/usr/share/genometools/gtdata/obo_files/so.obo is in genometools-common 1.5.10+ds-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895 1896 1897 1898 1899 1900 1901 1902 1903 1904 1905 1906 1907 1908 1909 1910 1911 1912 1913 1914 1915 1916 1917 1918 1919 1920 1921 1922 1923 1924 1925 1926 1927 1928 1929 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 1967 1968 1969 1970 1971 1972 1973 1974 1975 1976 1977 1978 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026 2027 2028 2029 2030 2031 2032 2033 2034 2035 2036 2037 2038 2039 2040 2041 2042 2043 2044 2045 2046 2047 2048 2049 2050 2051 2052 2053 2054 2055 2056 2057 2058 2059 2060 2061 2062 2063 2064 2065 2066 2067 2068 2069 2070 2071 2072 2073 2074 2075 2076 2077 2078 2079 2080 2081 2082 2083 2084 2085 2086 2087 2088 2089 2090 2091 2092 2093 2094 2095 2096 2097 2098 2099 2100 2101 2102 2103 2104 2105 2106 2107 2108 2109 2110 2111 2112 2113 2114 2115 2116 2117 2118 2119 2120 2121 2122 2123 2124 2125 2126 2127 2128 2129 2130 2131 2132 2133 2134 2135 2136 2137 2138 2139 2140 2141 2142 2143 2144 2145 2146 2147 2148 2149 2150 2151 2152 2153 2154 2155 2156 2157 2158 2159 2160 2161 2162 2163 2164 2165 2166 2167 2168 2169 2170 2171 2172 2173 2174 2175 2176 2177 2178 2179 2180 2181 2182 2183 2184 2185 2186 2187 2188 2189 2190 2191 2192 2193 2194 2195 2196 2197 2198 2199 2200 2201 2202 2203 2204 2205 2206 2207 2208 2209 2210 2211 2212 2213 2214 2215 2216 2217 2218 2219 2220 2221 2222 2223 2224 2225 2226 2227 2228 2229 2230 2231 2232 2233 2234 2235 2236 2237 2238 2239 2240 2241 2242 2243 2244 2245 2246 2247 2248 2249 2250 2251 2252 2253 2254 2255 2256 2257 2258 2259 2260 2261 2262 2263 2264 2265 2266 2267 2268 2269 2270 2271 2272 2273 2274 2275 2276 2277 2278 2279 2280 2281 2282 2283 2284 2285 2286 2287 2288 2289 2290 2291 2292 2293 2294 2295 2296 2297 2298 2299 2300 2301 2302 2303 2304 2305 2306 2307 2308 2309 2310 2311 2312 2313 2314 2315 2316 2317 2318 2319 2320 2321 2322 2323 2324 2325 2326 2327 2328 2329 2330 2331 2332 2333 2334 2335 2336 2337 2338 2339 2340 2341 2342 2343 2344 2345 2346 2347 2348 2349 2350 2351 2352 2353 2354 2355 2356 2357 2358 2359 2360 2361 2362 2363 2364 2365 2366 2367 2368 2369 2370 2371 2372 2373 2374 2375 2376 2377 2378 2379 2380 2381 2382 2383 2384 2385 2386 2387 2388 2389 2390 2391 2392 2393 2394 2395 2396 2397 2398 2399 2400 2401 2402 2403 2404 2405 2406 2407 2408 2409 2410 2411 2412 2413 2414 2415 2416 2417 2418 2419 2420 2421 2422 2423 2424 2425 2426 2427 2428 2429 2430 2431 2432 2433 2434 2435 2436 2437 2438 2439 2440 2441 2442 2443 2444 2445 2446 2447 2448 2449 2450 2451 2452 2453 2454 2455 2456 2457 2458 2459 2460 2461 2462 2463 2464 2465 2466 2467 2468 2469 2470 2471 2472 2473 2474 2475 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674 2675 2676 2677 2678 2679 2680 2681 2682 2683 2684 2685 2686 2687 2688 2689 2690 2691 2692 2693 2694 2695 2696 2697 2698 2699 2700 2701 2702 2703 2704 2705 2706 2707 2708 2709 2710 2711 2712 2713 2714 2715 2716 2717 2718 2719 2720 2721 2722 2723 2724 2725 2726 2727 2728 2729 2730 2731 2732 2733 2734 2735 2736 2737 2738 2739 2740 2741 2742 2743 2744 2745 2746 2747 2748 2749 2750 2751 2752 2753 2754 2755 2756 2757 2758 2759 2760 2761 2762 2763 2764 2765 2766 2767 2768 2769 2770 2771 2772 2773 2774 2775 2776 2777 2778 2779 2780 2781 2782 2783 2784 2785 2786 2787 2788 2789 2790 2791 2792 2793 2794 2795 2796 2797 2798 2799 2800 2801 2802 2803 2804 2805 2806 2807 2808 2809 2810 2811 2812 2813 2814 2815 2816 2817 2818 2819 2820 2821 2822 2823 2824 2825 2826 2827 2828 2829 2830 2831 2832 2833 2834 2835 2836 2837 2838 2839 2840 2841 2842 2843 2844 2845 2846 2847 2848 2849 2850 2851 2852 2853 2854 2855 2856 2857 2858 2859 2860 2861 2862 2863 2864 2865 2866 2867 2868 2869 2870 2871 2872 2873 2874 2875 2876 2877 2878 2879 2880 2881 2882 2883 2884 2885 2886 2887 2888 2889 2890 2891 2892 2893 2894 2895 2896 2897 2898 2899 2900 2901 2902 2903 2904 2905 2906 2907 2908 2909 2910 2911 2912 2913 2914 2915 2916 2917 2918 2919 2920 2921 2922 2923 2924 2925 2926 2927 2928 2929 2930 2931 2932 2933 2934 2935 2936 2937 2938 2939 2940 2941 2942 2943 2944 2945 2946 2947 2948 2949 2950 2951 2952 2953 2954 2955 2956 2957 2958 2959 2960 2961 2962 2963 2964 2965 2966 2967 2968 2969 2970 2971 2972 2973 2974 2975 2976 2977 2978 2979 2980 2981 2982 2983 2984 2985 2986 2987 2988 2989 2990 2991 2992 2993 2994 2995 2996 2997 2998 2999 3000 3001 3002 3003 3004 3005 3006 3007 3008 3009 3010 3011 3012 3013 3014 3015 3016 3017 3018 3019 3020 3021 3022 3023 3024 3025 3026 3027 3028 3029 3030 3031 3032 3033 3034 3035 3036 3037 3038 3039 3040 3041 3042 3043 3044 3045 3046 3047 3048 3049 3050 3051 3052 3053 3054 3055 3056 3057 3058 3059 3060 3061 3062 3063 3064 3065 3066 3067 3068 3069 3070 3071 3072 3073 3074 3075 3076 3077 3078 3079 3080 3081 3082 3083 3084 3085 3086 3087 3088 3089 3090 3091 3092 3093 3094 3095 3096 3097 3098 3099 3100 3101 3102 3103 3104 3105 3106 3107 3108 3109 3110 3111 3112 3113 3114 3115 3116 3117 3118 3119 3120 3121 3122 3123 3124 3125 3126 3127 3128 3129 3130 3131 3132 3133 3134 3135 3136 3137 3138 3139 3140 3141 3142 3143 3144 3145 3146 3147 3148 3149 3150 3151 3152 3153 3154 3155 3156 3157 3158 3159 3160 3161 3162 3163 3164 3165 3166 3167 3168 3169 3170 3171 3172 3173 3174 3175 3176 3177 3178 3179 3180 3181 3182 3183 3184 3185 3186 3187 3188 3189 3190 3191 3192 3193 3194 3195 3196 3197 3198 3199 3200 3201 3202 3203 3204 3205 3206 3207 3208 3209 3210 3211 3212 3213 3214 3215 3216 3217 3218 3219 3220 3221 3222 3223 3224 3225 3226 3227 3228 3229 3230 3231 3232 3233 3234 3235 3236 3237 3238 3239 3240 3241 3242 3243 3244 3245 3246 3247 3248 3249 3250 3251 3252 3253 3254 3255 3256 3257 3258 3259 3260 3261 3262 3263 3264 3265 3266 3267 3268 3269 3270 3271 3272 3273 3274 3275 3276 3277 3278 3279 3280 3281 3282 3283 3284 3285 3286 3287 3288 3289 3290 3291 3292 3293 3294 3295 3296 3297 3298 3299 3300 3301 3302 3303 3304 3305 3306 3307 3308 3309 3310 3311 3312 3313 3314 3315 3316 3317 3318 3319 3320 3321 3322 3323 3324 3325 3326 3327 3328 3329 3330 3331 3332 3333 3334 3335 3336 3337 3338 3339 3340 3341 3342 3343 3344 3345 3346 3347 3348 3349 3350 3351 3352 3353 3354 3355 3356 3357 3358 3359 3360 3361 3362 3363 3364 3365 3366 3367 3368 3369 3370 3371 3372 3373 3374 3375 3376 3377 3378 3379 3380 3381 3382 3383 3384 3385 3386 3387 3388 3389 3390 3391 3392 3393 3394 3395 3396 3397 3398 3399 3400 3401 3402 3403 3404 3405 3406 3407 3408 3409 3410 3411 3412 3413 3414 3415 3416 3417 3418 3419 3420 3421 3422 3423 3424 3425 3426 3427 3428 3429 3430 3431 3432 3433 3434 3435 3436 3437 3438 3439 3440 3441 3442 3443 3444 3445 3446 3447 3448 3449 3450 3451 3452 3453 3454 3455 3456 3457 3458 3459 3460 3461 3462 3463 3464 3465 3466 3467 3468 3469 3470 3471 3472 3473 3474 3475 3476 3477 3478 3479 3480 3481 3482 3483 3484 3485 3486 3487 3488 3489 3490 3491 3492 3493 3494 3495 3496 3497 3498 3499 3500 3501 3502 3503 3504 3505 3506 3507 3508 3509 3510 3511 3512 3513 3514 3515 3516 3517 3518 3519 3520 3521 3522 3523 3524 3525 3526 3527 3528 3529 3530 3531 3532 3533 3534 3535 3536 3537 3538 3539 3540 3541 3542 3543 3544 3545 3546 3547 3548 3549 3550 3551 3552 3553 3554 3555 3556 3557 3558 3559 3560 3561 3562 3563 3564 3565 3566 3567 3568 3569 3570 3571 3572 3573 3574 3575 3576 3577 3578 3579 3580 3581 3582 3583 3584 3585 3586 3587 3588 3589 3590 3591 3592 3593 3594 3595 3596 3597 3598 3599 3600 3601 3602 3603 3604 3605 3606 3607 3608 3609 3610 3611 3612 3613 3614 3615 3616 3617 3618 3619 3620 3621 3622 3623 3624 3625 3626 3627 3628 3629 3630 3631 3632 3633 3634 3635 3636 3637 3638 3639 3640 3641 3642 3643 3644 3645 3646 3647 3648 3649 3650 3651 3652 3653 3654 3655 3656 3657 3658 3659 3660 3661 3662 3663 3664 3665 3666 3667 3668 3669 3670 3671 3672 3673 3674 3675 3676 3677 3678 3679 3680 3681 3682 3683 3684 3685 3686 3687 3688 3689 3690 3691 3692 3693 3694 3695 3696 3697 3698 3699 3700 3701 3702 3703 3704 3705 3706 3707 3708 3709 3710 3711 3712 3713 3714 3715 3716 3717 3718 3719 3720 3721 3722 3723 3724 3725 3726 3727 3728 3729 3730 3731 3732 3733 3734 3735 3736 3737 3738 3739 3740 3741 3742 3743 3744 3745 3746 3747 3748 3749 3750 3751 3752 3753 3754 3755 3756 3757 3758 3759 3760 3761 3762 3763 3764 3765 3766 3767 3768 3769 3770 3771 3772 3773 3774 3775 3776 3777 3778 3779 3780 3781 3782 3783 3784 3785 3786 3787 3788 3789 3790 3791 3792 3793 3794 3795 3796 3797 3798 3799 3800 3801 3802 3803 3804 3805 3806 3807 3808 3809 3810 3811 3812 3813 3814 3815 3816 3817 3818 3819 3820 3821 3822 3823 3824 3825 3826 3827 3828 3829 3830 3831 3832 3833 3834 3835 3836 3837 3838 3839 3840 3841 3842 3843 3844 3845 3846 3847 3848 3849 3850 3851 3852 3853 3854 3855 3856 3857 3858 3859 3860 3861 3862 3863 3864 3865 3866 3867 3868 3869 3870 3871 3872 3873 3874 3875 3876 3877 3878 3879 3880 3881 3882 3883 3884 3885 3886 3887 3888 3889 3890 3891 3892 3893 3894 3895 3896 3897 3898 3899 3900 3901 3902 3903 3904 3905 3906 3907 3908 3909 3910 3911 3912 3913 3914 3915 3916 3917 3918 3919 3920 3921 3922 3923 3924 3925 3926 3927 3928 3929 3930 3931 3932 3933 3934 3935 3936 3937 3938 3939 3940 3941 3942 3943 3944 3945 3946 3947 3948 3949 3950 3951 3952 3953 3954 3955 3956 3957 3958 3959 3960 3961 3962 3963 3964 3965 3966 3967 3968 3969 3970 3971 3972 3973 3974 3975 3976 3977 3978 3979 3980 3981 3982 3983 3984 3985 3986 3987 3988 3989 3990 3991 3992 3993 3994 3995 3996 3997 3998 3999 4000 4001 4002 4003 4004 4005 4006 4007 4008 4009 4010 4011 4012 4013 4014 4015 4016 4017 4018 4019 4020 4021 4022 4023 4024 4025 4026 4027 4028 4029 4030 4031 4032 4033 4034 4035 4036 4037 4038 4039 4040 4041 4042 4043 4044 4045 4046 4047 4048 4049 4050 4051 4052 4053 4054 4055 4056 4057 4058 4059 4060 4061 4062 4063 4064 4065 4066 4067 4068 4069 4070 4071 4072 4073 4074 4075 4076 4077 4078 4079 4080 4081 4082 4083 4084 4085 4086 4087 4088 4089 4090 4091 4092 4093 4094 4095 4096 4097 4098 4099 4100 4101 4102 4103 4104 4105 4106 4107 4108 4109 4110 4111 4112 4113 4114 4115 4116 4117 4118 4119 4120 4121 4122 4123 4124 4125 4126 4127 4128 4129 4130 4131 4132 4133 4134 4135 4136 4137 4138 4139 4140 4141 4142 4143 4144 4145 4146 4147 4148 4149 4150 4151 4152 4153 4154 4155 4156 4157 4158 4159 4160 4161 4162 4163 4164 4165 4166 4167 4168 4169 4170 4171 4172 4173 4174 4175 4176 4177 4178 4179 4180 4181 4182 4183 4184 4185 4186 4187 4188 4189 4190 4191 4192 4193 4194 4195 4196 4197 4198 4199 4200 4201 4202 4203 4204 4205 4206 4207 4208 4209 4210 4211 4212 4213 4214 4215 4216 4217 4218 4219 4220 4221 4222 4223 4224 4225 4226 4227 4228 4229 4230 4231 4232 4233 4234 4235 4236 4237 4238 4239 4240 4241 4242 4243 4244 4245 4246 4247 4248 4249 4250 4251 4252 4253 4254 4255 4256 4257 4258 4259 4260 4261 4262 4263 4264 4265 4266 4267 4268 4269 4270 4271 4272 4273 4274 4275 4276 4277 4278 4279 4280 4281 4282 4283 4284 4285 4286 4287 4288 4289 4290 4291 4292 4293 4294 4295 4296 4297 4298 4299 4300 4301 4302 4303 4304 4305 4306 4307 4308 4309 4310 4311 4312 4313 4314 4315 4316 4317 4318 4319 4320 4321 4322 4323 4324 4325 4326 4327 4328 4329 4330 4331 4332 4333 4334 4335 4336 4337 4338 4339 4340 4341 4342 4343 4344 4345 4346 4347 4348 4349 4350 4351 4352 4353 4354 4355 4356 4357 4358 4359 4360 4361 4362 4363 4364 4365 4366 4367 4368 4369 4370 4371 4372 4373 4374 4375 4376 4377 4378 4379 4380 4381 4382 4383 4384 4385 4386 4387 4388 4389 4390 4391 4392 4393 4394 4395 4396 4397 4398 4399 4400 4401 4402 4403 4404 4405 4406 4407 4408 4409 4410 4411 4412 4413 4414 4415 4416 4417 4418 4419 4420 4421 4422 4423 4424 4425 4426 4427 4428 4429 4430 4431 4432 4433 4434 4435 4436 4437 4438 4439 4440 4441 4442 4443 4444 4445 4446 4447 4448 4449 4450 4451 4452 4453 4454 4455 4456 4457 4458 4459 4460 4461 4462 4463 4464 4465 4466 4467 4468 4469 4470 4471 4472 4473 4474 4475 4476 4477 4478 4479 4480 4481 4482 4483 4484 4485 4486 4487 4488 4489 4490 4491 4492 4493 4494 4495 4496 4497 4498 4499 4500 4501 4502 4503 4504 4505 4506 4507 4508 4509 4510 4511 4512 4513 4514 4515 4516 4517 4518 4519 4520 4521 4522 4523 4524 4525 4526 4527 4528 4529 4530 4531 4532 4533 4534 4535 4536 4537 4538 4539 4540 4541 4542 4543 4544 4545 4546 4547 4548 4549 4550 4551 4552 4553 4554 4555 4556 4557 4558 4559 4560 4561 4562 4563 4564 4565 4566 4567 4568 4569 4570 4571 4572 4573 4574 4575 4576 4577 4578 4579 4580 4581 4582 4583 4584 4585 4586 4587 4588 4589 4590 4591 4592 4593 4594 4595 4596 4597 4598 4599 4600 4601 4602 4603 4604 4605 4606 4607 4608 4609 4610 4611 4612 4613 4614 4615 4616 4617 4618 4619 4620 4621 4622 4623 4624 4625 4626 4627 4628 4629 4630 4631 4632 4633 4634 4635 4636 4637 4638 4639 4640 4641 4642 4643 4644 4645 4646 4647 4648 4649 4650 4651 4652 4653 4654 4655 4656 4657 4658 4659 4660 4661 4662 4663 4664 4665 4666 4667 4668 4669 4670 4671 4672 4673 4674 4675 4676 4677 4678 4679 4680 4681 4682 4683 4684 4685 4686 4687 4688 4689 4690 4691 4692 4693 4694 4695 4696 4697 4698 4699 4700 4701 4702 4703 4704 4705 4706 4707 4708 4709 4710 4711 4712 4713 4714 4715 4716 4717 4718 4719 4720 4721 4722 4723 4724 4725 4726 4727 4728 4729 4730 4731 4732 4733 4734 4735 4736 4737 4738 4739 4740 4741 4742 4743 4744 4745 4746 4747 4748 4749 4750 4751 4752 4753 4754 4755 4756 4757 4758 4759 4760 4761 4762 4763 4764 4765 4766 4767 4768 4769 4770 4771 4772 4773 4774 4775 4776 4777 4778 4779 4780 4781 4782 4783 4784 4785 4786 4787 4788 4789 4790 4791 4792 4793 4794 4795 4796 4797 4798 4799 4800 4801 4802 4803 4804 4805 4806 4807 4808 4809 4810 4811 4812 4813 4814 4815 4816 4817 4818 4819 4820 4821 4822 4823 4824 4825 4826 4827 4828 4829 4830 4831 4832 4833 4834 4835 4836 4837 4838 4839 4840 4841 4842 4843 4844 4845 4846 4847 4848 4849 4850 4851 4852 4853 4854 4855 4856 4857 4858 4859 4860 4861 4862 4863 4864 4865 4866 4867 4868 4869 4870 4871 4872 4873 4874 4875 4876 4877 4878 4879 4880 4881 4882 4883 4884 4885 4886 4887 4888 4889 4890 4891 4892 4893 4894 4895 4896 4897 4898 4899 4900 4901 4902 4903 4904 4905 4906 4907 4908 4909 4910 4911 4912 4913 4914 4915 4916 4917 4918 4919 4920 4921 4922 4923 4924 4925 4926 4927 4928 4929 4930 4931 4932 4933 4934 4935 4936 4937 4938 4939 4940 4941 4942 4943 4944 4945 4946 4947 4948 4949 4950 4951 4952 4953 4954 4955 4956 4957 4958 4959 4960 4961 4962 4963 4964 4965 4966 4967 4968 4969 4970 4971 4972 4973 4974 4975 4976 4977 4978 4979 4980 4981 4982 4983 4984 4985 4986 4987 4988 4989 4990 4991 4992 4993 4994 4995 4996 4997 4998 4999 5000 5001 5002 5003 5004 5005 5006 5007 5008 5009 5010 5011 5012 5013 5014 5015 5016 5017 5018 5019 5020 5021 5022 5023 5024 5025 5026 5027 5028 5029 5030 5031 5032 5033 5034 5035 5036 5037 5038 5039 5040 5041 5042 5043 5044 5045 5046 5047 5048 5049 5050 5051 5052 5053 5054 5055 5056 5057 5058 5059 5060 5061 5062 5063 5064 5065 5066 5067 5068 5069 5070 5071 5072 5073 5074 5075 5076 5077 5078 5079 5080 5081 5082 5083 5084 5085 5086 5087 5088 5089 5090 5091 5092 5093 5094 5095 5096 5097 5098 5099 5100 5101 5102 5103 5104 5105 5106 5107 5108 5109 5110 5111 5112 5113 5114 5115 5116 5117 5118 5119 5120 5121 5122 5123 5124 5125 5126 5127 5128 5129 5130 5131 5132 5133 5134 5135 5136 5137 5138 5139 5140 5141 5142 5143 5144 5145 5146 5147 5148 5149 5150 5151 5152 5153 5154 5155 5156 5157 5158 5159 5160 5161 5162 5163 5164 5165 5166 5167 5168 5169 5170 5171 5172 5173 5174 5175 5176 5177 5178 5179 5180 5181 5182 5183 5184 5185 5186 5187 5188 5189 5190 5191 5192 5193 5194 5195 5196 5197 5198 5199 5200 5201 5202 5203 5204 5205 5206 5207 5208 5209 5210 5211 5212 5213 5214 5215 5216 5217 5218 5219 5220 5221 5222 5223 5224 5225 5226 5227 5228 5229 5230 5231 5232 5233 5234 5235 5236 5237 5238 5239 5240 5241 5242 5243 5244 5245 5246 5247 5248 5249 5250 5251 5252 5253 5254 5255 5256 5257 5258 5259 5260 5261 5262 5263 5264 5265 5266 5267 5268 5269 5270 5271 5272 5273 5274 5275 5276 5277 5278 5279 5280 5281 5282 5283 5284 5285 5286 5287 5288 5289 5290 5291 5292 5293 5294 5295 5296 5297 5298 5299 5300 5301 5302 5303 5304 5305 5306 5307 5308 5309 5310 5311 5312 5313 5314 5315 5316 5317 5318 5319 5320 5321 5322 5323 5324 5325 5326 5327 5328 5329 5330 5331 5332 5333 5334 5335 5336 5337 5338 5339 5340 5341 5342 5343 5344 5345 5346 5347 5348 5349 5350 5351 5352 5353 5354 5355 5356 5357 5358 5359 5360 5361 5362 5363 5364 5365 5366 5367 5368 5369 5370 5371 5372 5373 5374 5375 5376 5377 5378 5379 5380 5381 5382 5383 5384 5385 5386 5387 5388 5389 5390 5391 5392 5393 5394 5395 5396 5397 5398 5399 5400 5401 5402 5403 5404 5405 5406 5407 5408 5409 5410 5411 5412 5413 5414 5415 5416 5417 5418 5419 5420 5421 5422 5423 5424 5425 5426 5427 5428 5429 5430 5431 5432 5433 5434 5435 5436 5437 5438 5439 5440 5441 5442 5443 5444 5445 5446 5447 5448 5449 5450 5451 5452 5453 5454 5455 5456 5457 5458 5459 5460 5461 5462 5463 5464 5465 5466 5467 5468 5469 5470 5471 5472 5473 5474 5475 5476 5477 5478 5479 5480 5481 5482 5483 5484 5485 5486 5487 5488 5489 5490 5491 5492 5493 5494 5495 5496 5497 5498 5499 5500 5501 5502 5503 5504 5505 5506 5507 5508 5509 5510 5511 5512 5513 5514 5515 5516 5517 5518 5519 5520 5521 5522 5523 5524 5525 5526 5527 5528 5529 5530 5531 5532 5533 5534 5535 5536 5537 5538 5539 5540 5541 5542 5543 5544 5545 5546 5547 5548 5549 5550 5551 5552 5553 5554 5555 5556 5557 5558 5559 5560 5561 5562 5563 5564 5565 5566 5567 5568 5569 5570 5571 5572 5573 5574 5575 5576 5577 5578 5579 5580 5581 5582 5583 5584 5585 5586 5587 5588 5589 5590 5591 5592 5593 5594 5595 5596 5597 5598 5599 5600 5601 5602 5603 5604 5605 5606 5607 5608 5609 5610 5611 5612 5613 5614 5615 5616 5617 5618 5619 5620 5621 5622 5623 5624 5625 5626 5627 5628 5629 5630 5631 5632 5633 5634 5635 5636 5637 5638 5639 5640 5641 5642 5643 5644 5645 5646 5647 5648 5649 5650 5651 5652 5653 5654 5655 5656 5657 5658 5659 5660 5661 5662 5663 5664 5665 5666 5667 5668 5669 5670 5671 5672 5673 5674 5675 5676 5677 5678 5679 5680 5681 5682 5683 5684 5685 5686 5687 5688 5689 5690 5691 5692 5693 5694 5695 5696 5697 5698 5699 5700 5701 5702 5703 5704 5705 5706 5707 5708 5709 5710 5711 5712 5713 5714 5715 5716 5717 5718 5719 5720 5721 5722 5723 5724 5725 5726 5727 5728 5729 5730 5731 5732 5733 5734 5735 5736 5737 5738 5739 5740 5741 5742 5743 5744 5745 5746 5747 5748 5749 5750 5751 5752 5753 5754 5755 5756 5757 5758 5759 5760 5761 5762 5763 5764 5765 5766 5767 5768 5769 5770 5771 5772 5773 5774 5775 5776 5777 5778 5779 5780 5781 5782 5783 5784 5785 5786 5787 5788 5789 5790 5791 5792 5793 5794 5795 5796 5797 5798 5799 5800 5801 5802 5803 5804 5805 5806 5807 5808 5809 5810 5811 5812 5813 5814 5815 5816 5817 5818 5819 5820 5821 5822 5823 5824 5825 5826 5827 5828 5829 5830 5831 5832 5833 5834 5835 5836 5837 5838 5839 5840 5841 5842 5843 5844 5845 5846 5847 5848 5849 5850 5851 5852 5853 5854 5855 5856 5857 5858 5859 5860 5861 5862 5863 5864 5865 5866 5867 5868 5869 5870 5871 5872 5873 5874 5875 5876 5877 5878 5879 5880 5881 5882 5883 5884 5885 5886 5887 5888 5889 5890 5891 5892 5893 5894 5895 5896 5897 5898 5899 5900 5901 5902 5903 5904 5905 5906 5907 5908 5909 5910 5911 5912 5913 5914 5915 5916 5917 5918 5919 5920 5921 5922 5923 5924 5925 5926 5927 5928 5929 5930 5931 5932 5933 5934 5935 5936 5937 5938 5939 5940 5941 5942 5943 5944 5945 5946 5947 5948 5949 5950 5951 5952 5953 5954 5955 5956 5957 5958 5959 5960 5961 5962 5963 5964 5965 5966 5967 5968 5969 5970 5971 5972 5973 5974 5975 5976 5977 5978 5979 5980 5981 5982 5983 5984 5985 5986 5987 5988 5989 5990 5991 5992 5993 5994 5995 5996 5997 5998 5999 6000 6001 6002 6003 6004 6005 6006 6007 6008 6009 6010 6011 6012 6013 6014 6015 6016 6017 6018 6019 6020 6021 6022 6023 6024 6025 6026 6027 6028 6029 6030 6031 6032 6033 6034 6035 6036 6037 6038 6039 6040 6041 6042 6043 6044 6045 6046 6047 6048 6049 6050 6051 6052 6053 6054 6055 6056 6057 6058 6059 6060 6061 6062 6063 6064 6065 6066 6067 6068 6069 6070 6071 6072 6073 6074 6075 6076 6077 6078 6079 6080 6081 6082 6083 6084 6085 6086 6087 6088 6089 6090 6091 6092 6093 6094 6095 6096 6097 6098 6099 6100 6101 6102 6103 6104 6105 6106 6107 6108 6109 6110 6111 6112 6113 6114 6115 6116 6117 6118 6119 6120 6121 6122 6123 6124 6125 6126 6127 6128 6129 6130 6131 6132 6133 6134 6135 6136 6137 6138 6139 6140 6141 6142 6143 6144 6145 6146 6147 6148 6149 6150 6151 6152 6153 6154 6155 6156 6157 6158 6159 6160 6161 6162 6163 6164 6165 6166 6167 6168 6169 6170 6171 6172 6173 6174 6175 6176 6177 6178 6179 6180 6181 6182 6183 6184 6185 6186 6187 6188 6189 6190 6191 6192 6193 6194 6195 6196 6197 6198 6199 6200 6201 6202 6203 6204 6205 6206 6207 6208 6209 6210 6211 6212 6213 6214 6215 6216 6217 6218 6219 6220 6221 6222 6223 6224 6225 6226 6227 6228 6229 6230 6231 6232 6233 6234 6235 6236 6237 6238 6239 6240 6241 6242 6243 6244 6245 6246 6247 6248 6249 6250 6251 6252 6253 6254 6255 6256 6257 6258 6259 6260 6261 6262 6263 6264 6265 6266 6267 6268 6269 6270 6271 6272 6273 6274 6275 6276 6277 6278 6279 6280 6281 6282 6283 6284 6285 6286 6287 6288 6289 6290 6291 6292 6293 6294 6295 6296 6297 6298 6299 6300 6301 6302 6303 6304 6305 6306 6307 6308 6309 6310 6311 6312 6313 6314 6315 6316 6317 6318 6319 6320 6321 6322 6323 6324 6325 6326 6327 6328 6329 6330 6331 6332 6333 6334 6335 6336 6337 6338 6339 6340 6341 6342 6343 6344 6345 6346 6347 6348 6349 6350 6351 6352 6353 6354 6355 6356 6357 6358 6359 6360 6361 6362 6363 6364 6365 6366 6367 6368 6369 6370 6371 6372 6373 6374 6375 6376 6377 6378 6379 6380 6381 6382 6383 6384 6385 6386 6387 6388 6389 6390 6391 6392 6393 6394 6395 6396 6397 6398 6399 6400 6401 6402 6403 6404 6405 6406 6407 6408 6409 6410 6411 6412 6413 6414 6415 6416 6417 6418 6419 6420 6421 6422 6423 6424 6425 6426 6427 6428 6429 6430 6431 6432 6433 6434 6435 6436 6437 6438 6439 6440 6441 6442 6443 6444 6445 6446 6447 6448 6449 6450 6451 6452 6453 6454 6455 6456 6457 6458 6459 6460 6461 6462 6463 6464 6465 6466 6467 6468 6469 6470 6471 6472 6473 6474 6475 6476 6477 6478 6479 6480 6481 6482 6483 6484 6485 6486 6487 6488 6489 6490 6491 6492 6493 6494 6495 6496 6497 6498 6499 6500 6501 6502 6503 6504 6505 6506 6507 6508 6509 6510 6511 6512 6513 6514 6515 6516 6517 6518 6519 6520 6521 6522 6523 6524 6525 6526 6527 6528 6529 6530 6531 6532 6533 6534 6535 6536 6537 6538 6539 6540 6541 6542 6543 6544 6545 6546 6547 6548 6549 6550 6551 6552 6553 6554 6555 6556 6557 6558 6559 6560 6561 6562 6563 6564 6565 6566 6567 6568 6569 6570 6571 6572 6573 6574 6575 6576 6577 6578 6579 6580 6581 6582 6583 6584 6585 6586 6587 6588 6589 6590 6591 6592 6593 6594 6595 6596 6597 6598 6599 6600 6601 6602 6603 6604 6605 6606 6607 6608 6609 6610 6611 6612 6613 6614 6615 6616 6617 6618 6619 6620 6621 6622 6623 6624 6625 6626 6627 6628 6629 6630 6631 6632 6633 6634 6635 6636 6637 6638 6639 6640 6641 6642 6643 6644 6645 6646 6647 6648 6649 6650 6651 6652 6653 6654 6655 6656 6657 6658 6659 6660 6661 6662 6663 6664 6665 6666 6667 6668 6669 6670 6671 6672 6673 6674 6675 6676 6677 6678 6679 6680 6681 6682 6683 6684 6685 6686 6687 6688 6689 6690 6691 6692 6693 6694 6695 6696 6697 6698 6699 6700 6701 6702 6703 6704 6705 6706 6707 6708 6709 6710 6711 6712 6713 6714 6715 6716 6717 6718 6719 6720 6721 6722 6723 6724 6725 6726 6727 6728 6729 6730 6731 6732 6733 6734 6735 6736 6737 6738 6739 6740 6741 6742 6743 6744 6745 6746 6747 6748 6749 6750 6751 6752 6753 6754 6755 6756 6757 6758 6759 6760 6761 6762 6763 6764 6765 6766 6767 6768 6769 6770 6771 6772 6773 6774 6775 6776 6777 6778 6779 6780 6781 6782 6783 6784 6785 6786 6787 6788 6789 6790 6791 6792 6793 6794 6795 6796 6797 6798 6799 6800 6801 6802 6803 6804 6805 6806 6807 6808 6809 6810 6811 6812 6813 6814 6815 6816 6817 6818 6819 6820 6821 6822 6823 6824 6825 6826 6827 6828 6829 6830 6831 6832 6833 6834 6835 6836 6837 6838 6839 6840 6841 6842 6843 6844 6845 6846 6847 6848 6849 6850 6851 6852 6853 6854 6855 6856 6857 6858 6859 6860 6861 6862 6863 6864 6865 6866 6867 6868 6869 6870 6871 6872 6873 6874 6875 6876 6877 6878 6879 6880 6881 6882 6883 6884 6885 6886 6887 6888 6889 6890 6891 6892 6893 6894 6895 6896 6897 6898 6899 6900 6901 6902 6903 6904 6905 6906 6907 6908 6909 6910 6911 6912 6913 6914 6915 6916 6917 6918 6919 6920 6921 6922 6923 6924 6925 6926 6927 6928 6929 6930 6931 6932 6933 6934 6935 6936 6937 6938 6939 6940 6941 6942 6943 6944 6945 6946 6947 6948 6949 6950 6951 6952 6953 6954 6955 6956 6957 6958 6959 6960 6961 6962 6963 6964 6965 6966 6967 6968 6969 6970 6971 6972 6973 6974 6975 6976 6977 6978 6979 6980 6981 6982 6983 6984 6985 6986 6987 6988 6989 6990 6991 6992 6993 6994 6995 6996 6997 6998 6999 7000 7001 7002 7003 7004 7005 7006 7007 7008 7009 7010 7011 7012 7013 7014 7015 7016 7017 7018 7019 7020 7021 7022 7023 7024 7025 7026 7027 7028 7029 7030 7031 7032 7033 7034 7035 7036 7037 7038 7039 7040 7041 7042 7043 7044 7045 7046 7047 7048 7049 7050 7051 7052 7053 7054 7055 7056 7057 7058 7059 7060 7061 7062 7063 7064 7065 7066 7067 7068 7069 7070 7071 7072 7073 7074 7075 7076 7077 7078 7079 7080 7081 7082 7083 7084 7085 7086 7087 7088 7089 7090 7091 7092 7093 7094 7095 7096 7097 7098 7099 7100 7101 7102 7103 7104 7105 7106 7107 7108 7109 7110 7111 7112 7113 7114 7115 7116 7117 7118 7119 7120 7121 7122 7123 7124 7125 7126 7127 7128 7129 7130 7131 7132 7133 7134 7135 7136 7137 7138 7139 7140 7141 7142 7143 7144 7145 7146 7147 7148 7149 7150 7151 7152 7153 7154 7155 7156 7157 7158 7159 7160 7161 7162 7163 7164 7165 7166 7167 7168 7169 7170 7171 7172 7173 7174 7175 7176 7177 7178 7179 7180 7181 7182 7183 7184 7185 7186 7187 7188 7189 7190 7191 7192 7193 7194 7195 7196 7197 7198 7199 7200 7201 7202 7203 7204 7205 7206 7207 7208 7209 7210 7211 7212 7213 7214 7215 7216 7217 7218 7219 7220 7221 7222 7223 7224 7225 7226 7227 7228 7229 7230 7231 7232 7233 7234 7235 7236 7237 7238 7239 7240 7241 7242 7243 7244 7245 7246 7247 7248 7249 7250 7251 7252 7253 7254 7255 7256 7257 7258 7259 7260 7261 7262 7263 7264 7265 7266 7267 7268 7269 7270 7271 7272 7273 7274 7275 7276 7277 7278 7279 7280 7281 7282 7283 7284 7285 7286 7287 7288 7289 7290 7291 7292 7293 7294 7295 7296 7297 7298 7299 7300 7301 7302 7303 7304 7305 7306 7307 7308 7309 7310 7311 7312 7313 7314 7315 7316 7317 7318 7319 7320 7321 7322 7323 7324 7325 7326 7327 7328 7329 7330 7331 7332 7333 7334 7335 7336 7337 7338 7339 7340 7341 7342 7343 7344 7345 7346 7347 7348 7349 7350 7351 7352 7353 7354 7355 7356 7357 7358 7359 7360 7361 7362 7363 7364 7365 7366 7367 7368 7369 7370 7371 7372 7373 7374 7375 7376 7377 7378 7379 7380 7381 7382 7383 7384 7385 7386 7387 7388 7389 7390 7391 7392 7393 7394 7395 7396 7397 7398 7399 7400 7401 7402 7403 7404 7405 7406 7407 7408 7409 7410 7411 7412 7413 7414 7415 7416 7417 7418 7419 7420 7421 7422 7423 7424 7425 7426 7427 7428 7429 7430 7431 7432 7433 7434 7435 7436 7437 7438 7439 7440 7441 7442 7443 7444 7445 7446 7447 7448 7449 7450 7451 7452 7453 7454 7455 7456 7457 7458 7459 7460 7461 7462 7463 7464 7465 7466 7467 7468 7469 7470 7471 7472 7473 7474 7475 7476 7477 7478 7479 7480 7481 7482 7483 7484 7485 7486 7487 7488 7489 7490 7491 7492 7493 7494 7495 7496 7497 7498 7499 7500 7501 7502 7503 7504 7505 7506 7507 7508 7509 7510 7511 7512 7513 7514 7515 7516 7517 7518 7519 7520 7521 7522 7523 7524 7525 7526 7527 7528 7529 7530 7531 7532 7533 7534 7535 7536 7537 7538 7539 7540 7541 7542 7543 7544 7545 7546 7547 7548 7549 7550 7551 7552 7553 7554 7555 7556 7557 7558 7559 7560 7561 7562 7563 7564 7565 7566 7567 7568 7569 7570 7571 7572 7573 7574 7575 7576 7577 7578 7579 7580 7581 7582 7583 7584 7585 7586 7587 7588 7589 7590 7591 7592 7593 7594 7595 7596 7597 7598 7599 7600 7601 7602 7603 7604 7605 7606 7607 7608 7609 7610 7611 7612 7613 7614 7615 7616 7617 7618 7619 7620 7621 7622 7623 7624 7625 7626 7627 7628 7629 7630 7631 7632 7633 7634 7635 7636 7637 7638 7639 7640 7641 7642 7643 7644 7645 7646 7647 7648 7649 7650 7651 7652 7653 7654 7655 7656 7657 7658 7659 7660 7661 7662 7663 7664 7665 7666 7667 7668 7669 7670 7671 7672 7673 7674 7675 7676 7677 7678 7679 7680 7681 7682 7683 7684 7685 7686 7687 7688 7689 7690 7691 7692 7693 7694 7695 7696 7697 7698 7699 7700 7701 7702 7703 7704 7705 7706 7707 7708 7709 7710 7711 7712 7713 7714 7715 7716 7717 7718 7719 7720 7721 7722 7723 7724 7725 7726 7727 7728 7729 7730 7731 7732 7733 7734 7735 7736 7737 7738 7739 7740 7741 7742 7743 7744 7745 7746 7747 7748 7749 7750 7751 7752 7753 7754 7755 7756 7757 7758 7759 7760 7761 7762 7763 7764 7765 7766 7767 7768 7769 7770 7771 7772 7773 7774 7775 7776 7777 7778 7779 7780 7781 7782 7783 7784 7785 7786 7787 7788 7789 7790 7791 7792 7793 7794 7795 7796 7797 7798 7799 7800 7801 7802 7803 7804 7805 7806 7807 7808 7809 7810 7811 7812 7813 7814 7815 7816 7817 7818 7819 7820 7821 7822 7823 7824 7825 7826 7827 7828 7829 7830 7831 7832 7833 7834 7835 7836 7837 7838 7839 7840 7841 7842 7843 7844 7845 7846 7847 7848 7849 7850 7851 7852 7853 7854 7855 7856 7857 7858 7859 7860 7861 7862 7863 7864 7865 7866 7867 7868 7869 7870 7871 7872 7873 7874 7875 7876 7877 7878 7879 7880 7881 7882 7883 7884 7885 7886 7887 7888 7889 7890 7891 7892 7893 7894 7895 7896 7897 7898 7899 7900 7901 7902 7903 7904 7905 7906 7907 7908 7909 7910 7911 7912 7913 7914 7915 7916 7917 7918 7919 7920 7921 7922 7923 7924 7925 7926 7927 7928 7929 7930 7931 7932 7933 7934 7935 7936 7937 7938 7939 7940 7941 7942 7943 7944 7945 7946 7947 7948 7949 7950 7951 7952 7953 7954 7955 7956 7957 7958 7959 7960 7961 7962 7963 7964 7965 7966 7967 7968 7969 7970 7971 7972 7973 7974 7975 7976 7977 7978 7979 7980 7981 7982 7983 7984 7985 7986 7987 7988 7989 7990 7991 7992 7993 7994 7995 7996 7997 7998 7999 8000 8001 8002 8003 8004 8005 8006 8007 8008 8009 8010 8011 8012 8013 8014 8015 8016 8017 8018 8019 8020 8021 8022 8023 8024 8025 8026 8027 8028 8029 8030 8031 8032 8033 8034 8035 8036 8037 8038 8039 8040 8041 8042 8043 8044 8045 8046 8047 8048 8049 8050 8051 8052 8053 8054 8055 8056 8057 8058 8059 8060 8061 8062 8063 8064 8065 8066 8067 8068 8069 8070 8071 8072 8073 8074 8075 8076 8077 8078 8079 8080 8081 8082 8083 8084 8085 8086 8087 8088 8089 8090 8091 8092 8093 8094 8095 8096 8097 8098 8099 8100 8101 8102 8103 8104 8105 8106 8107 8108 8109 8110 8111 8112 8113 8114 8115 8116 8117 8118 8119 8120 8121 8122 8123 8124 8125 8126 8127 8128 8129 8130 8131 8132 8133 8134 8135 8136 8137 8138 8139 8140 8141 8142 8143 8144 8145 8146 8147 8148 8149 8150 8151 8152 8153 8154 8155 8156 8157 8158 8159 8160 8161 8162 8163 8164 8165 8166 8167 8168 8169 8170 8171 8172 8173 8174 8175 8176 8177 8178 8179 8180 8181 8182 8183 8184 8185 8186 8187 8188 8189 8190 8191 8192 8193 8194 8195 8196 8197 8198 8199 8200 8201 8202 8203 8204 8205 8206 8207 8208 8209 8210 8211 8212 8213 8214 8215 8216 8217 8218 8219 8220 8221 8222 8223 8224 8225 8226 8227 8228 8229 8230 8231 8232 8233 8234 8235 8236 8237 8238 8239 8240 8241 8242 8243 8244 8245 8246 8247 8248 8249 8250 8251 8252 8253 8254 8255 8256 8257 8258 8259 8260 8261 8262 8263 8264 8265 8266 8267 8268 8269 8270 8271 8272 8273 8274 8275 8276 8277 8278 8279 8280 8281 8282 8283 8284 8285 8286 8287 8288 8289 8290 8291 8292 8293 8294 8295 8296 8297 8298 8299 8300 8301 8302 8303 8304 8305 8306 8307 8308 8309 8310 8311 8312 8313 8314 8315 8316 8317 8318 8319 8320 8321 8322 8323 8324 8325 8326 8327 8328 8329 8330 8331 8332 8333 8334 8335 8336 8337 8338 8339 8340 8341 8342 8343 8344 8345 8346 8347 8348 8349 8350 8351 8352 8353 8354 8355 8356 8357 8358 8359 8360 8361 8362 8363 8364 8365 8366 8367 8368 8369 8370 8371 8372 8373 8374 8375 8376 8377 8378 8379 8380 8381 8382 8383 8384 8385 8386 8387 8388 8389 8390 8391 8392 8393 8394 8395 8396 8397 8398 8399 8400 8401 8402 8403 8404 8405 8406 8407 8408 8409 8410 8411 8412 8413 8414 8415 8416 8417 8418 8419 8420 8421 8422 8423 8424 8425 8426 8427 8428 8429 8430 8431 8432 8433 8434 8435 8436 8437 8438 8439 8440 8441 8442 8443 8444 8445 8446 8447 8448 8449 8450 8451 8452 8453 8454 8455 8456 8457 8458 8459 8460 8461 8462 8463 8464 8465 8466 8467 8468 8469 8470 8471 8472 8473 8474 8475 8476 8477 8478 8479 8480 8481 8482 8483 8484 8485 8486 8487 8488 8489 8490 8491 8492 8493 8494 8495 8496 8497 8498 8499 8500 8501 8502 8503 8504 8505 8506 8507 8508 8509 8510 8511 8512 8513 8514 8515 8516 8517 8518 8519 8520 8521 8522 8523 8524 8525 8526 8527 8528 8529 8530 8531 8532 8533 8534 8535 8536 8537 8538 8539 8540 8541 8542 8543 8544 8545 8546 8547 8548 8549 8550 8551 8552 8553 8554 8555 8556 8557 8558 8559 8560 8561 8562 8563 8564 8565 8566 8567 8568 8569 8570 8571 8572 8573 8574 8575 8576 8577 8578 8579 8580 8581 8582 8583 8584 8585 8586 8587 8588 8589 8590 8591 8592 8593 8594 8595 8596 8597 8598 8599 8600 8601 8602 8603 8604 8605 8606 8607 8608 8609 8610 8611 8612 8613 8614 8615 8616 8617 8618 8619 8620 8621 8622 8623 8624 8625 8626 8627 8628 8629 8630 8631 8632 8633 8634 8635 8636 8637 8638 8639 8640 8641 8642 8643 8644 8645 8646 8647 8648 8649 8650 8651 8652 8653 8654 8655 8656 8657 8658 8659 8660 8661 8662 8663 8664 8665 8666 8667 8668 8669 8670 8671 8672 8673 8674 8675 8676 8677 8678 8679 8680 8681 8682 8683 8684 8685 8686 8687 8688 8689 8690 8691 8692 8693 8694 8695 8696 8697 8698 8699 8700 8701 8702 8703 8704 8705 8706 8707 8708 8709 8710 8711 8712 8713 8714 8715 8716 8717 8718 8719 8720 8721 8722 8723 8724 8725 8726 8727 8728 8729 8730 8731 8732 8733 8734 8735 8736 8737 8738 8739 8740 8741 8742 8743 8744 8745 8746 8747 8748 8749 8750 8751 8752 8753 8754 8755 8756 8757 8758 8759 8760 8761 8762 8763 8764 8765 8766 8767 8768 8769 8770 8771 8772 8773 8774 8775 8776 8777 8778 8779 8780 8781 8782 8783 8784 8785 8786 8787 8788 8789 8790 8791 8792 8793 8794 8795 8796 8797 8798 8799 8800 8801 8802 8803 8804 8805 8806 8807 8808 8809 8810 8811 8812 8813 8814 8815 8816 8817 8818 8819 8820 8821 8822 8823 8824 8825 8826 8827 8828 8829 8830 8831 8832 8833 8834 8835 8836 8837 8838 8839 8840 8841 8842 8843 8844 8845 8846 8847 8848 8849 8850 8851 8852 8853 8854 8855 8856 8857 8858 8859 8860 8861 8862 8863 8864 8865 8866 8867 8868 8869 8870 8871 8872 8873 8874 8875 8876 8877 8878 8879 8880 8881 8882 8883 8884 8885 8886 8887 8888 8889 8890 8891 8892 8893 8894 8895 8896 8897 8898 8899 8900 8901 8902 8903 8904 8905 8906 8907 8908 8909 8910 8911 8912 8913 8914 8915 8916 8917 8918 8919 8920 8921 8922 8923 8924 8925 8926 8927 8928 8929 8930 8931 8932 8933 8934 8935 8936 8937 8938 8939 8940 8941 8942 8943 8944 8945 8946 8947 8948 8949 8950 8951 8952 8953 8954 8955 8956 8957 8958 8959 8960 8961 8962 8963 8964 8965 8966 8967 8968 8969 8970 8971 8972 8973 8974 8975 8976 8977 8978 8979 8980 8981 8982 8983 8984 8985 8986 8987 8988 8989 8990 8991 8992 8993 8994 8995 8996 8997 8998 8999 9000 9001 9002 9003 9004 9005 9006 9007 9008 9009 9010 9011 9012 9013 9014 9015 9016 9017 9018 9019 9020 9021 9022 9023 9024 9025 9026 9027 9028 9029 9030 9031 9032 9033 9034 9035 9036 9037 9038 9039 9040 9041 9042 9043 9044 9045 9046 9047 9048 9049 9050 9051 9052 9053 9054 9055 9056 9057 9058 9059 9060 9061 9062 9063 9064 9065 9066 9067 9068 9069 9070 9071 9072 9073 9074 9075 9076 9077 9078 9079 9080 9081 9082 9083 9084 9085 9086 9087 9088 9089 9090 9091 9092 9093 9094 9095 9096 9097 9098 9099 9100 9101 9102 9103 9104 9105 9106 9107 9108 9109 9110 9111 9112 9113 9114 9115 9116 9117 9118 9119 9120 9121 9122 9123 9124 9125 9126 9127 9128 9129 9130 9131 9132 9133 9134 9135 9136 9137 9138 9139 9140 9141 9142 9143 9144 9145 9146 9147 9148 9149 9150 9151 9152 9153 9154 9155 9156 9157 9158 9159 9160 9161 9162 9163 9164 9165 9166 9167 9168 9169 9170 9171 9172 9173 9174 9175 9176 9177 9178 9179 9180 9181 9182 9183 9184 9185 9186 9187 9188 9189 9190 9191 9192 9193 9194 9195 9196 9197 9198 9199 9200 9201 9202 9203 9204 9205 9206 9207 9208 9209 9210 9211 9212 9213 9214 9215 9216 9217 9218 9219 9220 9221 9222 9223 9224 9225 9226 9227 9228 9229 9230 9231 9232 9233 9234 9235 9236 9237 9238 9239 9240 9241 9242 9243 9244 9245 9246 9247 9248 9249 9250 9251 9252 9253 9254 9255 9256 9257 9258 9259 9260 9261 9262 9263 9264 9265 9266 9267 9268 9269 9270 9271 9272 9273 9274 9275 9276 9277 9278 9279 9280 9281 9282 9283 9284 9285 9286 9287 9288 9289 9290 9291 9292 9293 9294 9295 9296 9297 9298 9299 9300 9301 9302 9303 9304 9305 9306 9307 9308 9309 9310 9311 9312 9313 9314 9315 9316 9317 9318 9319 9320 9321 9322 9323 9324 9325 9326 9327 9328 9329 9330 9331 9332 9333 9334 9335 9336 9337 9338 9339 9340 9341 9342 9343 9344 9345 9346 9347 9348 9349 9350 9351 9352 9353 9354 9355 9356 9357 9358 9359 9360 9361 9362 9363 9364 9365 9366 9367 9368 9369 9370 9371 9372 9373 9374 9375 9376 9377 9378 9379 9380 9381 9382 9383 9384 9385 9386 9387 9388 9389 9390 9391 9392 9393 9394 9395 9396 9397 9398 9399 9400 9401 9402 9403 9404 9405 9406 9407 9408 9409 9410 9411 9412 9413 9414 9415 9416 9417 9418 9419 9420 9421 9422 9423 9424 9425 9426 9427 9428 9429 9430 9431 9432 9433 9434 9435 9436 9437 9438 9439 9440 9441 9442 9443 9444 9445 9446 9447 9448 9449 9450 9451 9452 9453 9454 9455 9456 9457 9458 9459 9460 9461 9462 9463 9464 9465 9466 9467 9468 9469 9470 9471 9472 9473 9474 9475 9476 9477 9478 9479 9480 9481 9482 9483 9484 9485 9486 9487 9488 9489 9490 9491 9492 9493 9494 9495 9496 9497 9498 9499 9500 9501 9502 9503 9504 9505 9506 9507 9508 9509 9510 9511 9512 9513 9514 9515 9516 9517 9518 9519 9520 9521 9522 9523 9524 9525 9526 9527 9528 9529 9530 9531 9532 9533 9534 9535 9536 9537 9538 9539 9540 9541 9542 9543 9544 9545 9546 9547 9548 9549 9550 9551 9552 9553 9554 9555 9556 9557 9558 9559 9560 9561 9562 9563 9564 9565 9566 9567 9568 9569 9570 9571 9572 9573 9574 9575 9576 9577 9578 9579 9580 9581 9582 9583 9584 9585 9586 9587 9588 9589 9590 9591 9592 9593 9594 9595 9596 9597 9598 9599 9600 9601 9602 9603 9604 9605 9606 9607 9608 9609 9610 9611 9612 9613 9614 9615 9616 9617 9618 9619 9620 9621 9622 9623 9624 9625 9626 9627 9628 9629 9630 9631 9632 9633 9634 9635 9636 9637 9638 9639 9640 9641 9642 9643 9644 9645 9646 9647 9648 9649 9650 9651 9652 9653 9654 9655 9656 9657 9658 9659 9660 9661 9662 9663 9664 9665 9666 9667 9668 9669 9670 9671 9672 9673 9674 9675 9676 9677 9678 9679 9680 9681 9682 9683 9684 9685 9686 9687 9688 9689 9690 9691 9692 9693 9694 9695 9696 9697 9698 9699 9700 9701 9702 9703 9704 9705 9706 9707 9708 9709 9710 9711 9712 9713 9714 9715 9716 9717 9718 9719 9720 9721 9722 9723 9724 9725 9726 9727 9728 9729 9730 9731 9732 9733 9734 9735 9736 9737 9738 9739 9740 9741 9742 9743 9744 9745 9746 9747 9748 9749 9750 9751 9752 9753 9754 9755 9756 9757 9758 9759 9760 9761 9762 9763 9764 9765 9766 9767 9768 9769 9770 9771 9772 9773 9774 9775 9776 9777 9778 9779 9780 9781 9782 9783 9784 9785 9786 9787 9788 9789 9790 9791 9792 9793 9794 9795 9796 9797 9798 9799 9800 9801 9802 9803 9804 9805 9806 9807 9808 9809 9810 9811 9812 9813 9814 9815 9816 9817 9818 9819 9820 9821 9822 9823 9824 9825 9826 9827 9828 9829 9830 9831 9832 9833 9834 9835 9836 9837 9838 9839 9840 9841 9842 9843 9844 9845 9846 9847 9848 9849 9850 9851 9852 9853 9854 9855 9856 9857 9858 9859 9860 9861 9862 9863 9864 9865 9866 9867 9868 9869 9870 9871 9872 9873 9874 9875 9876 9877 9878 9879 9880 9881 9882 9883 9884 9885 9886 9887 9888 9889 9890 9891 9892 9893 9894 9895 9896 9897 9898 9899 9900 9901 9902 9903 9904 9905 9906 9907 9908 9909 9910 9911 9912 9913 9914 9915 9916 9917 9918 9919 9920 9921 9922 9923 9924 9925 9926 9927 9928 9929 9930 9931 9932 9933 9934 9935 9936 9937 9938 9939 9940 9941 9942 9943 9944 9945 9946 9947 9948 9949 9950 9951 9952 9953 9954 9955 9956 9957 9958 9959 9960 9961 9962 9963 9964 9965 9966 9967 9968 9969 9970 9971 9972 9973 9974 9975 9976 9977 9978 9979 9980 9981 9982 9983 9984 9985 9986 9987 9988 9989 9990 9991 9992 9993 9994 9995 9996 9997 9998 9999 10000 10001 10002 10003 10004 10005 10006 10007 10008 10009 10010 10011 10012 10013 10014 10015 10016 10017 10018 10019 10020 10021 10022 10023 10024 10025 10026 10027 10028 10029 10030 10031 10032 10033 10034 10035 10036 10037 10038 10039 10040 10041 10042 10043 10044 10045 10046 10047 10048 10049 10050 10051 10052 10053 10054 10055 10056 10057 10058 10059 10060 10061 10062 10063 10064 10065 10066 10067 10068 10069 10070 10071 10072 10073 10074 10075 10076 10077 10078 10079 10080 10081 10082 10083 10084 10085 10086 10087 10088 10089 10090 10091 10092 10093 10094 10095 10096 10097 10098 10099 10100 10101 10102 10103 10104 10105 10106 10107 10108 10109 10110 10111 10112 10113 10114 10115 10116 10117 10118 10119 10120 10121 10122 10123 10124 10125 10126 10127 10128 10129 10130 10131 10132 10133 10134 10135 10136 10137 10138 10139 10140 10141 10142 10143 10144 10145 10146 10147 10148 10149 10150 10151 10152 10153 10154 10155 10156 10157 10158 10159 10160 10161 10162 10163 10164 10165 10166 10167 10168 10169 10170 10171 10172 10173 10174 10175 10176 10177 10178 10179 10180 10181 10182 10183 10184 10185 10186 10187 10188 10189 10190 10191 10192 10193 10194 10195 10196 10197 10198 10199 10200 10201 10202 10203 10204 10205 10206 10207 10208 10209 10210 10211 10212 10213 10214 10215 10216 10217 10218 10219 10220 10221 10222 10223 10224 10225 10226 10227 10228 10229 10230 10231 10232 10233 10234 10235 10236 10237 10238 10239 10240 10241 10242 10243 10244 10245 10246 10247 10248 10249 10250 10251 10252 10253 10254 10255 10256 10257 10258 10259 10260 10261 10262 10263 10264 10265 10266 10267 10268 10269 10270 10271 10272 10273 10274 10275 10276 10277 10278 10279 10280 10281 10282 10283 10284 10285 10286 10287 10288 10289 10290 10291 10292 10293 10294 10295 10296 10297 10298 10299 10300 10301 10302 10303 10304 10305 10306 10307 10308 10309 10310 10311 10312 10313 10314 10315 10316 10317 10318 10319 10320 10321 10322 10323 10324 10325 10326 10327 10328 10329 10330 10331 10332 10333 10334 10335 10336 10337 10338 10339 10340 10341 10342 10343 10344 10345 10346 10347 10348 10349 10350 10351 10352 10353 10354 10355 10356 10357 10358 10359 10360 10361 10362 10363 10364 10365 10366 10367 10368 10369 10370 10371 10372 10373 10374 10375 10376 10377 10378 10379 10380 10381 10382 10383 10384 10385 10386 10387 10388 10389 10390 10391 10392 10393 10394 10395 10396 10397 10398 10399 10400 10401 10402 10403 10404 10405 10406 10407 10408 10409 10410 10411 10412 10413 10414 10415 10416 10417 10418 10419 10420 10421 10422 10423 10424 10425 10426 10427 10428 10429 10430 10431 10432 10433 10434 10435 10436 10437 10438 10439 10440 10441 10442 10443 10444 10445 10446 10447 10448 10449 10450 10451 10452 10453 10454 10455 10456 10457 10458 10459 10460 10461 10462 10463 10464 10465 10466 10467 10468 10469 10470 10471 10472 10473 10474 10475 10476 10477 10478 10479 10480 10481 10482 10483 10484 10485 10486 10487 10488 10489 10490 10491 10492 10493 10494 10495 10496 10497 10498 10499 10500 10501 10502 10503 10504 10505 10506 10507 10508 10509 10510 10511 10512 10513 10514 10515 10516 10517 10518 10519 10520 10521 10522 10523 10524 10525 10526 10527 10528 10529 10530 10531 10532 10533 10534 10535 10536 10537 10538 10539 10540 10541 10542 10543 10544 10545 10546 10547 10548 10549 10550 10551 10552 10553 10554 10555 10556 10557 10558 10559 10560 10561 10562 10563 10564 10565 10566 10567 10568 10569 10570 10571 10572 10573 10574 10575 10576 10577 10578 10579 10580 10581 10582 10583 10584 10585 10586 10587 10588 10589 10590 10591 10592 10593 10594 10595 10596 10597 10598 10599 10600 10601 10602 10603 10604 10605 10606 10607 10608 10609 10610 10611 10612 10613 10614 10615 10616 10617 10618 10619 10620 10621 10622 10623 10624 10625 10626 10627 10628 10629 10630 10631 10632 10633 10634 10635 10636 10637 10638 10639 10640 10641 10642 10643 10644 10645 10646 10647 10648 10649 10650 10651 10652 10653 10654 10655 10656 10657 10658 10659 10660 10661 10662 10663 10664 10665 10666 10667 10668 10669 10670 10671 10672 10673 10674 10675 10676 10677 10678 10679 10680 10681 10682 10683 10684 10685 10686 10687 10688 10689 10690 10691 10692 10693 10694 10695 10696 10697 10698 10699 10700 10701 10702 10703 10704 10705 10706 10707 10708 10709 10710 10711 10712 10713 10714 10715 10716 10717 10718 10719 10720 10721 10722 10723 10724 10725 10726 10727 10728 10729 10730 10731 10732 10733 10734 10735 10736 10737 10738 10739 10740 10741 10742 10743 10744 10745 10746 10747 10748 10749 10750 10751 10752 10753 10754 10755 10756 10757 10758 10759 10760 10761 10762 10763 10764 10765 10766 10767 10768 10769 10770 10771 10772 10773 10774 10775 10776 10777 10778 10779 10780 10781 10782 10783 10784 10785 10786 10787 10788 10789 10790 10791 10792 10793 10794 10795 10796 10797 10798 10799 10800 10801 10802 10803 10804 10805 10806 10807 10808 10809 10810 10811 10812 10813 10814 10815 10816 10817 10818 10819 10820 10821 10822 10823 10824 10825 10826 10827 10828 10829 10830 10831 10832 10833 10834 10835 10836 10837 10838 10839 10840 10841 10842 10843 10844 10845 10846 10847 10848 10849 10850 10851 10852 10853 10854 10855 10856 10857 10858 10859 10860 10861 10862 10863 10864 10865 10866 10867 10868 10869 10870 10871 10872 10873 10874 10875 10876 10877 10878 10879 10880 10881 10882 10883 10884 10885 10886 10887 10888 10889 10890 10891 10892 10893 10894 10895 10896 10897 10898 10899 10900 10901 10902 10903 10904 10905 10906 10907 10908 10909 10910 10911 10912 10913 10914 10915 10916 10917 10918 10919 10920 10921 10922 10923 10924 10925 10926 10927 10928 10929 10930 10931 10932 10933 10934 10935 10936 10937 10938 10939 10940 10941 10942 10943 10944 10945 10946 10947 10948 10949 10950 10951 10952 10953 10954 10955 10956 10957 10958 10959 10960 10961 10962 10963 10964 10965 10966 10967 10968 10969 10970 10971 10972 10973 10974 10975 10976 10977 10978 10979 10980 10981 10982 10983 10984 10985 10986 10987 10988 10989 10990 10991 10992 10993 10994 10995 10996 10997 10998 10999 11000 11001 11002 11003 11004 11005 11006 11007 11008 11009 11010 11011 11012 11013 11014 11015 11016 11017 11018 11019 11020 11021 11022 11023 11024 11025 11026 11027 11028 11029 11030 11031 11032 11033 11034 11035 11036 11037 11038 11039 11040 11041 11042 11043 11044 11045 11046 11047 11048 11049 11050 11051 11052 11053 11054 11055 11056 11057 11058 11059 11060 11061 11062 11063 11064 11065 11066 11067 11068 11069 11070 11071 11072 11073 11074 11075 11076 11077 11078 11079 11080 11081 11082 11083 11084 11085 11086 11087 11088 11089 11090 11091 11092 11093 11094 11095 11096 11097 11098 11099 11100 11101 11102 11103 11104 11105 11106 11107 11108 11109 11110 11111 11112 11113 11114 11115 11116 11117 11118 11119 11120 11121 11122 11123 11124 11125 11126 11127 11128 11129 11130 11131 11132 11133 11134 11135 11136 11137 11138 11139 11140 11141 11142 11143 11144 11145 11146 11147 11148 11149 11150 11151 11152 11153 11154 11155 11156 11157 11158 11159 11160 11161 11162 11163 11164 11165 11166 11167 11168 11169 11170 11171 11172 11173 11174 11175 11176 11177 11178 11179 11180 11181 11182 11183 11184 11185 11186 11187 11188 11189 11190 11191 11192 11193 11194 11195 11196 11197 11198 11199 11200 11201 11202 11203 11204 11205 11206 11207 11208 11209 11210 11211 11212 11213 11214 11215 11216 11217 11218 11219 11220 11221 11222 11223 11224 11225 11226 11227 11228 11229 11230 11231 11232 11233 11234 11235 11236 11237 11238 11239 11240 11241 11242 11243 11244 11245 11246 11247 11248 11249 11250 11251 11252 11253 11254 11255 11256 11257 11258 11259 11260 11261 11262 11263 11264 11265 11266 11267 11268 11269 11270 11271 11272 11273 11274 11275 11276 11277 11278 11279 11280 11281 11282 11283 11284 11285 11286 11287 11288 11289 11290 11291 11292 11293 11294 11295 11296 11297 11298 11299 11300 11301 11302 11303 11304 11305 11306 11307 11308 11309 11310 11311 11312 11313 11314 11315 11316 11317 11318 11319 11320 11321 11322 11323 11324 11325 11326 11327 11328 11329 11330 11331 11332 11333 11334 11335 11336 11337 11338 11339 11340 11341 11342 11343 11344 11345 11346 11347 11348 11349 11350 11351 11352 11353 11354 11355 11356 11357 11358 11359 11360 11361 11362 11363 11364 11365 11366 11367 11368 11369 11370 11371 11372 11373 11374 11375 11376 11377 11378 11379 11380 11381 11382 11383 11384 11385 11386 11387 11388 11389 11390 11391 11392 11393 11394 11395 11396 11397 11398 11399 11400 11401 11402 11403 11404 11405 11406 11407 11408 11409 11410 11411 11412 11413 11414 11415 11416 11417 11418 11419 11420 11421 11422 11423 11424 11425 11426 11427 11428 11429 11430 11431 11432 11433 11434 11435 11436 11437 11438 11439 11440 11441 11442 11443 11444 11445 11446 11447 11448 11449 11450 11451 11452 11453 11454 11455 11456 11457 11458 11459 11460 11461 11462 11463 11464 11465 11466 11467 11468 11469 11470 11471 11472 11473 11474 11475 11476 11477 11478 11479 11480 11481 11482 11483 11484 11485 11486 11487 11488 11489 11490 11491 11492 11493 11494 11495 11496 11497 11498 11499 11500 11501 11502 11503 11504 11505 11506 11507 11508 11509 11510 11511 11512 11513 11514 11515 11516 11517 11518 11519 11520 11521 11522 11523 11524 11525 11526 11527 11528 11529 11530 11531 11532 11533 11534 11535 11536 11537 11538 11539 11540 11541 11542 11543 11544 11545 11546 11547 11548 11549 11550 11551 11552 11553 11554 11555 11556 11557 11558 11559 11560 11561 11562 11563 11564 11565 11566 11567 11568 11569 11570 11571 11572 11573 11574 11575 11576 11577 11578 11579 11580 11581 11582 11583 11584 11585 11586 11587 11588 11589 11590 11591 11592 11593 11594 11595 11596 11597 11598 11599 11600 11601 11602 11603 11604 11605 11606 11607 11608 11609 11610 11611 11612 11613 11614 11615 11616 11617 11618 11619 11620 11621 11622 11623 11624 11625 11626 11627 11628 11629 11630 11631 11632 11633 11634 11635 11636 11637 11638 11639 11640 11641 11642 11643 11644 11645 11646 11647 11648 11649 11650 11651 11652 11653 11654 11655 11656 11657 11658 11659 11660 11661 11662 11663 11664 11665 11666 11667 11668 11669 11670 11671 11672 11673 11674 11675 11676 11677 11678 11679 11680 11681 11682 11683 11684 11685 11686 11687 11688 11689 11690 11691 11692 11693 11694 11695 11696 11697 11698 11699 11700 11701 11702 11703 11704 11705 11706 11707 11708 11709 11710 11711 11712 11713 11714 11715 11716 11717 11718 11719 11720 11721 11722 11723 11724 11725 11726 11727 11728 11729 11730 11731 11732 11733 11734 11735 11736 11737 11738 11739 11740 11741 11742 11743 11744 11745 11746 11747 11748 11749 11750 11751 11752 11753 11754 11755 11756 11757 11758 11759 11760 11761 11762 11763 11764 11765 11766 11767 11768 11769 11770 11771 11772 11773 11774 11775 11776 11777 11778 11779 11780 11781 11782 11783 11784 11785 11786 11787 11788 11789 11790 11791 11792 11793 11794 11795 11796 11797 11798 11799 11800 11801 11802 11803 11804 11805 11806 11807 11808 11809 11810 11811 11812 11813 11814 11815 11816 11817 11818 11819 11820 11821 11822 11823 11824 11825 11826 11827 11828 11829 11830 11831 11832 11833 11834 11835 11836 11837 11838 11839 11840 11841 11842 11843 11844 11845 11846 11847 11848 11849 11850 11851 11852 11853 11854 11855 11856 11857 11858 11859 11860 11861 11862 11863 11864 11865 11866 11867 11868 11869 11870 11871 11872 11873 11874 11875 11876 11877 11878 11879 11880 11881 11882 11883 11884 11885 11886 11887 11888 11889 11890 11891 11892 11893 11894 11895 11896 11897 11898 11899 11900 11901 11902 11903 11904 11905 11906 11907 11908 11909 11910 11911 11912 11913 11914 11915 11916 11917 11918 11919 11920 11921 11922 11923 11924 11925 11926 11927 11928 11929 11930 11931 11932 11933 11934 11935 11936 11937 11938 11939 11940 11941 11942 11943 11944 11945 11946 11947 11948 11949 11950 11951 11952 11953 11954 11955 11956 11957 11958 11959 11960 11961 11962 11963 11964 11965 11966 11967 11968 11969 11970 11971 11972 11973 11974 11975 11976 11977 11978 11979 11980 11981 11982 11983 11984 11985 11986 11987 11988 11989 11990 11991 11992 11993 11994 11995 11996 11997 11998 11999 12000 12001 12002 12003 12004 12005 12006 12007 12008 12009 12010 12011 12012 12013 12014 12015 12016 12017 12018 12019 12020 12021 12022 12023 12024 12025 12026 12027 12028 12029 12030 12031 12032 12033 12034 12035 12036 12037 12038 12039 12040 12041 12042 12043 12044 12045 12046 12047 12048 12049 12050 12051 12052 12053 12054 12055 12056 12057 12058 12059 12060 12061 12062 12063 12064 12065 12066 12067 12068 12069 12070 12071 12072 12073 12074 12075 12076 12077 12078 12079 12080 12081 12082 12083 12084 12085 12086 12087 12088 12089 12090 12091 12092 12093 12094 12095 12096 12097 12098 12099 12100 12101 12102 12103 12104 12105 12106 12107 12108 12109 12110 12111 12112 12113 12114 12115 12116 12117 12118 12119 12120 12121 12122 12123 12124 12125 12126 12127 12128 12129 12130 12131 12132 12133 12134 12135 12136 12137 12138 12139 12140 12141 12142 12143 12144 12145 12146 12147 12148 12149 12150 12151 12152 12153 12154 12155 12156 12157 12158 12159 12160 12161 12162 12163 12164 12165 12166 12167 12168 12169 12170 12171 12172 12173 12174 12175 12176 12177 12178 12179 12180 12181 12182 12183 12184 12185 12186 12187 12188 12189 12190 12191 12192 12193 12194 12195 12196 12197 12198 12199 12200 12201 12202 12203 12204 12205 12206 12207 12208 12209 12210 12211 12212 12213 12214 12215 12216 12217 12218 12219 12220 12221 12222 12223 12224 12225 12226 12227 12228 12229 12230 12231 12232 12233 12234 12235 12236 12237 12238 12239 12240 12241 12242 12243 12244 12245 12246 12247 12248 12249 12250 12251 12252 12253 12254 12255 12256 12257 12258 12259 12260 12261 12262 12263 12264 12265 12266 12267 12268 12269 12270 12271 12272 12273 12274 12275 12276 12277 12278 12279 12280 12281 12282 12283 12284 12285 12286 12287 12288 12289 12290 12291 12292 12293 12294 12295 12296 12297 12298 12299 12300 12301 12302 12303 12304 12305 12306 12307 12308 12309 12310 12311 12312 12313 12314 12315 12316 12317 12318 12319 12320 12321 12322 12323 12324 12325 12326 12327 12328 12329 12330 12331 12332 12333 12334 12335 12336 12337 12338 12339 12340 12341 12342 12343 12344 12345 12346 12347 12348 12349 12350 12351 12352 12353 12354 12355 12356 12357 12358 12359 12360 12361 12362 12363 12364 12365 12366 12367 12368 12369 12370 12371 12372 12373 12374 12375 12376 12377 12378 12379 12380 12381 12382 12383 12384 12385 12386 12387 12388 12389 12390 12391 12392 12393 12394 12395 12396 12397 12398 12399 12400 12401 12402 12403 12404 12405 12406 12407 12408 12409 12410 12411 12412 12413 12414 12415 12416 12417 12418 12419 12420 12421 12422 12423 12424 12425 12426 12427 12428 12429 12430 12431 12432 12433 12434 12435 12436 12437 12438 12439 12440 12441 12442 12443 12444 12445 12446 12447 12448 12449 12450 12451 12452 12453 12454 12455 12456 12457 12458 12459 12460 12461 12462 12463 12464 12465 12466 12467 12468 12469 12470 12471 12472 12473 12474 12475 12476 12477 12478 12479 12480 12481 12482 12483 12484 12485 12486 12487 12488 12489 12490 12491 12492 12493 12494 12495 12496 12497 12498 12499 12500 12501 12502 12503 12504 12505 12506 12507 12508 12509 12510 12511 12512 12513 12514 12515 12516 12517 12518 12519 12520 12521 12522 12523 12524 12525 12526 12527 12528 12529 12530 12531 12532 12533 12534 12535 12536 12537 12538 12539 12540 12541 12542 12543 12544 12545 12546 12547 12548 12549 12550 12551 12552 12553 12554 12555 12556 12557 12558 12559 12560 12561 12562 12563 12564 12565 12566 12567 12568 12569 12570 12571 12572 12573 12574 12575 12576 12577 12578 12579 12580 12581 12582 12583 12584 12585 12586 12587 12588 12589 12590 12591 12592 12593 12594 12595 12596 12597 12598 12599 12600 12601 12602 12603 12604 12605 12606 12607 12608 12609 12610 12611 12612 12613 12614 12615 12616 12617 12618 12619 12620 12621 12622 12623 12624 12625 12626 12627 12628 12629 12630 12631 12632 12633 12634 12635 12636 12637 12638 12639 12640 12641 12642 12643 12644 12645 12646 12647 12648 12649 12650 12651 12652 12653 12654 12655 12656 12657 12658 12659 12660 12661 12662 12663 12664 12665 12666 12667 12668 12669 12670 12671 12672 12673 12674 12675 12676 12677 12678 12679 12680 12681 12682 12683 12684 12685 12686 12687 12688 12689 12690 12691 12692 12693 12694 12695 12696 12697 12698 12699 12700 12701 12702 12703 12704 12705 12706 12707 12708 12709 12710 12711 12712 12713 12714 12715 12716 12717 12718 12719 12720 12721 12722 12723 12724 12725 12726 12727 12728 12729 12730 12731 12732 12733 12734 12735 12736 12737 12738 12739 12740 12741 12742 12743 12744 12745 12746 12747 12748 12749 12750 12751 12752 12753 12754 12755 12756 12757 12758 12759 12760 12761 12762 12763 12764 12765 12766 12767 12768 12769 12770 12771 12772 12773 12774 12775 12776 12777 12778 12779 12780 12781 12782 12783 12784 12785 12786 12787 12788 12789 12790 12791 12792 12793 12794 12795 12796 12797 12798 12799 12800 12801 12802 12803 12804 12805 12806 12807 12808 12809 12810 12811 12812 12813 12814 12815 12816 12817 12818 12819 12820 12821 12822 12823 12824 12825 12826 12827 12828 12829 12830 12831 12832 12833 12834 12835 12836 12837 12838 12839 12840 12841 12842 12843 12844 12845 12846 12847 12848 12849 12850 12851 12852 12853 12854 12855 12856 12857 12858 12859 12860 12861 12862 12863 12864 12865 12866 12867 12868 12869 12870 12871 12872 12873 12874 12875 12876 12877 12878 12879 12880 12881 12882 12883 12884 12885 12886 12887 12888 12889 12890 12891 12892 12893 12894 12895 12896 12897 12898 12899 12900 12901 12902 12903 12904 12905 12906 12907 12908 12909 12910 12911 12912 12913 12914 12915 12916 12917 12918 12919 12920 12921 12922 12923 12924 12925 12926 12927 12928 12929 12930 12931 12932 12933 12934 12935 12936 12937 12938 12939 12940 12941 12942 12943 12944 12945 12946 12947 12948 12949 12950 12951 12952 12953 12954 12955 12956 12957 12958 12959 12960 12961 12962 12963 12964 12965 12966 12967 12968 12969 12970 12971 12972 12973 12974 12975 12976 12977 12978 12979 12980 12981 12982 12983 12984 12985 12986 12987 12988 12989 12990 12991 12992 12993 12994 12995 12996 12997 12998 12999 13000 13001 13002 13003 13004 13005 13006 13007 13008 13009 13010 13011 13012 13013 13014 13015 13016 13017 13018 13019 13020 13021 13022 13023 13024 13025 13026 13027 13028 13029 13030 13031 13032 13033 13034 13035 13036 13037 13038 13039 13040 13041 13042 13043 13044 13045 13046 13047 13048 13049 13050 13051 13052 13053 13054 13055 13056 13057 13058 13059 13060 13061 13062 13063 13064 13065 13066 13067 13068 13069 13070 13071 13072 13073 13074 13075 13076 13077 13078 13079 13080 13081 13082 13083 13084 13085 13086 13087 13088 13089 13090 13091 13092 13093 13094 13095 13096 13097 13098 13099 13100 13101 13102 13103 13104 13105 13106 13107 13108 13109 13110 13111 13112 13113 13114 13115 13116 13117 13118 13119 13120 13121 13122 13123 13124 13125 13126 13127 13128 13129 13130 13131 13132 13133 13134 13135 13136 13137 13138 13139 13140 13141 13142 13143 13144 13145 13146 13147 13148 13149 13150 13151 13152 13153 13154 13155 13156 13157 13158 13159 13160 13161 13162 13163 13164 13165 13166 13167 13168 13169 13170 13171 13172 13173 13174 13175 13176 13177 13178 13179 13180 13181 13182 13183 13184 13185 13186 13187 13188 13189 13190 13191 13192 13193 13194 13195 13196 13197 13198 13199 13200 13201 13202 13203 13204 13205 13206 13207 13208 13209 13210 13211 13212 13213 13214 13215 13216 13217 13218 13219 13220 13221 13222 13223 13224 13225 13226 13227 13228 13229 13230 13231 13232 13233 13234 13235 13236 13237 13238 13239 13240 13241 13242 13243 13244 13245 13246 13247 13248 13249 13250 13251 13252 13253 13254 13255 13256 13257 13258 13259 13260 13261 13262 13263 13264 13265 13266 13267 13268 13269 13270 13271 13272 13273 13274 13275 13276 13277 13278 13279 13280 13281 13282 13283 13284 13285 13286 13287 13288 13289 13290 13291 13292 13293 13294 13295 13296 13297 13298 13299 13300 13301 13302 13303 13304 13305 13306 13307 13308 13309 13310 13311 13312 13313 13314 13315 13316 13317 13318 13319 13320 13321 13322 13323 13324 13325 13326 13327 13328 13329 13330 13331 13332 13333 13334 13335 13336 13337 13338 13339 13340 13341 13342 13343 13344 13345 13346 13347 13348 13349 13350 13351 13352 13353 13354 13355 13356 13357 13358 13359 13360 13361 13362 13363 13364 13365 13366 13367 13368 13369 13370 13371 13372 13373 13374 13375 13376 13377 13378 13379 13380 13381 13382 13383 13384 13385 13386 13387 13388 13389 13390 13391 13392 13393 13394 13395 13396 13397 13398 13399 13400 13401 13402 13403 13404 13405 13406 13407 13408 13409 13410 13411 13412 13413 13414 13415 13416 13417 13418 13419 13420 13421 13422 13423 13424 13425 13426 13427 13428 13429 13430 13431 13432 13433 13434 13435 13436 13437 13438 13439 13440 13441 13442 13443 13444 13445 13446 13447 13448 13449 13450 13451 13452 13453 13454 13455 13456 13457 13458 13459 13460 13461 13462 13463 13464 13465 13466 13467 13468 13469 13470 13471 13472 13473 13474 13475 13476 13477 13478 13479 13480 13481 13482 13483 13484 13485 13486 13487 13488 13489 13490 13491 13492 13493 13494 13495 13496 13497 13498 13499 13500 13501 13502 13503 13504 13505 13506 13507 13508 13509 13510 13511 13512 13513 13514 13515 13516 13517 13518 13519 13520 13521 13522 13523 13524 13525 13526 13527 13528 13529 13530 13531 13532 13533 13534 13535 13536 13537 13538 13539 13540 13541 13542 13543 13544 13545 13546 13547 13548 13549 13550 13551 13552 13553 13554 13555 13556 13557 13558 13559 13560 13561 13562 13563 13564 13565 13566 13567 13568 13569 13570 13571 13572 13573 13574 13575 13576 13577 13578 13579 13580 13581 13582 13583 13584 13585 13586 13587 13588 13589 13590 13591 13592 13593 13594 13595 13596 13597 13598 13599 13600 13601 13602 13603 13604 13605 13606 13607 13608 13609 13610 13611 13612 13613 13614 13615 13616 13617 13618 13619 13620 13621 13622 13623 13624 13625 13626 13627 13628 13629 13630 13631 13632 13633 13634 13635 13636 13637 13638 13639 13640 13641 13642 13643 13644 13645 13646 13647 13648 13649 13650 13651 13652 13653 13654 13655 13656 13657 13658 13659 13660 13661 13662 13663 13664 13665 13666 13667 13668 13669 13670 13671 13672 13673 13674 13675 13676 13677 13678 13679 13680 13681 13682 13683 13684 13685 13686 13687 13688 13689 13690 13691 13692 13693 13694 13695 13696 13697 13698 13699 13700 13701 13702 13703 13704 13705 13706 13707 13708 13709 13710 13711 13712 13713 13714 13715 13716 13717 13718 13719 13720 13721 13722 13723 13724 13725 13726 13727 13728 13729 13730 13731 13732 13733 13734 13735 13736 13737 13738 13739 13740 13741 13742 13743 13744 13745 13746 13747 13748 13749 13750 13751 13752 13753 13754 13755 13756 13757 13758 13759 13760 13761 13762 13763 13764 13765 13766 13767 13768 13769 13770 13771 13772 13773 13774 13775 13776 13777 13778 13779 13780 13781 13782 13783 13784 13785 13786 13787 13788 13789 13790 13791 13792 13793 13794 13795 13796 13797 13798 13799 13800 13801 13802 13803 13804 13805 13806 13807 13808 13809 13810 13811 13812 13813 13814 13815 13816 13817 13818 13819 13820 13821 13822 13823 13824 13825 13826 13827 13828 13829 13830 13831 13832 13833 13834 13835 13836 13837 13838 13839 13840 13841 13842 13843 13844 13845 13846 13847 13848 13849 13850 13851 13852 13853 13854 13855 13856 13857 13858 13859 13860 13861 13862 13863 13864 13865 13866 13867 13868 13869 13870 13871 13872 13873 13874 13875 13876 13877 13878 13879 13880 13881 13882 13883 13884 13885 13886 13887 13888 13889 13890 13891 13892 13893 13894 13895 13896 13897 13898 13899 13900 13901 13902 13903 13904 13905 13906 13907 13908 13909 13910 13911 13912 13913 13914 13915 13916 13917 13918 13919 13920 13921 13922 13923 13924 13925 13926 13927 13928 13929 13930 13931 13932 13933 13934 13935 13936 13937 13938 13939 13940 13941 13942 13943 13944 13945 13946 13947 13948 13949 13950 13951 13952 13953 13954 13955 13956 13957 13958 13959 13960 13961 13962 13963 13964 13965 13966 13967 13968 13969 13970 13971 13972 13973 13974 13975 13976 13977 13978 13979 13980 13981 13982 13983 13984 13985 13986 13987 13988 13989 13990 13991 13992 13993 13994 13995 13996 13997 13998 13999 14000 14001 14002 14003 14004 14005 14006 14007 14008 14009 14010 14011 14012 14013 14014 14015 14016 14017 14018 14019 14020 14021 14022 14023 14024 14025 14026 14027 14028 14029 14030 14031 14032 14033 14034 14035 14036 14037 14038 14039 14040 14041 14042 14043 14044 14045 14046 14047 14048 14049 14050 14051 14052 14053 14054 14055 14056 14057 14058 14059 14060 14061 14062 14063 14064 14065 14066 14067 14068 14069 14070 14071 14072 14073 14074 14075 14076 14077 14078 14079 14080 14081 14082 14083 14084 14085 14086 14087 14088 14089 14090 14091 14092 14093 14094 14095 14096 14097 14098 14099 14100 14101 14102 14103 14104 14105 14106 14107 14108 14109 14110 14111 14112 14113 14114 14115 14116 14117 14118 14119 14120 14121 14122 14123 14124 14125 14126 14127 14128 14129 14130 14131 14132 14133 14134 14135 14136 14137 14138 14139 14140 14141 14142 14143 14144 14145 14146 14147 14148 14149 14150 14151 14152 14153 14154 14155 14156 14157 14158 14159 14160 14161 14162 14163 14164 14165 14166 14167 14168 14169 14170 14171 14172 14173 14174 14175 14176 14177 14178 14179 14180 14181 14182 14183 14184 14185 14186 14187 14188 14189 14190 14191 14192 14193 14194 14195 14196 14197 14198 14199 14200 14201 14202 14203 14204 14205 14206 14207 14208 14209 14210 14211 14212 14213 14214 14215 14216 14217 14218 14219 14220 14221 14222 14223 14224 14225 14226 14227 14228 14229 14230 14231 14232 14233 14234 14235 14236 14237 14238 14239 14240 14241 14242 14243 14244 14245 14246 14247 14248 14249 14250 14251 14252 14253 14254 14255 14256 14257 14258 14259 14260 14261 14262 14263 14264 14265 14266 14267 14268 14269 14270 14271 14272 14273 14274 14275 14276 14277 14278 14279 14280 14281 14282 14283 14284 14285 14286 14287 14288 14289 14290 14291 14292 14293 14294 14295 14296 14297 14298 14299 14300 14301 14302 14303 14304 14305 14306 14307 14308 14309 14310 14311 14312 14313 14314 14315 14316 14317 14318 14319 14320 14321 14322 14323 14324 14325 14326 14327 14328 14329 14330 14331 14332 14333 14334 14335 14336 14337 14338 14339 14340 14341 14342 14343 14344 14345 14346 14347 14348 14349 14350 14351 14352 14353 14354 14355 14356 14357 14358 14359 14360 14361 14362 14363 14364 14365 14366 14367 14368 14369 14370 14371 14372 14373 14374 14375 14376 14377 14378 14379 14380 14381 14382 14383 14384 14385 14386 14387 14388 14389 14390 14391 14392 14393 14394 14395 14396 14397 14398 14399 14400 14401 14402 14403 14404 14405 14406 14407 14408 14409 14410 14411 14412 14413 14414 14415 14416 14417 14418 14419 14420 14421 14422 14423 14424 14425 14426 14427 14428 14429 14430 14431 14432 14433 14434 14435 14436 14437 14438 14439 14440 14441 14442 14443 14444 14445 14446 14447 14448 14449 14450 14451 14452 14453 14454 14455 14456 14457 14458 14459 14460 14461 14462 14463 14464 14465 14466 14467 14468 14469 14470 14471 14472 14473 14474 14475 14476 14477 14478 14479 14480 14481 14482 14483 14484 14485 14486 14487 14488 14489 14490 14491 14492 14493 14494 14495 14496 14497 14498 14499 14500 14501 14502 14503 14504 14505 14506 14507 14508 14509 14510 14511 14512 14513 14514 14515 14516 14517 14518 14519 14520 14521 14522 14523 14524 14525 14526 14527 14528 14529 14530 14531 14532 14533 14534 14535 14536 14537 14538 14539 14540 14541 14542 14543 14544 14545 14546 14547 14548 14549 14550 14551 14552 14553 14554 14555 14556 14557 14558 14559 14560 14561 14562 14563 14564 14565 14566 14567 14568 14569 14570 14571 14572 14573 14574 14575 14576 14577 14578 14579 14580 14581 14582 14583 14584 14585 14586 14587 14588 14589 14590 14591 14592 14593 14594 14595 14596 14597 14598 14599 14600 14601 14602 14603 14604 14605 14606 14607 14608 14609 14610 14611 14612 14613 14614 14615 14616 14617 14618 14619 14620 14621 14622 14623 14624 14625 14626 14627 14628 14629 14630 14631 14632 14633 14634 14635 14636 14637 14638 14639 14640 14641 14642 14643 14644 14645 14646 14647 14648 14649 14650 14651 14652 14653 14654 14655 14656 14657 14658 14659 14660 14661 14662 14663 14664 14665 14666 14667 14668 14669 14670 14671 14672 14673 14674 14675 14676 14677 14678 14679 14680 14681 14682 14683 14684 14685 14686 14687 14688 14689 14690 14691 14692 14693 14694 14695 14696 14697 14698 14699 14700 14701 14702 14703 14704 14705 14706 14707 14708 14709 14710 14711 14712 14713 14714 14715 14716 14717 14718 14719 14720 14721 14722 14723 14724 14725 14726 14727 14728 14729 14730 14731 14732 14733 14734 14735 14736 14737 14738 14739 14740 14741 14742 14743 14744 14745 14746 14747 14748 14749 14750 14751 14752 14753 14754 14755 14756 14757 14758 14759 14760 14761 14762 14763 14764 14765 14766 14767 14768 14769 14770 14771 14772 14773 14774 14775 14776 14777 14778 14779 14780 14781 14782 14783 14784 14785 14786 14787 14788 14789 14790 14791 14792 14793 14794 14795 14796 14797 14798 14799 14800 14801 14802 14803 14804 14805 14806 14807 14808 14809 14810 14811 14812 14813 14814 14815 14816 14817 14818 14819 14820 14821 14822 14823 14824 14825 14826 14827 14828 14829 14830 14831 14832 14833 14834 14835 14836 14837 14838 14839 14840 14841 14842 14843 14844 14845 14846 14847 14848 14849 14850 14851 14852 14853 14854 14855 14856 14857 14858 14859 14860 14861 14862 14863 14864 14865 14866 14867 14868 14869 14870 14871 14872 14873 14874 14875 14876 14877 14878 14879 14880 14881 14882 14883 14884 14885 14886 14887 14888 14889 14890 14891 14892 14893 14894 14895 14896 14897 14898 14899 14900 14901 14902 14903 14904 14905 14906 14907 14908 14909 14910 14911 14912 14913 14914 14915 14916 14917 14918 14919 14920 14921 14922 14923 14924 14925 14926 14927 14928 14929 14930 14931 14932 14933 14934 14935 14936 14937 14938 14939 14940 14941 14942 14943 14944 14945 14946 14947 14948 14949 14950 14951 14952 14953 14954 14955 14956 14957 14958 14959 14960 14961 14962 14963 14964 14965 14966 14967 14968 14969 14970 14971 14972 14973 14974 14975 14976 14977 14978 14979 14980 14981 14982 14983 14984 14985 14986 14987 14988 14989 14990 14991 14992 14993 14994 14995 14996 14997 14998 14999 15000 15001 15002 15003 15004 15005 15006 15007 15008 15009 15010 15011 15012 15013 15014 15015 15016 15017 15018 15019 15020 15021 15022 15023 15024 15025 15026 15027 15028 15029 15030 15031 15032 15033 15034 15035 15036 15037 15038 15039 15040 15041 15042 15043 15044 15045 15046 15047 15048 15049 15050 15051 15052 15053 15054 15055 15056 15057 15058 15059 15060 15061 15062 15063 15064 15065 15066 15067 15068 15069 15070 15071 15072 15073 15074 15075 15076 15077 15078 15079 15080 15081 15082 15083 15084 15085 15086 15087 15088 15089 15090 15091 15092 15093 15094 15095 15096 15097 15098 15099 15100 15101 15102 15103 15104 15105 15106 15107 15108 15109 15110 15111 15112 15113 15114 15115 15116 15117 15118 15119 15120 15121 15122 15123 15124 15125 15126 15127 15128 15129 15130 15131 15132 15133 15134 15135 15136 15137 15138 15139 15140 15141 15142 15143 15144 15145 15146 15147 15148 15149 15150 15151 15152 15153 15154 15155 15156 15157 15158 15159 15160 15161 15162 15163 15164 15165 15166 15167 15168 15169 15170 15171 15172 15173 15174 15175 15176 15177 15178 15179 15180 15181 15182 15183 15184 15185 15186 15187 15188 15189 15190 15191 15192 15193 15194 15195 15196 15197 15198 15199 15200 15201 15202 15203 15204 15205 15206 15207 15208 15209 15210 15211 15212 15213 15214 15215 15216 15217 15218 15219 15220 15221 15222 15223 15224 15225 15226 15227 15228 15229 15230 15231 15232 15233 15234 15235 15236 15237 15238 15239 15240 15241 15242 15243 15244 15245 15246 15247 15248 15249 15250 15251 15252 15253 15254 15255 15256 15257 15258 15259 15260 15261 15262 15263 15264 15265 15266 15267 15268 15269 15270 15271 15272 15273 15274 15275 15276 15277 15278 15279 15280 15281 15282 15283 15284 15285 15286 15287 15288 15289 15290 15291 15292 15293 15294 15295 15296 15297 15298 15299 15300 15301 15302 15303 15304 15305 15306 15307 15308 15309 15310 15311 15312 15313 15314 15315 15316 15317 15318 15319 15320 15321 15322 15323 15324 15325 15326 15327 15328 15329 15330 15331 15332 15333 15334 15335 15336 15337 15338 15339 15340 15341 15342 15343 15344 15345 15346 15347 15348 15349 15350 15351 15352 15353 15354 15355 15356 15357 15358 15359 15360 15361 15362 15363 15364 15365 15366 15367 15368 15369 15370 15371 15372 15373 15374 15375 15376 15377 15378 15379 15380 15381 15382 15383 15384 15385 15386 15387 15388 15389 15390 15391 15392 15393 15394 15395 15396 15397 15398 15399 15400 15401 15402 15403 15404 15405 15406 15407 15408 15409 15410 15411 15412 15413 15414 15415 15416 15417 15418 15419 15420 15421 15422 15423 15424 15425 15426 15427 15428 15429 15430 15431 15432 15433 15434 15435 15436 15437 15438 15439 15440 15441 15442 15443 15444 15445 15446 15447 15448 15449 15450 15451 15452 15453 15454 15455 15456 15457 15458 15459 15460 15461 15462 15463 15464 15465 15466 15467 15468 15469 15470 15471 15472 15473 15474 15475 15476 15477 15478 15479 15480 15481 15482 15483 15484 15485 15486 15487 15488 15489 15490 15491 15492 15493 15494 15495 15496 15497 15498 15499 15500 15501 15502 15503 15504 15505 15506 15507 15508 15509 15510 15511 15512 15513 15514 15515 15516 15517 15518 15519 15520 15521 15522 15523 15524 15525 15526 15527 15528 15529 15530 15531 15532 15533 15534 15535 15536 15537 15538 15539 15540 15541 15542 15543 15544 15545 15546 15547 15548 15549 15550 15551 15552 15553 15554 15555 15556 15557 15558 15559 15560 15561 15562 15563 15564 15565 15566 15567 15568 15569 15570 15571 15572 15573 15574 15575 15576 15577 15578 15579 15580 15581 15582 15583 15584 15585 15586 15587 15588 15589 15590 15591 15592 15593 15594 15595 15596 15597 15598 15599 15600 15601 15602 15603 15604 15605 15606 15607 15608 15609 15610 15611 15612 15613 15614 15615 15616 15617 15618 15619 15620 15621 15622 15623 15624 15625 15626 15627 15628 15629 15630 15631 15632 15633 15634 15635 15636 15637 15638 15639 15640 15641 15642 15643 15644 15645 15646 15647 15648 15649 15650 15651 15652 15653 15654 15655 15656 15657 15658 15659 15660 15661 15662 15663 15664 15665 15666 15667 15668 15669 15670 15671 15672 15673 15674 15675 15676 15677 15678 15679 15680 15681 15682 15683 15684 15685 15686 15687 15688 15689 15690 15691 15692 15693 15694 15695 15696 15697 15698 15699 15700 15701 15702 15703 15704 15705 15706 15707 15708 15709 15710 15711 15712 15713 15714 15715 15716 15717 15718 15719 15720 15721 15722 15723 15724 15725 15726 15727 15728 15729 15730 15731 15732 15733 15734 15735 15736 15737 15738 15739 15740 15741 15742 15743 15744 15745 15746 15747 15748 15749 15750 15751 15752 15753 15754 15755 15756 15757 15758 15759 15760 15761 15762 15763 15764 15765 15766 15767 15768 15769 15770 15771 15772 15773 15774 15775 15776 15777 15778 15779 15780 15781 15782 15783 15784 15785 15786 15787 15788 15789 15790 15791 15792 15793 15794 15795 15796 15797 15798 15799 15800 15801 15802 15803 15804 15805 15806 15807 15808 15809 15810 15811 15812 15813 15814 15815 15816 15817 15818 15819 15820 15821 15822 15823 15824 15825 15826 15827 15828 15829 15830 15831 15832 15833 15834 15835 15836 15837 15838 15839 15840 15841 15842 15843 15844 15845 15846 15847 15848 15849 15850 15851 15852 15853 15854 15855 15856 15857 15858 15859 15860 15861 15862 15863 15864 15865 15866 15867 15868 15869 15870 15871 15872 15873 15874 15875 15876 15877 15878 15879 15880 15881 15882 15883 15884 15885 15886 15887 15888 15889 15890 15891 15892 15893 15894 15895 15896 15897 15898 15899 15900 15901 15902 15903 15904 15905 15906 15907 15908 15909 15910 15911 15912 15913 15914 15915 15916 15917 15918 15919 15920 15921 15922 15923 15924 15925 15926 15927 15928 15929 15930 15931 15932 15933 15934 15935 15936 15937 15938 15939 15940 15941 15942 15943 15944 15945 15946 15947 15948 15949 15950 15951 15952 15953 15954 15955 15956 15957 15958 15959 15960 15961 15962 15963 15964 15965 15966 15967 15968 15969 15970 15971 15972 15973 15974 15975 15976 15977 15978 15979 15980 15981 15982 15983 15984 15985 15986 15987 15988 15989 15990 15991 15992 15993 15994 15995 15996 15997 15998 15999 16000 16001 16002 16003 16004 16005 16006 16007 16008 16009 16010 16011 16012 16013 16014 16015 16016 16017 16018 16019 16020 16021 16022 16023 16024 16025 16026 16027 16028 16029 16030 16031 16032 16033 16034 16035 16036 16037 16038 16039 16040 16041 16042 16043 16044 16045 16046 16047 16048 16049 16050 16051 16052 16053 16054 16055 16056 16057 16058 16059 16060 16061 16062 16063 16064 16065 16066 16067 16068 16069 16070 16071 16072 16073 16074 16075 16076 16077 16078 16079 16080 16081 16082 16083 16084 16085 16086 16087 16088 16089 16090 16091 16092 16093 16094 16095 16096 16097 16098 16099 16100 16101 16102 16103 16104 16105 16106 16107 16108 16109 16110 16111 16112 16113 16114 16115 16116 16117 16118 16119 16120 16121 16122 16123 16124 16125 16126 16127 16128 16129 16130 16131 16132 16133 16134 16135 16136 16137 16138 16139 16140 16141 16142 16143 16144 16145 16146 16147 16148 16149 16150 16151 16152 16153 16154 16155 16156 16157 16158 16159 16160 16161 16162 16163 16164 16165 16166 16167 16168 16169 16170 16171 16172 16173 16174 16175 16176 16177 16178 16179 16180 16181 16182 16183 16184 16185 16186 16187 16188 16189 16190 16191 16192 16193 16194 16195 16196 16197 16198 16199 16200 16201 16202 16203 16204 16205 16206 16207 16208 16209 16210 16211 16212 16213 16214 16215 16216 16217 16218 16219 16220 16221 16222 16223 16224 16225 16226 16227 16228 16229 16230 16231 16232 16233 16234 16235 16236 16237 16238 16239 16240 16241 16242 16243 16244 16245 16246 16247 16248 16249 16250 16251 16252 16253 16254 16255 16256 16257 16258 16259 16260 16261 16262 16263 16264 16265 16266 16267 16268 16269 16270 16271 16272 16273 16274 16275 16276 16277 16278 16279 16280 16281 16282 16283 16284 16285 16286 16287 16288 16289 16290 16291 16292 16293 16294 16295 16296 16297 16298 16299 16300 16301 16302 16303 16304 16305 16306 16307 16308 16309 16310 16311 16312 16313 16314 16315 16316 16317 16318 16319 16320 16321 16322 16323 16324 16325 16326 16327 16328 16329 16330 16331 16332 16333 16334 16335 16336 16337 16338 16339 16340 16341 16342 16343 16344 16345 16346 16347 16348 16349 16350 16351 16352 16353 16354 16355 16356 16357 16358 16359 16360 16361 16362 16363 16364 16365 16366 16367 16368 16369 16370 16371 16372 16373 16374 16375 16376 16377 16378 16379 16380 16381 16382 16383 16384 16385 16386 16387 16388 16389 16390 16391 16392 16393 16394 16395 16396 16397 16398 16399 16400 16401 16402 16403 16404 16405 16406 16407 16408 16409 16410 16411 16412 16413 16414 16415 16416 16417 16418 16419 16420 16421 16422 16423 16424 16425 16426 16427 16428 16429 16430 16431 16432 16433 16434 16435 16436 16437 16438 16439 16440 16441 16442 16443 16444 16445 16446 16447 16448 16449 16450 16451 16452 16453 16454 16455 16456 16457 16458 16459 16460 16461 16462 16463 16464 16465 16466 16467 16468 16469 16470 16471 16472 16473 16474 16475 16476 16477 16478 16479 16480 16481 16482 16483 16484 16485 16486 16487 16488 16489 16490 16491 16492 16493 16494 16495 16496 16497 16498 16499 16500 16501 16502 16503 16504 16505 16506 16507 16508 16509 16510 16511 16512 16513 16514 16515 16516 16517 16518 16519 16520 16521 16522 16523 16524 16525 16526 16527 16528 16529 16530 16531 16532 16533 16534 16535 16536 16537 16538 16539 16540 16541 16542 16543 16544 16545 16546 16547 16548 16549 16550 16551 16552 16553 16554 16555 16556 16557 16558 16559 16560 16561 16562 16563 16564 16565 16566 16567 16568 16569 16570 16571 16572 16573 16574 16575 16576 16577 16578 16579 16580 16581 16582 16583 16584 16585 16586 16587 16588 16589 16590 16591 16592 16593 16594 16595 16596 16597 16598 16599 16600 16601 16602 16603 16604 16605 16606 16607 16608 16609 16610 16611 16612 16613 16614 16615 16616 16617 16618 16619 16620 16621 16622 16623 16624 16625 16626 16627 16628 16629 16630 16631 16632 16633 16634 16635 16636 16637 16638 16639 16640 16641 16642 16643 16644 16645 16646 16647 16648 16649 16650 16651 16652 16653 16654 16655 16656 16657 16658 16659 16660 16661 16662 16663 16664 16665 16666 16667 16668 16669 16670 16671 16672 16673 16674 16675 16676 16677 16678 16679 16680 16681 16682 16683 16684 16685 16686 16687 16688 16689 16690 16691 16692 16693 16694 16695 16696 16697 16698 16699 16700 16701 16702 16703 16704 16705 16706 16707 16708 16709 16710 16711 16712 16713 16714 16715 16716 16717 16718 16719 16720 16721 16722 16723 16724 16725 16726 16727 16728 16729 16730 16731 16732 16733 16734 16735 16736 16737 16738 16739 16740 16741 16742 16743 16744 16745 16746 16747 16748 16749 16750 16751 16752 16753 16754 16755 16756 16757 16758 16759 16760 16761 16762 16763 16764 16765 16766 16767 16768 16769 16770 16771 16772 16773 16774 16775 16776 16777 16778 16779 16780 16781 16782 16783 16784 16785 16786 16787 16788 16789 16790 16791 16792 16793 16794 16795 16796 16797 16798 16799 16800 16801 16802 16803 16804 16805 16806 16807 16808 16809 16810 16811 16812 16813 16814 16815 16816 16817 16818 16819 16820 16821 16822 16823 16824 16825 16826 16827 16828 16829 16830 16831 16832 16833 16834 16835 16836 16837 16838 16839 16840 16841 16842 16843 16844 16845 16846 16847 16848 16849 16850 16851 16852 16853 16854 16855 16856 16857 16858 16859 16860 16861 16862 16863 16864 16865 16866 16867 16868 16869 16870 16871 16872 16873 16874 16875 16876 16877 16878 16879 16880 16881 16882 16883 16884 16885 16886 16887 16888 16889 16890 16891 16892 16893 16894 16895 16896 16897 16898 16899 16900 16901 16902 16903 16904 16905 16906 16907 16908 16909 16910 16911 16912 16913 16914 16915 16916 16917 16918 16919 16920 16921 16922 16923 16924 16925 16926 16927 16928 16929 16930 16931 16932 16933 16934 16935 16936 16937 16938 16939 16940 16941 16942 16943 16944 16945 16946 16947 16948 16949 16950 16951 16952 16953 16954 16955 16956 16957 16958 16959 16960 16961 16962 16963 16964 16965 16966 16967 16968 16969 16970 16971 16972 16973 16974 16975 16976 16977 16978 16979 16980 16981 16982 16983 16984 16985 16986 16987 16988 16989 16990 16991 16992 16993 16994 16995 16996 16997 16998 16999 17000 17001 17002 17003 17004 17005 17006 17007 17008 17009 17010 17011 17012 17013 17014 17015 17016 17017 17018 17019 17020 17021 17022 17023 17024 17025 17026 17027 17028 17029 17030 17031 17032 17033 17034 17035 17036 17037 17038 17039 17040 17041 17042 17043 17044 17045 17046 17047 17048 17049 17050 17051 17052 17053 17054 17055 17056 17057 17058 17059 17060 17061 17062 17063 17064 17065 17066 17067 17068 17069 17070 17071 17072 17073 17074 17075 17076 17077 17078 17079 17080 17081 17082 17083 17084 17085 17086 17087 17088 17089 17090 17091 17092 17093 17094 17095 17096 17097 17098 17099 17100 17101 17102 17103 17104 17105 17106 17107 17108 17109 17110 17111 17112 17113 17114 17115 17116 17117 17118 17119 17120 17121 17122 17123 17124 17125 17126 17127 17128 17129 17130 17131 17132 17133 17134 17135 17136 17137 17138 17139 17140 17141 17142 17143 17144 17145 17146 17147 17148 17149 17150 17151 17152 17153 17154 17155 17156 17157 17158 17159 17160 17161 17162 17163 17164 17165 17166 17167 17168 17169 17170 17171 17172 17173 17174 17175 17176 17177 17178 17179 17180 17181 17182 17183 17184 17185 17186 17187 17188 17189 17190 17191 17192 17193 17194 17195 17196 17197 17198 17199 17200 17201 17202 17203 17204 17205 17206 17207 17208 17209 17210 17211 17212 17213 17214 17215 17216 17217 17218 17219 17220 17221 17222 17223 17224 17225 17226 17227 17228 17229 17230 17231 17232 17233 17234 17235 17236 17237 17238 17239 17240 17241 17242 17243 17244 17245 17246 17247 17248 17249 17250 17251 17252 17253 17254 17255 17256 17257 17258 17259 17260 17261 17262 17263 17264 17265 17266 17267 17268 17269 17270 17271 17272 17273 17274 17275 17276 17277 17278 17279 17280 17281 17282 17283 17284 17285 17286 17287 17288 17289 17290 17291 17292 17293 17294 17295 17296 17297 17298 17299 17300 17301 17302 17303 17304 17305 17306 17307 17308 17309 17310 17311 17312 17313 17314 17315 17316 17317 17318 17319 17320 17321 17322 17323 17324 17325 17326 17327 17328 17329 17330 17331 17332 17333 17334 17335 17336 17337 17338 17339 17340 17341 17342 17343 17344 17345 17346 17347 17348 17349 17350 17351 17352 17353 17354 17355 17356 17357 17358 17359 17360 17361 17362 17363 17364 17365 17366 17367 17368 17369 17370 17371 17372 17373 17374 17375 17376 17377 17378 17379 17380 17381 17382 17383 17384 17385 17386 17387 17388 17389 17390 17391 17392 17393 17394 17395 17396 17397 17398 17399 17400 17401 17402 17403 17404 17405 17406 17407 17408 17409 17410 17411 17412 17413 17414 17415 17416 17417 17418 17419 17420 17421 17422 17423 17424 17425 17426 17427 17428 17429 17430 17431 17432 17433 17434 17435 17436 17437 17438 17439 17440 17441 17442 17443 17444 17445 17446 17447 17448 17449 17450 17451 17452 17453 17454 17455 17456 17457 17458 17459 17460 17461 17462 17463 17464 17465 17466 17467 17468 17469 17470 17471 17472 17473 17474 17475 17476 17477 17478 17479 17480 17481 17482 17483 17484 17485 17486 17487 17488 17489 17490 17491 17492 17493 17494 17495 17496 17497 17498 17499 17500 17501 17502 17503 17504 17505 17506 17507 17508 17509 17510 17511 17512 17513 17514 17515 17516 17517 17518 17519 17520 17521 17522 17523 17524 17525 17526 17527 17528 17529 17530 17531 17532 17533 17534 17535 17536 17537 17538 17539 17540 17541 17542 17543 17544 17545 17546 17547 17548 17549 17550 17551 17552 17553 17554 17555 17556 17557 17558 17559 17560 17561 17562 17563 17564 17565 17566 17567 17568 17569 17570 17571 17572 17573 17574 17575 17576 17577 17578 17579 17580 17581 17582 17583 17584 17585 17586 17587 17588 17589 17590 17591 17592 17593 17594 17595 17596 17597 17598 17599 17600 17601 17602 17603 17604 17605 17606 17607 17608 17609 17610 17611 17612 17613 17614 17615 17616 17617 17618 17619 17620 17621 17622 17623 17624 17625 17626 17627 17628 17629 17630 17631 17632 17633 17634 17635 17636 17637 17638 17639 17640 17641 17642 17643 17644 17645 17646 17647 17648 17649 17650 17651 17652 17653 17654 17655 17656 17657 17658 17659 17660 17661 17662 17663 17664 17665 17666 17667 17668 17669 17670 17671 17672 17673 17674 17675 17676 17677 17678 17679 17680 17681 17682 17683 17684 17685 17686 17687 17688 17689 17690 17691 17692 17693 17694 17695 17696 17697 17698 17699 17700 17701 17702 17703 17704 17705 17706 17707 17708 17709 17710 17711 17712 17713 17714 17715 17716 17717 17718 17719 17720 17721 17722 17723 17724 17725 17726 17727 17728 17729 17730 17731 17732 17733 17734 17735 17736 17737 17738 17739 17740 17741 17742 17743 17744 17745 17746 17747 17748 17749 17750 17751 17752 17753 17754 17755 17756 17757 17758 17759 17760 17761 17762 17763 17764 17765 17766 17767 17768 17769 17770 17771 17772 17773 17774 17775 17776 17777 17778 17779 17780 17781 17782 17783 17784 17785 17786 17787 17788 17789 17790 17791 17792 17793 17794 17795 17796 17797 17798 17799 17800 17801 17802 17803 17804 17805 17806 17807 17808 17809 17810 17811 17812 17813 17814 17815 17816 17817 17818 17819 17820 17821 17822 17823 17824 17825 17826 17827 17828 17829 17830 17831 17832 17833 17834 17835 17836 17837 17838 17839 17840 17841 17842 17843 17844 17845 17846 17847 17848 17849 17850 17851 17852 17853 17854 17855 17856 17857 17858 17859 17860 17861 17862 17863 17864 17865 17866 17867 17868 17869 17870 17871 17872 17873 17874 17875 17876 17877 17878 17879 17880 17881 17882 17883 17884 17885 17886 17887 17888 17889 17890 17891 17892 17893 17894 17895 17896 17897 17898 17899 17900 17901 17902 17903 17904 17905 17906 17907 17908 17909 17910 17911 17912 17913 17914 17915 17916 17917 17918 17919 17920 17921 17922 17923 17924 17925 17926 17927 17928 17929 17930 17931 17932 17933 17934 17935 17936 17937 17938 17939 17940 17941 17942 17943 17944 17945 17946 17947 17948 17949 17950 17951 17952 17953 17954 17955 17956 17957 17958 17959 17960 17961 17962 17963 17964 17965 17966 17967 17968 17969 17970 17971 17972 17973 17974 17975 17976 17977 17978 17979 17980 17981 17982 17983 17984 17985 17986 17987 17988 17989 17990 17991 17992 17993 17994 17995 17996 17997 17998 17999 18000 18001 18002 18003 18004 18005 18006 18007 18008 18009 18010 18011 18012 18013 18014 18015 18016 18017 18018 18019 18020 18021 18022 18023 18024 18025 18026 18027 18028 18029 18030 18031 18032 18033 18034 18035 18036 18037 18038 18039 18040 18041 18042 18043 18044 18045 18046 18047 18048 18049 18050 18051 18052 18053 18054 18055 18056 18057 18058 18059 18060 18061 18062 18063 18064 18065 18066 18067 18068 18069 18070 18071 18072 18073 18074 18075 18076 18077 18078 18079 18080 18081 18082 18083 18084 18085 18086 18087 18088 18089 18090 18091 18092 18093 18094 18095 18096 18097 18098 18099 18100 18101 18102 18103 18104 18105 18106 18107 18108 18109 18110 18111 18112 18113 18114 18115 18116 18117 18118 18119 18120 18121 18122 18123 18124 18125 18126 18127 18128 18129 18130 18131 18132 18133 18134 18135 18136 18137 18138 18139 18140 18141 18142 18143 18144 18145 18146 18147 18148 18149 18150 18151 18152 18153 18154 18155 18156 18157 18158 18159 18160 18161 18162 18163 18164 18165 18166 18167 18168 18169 18170 18171 18172 18173 18174 18175 18176 18177 18178 18179 18180 18181 18182 18183 18184 18185 18186 18187 18188 18189 18190 18191 18192 18193 18194 18195 18196 18197 18198 18199 18200 18201 18202 18203 18204 18205 18206 18207 18208 18209 18210 18211 18212 18213 18214 18215 18216 18217 18218 18219 18220 18221 18222 18223 18224 18225 18226 18227 18228 18229 18230 18231 18232 18233 18234 18235 18236 18237 18238 18239 18240 18241 18242 18243 18244 18245 18246 18247 18248 18249 18250 18251 18252 18253 18254 18255 18256 18257 18258 18259 18260 18261 18262 18263 18264 18265 18266 18267 18268 18269 18270 18271 18272 18273 18274 18275 18276 18277 18278 18279 18280 18281 18282 18283 18284 18285 18286 18287 18288 18289 18290 18291 18292 18293 18294 18295 18296 18297 18298 18299 18300 18301 18302 18303 18304 18305 18306 18307 18308 18309 18310 18311 18312 18313 18314 18315 18316 18317 18318 18319 18320 18321 18322 18323 18324 18325 18326 18327 18328 18329 18330 18331 18332 18333 18334 18335 18336 18337 18338 18339 18340 18341 18342 18343 18344 18345 18346 18347 18348 18349 18350 18351 18352 18353 18354 18355 18356 18357 18358 18359 18360 18361 18362 18363 18364 18365 18366 18367 18368 18369 18370 18371 18372 18373 18374 18375 18376 18377 18378 18379 18380 18381 18382 18383 18384 18385 18386 18387 18388 18389 18390 18391 18392 18393 18394 18395 18396 18397 18398 18399 18400 18401 18402 18403 18404 18405 18406 18407 18408 18409 18410 18411 18412 18413 18414 18415 18416 18417 18418 18419 18420 18421 18422 18423 18424 18425 18426 18427 18428 18429 18430 18431 18432 18433 18434 18435 18436 18437 18438 18439 18440 18441 18442 18443 18444 18445 18446 18447 18448 18449 18450 18451 18452 18453 18454 18455 18456 18457 18458 18459 18460 18461 18462 18463 18464 18465 18466 18467 18468 18469 18470 18471 18472 18473 18474 18475 18476 18477 18478 18479 18480 18481 18482 18483 18484 18485 18486 18487 18488 18489 18490 18491 18492 18493 18494 18495 18496 18497 18498 18499 18500 18501 18502 18503 18504 18505 18506 18507 18508 18509 18510 18511 18512 18513 18514 18515 18516 18517 18518 18519 18520 18521 18522 18523 18524 18525 18526 18527 18528 18529 18530 18531 18532 18533 18534 18535 18536 18537 18538 18539 18540 18541 18542 18543 18544 18545 18546 18547 18548 18549 18550 18551 18552 18553 18554 18555 18556 18557 18558 18559 18560 18561 18562 18563 18564 18565 18566 18567 18568 18569 18570 18571 18572 18573 18574 18575 18576 18577 18578 18579 18580 18581 18582 18583 18584 18585 18586 18587 18588 18589 18590 18591 18592 18593 18594 18595 18596 18597 18598 18599 18600 18601 18602 18603 18604 18605 18606 18607 18608 18609 18610 18611 18612 18613 18614 18615 18616 18617 18618 18619 18620 18621 18622 18623 18624 18625 18626 18627 18628 18629 18630 18631 18632 18633 18634 18635 18636 18637 18638 18639 18640 18641 18642 18643 18644 18645 18646 18647 18648 18649 18650 18651 18652 18653 18654 18655 18656 18657 18658 18659 18660 18661 18662 18663 18664 18665 18666 18667 18668 18669 18670 18671 18672 18673 18674 18675 18676 18677 18678 18679 18680 18681 18682 18683 18684 18685 18686 18687 18688 18689 18690 18691 18692 18693 18694 18695 18696 18697 18698 18699 18700 18701 18702 18703 18704 18705 18706 18707 18708 18709 18710 18711 18712 18713 18714 18715 18716 18717 18718 18719 18720 18721 18722 18723 18724 18725 18726 18727 18728 18729 18730 18731 18732 18733 18734 18735 18736 18737 18738 18739 18740 18741 18742 18743 18744 18745 18746 18747 18748 18749 18750 18751 18752 18753 18754 18755 18756 18757 18758 18759 18760 18761 18762 18763 18764 18765 18766 18767 18768 18769 18770 18771 18772 18773 18774 18775 18776 18777 18778 18779 18780 18781 18782 18783 18784 18785 18786 18787 18788 18789 18790 18791 18792 18793 18794 18795 18796 18797 18798 18799 18800 18801 18802 18803 18804 18805 18806 18807 18808 18809 18810 18811 18812 18813 18814 18815 18816 18817 18818 18819 18820 18821 18822 18823 18824 18825 18826 18827 18828 18829 18830 18831 18832 18833 18834 18835 18836 18837 18838 18839 18840 18841 18842 18843 18844 18845 18846 18847 18848 18849 18850 18851 18852 18853 18854 18855 18856 18857 18858 18859 18860 18861 18862 18863 18864 18865 18866 18867 18868 18869 18870 18871 18872 18873 18874 18875 18876 18877 18878 18879 18880 18881 18882 18883 18884 18885 18886 18887 18888 18889 18890 18891 18892 18893 18894 18895 18896 18897 18898 18899 18900 18901 18902 18903 18904 18905 18906 18907 18908 18909 18910 18911 18912 18913 18914 18915 18916 18917 18918 18919 18920 18921 18922 18923 18924 18925 18926 18927 18928 18929 18930 18931 18932 18933 18934 18935 18936 18937 18938 18939 18940 18941 18942 18943 18944 18945 18946 18947 18948 18949 18950 18951 18952 18953 18954 18955 18956 18957 18958 18959 18960 18961 18962 18963 18964 18965 18966 18967 18968 18969 18970 18971 18972 18973 18974 18975 18976 18977 18978 18979 18980 18981 18982 18983 18984 18985 18986 18987 18988 18989 18990 18991 18992 18993 18994 18995 18996 18997 18998 18999 19000 19001 19002 19003 19004 19005 19006 19007 19008 19009 19010 19011 19012 19013 19014 19015 19016 19017 19018 19019 19020 19021 19022 19023 19024 19025 19026 19027 19028 19029 19030 19031 19032 19033 19034 19035 19036 19037 19038 19039 19040 19041 19042 19043 19044 19045 19046 19047 19048 19049 19050 19051 19052 19053 19054 19055 19056 19057 19058 19059 19060 19061 19062 19063 19064 19065 19066 19067 19068 19069 19070 19071 19072 19073 19074 19075 19076 19077 19078 19079 19080 19081 19082 19083 19084 19085 19086 19087 19088 19089 19090 19091 19092 19093 19094 19095 19096 19097 19098 19099 19100 19101 19102 19103 19104 19105 19106 19107 19108 19109 19110 19111 19112 19113 19114 19115 19116 19117 19118 19119 19120 19121 19122 19123 19124 19125 19126 19127 19128 19129 19130 19131 19132 19133 19134 19135 19136 19137 19138 19139 19140 19141 19142 19143 19144 19145 19146 19147 19148 19149 19150 19151 19152 19153 19154 19155 19156 19157 19158 19159 19160 19161 19162 19163 19164 19165 19166 19167 19168 19169 19170 19171 19172 19173 19174 19175 19176 19177 19178 19179 19180 19181 19182 19183 19184 19185 19186 19187 19188 19189 19190 19191 19192 19193 19194 19195 19196 19197 19198 19199 19200 19201 19202 19203 19204 19205 19206 19207 19208 19209 19210 19211 19212 19213 19214 19215 19216 19217 19218 19219 19220 19221 19222 19223 19224 19225 19226 19227 19228 19229 19230 19231 19232 19233 19234 19235 19236 19237 19238 19239 19240 19241 19242 19243 19244 19245 19246 19247 19248 19249 19250 19251 19252 19253 19254 19255 19256 19257 19258 19259 19260 19261 19262 19263 19264 19265 19266 19267 19268 19269 19270 19271 19272 19273 19274 19275 19276 19277 19278 19279 19280 19281 19282 19283 19284 19285 19286 19287 19288 19289 19290 19291 19292 19293 19294 19295 19296 19297 19298 19299 19300 19301 19302 19303 19304 19305 19306 19307 19308 19309 19310 19311 19312 19313 19314 19315 19316 19317 19318 19319 19320 19321 19322 19323 19324 19325 19326 19327 19328 19329 19330 19331 19332 19333 19334 19335 19336 19337 19338 19339 19340 19341 19342 19343 19344 19345 19346 19347 19348 19349 19350 19351 19352 19353 19354 19355 19356 19357 19358 19359 19360 19361 19362 19363 19364 19365 19366 19367 19368 19369 19370 19371 19372 19373 19374 19375 19376 19377 19378 19379 19380 19381 19382 19383 19384 19385 19386 19387 19388 19389 19390 19391 19392 19393 19394 19395 19396 19397 19398 19399 19400 19401 19402 19403 19404 19405 19406 19407 19408 19409 19410 19411 19412 19413 19414 19415 19416 19417 19418 19419 19420 19421 19422 19423 19424 19425 19426 19427 19428 19429 19430 19431 19432 19433 19434 19435 19436 19437 19438 19439 19440 19441 19442 19443 19444 19445 19446 19447 19448 19449 19450 19451 19452 19453 19454 19455 19456 19457 19458 19459 19460 19461 19462 19463 19464 19465 19466 19467 19468 19469 19470 19471 19472 19473 19474 19475 19476 19477 19478 19479 19480 19481 19482 19483 19484 19485 19486 19487 19488 19489 19490 19491 19492 19493 19494 19495 19496 19497 19498 19499 19500 19501 19502 19503 19504 19505 19506 19507 19508 19509 19510 19511 19512 19513 19514 19515 19516 19517 19518 19519 19520 19521 19522 19523 19524 19525 19526 19527 19528 19529 19530 19531 19532 19533 19534 19535 19536 19537 19538 19539 19540 19541 19542 19543 19544 19545 19546 19547 19548 19549 19550 19551 19552 19553 19554 19555 19556 19557 19558 19559 19560 19561 19562 19563 19564 19565 19566 19567 19568 19569 19570 19571 19572 19573 19574 19575 19576 19577 19578 19579 19580 19581 19582 19583 19584 19585 19586 19587 19588 19589 19590 19591 19592 19593 19594 19595 19596 19597 19598 19599 19600 19601 19602 19603 19604 19605 19606 19607 19608 19609 19610 19611 19612 19613 19614 19615 19616 19617 19618 19619 19620 19621 19622 19623 19624 19625 19626 19627 19628 19629 19630 19631 19632 19633 19634 19635 19636 19637 19638 19639 19640 19641 19642 19643 19644 19645 19646 19647 19648 19649 19650 19651 19652 19653 19654 19655 19656 19657 19658 19659 19660 19661 19662 19663 19664 19665 19666 19667 19668 19669 19670 19671 19672 19673 19674 19675 19676 19677 19678 19679 19680 19681 19682 19683 19684 19685 19686 19687 19688 19689 19690 19691 19692 19693 19694 19695 19696 19697 19698 19699 19700 19701 19702 19703 19704 19705 19706 19707 19708 19709 19710 19711 19712 19713 19714 19715 19716 19717 19718 19719 19720 19721 19722 19723 19724 19725 19726 19727 19728 19729 19730 19731 19732 19733 19734 19735 19736 19737 19738 19739 19740 19741 19742 19743 19744 19745 19746 19747 19748 19749 19750 19751 19752 19753 19754 19755 19756 19757 19758 19759 19760 19761 19762 19763 19764 19765 19766 19767 19768 19769 19770 19771 19772 19773 19774 19775 19776 19777 19778 19779 19780 19781 19782 19783 19784 19785 19786 19787 19788 19789 19790 19791 19792 19793 19794 19795 19796 19797 19798 19799 19800 19801 19802 19803 19804 19805 19806 19807 19808 19809 19810 19811 19812 19813 19814 19815 19816 19817 19818 19819 19820 19821 19822 19823 19824 19825 19826 19827 19828 19829 19830 19831 19832 19833 19834 19835 19836 19837 19838 19839 19840 19841 19842 19843 19844 19845 19846 19847 19848 19849 19850 19851 19852 19853 19854 19855 19856 19857 19858 19859 19860 19861 19862 19863 19864 19865 19866 19867 19868 19869 19870 19871 19872 19873 19874 19875 19876 19877 19878 19879 19880 19881 19882 19883 19884 19885 19886 19887 19888 19889 19890 19891 19892 19893 19894 19895 19896 19897 19898 19899 19900 19901 19902 19903 19904 19905 19906 19907 19908 19909 19910 19911 19912 19913 19914 19915 19916 19917 19918 19919 19920 19921 19922 19923 19924 19925 19926 19927 19928 19929 19930 19931 19932 19933 19934 19935 19936 19937 19938 19939 19940 19941 19942 19943 19944 19945 19946 19947 19948 19949 19950 19951 19952 19953 19954 19955 19956 19957 19958 19959 19960 19961 19962 19963 19964 19965 19966 19967 19968 19969 19970 19971 19972 19973 19974 19975 19976 19977 19978 19979 19980 19981 19982 19983 19984 19985 19986 19987 19988 19989 19990 19991 19992 19993 19994 19995 19996 19997 19998 19999 20000 20001 20002 20003 20004 20005 20006 20007 20008 20009 20010 20011 20012 20013 20014 20015 20016 20017 20018 20019 20020 20021 20022 20023 20024 20025 20026 20027 20028 20029 20030 20031 20032 20033 20034 20035 20036 20037 20038 20039 20040 20041 20042 20043 20044 20045 20046 20047 20048 20049 20050 20051 20052 20053 20054 20055 20056 20057 20058 20059 20060 20061 20062 20063 20064 20065 20066 20067 20068 20069 20070 20071 20072 20073 20074 20075 20076 20077 20078 20079 20080 20081 20082 20083 20084 20085 20086 20087 20088 20089 20090 20091 20092 20093 20094 20095 20096 20097 20098 20099 20100 20101 20102 20103 20104 20105 20106 20107 20108 20109 20110 20111 20112 20113 20114 20115 20116 20117 20118 20119 20120 20121 20122 20123 20124 20125 20126 20127 20128 20129 20130 20131 20132 20133 20134 20135 20136 20137 20138 20139 20140 20141 20142 20143 20144 20145 20146 20147 20148 20149 20150 20151 20152 20153 20154 20155 20156 20157 20158 20159 20160 20161 20162 20163 20164 20165 20166 20167 20168 20169 20170 20171 20172 20173 20174 20175 20176 20177 20178 20179 20180 20181 20182 20183 20184 20185 20186 20187 20188 20189 20190 20191 20192 20193 20194 20195 20196 20197 20198 20199 20200 20201 20202 20203 20204 20205 20206 20207 20208 20209 20210 20211 20212 20213 20214 20215 20216 20217 20218 20219 20220 20221 20222 20223 20224 20225 20226 20227 20228 20229 20230 20231 20232 20233 20234 20235 20236 20237 20238 20239 20240 20241 20242 20243 20244 20245 20246 20247 20248 20249 20250 20251 20252 20253 20254 20255 20256 20257 20258 20259 20260 20261 20262 20263 20264 20265 20266 20267 20268 20269 20270 20271 20272 20273 20274 20275 20276 20277 20278 20279 20280 20281 20282 20283 20284 20285 20286 20287 20288 20289 20290 20291 20292 20293 20294 20295 20296 20297 20298 20299 20300 20301 20302 20303 20304 20305 20306 20307 20308 20309 20310 20311 20312 20313 20314 20315 20316 20317 20318 20319 20320 20321 20322 20323 20324 20325 20326 20327 20328 20329 20330 20331 20332 20333 20334 20335 20336 20337 20338 20339 20340 20341 20342 20343 20344 20345 20346 20347 20348 20349 20350 20351 20352 20353 20354 20355 20356 20357 20358 20359 20360 20361 20362 20363 20364 20365 20366 20367 20368 20369 20370 20371 20372 20373 20374 20375 20376 20377 20378 20379 20380 20381 20382 20383 20384 20385 20386 20387 20388 20389 20390 20391 20392 20393 20394 20395 20396 20397 20398 20399 20400 20401 20402 20403 20404 20405 20406 20407 20408 20409 20410 20411 20412 20413 20414 20415 20416 20417 20418 20419 20420 20421 20422 20423 20424 20425 20426 20427 20428 20429 20430 20431 20432 20433 20434 20435 20436 20437 20438 20439 20440 20441 20442 20443 20444 20445 20446 20447 20448 20449 20450 20451 20452 20453 20454 20455 20456 20457 20458 20459 20460 20461 20462 20463 20464 20465 20466 20467 20468 20469 20470 20471 20472 20473 20474 20475 20476 20477 20478 20479 20480 20481 20482 20483 20484 20485 20486 20487 20488 20489 20490 20491 20492 20493 20494 20495 20496 20497 20498 20499 20500 20501 20502 20503 20504 20505 20506 20507 20508 20509 20510 20511 20512 20513 20514 20515 20516 20517 20518 20519 20520 20521 20522 20523 20524 20525 20526 20527 20528 20529 20530 20531 20532 20533 20534 20535 20536 20537 20538 20539 20540 20541 20542 20543 20544 20545 20546 20547 20548 20549 20550 20551 20552 20553 20554 20555 20556 20557 20558 20559 20560 20561 20562 20563 20564 20565 20566 20567 20568 20569 20570 | format-version: 1.2
date: 22:06:2015 10:18
saved-by: kareneilbeck
auto-generated-by: OBO-Edit 2.3.1
subsetdef: biosapiens "biosapiens protein feature ontology"
subsetdef: DBVAR "database of genomic structural variation"
subsetdef: SOFA "SO feature annotation"
synonymtypedef: aa1 "amino acid 1 letter code"
synonymtypedef: aa3 "amino acid 3 letter code"
synonymtypedef: AAMOD "amino acid modification"
synonymtypedef: BS "biosapiens"
synonymtypedef: dbsnp "dbsnp variant terms"
synonymtypedef: dbvar "DBVAR"
synonymtypedef: ebi_variants "ensembl variant terms"
synonymtypedef: RNAMOD "RNA modification" EXACT
synonymtypedef: VAR "variant annotation term"
default-namespace: sequence
remark: autogenerated-by: DAG-Edit version 1.417\nsaved-by: eilbeck\ndate: Tue May 11 15:18:44 PDT 2004\nversion: $Revision: 1.45 $
ontology: so-xp.obo
[Term]
id: SO:0000000
name: Sequence_Ontology
subset: SOFA
is_obsolete: true
[Term]
id: SO:0000001
name: region
def: "A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids." [SO:ke]
subset: SOFA
synonym: "sequence" EXACT []
is_a: SO:0000110 ! sequence_feature
disjoint_from: SO:0000699 ! junction
[Term]
id: SO:0000002
name: sequence_secondary_structure
def: "A folded sequence." [SO:ke]
synonym: "sequence secondary structure" EXACT []
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000003
name: G_quartet
def: "G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet." [http://www.ncbi.nlm.nih.gov/pubmed/7919797?dopt=Abstract]
synonym: "G quartet" EXACT []
synonym: "G tetrad" EXACT []
synonym: "G-quadruplex" EXACT []
synonym: "G-quartet" EXACT []
synonym: "G-tetrad" EXACT []
synonym: "G_quadruplex" EXACT []
synonym: "guanine tetrad" EXACT []
xref: http://en.wikipedia.org/wiki/G-quadruplex "wiki"
is_a: SO:0000002 ! sequence_secondary_structure
[Term]
id: SO:0000004
name: interior_coding_exon
subset: SOFA
synonym: "interior coding exon" EXACT []
is_a: SO:0000195 ! coding_exon
[Term]
id: SO:0000005
name: satellite_DNA
def: "The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "satellite DNA" EXACT []
xref: http://en.wikipedia.org/wiki/Satellite_DNA "wiki"
is_a: SO:0000705 ! tandem_repeat
[Term]
id: SO:0000006
name: PCR_product
def: "A region amplified by a PCR reaction." [SO:ke]
comment: This term is mapped to MGED. This term is now located in OBI, with the following ID OBI_0000406.
subset: SOFA
synonym: "amplicon" RELATED []
synonym: "PCR product" EXACT []
xref: http://en.wikipedia.org/wiki/RAPD "wiki"
is_a: SO:0000695 ! reagent
[Term]
id: SO:0000007
name: read_pair
def: "One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert." [SO:ls]
subset: SOFA
synonym: "mate pair" EXACT []
synonym: "read-pair" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000149 ! contig
relationship: part_of SO:0001790 ! paired_end_fragment
[Term]
id: SO:0000008
name: gene_sensu_your_favorite_organism
is_obsolete: true
[Term]
id: SO:0000009
name: gene_class
is_obsolete: true
[Term]
id: SO:0000010
name: protein_coding
synonym: "protein-coding" EXACT []
is_a: SO:0000401 ! gene_attribute
[Term]
id: SO:0000011
name: non_protein_coding
synonym: "non protein-coding" EXACT []
is_a: SO:0000401 ! gene_attribute
[Term]
id: SO:0000012
name: scRNA_primary_transcript
def: "The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote." [http://www.ebi.ac.uk/embl/WebFeat/align/scRNA_s.html]
synonym: "scRNA primary transcript" EXACT []
synonym: "scRNA transcript" EXACT []
synonym: "small cytoplasmic RNA" RELATED []
synonym: "small cytoplasmic RNA transcript" EXACT []
synonym: "small_cytoplasmic_RNA" RELATED []
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000013
name: scRNA
def: "A small non coding RNA sequence, present in the cytoplasm." [SO:ke]
subset: SOFA
synonym: "small cytoplasmic RNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000012 ! scRNA_primary_transcript
[Term]
id: SO:0000014
name: INR_motif
def: "A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element." [PMID:12651739, PMID:16858867]
comment: Binds TAF1, TAF2.
synonym: "DMp2" RELATED []
synonym: "initiator" EXACT []
synonym: "initiator motif" EXACT []
synonym: "INR motif" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
[Term]
id: SO:0000015
name: DPE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C)." [PMID:12651739:12537576, PMID:16858867]
comment: Binds TAF6, TAF9.
synonym: "CRWMGCGWKCGCTTS" NARROW []
synonym: "downstream core promoter element" EXACT []
synonym: "DPE motif" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
[Term]
id: SO:0000016
name: BREu_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB." [PMID:12651739, PMID:16858867]
comment: Binds TFIIB.
synonym: "B-recognition element" EXACT []
synonym: "BRE motif" EXACT []
synonym: "BREu" RELATED []
synonym: "BREu motif" EXACT []
synonym: "TFIIB recognition element" RELATED []
synonym: "transcription factor B-recognition element" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
[Term]
id: SO:0000017
name: PSE_motif
def: "A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G)." [PMID:12651739]
synonym: "proximal sequence element" EXACT []
synonym: "PSE motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000167 ! promoter
[Term]
id: SO:0000018
name: linkage_group
def: "A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned." [ISBN:038752046]
synonym: "linkage group" EXACT []
xref: http://en.wikipedia.org/wiki/Linkage_group "wiki"
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000020
name: RNA_internal_loop
def: "A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge." [SO:ke]
synonym: "RNA internal loop" EXACT []
is_a: SO:0000715 ! RNA_motif
[Term]
id: SO:0000021
name: asymmetric_RNA_internal_loop
def: "An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand." [SO:ke]
synonym: "asymmetric RNA internal loop" EXACT []
is_a: SO:0000020 ! RNA_internal_loop
[Term]
id: SO:0000022
name: A_minor_RNA_motif
def: "A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix." [SO:ke]
synonym: "A minor RNA motif" EXACT []
is_a: SO:0000715 ! RNA_motif
[Term]
id: SO:0000023
name: K_turn_RNA_motif
def: "The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices." [SO:ke]
synonym: "K turn RNA motif" EXACT []
synonym: "K-turn" EXACT []
synonym: "kink turn" EXACT []
synonym: "kink-turn motif" EXACT []
xref: http://en.wikipedia.org/wiki/K-turn "wiki"
is_a: SO:0000021 ! asymmetric_RNA_internal_loop
[Term]
id: SO:0000024
name: sarcin_like_RNA_motif
def: "A loop in ribosomal RNA containing the sites of attack for ricin and sarcin." [http://www.ncbi.nlm.nih.gov/pubmed/7897662]
synonym: "sarcin like RNA motif" EXACT []
synonym: "sarcin/ricin domain" EXACT []
synonym: "sarcin/ricin loop" EXACT []
synonym: "sarcin/ricin RNA domain" EXACT []
is_a: SO:0000021 ! asymmetric_RNA_internal_loop
[Term]
id: SO:0000025
name: symmetric_RNA_internal_loop
def: "An internal RNA loop where the extent of the loop on both stands is the same size." [SO:ke]
synonym: "A-minor RNA motif" EXACT []
is_a: SO:0000020 ! RNA_internal_loop
[Term]
id: SO:0000026
name: RNA_junction_loop
synonym: "RNA junction loop" EXACT []
is_a: SO:0000715 ! RNA_motif
[Term]
id: SO:0000027
name: RNA_hook_turn
synonym: "hook turn" RELATED []
synonym: "hook-turn motif" EXACT []
synonym: "RNA hook turn" EXACT []
is_a: SO:0000026 ! RNA_junction_loop
[Term]
id: SO:0000028
name: base_pair
synonym: "base pair" EXACT []
xref: http://en.wikipedia.org/wiki/Base_pair "wiki"
is_a: SO:0000002 ! sequence_secondary_structure
[Term]
id: SO:0000029
name: WC_base_pair
def: "The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation." [PMID:12177293]
synonym: "canonical base pair" EXACT []
synonym: "Watson Crick base pair" EXACT []
synonym: "Watson-Crick base pair" RELATED []
synonym: "Watson-Crick pair" EXACT []
synonym: "WC base pair" EXACT []
is_a: SO:0000028 ! base_pair
[Term]
id: SO:0000030
name: sugar_edge_base_pair
def: "A type of non-canonical base-pairing." [PMID:12177293]
synonym: "sugar edge base pair" EXACT []
is_a: SO:0000028 ! base_pair
[Term]
id: SO:0000031
name: aptamer
def: "DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]
xref: http://en.wikipedia.org/wiki/Aptamer "wiki"
is_a: SO:0000696 ! oligo
[Term]
id: SO:0000032
name: DNA_aptamer
def: "DNA molecules that have been selected from random pools based on their ability to bind other molecules." [http:aptamer.icmb.utexas.edu]
synonym: "DNA aptamer" EXACT []
is_a: SO:0000031 ! aptamer
[Term]
id: SO:0000033
name: RNA_aptamer
def: "RNA molecules that have been selected from random pools based on their ability to bind other molecules." [http://aptamer.icmb.utexas.edu]
synonym: "RNA aptamer" EXACT []
is_a: SO:0000031 ! aptamer
[Term]
id: SO:0000034
name: morpholino_oligo
def: "Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino." [http://www.gene-tools.com/]
synonym: "morphant" BROAD []
synonym: "morpholino" EXACT []
synonym: "morpholino oligo" EXACT []
is_a: SO:0001247 ! synthetic_oligo
relationship: has_quality SO:0001183 ! morpholino_backbone
[Term]
id: SO:0000035
name: riboswitch
def: "A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites." [PMID:2820954]
synonym: "riboswitch RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Riboswitch "wiki"
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000234 ! mRNA
[Term]
id: SO:0000036
name: matrix_attachment_site
def: "A DNA region that is required for the binding of chromatin to the nuclear matrix." [SO:ma]
synonym: "MAR" EXACT []
synonym: "matrix association region" EXACT []
synonym: "matrix attachment region" EXACT []
synonym: "matrix attachment site" EXACT []
synonym: "nuclear matrix association region" EXACT []
synonym: "nuclear matrix attachment site" EXACT []
synonym: "S/MAR" EXACT []
synonym: "S/MAR element" RELATED []
synonym: "scaffold attachment site" EXACT []
synonym: "scaffold matrix attachment region" EXACT []
synonym: "SMAR" EXACT []
xref: http://en.wikipedia.org/wiki/Matrix_attachment_site "wiki"
is_a: SO:0000626 ! chromosomal_regulatory_element
[Term]
id: SO:0000037
name: locus_control_region
def: "A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene." [SO:ma]
synonym: "LCR" EXACT []
synonym: "locus control element" RELATED []
synonym: "locus control region" EXACT []
xref: http://en.wikipedia.org/wiki/Locus_control_region "wiki"
is_a: SO:0000727 ! CRM
[Term]
id: SO:0000038
name: match_set
def: "A collection of match parts." [SO:ke]
subset: SOFA
is_obsolete: true
[Term]
id: SO:0000039
name: match_part
def: "A part of a match, for example an hsp from blast is a match_part." [SO:ke]
subset: SOFA
synonym: "match part" EXACT []
is_a: SO:0001410 ! experimental_feature
relationship: part_of SO:0000343 ! match
[Term]
id: SO:0000040
name: genomic_clone
def: "A clone of a DNA region of a genome." [SO:ma]
synonym: "genomic clone" EXACT []
is_a: SO:0000151 ! clone
relationship: has_quality SO:0000991 ! genomic_DNA
[Term]
id: SO:0000041
name: sequence_operation
def: "An operation that can be applied to a sequence, that results in a change." [SO:ke]
synonym: "sequence operation" EXACT []
is_obsolete: true
[Term]
id: SO:0000042
name: pseudogene_attribute
def: "An attribute of a pseudogene (SO:0000336)." [SO:ma]
synonym: "pseudogene attribute" EXACT []
is_obsolete: true
[Term]
id: SO:0000043
name: processed_pseudogene
def: "A pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promoters, but often including a polyA tail." [SO:xp]
comment: Please not the synonym R psi M uses the spelled out form of the greek letter.
synonym: "processed pseudogene" EXACT []
synonym: "pseudogene by reverse transcription" RELATED []
synonym: "R psi G" RELATED []
synonym: "retropseudogene" EXACT []
is_a: SO:0000336 ! pseudogene
[Term]
id: SO:0000044
name: pseudogene_by_unequal_crossing_over
def: "A pseudogene caused by unequal crossing over at recombination." [SO:ke]
synonym: "pseudogene by unequal crossing over" EXACT []
is_a: SO:0001760 ! non_processed_pseudogene
[Term]
id: SO:0000045
name: delete
def: "To remove a subsection of sequence." [SO:ke]
is_obsolete: true
[Term]
id: SO:0000046
name: insert
def: "To insert a subsection of sequence." [SO:ke]
is_obsolete: true
[Term]
id: SO:0000047
name: invert
def: "To invert a subsection of sequence." [SO:ke]
is_obsolete: true
[Term]
id: SO:0000048
name: substitute
def: "To substitute a subsection of sequence for another." [SO:ke]
is_obsolete: true
[Term]
id: SO:0000049
name: translocate
def: "To translocate a subsection of sequence." [SO:ke]
is_obsolete: true
[Term]
id: SO:0000050
name: gene_part
def: "A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene." [SO:ke]
subset: SOFA
is_obsolete: true
[Term]
id: SO:0000051
name: probe
def: "A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid." [SO:ma]
xref: http://en.wikipedia.org/wiki/Hybridization_probe "wiki"
is_a: SO:0000696 ! oligo
[Term]
id: SO:0000052
name: assortment_derived_deficiency
synonym: "assortment-derived_deficiency" RELATED []
is_obsolete: true
[Term]
id: SO:0000053
name: sequence_variant_affecting_regulatory_region
def: "A sequence_variant_effect which changes the regulatory region of a gene." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting regulatory region" RELATED []
synonym: "sequence variant affecting regulatory region" EXACT []
is_obsolete: true
replaced_by: SO:0001556
[Term]
id: SO:0000054
name: aneuploid
def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
xref: http://en.wikipedia.org/wiki/Aneuploid "wiki"
is_a: SO:1000182 ! chromosome_number_variation
[Term]
id: SO:0000055
name: hyperploid
def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present." [SO:ke]
xref: http://en.wikipedia.org/wiki/Hyperploid "wiki"
is_a: SO:0000054 ! aneuploid
[Term]
id: SO:0000056
name: hypoploid
def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing." [SO:ke]
xref: http://en.wikipedia.org/wiki/Hypoploid "wiki"
is_a: SO:0000054 ! aneuploid
[Term]
id: SO:0000057
name: operator
def: "A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon." [SO:ma]
subset: SOFA
synonym: "operator segment" EXACT []
xref: http://en.wikipedia.org/wiki/Operator_(biology)#Operator "wiki"
is_a: SO:0000752 ! gene_group_regulatory_region
[Term]
id: SO:0000058
name: assortment_derived_aneuploid
synonym: "assortment-derived_aneuploid" RELATED []
is_obsolete: true
[Term]
id: SO:0000059
name: nuclease_binding_site
def: "A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease." [SO:cb]
subset: SOFA
synonym: "nuclease binding site" EXACT []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site
[Term]
id: SO:0000060
name: compound_chromosome_arm
comment: FLAG - this term is should probably be a part of rather than an is_a.
synonym: "compound chromosome arm" EXACT []
is_a: SO:1000042 ! compound_chromosome
[Term]
id: SO:0000061
name: restriction_enzyme_binding_site
def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme." [SO:cb]
comment: A region of a molecule that binds to a restriction enzyme.
synonym: "restriction endonuclease binding site" EXACT []
synonym: "restriction enzyme binding site" EXACT []
is_a: SO:0000059 ! nuclease_binding_site
[Term]
id: SO:0000062
name: deficient_intrachromosomal_transposition
def: "An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]
synonym: "deficient intrachromosomal transposition" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000041 ! intrachromosomal_transposition
relationship: has_part SO:0000159 ! deletion
[Term]
id: SO:0000063
name: deficient_interchromosomal_transposition
def: "An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining." [SO:ke]
synonym: "deficient interchromosomal transposition" EXACT []
is_a: SO:1000155 ! interchromosomal_transposition
[Term]
id: SO:0000064
name: gene_by_transcript_attribute
comment: This classes of attributes was added by MA to allow the broad description of genes based on qualities of the transcript(s). A product of SO meeting 2004.
is_obsolete: true
[Term]
id: SO:0000065
name: free_chromosome_arm
def: "A chromosome structure variation whereby an arm exists as an individual chromosome element." [SO:ke]
synonym: "free chromosome arm" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation
[Term]
id: SO:0000066
name: gene_by_polyadenylation_attribute
is_obsolete: true
[Term]
id: SO:0000067
name: gene_to_gene_feature
synonym: "gene to gene feature" EXACT []
is_a: SO:0000401 ! gene_attribute
[Term]
id: SO:0000068
name: overlapping
def: "An attribute describing a gene that has a sequence that overlaps the sequence of another gene." [SO:ke]
is_a: SO:0000067 ! gene_to_gene_feature
[Term]
id: SO:0000069
name: inside_intron
def: "An attribute to describe a gene when it is located within the intron of another gene." [SO:ke]
synonym: "inside intron" EXACT []
is_a: SO:0000068 ! overlapping
[Term]
id: SO:0000070
name: inside_intron_antiparallel
def: "An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand." [SO:ke]
synonym: "inside intron antiparallel" EXACT []
is_a: SO:0000069 ! inside_intron
[Term]
id: SO:0000071
name: inside_intron_parallel
def: "An attribute to describe a gene when it is located within the intron of another gene and on the same strand." [SO:ke]
synonym: "inside intron parallel" EXACT []
is_a: SO:0000069 ! inside_intron
[Term]
id: SO:0000072
name: end_overlapping_gene
is_obsolete: true
[Term]
id: SO:0000073
name: five_prime_three_prime_overlap
def: "An attribute to describe a gene when the five prime region overlaps with another gene's 3' region." [SO:ke]
synonym: "five prime-three prime overlap" EXACT []
is_a: SO:0000068 ! overlapping
[Term]
id: SO:0000074
name: five_prime_five_prime_overlap
def: "An attribute to describe a gene when the five prime region overlaps with another gene's five prime region." [SO:ke]
synonym: "five prime-five prime overlap" EXACT []
is_a: SO:0000068 ! overlapping
[Term]
id: SO:0000075
name: three_prime_three_prime_overlap
def: "An attribute to describe a gene when the 3' region overlaps with another gene's 3' region." [SO:ke]
synonym: "three prime-three prime overlap" EXACT []
is_a: SO:0000068 ! overlapping
[Term]
id: SO:0000076
name: three_prime_five_prime_overlap
def: "An attribute to describe a gene when the 3' region overlaps with another gene's 5' region." [SO:ke]
synonym: "5' 3' overlap" EXACT []
synonym: "three prime five prime overlap" EXACT []
is_a: SO:0000068 ! overlapping
[Term]
id: SO:0000077
name: antisense
def: "A region sequence that is complementary to a sequence of messenger RNA." [SO:ke]
xref: http://en.wikipedia.org/wiki/Antisense "wiki"
is_a: SO:0000068 ! overlapping
[Term]
id: SO:0000078
name: polycistronic_transcript
def: "A transcript that is polycistronic." [SO:xp]
synonym: "polycistronic transcript" EXACT []
is_a: SO:0000673 ! transcript
relationship: has_quality SO:0000880 ! polycistronic
[Term]
id: SO:0000079
name: dicistronic_transcript
def: "A transcript that is dicistronic." [SO:ke]
synonym: "dicistronic transcript" EXACT []
is_a: SO:0000078 ! polycistronic_transcript
relationship: has_quality SO:0000879 ! dicistronic
[Term]
id: SO:0000080
name: operon_member
synonym: "operon member" EXACT []
is_a: SO:0000081 ! gene_array_member
[Term]
id: SO:0000081
name: gene_array_member
synonym: "gene array member" EXACT []
is_a: SO:0000401 ! gene_attribute
[Term]
id: SO:0000082
name: processed_transcript_attribute
is_obsolete: true
[Term]
id: SO:0000083
name: macronuclear_sequence
synonym: "macronuclear sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence
[Term]
id: SO:0000084
name: micronuclear_sequence
synonym: "micronuclear sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence
[Term]
id: SO:0000085
name: gene_by_genome_location
is_obsolete: true
[Term]
id: SO:0000086
name: gene_by_organelle_of_genome
is_obsolete: true
[Term]
id: SO:0000087
name: nuclear_gene
def: "A gene from nuclear sequence." [SO:xp]
synonym: "nuclear gene" EXACT []
xref: http://en.wikipedia.org/wiki/Nuclear_gene "wiki"
is_a: SO:0000704 ! gene
relationship: has_origin SO:0000738 ! nuclear_sequence
[Term]
id: SO:0000088
name: mt_gene
def: "A gene located in mitochondrial sequence." [SO:xp]
synonym: "mitochondrial gene" EXACT []
synonym: "mt gene" EXACT []
xref: http://en.wikipedia.org/wiki/Mitochondrial_gene "wiki"
is_a: SO:0000704 ! gene
relationship: has_origin SO:0000737 ! mitochondrial_sequence
[Term]
id: SO:0000089
name: kinetoplast_gene
def: "A gene located in kinetoplast sequence." [SO:xp]
synonym: "kinetoplast gene" EXACT []
is_a: SO:0000088 ! mt_gene
relationship: has_origin SO:0000741 ! kinetoplast
[Term]
id: SO:0000090
name: plastid_gene
def: "A gene from plastid sequence." [SO:xp]
synonym: "plastid gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_origin SO:0000740 ! plastid_sequence
[Term]
id: SO:0000091
name: apicoplast_gene
def: "A gene from apicoplast sequence." [SO:xp]
synonym: "apicoplast gene" EXACT []
is_a: SO:0000090 ! plastid_gene
relationship: has_origin SO:0000743 ! apicoplast_sequence
[Term]
id: SO:0000092
name: ct_gene
def: "A gene from chloroplast sequence." [SO:xp]
synonym: "chloroplast gene" EXACT []
synonym: "ct gene" EXACT []
is_a: SO:0000090 ! plastid_gene
relationship: has_origin SO:0000745 ! chloroplast_sequence
[Term]
id: SO:0000093
name: chromoplast_gene
def: "A gene from chromoplast_sequence." [SO:xp]
synonym: "chromoplast gene" EXACT []
is_a: SO:0000090 ! plastid_gene
relationship: has_origin SO:0000744 ! chromoplast_sequence
[Term]
id: SO:0000094
name: cyanelle_gene
def: "A gene from cyanelle sequence." [SO:xp]
synonym: "cyanelle gene" EXACT []
is_a: SO:0000090 ! plastid_gene
relationship: has_origin SO:0000746 ! cyanelle_sequence
[Term]
id: SO:0000095
name: leucoplast_gene
def: "A plastid gene from leucoplast sequence." [SO:xp]
synonym: "leucoplast gene" EXACT []
is_a: SO:0000090 ! plastid_gene
relationship: has_origin SO:0000747 ! leucoplast_sequence
[Term]
id: SO:0000096
name: proplastid_gene
def: "A gene from proplastid sequence." [SO:ke]
synonym: "proplastid gene" EXACT []
is_a: SO:0000090 ! plastid_gene
relationship: has_origin SO:0000748 ! proplastid_sequence
[Term]
id: SO:0000097
name: nucleomorph_gene
def: "A gene from nucleomorph sequence." [SO:xp]
synonym: "nucleomorph gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_origin SO:0000739 ! nucleomorphic_sequence
[Term]
id: SO:0000098
name: plasmid_gene
def: "A gene from plasmid sequence." [SO:xp]
synonym: "plasmid gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_origin SO:0000749 ! plasmid_location
[Term]
id: SO:0000099
name: proviral_gene
def: "A gene from proviral sequence." [SO:xp]
synonym: "proviral gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_origin SO:0000751 ! proviral_location
[Term]
id: SO:0000100
name: endogenous_retroviral_gene
def: "A proviral gene with origin endogenous retrovirus." [SO:xp]
synonym: "endogenous retroviral gene" EXACT []
is_a: SO:0000099 ! proviral_gene
relationship: has_origin SO:0000903 ! endogenous_retroviral_sequence
[Term]
id: SO:0000101
name: transposable_element
def: "A transposon or insertion sequence. An element that can insert in a variety of DNA sequences." [http://www.sci.sdsu.edu/~smaloy/Glossary/T.html]
subset: SOFA
synonym: "transposable element" EXACT []
synonym: "transposon" EXACT []
xref: http://en.wikipedia.org/wiki/Transposable_element "wiki"
is_a: SO:0001039 ! integrated_mobile_genetic_element
[Term]
id: SO:0000102
name: expressed_sequence_match
def: "A match to an EST or cDNA sequence." [SO:ke]
subset: SOFA
synonym: "expressed sequence match" EXACT []
is_a: SO:0000347 ! nucleotide_match
[Term]
id: SO:0000103
name: clone_insert_end
def: "The end of the clone insert." [SO:ke]
subset: SOFA
synonym: "clone insert end" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000753 ! clone_insert
[Term]
id: SO:0000104
name: polypeptide
alt_id: SO:0000358
def: "A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The term 'protein' was merged with 'polypeptide'. Although 'protein' was a sequence_attribute and therefore meant to describe the quality rather than an actual feature, it was being used erroneously. It is replaced by 'peptidyl' as the polymer attribute.
subset: SOFA
synonym: "protein" EXACT []
xref: http://en.wikipedia.org/wiki/Polypeptide "wiki"
is_a: SO:0001411 ! biological_region
relationship: derives_from SO:0000316 ! CDS
[Term]
id: SO:0000105
name: chromosome_arm
def: "A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere." [http://www.medterms.com/script/main/art.asp?articlekey=5152]
synonym: "chromosome arm" EXACT []
is_a: SO:0000830 ! chromosome_part
[Term]
id: SO:0000106
name: non_capped_primary_transcript
is_obsolete: true
[Term]
id: SO:0000107
name: sequencing_primer
synonym: "sequencing primer" EXACT []
is_a: SO:0000112 ! primer
[Term]
id: SO:0000108
name: mRNA_with_frameshift
def: "An mRNA with a frameshift." [SO:xp]
synonym: "frameshifted mRNA" EXACT []
synonym: "mRNA with frameshift" EXACT []
is_a: SO:0000234 ! mRNA
relationship: has_quality SO:0000865 ! frameshift
[Term]
id: SO:0000109
name: sequence_variant_obs
def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
subset: SOFA
synonym: "mutation" RELATED []
is_obsolete: true
[Term]
id: SO:0000110
name: sequence_feature
def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke]
subset: SOFA
synonym: "located sequence feature" RELATED []
synonym: "located_sequence_feature" EXACT []
synonym: "sequence feature" EXACT []
disjoint_from: SO:0000400 ! sequence_attribute
[Term]
id: SO:0000111
name: transposable_element_gene
def: "A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast." [SO:ke]
synonym: "transposable element gene" EXACT []
is_a: SO:0000704 ! gene
relationship: part_of SO:0000101 ! transposable_element
[Term]
id: SO:0000112
name: primer
def: "An oligo to which new deoxyribonucleotides can be added by DNA polymerase." [SO:ke]
subset: SOFA
synonym: "DNA primer" EXACT []
synonym: "primer oligonucleotide" EXACT []
synonym: "primer polynucleotide" EXACT []
synonym: "primer sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Primer_(molecular_biology) "wiki"
is_a: SO:0000441 ! ss_oligo
[Term]
id: SO:0000113
name: proviral_region
def: "A viral sequence which has integrated into a host genome." [SO:ke]
subset: SOFA
synonym: "proviral region" EXACT []
synonym: "proviral sequence" RELATED []
is_a: SO:0001039 ! integrated_mobile_genetic_element
[Term]
id: SO:0000114
name: methylated_cytosine
def: "A methylated deoxy-cytosine." [SO:ke]
subset: SOFA
synonym: "methylated C" EXACT []
synonym: "methylated cytosine" EXACT []
synonym: "methylated cytosine base" EXACT []
synonym: "methylated cytosine residue" EXACT []
synonym: "methylated_C" EXACT []
is_a: SO:0000306 ! methylated_DNA_base_feature
is_a: SO:0001963 ! modified_cytosine
[Term]
id: SO:0000115
name: transcript_feature
is_obsolete: true
[Term]
id: SO:0000116
name: edited
def: "An attribute describing a sequence that is modified by editing." [SO:ke]
is_a: SO:0000237 ! transcript_attribute
[Term]
id: SO:0000117
name: transcript_with_readthrough_stop_codon
is_obsolete: true
[Term]
id: SO:0000118
name: transcript_with_translational_frameshift
def: "A transcript with a translational frameshift." [SO:xp]
synonym: "transcript with translational frameshift" EXACT []
is_a: SO:0000673 ! transcript
relationship: has_quality SO:0000887 ! translationally_frameshifted
[Term]
id: SO:0000119
name: regulated
def: "An attribute to describe a sequence that is regulated." [SO:ke]
is_a: SO:0000401 ! gene_attribute
[Term]
id: SO:0000120
name: protein_coding_primary_transcript
def: "A primary transcript that, at least in part, encodes one or more proteins." [SO:ke]
comment: May contain introns.
subset: SOFA
synonym: "pre mRNA" RELATED []
synonym: "protein coding primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript
[Term]
id: SO:0000121
name: forward_primer
def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "DNA forward primer" EXACT []
synonym: "forward DNA primer" EXACT []
synonym: "forward primer" EXACT []
synonym: "forward primer oligo" EXACT []
synonym: "forward primer oligonucleotide" EXACT []
synonym: "forward primer polynucleotide" EXACT []
synonym: "forward primer sequence" EXACT []
is_a: SO:0000112 ! primer
relationship: has_quality SO:0001030 ! forward
[Term]
id: SO:0000122
name: RNA_sequence_secondary_structure
def: "A folded RNA sequence." [SO:ke]
synonym: "RNA sequence secondary structure" EXACT []
is_a: SO:0000002 ! sequence_secondary_structure
[Term]
id: SO:0000123
name: transcriptionally_regulated
def: "An attribute describing a gene that is regulated at transcription." [SO:ma]
comment: By:<protein_id>.
synonym: "transcriptionally regulated" EXACT []
is_a: SO:0000119 ! regulated
[Term]
id: SO:0000124
name: transcriptionally_constitutive
def: "Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate." [SO:ke]
synonym: "transcriptionally constitutive" EXACT []
is_a: SO:0000123 ! transcriptionally_regulated
[Term]
id: SO:0000125
name: transcriptionally_induced
def: "An inducer molecule is required for transcription to occur." [SO:ke]
synonym: "transcriptionally induced" EXACT []
is_a: SO:0000123 ! transcriptionally_regulated
[Term]
id: SO:0000126
name: transcriptionally_repressed
def: "A repressor molecule is required for transcription to stop." [SO:ke]
synonym: "transcriptionally repressed" EXACT []
is_a: SO:0000123 ! transcriptionally_regulated
[Term]
id: SO:0000127
name: silenced_gene
def: "A gene that is silenced." [SO:xp]
synonym: "silenced gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000893 ! silenced
[Term]
id: SO:0000128
name: gene_silenced_by_DNA_modification
def: "A gene that is silenced by DNA modification." [SO:xp]
synonym: "gene silenced by DNA modification" EXACT []
is_a: SO:0000127 ! silenced_gene
relationship: has_quality SO:0000894 ! silenced_by_DNA_modification
[Term]
id: SO:0000129
name: gene_silenced_by_DNA_methylation
def: "A gene that is silenced by DNA methylation." [SO:xp]
synonym: "gene silenced by DNA methylation" EXACT []
synonym: "methylation-silenced gene" EXACT []
is_a: SO:0000128 ! gene_silenced_by_DNA_modification
relationship: has_quality SO:0000895 ! silenced_by_DNA_methylation
[Term]
id: SO:0000130
name: post_translationally_regulated
def: "An attribute describing a gene that is regulated after it has been translated." [SO:ke]
synonym: "post translationally regulated" EXACT []
synonym: "post-translationally regulated" EXACT []
is_a: SO:0000119 ! regulated
[Term]
id: SO:0000131
name: translationally_regulated
def: "An attribute describing a gene that is regulated as it is translated." [SO:ke]
synonym: "translationally regulated" EXACT []
is_a: SO:0000119 ! regulated
[Term]
id: SO:0000132
name: reverse_primer
def: "A single stranded oligo used for polymerase chain reaction." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "DNA reverse primer" EXACT []
synonym: "reverse DNA primer" EXACT []
synonym: "reverse primer" EXACT []
synonym: "reverse primer oligo" EXACT []
synonym: "reverse primer oligonucleotide" EXACT []
synonym: "reverse primer sequence" EXACT []
is_a: SO:0000112 ! primer
relationship: has_quality SO:0001031 ! reverse
[Term]
id: SO:0000133
name: epigenetically_modified
def: "This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones." [SO:ke]
synonym: "epigenetically modified" EXACT []
is_a: SO:0000401 ! gene_attribute
[Term]
id: SO:0000134
name: genomically_imprinted
def: "Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin." [SO:ke]
synonym: "genomically imprinted" EXACT []
synonym: "imprinted" BROAD []
xref: http:http://en.wikipedia.org/wiki/Genomic_imprinting "wiki"
is_a: SO:0000119 ! regulated
is_a: SO:0000133 ! epigenetically_modified
[Term]
id: SO:0000135
name: maternally_imprinted
def: "The maternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]
synonym: "maternally imprinted" EXACT []
is_a: SO:0000134 ! genomically_imprinted
[Term]
id: SO:0000136
name: paternally_imprinted
def: "The paternal copy of the gene is modified, rendering it transcriptionally silent." [SO:ke]
synonym: "paternally imprinted" EXACT []
is_a: SO:0000134 ! genomically_imprinted
[Term]
id: SO:0000137
name: allelically_excluded
def: "Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell." [SO:ke]
comment: Examples are x-inactivation and immunoglobulin formation.
synonym: "allelically excluded" EXACT []
is_a: SO:0000133 ! epigenetically_modified
[Term]
id: SO:0000138
name: gene_rearranged_at_DNA_level
def: "An epigenetically modified gene, rearranged at the DNA level." [SO:xp]
synonym: "gene rearranged at DNA level" EXACT []
is_a: SO:0000898 ! epigenetically_modified_gene
relationship: has_quality SO:0000904 ! rearranged_at_DNA_level
[Term]
id: SO:0000139
name: ribosome_entry_site
def: "Region in mRNA where ribosome assembles." [SO:ke]
subset: SOFA
synonym: "ribosome entry site" EXACT []
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000204 ! five_prime_UTR
[Term]
id: SO:0000140
name: attenuator
def: "A sequence segment located within the five prime end of an mRNA that causes premature termination of translation." [SO:as]
subset: SOFA
synonym: "attenuator sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Attenuator "wiki"
is_a: SO:0001680 ! translation_regulatory_region
relationship: part_of SO:0000234 ! mRNA
[Term]
id: SO:0000141
name: terminator
def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "terminator sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Terminator_(genetics) "wiki"
is_a: SO:0001679 ! transcription_regulatory_region
relationship: part_of SO:0000673 ! transcript
[Term]
id: SO:0000142
name: DNA_sequence_secondary_structure
def: "A folded DNA sequence." [SO:ke]
synonym: "DNA sequence secondary structure" EXACT []
is_a: SO:0000002 ! sequence_secondary_structure
[Term]
id: SO:0000143
name: assembly_component
def: "A region of known length which may be used to manufacture a longer region." [SO:ke]
subset: SOFA
synonym: "assembly component" EXACT []
is_a: SO:0001410 ! experimental_feature
[Term]
id: SO:0000144
name: primary_transcript_attribute
is_obsolete: true
[Term]
id: SO:0000145
name: recoded_codon
def: "A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough." [SO:xp]
synonym: "recoded codon" EXACT []
is_a: SO:0000360 ! codon
[Term]
id: SO:0000146
name: capped
def: "An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end." [SO:ke]
is_a: SO:0000237 ! transcript_attribute
[Term]
id: SO:0000147
name: exon
def: "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Exon "wiki"
is_a: SO:0000833 ! transcript_region
[Term]
id: SO:0000148
name: supercontig
def: "One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's." [SO:ls]
subset: SOFA
synonym: "scaffold" RELATED []
is_a: SO:0001876 ! partial_genomic_sequence_assembly
relationship: part_of SO:0000719 ! ultracontig
[Term]
id: SO:0000149
name: contig
def: "A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases." [SO:ls]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Contig "wiki"
is_a: SO:0000143 ! assembly_component
is_a: SO:0000353 ! sequence_assembly
relationship: part_of SO:0000148 ! supercontig
[Term]
id: SO:0000150
name: read
def: "A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine." [SO:rd]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000149 ! contig
[Term]
id: SO:0000151
name: clone
def: "A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism." [SO:ke]
subset: SOFA
xref: http:http://en.wikipedia.org/wiki/Clone_(genetics) "wiki"
is_a: SO:0000695 ! reagent
[Term]
id: SO:0000152
name: YAC
def: "Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "yeast artificial chromosome" EXACT []
is_a: SO:0000440 ! vector_replicon
[Term]
id: SO:0000153
name: BAC
def: "Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "bacterial artificial chromosome" EXACT []
is_a: SO:0000440 ! vector_replicon
[Term]
id: SO:0000154
name: PAC
def: "The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells." [http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. Drosophila melanogaster PACs carry an average insert size of 80 kb. The library represents a 6-fold coverage of the genome.
synonym: "P1" EXACT []
synonym: "P1 artificial chromosome" EXACT []
xref: http://en.wikipedia.org/wiki/P1-derived_artificial_chromosome "wiki"
is_a: SO:0000440 ! vector_replicon
[Term]
id: SO:0000155
name: plasmid
def: "A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "plasmid sequence" EXACT []
is_a: SO:0001235 ! replicon
[Term]
id: SO:0000156
name: cosmid
def: "A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites." [SO:ma]
comment: Paper: vans GA et al. High efficiency vectors for cosmid microcloning and genomic analysis. Gene 1989; 79(1):9-20. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "cosmid vector" EXACT []
xref: http://en.wikipedia.org/wiki/Cosmid "wiki"
is_a: SO:0000440 ! vector_replicon
[Term]
id: SO:0000157
name: phagemid
def: "A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with \"helper\" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids." [SO:ma]
synonym: "phagemid vector" RELATED []
xref: http://en.wikipedia.org/wiki/Phagemid "wiki"
is_a: SO:0000440 ! vector_replicon
[Term]
id: SO:0000158
name: fosmid
def: "A cloning vector that utilizes the E. coli F factor." [SO:ma]
comment: Birren BW et al. A human chromosome 22 fosmid resource: mapping and analysis of 96 clones. Genomics 1996.
synonym: "fosmid vector" RELATED []
xref: http://en.wikipedia.org/wiki/Fosmid "wiki"
is_a: SO:0000440 ! vector_replicon
[Term]
id: SO:0000159
name: deletion
alt_id: SO:1000033
def: "The point at which one or more contiguous nucleotides were excised." [SO:ke]
subset: SOFA
synonym: "deleted_sequence" EXACT []
synonym: "nucleotide deletion" EXACT []
synonym: "nucleotide_deletion" EXACT []
xref: http://en.wikipedia.org/wiki/Nucleotide_deletion "wiki"
xref: loinc:LA6692-3 "Deletion"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000160
name: lambda_clone
def: "A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]
is_obsolete: true
[Term]
id: SO:0000161
name: methylated_adenine
def: "A modified base in which adenine has been methylated." [SO:ke]
subset: SOFA
synonym: "methylated A" EXACT []
synonym: "methylated adenine" EXACT []
synonym: "methylated adenine base" EXACT []
synonym: "methylated adenine residue" EXACT []
synonym: "methylated_A" EXACT []
is_a: SO:0000306 ! methylated_DNA_base_feature
is_a: SO:0001962 ! modified_adenine
[Term]
id: SO:0000162
name: splice_site
def: "Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction." [SO:cjm, SO:ke]
comment: With spliceosomal introns, the splice sites bind the spliceosomal machinery.
subset: SOFA
synonym: "splice site" EXACT []
xref: http://en.wikipedia.org/wiki/Splice_site "wiki"
is_a: SO:0000835 ! primary_transcript_region
[Term]
id: SO:0000163
name: five_prime_cis_splice_site
def: "Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]
subset: SOFA
synonym: "5' splice site" EXACT []
synonym: "donor" RELATED []
synonym: "donor splice site" EXACT []
synonym: "five prime splice site" EXACT []
synonym: "splice donor site" EXACT []
is_a: SO:0001419 ! cis_splice_site
[Term]
id: SO:0000164
name: three_prime_cis_splice_site
def: "Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html, SO:cjm, SO:ke]
subset: SOFA
synonym: "3' splice site" RELATED []
synonym: "acceptor" RELATED []
synonym: "acceptor splice site" EXACT []
synonym: "splice acceptor site" EXACT []
synonym: "three prime splice site" EXACT []
is_a: SO:0001419 ! cis_splice_site
[Term]
id: SO:0000165
name: enhancer
def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki"
is_a: SO:0000727 ! CRM
[Term]
id: SO:0000166
name: enhancer_bound_by_factor
def: "An enhancer bound by a factor." [SO:xp]
synonym: "enhancer bound by factor" EXACT []
is_a: SO:0000165 ! enhancer
relationship: has_quality SO:0000277 ! bound_by_factor
[Term]
id: SO:0000167
name: promoter
def: "A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the basal transcription machinery." [SO:regcreative]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription.
subset: SOFA
synonym: "promoter sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Promoter "wiki"
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
[Term]
id: SO:0000168
name: restriction_enzyme_cut_site
def: "A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA." [SO:ma]
is_obsolete: true
[Term]
id: SO:0000169
name: RNApol_I_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription." [SO:ke]
synonym: "pol I promoter" EXACT []
synonym: "polymerase I promoter" EXACT []
synonym: "RNA polymerase A promoter" EXACT []
synonym: "RNApol I promoter" EXACT []
is_a: SO:0001203 ! RNA_polymerase_promoter
[Term]
id: SO:0000170
name: RNApol_II_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke]
synonym: "pol II promoter" RELATED []
synonym: "polymerase II promoter" EXACT []
synonym: "RNA polymerase B promoter" EXACT []
synonym: "RNApol II promoter" EXACT []
is_a: SO:0001203 ! RNA_polymerase_promoter
[Term]
id: SO:0000171
name: RNApol_III_promoter
def: "A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription." [SO:ke]
synonym: "pol III promoter" EXACT []
synonym: "polymerase III promoter" EXACT []
synonym: "RNA polymerase C promoter" EXACT []
synonym: "RNApol III promoter" EXACT []
is_a: SO:0001203 ! RNA_polymerase_promoter
[Term]
id: SO:0000172
name: CAAT_signal
def: "Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "CAAT box" EXACT []
synonym: "CAAT signal" EXACT []
synonym: "CAAT-box" EXACT []
xref: http://en.wikipedia.org/wiki/CAAT_box "wiki"
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0000173
name: GC_rich_promoter_region
def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "GC rich promoter region" EXACT []
synonym: "GC-rich region" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0000174
name: TATA_box
def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:16858867]
comment: Binds TBP.
synonym: "Goldstein-Hogness box" EXACT []
synonym: "TATA box" EXACT []
xref: http://en.wikipedia.org/wiki/TATA_box "wiki"
is_a: SO:0001660 ! core_promoter_element
[Term]
id: SO:0000175
name: minus_10_signal
def: "A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "-10 signal" EXACT []
synonym: "minus 10 signal" EXACT []
synonym: "Pribnow box" EXACT []
synonym: "Pribnow Schaller box" EXACT []
synonym: "Pribnow-Schaller box" EXACT []
xref: http://en.wikipedia.org/wiki/Pribnow_box "wiki"
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70
relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf
[Term]
id: SO:0000176
name: minus_35_signal
def: "A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "-35 signal" EXACT []
synonym: "minus 35 signal" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001671 ! bacterial_RNApol_promoter_sigma_70
relationship: part_of SO:0001913 ! bacterial_RNApol_promoter_sigma_ecf
[Term]
id: SO:0000177
name: cross_genome_match
def: "A nucleotide match against a sequence from another organism." [SO:ma]
subset: SOFA
synonym: "cross genome match" EXACT []
is_a: SO:0000347 ! nucleotide_match
[Term]
id: SO:0000178
name: operon
def: "A group of contiguous genes transcribed as a single (polycistronic) mRNA from a single regulatory region." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Operon "wiki"
is_a: SO:0005855 ! gene_group
[Term]
id: SO:0000179
name: clone_insert_start
def: "The start of the clone insert." [SO:ke]
subset: SOFA
synonym: "clone insert start" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000753 ! clone_insert
[Term]
id: SO:0000180
name: retrotransposon
def: "A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase." [http://www.dddmag.com/Glossary.aspx#r]
synonym: "class I" RELATED []
synonym: "class I transposon" EXACT []
synonym: "retrotransposon element" EXACT []
xref: http://en.wikipedia.org/wiki/Retrotransposon "wiki"
is_a: SO:0000101 ! transposable_element
[Term]
id: SO:0000181
name: translated_nucleotide_match
def: "A match against a translated sequence." [SO:ke]
subset: SOFA
synonym: "translated nucleotide match" EXACT []
is_a: SO:0000347 ! nucleotide_match
[Term]
id: SO:0000182
name: DNA_transposon
def: "A transposon where the mechanism of transposition is via a DNA intermediate." [SO:ke]
synonym: "class II" RELATED []
synonym: "class II transposon" EXACT []
synonym: "DNA transposon" EXACT []
is_a: SO:0000101 ! transposable_element
[Term]
id: SO:0000183
name: non_transcribed_region
def: "A region of the gene which is not transcribed." [SO:ke]
subset: SOFA
synonym: "non transcribed region" EXACT []
synonym: "non-transcribed sequence" EXACT []
synonym: "nontranscribed region" EXACT []
synonym: "nontranscribed sequence" EXACT []
is_a: SO:0000842 ! gene_component_region
[Term]
id: SO:0000184
name: U2_intron
def: "A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs." [PMID:9428511]
comment: May have either GT-AG or AT-AG 5' and 3' boundaries.
synonym: "U2 intron" EXACT []
is_a: SO:0000662 ! spliceosomal_intron
[Term]
id: SO:0000185
name: primary_transcript
def: "A transcript that in its initial state requires modification to be functional." [SO:ma]
subset: SOFA
synonym: "precursor RNA" EXACT []
synonym: "primary transcript" EXACT []
xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki"
is_a: SO:0000673 ! transcript
[Term]
id: SO:0000186
name: LTR_retrotransposon
def: "A retrotransposon flanked by long terminal repeat sequences." [SO:ke]
synonym: "long terminal repeat retrotransposon" EXACT []
synonym: "LTR retrotransposon" EXACT []
is_a: SO:0000180 ! retrotransposon
[Term]
id: SO:0000187
name: repeat_family
def: "A group of characterized repeat sequences." [SO:ke]
subset: SOFA
is_obsolete: true
[Term]
id: SO:0000188
name: intron
def: "A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Intron "wiki"
is_a: SO:0000835 ! primary_transcript_region
[Term]
id: SO:0000189
name: non_LTR_retrotransposon
def: "A retrotransposon without long terminal repeat sequences." [SO:ke]
synonym: "non LTR retrotransposon" EXACT []
is_a: SO:0000180 ! retrotransposon
[Term]
id: SO:0000190
name: five_prime_intron
synonym: "5' intron" EXACT []
synonym: "5' intron sequence" EXACT []
synonym: "five prime intron" EXACT []
is_a: SO:0000188 ! intron
[Term]
id: SO:0000191
name: interior_intron
synonym: "interior intron" EXACT []
is_a: SO:0000188 ! intron
[Term]
id: SO:0000192
name: three_prime_intron
synonym: "3' intron" EXACT []
synonym: "3' intron sequence" RELATED []
synonym: "three prime intron" EXACT []
is_a: SO:0000188 ! intron
[Term]
id: SO:0000193
name: RFLP_fragment
def: "A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme." [GOC:pj]
subset: SOFA
synonym: "restriction fragment length polymorphism" EXACT []
synonym: "RFLP" EXACT []
synonym: "RFLP fragment" EXACT []
xref: http://en.wikipedia.org/wiki/Restriction_fragment_length_polymorphism "wiki"
is_a: SO:0000412 ! restriction_fragment
[Term]
id: SO:0000194
name: LINE_element
def: "A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
synonym: "LINE" EXACT []
synonym: "LINE element" EXACT []
synonym: "Long interspersed element" EXACT []
synonym: "Long interspersed nuclear element" EXACT []
is_a: SO:0000189 ! non_LTR_retrotransposon
[Term]
id: SO:0000195
name: coding_exon
def: "An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon)." [SO:ke]
subset: SOFA
synonym: "coding exon" EXACT []
is_a: SO:0000147 ! exon
[Term]
id: SO:0000196
name: five_prime_coding_exon_coding_region
def: "The sequence of the five_prime_coding_exon that codes for protein." [SO:cjm]
subset: SOFA
synonym: "five prime exon coding region" EXACT []
is_a: SO:0001215 ! coding_region_of_exon
relationship: part_of SO:0000200 ! five_prime_coding_exon
[Term]
id: SO:0000197
name: three_prime_coding_exon_coding_region
def: "The sequence of the three_prime_coding_exon that codes for protein." [SO:cjm]
subset: SOFA
synonym: "three prime exon coding region" EXACT []
is_a: SO:0001215 ! coding_region_of_exon
relationship: part_of SO:0000202 ! three_prime_coding_exon
[Term]
id: SO:0000198
name: noncoding_exon
def: "An exon that does not contain any codons." [SO:ke]
subset: SOFA
synonym: "noncoding exon" EXACT []
is_a: SO:0000147 ! exon
[Term]
id: SO:0000199
name: translocation
def: "A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions." [NCBI:th, SO:ke]
subset: DBVAR
synonym: "transchr" RELATED [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "translocated sequence" EXACT []
is_a: SO:0001785 ! structural_alteration
[Term]
id: SO:0000200
name: five_prime_coding_exon
def: "The 5' most coding exon." [SO:ke]
subset: SOFA
synonym: "5' coding exon" EXACT []
synonym: "five prime coding exon" EXACT []
is_a: SO:0000195 ! coding_exon
[Term]
id: SO:0000201
name: interior_exon
def: "An exon that is bounded by 5' and 3' splice sites." [PMID:10373547]
synonym: "interior exon" EXACT []
is_a: SO:0000147 ! exon
[Term]
id: SO:0000202
name: three_prime_coding_exon
def: "The coding exon that is most 3-prime on a given transcript." [SO:ma]
synonym: "3' coding exon" RELATED []
synonym: "three prime coding exon" EXACT []
is_a: SO:0000195 ! coding_exon
[Term]
id: SO:0000203
name: UTR
def: "Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated." [SO:ke]
subset: SOFA
synonym: "untranslated region" EXACT []
is_a: SO:0000836 ! mRNA_region
[Term]
id: SO:0000204
name: five_prime_UTR
def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "5' UTR" EXACT []
synonym: "five prime UTR" EXACT []
synonym: "five_prime_untranslated_region" EXACT []
xref: http://en.wikipedia.org/wiki/5'_UTR "wiki"
is_a: SO:0000203 ! UTR
[Term]
id: SO:0000205
name: three_prime_UTR
def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "three prime untranslated region" EXACT []
synonym: "three prime UTR" EXACT []
xref: http://en.wikipedia.org/wiki/Three_prime_untranslated_region "wiki"
is_a: SO:0000203 ! UTR
[Term]
id: SO:0000206
name: SINE_element
def: "A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element." [SO:ke]
synonym: "Short interspersed element" EXACT []
synonym: "Short interspersed nuclear element" EXACT []
synonym: "SINE element" EXACT []
xref: http://en.wikipedia.org/wiki/Short_interspersed_nuclear_element "wiki"
is_a: SO:0000189 ! non_LTR_retrotransposon
[Term]
id: SO:0000207
name: simple_sequence_length_variation
synonym: "simple sequence length polymorphism" RELATED []
synonym: "simple sequence length variation" EXACT []
synonym: "SSLP" RELATED []
is_a: SO:0000248 ! sequence_length_variation
[Term]
id: SO:0000208
name: terminal_inverted_repeat_element
def: "A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]
synonym: "terminal inverted repeat element" EXACT []
synonym: "TIR element" EXACT []
is_a: SO:0000182 ! DNA_transposon
[Term]
id: SO:0000209
name: rRNA_primary_transcript
def: "A primary transcript encoding a ribosomal RNA." [SO:ke]
subset: SOFA
synonym: "ribosomal RNA primary transcript" EXACT []
synonym: "rRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000210
name: tRNA_primary_transcript
def: "A primary transcript encoding a transfer RNA (SO:0000253)." [SO:ke]
synonym: "tRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000211
name: alanine_tRNA_primary_transcript
def: "A primary transcript encoding alanyl tRNA." [SO:ke]
synonym: "alanine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000212
name: arginine_tRNA_primary_transcript
def: "A primary transcript encoding arginyl tRNA (SO:0000255)." [SO:ke]
synonym: "arginine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000213
name: asparagine_tRNA_primary_transcript
def: "A primary transcript encoding asparaginyl tRNA (SO:0000256)." [SO:ke]
synonym: "asparagine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000214
name: aspartic_acid_tRNA_primary_transcript
def: "A primary transcript encoding aspartyl tRNA (SO:0000257)." [SO:ke]
synonym: "aspartic acid tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000215
name: cysteine_tRNA_primary_transcript
def: "A primary transcript encoding cysteinyl tRNA (SO:0000258)." [SO:ke]
synonym: "cysteine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000216
name: glutamic_acid_tRNA_primary_transcript
def: "A primary transcript encoding glutaminyl tRNA (SO:0000260)." [SO:ke]
synonym: "glutamic acid tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000217
name: glutamine_tRNA_primary_transcript
def: "A primary transcript encoding glutamyl tRNA (SO:0000260)." [SO:ke]
synonym: "glutamine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000218
name: glycine_tRNA_primary_transcript
def: "A primary transcript encoding glycyl tRNA (SO:0000263)." [SO:ke]
synonym: "glycine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000219
name: histidine_tRNA_primary_transcript
def: "A primary transcript encoding histidyl tRNA (SO:0000262)." [SO:ke]
synonym: "histidine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000220
name: isoleucine_tRNA_primary_transcript
def: "A primary transcript encoding isoleucyl tRNA (SO:0000263)." [SO:ke]
synonym: "isoleucine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000221
name: leucine_tRNA_primary_transcript
def: "A primary transcript encoding leucyl tRNA (SO:0000264)." [SO:ke]
synonym: "leucine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000222
name: lysine_tRNA_primary_transcript
def: "A primary transcript encoding lysyl tRNA (SO:0000265)." [SO:ke]
synonym: "lysine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000223
name: methionine_tRNA_primary_transcript
def: "A primary transcript encoding methionyl tRNA (SO:0000266)." [SO:ke]
synonym: "methionine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000224
name: phenylalanine_tRNA_primary_transcript
def: "A primary transcript encoding phenylalanyl tRNA (SO:0000267)." [SO:ke]
synonym: "phenylalanine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000225
name: proline_tRNA_primary_transcript
def: "A primary transcript encoding prolyl tRNA (SO:0000268)." [SO:ke]
synonym: "proline tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000226
name: serine_tRNA_primary_transcript
def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
synonym: "serine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000227
name: threonine_tRNA_primary_transcript
def: "A primary transcript encoding threonyl tRNA (SO:000270)." [SO:ke]
synonym: "threonine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000228
name: tryptophan_tRNA_primary_transcript
def: "A primary transcript encoding tryptophanyl tRNA (SO:000271)." [SO:ke]
synonym: "tryptophan tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000229
name: tyrosine_tRNA_primary_transcript
def: "A primary transcript encoding tyrosyl tRNA (SO:000272)." [SO:ke]
synonym: "tyrosine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000230
name: valine_tRNA_primary_transcript
def: "A primary transcript encoding valyl tRNA (SO:000273)." [SO:ke]
synonym: "valine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000231
name: snRNA_primary_transcript
def: "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke]
synonym: "snRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000232
name: snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar mRNA (SO:0000275)." [SO:ke]
synonym: "snoRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000233
name: mature_transcript
def: "A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified." [SO:ke]
comment: A processed transcript cannot contain introns.
subset: SOFA
synonym: "mature transcript" EXACT []
xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki"
is_a: SO:0000673 ! transcript
relationship: derives_from SO:0000185 ! primary_transcript
[Term]
id: SO:0000234
name: mRNA
def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma]
comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "messenger RNA" EXACT []
xref: http://en.wikipedia.org/wiki/MRNA "wiki"
is_a: SO:0000233 ! mature_transcript
[Term]
id: SO:0000235
name: TF_binding_site
def: "A region of a nucleotide molecule that binds a Transcription Factor or Transcription Factor complex [GO:0005667]." [SO:ke]
subset: SOFA
synonym: "TF binding site" EXACT []
synonym: "transcription factor binding site" EXACT []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site
is_a: SO:0001679 ! transcription_regulatory_region
[Term]
id: SO:0000236
name: ORF
def: "The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER." [SGD:rb, SO:ma]
comment: The definition was modified by Rama. ORF is defined by the sequence, whereas the CDS is defined according to whether a polypeptide is made. This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "open reading frame" EXACT []
is_a: SO:0000717 ! reading_frame
[Term]
id: SO:0000237
name: transcript_attribute
synonym: "transcript attribute" EXACT []
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000238
name: foldback_element
def: "A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats." [http://www.genetics.org/cgi/reprint/156/4/1983.pdf]
synonym: "foldback element" EXACT []
synonym: "long inverted repeat element" RELATED []
synonym: "LVR element" RELATED []
is_a: SO:0000182 ! DNA_transposon
[Term]
id: SO:0000239
name: flanking_region
def: "The sequences extending on either side of a specific region." [SO:ke]
subset: SOFA
synonym: "flanking region" EXACT []
is_a: SO:0001412 ! topologically_defined_region
[Term]
id: SO:0000240
name: chromosome_variation
synonym: "chromosome variation" EXACT []
is_a: SO:0001507 ! variant_collection
disjoint_from: SO:0000400 ! sequence_attribute
relationship: part_of SO:0001524 ! chromosomally_aberrant_genome
[Term]
id: SO:0000241
name: internal_UTR
def: "A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal." [SO:cjm]
synonym: "internal UTR" EXACT []
is_a: SO:0000203 ! UTR
[Term]
id: SO:0000242
name: untranslated_region_polycistronic_mRNA
def: "The untranslated sequence separating the 'cistrons' of multicistronic mRNA." [SO:ke]
synonym: "untranslated region polycistronic mRNA" EXACT []
is_a: SO:0000203 ! UTR
[Term]
id: SO:0000243
name: internal_ribosome_entry_site
def: "Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation." [SO:ke]
synonym: "internal ribosomal entry sequence" EXACT []
synonym: "internal ribosomal entry site" EXACT []
synonym: "internal ribosome entry sequence" RELATED []
synonym: "internal ribosome entry site" EXACT []
synonym: "IRES" EXACT []
xref: http://en.wikipedia.org/wiki/Internal_ribosome_entry_site "wiki"
is_a: SO:0000139 ! ribosome_entry_site
[Term]
id: SO:0000244
name: four_cutter_restriction_site
synonym: "4-cutter_restriction_site" RELATED []
synonym: "four-cutter_restriction_sit" RELATED []
is_obsolete: true
[Term]
id: SO:0000245
name: mRNA_by_polyadenylation_status
is_obsolete: true
[Term]
id: SO:0000246
name: polyadenylated
def: "A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute
[Term]
id: SO:0000247
name: mRNA_not_polyadenylated
is_obsolete: true
[Term]
id: SO:0000248
name: sequence_length_variation
synonym: "sequence length variation" EXACT []
is_a: SO:1000002 ! substitution
[Term]
id: SO:0000249
name: six_cutter_restriction_site
synonym: "6-cutter_restriction_site" RELATED []
synonym: "six-cutter_restriction_site" RELATED []
is_obsolete: true
[Term]
id: SO:0000250
name: modified_RNA_base_feature
def: "A post_transcriptionally modified base." [SO:ke]
synonym: "modified RNA base feature" EXACT []
is_a: SO:0001236 ! base
[Term]
id: SO:0000251
name: eight_cutter_restriction_site
synonym: "8-cutter_restriction_site" RELATED []
synonym: "eight-cutter_restriction_site" RELATED []
is_obsolete: true
[Term]
id: SO:0000252
name: rRNA
def: "RNA that comprises part of a ribosome, and that can provide both structural scaffolding and catalytic activity." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, ISBN:0198506732]
subset: SOFA
synonym: "ribosomal ribonucleic acid" EXACT []
synonym: "ribosomal RNA" EXACT []
xref: http://en.wikipedia.org/wiki/RRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000209 ! rRNA_primary_transcript
[Term]
id: SO:0000253
name: tRNA
def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "transfer ribonucleic acid" RELATED []
synonym: "transfer RNA" RELATED []
xref: http://en.wikipedia.org/wiki/TRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0000254
name: alanyl_tRNA
def: "A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region." [SO:ke]
synonym: "alanyl tRNA" EXACT []
synonym: "alanyl-transfer ribonucleic acid" EXACT []
synonym: "alanyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000211 ! alanine_tRNA_primary_transcript
[Term]
id: SO:0000255
name: rRNA_small_subunit_primary_transcript
def: "A primary transcript encoding a small ribosomal subunit RNA." [SO:ke]
synonym: "rRNA small subunit primary transcript" EXACT []
is_a: SO:0000209 ! rRNA_primary_transcript
[Term]
id: SO:0000256
name: asparaginyl_tRNA
def: "A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region." [SO:ke]
synonym: "asparaginyl tRNA" EXACT []
synonym: "asparaginyl-transfer ribonucleic acid" EXACT []
synonym: "asparaginyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000213 ! asparagine_tRNA_primary_transcript
[Term]
id: SO:0000257
name: aspartyl_tRNA
def: "A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region." [SO:ke]
synonym: "aspartyl tRNA" EXACT []
synonym: "aspartyl-transfer ribonucleic acid" EXACT []
synonym: "aspartyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000214 ! aspartic_acid_tRNA_primary_transcript
[Term]
id: SO:0000258
name: cysteinyl_tRNA
def: "A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region." [SO:ke]
synonym: "cysteinyl tRNA" EXACT []
synonym: "cysteinyl-transfer ribonucleic acid" EXACT []
synonym: "cysteinyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000215 ! cysteine_tRNA_primary_transcript
[Term]
id: SO:0000259
name: glutaminyl_tRNA
def: "A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region." [SO:ke]
synonym: "glutaminyl tRNA" EXACT []
synonym: "glutaminyl-transfer ribonucleic acid" EXACT []
synonym: "glutaminyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000216 ! glutamic_acid_tRNA_primary_transcript
[Term]
id: SO:0000260
name: glutamyl_tRNA
def: "A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region." [SO:ke]
synonym: "glutamyl tRNA" EXACT []
synonym: "glutamyl-transfer ribonucleic acid" EXACT []
synonym: "glutamyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000217 ! glutamine_tRNA_primary_transcript
[Term]
id: SO:0000261
name: glycyl_tRNA
def: "A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region." [SO:ke]
synonym: "glycyl tRNA" EXACT []
synonym: "glycyl-transfer ribonucleic acid" RELATED []
synonym: "glycyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000218 ! glycine_tRNA_primary_transcript
[Term]
id: SO:0000262
name: histidyl_tRNA
def: "A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region." [SO:ke]
synonym: "histidyl tRNA" EXACT []
synonym: "histidyl-transfer ribonucleic acid" EXACT []
synonym: "histidyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000219 ! histidine_tRNA_primary_transcript
[Term]
id: SO:0000263
name: isoleucyl_tRNA
def: "A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region." [SO:ke]
synonym: "isoleucyl tRNA" EXACT []
synonym: "isoleucyl-transfer ribonucleic acid" EXACT []
synonym: "isoleucyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000220 ! isoleucine_tRNA_primary_transcript
[Term]
id: SO:0000264
name: leucyl_tRNA
def: "A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region." [SO:ke]
synonym: "leucyl tRNA" EXACT []
synonym: "leucyl-transfer ribonucleic acid" EXACT []
synonym: "leucyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000221 ! leucine_tRNA_primary_transcript
[Term]
id: SO:0000265
name: lysyl_tRNA
def: "A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region." [SO:ke]
synonym: "lysyl tRNA" EXACT []
synonym: "lysyl-transfer ribonucleic acid" EXACT []
synonym: "lysyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000222 ! lysine_tRNA_primary_transcript
[Term]
id: SO:0000266
name: methionyl_tRNA
def: "A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region." [SO:ke]
synonym: "methionyl tRNA" EXACT []
synonym: "methionyl-transfer ribonucleic acid" EXACT []
synonym: "methionyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000223 ! methionine_tRNA_primary_transcript
[Term]
id: SO:0000267
name: phenylalanyl_tRNA
def: "A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region." [SO:ke]
synonym: "phenylalanyl tRNA" EXACT []
synonym: "phenylalanyl-transfer ribonucleic acid" EXACT []
synonym: "phenylalanyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000224 ! phenylalanine_tRNA_primary_transcript
[Term]
id: SO:0000268
name: prolyl_tRNA
def: "A tRNA sequence that has a proline anticodon, and a 3' proline binding region." [SO:ke]
synonym: "prolyl tRNA" EXACT []
synonym: "prolyl-transfer ribonucleic acid" EXACT []
synonym: "prolyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000225 ! proline_tRNA_primary_transcript
[Term]
id: SO:0000269
name: seryl_tRNA
def: "A tRNA sequence that has a serine anticodon, and a 3' serine binding region." [SO:ke]
synonym: "seryl tRNA" EXACT []
synonym: "seryl-transfer ribonucleic acid" RELATED []
synonym: "seryl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000226 ! serine_tRNA_primary_transcript
[Term]
id: SO:0000270
name: threonyl_tRNA
def: "A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region." [SO:ke]
synonym: "threonyl tRNA" EXACT []
synonym: "threonyl-transfer ribonucleic acid" EXACT []
synonym: "threonyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000227 ! threonine_tRNA_primary_transcript
[Term]
id: SO:0000271
name: tryptophanyl_tRNA
def: "A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region." [SO:ke]
synonym: "tryptophanyl tRNA" EXACT []
synonym: "tryptophanyl-transfer ribonucleic acid" EXACT []
synonym: "tryptophanyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000228 ! tryptophan_tRNA_primary_transcript
[Term]
id: SO:0000272
name: tyrosyl_tRNA
def: "A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region." [SO:ke]
synonym: "tyrosyl tRNA" EXACT []
synonym: "tyrosyl-transfer ribonucleic acid" EXACT []
synonym: "tyrosyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000229 ! tyrosine_tRNA_primary_transcript
[Term]
id: SO:0000273
name: valyl_tRNA
def: "A tRNA sequence that has a valine anticodon, and a 3' valine binding region." [SO:ke]
synonym: "valyl tRNA" EXACT []
synonym: "valyl-transfer ribonucleic acid" EXACT []
synonym: "valyl-transfer RNA" RELATED []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000230 ! valine_tRNA_primary_transcript
[Term]
id: SO:0000274
name: snRNA
def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, PMID:11733745, WB:ems]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "small nuclear RNA" EXACT []
xref: http://en.wikipedia.org/wiki/SnRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000231 ! snRNA_primary_transcript
[Term]
id: SO:0000275
name: snoRNA
def: "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." [GOC:kgc]
subset: SOFA
synonym: "small nucleolar RNA" EXACT []
xref: http://en.wikipedia.org/wiki/SnoRNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000232 ! snoRNA_primary_transcript
[Term]
id: SO:0000276
name: miRNA
alt_id: SO:0000649
def: "Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes. Micro RNAs are produced from precursor molecules (SO:0000647) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors." [PMID:11081512, PMID:12592000]
subset: SOFA
synonym: "micro RNA" EXACT []
synonym: "microRNA" EXACT []
synonym: "small temporal RNA" EXACT []
synonym: "stRNA" EXACT []
xref: http://en.wikipedia.org/wiki/MiRNA "wiki"
xref: http://en.wikipedia.org/wiki/StRNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA
relationship: part_of SO:0001244 ! pre_miRNA
[Term]
id: SO:0000277
name: bound_by_factor
def: "An attribute describing a sequence that is bound by another molecule." [SO:ke]
comment: Formerly called transcript_by_bound_factor.
synonym: "bound by factor" EXACT []
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000278
name: transcript_bound_by_nucleic_acid
def: "A transcript that is bound by a nucleic acid." [SO:xp]
comment: Formerly called transcript_by_bound_nucleic_acid.
synonym: "transcript bound by nucleic acid" EXACT []
is_a: SO:0000673 ! transcript
relationship: has_quality SO:0000876 ! bound_by_nucleic_acid
[Term]
id: SO:0000279
name: transcript_bound_by_protein
def: "A transcript that is bound by a protein." [SO:xp]
comment: Formerly called transcript_by_bound_protein.
synonym: "transcript bound by protein" EXACT []
is_a: SO:0000673 ! transcript
relationship: has_quality SO:0000875 ! bound_by_protein
[Term]
id: SO:0000280
name: engineered_gene
def: "A gene that is engineered." [SO:xp]
synonym: "engineered gene" EXACT []
is_a: SO:0000704 ! gene
is_a: SO:0000804 ! engineered_region
relationship: has_quality SO:0000783 ! engineered
[Term]
id: SO:0000281
name: engineered_foreign_gene
def: "A gene that is engineered and foreign." [SO:xp]
synonym: "engineered foreign gene" EXACT []
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000285 ! foreign_gene
is_a: SO:0000805 ! engineered_foreign_region
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign
[Term]
id: SO:0000282
name: mRNA_with_minus_1_frameshift
def: "An mRNA with a minus 1 frameshift." [SO:xp]
synonym: "mRNA with minus 1 frameshift" EXACT []
is_a: SO:0000108 ! mRNA_with_frameshift
relationship: has_quality SO:0000866 ! minus_1_frameshift
[Term]
id: SO:0000283
name: engineered_foreign_transposable_element_gene
def: "A transposable_element that is engineered and foreign." [SO:xp]
synonym: "engineered foreign transposable element gene" EXACT []
is_a: SO:0000111 ! transposable_element_gene
is_a: SO:0000281 ! engineered_foreign_gene
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign
[Term]
id: SO:0000284
name: type_I_enzyme_restriction_site
def: "The recognition site is bipartite and interrupted." [http://www.promega.com]
is_obsolete: true
[Term]
id: SO:0000285
name: foreign_gene
def: "A gene that is foreign." [SO:xp]
synonym: "foreign gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000784 ! foreign
[Term]
id: SO:0000286
name: long_terminal_repeat
def: "A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "direct terminal repeat" RELATED []
synonym: "long terminal repeat" EXACT []
synonym: "LTR" EXACT []
xref: http://en.wikipedia.org/wiki/Long_terminal_repeat "wiki"
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000186 ! LTR_retrotransposon
[Term]
id: SO:0000287
name: fusion_gene
def: "A gene that is a fusion." [SO:xp]
synonym: "fusion gene" EXACT []
xref: http://en.wikipedia.org/wiki/Fusion_gene "wiki"
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000806 ! fusion
[Term]
id: SO:0000288
name: engineered_fusion_gene
def: "A fusion gene that is engineered." [SO:xp]
synonym: "engineered fusion gene" EXACT []
is_a: SO:0000280 ! engineered_gene
is_a: SO:0000287 ! fusion_gene
relationship: has_quality SO:0000783 ! engineered
[Term]
id: SO:0000289
name: microsatellite
def: "A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem." [http://www.informatics.jax.org/silver/glossary.shtml, NCBI:th]
subset: SOFA
synonym: "microsatellite locus" EXACT []
synonym: "microsatellite marker" EXACT []
synonym: "VNTR" EXACT []
xref: http://en.wikipedia.org/wiki/Microsatellite "wiki"
is_a: SO:0000005 ! satellite_DNA
[Term]
id: SO:0000290
name: dinucleotide_repeat_microsatellite_feature
synonym: "dinucleotide repeat microsatellite" EXACT []
synonym: "dinucleotide repeat microsatellite feature" EXACT []
synonym: "dinucleotide repeat microsatellite locus" EXACT []
synonym: "dinucleotide repeat microsatellite marker" EXACT []
is_a: SO:0000289 ! microsatellite
[Term]
id: SO:0000291
name: trinucleotide_repeat_microsatellite_feature
synonym: "dinucleotide repeat microsatellite marker" RELATED []
synonym: "rinucleotide repeat microsatellite" EXACT []
synonym: "trinucleotide repeat microsatellite feature" EXACT []
synonym: "trinucleotide repeat microsatellite locus" EXACT []
is_a: SO:0000289 ! microsatellite
[Term]
id: SO:0000292
name: repetitive_element
is_obsolete: true
[Term]
id: SO:0000293
name: engineered_foreign_repetitive_element
def: "A repetitive element that is engineered and foreign." [SO:xp]
synonym: "engineered foreign repetitive element" EXACT []
is_a: SO:0000657 ! repeat_region
is_a: SO:0000805 ! engineered_foreign_region
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign
[Term]
id: SO:0000294
name: inverted_repeat
def: "The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC." [SO:ke]
subset: SOFA
synonym: "inverted repeat" EXACT []
synonym: "inverted repeat sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Inverted_repeat "wiki"
is_a: SO:0000657 ! repeat_region
[Term]
id: SO:0000295
name: U12_intron
def: "A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs." [PMID:9428511]
comment: May have either GT-AC or AT-AC 5' and 3' boundaries.
synonym: "U12 intron" EXACT []
synonym: "U12-dependent intron" EXACT []
is_a: SO:0000662 ! spliceosomal_intron
[Term]
id: SO:0000296
name: origin_of_replication
def: "The origin of replication; starting site for duplication of a nucleic acid molecule to give two identical copies." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "ori" EXACT []
synonym: "origin of replication" EXACT []
xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki"
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0001235 ! replicon
[Term]
id: SO:0000297
name: D_loop
def: "Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "D-loop" EXACT []
synonym: "displacement loop" RELATED []
xref: http://en.wikipedia.org/wiki/D_loop "wiki"
is_a: SO:0000296 ! origin_of_replication
[Term]
id: SO:0000298
name: recombination_feature
synonym: "recombination feature" EXACT []
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000299
name: specific_recombination_site
synonym: "specific recombination site" EXACT []
is_a: SO:0000669 ! sequence_rearrangement_feature
[Term]
id: SO:0000300
name: recombination_feature_of_rearranged_gene
synonym: "recombination feature of rearranged gene" EXACT []
is_a: SO:0000299 ! specific_recombination_site
[Term]
id: SO:0000301
name: vertebrate_immune_system_gene_recombination_feature
synonym: "vertebrate immune system gene recombination feature" EXACT []
is_a: SO:0000300 ! recombination_feature_of_rearranged_gene
[Term]
id: SO:0000302
name: J_gene_recombination_feature
def: "Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J gene recombination feature" EXACT []
synonym: "J-RS" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
[Term]
id: SO:0000303
name: clip
def: "Part of the primary transcript that is clipped off during processing." [SO:ke]
subset: SOFA
is_a: SO:0000835 ! primary_transcript_region
[Term]
id: SO:0000304
name: type_II_enzyme_restriction_site
def: "The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site." [http://www.promega.com]
is_obsolete: true
[Term]
id: SO:0000305
name: modified_DNA_base
def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Modified base:<modified_base>.
subset: SOFA
synonym: "modified base site" EXACT []
is_a: SO:0001236 ! base
is_a: SO:0001720 ! epigenetically_modified_region
[Term]
id: SO:0000306
name: methylated_DNA_base_feature
def: "A nucleotide modified by methylation." [SO:ke]
subset: SOFA
synonym: "methylated base feature" EXACT []
is_a: SO:0000305 ! modified_DNA_base
[Term]
id: SO:0000307
name: CpG_island
def: "Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes." [SO:rd]
subset: SOFA
synonym: "CG island" EXACT []
synonym: "CpG island" EXACT []
xref: http://en.wikipedia.org/wiki/CpG_island "wiki"
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000308
name: sequence_feature_locating_method
is_obsolete: true
[Term]
id: SO:0000309
name: computed_feature
is_obsolete: true
[Term]
id: SO:0000310
name: predicted_ab_initio_computation
is_obsolete: true
[Term]
id: SO:0000311
name: computed_feature_by_similarity
def: "." [SO:ma]
comment: similar to:<sequence_id>
is_obsolete: true
[Term]
id: SO:0000312
name: experimentally_determined
def: "Attribute to describe a feature that has been experimentally verified." [SO:ke]
synonym: "experimentally determined" EXACT []
is_a: SO:0000789 ! validated
[Term]
id: SO:0000313
name: stem_loop
alt_id: SO:0000019
def: "A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "RNA_hairpin_loop" EXACT []
synonym: "stem loop" EXACT []
synonym: "stem-loop" EXACT []
xref: http://en.wikipedia.org/wiki/Stem_loop "wiki"
is_a: SO:0000122 ! RNA_sequence_secondary_structure
[Term]
id: SO:0000314
name: direct_repeat
def: "A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA." [SO:ke]
subset: SOFA
synonym: "direct repeat" EXACT []
xref: http://en.wikipedia.org/wiki/Direct_repeat "wiki"
is_a: SO:0000657 ! repeat_region
[Term]
id: SO:0000315
name: TSS
def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke]
subset: SOFA
synonym: "transcription start site" EXACT []
synonym: "transcription_start_site" EXACT []
is_a: SO:0000835 ! primary_transcript_region
[Term]
id: SO:0000316
name: CDS
def: "A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon." [SO:ma]
subset: SOFA
synonym: "coding sequence" EXACT []
synonym: "coding_sequence" EXACT []
is_a: SO:0000836 ! mRNA_region
[Term]
id: SO:0000317
name: cDNA_clone
def: "Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "cDNA clone" EXACT []
is_a: SO:0000151 ! clone
relationship: has_quality SO:0000756 ! cDNA
[Term]
id: SO:0000318
name: start_codon
def: "First codon to be translated by a ribosome." [SO:ke]
subset: SOFA
synonym: "initiation codon" EXACT []
synonym: "start codon" EXACT []
xref: http://en.wikipedia.org/wiki/Start_codon "wiki"
is_a: SO:0000360 ! codon
[Term]
id: SO:0000319
name: stop_codon
def: "In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis." [SO:ke]
subset: SOFA
synonym: "stop codon" EXACT []
xref: http://en.wikipedia.org/wiki/Stop_codon "wiki"
is_a: SO:0000360 ! codon
[Term]
id: SO:0000320
name: intronic_splice_enhancer
def: "Sequences within the intron that modulate splice site selection for some introns." [SO:ke]
synonym: "intronic splice enhancer" EXACT []
is_a: SO:0000344 ! splice_enhancer
relationship: part_of SO:0000841 ! spliceosomal_intron_region
[Term]
id: SO:0000321
name: mRNA_with_plus_1_frameshift
def: "An mRNA with a plus 1 frameshift." [SO:ke]
synonym: "mRNA with plus 1 frameshift" EXACT []
is_a: SO:0000108 ! mRNA_with_frameshift
relationship: has_quality SO:0000868 ! plus_1_frameshift
[Term]
id: SO:0000322
name: nuclease_hypersensitive_site
synonym: "nuclease hypersensitive site" EXACT []
is_a: SO:0000684 ! nuclease_sensitive_site
[Term]
id: SO:0000323
name: coding_start
def: "The first base to be translated into protein." [SO:ke]
synonym: "coding start" EXACT []
synonym: "translation initiation site" EXACT []
synonym: "translation start" RELATED []
is_a: SO:0000851 ! CDS_region
[Term]
id: SO:0000324
name: tag
def: "A nucleotide sequence that may be used to identify a larger sequence." [SO:ke]
subset: SOFA
is_a: SO:0000696 ! oligo
[Term]
id: SO:0000325
name: rRNA_large_subunit_primary_transcript
def: "A primary transcript encoding a large ribosomal subunit RNA." [SO:ke]
subset: SOFA
synonym: "35S rRNA primary transcript" EXACT []
synonym: "rRNA large subunit primary transcript" EXACT []
is_a: SO:0000209 ! rRNA_primary_transcript
[Term]
id: SO:0000326
name: SAGE_tag
def: "A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=7570003&dopt=Abstract]
subset: SOFA
synonym: "SAGE tag" EXACT []
is_a: SO:0000324 ! tag
[Term]
id: SO:0000327
name: coding_end
def: "The last base to be translated into protein. It does not include the stop codon." [SO:ke]
synonym: "coding end" EXACT []
synonym: "translation termination site" EXACT []
synonym: "translation_end" EXACT []
is_a: SO:0000851 ! CDS_region
[Term]
id: SO:0000328
name: microarray_oligo
synonym: "microarray oligo" EXACT []
synonym: "microarray oligonucleotide" EXACT []
is_a: SO:0000051 ! probe
[Term]
id: SO:0000329
name: mRNA_with_plus_2_frameshift
def: "An mRNA with a plus 2 frameshift." [SO:xp]
synonym: "mRNA with plus 2 frameshift" EXACT []
is_a: SO:0000108 ! mRNA_with_frameshift
relationship: has_quality SO:0000869 ! plus_2_framshift
[Term]
id: SO:0000330
name: conserved_region
def: "Region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
synonym: "conserved region" EXACT []
xref: http://en.wikipedia.org/wiki/Conserved_region "wiki"
is_a: SO:0001410 ! experimental_feature
[Term]
id: SO:0000331
name: STS
def: "Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known." [http://www.biospace.com]
subset: SOFA
synonym: "sequence tag site" EXACT []
is_a: SO:0000324 ! tag
[Term]
id: SO:0000332
name: coding_conserved_region
def: "Coding region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
synonym: "coding conserved region" EXACT []
is_a: SO:0000330 ! conserved_region
[Term]
id: SO:0000333
name: exon_junction
def: "The boundary between two exons in a processed transcript." [SO:ke]
subset: SOFA
synonym: "exon junction" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000233 ! mature_transcript
[Term]
id: SO:0000334
name: nc_conserved_region
def: "Non-coding region of sequence similarity by descent from a common ancestor." [SO:ke]
subset: SOFA
synonym: "nc conserved region" EXACT []
synonym: "noncoding conserved region" EXACT []
is_a: SO:0000330 ! conserved_region
[Term]
id: SO:0000335
name: mRNA_with_minus_2_frameshift
def: "A mRNA with a minus 2 frameshift." [SO:ke]
synonym: "mRNA with minus 2 frameshift" EXACT []
is_a: SO:0000108 ! mRNA_with_frameshift
relationship: has_quality SO:0000867 ! minus_2_frameshift
[Term]
id: SO:0000336
name: pseudogene
def: "A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their \"normal\" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its \"normal\" paralog)." [http://www.ucl.ac.uk/~ucbhjow/b241/glossary.html]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Pseudogene "wiki"
is_a: SO:0001411 ! biological_region
relationship: non_functional_homolog_of SO:0000704 ! gene
[Term]
id: SO:0000337
name: RNAi_reagent
def: "A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference." [SO:rd]
subset: SOFA
synonym: "RNAi reagent" EXACT []
is_a: SO:0000442 ! ds_oligo
[Term]
id: SO:0000338
name: MITE
def: "A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins." [http://www.pnas.org/cgi/content/full/97/18/10083]
synonym: "miniature inverted repeat transposable element" EXACT []
is_a: SO:0000208 ! terminal_inverted_repeat_element
[Term]
id: SO:0000339
name: recombination_hotspot
def: "A region in a genome which promotes recombination." [SO:rd]
synonym: "recombination hotspot" EXACT []
xref: http://en.wikipedia.org/wiki/Recombination_hotspot "wiki"
is_a: SO:0000298 ! recombination_feature
[Term]
id: SO:0000340
name: chromosome
def: "Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Chromosome "wiki"
is_a: SO:0001235 ! replicon
[Term]
id: SO:0000341
name: chromosome_band
def: "A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark." [SO:ma]
subset: SOFA
synonym: "chromosome band" EXACT []
synonym: "cytoband" EXACT []
synonym: "cytological band" EXACT []
xref: http://en.wikipedia.org/wiki/Cytological_band "wiki"
is_a: SO:0000830 ! chromosome_part
[Term]
id: SO:0000342
name: site_specific_recombination_target_region
synonym: "site specific recombination target region" EXACT []
is_a: SO:0000299 ! specific_recombination_site
[Term]
id: SO:0000343
name: match
def: "A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4." [SO:ke]
subset: SOFA
is_a: SO:0001410 ! experimental_feature
[Term]
id: SO:0000344
name: splice_enhancer
def: "Region of a transcript that regulates splicing." [SO:ke]
subset: SOFA
synonym: "splice enhancer" EXACT []
is_a: SO:0000165 ! enhancer
is_a: SO:0001056 ! splicing_regulatory_region
[Term]
id: SO:0000345
name: EST
def: "A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "expressed sequence tag" EXACT []
is_a: SO:0000324 ! tag
relationship: derives_from SO:0000234 ! mRNA
[Term]
id: SO:0000346
name: loxP_site
synonym: "Cre-recombination target region" RELATED []
synonym: "loxP site" EXACT []
is_a: SO:0000947 ! resolution_site
[Term]
id: SO:0000347
name: nucleotide_match
def: "A match against a nucleotide sequence." [SO:ke]
subset: SOFA
synonym: "nucleotide match" EXACT []
is_a: SO:0000343 ! match
[Term]
id: SO:0000348
name: nucleic_acid
def: "An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone." [CHEBI:33696, RSC:cb]
synonym: "nucleic acid" EXACT []
xref: http://en.wikipedia.org/wiki/Nucleic_acid "wiki"
is_a: SO:0000443 ! polymer_attribute
[Term]
id: SO:0000349
name: protein_match
def: "A match against a protein sequence." [SO:ke]
subset: SOFA
synonym: "protein match" EXACT []
is_a: SO:0000343 ! match
[Term]
id: SO:0000350
name: FRT_site
def: "An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid." [SO:ma]
synonym: "FLP recombination target region" EXACT []
synonym: "FRT site" EXACT []
is_a: SO:0000948 ! inversion_site
[Term]
id: SO:0000351
name: synthetic_sequence
def: "An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence." [SO:ma]
synonym: "synthetic sequence" EXACT []
is_a: SO:0000443 ! polymer_attribute
[Term]
id: SO:0000352
name: DNA
def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone." [RSC:cb]
is_a: SO:0000348 ! nucleic_acid
[Term]
id: SO:0000353
name: sequence_assembly
def: "A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences." [SO:ma]
subset: SOFA
synonym: "sequence assembly" EXACT []
xref: http://en.wikipedia.org/wiki/Sequence_assembly "wiki"
is_a: SO:0001248 ! assembly
[Term]
id: SO:0000354
name: group_1_intron_homing_endonuclease_target_region
def: "A region of intronic nucleotide sequence targeted by a nuclease enzyme." [SO:ke]
synonym: "group 1 intron homing endonuclease target region" EXACT []
is_a: SO:0000684 ! nuclease_sensitive_site
[Term]
id: SO:0000355
name: haplotype_block
def: "A region of the genome which is co-inherited as the result of the lack of historic recombination within it." [SO:ma]
synonym: "haplotype block" EXACT []
is_a: SO:0000298 ! recombination_feature
[Term]
id: SO:0000356
name: RNA
def: "An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone." [RSC:cb]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
is_a: SO:0000348 ! nucleic_acid
[Term]
id: SO:0000357
name: flanked
def: "An attribute describing a region that is bounded either side by a particular kind of region." [SO:ke]
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000359
name: floxed
def: "An attribute describing sequence that is flanked by Lox-P sites." [SO:ke]
xref: http://en.wikipedia.org/wiki/Floxed "wiki"
is_a: SO:0000357 ! flanked
[Term]
id: SO:0000360
name: codon
def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS." [http://www.everythingbio.com/glos/definition.php?word=codon, SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Codon "wiki"
is_a: SO:0000851 ! CDS_region
[Term]
id: SO:0000361
name: FRT_flanked
def: "An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT." [SO:ke]
synonym: "FRT flanked" EXACT []
is_a: SO:0000357 ! flanked
[Term]
id: SO:0000362
name: invalidated_by_chimeric_cDNA
def: "A cDNA clone constructed from more than one mRNA. Usually an experimental artifact." [SO:ma]
synonym: "invalidated by chimeric cDNA" EXACT []
is_a: SO:0000790 ! invalidated
[Term]
id: SO:0000363
name: floxed_gene
def: "A transgene that is floxed." [SO:xp]
synonym: "floxed gene" EXACT []
is_a: SO:0000902 ! transgene
relationship: has_quality SO:0000359 ! floxed
[Term]
id: SO:0000364
name: transposable_element_flanking_region
def: "The region of sequence surrounding a transposable element." [SO:ke]
synonym: "transposable element flanking region" EXACT []
is_a: SO:0000239 ! flanking_region
[Term]
id: SO:0000365
name: integron
def: "A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site." [SO:as]
xref: http://en.wikipedia.org/wiki/Integron "wiki"
is_a: SO:0001039 ! integrated_mobile_genetic_element
[Term]
id: SO:0000366
name: insertion_site
def: "The junction where an insertion occurred." [SO:ke]
subset: SOFA
synonym: "insertion site" EXACT []
is_a: SO:0000699 ! junction
[Term]
id: SO:0000367
name: attI_site
def: "A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place." [SO:as]
synonym: "attI site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0000365 ! integron
[Term]
id: SO:0000368
name: transposable_element_insertion_site
def: "The junction in a genome where a transposable_element has inserted." [SO:ke]
subset: SOFA
synonym: "transposable element insertion site" EXACT []
is_a: SO:0000366 ! insertion_site
[Term]
id: SO:0000369
name: integrase_coding_region
is_obsolete: true
[Term]
id: SO:0000370
name: small_regulatory_ncRNA
def: "A non-coding RNA, usually with a specific secondary structure, that acts to regulate gene expression." [SO:ma]
subset: SOFA
synonym: "small regulatory ncRNA" EXACT []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000371
name: conjugative_transposon
def: "A transposon that encodes function required for conjugation." [http://www.sci.sdsu.edu/~smaloy/Glossary/C.html]
synonym: "conjugative transposon" EXACT []
is_a: SO:0000182 ! DNA_transposon
[Term]
id: SO:0000372
name: enzymatic_RNA
def: "An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
comment: This was moved to be a child of transcript (SO:0000673) because some enzymatic RNA regions are part of primary transcripts and some are part of processed transcripts.
subset: SOFA
synonym: "enzymatic RNA" EXACT []
is_a: SO:0000673 ! transcript
relationship: has_quality SO:0001185 ! enzymatic
[Term]
id: SO:0000373
name: recombinationally_inverted_gene
def: "A recombinationally rearranged gene by inversion." [SO:xp]
synonym: "recombinationally inverted gene" EXACT []
is_a: SO:0000456 ! recombinationally_rearranged_gene
relationship: has_quality SO:1000036 ! inversion
[Term]
id: SO:0000374
name: ribozyme
def: "An RNA with catalytic activity." [SO:ma]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Ribozyme "wiki"
is_a: SO:0000372 ! enzymatic_RNA
relationship: has_quality SO:0001186 ! ribozymic
[Term]
id: SO:0000375
name: rRNA_5_8S
def: "5_8S ribosomal RNA (5. 8S rRNA) is a component of the large subunit of the eukaryotic ribosome. It is transcribed by RNA polymerase I as part of the 45S precursor that also contains 18S and 28S rRNA. Functionally, it is thought that 5.8S rRNA may be involved in ribosome translocation. It is also known to form covalent linkage to the p53 tumour suppressor protein. 5_8S rRNA is also found in archaea." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00002]
subset: SOFA
synonym: "5.8S LSU rRNA" EXACT []
synonym: "5.8S ribosomal RNA" EXACT []
synonym: "5.8S rRNA" EXACT []
synonym: "rRNA 5 8S" EXACT []
xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki"
is_a: SO:0000651 ! large_subunit_rRNA
[Term]
id: SO:0000376
name: RNA_6S
def: "A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00013]
synonym: "6S RNA" EXACT []
synonym: "RNA 6S" EXACT []
xref: http://en.wikipedia.org/wiki/6S_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000377
name: CsrB_RsmB_RNA
def: "An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00018]
synonym: "CsrB RsmB RNA" EXACT []
synonym: "CsrB-RsmB RNA" EXACT []
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000378
name: DsrA_RNA
def: "DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00014]
synonym: "DsrA RNA" EXACT []
xref: http://en.wikipedia.org/wiki/DsrA_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000379
name: GcvB_RNA
def: "A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00022]
synonym: "GcvB RNA" EXACT []
xref: http://en.wikipedia.org/wiki/GcvB_RNA "wiki"
is_a: SO:0000378 ! DsrA_RNA
[Term]
id: SO:0000380
name: hammerhead_ribozyme
def: "A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs." [PMID:2436805]
subset: SOFA
synonym: "hammerhead ribozyme" EXACT []
xref: http://en.wikipedia.org/wiki/Hammerhead_ribozyme "wiki"
is_a: SO:0000715 ! RNA_motif
relationship: has_quality SO:0001186 ! ribozymic
[Term]
id: SO:0000381
name: group_IIA_intron
synonym: "group IIA intron" EXACT []
is_a: SO:0000603 ! group_II_intron
[Term]
id: SO:0000382
name: group_IIB_intron
synonym: "group IIB intron" EXACT []
is_a: SO:0000603 ! group_II_intron
[Term]
id: SO:0000383
name: MicF_RNA
def: "A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00033]
synonym: "MicF RNA" EXACT []
xref: http://en.wikipedia.org/wiki/MicF_RNA "wiki"
is_a: SO:0000644 ! antisense_RNA
[Term]
id: SO:0000384
name: OxyS_RNA
def: "A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00035]
synonym: "OxyS RNA" EXACT []
xref: http://en.wikipedia.org/wiki/OxyS_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000385
name: RNase_MRP_RNA
def: "The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00030]
subset: SOFA
synonym: "RNase MRP RNA" EXACT []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000386
name: RNase_P_RNA
def: "The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00010]
subset: SOFA
synonym: "RNase P RNA" EXACT []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000387
name: RprA_RNA
def: "Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00034]
synonym: "RprA RNA" EXACT []
xref: http://en.wikipedia.org/wiki/RprA_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000388
name: RRE_RNA
def: "The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00036]
synonym: "RRE RNA" EXACT []
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000389
name: spot_42_RNA
def: "A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00021]
synonym: "spot-42 RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Spot_42_RNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000390
name: telomerase_RNA
def: "The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00025]
subset: SOFA
synonym: "telomerase RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Telomerase_RNA "wiki"
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000391
name: U1_snRNA
def: "U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00003]
subset: SOFA
synonym: "small nuclear RNA U1" EXACT [RSC:cb]
synonym: "snRNA U1" EXACT [RSC:cb]
synonym: "U1 small nuclear RNA" EXACT [RSC:cb]
synonym: "U1 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U1_snRNA "wiki"
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000392
name: U2_snRNA
def: "U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00004]
subset: SOFA
synonym: "small nuclear RNA U2" EXACT [RSC:CB]
synonym: "snRNA U2" EXACT [RSC:CB]
synonym: "U2 small nuclear RNA" EXACT [RSC:CB]
synonym: "U2 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U2_snRNA "wiki"
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000393
name: U4_snRNA
def: "U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
subset: SOFA
synonym: "small nuclear RNA U4" EXACT [RSC:cb]
synonym: "snRNA U4" EXACT [RSC:cb]
synonym: "U4 small nuclear RNA" EXACT [RSC:cb]
synonym: "U4 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U4_snRNA "wiki"
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000394
name: U4atac_snRNA
def: "An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397)." [PMID:=12409455]
subset: SOFA
synonym: "small nuclear RNA U4atac" EXACT [RSC:cb]
synonym: "snRNA U4atac" EXACT [RSC:cb]
synonym: "U4atac small nuclear RNA" EXACT [RSC:cb]
synonym: "U4atac snRNA" EXACT []
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000395
name: U5_snRNA
def: "U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00020]
subset: SOFA
synonym: "small nuclear RNA U5" EXACT [RSC:cb]
synonym: "snRNA U5" EXACT [RSC:cb]
synonym: "U5 small nuclear RNA" EXACT [RSC:cb]
synonym: "U5 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U5_snRNA "wiki"
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000396
name: U6_snRNA
def: "U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00015]
subset: SOFA
synonym: "small nuclear RNA U6" EXACT [RSC:cb]
synonym: "snRNA U6" EXACT [RSC:cb]
synonym: "U6 small nuclear RNA" EXACT [RSC:cb]
synonym: "U6 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U6_snRNA "wiki"
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000397
name: U6atac_snRNA
def: "U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394)." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=12409455&dopt=Abstract]
subset: SOFA
synonym: "snRNA U6atac" EXACT [RSC:cb]
synonym: "U6atac small nuclear RNA" EXACT [RSC:cb]
synonym: "U6atac snRNA" EXACT [RSC:cb]
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000398
name: U11_snRNA
def: "U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence." [PMID:9622129]
subset: SOFA
synonym: "small nuclear RNA U11" EXACT [RSC:cb]
synonym: "snRNA U11" EXACT [RSC:cb]
synonym: "U11 small nuclear RNA" EXACT [RSC:cb]
synonym: "U11 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U11_snRNA "wiki"
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000399
name: U12_snRNA
def: "The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00007]
subset: SOFA
synonym: "small nuclear RNA U12" EXACT [RSC:cb]
synonym: "snRNA U12" EXACT [RSC:cb]
synonym: "U12 small nuclear RNA" EXACT [RSC:cb]
synonym: "U12 snRNA" EXACT []
xref: http://en.wikipedia.org/wiki/U12_snRNA "wiki"
is_a: SO:0000274 ! snRNA
[Term]
id: SO:0000400
name: sequence_attribute
def: "An attribute describes a quality of sequence." [SO:ke]
synonym: "sequence attribute" EXACT []
[Term]
id: SO:0000401
name: gene_attribute
synonym: "gene attribute" EXACT []
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000402
name: enhancer_attribute
is_obsolete: true
[Term]
id: SO:0000403
name: U14_snoRNA
alt_id: SO:0005839
def: "U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00016, PMID:2551119]
comment: An evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA.
subset: SOFA
synonym: "small nucleolar RNA U14" EXACT []
synonym: "snoRNA U14" EXACT []
synonym: "U14 small nucleolar RNA" EXACT []
synonym: "U14 snoRNA" EXACT []
is_a: SO:0000593 ! C_D_box_snoRNA
relationship: derives_from SO:0005837 ! U14_snoRNA_primary_transcript
[Term]
id: SO:0000404
name: vault_RNA
def: "A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00006]
subset: SOFA
synonym: "vault RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Vault_RNA "wiki"
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000405
name: Y_RNA
def: "Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00019]
subset: SOFA
synonym: "Y RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Y_RNA "wiki"
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000406
name: twintron
def: "An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed." [PMID:1899376, PMID:7823908]
xref: http://en.wikipedia.org/wiki/Twintron "wiki"
is_a: SO:0000188 ! intron
[Term]
id: SO:0000407
name: rRNA_18S
def: "A large polynucleotide in eukaryotes, which functions as the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "18S ribosomal RNA" EXACT []
synonym: "18S rRNA" EXACT []
synonym: "rRNA 18S" EXACT []
xref: http://en.wikipedia.org/wiki/18S_ribosomal_RNA "wiki"
is_a: SO:0000650 ! small_subunit_rRNA
[Term]
id: SO:0000408
name: site
def: "The interbase position where something (eg an aberration) occurred." [SO:ke]
is_obsolete: true
[Term]
id: SO:0000409
name: binding_site
alt_id: BS:00033
def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]
comment: See GO:0005488 : binding.
subset: biosapiens
subset: SOFA
synonym: "binding_or_interaction_site" EXACT []
synonym: "site" RELATED []
xref: http://en.wikipedia.org/wiki/Binding_site "wiki"
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000410
name: protein_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke]
comment: See GO:0042277 : peptide binding.
subset: SOFA
synonym: "protein binding site" EXACT []
is_a: SO:0000409 ! binding_site
[Term]
id: SO:0000411
name: rescue_region
def: "A region that rescues." [SO:xp]
synonym: "rescue fragment" EXACT []
synonym: "rescue region" EXACT []
synonym: "rescue segment" RELATED []
is_a: SO:0000695 ! reagent
relationship: has_quality SO:0000814 ! rescue
[Term]
id: SO:0000412
name: restriction_fragment
def: "A region of polynucleotide sequence produced by digestion with a restriction endonuclease." [SO:ke]
subset: SOFA
synonym: "restriction fragment" EXACT []
xref: http://en.wikipedia.org/wiki/Restriction_fragment "wiki"
is_a: SO:0000143 ! assembly_component
[Term]
id: SO:0000413
name: sequence_difference
def: "A region where the sequence differs from that of a specified sequence." [SO:ke]
subset: SOFA
synonym: "sequence difference" EXACT []
is_a: SO:0000700 ! remark
[Term]
id: SO:0000414
name: invalidated_by_genomic_contamination
def: "An attribute to describe a feature that is invalidated due to genomic contamination." [SO:ke]
synonym: "invalidated by genomic contamination" EXACT []
is_a: SO:0000790 ! invalidated
[Term]
id: SO:0000415
name: invalidated_by_genomic_polyA_primed_cDNA
def: "An attribute to describe a feature that is invalidated due to polyA priming." [SO:ke]
synonym: "invalidated by genomic polyA primed cDNA" EXACT []
is_a: SO:0000790 ! invalidated
[Term]
id: SO:0000416
name: invalidated_by_partial_processing
def: "An attribute to describe a feature that is invalidated due to partial processing." [SO:ke]
synonym: "invalidated by partial processing" EXACT []
is_a: SO:0000790 ! invalidated
[Term]
id: SO:0000417
name: polypeptide_domain
alt_id: BS:00012
alt_id: BS:00134
alt_id: SO:0001069
def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]
comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
subset: biosapiens
synonym: "domain" BROAD BS [uniprot:feature_type]
synonym: "polypeptide domain" EXACT []
synonym: "polypeptide_structural_domain" EXACT BS []
synonym: "structural domain" BROAD BS []
is_a: SO:0001070 ! polypeptide_structural_region
is_a: SO:0100021 ! polypeptide_conserved_region
[Term]
id: SO:0000418
name: signal_peptide
alt_id: BS:00159
def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
subset: biosapiens
subset: SOFA
synonym: "signal" RELATED [uniprot:feature_type]
synonym: "signal peptide" EXACT []
synonym: "signal peptide coding sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki"
is_a: SO:0001527 ! peptide_localization_signal
relationship: part_of SO:0001062 ! propeptide
[Term]
id: SO:0000419
name: mature_protein_region
alt_id: BS:00149
def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html, SO:cb]
comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
subset: biosapiens
subset: SOFA
synonym: "chain" RELATED [uniprot:feature_type]
synonym: "mature peptide" RELATED []
synonym: "mature protein region" EXACT []
is_a: SO:0000839 ! polypeptide_region
relationship: part_of SO:0001063 ! immature_peptide_region
[Term]
id: SO:0000420
name: five_prime_terminal_inverted_repeat
synonym: "5' TIR" EXACT []
synonym: "five prime terminal inverted repeat" EXACT []
is_a: SO:0000481 ! terminal_inverted_repeat
[Term]
id: SO:0000421
name: three_prime_terminal_inverted_repeat
synonym: "3' TIR" EXACT []
synonym: "three prime terminal inverted repeat" EXACT []
is_a: SO:0000481 ! terminal_inverted_repeat
[Term]
id: SO:0000422
name: U5_LTR_region
synonym: "U5 long terminal repeat region" EXACT []
synonym: "U5 LTR region" EXACT []
is_a: SO:0000848 ! LTR_component
[Term]
id: SO:0000423
name: R_LTR_region
synonym: "R long terminal repeat region" EXACT []
synonym: "R LTR region" EXACT []
is_a: SO:0000848 ! LTR_component
[Term]
id: SO:0000424
name: U3_LTR_region
synonym: "U3 long terminal repeat region" EXACT []
synonym: "U3 LTR region" EXACT []
is_a: SO:0000848 ! LTR_component
[Term]
id: SO:0000425
name: five_prime_LTR
synonym: "5' long terminal repeat" EXACT []
synonym: "5' LTR" EXACT []
synonym: "five prime LTR" EXACT []
is_a: SO:0000286 ! long_terminal_repeat
[Term]
id: SO:0000426
name: three_prime_LTR
synonym: "3' long terminal repeat" EXACT []
synonym: "3' LTR" EXACT []
synonym: "three prime LTR" EXACT []
is_a: SO:0000286 ! long_terminal_repeat
[Term]
id: SO:0000427
name: R_five_prime_LTR_region
synonym: "R 5' long term repeat region" EXACT []
synonym: "R five prime LTR region" EXACT []
is_a: SO:0000423 ! R_LTR_region
is_a: SO:0000850 ! five_prime_LTR_component
[Term]
id: SO:0000428
name: U5_five_prime_LTR_region
synonym: "U5 5' long terminal repeat region" EXACT []
synonym: "U5 five prime LTR region" EXACT []
is_a: SO:0000422 ! U5_LTR_region
is_a: SO:0000850 ! five_prime_LTR_component
[Term]
id: SO:0000429
name: U3_five_prime_LTR_region
synonym: "U3 5' long term repeat region" EXACT []
synonym: "U3 five prime LTR region" EXACT []
is_a: SO:0000424 ! U3_LTR_region
is_a: SO:0000850 ! five_prime_LTR_component
[Term]
id: SO:0000430
name: R_three_prime_LTR_region
synonym: "R 3' long terminal repeat region" EXACT []
synonym: "R three prime LTR region" EXACT []
is_a: SO:0000849 ! three_prime_LTR_component
[Term]
id: SO:0000431
name: U3_three_prime_LTR_region
synonym: "U3 3' long terminal repeat region" EXACT []
synonym: "U3 three prime LTR region" EXACT []
is_a: SO:0000849 ! three_prime_LTR_component
[Term]
id: SO:0000432
name: U5_three_prime_LTR_region
synonym: "U5 3' long terminal repeat region" EXACT []
synonym: "U5 three prime LTR region" EXACT []
is_a: SO:0000849 ! three_prime_LTR_component
[Term]
id: SO:0000433
name: non_LTR_retrotransposon_polymeric_tract
def: "A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon." [SO:ke]
synonym: "non LTR retrotransposon polymeric tract" EXACT []
is_a: SO:0000657 ! repeat_region
is_a: SO:0000840 ! repeat_component
relationship: part_of SO:0000189 ! non_LTR_retrotransposon
[Term]
id: SO:0000434
name: target_site_duplication
def: "A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion." [http://www.koko.gov.my/CocoaBioTech/Glossaryt.html]
synonym: "target site duplication" EXACT []
is_a: SO:0000314 ! direct_repeat
relationship: derives_from SO:0000101 ! transposable_element
[Term]
id: SO:0000435
name: RR_tract
def: "A polypurine tract within an LTR_retrotransposon." [SO:ke]
synonym: "LTR retrotransposon poly purine tract" RELATED []
synonym: "RR tract" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0000186 ! LTR_retrotransposon
[Term]
id: SO:0000436
name: ARS
def: "A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host." [SO:ma]
subset: SOFA
synonym: "autonomously replicating sequence" EXACT []
is_a: SO:0000296 ! origin_of_replication
[Term]
id: SO:0000437
name: assortment_derived_duplication
is_obsolete: true
[Term]
id: SO:0000438
name: gene_not_polyadenylated
is_obsolete: true
[Term]
id: SO:0000439
name: inverted_ring_chromosome
synonym: "inverted ring chromosome" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000045 ! ring_chromosome
[Term]
id: SO:0000440
name: vector_replicon
def: "A replicon that has been modified to act as a vector for foreign sequence." [SO:ma]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "vector" EXACT []
synonym: "vector replicon" EXACT []
xref: http://en.wikipedia.org/wiki/Vector_(molecular_biology) "wiki"
is_a: SO:0001235 ! replicon
relationship: part_of SO:0000151 ! clone
[Term]
id: SO:0000441
name: ss_oligo
def: "A single stranded oligonucleotide." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "single strand oligo" EXACT []
synonym: "single strand oligonucleotide" EXACT []
synonym: "single stranded oligonucleotide" EXACT []
synonym: "ss oligo" EXACT []
synonym: "ss oligonucleotide" EXACT []
is_a: SO:0000696 ! oligo
[Term]
id: SO:0000442
name: ds_oligo
def: "A double stranded oligonucleotide." [SO:ke]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "double stranded oligonucleotide" EXACT []
synonym: "ds oligo" EXACT []
synonym: "ds-oligonucleotide" EXACT []
is_a: SO:0000696 ! oligo
[Term]
id: SO:0000443
name: polymer_attribute
def: "An attribute to describe the kind of biological sequence." [SO:ke]
synonym: "polymer attribute" EXACT []
is_a: SO:0000400 ! sequence_attribute
[Term]
id: SO:0000444
name: three_prime_noncoding_exon
def: "Non-coding exon in the 3' UTR." [SO:ke]
synonym: "three prime noncoding exon" EXACT []
is_a: SO:0000198 ! noncoding_exon
[Term]
id: SO:0000445
name: five_prime_noncoding_exon
def: "Non-coding exon in the 5' UTR." [SO:ke]
synonym: "5' nc exon" EXACT []
synonym: "5' non coding exon" EXACT []
synonym: "five prime noncoding exon" EXACT []
is_a: SO:0000198 ! noncoding_exon
[Term]
id: SO:0000446
name: UTR_intron
def: "Intron located in the untranslated region." [SO:ke]
synonym: "UTR intron" EXACT []
is_a: SO:0000188 ! intron
[Term]
id: SO:0000447
name: five_prime_UTR_intron
def: "An intron located in the 5' UTR." [SO:ke]
synonym: "five prime UTR intron" EXACT []
is_a: SO:0000446 ! UTR_intron
[Term]
id: SO:0000448
name: three_prime_UTR_intron
def: "An intron located in the 3' UTR." [SO:ke]
synonym: "three prime UTR intron" EXACT []
is_a: SO:0000446 ! UTR_intron
[Term]
id: SO:0000449
name: random_sequence
def: "A sequence of nucleotides or amino acids which, by design, has a \"random\" order of components, given a predetermined input frequency of these components." [SO:ma]
synonym: "random sequence" EXACT []
is_a: SO:0000351 ! synthetic_sequence
[Term]
id: SO:0000450
name: interband
def: "A light region between two darkly staining bands in a polytene chromosome." [SO:ma]
synonym: "chromosome interband" RELATED []
is_a: SO:0000830 ! chromosome_part
[Term]
id: SO:0000451
name: gene_with_polyadenylated_mRNA
def: "A gene that encodes a polyadenylated mRNA." [SO:xp]
synonym: "gene with polyadenylated mRNA" EXACT []
is_a: SO:0001217 ! protein_coding_gene
relationship: transcribed_to SO:0000871 ! polyadenylated_mRNA
[Term]
id: SO:0000452
name: transgene_attribute
is_obsolete: true
[Term]
id: SO:0000453
name: chromosomal_transposition
def: "A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type." [FB:reference_manual, SO:ke]
synonym: "chromosomal transposition" EXACT []
synonym: "transposition" NARROW []
is_a: SO:1000183 ! chromosome_structure_variation
[Term]
id: SO:0000454
name: rasiRNA
def: "A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements." [http://www.developmentalcell.com/content/article/abstract?uid=PIIS1534580703002284]
subset: SOFA
synonym: "repeat associated small interfering RNA" EXACT []
xref: http://en.wikipedia.org/wiki/RasiRNA "wiki"
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000455
name: gene_with_mRNA_with_frameshift
def: "A gene that encodes an mRNA with a frameshift." [SO:xp]
synonym: "gene with mRNA with frameshift" EXACT []
is_a: SO:0001217 ! protein_coding_gene
relationship: has_quality SO:0000865 ! frameshift
[Term]
id: SO:0000456
name: recombinationally_rearranged_gene
def: "A gene that is recombinationally rearranged." [SO:ke]
synonym: "recombinationally rearranged gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000940 ! recombinationally_rearranged
[Term]
id: SO:0000457
name: interchromosomal_duplication
def: "A chromosome duplication involving an insertion from another chromosome." [SO:ke]
synonym: "interchromosomal duplication" EXACT []
is_a: SO:1000037 ! chromosomal_duplication
[Term]
id: SO:0000458
name: D_gene_segment
def: "Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D gene" EXACT []
synonym: "D-GENE" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
[Term]
id: SO:0000459
name: gene_with_trans_spliced_transcript
def: "A gene with a transcript that is trans-spliced." [SO:xp]
synonym: "gene with trans spliced transcript" EXACT []
is_a: SO:0000704 ! gene
relationship: transcribed_to SO:0000479 ! trans_spliced_transcript
[Term]
id: SO:0000460
name: vertebrate_immunoglobulin_T_cell_receptor_segment
comment: I am using the term segment instead of gene here to avoid confusion with the region 'gene'.
synonym: "vertebrate immunoglobulin T cell receptor segment" EXACT []
synonym: "vertebrate_immunoglobulin/T-cell receptor gene" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
[Term]
id: SO:0000461
name: inversion_derived_bipartite_deficiency
def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion." [FB:km]
synonym: "inversion derived bipartite deficiency" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
[Term]
id: SO:0000462
name: pseudogenic_region
def: "A non-functional descendant of a functional entity." [SO:cjm]
subset: SOFA
synonym: "pseudogenic region" EXACT []
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000463
name: encodes_alternately_spliced_transcripts
def: "A gene that encodes more than one transcript." [SO:ke]
synonym: "encodes alternately spliced transcripts" EXACT []
is_a: SO:0000401 ! gene_attribute
[Term]
id: SO:0000464
name: decayed_exon
def: "A non-functional descendant of an exon." [SO:ke]
subset: SOFA
synonym: "decayed exon" EXACT []
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000147 ! exon
[Term]
id: SO:0000465
name: inversion_derived_deficiency_plus_duplication
def: "A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion." [FB:km]
synonym: "inversion derived deficiency plus duplication" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000038 ! intrachromosomal_duplication
[Term]
id: SO:0000466
name: V_gene_segment
def: "Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V gene" EXACT []
synonym: "V-GENE" EXACT []
synonym: "variable_gene" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
[Term]
id: SO:0000467
name: post_translationally_regulated_by_protein_stability
def: "An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein." [SO:ke]
synonym: "post translationally regulated by protein stability" EXACT []
synonym: "post-translationally regulated by protein stability" EXACT []
is_a: SO:0000130 ! post_translationally_regulated
[Term]
id: SO:0000468
name: golden_path_fragment
def: "One of the pieces of sequence that make up a golden path." [SO:rd]
subset: SOFA
synonym: "golden path fragment" EXACT []
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000688 ! golden_path
[Term]
id: SO:0000469
name: post_translationally_regulated_by_protein_modification
def: "An attribute describing a gene sequence where the resulting protein is modified to regulate it." [SO:ke]
synonym: "post translationally regulated by protein modification" EXACT []
synonym: "post-translationally regulated by protein modification" EXACT []
is_a: SO:0000130 ! post_translationally_regulated
[Term]
id: SO:0000470
name: J_gene_segment
def: "Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J gene" EXACT []
synonym: "J-GENE" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
[Term]
id: SO:0000471
name: autoregulated
def: "The gene product is involved in its own transcriptional regulation." [SO:ke]
is_a: SO:0000123 ! transcriptionally_regulated
[Term]
id: SO:0000472
name: tiling_path
def: "A set of regions which overlap with minimal polymorphism to form a linear sequence." [SO:cjm]
subset: SOFA
synonym: "tiling path" EXACT []
is_a: SO:0000353 ! sequence_assembly
[Term]
id: SO:0000473
name: negatively_autoregulated
def: "The gene product is involved in its own transcriptional regulation where it decreases transcription." [SO:ke]
synonym: "negatively autoregulated" EXACT []
is_a: SO:0000126 ! transcriptionally_repressed
is_a: SO:0000471 ! autoregulated
[Term]
id: SO:0000474
name: tiling_path_fragment
def: "A piece of sequence that makes up a tiling_path (SO:0000472)." [SO:ke]
subset: SOFA
synonym: "tiling path fragment" EXACT []
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000472 ! tiling_path
[Term]
id: SO:0000475
name: positively_autoregulated
def: "The gene product is involved in its own transcriptional regulation, where it increases transcription." [SO:ke]
synonym: "positively autoregulated" EXACT []
is_a: SO:0000125 ! transcriptionally_induced
is_a: SO:0000471 ! autoregulated
[Term]
id: SO:0000476
name: contig_read
def: "A DNA sequencer read which is part of a contig." [SO:ke]
synonym: "contig read" EXACT []
is_a: SO:0000150 ! read
[Term]
id: SO:0000477
name: polycistronic_gene
def: "A gene that is polycistronic." [SO:ke]
is_obsolete: true
[Term]
id: SO:0000478
name: C_gene_segment
def: "Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "C gene" EXACT []
synonym: "C_GENE" EXACT []
synonym: "constant gene" EXACT []
is_a: SO:0000460 ! vertebrate_immunoglobulin_T_cell_receptor_segment
[Term]
id: SO:0000479
name: trans_spliced_transcript
def: "A transcript that is trans-spliced." [SO:xp]
synonym: "trans spliced transcript" EXACT []
synonym: "trans-spliced transcript" EXACT []
is_a: SO:0000673 ! transcript
relationship: has_quality SO:0000870 ! trans_spliced
[Term]
id: SO:0000480
name: tiling_path_clone
def: "A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly." [SO:ke]
synonym: "tiling path clone" EXACT []
is_a: SO:0000151 ! clone
is_a: SO:0000474 ! tiling_path_fragment
[Term]
id: SO:0000481
name: terminal_inverted_repeat
def: "An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon." [SO:ke]
synonym: "terminal inverted repeat" EXACT []
synonym: "TIR" EXACT []
is_a: SO:0000294 ! inverted_repeat
relationship: part_of SO:0000208 ! terminal_inverted_repeat_element
[Term]
id: SO:0000482
name: vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
synonym: "vertebrate immunoglobulin T cell receptor gene cluster" EXACT []
synonym: "vertebrate_immunoglobulin/T-cell receptor gene cluster" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
[Term]
id: SO:0000483
name: nc_primary_transcript
def: "A primary transcript that is never translated into a protein." [SO:ke]
subset: SOFA
synonym: "nc primary transcript" EXACT []
synonym: "noncoding primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript
[Term]
id: SO:0000484
name: three_prime_coding_exon_noncoding_region
def: "The sequence of the 3' exon that is not coding." [SO:ke]
subset: SOFA
synonym: "three prime coding exon noncoding region" EXACT []
synonym: "three_prime_exon_noncoding_region" EXACT []
is_a: SO:0001214 ! noncoding_region_of_exon
relationship: part_of SO:0000202 ! three_prime_coding_exon
[Term]
id: SO:0000485
name: DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(DJ)-J-CLUSTER" EXACT []
synonym: "DJ J cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000486
name: five_prime_coding_exon_noncoding_region
def: "The sequence of the 5' exon preceding the start codon." [SO:ke]
subset: SOFA
synonym: "five prime coding exon noncoding region" EXACT []
synonym: "five_prime_exon_noncoding_region" EXACT []
is_a: SO:0001214 ! noncoding_region_of_exon
relationship: part_of SO:0000200 ! five_prime_coding_exon
[Term]
id: SO:0000487
name: VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VDJ)-J-C-CLUSTER" EXACT []
synonym: "VDJ J C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment
[Term]
id: SO:0000488
name: VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VDJ)-J-CLUSTER" EXACT []
synonym: "VDJ J cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment
[Term]
id: SO:0000489
name: VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VJ)-C-CLUSTER" RELATED []
synonym: "VJ C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment
[Term]
id: SO:0000490
name: VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VJ)-J-C-CLUSTER" EXACT []
synonym: "VJ J C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment
[Term]
id: SO:0000491
name: VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VJ)-J-CLUSTER" EXACT []
synonym: "VJ J cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment
[Term]
id: SO:0000492
name: D_gene_recombination_feature
synonym: "D gene recombination feature" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
[Term]
id: SO:0000493
name: three_prime_D_heptamer
def: "7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "3'D-HEPTAMER" EXACT []
synonym: "three prime D heptamer" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence
[Term]
id: SO:0000494
name: three_prime_D_nonamer
def: "A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "3'D-NOMAMER" EXACT []
synonym: "three prime D nonamer" EXACT []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence
[Term]
id: SO:0000495
name: three_prime_D_spacer
def: "A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "3'D-SPACER" EXACT []
synonym: "three prime D spacer" EXACT []
is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
relationship: part_of SO:0000570 ! three_prime_D_recombination_signal_sequence
[Term]
id: SO:0000496
name: five_prime_D_heptamer
def: "7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "5'D-HEPTAMER" EXACT []
synonym: "five prime D heptamer" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence
[Term]
id: SO:0000497
name: five_prime_D_nonamer
def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "5'D-NONAMER" EXACT []
synonym: "five prime D nonamer" EXACT []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence
[Term]
id: SO:0000498
name: five_prime_D_spacer
def: "12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "5'-SPACER" EXACT []
synonym: "five prime D spacer" EXACT []
synonym: "five prime D-spacer" EXACT []
is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
relationship: part_of SO:0000556 ! five_prime_D_recombination_signal_sequence
[Term]
id: SO:0000499
name: virtual_sequence
def: "A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database." [SO:ke]
subset: SOFA
synonym: "virtual sequence" EXACT []
is_a: SO:0000353 ! sequence_assembly
[Term]
id: SO:0000500
name: Hoogsteen_base_pair
def: "A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds." [PMID:12177293]
synonym: "Hoogsteen base pair" EXACT []
xref: http://en.wikipedia.org/wiki/Hoogsteen_base_pair "wiki"
is_a: SO:0000028 ! base_pair
[Term]
id: SO:0000501
name: reverse_Hoogsteen_base_pair
def: "A type of non-canonical base-pairing." [SO:ke]
synonym: "reverse Hoogsteen base pair" EXACT []
is_a: SO:0000028 ! base_pair
[Term]
id: SO:0000502
name: transcribed_region
def: "A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes." [SO:ke]
comment: This concept cam about as a direct result of the SO meeting August 2004.nThe exact nature of the relationship between transcribed_region and gene is still up for discussion. We are going with 'associated_with' for the time being.
subset: SOFA
is_obsolete: true
[Term]
id: SO:0000503
name: alternately_spliced_gene_encodeing_one_transcript
is_obsolete: true
[Term]
id: SO:0000504
name: D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D DJ C cluster" EXACT []
synonym: "D-(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000505
name: D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D DJ cluster" EXACT []
synonym: "D-(DJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000506
name: D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D DJ J C cluster" EXACT []
synonym: "D-(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000507
name: pseudogenic_exon
def: "A non functional descendant of an exon, part of a pseudogene." [SO:ke]
comment: This is the analog of the exon of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
synonym: "pseudogenic exon" EXACT []
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000147 ! exon
relationship: part_of SO:0000516 ! pseudogenic_transcript
[Term]
id: SO:0000508
name: D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D DJ J cluster" EXACT []
synonym: "D-(DJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000509
name: D_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D J C cluster" EXACT []
synonym: "D-J-C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
[Term]
id: SO:0000510
name: VD_gene_segment
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V_D_GENE" EXACT []
synonym: "VD gene" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
[Term]
id: SO:0000511
name: J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J C cluster" EXACT []
synonym: "J-C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
[Term]
id: SO:0000512
name: inversion_derived_deficiency_plus_aneuploid
def: "A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]
synonym: "inversion derived deficiency plus aneuploid" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
[Term]
id: SO:0000513
name: J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J cluster" EXACT []
synonym: "J-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
[Term]
id: SO:0000514
name: J_nonamer
def: "9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J nonamer" EXACT []
synonym: "J-NONAMER" EXACT []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000302 ! J_gene_recombination_feature
[Term]
id: SO:0000515
name: J_heptamer
def: "7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J heptamer" EXACT []
synonym: "J-HEPTAMER" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000302 ! J_gene_recombination_feature
[Term]
id: SO:0000516
name: pseudogenic_transcript
def: "A non functional descendant of a transcript, part of a pseudogene." [SO:ke]
comment: This is the analog of the transcript of a functional gene. The term was requested by Rama - SGD to allow the annotation of the parts of a pseudogene. Non-functional is defined as either its transcription or translation (or both) are prevented due to one or more mutations.
synonym: "pseudogenic transcript" EXACT []
is_a: SO:0000462 ! pseudogenic_region
relationship: non_functional_homolog_of SO:0000673 ! transcript
relationship: part_of SO:0000336 ! pseudogene
[Term]
id: SO:0000517
name: J_spacer
def: "12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "J spacer" EXACT []
synonym: "J-SPACER" EXACT []
is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
relationship: part_of SO:0000302 ! J_gene_recombination_feature
[Term]
id: SO:0000518
name: V_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V DJ cluster" EXACT []
synonym: "V-(DJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000519
name: V_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V DJ J cluster" EXACT []
synonym: "V-(DJ)-J-CLUSTER" RELATED []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000520
name: V_VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VDJ C cluster" EXACT []
synonym: "V-(VDJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment
[Term]
id: SO:0000521
name: V_VDJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VDJ cluster" EXACT []
synonym: "V-(VDJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment
[Term]
id: SO:0000522
name: V_VDJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VDJ J cluster" EXACT []
synonym: "V-(VDJ)-J-CLUSTER" RELATED []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment
[Term]
id: SO:0000523
name: V_VJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VJ C cluster" EXACT []
synonym: "V-(VJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment
[Term]
id: SO:0000524
name: V_VJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VJ cluster" EXACT []
synonym: "V-(VJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment
[Term]
id: SO:0000525
name: V_VJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VJ J cluster" EXACT []
synonym: "V-(VJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment
[Term]
id: SO:0000526
name: V_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V cluster" EXACT []
synonym: "V-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
[Term]
id: SO:0000527
name: V_D_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D DJ C cluster" EXACT []
synonym: "V-D-(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000528
name: V_D_DJ_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D DJ cluster" EXACT []
synonym: "V-D-(DJ)-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000529
name: V_D_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D DJ J C cluster" EXACT []
synonym: "V-D-(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000530
name: V_D_DJ_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D DJ J cluster" EXACT []
synonym: "V-D-(DJ)-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000531
name: V_D_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D J C cluster" EXACT []
synonym: "V-D-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
[Term]
id: SO:0000532
name: V_D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V D J cluster" EXACT []
synonym: "V-D-J-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
[Term]
id: SO:0000533
name: V_heptamer
def: "7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V heptamer" EXACT []
synonym: "V-HEPTAMER" EXACT []
is_a: SO:0000561 ! heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000538 ! V_gene_recombination_feature
[Term]
id: SO:0000534
name: V_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V J cluster" EXACT []
synonym: "V-J-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
[Term]
id: SO:0000535
name: V_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V J C cluster" EXACT []
synonym: "V-J-C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
[Term]
id: SO:0000536
name: V_nonamer
def: "9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V nonamer" EXACT []
synonym: "V-NONAMER" EXACT []
is_a: SO:0000562 ! nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
relationship: part_of SO:0000538 ! V_gene_recombination_feature
[Term]
id: SO:0000537
name: V_spacer
def: "12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V spacer" EXACT []
synonym: "V-SPACER" EXACT []
is_a: SO:0000563 ! vertebrate_immune_system_gene_recombination_spacer
relationship: part_of SO:0000538 ! V_gene_recombination_feature
[Term]
id: SO:0000538
name: V_gene_recombination_feature
def: "Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V gene recombination feature" EXACT []
synonym: "V-RS" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
[Term]
id: SO:0000539
name: DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(DJ)-C-CLUSTER" EXACT []
synonym: "DJ C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000540
name: DJ_J_C_cluster
def: "Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(DJ)-J-C-CLUSTER" EXACT []
synonym: "DJ J C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000541
name: VDJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "(VDJ)-C-CLUSTER" EXACT []
synonym: "VDJ C cluster" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment
[Term]
id: SO:0000542
name: V_DJ_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V DJ C cluster" EXACT []
synonym: "V-(DJ)-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000543
name: alternately_spliced_gene_encoding_greater_than_one_transcript
is_obsolete: true
[Term]
id: SO:0000544
name: helitron
def: "A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons." [http://www.pnas.org/cgi/content/full/100/11/6569]
synonym: "ISCR" RELATED []
xref: http://en.wikipedia.org/wiki/Helitron "wiki"
is_a: SO:0000182 ! DNA_transposon
[Term]
id: SO:0000545
name: recoding_pseudoknot
def: "The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding." [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=33937]
synonym: "recoding pseudoknot" EXACT []
is_a: SO:0000591 ! pseudoknot
relationship: part_of SO:1001268 ! recoding_stimulatory_region
[Term]
id: SO:0000546
name: designed_sequence
synonym: "designed sequence" EXACT []
is_a: SO:0000351 ! synthetic_sequence
[Term]
id: SO:0000547
name: inversion_derived_bipartite_duplication
def: "A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion." [FB:km]
synonym: "inversion derived bipartite duplication" EXACT []
is_a: SO:1000038 ! intrachromosomal_duplication
[Term]
id: SO:0000548
name: gene_with_edited_transcript
def: "A gene that encodes a transcript that is edited." [SO:xp]
synonym: "gene with edited transcript" EXACT []
is_a: SO:0001217 ! protein_coding_gene
relationship: transcribed_to SO:0000873 ! edited_transcript
[Term]
id: SO:0000549
name: inversion_derived_duplication_plus_aneuploid
def: "A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion." [FB:km]
synonym: "inversion derived duplication plus aneuploid" EXACT []
is_a: SO:1000038 ! intrachromosomal_duplication
[Term]
id: SO:0000550
name: aneuploid_chromosome
def: "A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking." [SO:ke]
comment: Examples are Nullo-4, Haplo-4 and triplo-4 in Drosophila.
synonym: "aneuploid chromosome" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation
[Term]
id: SO:0000551
name: polyA_signal_sequence
def: "The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "poly(A) signal" EXACT []
synonym: "polyA signal sequence" EXACT []
synonym: "polyadenylation termination signal" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
[Term]
id: SO:0000552
name: Shine_Dalgarno_sequence
def: "A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex." [SO:jh]
comment: Not found in Eukaryotic sequence.
synonym: "five prime ribosome binding site" EXACT []
synonym: "RBS" RELATED []
synonym: "Shine Dalgarno sequence" EXACT []
synonym: "Shine-Dalgarno sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Shine-Dalgarno_sequence "wiki"
is_a: SO:0000139 ! ribosome_entry_site
[Term]
id: SO:0000553
name: polyA_site
alt_id: SO:0001430
def: "The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "polyA cleavage site" EXACT []
synonym: "polyA junction" EXACT []
synonym: "polyA site" EXACT []
synonym: "polyA_junction" EXACT []
synonym: "polyadenylation site" RELATED []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000205 ! three_prime_UTR
relationship: part_of SO:0000233 ! mature_transcript
[Term]
id: SO:0000554
name: assortment_derived_deficiency_plus_duplication
is_obsolete: true
[Term]
id: SO:0000555
name: five_prime_clip
def: "5' most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "5' clip" RELATED []
synonym: "five prime clip" EXACT []
is_a: SO:0000303 ! clip
[Term]
id: SO:0000556
name: five_prime_D_recombination_signal_sequence
def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "5'RS" EXACT []
synonym: "five prime D recombination signal sequence" EXACT []
synonym: "five prime D-recombination signal sequence" EXACT []
is_a: SO:0000492 ! D_gene_recombination_feature
[Term]
id: SO:0000557
name: three_prime_clip
def: "3'-most region of a precursor transcript that is clipped off during processing." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "3'-clip" EXACT []
synonym: "three prime clip" EXACT []
is_a: SO:0000303 ! clip
[Term]
id: SO:0000558
name: C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "C cluster" EXACT []
synonym: "C-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000478 ! C_gene_segment
[Term]
id: SO:0000559
name: D_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D cluster" EXACT []
synonym: "D-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
[Term]
id: SO:0000560
name: D_J_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D J cluster" EXACT []
synonym: "D-J-CLUSTER" EXACT []
is_a: SO:0000482 ! vertebrate_immunoglobulin_T_cell_receptor_gene_cluster
relationship: has_part SO:0000458 ! D_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
[Term]
id: SO:0000561
name: heptamer_of_recombination_feature_of_vertebrate_immune_system_gene
def: "Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "HEPTAMER" RELATED []
synonym: "heptamer of recombination feature of vertebrate immune system gene" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
[Term]
id: SO:0000562
name: nonamer_of_recombination_feature_of_vertebrate_immune_system_gene
synonym: "nonamer of recombination feature of vertebrate immune system gene" EXACT []
is_a: SO:0000939 ! vertebrate_immune_system_gene_recombination_signal_feature
[Term]
id: SO:0000563
name: vertebrate_immune_system_gene_recombination_spacer
synonym: "vertebrate immune system gene recombination spacer" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
[Term]
id: SO:0000564
name: V_DJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V DJ J C cluster" EXACT []
synonym: "V-(DJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000572 ! DJ_gene_segment
[Term]
id: SO:0000565
name: V_VDJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VDJ J C cluster" EXACT []
synonym: "V-(VDJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000574 ! VDJ_gene_segment
[Term]
id: SO:0000566
name: V_VJ_J_C_cluster
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V VJ J C cluster" EXACT []
synonym: "V-(VJ)-J-C-CLUSTER" EXACT []
is_a: SO:0000938 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
relationship: has_part SO:0000466 ! V_gene_segment
relationship: has_part SO:0000470 ! J_gene_segment
relationship: has_part SO:0000478 ! C_gene_segment
relationship: has_part SO:0000576 ! VJ_gene_segment
[Term]
id: SO:0000567
name: inversion_derived_aneuploid_chromosome
def: "A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion." [FB:km]
synonym: "inversion derived aneuploid chromosome" EXACT []
is_a: SO:0000550 ! aneuploid_chromosome
[Term]
id: SO:0000568
name: bidirectional_promoter
def: "An unregulated promoter that allows continuous expression." [SO:ke]
synonym: "bidirectional promoter" EXACT []
is_a: SO:0000167 ! promoter
[Term]
id: SO:0000569
name: retrotransposed
alt_id: SO:0100042
def: "An attribute of a feature that occurred as the product of a reverse transcriptase mediated event." [SO:ke]
comment: GO:0003964 RNA-directed DNA polymerase activity.
xref: http://en.wikipedia.org/wiki/Retrotransposed "wiki"
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000570
name: three_prime_D_recombination_signal_sequence
def: "Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "3'D-RS" EXACT []
synonym: "three prime D recombination signal sequence" EXACT []
synonym: "three_prime_D-recombination_signal_sequence" EXACT []
is_a: SO:0000492 ! D_gene_recombination_feature
[Term]
id: SO:0000571
name: miRNA_encoding
synonym: "miRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000572
name: DJ_gene_segment
def: "Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "D-J-GENE" EXACT []
synonym: "DJ gene" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
[Term]
id: SO:0000573
name: rRNA_encoding
synonym: "rRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000574
name: VDJ_gene_segment
def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V-D-J-GENE" EXACT []
synonym: "VDJ gene" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
[Term]
id: SO:0000575
name: scRNA_encoding
synonym: "scRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000576
name: VJ_gene_segment
def: "Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205)." [http://www.imgt.org/cgi-bin/IMGTlect.jv?query=7#]
synonym: "V-J-GENE" EXACT []
synonym: "VJ gene" EXACT []
is_a: SO:0000936 ! vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
[Term]
id: SO:0000577
name: centromere
def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Centromere "wiki"
is_a: SO:0000628 ! chromosomal_structural_element
[Term]
id: SO:0000578
name: snoRNA_encoding
synonym: "snoRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000579
name: edited_transcript_feature
def: "A locatable feature on a transcript that is edited." [SO:ma]
synonym: "edited transcript feature" EXACT []
is_a: SO:0000833 ! transcript_region
[Term]
id: SO:0000580
name: methylation_guide_snoRNA_primary_transcript
def: "A primary transcript encoding a methylation guide small nucleolar RNA." [SO:ke]
synonym: "methylation guide snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript
[Term]
id: SO:0000581
name: cap
def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA." [http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/mbglossary/mbgloss.html]
subset: SOFA
xref: http://en.wikipedia.org/wiki/5%27_cap "wiki"
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000582
name: rRNA_cleavage_snoRNA_primary_transcript
def: "A primary transcript encoding an rRNA cleavage snoRNA." [SO:ke]
synonym: "rRNA cleavage snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript
[Term]
id: SO:0000583
name: pre_edited_region
def: "The region of a transcript that will be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]
synonym: "pre edited region" EXACT []
synonym: "pre-edited region" EXACT []
is_a: SO:0000579 ! edited_transcript_feature
[Term]
id: SO:0000584
name: tmRNA
def: "A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00023]
synonym: "10Sa RNA" RELATED []
synonym: "ssrA" RELATED []
xref: http://en.wikipedia.org/wiki/TmRNA "wiki"
is_a: SO:0000370 ! small_regulatory_ncRNA
[Term]
id: SO:0000585
name: C_D_box_snoRNA_encoding
synonym: "C/D box snoRNA encoding" EXACT []
is_a: SO:0000578 ! snoRNA_encoding
[Term]
id: SO:0000586
name: tmRNA_primary_transcript
def: "A primary transcript encoding a tmRNA (SO:0000584)." [SO:ke]
synonym: "10Sa RNA primary transcript" RELATED []
synonym: "ssrA RNA primary transcript" RELATED []
synonym: "tmRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000587
name: group_I_intron
def: "Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028]
comment: GO:0000372.
subset: SOFA
synonym: "group I intron" EXACT []
xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki"
is_a: SO:0000588 ! autocatalytically_spliced_intron
[Term]
id: SO:0000588
name: autocatalytically_spliced_intron
def: "A self spliced intron." [SO:ke]
subset: SOFA
synonym: "autocatalytically spliced intron" EXACT []
is_a: SO:0000188 ! intron
relationship: has_quality SO:0001186 ! ribozymic
[Term]
id: SO:0000589
name: SRP_RNA_primary_transcript
def: "A primary transcript encoding a signal recognition particle RNA." [SO:ke]
synonym: "SRP RNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
[Term]
id: SO:0000590
name: SRP_RNA
def: "The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00017]
subset: SOFA
synonym: "7S RNA" RELATED []
synonym: "signal recognition particle RNA" RELATED []
synonym: "SRP RNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000589 ! SRP_RNA_primary_transcript
[Term]
id: SO:0000591
name: pseudoknot
def: "A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop." [RSC:cb]
xref: http://en.wikipedia.org/wiki/Pseudoknot "wiki"
is_a: SO:0000002 ! sequence_secondary_structure
[Term]
id: SO:0000592
name: H_pseudoknot
def: "A pseudoknot which contains two stems and at least two loops." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=10334330&dopt=Abstract]
synonym: "classical pseudoknot" EXACT []
synonym: "H pseudoknot" EXACT []
synonym: "H-pseudoknot" EXACT []
synonym: "H-type pseudoknot" EXACT []
synonym: "hairpin-type pseudoknot" EXACT []
is_a: SO:0000591 ! pseudoknot
[Term]
id: SO:0000593
name: C_D_box_snoRNA
def: "Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
subset: SOFA
synonym: "box C/D snoRNA" EXACT []
synonym: "C D box snoRNA" EXACT []
synonym: "C/D box snoRNA" EXACT []
is_a: SO:0000275 ! snoRNA
relationship: derives_from SO:0000595 ! C_D_box_snoRNA_primary_transcript
[Term]
id: SO:0000594
name: H_ACA_box_snoRNA
def: "Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains." [http://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html]
synonym: "box H/ACA snoRNA" EXACT []
synonym: "H ACA box snoRNA" EXACT []
synonym: "H/ACA box snoRNA" EXACT []
is_a: SO:0000275 ! snoRNA
relationship: derives_from SO:0000596 ! H_ACA_box_snoRNA_primary_transcript
[Term]
id: SO:0000595
name: C_D_box_snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar RNA of the box C/D family." [SO:ke]
synonym: "C/D box snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript
[Term]
id: SO:0000596
name: H_ACA_box_snoRNA_primary_transcript
def: "A primary transcript encoding a small nucleolar RNA of the box H/ACA family." [SO:ke]
synonym: "H ACA box snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript
[Term]
id: SO:0000597
name: transcript_edited_by_U_insertion/deletion
def: "The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa." [http://www.rna.ucla.edu/index.html]
is_obsolete: true
[Term]
id: SO:0000598
name: edited_by_C_insertion_and_dinucleotide_insertion
synonym: "transcript_edited_by_C-insertion_and_dinucleotide_insertion" RELATED []
is_obsolete: true
[Term]
id: SO:0000599
name: edited_by_C_to_U_substitution
is_obsolete: true
[Term]
id: SO:0000600
name: edited_by_A_to_I_substitution
is_obsolete: true
[Term]
id: SO:0000601
name: edited_by_G_addition
is_obsolete: true
[Term]
id: SO:0000602
name: guide_RNA
def: "A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA." [http://www.rna.ucla.edu/index.html]
subset: SOFA
synonym: "gRNA" EXACT []
synonym: "guide RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Guide_RNA "wiki"
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000603
name: group_II_intron
def: "Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny." [http://www.sanger.ac.uk/Software/Rfam/browse/index.shtml]
comment: GO:0000373.
subset: SOFA
synonym: "group II intron" EXACT []
xref: http://en.wikipedia.org/wiki/Group_II_intron "wiki"
is_a: SO:0000588 ! autocatalytically_spliced_intron
[Term]
id: SO:0000604
name: editing_block
def: "Edited mRNA sequence mediated by a single guide RNA (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]
synonym: "editing block" EXACT []
is_a: SO:0000579 ! edited_transcript_feature
[Term]
id: SO:0000605
name: intergenic_region
def: "A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome." [SO:cjm]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
subset: SOFA
synonym: "intergenic region" EXACT []
xref: http://en.wikipedia.org/wiki/Intergenic_region "wiki"
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000606
name: editing_domain
def: "Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602)." [http://dna.kdna.ucla.edu/rna/index.aspx]
synonym: "editing domain" EXACT []
is_a: SO:0000579 ! edited_transcript_feature
[Term]
id: SO:0000607
name: unedited_region
def: "The region of an edited transcript that will not be edited." [http://dna.kdna.ucla.edu/rna/index.aspx]
synonym: "unedited region" EXACT []
is_a: SO:0000579 ! edited_transcript_feature
[Term]
id: SO:0000608
name: H_ACA_box_snoRNA_encoding
synonym: "H ACA box snoRNA encoding" EXACT []
is_a: SO:0000578 ! snoRNA_encoding
[Term]
id: SO:0000609
name: oligo_U_tail
def: "The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602)." [http://www.rna.ucla.edu/]
synonym: "oligo U tail" EXACT []
is_a: SO:0001411 ! biological_region
relationship: adjacent_to SO:0000602 ! guide_RNA
[Term]
id: SO:0000610
name: polyA_sequence
def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:ke]
subset: SOFA
synonym: "polyA sequence" EXACT []
is_a: SO:0001411 ! biological_region
relationship: adjacent_to SO:0000234 ! mRNA
[Term]
id: SO:0000611
name: branch_site
def: "A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat." [SO:ke]
subset: SOFA
synonym: "branch point" EXACT []
synonym: "branch site" EXACT []
synonym: "branch_point" EXACT []
is_a: SO:0000841 ! spliceosomal_intron_region
[Term]
id: SO:0000612
name: polypyrimidine_tract
def: "The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing." [http://nar.oupjournals.org/cgi/content/full/25/4/888]
subset: SOFA
synonym: "polypyrimidine tract" EXACT []
xref: http://en.wikipedia.org/wiki/Polypyrimidine_tract "wiki"
is_a: SO:0000841 ! spliceosomal_intron_region
[Term]
id: SO:0000613
name: bacterial_RNApol_promoter
def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke]
synonym: "bacterial RNApol promoter" EXACT []
is_a: SO:0000752 ! gene_group_regulatory_region
is_a: SO:0001203 ! RNA_polymerase_promoter
[Term]
id: SO:0000614
name: bacterial_terminator
def: "A terminator signal for bacterial transcription." [SO:ke]
synonym: "bacterial terminator" EXACT []
is_a: SO:0000141 ! terminator
is_a: SO:0000752 ! gene_group_regulatory_region
[Term]
id: SO:0000615
name: terminator_of_type_2_RNApol_III_promoter
def: "A terminator signal for RNA polymerase III transcription." [SO:ke]
synonym: "terminator of type 2 RNApol III promoter" EXACT []
is_a: SO:0000951 ! eukaryotic_terminator
[Term]
id: SO:0000616
name: transcription_end_site
def: "The base where transcription ends." [SO:ke]
subset: SOFA
synonym: "transcription end site" EXACT []
is_a: SO:0000835 ! primary_transcript_region
[Term]
id: SO:0000617
name: RNApol_III_promoter_type_1
synonym: "RNApol III promoter type 1" EXACT []
is_a: SO:0000171 ! RNApol_III_promoter
[Term]
id: SO:0000618
name: RNApol_III_promoter_type_2
synonym: "RNApol III promoter type 2" EXACT []
synonym: "tRNA promoter" RELATED []
is_a: SO:0000171 ! RNApol_III_promoter
[Term]
id: SO:0000619
name: A_box
def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG." [SO:ke]
comment: Binds TFIIIC.
synonym: "A-box" EXACT []
xref: http://en.wikipedia.org/wiki/A-box "wiki"
is_a: SO:0001660 ! core_promoter_element
[Term]
id: SO:0000620
name: B_box
def: "A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC." [SO:ke]
comment: Binds TFIIIC.
synonym: "B-box" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2
[Term]
id: SO:0000621
name: RNApol_III_promoter_type_3
synonym: "RNApol III promoter type 3" EXACT []
is_a: SO:0000171 ! RNApol_III_promoter
[Term]
id: SO:0000622
name: C_box
def: "An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn." [SO:ke]
synonym: "C-box" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
[Term]
id: SO:0000623
name: snRNA_encoding
synonym: "snRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000624
name: telomere
def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma]
subset: SOFA
synonym: "telomeric DNA" EXACT []
synonym: "telomeric sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Telomere "wiki"
is_a: SO:0000628 ! chromosomal_structural_element
[Term]
id: SO:0000625
name: silencer
def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki"
is_a: SO:0000727 ! CRM
[Term]
id: SO:0000626
name: chromosomal_regulatory_element
synonym: "chromosomal regulatory element" EXACT []
is_a: SO:0000830 ! chromosome_part
[Term]
id: SO:0000627
name: insulator
def: "A transcriptional cis regulatory region that when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression." [SO:regcreative]
subset: SOFA
synonym: "insulator element" EXACT []
xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki"
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
[Term]
id: SO:0000628
name: chromosomal_structural_element
subset: SOFA
synonym: "chromosomal structural element" EXACT []
is_a: SO:0000830 ! chromosome_part
[Term]
id: SO:0000629
name: five_prime_open_reading_frame
synonym: "five prime open reading frame" EXACT []
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000204 ! five_prime_UTR
[Term]
id: SO:0000630
name: upstream_AUG_codon
def: "A start codon upstream of the ORF." [SO:ke]
synonym: "upstream AUG codon" EXACT []
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000203 ! UTR
[Term]
id: SO:0000631
name: polycistronic_primary_transcript
def: "A primary transcript encoding for more than one gene product." [SO:ke]
synonym: "polycistronic primary transcript" EXACT []
is_a: SO:0000078 ! polycistronic_transcript
is_a: SO:0000185 ! primary_transcript
relationship: has_quality SO:0000880 ! polycistronic
[Term]
id: SO:0000632
name: monocistronic_primary_transcript
def: "A primary transcript encoding for one gene product." [SO:ke]
synonym: "monocistronic primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript
is_a: SO:0000665 ! monocistronic_transcript
relationship: has_quality SO:0000878 ! monocistronic
[Term]
id: SO:0000633
name: monocistronic_mRNA
def: "An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap." [SO:rd]
synonym: "monocistronic mRNA" EXACT []
synonym: "monocistronic processed transcript" EXACT []
xref: http://en.wikipedia.org/wiki/Monocistronic_mRNA "wiki"
is_a: SO:0000234 ! mRNA
is_a: SO:0000665 ! monocistronic_transcript
relationship: has_quality SO:0000878 ! monocistronic
[Term]
id: SO:0000634
name: polycistronic_mRNA
def: "An mRNA that encodes multiple proteins from at least two non-overlapping regions." [SO:rd]
synonym: "polycistronic mRNA" EXACT []
synonym: "polycistronic processed transcript" RELATED []
xref: http://en.wikipedia.org/wiki/Polycistronic_mRNA "wiki"
is_a: SO:0000078 ! polycistronic_transcript
is_a: SO:0000234 ! mRNA
relationship: has_quality SO:0000880 ! polycistronic
[Term]
id: SO:0000635
name: mini_exon_donor_RNA
def: "A primary transcript that donates the spliced leader to other mRNA." [SO:ke]
synonym: "mini exon donor RNA" EXACT []
synonym: "mini-exon donor RNA" EXACT []
is_a: SO:0000185 ! primary_transcript
[Term]
id: SO:0000636
name: spliced_leader_RNA
synonym: "mini-exon" RELATED []
synonym: "spliced leader RNA" EXACT []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000635 ! mini_exon_donor_RNA
[Term]
id: SO:0000637
name: engineered_plasmid
def: "A plasmid that is engineered." [SO:xp]
synonym: "engineered plasmid" EXACT []
synonym: "engineered plasmid gene" RELATED []
is_a: SO:0000155 ! plasmid
is_a: SO:0000804 ! engineered_region
relationship: has_quality SO:0000783 ! engineered
[Term]
id: SO:0000638
name: transcribed_spacer_region
def: "Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA." [http://oregonstate.edu/instruction/bb492/general/glossary.html]
synonym: "transcribed spacer region" EXACT []
is_a: SO:0000838 ! rRNA_primary_transcript_region
[Term]
id: SO:0000639
name: internal_transcribed_spacer_region
def: "Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs." [SO:ke]
synonym: "internal transcribed spacer region" EXACT []
is_a: SO:0000638 ! transcribed_spacer_region
[Term]
id: SO:0000640
name: external_transcribed_spacer_region
def: "Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA." [SO:ke]
synonym: "external transcribed spacer region" EXACT []
is_a: SO:0000638 ! transcribed_spacer_region
[Term]
id: SO:0000641
name: tetranucleotide_repeat_microsatellite_feature
synonym: "tetranucleotide repeat microsatellite feature" EXACT []
is_a: SO:0000289 ! microsatellite
[Term]
id: SO:0000642
name: SRP_RNA_encoding
synonym: "SRP RNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000643
name: minisatellite
def: "A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp." [http://www.informatics.jax.org/silver/glossary.shtml]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Minisatellite "wiki"
is_a: SO:0000005 ! satellite_DNA
[Term]
id: SO:0000644
name: antisense_RNA
def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke]
subset: SOFA
synonym: "antisense RNA" EXACT []
xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki"
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000645 ! antisense_primary_transcript
[Term]
id: SO:0000645
name: antisense_primary_transcript
def: "The reverse complement of the primary transcript." [SO:ke]
subset: SOFA
synonym: "antisense primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript
[Term]
id: SO:0000646
name: siRNA
def: "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." [PMID:12592000]
subset: SOFA
synonym: "small interfering RNA" EXACT []
xref: http://en.wikipedia.org/wiki/SiRNA "wiki"
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000647
name: miRNA_primary_transcript
alt_id: SO:0000648
def: "A primary transcript encoding a micro RNA." [SO:ke]
synonym: "micro RNA primary transcript" EXACT []
synonym: "miRNA primary transcript" EXACT []
synonym: "small temporal RNA primary transcript" EXACT []
synonym: "stRNA primary transcript" EXACT []
synonym: "stRNA_primary_transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
[Term]
id: SO:0000650
name: small_subunit_rRNA
def: "Ribosomal RNA transcript that structures the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "small subunit rRNA" EXACT []
synonym: "SSU RNA" EXACT [RSC:cb]
synonym: "SSU rRNA" EXACT [RSC:cb]
is_a: SO:0000252 ! rRNA
relationship: derives_from SO:0000255 ! rRNA_small_subunit_primary_transcript
[Term]
id: SO:0000651
name: large_subunit_rRNA
def: "Ribosomal RNA transcript that structures the large subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "large subunit rRNA" EXACT []
synonym: "LSU RNA" EXACT [RSC:cb]
synonym: "LSU rRNA" EXACT [RSC:cb]
is_a: SO:0000252 ! rRNA
relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript
[Term]
id: SO:0000652
name: rRNA_5S
def: "5S ribosomal RNA (5S rRNA) is a component of the large ribosomal subunit in both prokaryotes and eukaryotes. In eukaryotes, it is synthesised by RNA polymerase III (the other eukaryotic rRNAs are cleaved from a 45S precursor synthesised by RNA polymerase I). In Xenopus oocytes, it has been shown that fingers 4-7 of the nine-zinc finger transcription factor TFIIIA can bind to the central region of 5S RNA. Thus, in addition to positively regulating 5S rRNA transcription, TFIIIA also stabilizes 5S rRNA until it is required for transcription." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00001]
subset: SOFA
synonym: "5S LSU rRNA" EXACT []
synonym: "5S ribosomal RNA" EXACT []
synonym: "5S rRNA" EXACT []
synonym: "rRNA 5S" EXACT []
xref: http://en.wikipedia.org/wiki/5S_ribosomal_RNA "wiki"
is_a: SO:0000651 ! large_subunit_rRNA
[Term]
id: SO:0000653
name: rRNA_28S
def: "A component of the large ribosomal subunit." [SO:ke]
subset: SOFA
synonym: "28S LSU rRNA" EXACT []
synonym: "28S ribosomal RNA" EXACT []
synonym: "28S rRNA" EXACT []
synonym: "rRNA 28S" EXACT []
xref: http://en.wikipedia.org/wiki/28S_ribosomal_RNA "wiki"
is_a: SO:0000651 ! large_subunit_rRNA
[Term]
id: SO:0000654
name: maxicircle_gene
def: "A mitochondrial gene located in a maxicircle." [SO:xp]
synonym: "maxi-circle gene" EXACT []
synonym: "maxicircle gene" EXACT []
is_a: SO:0000089 ! kinetoplast_gene
relationship: part_of SO:0000742 ! maxicircle
[Term]
id: SO:0000655
name: ncRNA
def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke]
comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript.
subset: SOFA
synonym: "noncoding RNA" EXACT []
xref: http://en.wikipedia.org/wiki/NcRNA "wiki"
is_a: SO:0000233 ! mature_transcript
[Term]
id: SO:0000656
name: stRNA_encoding
synonym: "stRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000657
name: repeat_region
def: "A region of sequence containing one or more repeat units." [SO:ke]
subset: SOFA
synonym: "repeat region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: has_part SO:0000726 ! repeat_unit
[Term]
id: SO:0000658
name: dispersed_repeat
def: "A repeat that is located at dispersed sites in the genome." [SO:ke]
subset: SOFA
synonym: "dispersed repeat" EXACT []
synonym: "interspersed repeat" EXACT []
xref: http://en.wikipedia.org/wiki/Interspersed_repeat "wiki"
is_a: SO:0000657 ! repeat_region
[Term]
id: SO:0000659
name: tmRNA_encoding
synonym: "tmRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000660
name: DNA_invertase_target_sequence
is_obsolete: true
[Term]
id: SO:0000661
name: intron_attribute
is_obsolete: true
[Term]
id: SO:0000662
name: spliceosomal_intron
def: "An intron which is spliced by the spliceosome." [SO:ke]
comment: GO:0000398.
subset: SOFA
synonym: "spliceosomal intron" EXACT []
is_a: SO:0000188 ! intron
[Term]
id: SO:0000663
name: tRNA_encoding
synonym: "tRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000664
name: introgressed_chromosome_region
synonym: "introgressed chromosome region" EXACT []
is_a: SO:0000830 ! chromosome_part
[Term]
id: SO:0000665
name: monocistronic_transcript
def: "A transcript that is monocistronic." [SO:xp]
synonym: "monocistronic transcript" EXACT []
is_a: SO:0000673 ! transcript
relationship: has_quality SO:0000878 ! monocistronic
[Term]
id: SO:0000666
name: mobile_intron
def: "An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility." [SO:ke]
synonym: "mobile intron" EXACT []
is_a: SO:0000188 ! intron
is_a: SO:0001037 ! mobile_genetic_element
relationship: has_quality SO:0001234 ! mobile
[Term]
id: SO:0000667
name: insertion
alt_id: SO:1000034
def: "The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence." [SO:ke]
subset: DBVAR
subset: SOFA
synonym: "insertion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "nucleotide insertion" EXACT []
synonym: "nucleotide_insertion" EXACT []
xref: loinc:LA6687-3 "Insertion"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000668
name: EST_match
def: "A match against an EST sequence." [SO:ke]
subset: SOFA
synonym: "EST match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match
[Term]
id: SO:0000669
name: sequence_rearrangement_feature
synonym: "sequence rearrangement feature" EXACT []
is_a: SO:0000298 ! recombination_feature
[Term]
id: SO:0000670
name: chromosome_breakage_sequence
def: "A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation." [SO:ma]
synonym: "chromosome breakage sequence" EXACT []
is_a: SO:0000669 ! sequence_rearrangement_feature
[Term]
id: SO:0000671
name: internal_eliminated_sequence
def: "A sequence eliminated from the genome of ciliates during nuclear differentiation." [SO:ma]
synonym: "internal eliminated sequence" EXACT []
is_a: SO:0000669 ! sequence_rearrangement_feature
[Term]
id: SO:0000672
name: macronucleus_destined_segment
def: "A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome." [SO:ma]
synonym: "macronucleus destined segment" EXACT []
is_a: SO:0000669 ! sequence_rearrangement_feature
[Term]
id: SO:0000673
name: transcript
def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma]
subset: SOFA
xref: http://en.wikipedia.org/wiki/RNA "wiki"
is_a: SO:0000831 ! gene_member_region
[Term]
id: SO:0000674
name: non_canonical_splice_site
def: "A splice site where the donor and acceptor sites differ from the canonical form." [SO:ke]
synonym: "non canonical splice site" EXACT []
synonym: "non-canonical splice site" EXACT []
is_obsolete: true
consider: SO:0000678
consider: SO:0000679
[Term]
id: SO:0000675
name: canonical_splice_site
def: "The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively." [SO:ke]
synonym: "canonical splice site" EXACT []
is_obsolete: true
consider: SO:0000676
consider: SO:0000677
[Term]
id: SO:0000676
name: canonical_three_prime_splice_site
def: "The canonical 3' splice site has the sequence \"AG\"." [SO:ke]
synonym: "canonical 3' splice site" EXACT []
synonym: "canonical three prime splice site" EXACT []
is_a: SO:0000164 ! three_prime_cis_splice_site
[Term]
id: SO:0000677
name: canonical_five_prime_splice_site
def: "The canonical 5' splice site has the sequence \"GT\"." [SO:ke]
synonym: "canonical 5' splice site" EXACT []
synonym: "canonical five prime splice site" EXACT []
is_a: SO:0000163 ! five_prime_cis_splice_site
[Term]
id: SO:0000678
name: non_canonical_three_prime_splice_site
def: "A 3' splice site that does not have the sequence \"AG\"." [SO:ke]
synonym: "non canonical 3' splice site" RELATED []
synonym: "non canonical three prime splice site" EXACT []
synonym: "non-canonical three prime splice site" EXACT []
is_a: SO:0000164 ! three_prime_cis_splice_site
[Term]
id: SO:0000679
name: non_canonical_five_prime_splice_site
def: "A 5' splice site which does not have the sequence \"GT\"." [SO:ke]
synonym: "non canonical 5' splice site" EXACT []
synonym: "non canonical five prime splice site" EXACT []
synonym: "non-canonical five prime splice site" EXACT []
is_a: SO:0000163 ! five_prime_cis_splice_site
[Term]
id: SO:0000680
name: non_canonical_start_codon
def: "A start codon that is not the usual AUG sequence." [SO:ke]
synonym: "non ATG start codon" EXACT []
synonym: "non canonical start codon" EXACT []
synonym: "non-canonical start codon" EXACT []
is_a: SO:0000318 ! start_codon
[Term]
id: SO:0000681
name: aberrant_processed_transcript
def: "A transcript that has been processed \"incorrectly\", for example by the failure of splicing of one or more exons." [SO:ke]
synonym: "aberrant processed transcript" EXACT []
is_a: SO:0000673 ! transcript
[Term]
id: SO:0000682
name: splicing_feature
is_obsolete: true
[Term]
id: SO:0000683
name: exonic_splice_enhancer
def: "Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12403462&dopt=Abstract]
synonym: "exonic splice enhancer" EXACT []
is_a: SO:0000344 ! splice_enhancer
[Term]
id: SO:0000684
name: nuclease_sensitive_site
def: "A region of nucleotide sequence targeted by a nuclease enzyme." [SO:ma]
subset: SOFA
synonym: "nuclease sensitive site" EXACT []
is_a: SO:0000059 ! nuclease_binding_site
[Term]
id: SO:0000685
name: DNAseI_hypersensitive_site
synonym: "DHS" EXACT []
synonym: "DNAseI hypersensitive site" EXACT []
is_a: SO:0000322 ! nuclease_hypersensitive_site
[Term]
id: SO:0000686
name: translocation_element
def: "A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations." [SO:ma]
synonym: "translocation element" EXACT []
is_a: SO:1000044 ! chromosomal_translocation
[Term]
id: SO:0000687
name: deletion_junction
def: "The space between two bases in a sequence which marks the position where a deletion has occurred." [SO:ke]
subset: SOFA
synonym: "deletion junction" EXACT []
is_a: SO:0000699 ! junction
[Term]
id: SO:0000688
name: golden_path
def: "A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence." [SO:ls]
subset: SOFA
synonym: "golden path" EXACT []
is_a: SO:0000353 ! sequence_assembly
[Term]
id: SO:0000689
name: cDNA_match
def: "A match against cDNA sequence." [SO:ke]
subset: SOFA
synonym: "cDNA match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match
[Term]
id: SO:0000690
name: gene_with_polycistronic_transcript
def: "A gene that encodes a polycistronic transcript." [SO:xp]
synonym: "gene with polycistronic transcript" EXACT []
is_a: SO:0000704 ! gene
relationship: transcribed_to SO:0000078 ! polycistronic_transcript
[Term]
id: SO:0000691
name: cleaved_initiator_methionine
alt_id: BS:00067
def: "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]
subset: biosapiens
synonym: "cleaved initiator methionine" EXACT []
synonym: "init_met" RELATED [uniprot:feature_type]
synonym: "initiator methionine" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
[Term]
id: SO:0000692
name: gene_with_dicistronic_transcript
def: "A gene that encodes a dicistronic transcript." [SO:xp]
synonym: "gene with dicistronic transcript" EXACT []
is_a: SO:0000690 ! gene_with_polycistronic_transcript
relationship: transcribed_to SO:0000079 ! dicistronic_transcript
[Term]
id: SO:0000693
name: gene_with_recoded_mRNA
def: "A gene that encodes an mRNA that is recoded." [SO:xp]
synonym: "gene with recoded mRNA" EXACT []
is_a: SO:0001217 ! protein_coding_gene
relationship: has_quality SO:0000881 ! recoded
[Term]
id: SO:0000694
name: SNP
def: "SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater." [SO:cb]
subset: SOFA
synonym: "single nucleotide polymorphism" EXACT []
is_a: SO:0001483 ! SNV
[Term]
id: SO:0000695
name: reagent
def: "A sequence used in experiment." [SO:ke]
comment: Requested by Lynn Crosby, jan 2006.
subset: SOFA
is_a: SO:0001409 ! biomaterial_region
[Term]
id: SO:0000696
name: oligo
def: "A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded." [SO:ma]
subset: SOFA
synonym: "oligonucleotide" EXACT []
xref: http://en.wikipedia.org/wiki/Oligonucleotide "wiki"
is_a: SO:0000695 ! reagent
[Term]
id: SO:0000697
name: gene_with_stop_codon_read_through
def: "A gene that encodes a transcript with stop codon readthrough." [SO:xp]
synonym: "gene with stop codon read through" EXACT []
is_a: SO:0000693 ! gene_with_recoded_mRNA
relationship: has_part SO:0000883 ! stop_codon_read_through
[Term]
id: SO:0000698
name: gene_with_stop_codon_redefined_as_pyrrolysine
def: "A gene encoding an mRNA that has the stop codon redefined as pyrrolysine." [SO:xp]
synonym: "gene with stop codon redefined as pyrrolysine" EXACT []
is_a: SO:0000697 ! gene_with_stop_codon_read_through
relationship: has_part SO:0000884 ! stop_codon_redefined_as_pyrrolysine
[Term]
id: SO:0000699
name: junction
def: "A sequence_feature with an extent of zero." [SO:ke]
comment: A junction is a boundary between regions. A boundary has an extent of zero.
subset: SOFA
synonym: "boundary" EXACT []
synonym: "breakpoint" EXACT []
is_a: SO:0000110 ! sequence_feature
[Term]
id: SO:0000700
name: remark
def: "A comment about the sequence." [SO:ke]
subset: SOFA
is_a: SO:0001410 ! experimental_feature
[Term]
id: SO:0000701
name: possible_base_call_error
def: "A region of sequence where the validity of the base calling is questionable." [SO:ke]
subset: SOFA
synonym: "possible base call error" EXACT []
is_a: SO:0000413 ! sequence_difference
[Term]
id: SO:0000702
name: possible_assembly_error
def: "A region of sequence where there may have been an error in the assembly." [SO:ke]
subset: SOFA
synonym: "possible assembly error" EXACT []
is_a: SO:0000413 ! sequence_difference
[Term]
id: SO:0000703
name: experimental_result_region
def: "A region of sequence implicated in an experimental result." [SO:ke]
subset: SOFA
synonym: "experimental result region" EXACT []
is_a: SO:0000700 ! remark
[Term]
id: SO:0000704
name: gene
def: "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions." [SO:immuno_workshop]
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
subset: SOFA
xref: http://en.wikipedia.org/wiki/Gene "wiki"
is_a: SO:0001411 ! biological_region
relationship: member_of SO:0005855 ! gene_group
[Term]
id: SO:0000705
name: tandem_repeat
def: "Two or more adjacent copies of a region (of length greater than 1)." [SO:ke]
subset: SOFA
synonym: "tandem repeat" EXACT []
xref: http://en.wikipedia.org/wiki/Tandem_repeat "wiki"
xref: http://www.sci.sdsu.edu/~smaloy/Glossary/T.html
is_a: SO:0000657 ! repeat_region
[Term]
id: SO:0000706
name: trans_splice_acceptor_site
def: "The 3' splice site of the acceptor primary transcript." [SO:ke]
comment: This region contains a polypyridine tract and AG dinucleotide in some organisms and is UUUCAG in C. elegans.
subset: SOFA
synonym: "3' trans splice site" RELATED []
synonym: "trans splice acceptor site" EXACT []
is_a: SO:0001420 ! trans_splice_site
[Term]
id: SO:0000707
name: trans_splice_donor_site
def: "The 5' five prime splice site region of the donor RNA." [SO:ke]
comment: SL RNA contains a donor site.
synonym: "5 prime trans splice site" RELATED []
synonym: "trans splice donor site" EXACT []
synonym: "trans-splice donor site" EXACT []
is_a: SO:0001420 ! trans_splice_site
[Term]
id: SO:0000708
name: SL1_acceptor_site
def: "A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs." [SO:nlw]
synonym: "SL1 acceptor site" EXACT []
is_a: SO:0000706 ! trans_splice_acceptor_site
[Term]
id: SO:0000709
name: SL2_acceptor_site
def: "A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL2 acceptor site" EXACT []
is_a: SO:0000706 ! trans_splice_acceptor_site
[Term]
id: SO:0000710
name: gene_with_stop_codon_redefined_as_selenocysteine
def: "A gene encoding an mRNA that has the stop codon redefined as selenocysteine." [SO:xp]
synonym: "gene with stop codon redefined as selenocysteine" EXACT []
is_a: SO:0000697 ! gene_with_stop_codon_read_through
relationship: has_part SO:0000885 ! stop_codon_redefined_as_selenocysteine
[Term]
id: SO:0000711
name: gene_with_mRNA_recoded_by_translational_bypass
def: "A gene with mRNA recoded by translational bypass." [SO:xp]
synonym: "gene with mRNA recoded by translational bypass" EXACT []
is_a: SO:0000693 ! gene_with_recoded_mRNA
relationship: has_quality SO:0000886 ! recoded_by_translational_bypass
[Term]
id: SO:0000712
name: gene_with_transcript_with_translational_frameshift
def: "A gene encoding a transcript that has a translational frameshift." [SO:xp]
synonym: "gene with transcript with translational frameshift" EXACT []
is_a: SO:0000693 ! gene_with_recoded_mRNA
relationship: has_quality SO:0000887 ! translationally_frameshifted
[Term]
id: SO:0000713
name: DNA_motif
def: "A motif that is active in the DNA form of the sequence." [SO:ke]
synonym: "DNA motif" EXACT []
xref: http://en.wikipedia.org/wiki/DNA_motif "wiki"
is_a: SO:0000714 ! nucleotide_motif
[Term]
id: SO:0000714
name: nucleotide_motif
def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke]
subset: SOFA
synonym: "nucleotide motif" EXACT []
is_a: SO:0001683 ! sequence_motif
[Term]
id: SO:0000715
name: RNA_motif
def: "A motif that is active in RNA sequence." [SO:ke]
subset: SOFA
synonym: "RNA motif" EXACT []
is_a: SO:0000714 ! nucleotide_motif
[Term]
id: SO:0000716
name: dicistronic_mRNA
def: "An mRNA that has the quality dicistronic." [SO:ke]
synonym: "dicistronic mRNA" EXACT []
synonym: "dicistronic processed transcript" RELATED []
is_a: SO:0000079 ! dicistronic_transcript
is_a: SO:0000634 ! polycistronic_mRNA
relationship: has_quality SO:0000879 ! dicistronic
[Term]
id: SO:0000717
name: reading_frame
def: "A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon." [SGD:rb]
comment: This term was added after a request by SGD. August 2004. Modified after SO meeting in Cambridge to not include start or stop.
subset: SOFA
synonym: "reading frame" EXACT []
xref: http://en.wikipedia.org/wiki/Reading_frame "wiki"
is_a: SO:0001410 ! experimental_feature
[Term]
id: SO:0000718
name: blocked_reading_frame
def: "A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons." [SGD:rb]
comment: Term requested by Rama from SGD.
synonym: "blocked reading frame" EXACT []
is_a: SO:0000717 ! reading_frame
[Term]
id: SO:0000719
name: ultracontig
def: "An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers." [FB:WG]
subset: SOFA
synonym: "superscaffold" RELATED []
is_a: SO:0001876 ! partial_genomic_sequence_assembly
[Term]
id: SO:0000720
name: foreign_transposable_element
def: "A transposable element that is foreign." [SO:ke]
comment: requested by Michael on 19 Nov 2004.
synonym: "foreign transposable element" EXACT []
is_a: SO:0000101 ! transposable_element
relationship: has_quality SO:0000784 ! foreign
[Term]
id: SO:0000721
name: gene_with_dicistronic_primary_transcript
def: "A gene that encodes a dicistronic primary transcript." [SO:xp]
comment: Requested by Michael, 19 nov 2004.
synonym: "gene with dicistronic primary transcript" EXACT []
is_a: SO:0000692 ! gene_with_dicistronic_transcript
relationship: transcribed_to SO:1001197 ! dicistronic_primary_transcript
[Term]
id: SO:0000722
name: gene_with_dicistronic_mRNA
def: "A gene that encodes a polycistronic mRNA." [SO:xp]
comment: Requested by MA nov 19 2004.
synonym: "gene with dicistronic mRNA" EXACT []
synonym: "gene with dicistronic processed transcript" EXACT []
is_a: SO:0000692 ! gene_with_dicistronic_transcript
relationship: transcribed_to SO:0000716 ! dicistronic_mRNA
[Term]
id: SO:0000723
name: iDNA
def: "Genomic sequence removed from the genome, as a normal event, by a process of recombination." [SO:ma]
synonym: "intervening DNA" EXACT []
xref: http://en.wikipedia.org/wiki/IDNA "wiki"
is_a: SO:0000298 ! recombination_feature
[Term]
id: SO:0000724
name: oriT
def: "A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
subset: SOFA
synonym: "origin of transfer" EXACT []
xref: http://en.wikipedia.org/wiki/Origin_of_transfer "wiki"
is_a: SO:0000296 ! origin_of_replication
[Term]
id: SO:0000725
name: transit_peptide
alt_id: BS:00055
def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
comment: Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
subset: biosapiens
subset: SOFA
synonym: "signal" RELATED []
synonym: "transit" RELATED [uniprot:feature_type]
synonym: "transit peptide" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
[Term]
id: SO:0000726
name: repeat_unit
def: "The simplest repeated component of a repeat region. A single repeat." [SO:ke]
comment: Added to comply with the feature table. A single repeat.
synonym: "repeat unit" EXACT []
xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000727
name: CRM
def: "A regulatory region where transcription factor binding sites clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundred kb upstream of the basal promoter, in the coding sequence, within introns, or in the downstream 3'UTR sequences, as well as on different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network." [PMID:19660565, SO:SG]
comment: Requested by Stephen Grossmann Dec 2004.
subset: SOFA
synonym: "cis regulatory module" EXACT []
synonym: "TF module" EXACT []
synonym: "transcription factor module" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
relationship: has_part SO:0000235 ! TF_binding_site
[Term]
id: SO:0000728
name: intein
def: "A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond." [SO:ke]
comment: Intein-mediated protein splicing occurs after mRNA has been translated into a protein.
synonym: "protein intron" RELATED []
xref: http://en.wikipedia.org/wiki/Intein "wiki"
is_a: SO:0100011 ! cleaved_peptide_region
[Term]
id: SO:0000729
name: intein_containing
def: "An attribute of protein-coding genes where the initial protein product contains an intein." [SO:ke]
synonym: "intein containing" EXACT []
is_a: SO:0000010 ! protein_coding
[Term]
id: SO:0000730
name: gap
def: "A gap in the sequence of known length. The unknown bases are filled in with N's." [SO:ke]
subset: SOFA
is_a: SO:0000143 ! assembly_component
relationship: part_of SO:0000353 ! sequence_assembly
[Term]
id: SO:0000731
name: fragmentary
def: "An attribute to describe a feature that is incomplete." [SO:ke]
comment: Term added because of request by MO people.
synonym: "fragment" EXACT []
is_a: SO:0000905 ! status
[Term]
id: SO:0000732
name: predicted
def: "An attribute describing an unverified region." [SO:ke]
xref: http://en.wikipedia.org/wiki/Predicted "wiki"
is_a: SO:0000905 ! status
[Term]
id: SO:0000733
name: feature_attribute
def: "An attribute describing a located_sequence_feature." [SO:ke]
synonym: "feature attribute" EXACT []
is_a: SO:0000400 ! sequence_attribute
[Term]
id: SO:0000734
name: exemplar_mRNA
def: "An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group." [http://mged.sourceforge.net/ontologies/MGEDontology.php]
comment: Added for the MO people.
synonym: "exemplar mRNA" EXACT []
is_a: SO:0000234 ! mRNA
relationship: has_quality SO:0000864 ! exemplar
[Term]
id: SO:0000735
name: sequence_location
synonym: "sequence location" EXACT []
is_a: SO:0000400 ! sequence_attribute
[Term]
id: SO:0000736
name: organelle_sequence
synonym: "organelle sequence" EXACT []
is_a: SO:0000735 ! sequence_location
[Term]
id: SO:0000737
name: mitochondrial_sequence
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "mitochondrial sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence
[Term]
id: SO:0000738
name: nuclear_sequence
synonym: "nuclear sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence
[Term]
id: SO:0000739
name: nucleomorphic_sequence
synonym: "nucleomorphic sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence
[Term]
id: SO:0000740
name: plastid_sequence
synonym: "plastid sequence" EXACT []
is_a: SO:0000736 ! organelle_sequence
[Term]
id: SO:0000741
name: kinetoplast
alt_id: SO:0000826
def: "A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species." [PMID:8395055]
synonym: "kinetoplast_chromosome" EXACT []
xref: http://en.wikipedia.org/wiki/Kinetoplast "wiki"
is_a: SO:0001026 ! genome
relationship: has_part SO:0000742 ! maxicircle
relationship: has_part SO:0000980 ! minicircle
[Term]
id: SO:0000742
name: maxicircle
alt_id: SO:0000827
def: "A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method." [PMID:8395055]
synonym: "maxicircle_chromosome" EXACT []
is_a: SO:0001235 ! replicon
[Term]
id: SO:0000743
name: apicoplast_sequence
synonym: "apicoplast sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence
[Term]
id: SO:0000744
name: chromoplast_sequence
synonym: "chromoplast sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence
[Term]
id: SO:0000745
name: chloroplast_sequence
synonym: "chloroplast sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence
[Term]
id: SO:0000746
name: cyanelle_sequence
synonym: "cyanelle sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence
[Term]
id: SO:0000747
name: leucoplast_sequence
synonym: "leucoplast sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence
[Term]
id: SO:0000748
name: proplastid_sequence
synonym: "proplastid sequence" EXACT []
is_a: SO:0000740 ! plastid_sequence
[Term]
id: SO:0000749
name: plasmid_location
synonym: "plasmid location" EXACT []
is_a: SO:0000735 ! sequence_location
[Term]
id: SO:0000750
name: amplification_origin
def: "An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence." [SO:ma]
synonym: "amplification origin" EXACT []
is_a: SO:0000296 ! origin_of_replication
[Term]
id: SO:0000751
name: proviral_location
synonym: "proviral location" EXACT []
is_a: SO:0000735 ! sequence_location
[Term]
id: SO:0000752
name: gene_group_regulatory_region
subset: SOFA
synonym: "gene group regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
relationship: member_of SO:0005855 ! gene_group
[Term]
id: SO:0000753
name: clone_insert
def: "The region of sequence that has been inserted and is being propagated by the clone." [SO:ke]
subset: SOFA
synonym: "clone insert" EXACT []
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000151 ! clone
[Term]
id: SO:0000754
name: lambda_vector
def: "The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome." [ISBN:0-1767-2380-8]
synonym: "lambda vector" EXACT []
is_a: SO:0000440 ! vector_replicon
[Term]
id: SO:0000755
name: plasmid_vector
synonym: "plasmid vector" EXACT []
xref: http://en.wikipedia.org/wiki/Plasmid_vector#Vectors "wiki"
is_a: SO:0000440 ! vector_replicon
relationship: derives_from SO:0000155 ! plasmid
[Term]
id: SO:0000756
name: cDNA
def: "DNA synthesized by reverse transcriptase using RNA as a template." [SO:ma]
synonym: "complementary DNA" EXACT []
xref: http://en.wikipedia.org/wiki/CDNA "wiki"
is_a: SO:0000352 ! DNA
[Term]
id: SO:0000757
name: single_stranded_cDNA
synonym: "single strand cDNA" EXACT []
synonym: "single stranded cDNA" EXACT []
synonym: "single-strand cDNA" RELATED []
is_a: SO:0000756 ! cDNA
[Term]
id: SO:0000758
name: double_stranded_cDNA
synonym: "double strand cDNA" RELATED []
synonym: "double stranded cDNA" EXACT []
synonym: "double-strand cDNA" RELATED []
is_a: SO:0000756 ! cDNA
[Term]
id: SO:0000759
name: plasmid_clone
is_obsolete: true
[Term]
id: SO:0000760
name: YAC_clone
is_obsolete: true
[Term]
id: SO:0000761
name: phagemid_clone
is_obsolete: true
[Term]
id: SO:0000762
name: PAC_clone
synonym: "P1_clone" RELATED []
is_obsolete: true
[Term]
id: SO:0000763
name: fosmid_clone
is_obsolete: true
[Term]
id: SO:0000764
name: BAC_clone
is_obsolete: true
[Term]
id: SO:0000765
name: cosmid_clone
is_obsolete: true
[Term]
id: SO:0000766
name: pyrrolysyl_tRNA
def: "A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region." [SO:ke]
synonym: "pyrrolysyl tRNA" EXACT []
synonym: "pyrrolysyl-transfer ribonucleic acid" EXACT []
synonym: "pyrrolysyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0001178 ! pyrrolysine_tRNA_primary_transcript
[Term]
id: SO:0000767
name: clone_insert_start
is_obsolete: true
[Term]
id: SO:0000768
name: episome
def: "A plasmid that may integrate with a chromosome." [SO:ma]
is_a: SO:0000155 ! plasmid
[Term]
id: SO:0000769
name: tmRNA_coding_piece
def: "The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw, issn:1362-4962]
comment: Added in response to comment from Kelly Williams from Indiana. Nov 2005.
synonym: "tmRNA coding piece" EXACT []
is_a: SO:0000847 ! tmRNA_region
[Term]
id: SO:0000770
name: tmRNA_acceptor_piece
def: "The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together." [doi:10.1093/nar/gkh795, Indiana:kw]
comment: Added in response to Kelly Williams from Indiana. Date: Nov 2005.
synonym: "tmRNA acceptor piece" EXACT []
is_a: SO:0000847 ! tmRNA_region
[Term]
id: SO:0000771
name: QTL
def: "A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci." [http://rgd.mcw.edu/tu/qtls/]
comment: Added in respose to request by Simon Twigger November 14th 2005.
synonym: "quantitative trait locus" EXACT []
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0000772
name: genomic_island
def: "A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility." [Phigo:at, SO:ke]
comment: Genomic islands are transmissible elements characterized by large size (>10kb).
synonym: "genomic island" EXACT []
xref: http://en.wikipedia.org/wiki/Genomic_island "wiki"
is_a: SO:0001039 ! integrated_mobile_genetic_element
[Term]
id: SO:0000773
name: pathogenic_island
def: "Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species." [SO:ke]
comment: Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
synonym: "pathogenic island" EXACT []
is_a: SO:0000772 ! genomic_island
[Term]
id: SO:0000774
name: metabolic_island
def: "A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
comment: Genes for phenolic compound degradation in Pseudomonas putida are found on metabolic islands.
synonym: "metabolic island" EXACT []
is_a: SO:0000772 ! genomic_island
[Term]
id: SO:0000775
name: adaptive_island
def: "An adaptive island is a genomic island that provides an adaptive advantage to the host." [SO:ke]
comment: The iron-uptake ability of many pathogens are conveyed by adaptive islands. Nature Reviews Microbiology 2, 414-424 (2004); doi:10.1038 micro 884 GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel & Jorg Hacker.
synonym: "adaptive island" EXACT []
is_a: SO:0000772 ! genomic_island
[Term]
id: SO:0000776
name: symbiosis_island
def: "A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria." [SO:ke]
comment: Nitrogen fixation in Rhizobiaceae species is encoded by symbiosis islands. Evolution of rhizobia by acquisition of a 500-kb symbiosis island that integrates into a phe-tRNA gene. John T. Sullivan and Clive W. Ronso PNAS 1998 Apr 28 95 (9) 5145-5149.
synonym: "symbiosis island" EXACT []
is_a: SO:0000772 ! genomic_island
[Term]
id: SO:0000777
name: pseudogenic_rRNA
def: "A non functional descendant of an rRNA." [SO:ke]
comment: Added Jan 2006 to allow the annotation of the pseudogenic rRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
subset: SOFA
synonym: "pseudogenic rRNA" EXACT []
is_a: SO:0000462 ! pseudogenic_region
[Term]
id: SO:0000778
name: pseudogenic_tRNA
def: "A non functional descendent of a tRNA." [SO:ke]
comment: Added Jan 2006 to allow the annotation of the pseudogenic tRNA by flybase. Non-functional is defined as its transcription is prevented due to one or more mutatations.
subset: SOFA
synonym: "pseudogenic tRNA" EXACT []
is_a: SO:0000462 ! pseudogenic_region
[Term]
id: SO:0000779
name: engineered_episome
def: "An episome that is engineered." [SO:xp]
comment: Requested by Lynn Crosby Jan 2006.
synonym: "engineered episome" EXACT []
is_a: SO:0000637 ! engineered_plasmid
is_a: SO:0000768 ! episome
relationship: has_quality SO:0000783 ! engineered
[Term]
id: SO:0000780
name: transposable_element_attribute
comment: Added by KE Jan 2006 to capture the kinds of attributes of TEs
is_obsolete: true
[Term]
id: SO:0000781
name: transgenic
def: "Attribute describing sequence that has been integrated with foreign sequence." [SO:ke]
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000782
name: natural
def: "An attribute describing a feature that occurs in nature." [SO:ke]
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000783
name: engineered
def: "An attribute to describe a region that was modified in vitro." [SO:ke]
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000784
name: foreign
def: "An attribute to describe a region from another species." [SO:ke]
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000785
name: cloned_region
comment: Added in response to Lynn Crosby. A clone insert may be composed of many cloned regions.
synonym: "cloned region" EXACT []
synonym: "cloned segment" EXACT []
is_a: SO:0000695 ! reagent
relationship: part_of SO:0000753 ! clone_insert
[Term]
id: SO:0000786
name: reagent_attribute
comment: Added jan 2006 by KE.
synonym: "reagent attribute" EXACT []
is_obsolete: true
[Term]
id: SO:0000787
name: clone_attribute
is_obsolete: true
[Term]
id: SO:0000788
name: cloned
is_obsolete: true
[Term]
id: SO:0000789
name: validated
def: "An attribute to describe a feature that has been proven." [SO:ke]
is_a: SO:0000905 ! status
[Term]
id: SO:0000790
name: invalidated
def: "An attribute describing a feature that is invalidated." [SO:ke]
is_a: SO:0000905 ! status
[Term]
id: SO:0000791
name: cloned_genomic
is_obsolete: true
[Term]
id: SO:0000792
name: cloned_cDNA
is_obsolete: true
[Term]
id: SO:0000793
name: engineered_DNA
is_obsolete: true
[Term]
id: SO:0000794
name: engineered_rescue_region
def: "A rescue region that is engineered." [SO:xp]
synonym: "engineered rescue fragment" EXACT []
synonym: "engineered rescue region" EXACT []
synonym: "engineered rescue segment" EXACT []
is_a: SO:0000411 ! rescue_region
is_a: SO:0000804 ! engineered_region
relationship: has_quality SO:0000783 ! engineered
[Term]
id: SO:0000795
name: rescue_mini_gene
def: "A mini_gene that rescues." [SO:xp]
synonym: "rescue mini gene" EXACT []
synonym: "rescue mini-gene" EXACT []
is_a: SO:0000815 ! mini_gene
relationship: has_quality SO:0000814 ! rescue
[Term]
id: SO:0000796
name: transgenic_transposable_element
def: "TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE." [FB:mc]
comment: Modified as requested by Lynn - FB. May 2007.
synonym: "transgenic transposable element" EXACT []
is_a: SO:0000101 ! transposable_element
relationship: derives_from SO:0000151 ! clone
relationship: has_quality SO:0000781 ! transgenic
[Term]
id: SO:0000797
name: natural_transposable_element
def: "TE that exists (or existed) in nature." [FB:mc]
synonym: "natural transposable element" EXACT []
is_a: SO:0000101 ! transposable_element
is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
relationship: has_quality SO:0000782 ! natural
[Term]
id: SO:0000798
name: engineered_transposable_element
def: "TE that has been modified by manipulations in vitro." [FB:mc]
synonym: "engineered transposable element" EXACT []
is_a: SO:0000101 ! transposable_element
is_a: SO:0000804 ! engineered_region
relationship: has_quality SO:0000783 ! engineered
[Term]
id: SO:0000799
name: engineered_foreign_transposable_element
def: "A transposable_element that is engineered and foreign." [FB:mc]
synonym: "engineered foreign transposable element" EXACT []
is_a: SO:0000720 ! foreign_transposable_element
is_a: SO:0000798 ! engineered_transposable_element
is_a: SO:0000805 ! engineered_foreign_region
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign
[Term]
id: SO:0000800
name: assortment_derived_duplication
def: "A multi-chromosome duplication aberration generated by reassortment of other aberration components." [FB:gm]
synonym: "assortment derived duplication" EXACT []
is_a: SO:0001504 ! assortment_derived_variation
[Term]
id: SO:0000801
name: assortment_derived_deficiency_plus_duplication
def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication." [FB:gm]
synonym: "assortment derived deficiency plus duplication" EXACT []
is_a: SO:0001504 ! assortment_derived_variation
[Term]
id: SO:0000802
name: assortment_derived_deficiency
def: "A multi-chromosome deficiency aberration generated by reassortment of other aberration components." [FB:gm]
synonym: "assortment-derived deficiency" EXACT []
is_a: SO:0001504 ! assortment_derived_variation
[Term]
id: SO:0000803
name: assortment_derived_aneuploid
def: "A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication." [FB:gm]
synonym: "assortment derived aneuploid" EXACT []
is_a: SO:0001504 ! assortment_derived_variation
[Term]
id: SO:0000804
name: engineered_region
def: "A region that is engineered." [SO:xp]
synonym: "construct" EXACT []
synonym: "engineered region" EXACT []
synonym: "engineered sequence" EXACT []
is_a: SO:0001409 ! biomaterial_region
relationship: has_quality SO:0000783 ! engineered
[Term]
id: SO:0000805
name: engineered_foreign_region
def: "A region that is engineered and foreign." [SO:xp]
synonym: "engineered foreign region" EXACT []
is_a: SO:0000804 ! engineered_region
relationship: has_quality SO:0000783 ! engineered
relationship: has_quality SO:0000784 ! foreign
[Term]
id: SO:0000806
name: fusion
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000807
name: engineered_tag
def: "A tag that is engineered." [SO:xp]
synonym: "engineered tag" EXACT []
is_a: SO:0000324 ! tag
is_a: SO:0000804 ! engineered_region
relationship: has_quality SO:0000783 ! engineered
[Term]
id: SO:0000808
name: validated_cDNA_clone
def: "A cDNA clone that has been validated." [SO:xp]
synonym: "validated cDNA clone" EXACT []
is_a: SO:0000317 ! cDNA_clone
relationship: has_quality SO:0000789 ! validated
[Term]
id: SO:0000809
name: invalidated_cDNA_clone
def: "A cDNA clone that is invalid." [SO:xp]
synonym: "invalidated cDNA clone" EXACT []
is_a: SO:0000317 ! cDNA_clone
relationship: has_quality SO:0000790 ! invalidated
[Term]
id: SO:0000810
name: chimeric_cDNA_clone
def: "A cDNA clone invalidated because it is chimeric." [SO:xp]
synonym: "chimeric cDNA clone" EXACT []
is_a: SO:0000809 ! invalidated_cDNA_clone
relationship: has_quality SO:0000362 ! invalidated_by_chimeric_cDNA
[Term]
id: SO:0000811
name: genomically_contaminated_cDNA_clone
def: "A cDNA clone invalidated by genomic contamination." [SO:xp]
synonym: "genomically contaminated cDNA clone" EXACT []
is_a: SO:0000809 ! invalidated_cDNA_clone
relationship: has_quality SO:0000414 ! invalidated_by_genomic_contamination
[Term]
id: SO:0000812
name: polyA_primed_cDNA_clone
def: "A cDNA clone invalidated by polyA priming." [SO:xp]
synonym: "polyA primed cDNA clone" EXACT []
is_a: SO:0000809 ! invalidated_cDNA_clone
relationship: has_quality SO:0000415 ! invalidated_by_genomic_polyA_primed_cDNA
[Term]
id: SO:0000813
name: partially_processed_cDNA_clone
def: "A cDNA invalidated clone by partial processing." [SO:xp]
synonym: "partially processed cDNA clone" EXACT []
is_a: SO:0000809 ! invalidated_cDNA_clone
relationship: has_quality SO:0000416 ! invalidated_by_partial_processing
[Term]
id: SO:0000814
name: rescue
def: "An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype." [SO:ke]
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000815
name: mini_gene
def: "By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA." [PMID:15992143]
synonym: "mini gene" EXACT []
is_a: SO:0000236 ! ORF
[Term]
id: SO:0000816
name: rescue_gene
def: "A gene that rescues." [SO:xp]
synonym: "rescue gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000814 ! rescue
[Term]
id: SO:0000817
name: wild_type
def: "An attribute describing sequence with the genotype found in nature and/or standard laboratory stock." [SO:ke]
synonym: "wild type" EXACT []
xref: http://en.wikipedia.org/wiki/Wild_type "wiki"
xref: loinc:LA9658-1 "wild type"
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000818
name: wild_type_rescue_gene
def: "A gene that rescues." [SO:xp]
synonym: "wild type rescue gene" EXACT []
is_a: SO:0000816 ! rescue_gene
relationship: has_quality SO:0000817 ! wild_type
[Term]
id: SO:0000819
name: mitochondrial_chromosome
def: "A chromosome originating in a mitochondria." [SO:xp]
synonym: "mitochondrial chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000737 ! mitochondrial_sequence
[Term]
id: SO:0000820
name: chloroplast_chromosome
def: "A chromosome originating in a chloroplast." [SO:xp]
synonym: "chloroplast chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000745 ! chloroplast_sequence
[Term]
id: SO:0000821
name: chromoplast_chromosome
def: "A chromosome originating in a chromoplast." [SO:xp]
synonym: "chromoplast chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000744 ! chromoplast_sequence
[Term]
id: SO:0000822
name: cyanelle_chromosome
def: "A chromosome originating in a cyanelle." [SO:xp]
synonym: "cyanelle chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000746 ! cyanelle_sequence
[Term]
id: SO:0000823
name: leucoplast_chromosome
def: "A chromosome with origin in a leucoplast." [SO:xp]
synonym: "leucoplast chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000747 ! leucoplast_sequence
[Term]
id: SO:0000824
name: macronuclear_chromosome
def: "A chromosome originating in a macronucleus." [SO:xp]
synonym: "macronuclear chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000083 ! macronuclear_sequence
[Term]
id: SO:0000825
name: micronuclear_chromosome
def: "A chromosome originating in a micronucleus." [SO:xp]
synonym: "micronuclear chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000084 ! micronuclear_sequence
[Term]
id: SO:0000828
name: nuclear_chromosome
def: "A chromosome originating in a nucleus." [SO:xp]
synonym: "nuclear chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000738 ! nuclear_sequence
[Term]
id: SO:0000829
name: nucleomorphic_chromosome
def: "A chromosome originating in a nucleomorph." [SO:xp]
synonym: "nucleomorphic chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000739 ! nucleomorphic_sequence
[Term]
id: SO:0000830
name: chromosome_part
def: "A region of a chromosome." [SO:ke]
comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root.
subset: SOFA
synonym: "chromosome part" EXACT []
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000340 ! chromosome
[Term]
id: SO:0000831
name: gene_member_region
def: "A region of a gene." [SO:ke]
comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root.
subset: SOFA
synonym: "gene member region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: member_of SO:0000704 ! gene
[Term]
id: SO:0000832
name: promoter_region
def: "A region of sequence which is part of a promoter." [SO:ke]
comment: This is a manufactured term to allow the parts of promoter to have an is_a path back to the root.
is_obsolete: true
[Term]
id: SO:0000833
name: transcript_region
def: "A region of a transcript." [SO:ke]
comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root.
subset: SOFA
synonym: "transcript region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000673 ! transcript
[Term]
id: SO:0000834
name: mature_transcript_region
def: "A region of a mature transcript." [SO:ke]
comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
subset: SOFA
synonym: "mature transcript region" EXACT []
is_a: SO:0000833 ! transcript_region
[Term]
id: SO:0000835
name: primary_transcript_region
def: "A part of a primary transcript." [SO:ke]
comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root.
subset: SOFA
synonym: "primary transcript region" EXACT []
is_a: SO:0000833 ! transcript_region
relationship: part_of SO:0000185 ! primary_transcript
[Term]
id: SO:0000836
name: mRNA_region
def: "A region of an mRNA." [SO:cb]
comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root.
subset: SOFA
synonym: "mRNA region" EXACT []
is_a: SO:0000834 ! mature_transcript_region
relationship: part_of SO:0000234 ! mRNA
[Term]
id: SO:0000837
name: UTR_region
def: "A region of UTR." [SO:ke]
comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root.
subset: SOFA
synonym: "UTR region" EXACT []
is_a: SO:0000836 ! mRNA_region
[Term]
id: SO:0000838
name: rRNA_primary_transcript_region
def: "A region of an rRNA primary transcript." [SO:ke]
comment: To allow transcribed_spacer_region to have a path to the root.
synonym: "rRNA primary transcript region" EXACT []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000209 ! rRNA_primary_transcript
[Term]
id: SO:0000839
name: polypeptide_region
alt_id: BS:00124
alt_id: BS:00331
def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]
comment: Added to allow the polypeptide regions to have is_a paths back to the root.
subset: biosapiens
subset: SOFA
synonym: "positional" RELATED []
synonym: "positional polypeptide feature" RELATED []
synonym: "region" NARROW [uniprot:feature_type]
synonym: "region or site annotation" RELATED []
synonym: "site" NARROW [uniprot:feature_type]
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000104 ! polypeptide
[Term]
id: SO:0000840
name: repeat_component
def: "A region of a repeated sequence." [SO:ke]
comment: A manufactured to group the parts of repeats, to give them an is_a path back to the root.
synonym: "repeat component" EXACT []
is_a: SO:0001412 ! topologically_defined_region
[Term]
id: SO:0000841
name: spliceosomal_intron_region
def: "A region within an intron." [SO:ke]
comment: A terms added to allow the parts of introns to have is_a paths to the root.
subset: SOFA
synonym: "spliceosomal intron region" EXACT []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000662 ! spliceosomal_intron
[Term]
id: SO:0000842
name: gene_component_region
subset: SOFA
synonym: "gene component region" EXACT []
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000704 ! gene
[Term]
id: SO:0000843
name: bacterial_RNApol_promoter_region
def: "A region which is part of a bacterial RNA polymerase promoter." [SO:ke]
comment: This is a manufactured term to allow the parts of bacterial_RNApol_promoter to have an is_a path back to the root.
is_obsolete: true
[Term]
id: SO:0000844
name: RNApol_II_promoter_region
def: "A region of sequence which is a promoter for RNA polymerase II." [SO:ke]
comment: This is a manufactured term to allow the parts of RNApol_II_promoter to have an is_a path back to the root.
is_obsolete: true
[Term]
id: SO:0000845
name: RNApol_III_promoter_type_1_region
def: "A region of sequence which is a promoter for RNA polymerase III type 1." [SO:ke]
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_1 to have an is_a path back to the root.
is_obsolete: true
[Term]
id: SO:0000846
name: RNApol_III_promoter_type_2_region
def: "A region of sequence which is a promoter for RNA polymerase III type 2." [SO:ke]
comment: This is a manufactured term to allow the parts of RNApol_III_promoter_type_2 to have an is_a path back to the root.
is_obsolete: true
[Term]
id: SO:0000847
name: tmRNA_region
def: "A region of a tmRNA." [SO:cb]
comment: This term was added to provide a grouping term for the region parts of tmRNA, thus giving them an is_a path back to the root.
synonym: "tmRNA region" EXACT []
is_a: SO:0000834 ! mature_transcript_region
relationship: part_of SO:0000584 ! tmRNA
[Term]
id: SO:0000848
name: LTR_component
synonym: "long term repeat component" EXACT []
synonym: "LTR component" EXACT []
is_a: SO:0000840 ! repeat_component
relationship: part_of SO:0000286 ! long_terminal_repeat
[Term]
id: SO:0000849
name: three_prime_LTR_component
synonym: "3' long terminal repeat component" EXACT []
synonym: "three prime LTR component" EXACT []
is_a: SO:0000848 ! LTR_component
relationship: part_of SO:0000426 ! three_prime_LTR
[Term]
id: SO:0000850
name: five_prime_LTR_component
synonym: "5' long term repeat component" EXACT []
synonym: "five prime LTR component" EXACT []
is_a: SO:0000848 ! LTR_component
relationship: part_of SO:0000425 ! five_prime_LTR
[Term]
id: SO:0000851
name: CDS_region
def: "A region of a CDS." [SO:cb]
subset: SOFA
synonym: "CDS region" EXACT []
is_a: SO:0000836 ! mRNA_region
relationship: part_of SO:0000316 ! CDS
[Term]
id: SO:0000852
name: exon_region
def: "A region of an exon." [RSC:cb]
subset: SOFA
synonym: "exon region" EXACT []
is_a: SO:0000833 ! transcript_region
relationship: part_of SO:0000147 ! exon
[Term]
id: SO:0000853
name: homologous_region
def: "A region that is homologous to another region." [SO:ke]
synonym: "homolog" EXACT []
synonym: "homologous region" EXACT []
synonym: "homologue" EXACT []
xref: http://en.wikipedia.org/wiki/Homology_(biology) "wiki"
is_a: SO:0000330 ! conserved_region
relationship: has_quality SO:0000857 ! homologous
[Term]
id: SO:0000854
name: paralogous_region
def: "A homologous_region that is paralogous to another region." [SO:ke]
comment: A term to be used in conjunction with the paralogous_to relationship.
synonym: "paralog" EXACT []
synonym: "paralogous region" EXACT []
synonym: "paralogue" EXACT []
xref: http://en.wikipedia.org/wiki/Paralog#Paralogy "wiki"
is_a: SO:0000853 ! homologous_region
relationship: has_quality SO:0000859 ! paralogous
[Term]
id: SO:0000855
name: orthologous_region
def: "A homologous_region that is orthologous to another region." [SO:ke]
comment: This term should be used in conjunction with the similarity relationships defined in SO.
synonym: "ortholog" EXACT []
synonym: "orthologous region" EXACT []
synonym: "orthologue" EXACT []
xref: http://en.wikipedia.org/wiki/Ortholog#Orthology "wiki"
is_a: SO:0000853 ! homologous_region
relationship: has_quality SO:0000858 ! orthologous
[Term]
id: SO:0000856
name: conserved
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000857
name: homologous
def: "Similarity due to common ancestry." [SO:ke]
is_a: SO:0000856 ! conserved
[Term]
id: SO:0000858
name: orthologous
def: "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke]
is_a: SO:0000857 ! homologous
[Term]
id: SO:0000859
name: paralogous
def: "An attribute describing a kind of homology where divergence occurred after a duplication event." [SO:ke]
is_a: SO:0000857 ! homologous
[Term]
id: SO:0000860
name: syntenic
def: "Attribute describing sequence regions occurring in same order on chromosome of different species." [SO:ke]
xref: http://en.wikipedia.org/wiki/Syntenic "wiki"
is_a: SO:0000856 ! conserved
[Term]
id: SO:0000861
name: capped_primary_transcript
def: "A primary transcript that is capped." [SO:xp]
synonym: "capped primary transcript" EXACT []
is_a: SO:0000185 ! primary_transcript
relationship: adjacent_to SO:0000581 ! cap
relationship: has_quality SO:0000146 ! capped
[Term]
id: SO:0000862
name: capped_mRNA
def: "An mRNA that is capped." [SO:xp]
synonym: "capped mRNA" EXACT []
is_a: SO:0000234 ! mRNA
relationship: adjacent_to SO:0000581 ! cap
relationship: has_quality SO:0000146 ! capped
[Term]
id: SO:0000863
name: mRNA_attribute
def: "An attribute describing an mRNA feature." [SO:ke]
synonym: "mRNA attribute" EXACT []
is_a: SO:0000237 ! transcript_attribute
[Term]
id: SO:0000864
name: exemplar
def: "An attribute describing a sequence is representative of a class of similar sequences." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute
[Term]
id: SO:0000865
name: frameshift
def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3." [SO:ke]
xref: http://en.wikipedia.org/wiki/Frameshift "wiki"
is_a: SO:0000863 ! mRNA_attribute
[Term]
id: SO:0000866
name: minus_1_frameshift
def: "A frameshift caused by deleting one base." [SO:ke]
synonym: "minus 1 frameshift" EXACT []
is_a: SO:0000865 ! frameshift
[Term]
id: SO:0000867
name: minus_2_frameshift
def: "A frameshift caused by deleting two bases." [SO:ke]
synonym: "minus 2 frameshift" EXACT []
is_a: SO:0000865 ! frameshift
[Term]
id: SO:0000868
name: plus_1_frameshift
def: "A frameshift caused by inserting one base." [SO:ke]
synonym: "plus 1 frameshift" EXACT []
is_a: SO:0000865 ! frameshift
[Term]
id: SO:0000869
name: plus_2_framshift
def: "A frameshift caused by inserting two bases." [SO:ke]
synonym: "plus 2 framshift" EXACT []
is_a: SO:0000865 ! frameshift
[Term]
id: SO:0000870
name: trans_spliced
def: "An attribute describing transcript sequence that is created by splicing exons from diferent genes." [SO:ke]
synonym: "trans-spliced" EXACT []
is_a: SO:0000237 ! transcript_attribute
[Term]
id: SO:0000871
name: polyadenylated_mRNA
def: "An mRNA that is polyadenylated." [SO:xp]
synonym: "polyadenylated mRNA" EXACT []
is_a: SO:0000234 ! mRNA
relationship: adjacent_to SO:0000610 ! polyA_sequence
relationship: has_quality SO:0000246 ! polyadenylated
[Term]
id: SO:0000872
name: trans_spliced_mRNA
def: "An mRNA that is trans-spliced." [SO:xp]
synonym: "trans-spliced mRNA" EXACT []
is_a: SO:0000234 ! mRNA
is_a: SO:0000479 ! trans_spliced_transcript
relationship: adjacent_to SO:0000636 ! spliced_leader_RNA
relationship: has_quality SO:0000870 ! trans_spliced
[Term]
id: SO:0000873
name: edited_transcript
def: "A transcript that is edited." [SO:ke]
synonym: "edited transcript" EXACT []
is_a: SO:0000673 ! transcript
relationship: guided_by SO:0000602 ! guide_RNA
relationship: has_part SO:0000977 ! anchor_binding_site
relationship: has_quality SO:0000116 ! edited
[Term]
id: SO:0000874
name: edited_transcript_by_A_to_I_substitution
def: "A transcript that has been edited by A to I substitution." [SO:ke]
synonym: "edited transcript by A to I substitution" EXACT []
is_a: SO:0000873 ! edited_transcript
[Term]
id: SO:0000875
name: bound_by_protein
def: "An attribute describing a sequence that is bound by a protein." [SO:ke]
synonym: "bound by protein" EXACT []
is_a: SO:0000277 ! bound_by_factor
[Term]
id: SO:0000876
name: bound_by_nucleic_acid
def: "An attribute describing a sequence that is bound by a nucleic acid." [SO:ke]
synonym: "bound by nucleic acid" EXACT []
is_a: SO:0000277 ! bound_by_factor
[Term]
id: SO:0000877
name: alternatively_spliced
def: "An attribute describing a situation where a gene may encode for more than 1 transcript." [SO:ke]
synonym: "alternatively spliced" EXACT []
is_a: SO:0000237 ! transcript_attribute
[Term]
id: SO:0000878
name: monocistronic
def: "An attribute describing a sequence that contains the code for one gene product." [SO:ke]
is_a: SO:0000237 ! transcript_attribute
[Term]
id: SO:0000879
name: dicistronic
def: "An attribute describing a sequence that contains the code for two gene products." [SO:ke]
is_a: SO:0000880 ! polycistronic
[Term]
id: SO:0000880
name: polycistronic
def: "An attribute describing a sequence that contains the code for more than one gene product." [SO:ke]
is_a: SO:0000237 ! transcript_attribute
[Term]
id: SO:0000881
name: recoded
def: "An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute
[Term]
id: SO:0000882
name: codon_redefined
def: "An attribute describing the alteration of codon meaning." [SO:ke]
synonym: "codon redefined" EXACT []
is_a: SO:0000881 ! recoded
[Term]
id: SO:0000883
name: stop_codon_read_through
def: "A stop codon redefined to be a new amino acid." [SO:ke]
synonym: "stop codon read through" EXACT []
synonym: "stop codon readthrough" RELATED []
is_a: SO:0000145 ! recoded_codon
[Term]
id: SO:0000884
name: stop_codon_redefined_as_pyrrolysine
def: "A stop codon redefined to be the new amino acid, pyrrolysine." [SO:ke]
synonym: "stop codon redefined as pyrrolysine" EXACT []
is_a: SO:0000883 ! stop_codon_read_through
[Term]
id: SO:0000885
name: stop_codon_redefined_as_selenocysteine
def: "A stop codon redefined to be the new amino acid, selenocysteine." [SO:ke]
synonym: "stop codon redefined as selenocysteine" EXACT []
is_a: SO:0000883 ! stop_codon_read_through
[Term]
id: SO:0000886
name: recoded_by_translational_bypass
def: "Recoded mRNA where a block of nucleotides is not translated." [SO:ke]
synonym: "recoded by translational bypass" EXACT []
is_a: SO:0000881 ! recoded
[Term]
id: SO:0000887
name: translationally_frameshifted
def: "Recoding by frameshifting a particular site." [SO:ke]
synonym: "translationally frameshifted" EXACT []
is_a: SO:0000881 ! recoded
[Term]
id: SO:0000888
name: maternally_imprinted_gene
def: "A gene that is maternally_imprinted." [SO:xp]
synonym: "maternally imprinted gene" EXACT []
is_a: SO:0000898 ! epigenetically_modified_gene
relationship: has_quality SO:0000135 ! maternally_imprinted
[Term]
id: SO:0000889
name: paternally_imprinted_gene
def: "A gene that is paternally imprinted." [SO:xp]
synonym: "paternally imprinted gene" EXACT []
is_a: SO:0000898 ! epigenetically_modified_gene
relationship: has_quality SO:0000136 ! paternally_imprinted
[Term]
id: SO:0000890
name: post_translationally_regulated_gene
def: "A gene that is post translationally regulated." [SO:xp]
synonym: "post translationally regulated gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000130 ! post_translationally_regulated
[Term]
id: SO:0000891
name: negatively_autoregulated_gene
def: "A gene that is negatively autoreguated." [SO:xp]
synonym: "negatively autoregulated gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000473 ! negatively_autoregulated
[Term]
id: SO:0000892
name: positively_autoregulated_gene
def: "A gene that is positively autoregulated." [SO:xp]
synonym: "positively autoregulated gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000475 ! positively_autoregulated
[Term]
id: SO:0000893
name: silenced
def: "An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level." [SO:ke]
xref: http://en.wikipedia.org/wiki/Silenced "wiki"
is_a: SO:0000126 ! transcriptionally_repressed
[Term]
id: SO:0000894
name: silenced_by_DNA_modification
def: "An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription." [SO:ke]
synonym: "silenced by DNA modification" EXACT []
is_a: SO:0000893 ! silenced
[Term]
id: SO:0000895
name: silenced_by_DNA_methylation
def: "An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription." [SO:ke]
synonym: "silenced by DNA methylation" EXACT []
is_a: SO:0000894 ! silenced_by_DNA_modification
[Term]
id: SO:0000896
name: translationally_regulated_gene
def: "A gene that is translationally regulated." [SO:xp]
synonym: "translationally regulated gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000131 ! translationally_regulated
[Term]
id: SO:0000897
name: allelically_excluded_gene
def: "A gene that is allelically_excluded." [SO:xp]
synonym: "allelically excluded gene" EXACT []
is_a: SO:0000898 ! epigenetically_modified_gene
relationship: has_quality SO:0000137 ! allelically_excluded
[Term]
id: SO:0000898
name: epigenetically_modified_gene
def: "A gene that is epigenetically modified." [SO:ke]
synonym: "epigenetically modified gene" EXACT []
is_a: SO:0000704 ! gene
is_a: SO:0001720 ! epigenetically_modified_region
relationship: has_quality SO:0000133 ! epigenetically_modified
[Term]
id: SO:0000899
name: nuclear_mitochondrial
def: "An attribute describing a nuclear pseudogene of a mitochndrial gene." [SO:ke]
synonym: "nuclear mitochondrial" EXACT []
is_obsolete: true
[Term]
id: SO:0000900
name: processed
def: "An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail." [SO:ke]
is_obsolete: true
[Term]
id: SO:0000901
name: unequally_crossed_over
def: "An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination." [SO:ke]
synonym: "unequally crossed over" EXACT []
is_obsolete: true
[Term]
id: SO:0000902
name: transgene
def: "A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another." [SO:xp]
xref: http://en.wikipedia.org/wiki/Transgene "wiki"
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000781 ! transgenic
[Term]
id: SO:0000903
name: endogenous_retroviral_sequence
synonym: "endogenous retroviral sequence" EXACT []
is_a: SO:0000751 ! proviral_location
[Term]
id: SO:0000904
name: rearranged_at_DNA_level
def: "An attribute to describe the sequence of a feature, where the DNA is rearranged." [SO:ke]
synonym: "rearranged at DNA level" EXACT []
is_a: SO:0000133 ! epigenetically_modified
[Term]
id: SO:0000905
name: status
def: "An attribute describing the status of a feature, based on the available evidence." [SO:ke]
comment: This term is the hypernym of attributes and should not be annotated to.
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000906
name: independently_known
def: "Attribute to describe a feature that is independently known - not predicted." [SO:ke]
synonym: "independently known" EXACT []
is_a: SO:0000905 ! status
[Term]
id: SO:0000907
name: supported_by_sequence_similarity
def: "An attribute to describe a feature that has been predicted using sequence similarity techniques." [SO:ke]
synonym: "supported by sequence similarity" EXACT []
is_a: SO:0000732 ! predicted
[Term]
id: SO:0000908
name: supported_by_domain_match
def: "An attribute to describe a feature that has been predicted using sequence similarity of a known domain." [SO:ke]
synonym: "supported by domain match" EXACT []
is_a: SO:0000907 ! supported_by_sequence_similarity
[Term]
id: SO:0000909
name: supported_by_EST_or_cDNA
def: "An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data." [SO:ke]
synonym: "supported by EST or cDNA" EXACT []
is_a: SO:0000907 ! supported_by_sequence_similarity
[Term]
id: SO:0000910
name: orphan
is_a: SO:0000732 ! predicted
[Term]
id: SO:0000911
name: predicted_by_ab_initio_computation
def: "An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity." [SO:ke]
synonym: "predicted by ab initio computation" EXACT []
is_a: SO:0000732 ! predicted
[Term]
id: SO:0000912
name: asx_turn
alt_id: BS:00203
def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif
[Term]
id: SO:0000913
name: cloned_cDNA_insert
def: "A clone insert made from cDNA." [SO:xp]
synonym: "cloned cDNA insert" EXACT []
is_a: SO:0000753 ! clone_insert
relationship: has_quality SO:0000756 ! cDNA
[Term]
id: SO:0000914
name: cloned_genomic_insert
def: "A clone insert made from genomic DNA." [SO:xp]
synonym: "cloned genomic insert" EXACT []
is_a: SO:0000753 ! clone_insert
relationship: has_quality SO:0000991 ! genomic_DNA
[Term]
id: SO:0000915
name: engineered_insert
def: "A clone insert that is engineered." [SO:xp]
synonym: "engineered insert" EXACT []
is_a: SO:0000753 ! clone_insert
is_a: SO:0000804 ! engineered_region
relationship: has_quality SO:0000783 ! engineered
[Term]
id: SO:0000916
name: edit_operation
synonym: "edit operation" EXACT []
is_obsolete: true
[Term]
id: SO:0000917
name: insert_U
def: "An edit to insert a U." [SO:ke]
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
synonym: "insert U" EXACT []
is_obsolete: true
[Term]
id: SO:0000918
name: delete_U
def: "An edit to delete a uridine." [SO:ke]
comment: The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa.
synonym: "delete U" EXACT []
is_obsolete: true
[Term]
id: SO:0000919
name: substitute_A_to_I
def: "An edit to substitute an I for an A." [SO:ke]
synonym: "substitute A to I" EXACT []
is_obsolete: true
[Term]
id: SO:0000920
name: insert_C
def: "An edit to insert a cytidine." [SO:ke]
synonym: "insert C" EXACT []
is_obsolete: true
[Term]
id: SO:0000921
name: insert_dinucleotide
def: "An edit to insert a dinucleotide." [SO:ke]
synonym: "insert dinucleotide" EXACT []
is_obsolete: true
[Term]
id: SO:0000922
name: substitute_C_to_U
def: "An edit to substitute an U for a C." [SO:ke]
synonym: "substitute C to U" EXACT []
is_obsolete: true
[Term]
id: SO:0000923
name: insert_G
def: "An edit to insert a G." [SO:ke]
synonym: "insert G" EXACT []
is_obsolete: true
[Term]
id: SO:0000924
name: insert_GC
def: "An edit to insert a GC dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert GC" EXACT []
is_obsolete: true
[Term]
id: SO:0000925
name: insert_GU
def: "An edit to insert a GU dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert GU" EXACT []
is_obsolete: true
[Term]
id: SO:0000926
name: insert_CU
def: "An edit to insert a CU dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert CU" EXACT []
is_obsolete: true
[Term]
id: SO:0000927
name: insert_AU
def: "An edit to insert a AU dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert AU" EXACT []
is_obsolete: true
[Term]
id: SO:0000928
name: insert_AA
def: "An edit to insert a AA dinucleotide." [SO:ke]
comment: The type of RNA editing found in the mitochondria of Myxomycota, characterized by the insertion of mono- and dinucleotides in RNAs relative to their mtDNA template and in addition, C to U base conversion. The most common mononucleotide insertion is cytidine, although a number of uridine mononucleotides are inserted at specific sites. Adenine and guanine have not been observed in mononucleotide insertions. Five different dinucleotide insertions have been observed, GC, GU, CU, AU and AA. Both mono- and dinucleotide insertions create open reading frames in mRNA and contribute to highly conserved structural features of rRNAs and tRNAs.
synonym: "insert AA" EXACT []
is_obsolete: true
[Term]
id: SO:0000929
name: edited_mRNA
def: "An mRNA that is edited." [SO:xp]
synonym: "edited mRNA" EXACT []
is_a: SO:0000234 ! mRNA
is_a: SO:0000873 ! edited_transcript
relationship: has_quality SO:0000116 ! edited
[Term]
id: SO:0000930
name: guide_RNA_region
def: "A region of guide RNA." [SO:ma]
synonym: "guide RNA region" EXACT []
is_a: SO:0000834 ! mature_transcript_region
relationship: part_of SO:0000602 ! guide_RNA
[Term]
id: SO:0000931
name: anchor_region
def: "A region of a guide_RNA that base-pairs to a target mRNA." [SO:jk]
synonym: "anchor region" EXACT []
is_a: SO:0000930 ! guide_RNA_region
[Term]
id: SO:0000932
name: pre_edited_mRNA
synonym: "pre-edited mRNA" EXACT []
is_a: SO:0000120 ! protein_coding_primary_transcript
[Term]
id: SO:0000933
name: intermediate
def: "An attribute to describe a feature between stages of processing." [SO:ke]
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000934
name: miRNA_target_site
def: "A miRNA target site is a binding site where the molecule is a micro RNA." [FB:cds]
synonym: "miRNA target site" EXACT []
is_a: SO:0001655 ! nucleotide_binding_site
[Term]
id: SO:0000935
name: edited_CDS
def: "A CDS that is edited." [SO:xp]
synonym: "edited CDS" EXACT []
is_a: SO:0000316 ! CDS
relationship: has_quality SO:0000116 ! edited
[Term]
id: SO:0000936
name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment
synonym: "vertebrate immunoglobulin T cell receptor rearranged segment" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
[Term]
id: SO:0000937
name: vertebrate_immune_system_feature
is_obsolete: true
[Term]
id: SO:0000938
name: vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster
synonym: "vertebrate immunoglobulin T cell receptor rearranged gene cluster" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
[Term]
id: SO:0000939
name: vertebrate_immune_system_gene_recombination_signal_feature
synonym: "vertebrate immune system gene recombination signal feature" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
[Term]
id: SO:0000940
name: recombinationally_rearranged
synonym: "recombinationally rearranged" EXACT []
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000941
name: recombinationally_rearranged_vertebrate_immune_system_gene
def: "A recombinationally rearranged gene of the vertebrate immune system." [SO:xp]
synonym: "recombinationally rearranged vertebrate immune system gene" EXACT []
is_a: SO:0000456 ! recombinationally_rearranged_gene
[Term]
id: SO:0000942
name: attP_site
def: "An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome." [SO:as]
synonym: "attP site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0001042 ! phage_sequence
[Term]
id: SO:0000943
name: attB_site
def: "An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site." [SO:as]
synonym: "attB site" EXACT []
is_a: SO:0000946 ! integration_excision_site
[Term]
id: SO:0000944
name: attL_site
def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site." [SO:as]
synonym: "attBP'" RELATED []
synonym: "attL site" RELATED []
is_a: SO:0000946 ! integration_excision_site
[Term]
id: SO:0000945
name: attR_site
def: "A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site." [SO:as]
synonym: "attPB'" RELATED []
synonym: "attR site" EXACT []
is_a: SO:0000946 ! integration_excision_site
[Term]
id: SO:0000946
name: integration_excision_site
def: "A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site." [SO:as]
synonym: "attachment site" RELATED []
synonym: "integration excision site" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region
[Term]
id: SO:0000947
name: resolution_site
def: "A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles." [SO:as]
synonym: "res site" EXACT []
synonym: "resolution site" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region
[Term]
id: SO:0000948
name: inversion_site
def: "A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites." [SO:ma]
comment: A target region for site-specific inversion of a DNA region and which carries binding sites for a site-specific recombinase and accessory proteins as well as the site for specific cleavage by the recombinase.
synonym: "inversion site" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region
[Term]
id: SO:0000949
name: dif_site
def: "A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase." [SO:as]
synonym: "dif site" EXACT []
is_a: SO:0000947 ! resolution_site
[Term]
id: SO:0000950
name: attC_site
def: "An attC site is a sequence required for the integration of a DNA of an integron." [SO:as]
synonym: "attC site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0000365 ! integron
[Term]
id: SO:0000951
name: eukaryotic_terminator
synonym: "eukaryotic terminator" EXACT []
is_a: SO:0000141 ! terminator
[Term]
id: SO:0000952
name: oriV
def: "An origin of vegetative replication in plasmids and phages." [SO:as]
synonym: "origin of vegetative replication" EXACT []
is_a: SO:0000296 ! origin_of_replication
[Term]
id: SO:0000953
name: oriC
def: "An origin of bacterial chromosome replication." [SO:as]
synonym: "origin of bacterial chromosome replication" EXACT []
is_a: SO:0000296 ! origin_of_replication
[Term]
id: SO:0000954
name: DNA_chromosome
def: "Structural unit composed of a self-replicating, DNA molecule." [SO:ma]
synonym: "DNA chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_quality SO:0000352 ! DNA
[Term]
id: SO:0000955
name: double_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded DNA molecule." [SO:ma]
synonym: "double stranded DNA chromosome" EXACT []
is_a: SO:0000954 ! DNA_chromosome
relationship: has_quality SO:0000985 ! double
[Term]
id: SO:0000956
name: single_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded DNA molecule." [SO:ma]
synonym: "single stranded DNA chromosome" EXACT []
is_a: SO:0000954 ! DNA_chromosome
relationship: has_quality SO:0000984 ! single
[Term]
id: SO:0000957
name: linear_double_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, linear DNA molecule." [SO:ma]
synonym: "linear double stranded DNA chromosome" EXACT []
is_a: SO:0000955 ! double_stranded_DNA_chromosome
relationship: has_quality SO:0000987 ! linear
[Term]
id: SO:0000958
name: circular_double_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, circular DNA molecule." [SO:ma]
synonym: "circular double stranded DNA chromosome" EXACT []
is_a: SO:0000955 ! double_stranded_DNA_chromosome
relationship: has_quality SO:0000988 ! circular
[Term]
id: SO:0000959
name: linear_single_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, linear DNA molecule." [SO:ma]
synonym: "linear single stranded DNA chromosome" EXACT []
is_a: SO:0000956 ! single_stranded_DNA_chromosome
relationship: has_quality SO:0000987 ! linear
[Term]
id: SO:0000960
name: circular_single_stranded_DNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
synonym: "circular single stranded DNA chromosome" EXACT []
is_a: SO:0000956 ! single_stranded_DNA_chromosome
relationship: has_quality SO:0000988 ! circular
[Term]
id: SO:0000961
name: RNA_chromosome
def: "Structural unit composed of a self-replicating, RNA molecule." [SO:ma]
synonym: "RNA chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_quality SO:0000356 ! RNA
[Term]
id: SO:0000962
name: single_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded RNA molecule." [SO:ma]
synonym: "single stranded RNA chromosome" EXACT []
is_a: SO:0000961 ! RNA_chromosome
relationship: has_quality SO:0000984 ! single
[Term]
id: SO:0000963
name: linear_single_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, linear RNA molecule." [SO:ma]
synonym: "linear single stranded RNA chromosome" EXACT []
is_a: SO:0000962 ! single_stranded_RNA_chromosome
relationship: has_quality SO:0000987 ! linear
[Term]
id: SO:0000964
name: linear_double_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, linear RNA molecule." [SO:ma]
synonym: "linear double stranded RNA chromosome" EXACT []
is_a: SO:0000965 ! double_stranded_RNA_chromosome
relationship: has_quality SO:0000987 ! linear
[Term]
id: SO:0000965
name: double_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded RNA molecule." [SO:ma]
synonym: "double stranded RNA chromosome" EXACT []
is_a: SO:0000961 ! RNA_chromosome
relationship: has_quality SO:0000985 ! double
[Term]
id: SO:0000966
name: circular_single_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, single-stranded, circular DNA molecule." [SO:ma]
synonym: "circular single stranded RNA chromosome" EXACT []
is_a: SO:0000962 ! single_stranded_RNA_chromosome
relationship: has_quality SO:0000988 ! circular
[Term]
id: SO:0000967
name: circular_double_stranded_RNA_chromosome
def: "Structural unit composed of a self-replicating, double-stranded, circular RNA molecule." [SO:ma]
synonym: "circular double stranded RNA chromosome" EXACT []
is_a: SO:0000965 ! double_stranded_RNA_chromosome
relationship: has_quality SO:0000988 ! circular
[Term]
id: SO:0000968
name: sequence_replication_mode
comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
synonym: "sequence replication mode" EXACT []
is_obsolete: true
[Term]
id: SO:0000969
name: rolling_circle
comment: This has been obsoleted as it represents a process. replaced_by: GO:0070581.
synonym: "rolling circle" EXACT []
xref: http://en.wikipedia.org/wiki/Rolling_circle "wiki"
is_obsolete: true
[Term]
id: SO:0000970
name: theta_replication
comment: This has been obsoleted as it represents a process. replaced_by: GO:0070582
synonym: "theta replication" EXACT []
is_obsolete: true
[Term]
id: SO:0000971
name: DNA_replication_mode
comment: This has been obsoleted as it represents a process. replaced_by: GO:0006260.
synonym: "DNA replication mode" EXACT []
is_obsolete: true
[Term]
id: SO:0000972
name: RNA_replication_mode
comment: This has been obsoleted as it represents a process. replaced_by: GO:0034961.
synonym: "RNA replication mode" EXACT []
is_obsolete: true
[Term]
id: SO:0000973
name: insertion_sequence
def: "A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats." [SO:as]
synonym: "insertion sequence" EXACT []
synonym: "IS" RELATED []
xref: http://en.wikipedia.org/wiki/Insertion_sequence "wiki"
is_a: SO:0000208 ! terminal_inverted_repeat_element
[Term]
id: SO:0000975
name: minicircle_gene
synonym: "minicircle gene" EXACT []
is_a: SO:0000089 ! kinetoplast_gene
relationship: part_of SO:0000980 ! minicircle
[Term]
id: SO:0000976
name: cryptic
def: "A feature_attribute describing a feature that is not manifest under normal conditions." [SO:ke]
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000977
name: anchor_binding_site
comment: Part of an edited transcript only.
synonym: "anchor binding site" EXACT []
is_a: SO:0000833 ! transcript_region
[Term]
id: SO:0000978
name: template_region
def: "A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA." [SO:jk]
synonym: "information region" EXACT []
synonym: "template region" EXACT []
is_a: SO:0000930 ! guide_RNA_region
[Term]
id: SO:0000979
name: gRNA_encoding
def: "A non-protein_coding gene that encodes a guide_RNA." [SO:ma]
synonym: "gRNA encoding" EXACT []
is_a: SO:0000011 ! non_protein_coding
[Term]
id: SO:0000980
name: minicircle
alt_id: SO:0000974
def: "A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs." [PMID:8395055]
synonym: "minicircle_chromosome" EXACT []
xref: http://en.wikipedia.org/wiki/Minicircle "wiki"
is_a: SO:0001235 ! replicon
[Term]
id: SO:0000981
name: rho_dependent_bacterial_terminator
synonym: "rho dependent bacterial terminator" EXACT []
is_a: SO:0000614 ! bacterial_terminator
[Term]
id: SO:0000982
name: rho_independent_bacterial_terminator
synonym: "rho independent bacterial terminator" EXACT []
is_a: SO:0000614 ! bacterial_terminator
[Term]
id: SO:0000983
name: strand_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
synonym: "strand attribute" EXACT []
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0000984
name: single
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000983 ! strand_attribute
[Term]
id: SO:0000985
name: double
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
is_a: SO:0000983 ! strand_attribute
[Term]
id: SO:0000986
name: topology_attribute
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
synonym: "topology attribute" EXACT []
is_a: SO:0000443 ! polymer_attribute
[Term]
id: SO:0000987
name: linear
def: "A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue." [SO:cb]
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
synonym: "two-ended" RELATED []
is_a: SO:0000986 ! topology_attribute
disjoint_from: SO:0000988 ! circular
[Term]
id: SO:0000988
name: circular
def: "A quality of a nucleotide polymer that has no terminal nucleotide residues." [SO:cb]
comment: Attributes added to describe the different kinds of replicon. SO workshop, September 2006.
synonym: "zero-ended" RELATED []
is_a: SO:0000986 ! topology_attribute
[Term]
id: SO:0000989
name: class_II_RNA
def: "Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]
synonym: "class II RNA" EXACT []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000990
name: class_I_RNA
def: "Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm." [PMID:15333696]
comment: Requested by Karen Pilcher - Dictybase. song-Term Tracker-1574577.
synonym: "class I RNA" EXACT []
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0000991
name: genomic_DNA
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "genomic DNA" EXACT []
is_a: SO:0000352 ! DNA
[Term]
id: SO:0000992
name: BAC_cloned_genomic_insert
comment: Requested by Andy Schroder - Flybase Harvard, Nov 2006.
synonym: "BAC cloned genomic insert" EXACT []
is_a: SO:0000914 ! cloned_genomic_insert
relationship: derives_from SO:0000153 ! BAC
[Term]
id: SO:0000993
name: consensus
comment: Term added Dec 06 to comply with mapping to MGED terms. It should be used to generate consensus regions. The specific cross product terms they require are consensus_region and consensus_mRNA.
is_a: SO:0000905 ! status
[Term]
id: SO:0000994
name: consensus_region
comment: DO not obsolete without considering MGED mapping.
synonym: "consensus region" EXACT []
is_a: SO:0001410 ! experimental_feature
relationship: has_quality SO:0000993 ! consensus
[Term]
id: SO:0000995
name: consensus_mRNA
comment: DO not obsolete without considering MGED mapping.
synonym: "consensus mRNA" EXACT []
is_a: SO:0000234 ! mRNA
is_a: SO:0000994 ! consensus_region
relationship: has_quality SO:0000993 ! consensus
[Term]
id: SO:0000996
name: predicted_gene
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "predicted gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000732 ! predicted
[Term]
id: SO:0000997
name: gene_fragment
comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
synonym: "gene fragment" EXACT []
is_a: SO:0000842 ! gene_component_region
relationship: has_quality SO:0000731 ! fragmentary
[Term]
id: SO:0000998
name: recursive_splice_site
def: "A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons." [http://www.genetics.org/cgi/content/full/170/2/661]
synonym: "recursive splice site" EXACT []
is_a: SO:0001419 ! cis_splice_site
[Term]
id: SO:0000999
name: BAC_end
def: "A region of sequence from the end of a BAC clone that may provide a highly specific marker." [SO:ke]
comment: Requested by Keith Boroevich December, 2006.
synonym: "BAC end" EXACT []
synonym: "BAC end sequence" EXACT []
synonym: "BES" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000153 ! BAC
[Term]
id: SO:0001000
name: rRNA_16S
def: "A large polynucleotide in Bacteria and Archaea, which functions as the small subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "16S ribosomal RNA" EXACT []
synonym: "16S rRNA" RELATED []
synonym: "16S SSU RNA" EXACT []
synonym: "rRNA 16S" EXACT []
xref: http://en.wikipedia.org/wiki/16S_ribosomal_RNA "wiki"
is_a: SO:0000650 ! small_subunit_rRNA
[Term]
id: SO:0001001
name: rRNA_23S
def: "A large polynucleotide in Bacteria and Archaea, which functions as the large subunit of the ribosome." [SO:ke]
subset: SOFA
synonym: "23S LSU rRNA" EXACT []
synonym: "23S ribosomal RNA" RELATED []
synonym: "23S rRNA" EXACT []
synonym: "rRNA 23S" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA
[Term]
id: SO:0001002
name: rRNA_25S
def: "A large polynucleotide which functions as part of the large subunit of the ribosome in some eukaryotes." [RSC:cb]
subset: SOFA
synonym: "25S LSU rRNA" EXACT []
synonym: "25S ribosomal RNA" EXACT []
synonym: "25S rRNA" EXACT []
synonym: "rRNA 25S" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA
[Term]
id: SO:0001003
name: solo_LTR
def: "A recombination product between the 2 LTR of the same element." [SO:ke]
comment: Requested by Hadi Quesneville January 2007.
synonym: "solo LTR" EXACT []
is_a: SO:0000286 ! long_terminal_repeat
[Term]
id: SO:0001004
name: low_complexity
synonym: "low complexity" EXACT []
is_a: SO:0000905 ! status
[Term]
id: SO:0001005
name: low_complexity_region
synonym: "low complexity region" EXACT []
is_a: SO:0001410 ! experimental_feature
relationship: has_quality SO:0001004 ! low_complexity
[Term]
id: SO:0001006
name: prophage
def: "A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated \"island\"." [GOC:jl]
xref: http://en.wikipedia.org/wiki/Prophage "wiki"
is_a: SO:0000113 ! proviral_region
[Term]
id: SO:0001007
name: cryptic_prophage
def: "A remnant of an integrated prophage in the host genome or an \"island\" in the host genome that includes phage like-genes." [GOC:jl]
comment: This is not cryptic in the same sense as a cryptic gene or cryptic splice site.
synonym: "cryptic prophage" EXACT []
xref: http://ecoliwiki.net/colipedia/index.php/Category:Cryptic_Prophage.w
is_a: SO:0000772 ! genomic_island
[Term]
id: SO:0001008
name: tetraloop
def: "A base-paired stem with loop of 4 non-hydrogen bonded nucleotides." [SO:ke]
xref: http://en.wikipedia.org/wiki/Tetraloop "wiki"
is_a: SO:0000313 ! stem_loop
[Term]
id: SO:0001009
name: DNA_constraint_sequence
def: "A double-stranded DNA used to control macromolecular structure and function." [http:/www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=pubmed&term=SILVERMAN+SK[au\]&dispmax=50]
synonym: "DNA constraint" EXACT []
synonym: "DNA constraint sequence" EXACT []
is_a: SO:0000442 ! ds_oligo
[Term]
id: SO:0001010
name: i_motif
def: "A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH." [PMID:9753739]
synonym: "i motif" EXACT []
synonym: "short intercalated motif" EXACT []
is_a: SO:0000142 ! DNA_sequence_secondary_structure
[Term]
id: SO:0001011
name: PNA_oligo
def: "Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [SO:ke]
synonym: "peptide nucleic acid" EXACT []
synonym: "PNA oligo" EXACT []
xref: http://en.wikipedia.org/wiki/Peptide_nucleic_acid "wiki"
is_a: SO:0001247 ! synthetic_oligo
relationship: has_quality SO:0001184 ! PNA
[Term]
id: SO:0001012
name: DNAzyme
def: "A DNA sequence with catalytic activity." [SO:cb]
comment: Added by request from Colin Batchelor.
synonym: "catalytic DNA" EXACT []
synonym: "deoxyribozyme" RELATED []
synonym: "DNA enzyme" EXACT []
is_a: SO:0000696 ! oligo
relationship: has_quality SO:0001185 ! enzymatic
[Term]
id: SO:0001013
name: MNP
def: "A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT." [http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?rs=rs2067431]
synonym: "multiple nucleotide polymorphism" RELATED []
is_a: SO:0002007 ! MNV
[Term]
id: SO:0001014
name: intron_domain
comment: Requested by Colin Batchelor, Feb 2007.
synonym: "intron domain" EXACT []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000188 ! intron
[Term]
id: SO:0001015
name: wobble_base_pair
def: "A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C." [PMID:11256617]
synonym: "wobble base pair" EXACT []
synonym: "wobble pair" EXACT []
xref: http://en.wikipedia.org/wiki/Wobble_base_pair "wiki"
is_a: SO:0000028 ! base_pair
[Term]
id: SO:0001016
name: internal_guide_sequence
def: "A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity." [SO:cb]
synonym: "IGS" EXACT []
synonym: "internal guide sequence" EXACT []
is_a: SO:0001014 ! intron_domain
relationship: part_of SO:0000587 ! group_I_intron
[Term]
id: SO:0001017
name: silent_mutation
def: "A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation." [SO:ke]
comment: Added in March 2007 in after meeting with PharmGKB. Although this term is in common usage, it is better to annotate with the most specific term possible, such as synonymous codon, intron variant etc.
synonym: "silent mutation" EXACT []
xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
xref: loinc:LA6700-4 "Silent"
is_a: SO:0001878 ! feature_variant
[Term]
id: SO:0001018
name: epitope
def: "A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells." [http://en.wikipedia.org/wiki/Epitope, SO:cb]
comment: Requested by Trish Whetzel.
xref: http://en.wikipedia.org/wiki/Epitope "wiki"
is_a: SO:0000409 ! binding_site
[Term]
id: SO:0001019
name: copy_number_variation
def: "A variation that increases or decreases the copy number of a given region." [SO:ke]
subset: SOFA
synonym: "CNP" EXACT []
synonym: "CNV" EXACT []
synonym: "copy number polymorphism" EXACT []
synonym: "copy number variation" EXACT []
xref: http://en.wikipedia.org/wiki/Copy_number_variation "wiki"
is_a: SO:0001059 ! sequence_alteration
[Term]
id: SO:0001020
name: sequence_variant_affecting_copy_number
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting copy number" EXACT []
synonym: "sequence variant affecting copy number" EXACT []
is_obsolete: true
replaced_by: SO:0001563
[Term]
id: SO:0001021
name: chromosome_breakpoint
alt_id: SO:0001242
synonym: "aberration breakpoint" EXACT []
synonym: "aberration_junction" EXACT []
synonym: "chromosome breakpoint" EXACT []
is_a: SO:0000699 ! junction
relationship: part_of SO:0000340 ! chromosome
[Term]
id: SO:0001022
name: inversion_breakpoint
def: "The point within a chromosome where an inversion begins or ends." [SO:cb]
synonym: "inversion breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint
[Term]
id: SO:0001023
name: allele
def: "An allele is one of a set of coexisting sequence variants of a gene." [SO:immuno_workshop]
synonym: "allelomorph" EXACT []
xref: http://en.wikipedia.org/wiki/Allele "wiki"
is_a: SO:0001507 ! variant_collection
relationship: variant_of SO:0000704 ! gene
[Term]
id: SO:0001024
name: haplotype
def: "A haplotype is one of a set of coexisting sequence variants of a haplotype block." [SO:immuno_workshop]
xref: http://en.wikipedia.org/wiki/Haplotype "wiki"
is_a: SO:0001507 ! variant_collection
relationship: variant_of SO:0000355 ! haplotype_block
[Term]
id: SO:0001025
name: polymorphic_sequence_variant
def: "A sequence variant that is segregating in one or more natural populations of a species." [SO:immuno_workshop]
synonym: "polymorphic sequence variant" EXACT []
is_a: SO:0001023 ! allele
[Term]
id: SO:0001026
name: genome
def: "A genome is the sum of genetic material within a cell or virion." [SO:immuno_workshop]
xref: http://en.wikipedia.org/wiki/Genome "wiki"
is_a: SO:0001260 ! sequence_collection
relationship: has_part SO:0001235 ! replicon
[Term]
id: SO:0001027
name: genotype
def: "A genotype is a variant genome, complete or incomplete." [SO:immuno_workshop]
xref: http://en.wikipedia.org/wiki/Genotype "wiki"
is_a: SO:0001507 ! variant_collection
relationship: variant_of SO:0001026 ! genome
[Term]
id: SO:0001028
name: diplotype
def: "A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known." [SO:immuno_workshop]
is_a: SO:0001507 ! variant_collection
[Term]
id: SO:0001029
name: direction_attribute
synonym: "direction attribute" EXACT []
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0001030
name: forward
def: "Forward is an attribute of the feature, where the feature is in the 5' to 3' direction." [SO:ke]
is_a: SO:0001029 ! direction_attribute
[Term]
id: SO:0001031
name: reverse
def: "Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer." [SO:ke]
is_a: SO:0001029 ! direction_attribute
[Term]
id: SO:0001032
name: mitochondrial_DNA
comment: This terms is used by MO.
synonym: "mitochondrial DNA" EXACT []
synonym: "mtDNA" EXACT []
xref: http://en.wikipedia.org/wiki/Mitochondrial_DNA "wiki"
is_a: SO:0000737 ! mitochondrial_sequence
relationship: has_quality SO:0000352 ! DNA
[Term]
id: SO:0001033
name: chloroplast_DNA
comment: This term is used by MO.
synonym: "chloroplast DNA" EXACT []
is_a: SO:0000745 ! chloroplast_sequence
relationship: has_quality SO:0000352 ! DNA
[Term]
id: SO:0001034
name: miRtron
def: "A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage." [PMID:17589500, SO:ma]
comment: Ruby et al. Nature 448:83 describe a new class of miRNAs that are derived from de-branched introns.
is_a: SO:0001014 ! intron_domain
relationship: has_part SO:0001244 ! pre_miRNA
[Term]
id: SO:0001035
name: piRNA
def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke]
synonym: "piwi-associated RNA" EXACT []
xref: http://en.wikipedia.org/wiki/PiRNA "wiki"
is_a: SO:0000655 ! ncRNA
[Term]
id: SO:0001036
name: arginyl_tRNA
def: "A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region." [SO:ke]
synonym: "arginyl tRNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0000212 ! arginine_tRNA_primary_transcript
[Term]
id: SO:0001037
name: mobile_genetic_element
def: "A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome." [PMID:14681355]
subset: SOFA
synonym: "MGE" EXACT []
synonym: "mobile genetic element" EXACT []
xref: http://en.wikipedia.org/wiki/Mobile_genetic_element "wiki"
is_a: SO:0001411 ! biological_region
relationship: has_quality SO:0001234 ! mobile
[Term]
id: SO:0001038
name: extrachromosomal_mobile_genetic_element
def: "An MGE that is not integrated into the host chromosome." [SO:ke]
synonym: "extrachromosomal mobile genetic element" EXACT []
is_a: SO:0001037 ! mobile_genetic_element
[Term]
id: SO:0001039
name: integrated_mobile_genetic_element
def: "An MGE that is integrated into the host chromosome." [SO:ke]
subset: SOFA
synonym: "integrated mobile genetic element" EXACT []
is_a: SO:0001037 ! mobile_genetic_element
[Term]
id: SO:0001040
name: integrated_plasmid
def: "A plasmid sequence that is integrated within the host chromosome." [SO:ke]
synonym: "integrated plasmid" EXACT []
is_a: SO:0001039 ! integrated_mobile_genetic_element
relationship: derives_from SO:0000155 ! plasmid
[Term]
id: SO:0001041
name: viral_sequence
def: "The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell." [SO:ke]
comment: The definitions of the children of this term were revised Decemeber 2007 after discussion on song-devel. The resulting definitions are slightly unweildy but hopefully more logically correct.
synonym: "viral sequence" EXACT []
synonym: "virus sequence" EXACT []
is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
is_a: SO:0001235 ! replicon
[Term]
id: SO:0001042
name: phage_sequence
def: "The nucleotide sequence of a virus that infects bacteria." [SO:ke]
synonym: "bacteriophage" EXACT []
synonym: "phage" EXACT []
synonym: "phage sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Bacteriophage "wiki"
is_a: SO:0001041 ! viral_sequence
[Term]
id: SO:0001043
name: attCtn_site
def: "An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon." [Phigo:at]
synonym: "attCtn site" EXACT []
is_a: SO:0000946 ! integration_excision_site
relationship: part_of SO:0000371 ! conjugative_transposon
[Term]
id: SO:0001044
name: nuclear_mt_pseudogene
def: "A nuclear pseudogene of either coding or non-coding mitochondria derived sequence." [SO:xp]
comment: Definition change requested by Val, 3172757.
synonym: "nuclear mitochondrial pseudogene" EXACT []
synonym: "nuclear mt pseudogene" EXACT []
synonym: "NUMT" EXACT []
xref: http://en.wikipedia.org/wiki/Numt "wikipedia"
is_a: SO:0001760 ! non_processed_pseudogene
[Term]
id: SO:0001045
name: cointegrated_plasmid
def: "A MGE region consisting of two fused plasmids resulting from a replicative transposition event." [phigo:at]
synonym: "cointegrated plasmid" EXACT []
synonym: "cointegrated replicon" EXACT []
is_a: SO:0001039 ! integrated_mobile_genetic_element
[Term]
id: SO:0001046
name: IRLinv_site
def: "Component of the inversion site located at the left of a region susceptible to site-specific inversion." [Phigo:at]
synonym: "IRLinv site" EXACT []
is_a: SO:0001048 ! inversion_site_part
relationship: part_of SO:0000948 ! inversion_site
[Term]
id: SO:0001047
name: IRRinv_site
def: "Component of the inversion site located at the right of a region susceptible to site-specific inversion." [Phigo:at]
synonym: "IRRinv site" EXACT []
is_a: SO:0001048 ! inversion_site_part
relationship: part_of SO:0000948 ! inversion_site
[Term]
id: SO:0001048
name: inversion_site_part
def: "A region located within an inversion site." [SO:ke]
comment: A term created to allow the parts of an inversion site have an is_a path back to the root.
synonym: "inversion site part" EXACT []
is_a: SO:0000342 ! site_specific_recombination_target_region
[Term]
id: SO:0001049
name: defective_conjugative_transposon
def: "An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon." [Phigo:ariane]
synonym: "defective conjugative transposon" EXACT []
is_a: SO:0000772 ! genomic_island
[Term]
id: SO:0001050
name: repeat_fragment
def: "A portion of a repeat, interrupted by the insertion of another element." [SO:ke]
comment: Requested by Chris Smith, and others at Flybase to help annotate nested repeats.
synonym: "repeat fragment" EXACT []
is_a: SO:0000840 ! repeat_component
relationship: part_of SO:0001649 ! nested_repeat
[Term]
id: SO:0001051
name: nested_region
is_obsolete: true
[Term]
id: SO:0001052
name: nested_repeat
is_obsolete: true
[Term]
id: SO:0001053
name: nested_transposon
is_obsolete: true
[Term]
id: SO:0001054
name: transposon_fragment
def: "A portion of a transposon, interrupted by the insertion of another element." [SO:ke]
synonym: "transposon fragment" EXACT []
is_a: SO:0000840 ! repeat_component
relationship: part_of SO:0001648 ! nested_transposon
[Term]
id: SO:0001055
name: transcriptional_cis_regulatory_region
def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative]
subset: SOFA
synonym: "transcription-control region" EXACT []
synonym: "transcriptional cis regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
[Term]
id: SO:0001056
name: splicing_regulatory_region
def: "A regulatory_region that modulates splicing." [SO:ke]
subset: SOFA
synonym: "splicing regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
[Term]
id: SO:0001057
name: enhanceosome
is_obsolete: true
[Term]
id: SO:0001058
name: promoter_targeting_sequence
def: "A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter." [SO:regcreative]
synonym: "promoter targeting sequence" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
[Term]
id: SO:0001059
name: sequence_alteration
alt_id: SO:1000004
alt_id: SO:1000007
def: "A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence." [SO:ke]
comment: Merged with partially characterized change in nucleotide sequence.
subset: SOFA
synonym: "partially characterised change in DNA sequence" NARROW []
synonym: "partially_characterised_change_in_DNA_sequence" NARROW []
synonym: "sequence alteration" EXACT []
synonym: "sequence variation" RELATED []
synonym: "uncharacterised_change_in_nucleotide_sequence" NARROW []
is_a: SO:0000110 ! sequence_feature
[Term]
id: SO:0001060
name: sequence_variant
def: "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." [SO:ke]
synonym: "ANNOVAR:unknown" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "sequence variant" EXACT []
synonym: "VAAST:sequence_variant" EXACT VAR []
[Term]
id: SO:0001061
name: propeptide_cleavage_site
alt_id: BS:00063
def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]
comment: Discrete.
subset: biosapiens
synonym: "propeptide cleavage site" EXACT []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0001062 ! propeptide
[Term]
id: SO:0001062
name: propeptide
alt_id: BS:00077
def: "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "propep" RELATED [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Propeptide "wiki"
is_a: SO:0100011 ! cleaved_peptide_region
[Term]
id: SO:0001063
name: immature_peptide_region
alt_id: BS:00129
def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]
comment: Range.
subset: biosapiens
subset: SOFA
synonym: "immature peptide region" EXACT []
is_a: SO:0000839 ! polypeptide_region
[Term]
id: SO:0001064
name: active_peptide
alt_id: BS:00076
def: "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]
comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
subset: biosapiens
synonym: "active peptide" EXACT []
synonym: "peptide" BROAD [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Peptide "wiki"
is_a: SO:0000419 ! mature_protein_region
[Term]
id: SO:0001066
name: compositionally_biased_region_of_peptide
alt_id: BS:00068
def: "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "compbias" RELATED [uniprot:feature_type]
synonym: "compositional bias" RELATED []
synonym: "compositionally biased" RELATED []
synonym: "compositionally biased region of peptide" RELATED []
synonym: "compositionally_biased_region" EXACT []
is_a: SO:0000839 ! polypeptide_region
[Term]
id: SO:0001067
name: polypeptide_motif
alt_id: BS:00032
def: "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "motif" BROAD [uniprot:feature_type]
synonym: "polypeptide motif" EXACT []
is_a: SO:0100021 ! polypeptide_conserved_region
[Term]
id: SO:0001068
name: polypeptide_repeat
alt_id: BS:00070
def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "polypeptide repeat" EXACT []
synonym: "repeat" RELATED [uniprot:feature_type]
is_a: SO:0100021 ! polypeptide_conserved_region
[Term]
id: SO:0001070
name: polypeptide_structural_region
alt_id: BS:00337
def: "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]
comment: Range.
subset: biosapiens
synonym: "polypeptide structural region" EXACT []
synonym: "structural_region" RELATED []
is_a: SO:0000839 ! polypeptide_region
[Term]
id: SO:0001071
name: membrane_structure
alt_id: BS:00128
def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "membrane structure" EXACT []
is_a: SO:0001070 ! polypeptide_structural_region
[Term]
id: SO:0001072
name: extramembrane_polypeptide_region
alt_id: BS:00154
def: "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]
comment: Range.
subset: biosapiens
synonym: "extramembrane" RELATED BS []
synonym: "extramembrane polypeptide region" EXACT []
synonym: "extramembrane_region" RELATED BS []
synonym: "topo_dom" RELATED BS [uniprot:feature_type]
is_a: SO:0001070 ! polypeptide_structural_region
relationship: part_of SO:0001071 ! membrane_structure
[Term]
id: SO:0001073
name: cytoplasmic_polypeptide_region
alt_id: BS:00145
def: "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "cytoplasm_location" EXACT BS []
synonym: "cytoplasmic polypeptide region" EXACT []
synonym: "inside" RELATED BS []
is_a: SO:0001072 ! extramembrane_polypeptide_region
[Term]
id: SO:0001074
name: non_cytoplasmic_polypeptide_region
alt_id: BS:00144
def: "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]
comment: This could be inside an organelle within the cell.
subset: biosapiens
synonym: "non cytoplasmic polypeptide region" EXACT []
synonym: "non_cytoplasm_location" EXACT BS []
synonym: "outside" RELATED BS []
is_a: SO:0001072 ! extramembrane_polypeptide_region
[Term]
id: SO:0001075
name: intramembrane_polypeptide_region
alt_id: BS:00156
def: "Polypeptide region present in the lipid bilayer." [EBIBS:GAR]
subset: biosapiens
synonym: "intramembrane" RELATED BS []
synonym: "intramembrane polypeptide region" EXACT []
is_a: SO:0001070 ! polypeptide_structural_region
relationship: part_of SO:0001071 ! membrane_structure
[Term]
id: SO:0001076
name: membrane_peptide_loop
alt_id: BS:00155
def: "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "membrane peptide loop" EXACT []
synonym: "membrane_loop" RELATED BS []
is_a: SO:0001075 ! intramembrane_polypeptide_region
[Term]
id: SO:0001077
name: transmembrane_polypeptide_region
alt_id: BS:00158
def: "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]
subset: biosapiens
synonym: "transmem" RELATED BS [uniprot:feature_type]
synonym: "transmembrane" RELATED BS []
synonym: "transmembrane polypeptide region" EXACT []
is_a: SO:0001075 ! intramembrane_polypeptide_region
[Term]
id: SO:0001078
name: polypeptide_secondary_structure
alt_id: BS:00003
def: "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]
comment: Biosapien term was secondary_structure.
subset: biosapiens
synonym: "2nary structure" RELATED BS []
synonym: "polypeptide secondary structure" EXACT []
synonym: "secondary structure" RELATED BS []
synonym: "secondary structure region" RELATED BS []
synonym: "secondary_structure" RELATED BS []
xref: http://en.wikipedia.org/wiki/Secondary_structure "wiki"
is_a: SO:0001070 ! polypeptide_structural_region
[Term]
id: SO:0001079
name: polypeptide_structural_motif
alt_id: BS:0000338
def: "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]
subset: biosapiens
synonym: "polypeptide structural motif" RELATED []
synonym: "structural_motif" RELATED BS []
xref: http://en.wikipedia.org/wiki/Structural_motif "wiki"
is_a: SO:0001070 ! polypeptide_structural_region
[Term]
id: SO:0001080
name: coiled_coil
alt_id: BS:00041
def: "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "coiled" RELATED BS [uniprot:feature_type]
synonym: "coiled coil" EXACT []
xref: http://en.wikipedia.org/wiki/Coiled_coil "wiki"
is_a: SO:0001079 ! polypeptide_structural_motif
[Term]
id: SO:0001081
name: helix_turn_helix
alt_id: BS:00147
def: "A motif comprising two helices separated by a turn." [EBIBS:GAR]
subset: biosapiens
synonym: "helix turn helix" EXACT []
synonym: "helix-turn-helix" EXACT []
synonym: "HTH" RELATED BS []
is_a: SO:0001079 ! polypeptide_structural_motif
relationship: has_part SO:0001114 ! peptide_helix
relationship: has_part SO:0001128 ! polypeptide_turn_motif
[Term]
id: SO:0001082
name: polypeptide_sequencing_information
alt_id: BS:00125
def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "sequencing_information" EXACT []
is_a: SO:0000700 ! remark
[Term]
id: SO:0001083
name: non_adjacent_residues
alt_id: BS:00182
def: "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "non consecutive" EXACT []
synonym: "non_cons" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information
[Term]
id: SO:0001084
name: non_terminal_residue
alt_id: BS:00072
def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "non terminal" EXACT []
synonym: "non_ter" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information
[Term]
id: SO:0001085
name: sequence_conflict
alt_id: BS:00069
def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "conflict" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information
[Term]
id: SO:0001086
name: sequence_uncertainty
alt_id: BS:00181
def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "unsure" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information
[Term]
id: SO:0001087
name: cross_link
alt_id: BS:00178
def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "cross link" EXACT []
synonym: "crosslink" RELATED []
is_obsolete: true
[Term]
id: SO:0001088
name: disulfide_bond
alt_id: BS:00028
def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual]
comment: 2 discreet & joined.
subset: biosapiens
synonym: "disulfid" RELATED []
synonym: "disulfide" RELATED []
synonym: "disulfide bond" RELATED []
synonym: "disulphide" EXACT []
synonym: "disulphide bond" RELATED []
is_obsolete: true
[Term]
id: SO:0001089
name: post_translationally_modified_region
alt_id: BS:00052
def: "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "mod_res" EXACT [uniprot:feature_type]
synonym: "modified residue" EXACT []
synonym: "post_translational_modification" EXACT []
xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki"
is_a: SO:0100001 ! biochemical_region_of_peptide
[Term]
id: SO:0001090
name: covalent_binding_site
alt_id: BS:00246
def: "Binding involving a covalent bond." [EBIBS:GAR]
subset: biosapiens
synonym: "covalent binding site" EXACT []
is_obsolete: true
[Term]
id: SO:0001091
name: non_covalent_binding_site
alt_id: BS:00029
def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR]
comment: Discrete.
subset: biosapiens
synonym: "binding" RELATED [uniprot:curation]
synonym: "binding site" RELATED []
synonym: "non covalent binding site" EXACT []
is_obsolete: true
[Term]
id: SO:0001092
name: polypeptide_metal_contact
alt_id: BS:00027
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]
comment: Residue is part of a binding site for a metal ion.
subset: biosapiens
synonym: "metal_binding" RELATED []
is_a: SO:0001656 ! metal_binding_site
is_a: SO:0100002 ! molecular_contact_region
[Term]
id: SO:0001093
name: protein_protein_contact
alt_id: BS:00131
def: "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]
subset: biosapiens
synonym: "protein protein contact" EXACT []
synonym: "protein protein contact site" EXACT []
synonym: "protein_protein_interaction" RELATED []
xref: http://en.wikipedia.org/wiki/Protein_protein_interaction "wiki"
is_a: SO:0000410 ! protein_binding_site
is_a: SO:0100002 ! molecular_contact_region
[Term]
id: SO:0001094
name: polypeptide_calcium_ion_contact_site
alt_id: BS:00186
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]
comment: Residue involved in contact with calcium.
subset: biosapiens
synonym: "ca bind" RELATED []
synonym: "ca_bind" EXACT BS [uniprot:feature_type]
synonym: "Ca_contact_site" EXACT []
synonym: "polypeptide calcium ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001095
name: polypeptide_cobalt_ion_contact_site
alt_id: BS:00136
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Co_contact_site" EXACT []
synonym: "polypeptide cobalt ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001096
name: polypeptide_copper_ion_contact_site
alt_id: BS:00146
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Cu_contact_site" EXACT []
synonym: "polypeptide copper ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001097
name: polypeptide_iron_ion_contact_site
alt_id: BS:00137
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Fe_contact_site" EXACT []
synonym: "polypeptide iron ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001098
name: polypeptide_magnesium_ion_contact_site
alt_id: BS:00187
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Mg_contact_site" EXACT []
synonym: "polypeptide magnesium ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001099
name: polypeptide_manganese_ion_contact_site
alt_id: BS:00140
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Mn_contact_site" EXACT []
synonym: "polypeptide manganese ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001100
name: polypeptide_molybdenum_ion_contact_site
alt_id: BS:00141
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Mo_contact_site" EXACT []
synonym: "polypeptide molybdenum ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001101
name: polypeptide_nickel_ion_contact_site
alt_id: BS:00142
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]
subset: biosapiens
synonym: "Ni_contact_site" EXACT []
synonym: "polypeptide nickel ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001102
name: polypeptide_tungsten_ion_contact_site
alt_id: BS:00143
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "polypeptide tungsten ion contact site" EXACT []
synonym: "W_contact_site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001103
name: polypeptide_zinc_ion_contact_site
alt_id: BS:00185
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "polypeptide zinc ion contact site" EXACT []
synonym: "Zn_contact_site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact
[Term]
id: SO:0001104
name: catalytic_residue
alt_id: BS:00026
def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "act_site" RELATED [uniprot:feature_type]
synonym: "active site residue" EXACT []
synonym: "catalytic residue" EXACT []
is_a: SO:0001237 ! amino_acid
relationship: part_of SO:0100019 ! polypeptide_catalytic_motif
[Term]
id: SO:0001105
name: polypeptide_ligand_contact
alt_id: BS:00157
def: "Residues which interact with a ligand." [EBIBS:GAR]
subset: biosapiens
synonym: "polypeptide ligand contact" EXACT []
synonym: "protein-ligand interaction" RELATED []
is_a: SO:0001657 ! ligand_binding_site
is_a: SO:0100002 ! molecular_contact_region
[Term]
id: SO:0001106
name: asx_motif
alt_id: BS:00202
def: "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001107
name: beta_bulge
alt_id: BS:00208
def: "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge" EXACT []
xref: http://en.wikipedia.org/wiki/Beta_bulge "wiki"
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001108
name: beta_bulge_loop
alt_id: BS:00209
def: "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge loop" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001109
name: beta_bulge_loop_five
alt_id: BS:00210
def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge loop five" EXACT []
is_a: SO:0001108 ! beta_bulge_loop
[Term]
id: SO:0001110
name: beta_bulge_loop_six
alt_id: BS:00211
def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge loop six" EXACT []
is_a: SO:0001108 ! beta_bulge_loop
[Term]
id: SO:0001111
name: beta_strand
alt_id: BS:00042
def: "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "strand" RELATED BS [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Beta_sheet "wiki"
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001112
name: antiparallel_beta_strand
alt_id: BS:0000341
def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "antiparallel beta strand" EXACT []
is_a: SO:0001111 ! beta_strand
[Term]
id: SO:0001113
name: parallel_beta_strand
alt_id: BS:00151
def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "parallel beta strand" EXACT []
is_a: SO:0001111 ! beta_strand
[Term]
id: SO:0001114
name: peptide_helix
alt_id: BS:00152
def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "helix" RELATED BS []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001115
name: left_handed_peptide_helix
alt_id: BS:00222
def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]
subset: biosapiens
synonym: "helix-l" RELATED []
synonym: "left handed helix" EXACT []
is_a: SO:0001114 ! peptide_helix
[Term]
id: SO:0001116
name: right_handed_peptide_helix
alt_id: BS:0000339
def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]
subset: biosapiens
synonym: "helix" RELATED BS []
synonym: "right handed helix" EXACT []
is_a: SO:0001114 ! peptide_helix
[Term]
id: SO:0001117
name: alpha_helix
alt_id: BS:00040
def: "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "a-helix" RELATED BS []
synonym: "helix" RELATED BS [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Alpha_helix "wiki"
is_a: SO:0001116 ! right_handed_peptide_helix
[Term]
id: SO:0001118
name: pi_helix
alt_id: BS:00153
def: "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "pi helix" EXACT []
xref: http://en.wikipedia.org/wiki/Pi_helix "wiki"
is_a: SO:0001116 ! right_handed_peptide_helix
[Term]
id: SO:0001119
name: three_ten_helix
alt_id: BS:0000340
def: "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "3(10) helix" EXACT []
synonym: "3-10 helix" EXACT []
synonym: "310 helix" EXACT []
synonym: "three ten helix" EXACT []
xref: http://en.wikipedia.org/wiki/310_helix "wiki"
is_a: SO:0001116 ! right_handed_peptide_helix
[Term]
id: SO:0001120
name: polypeptide_nest_motif
alt_id: BS:00223
def: "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest" RELATED BS []
synonym: "nest_motif" EXACT []
synonym: "polypeptide nest motif" RELATED []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001121
name: polypeptide_nest_left_right_motif
alt_id: BS:00224
def: "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest_left_right" EXACT []
synonym: "nest_lr" EXACT []
synonym: "polypeptide nest left right motif" EXACT []
is_a: SO:0001120 ! polypeptide_nest_motif
[Term]
id: SO:0001122
name: polypeptide_nest_right_left_motif
alt_id: BS:00225
def: "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest_right_left" EXACT []
synonym: "nest_rl" EXACT []
synonym: "polypeptide nest right left motif" EXACT []
is_a: SO:0001120 ! polypeptide_nest_motif
[Term]
id: SO:0001123
name: schellmann_loop
alt_id: BS:00226
def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "paperclip" RELATED BS []
synonym: "paperclip loop" RELATED []
synonym: "schellmann loop" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001124
name: schellmann_loop_seven
alt_id: BS:00228
def: "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "schellmann loop seven" EXACT []
synonym: "seven-residue schellmann loop" EXACT []
is_a: SO:0001123 ! schellmann_loop
[Term]
id: SO:0001125
name: schellmann_loop_six
alt_id: BS:00227
def: "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "schellmann loop six" EXACT []
synonym: "six-residue schellmann loop" EXACT []
is_a: SO:0001123 ! schellmann_loop
[Term]
id: SO:0001126
name: serine_threonine_motif
alt_id: BS:00229
def: "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "serine/threonine motif" EXACT []
synonym: "st motif" EXACT []
synonym: "st_motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001127
name: serine_threonine_staple_motif
alt_id: BS:00230
def: "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "serine threonine staple motif" EXACT []
synonym: "st_staple" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001128
name: polypeptide_turn_motif
alt_id: BS:00148
def: "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]
comment: Range.
subset: biosapiens
synonym: "turn" RELATED BS []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0001129
name: asx_turn_left_handed_type_one
alt_id: BS:00206
def: "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn left handed type one" EXACT []
synonym: "asx_turn_il" RELATED []
is_a: SO:0000912 ! asx_turn
[Term]
id: SO:0001130
name: asx_turn_left_handed_type_two
alt_id: BS:00204
def: "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn left handed type two" EXACT []
synonym: "asx_turn_iil" EXACT []
is_a: SO:0000912 ! asx_turn
[Term]
id: SO:0001131
name: asx_turn_right_handed_type_two
alt_id: BS:00205
def: "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn right handed type two" EXACT []
synonym: "asx_turn_iir" EXACT []
is_a: SO:0000912 ! asx_turn
[Term]
id: SO:0001132
name: asx_turn_right_handed_type_one
alt_id: BS:00207
def: "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn type right handed type one" EXACT []
synonym: "asx_turn_ir" EXACT []
is_a: SO:0000912 ! asx_turn
[Term]
id: SO:0001133
name: beta_turn
alt_id: BS:00212
def: "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif
[Term]
id: SO:0001134
name: beta_turn_left_handed_type_one
alt_id: BS:00215
def: "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn left handed type one" EXACT []
synonym: "beta_turn_il" EXACT []
synonym: "type I' beta turn" EXACT []
synonym: "type I' turn" EXACT []
is_a: SO:0001133 ! beta_turn
[Term]
id: SO:0001135
name: beta_turn_left_handed_type_two
alt_id: BS:00213
def: "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn left handed type two" EXACT []
synonym: "beta_turn_iil" EXACT []
synonym: "type II' beta turn" EXACT []
synonym: "type II' turn" EXACT []
is_a: SO:0001133 ! beta_turn
[Term]
id: SO:0001136
name: beta_turn_right_handed_type_one
alt_id: BS:00216
def: "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn right handed type one" EXACT []
synonym: "beta_turn_ir" EXACT []
synonym: "type I beta turn" EXACT []
synonym: "type I turn" EXACT []
is_a: SO:0001133 ! beta_turn
[Term]
id: SO:0001137
name: beta_turn_right_handed_type_two
alt_id: BS:00214
def: "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn right handed type two" EXACT []
synonym: "beta_turn_iir" EXACT []
synonym: "type II beta turn" EXACT []
synonym: "type II turn" EXACT []
is_a: SO:0001133 ! beta_turn
[Term]
id: SO:0001138
name: gamma_turn
alt_id: BS:00219
def: "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "gamma turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif
[Term]
id: SO:0001139
name: gamma_turn_classic
alt_id: BS:00220
def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "classic gamma turn" EXACT []
synonym: "gamma turn classic" EXACT []
is_a: SO:0001138 ! gamma_turn
[Term]
id: SO:0001140
name: gamma_turn_inverse
alt_id: BS:00221
def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "gamma turn inverse" EXACT []
is_a: SO:0001138 ! gamma_turn
[Term]
id: SO:0001141
name: serine_threonine_turn
alt_id: BS:00231
def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "serine/threonine turn" EXACT []
synonym: "st_turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif
[Term]
id: SO:0001142
name: st_turn_left_handed_type_one
alt_id: BS:00234
def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn left handed type one" EXACT []
synonym: "st_turn_il" EXACT []
is_a: SO:0001141 ! serine_threonine_turn
[Term]
id: SO:0001143
name: st_turn_left_handed_type_two
alt_id: BS:00232
def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn left handed type two" EXACT []
synonym: "st_turn_iil" EXACT []
is_a: SO:0001141 ! serine_threonine_turn
[Term]
id: SO:0001144
name: st_turn_right_handed_type_one
alt_id: BS:00235
def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn right handed type one" EXACT []
synonym: "st_turn_ir" EXACT []
is_a: SO:0001141 ! serine_threonine_turn
[Term]
id: SO:0001145
name: st_turn_right_handed_type_two
alt_id: BS:00233
def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn right handed type two" EXACT []
synonym: "st_turn_iir" EXACT []
is_a: SO:0001141 ! serine_threonine_turn
[Term]
id: SO:0001146
name: polypeptide_variation_site
alt_id: BS:00336
def: "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]
comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
subset: biosapiens
synonym: "sequence_variations" EXACT []
is_a: SO:0000839 ! polypeptide_region
[Term]
id: SO:0001147
name: natural_variant_site
alt_id: BS:00071
def: "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "natural_variant" BROAD []
synonym: "sequence variation" BROAD []
synonym: "variant" BROAD [uniprot:feature_type]
is_a: SO:0001146 ! polypeptide_variation_site
[Term]
id: SO:0001148
name: mutated_variant_site
alt_id: BS:00036
def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "mutagen" EXACT BS [uniprot:feature_type]
synonym: "mutagenesis" EXACT []
synonym: "mutated_site" EXACT []
is_a: SO:0001146 ! polypeptide_variation_site
[Term]
id: SO:0001149
name: alternate_sequence_site
alt_id: BS:00073
alt_id: SO:0001065
def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "alternative_sequence" EXACT []
synonym: "isoform" NARROW []
synonym: "sequence variation" NARROW []
synonym: "var_seq" EXACT [uniprot:feature_type]
synonym: "varsplic" NARROW []
is_a: SO:0001146 ! polypeptide_variation_site
[Term]
id: SO:0001150
name: beta_turn_type_six
def: "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]
subset: biosapiens
synonym: "beta turn type six" EXACT []
synonym: "cis-proline loop" EXACT []
synonym: "type VI beta turn" EXACT []
synonym: "type VI turn" EXACT []
is_a: SO:0001133 ! beta_turn
[Term]
id: SO:0001151
name: beta_turn_type_six_a
def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]
subset: biosapiens
synonym: "beta turn type six a" EXACT []
synonym: "type VIa beta turn" EXACT []
synonym: "type VIa turn" EXACT []
is_a: SO:0001150 ! beta_turn_type_six
[Term]
id: SO:0001152
name: beta_turn_type_six_a_one
subset: biosapiens
synonym: "beta turn type six a one" EXACT []
synonym: "type VIa1 beta turn" EXACT []
synonym: "type VIa1 turn" EXACT []
is_a: SO:0001151 ! beta_turn_type_six_a
[Term]
id: SO:0001153
name: beta_turn_type_six_a_two
subset: biosapiens
synonym: "beta turn type six a two" EXACT []
synonym: "type VIa2 beta turn" EXACT []
synonym: "type VIa2 turn" EXACT []
is_a: SO:0001151 ! beta_turn_type_six_a
[Term]
id: SO:0001154
name: beta_turn_type_six_b
def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]
subset: biosapiens
synonym: "beta turn type six b" EXACT []
synonym: "type VIb beta turn" EXACT []
synonym: "type VIb turn" EXACT []
is_a: SO:0001150 ! beta_turn_type_six
[Term]
id: SO:0001155
name: beta_turn_type_eight
def: "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]
subset: biosapiens
synonym: "beta turn type eight" EXACT []
synonym: "type VIII beta turn" EXACT []
synonym: "type VIII turn" EXACT []
is_a: SO:0001133 ! beta_turn
[Term]
id: SO:0001156
name: DRE_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW." [PMID:12537576]
comment: This consensus sequence was identified computationally using the MEME algorithm within core promoter sequences from -60 to +40, with an E value of 1.7e-183. Tends to co-occur with Motif 7. Tends to not occur with DPE motif (SO:0000015) or motif 10.
synonym: "DRE motif" EXACT []
synonym: "NDM4" EXACT []
synonym: "WATCGATW_motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001157
name: DMv4_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014)." [PMID:16827941:12537576]
synonym: "directional motif v4" EXACT []
synonym: "DMv4" EXACT []
synonym: "DMv4 motif" EXACT []
synonym: "motif 1 element" EXACT []
synonym: "promoter motif 1" EXACT []
synonym: "YGGTCACATR" NARROW []
is_a: SO:0001659 ! promoter_element
[Term]
id: SO:0001158
name: E_box_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015)." [PMID:12537576:16827941]
synonym: "AWCAGCTGWT" NARROW []
synonym: "E box motif" EXACT []
synonym: "generic E box motif" EXACT []
synonym: "NDM5" RELATED []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001159
name: DMv5_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]
synonym: "directional motif v5" EXACT []
synonym: "DMv5" EXACT []
synonym: "DMv5 motif" EXACT []
synonym: "KTYRGTATWTTT" NARROW []
synonym: "promoter motif 6" RELATED []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001160
name: DMv3_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162)." [PMID:12537576:16827941]
synonym: "directional motif v3" EXACT []
synonym: "DMv3" EXACT []
synonym: "DMv3 motif" EXACT []
synonym: "KNNCAKCNCTRNY" NARROW []
synonym: "promoter motif 7" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001161
name: DMv2_motif
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162)." [PMID:12537576:16827941]
synonym: "directional motif v2" EXACT []
synonym: "DMv2" EXACT []
synonym: "DMv2 motif" EXACT []
synonym: "MKSYGGCARCGSYSS" NARROW []
synonym: "promoter motif 8" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001162
name: MTE
def: "A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159)." [PMID:12537576:15231738, PMID:16858867]
synonym: "CSARCSSAACGS" NARROW []
synonym: "motif ten element" EXACT []
synonym: "motif_ten_element" EXACT []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
[Term]
id: SO:0001163
name: INR1_motif
def: "A promoter motif with consensus sequence TCATTCG." [PMID:16827941]
synonym: "directional motif p3" EXACT []
synonym: "directional promoter motif 3" EXACT []
synonym: "DMp3" EXACT []
synonym: "INR1 motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001164
name: DPE1_motif
def: "A promoter motif with consensus sequence CGGACGT." [PMID:16827941]
synonym: "directional motif 5" EXACT []
synonym: "directional promoter motif 5" RELATED []
synonym: "DMp5" EXACT []
synonym: "DPE1 motif" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001165
name: DMv1_motif
def: "A promoter motif with consensus sequence CARCCCT." [PMID:16827941]
synonym: "directional promoter motif v1" RELATED []
synonym: "DMv1" RELATED []
synonym: "DMv1 motif" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001166
name: GAGA_motif
def: "A non directional promoter motif with consensus sequence GAGAGCG." [PMID:16827941]
synonym: "GAGA" EXACT []
synonym: "GAGA motif" EXACT []
synonym: "NDM1" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001167
name: NDM2_motif
def: "A non directional promoter motif with consensus CGMYGYCR." [PMID:16827941]
synonym: "NDM2" EXACT []
synonym: "NDM2 motif" EXACT []
synonym: "non directional promoter motif 2" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001168
name: NDM3_motif
def: "A non directional promoter motif with consensus sequence GAAAGCT." [PMID:16827941]
synonym: "NDM3" EXACT []
synonym: "NDM3 motif" EXACT []
synonym: "non directional motif 3" EXACT []
is_a: SO:0001659 ! promoter_element
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001169
name: ds_RNA_viral_sequence
def: "A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA." [SO:ke]
synonym: "double stranded RNA virus sequence" EXACT []
synonym: "ds RNA viral sequence" EXACT []
is_a: SO:0001041 ! viral_sequence
[Term]
id: SO:0001170
name: polinton
def: "A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements." [PMID:16537396]
synonym: "maverick element" RELATED []
is_a: SO:0000208 ! terminal_inverted_repeat_element
[Term]
id: SO:0001171
name: rRNA_21S
def: "A component of the large ribosomal subunit in mitochondrial rRNA." [RSC:cb]
synonym: "21S LSU rRNA" EXACT []
synonym: "21S ribosomal RNA" EXACT []
synonym: "21S rRNA" EXACT []
synonym: "rRNA 21S" EXACT []
is_a: SO:0000651 ! large_subunit_rRNA
[Term]
id: SO:0001172
name: tRNA_region
def: "A region of a tRNA." [RSC:cb]
synonym: "tRNA region" EXACT []
is_a: SO:0000834 ! mature_transcript_region
relationship: part_of SO:0000253 ! tRNA
[Term]
id: SO:0001173
name: anticodon_loop
def: "A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3." [ISBN:0716719207]
synonym: "anti-codon loop" EXACT []
synonym: "anticodon loop" EXACT []
is_a: SO:0001172 ! tRNA_region
[Term]
id: SO:0001174
name: anticodon
def: "A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA." [RSC:cb]
synonym: "anti-codon" EXACT []
xref: http://en.wikipedia.org/wiki/Anticodon "wiki"
is_a: SO:0001172 ! tRNA_region
relationship: part_of SO:0001173 ! anticodon_loop
[Term]
id: SO:0001175
name: CCA_tail
def: "Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid." [ISBN:0716719207]
synonym: "CCA sequence" EXACT []
synonym: "CCA tail" EXACT []
is_a: SO:0001172 ! tRNA_region
[Term]
id: SO:0001176
name: DHU_loop
def: "Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues." [ISBN:071671920]
synonym: "D loop" RELATED []
synonym: "DHU loop" EXACT []
is_a: SO:0001172 ! tRNA_region
[Term]
id: SO:0001177
name: T_loop
def: "Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C." [ISBN:0716719207]
synonym: "T loop" EXACT []
synonym: "TpsiC loop" EXACT []
is_a: SO:0001172 ! tRNA_region
[Term]
id: SO:0001178
name: pyrrolysine_tRNA_primary_transcript
def: "A primary transcript encoding pyrrolysyl tRNA (SO:0000766)." [RSC:cb]
synonym: "pyrrolysine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0001179
name: U3_snoRNA
def: "U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00012]
comment: The definition is most of the old definition for snoRNA (SO:0000275).
synonym: "small nucleolar RNA U3" EXACT []
synonym: "snoRNA U3" EXACT []
synonym: "U3 small nucleolar RNA" EXACT []
synonym: "U3 snoRNA" EXACT []
xref: http://en.wikipedia.org/wiki/Small_nucleolar_RNA_U3 "wiki"
is_a: SO:0000593 ! C_D_box_snoRNA
[Term]
id: SO:0001180
name: AU_rich_element
def: "A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable." [PMID:7892223]
synonym: "ARE" RELATED []
synonym: "AU rich element" EXACT []
synonym: "AU-rich element" EXACT []
xref: http://en.wikipedia.org/wiki/AU-rich_element "wiki"
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000205 ! three_prime_UTR
[Term]
id: SO:0001181
name: Bruno_response_element
def: "A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs." [PMID:10893231]
comment: Not to be confused with BRE_motif (SO:0000016), which binds transcription factor II B.
synonym: "BRE" RELATED []
synonym: "Bruno response element" EXACT []
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000205 ! three_prime_UTR
[Term]
id: SO:0001182
name: iron_responsive_element
def: "A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins." [PMID:3198610, PMID:8710843]
synonym: "IRE" EXACT []
synonym: "iron responsive element" EXACT []
xref: http://en.wikipedia.org/wiki/Iron_responsive_element "wiki"
is_a: SO:0000837 ! UTR_region
relationship: part_of SO:0000203 ! UTR
[Term]
id: SO:0001183
name: morpholino_backbone
def: "An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages." [RSC:cb]
comment: Do not use this for feature annotation. Use morpholino_oligo (SO:0000034) instead.
synonym: "morpholino backbone" EXACT []
xref: http://en.wikipedia.org/wiki/Morpholino "wiki"
is_a: SO:0000348 ! nucleic_acid
[Term]
id: SO:0001184
name: PNA
def: "An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds." [RSC:cb]
comment: Do not use this term for feature annotation. Use PNA_oligo (SO:0001011) instead.
synonym: "peptide nucleic acid" RELATED []
is_a: SO:0000348 ! nucleic_acid
[Term]
id: SO:0001185
name: enzymatic
def: "An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein." [RSC:cb]
comment: Do not use this for feature annotation. Use enzymatic_RNA (SO:0000372) instead.
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0001186
name: ribozymic
def: "An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein." [RSC:cb]
comment: Do not use this for feature annotation. Use ribozyme (SO:0000374) instead.
is_a: SO:0001185 ! enzymatic
[Term]
id: SO:0001187
name: pseudouridylation_guide_snoRNA
def: "A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]
comment: Has RNA pseudouridylation guide activity (GO:0030558).
synonym: "pseudouridylation guide snoRNA" EXACT []
is_a: SO:0000594 ! H_ACA_box_snoRNA
[Term]
id: SO:0001188
name: LNA
def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link." [CHEBI:48010]
comment: Do not use this term for feature annotation. Use LNA_oligo (SO:0001189) instead.
is_a: SO:0000348 ! nucleic_acid
[Term]
id: SO:0001189
name: LNA_oligo
def: "An oligo composed of LNA residues." [RSC:cb]
synonym: "LNA oligo" EXACT []
synonym: "locked nucleic acid" EXACT []
xref: http://en.wikipedia.org/wiki/Locked_nucleic_acid "wiki"
is_a: SO:0001247 ! synthetic_oligo
relationship: has_quality SO:0001188 ! LNA
[Term]
id: SO:0001190
name: TNA
def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone." [CHEBI:48019]
comment: Do not use this term for feature annotation. Use TNA_oligo (SO:0001191) instead.
is_a: SO:0000348 ! nucleic_acid
[Term]
id: SO:0001191
name: TNA_oligo
def: "An oligo composed of TNA residues." [RSC:cb]
synonym: "threose nucleic acid" EXACT []
synonym: "TNA oligo" EXACT []
xref: http://en.wikipedia.org/wiki/Threose_nucleic_acid "wiki"
is_a: SO:0001247 ! synthetic_oligo
relationship: has_quality SO:0001190 ! TNA
[Term]
id: SO:0001192
name: GNA
def: "An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA." [CHEBI:48015]
comment: Do not use this term for feature annotation. Use GNA_oligo (SO:0001192) instead.
is_a: SO:0000348 ! nucleic_acid
[Term]
id: SO:0001193
name: GNA_oligo
def: "An oligo composed of GNA residues." [RSC:cb]
synonym: "glycerol nucleic acid" EXACT []
synonym: "glycol nucleic acid" EXACT []
synonym: "GNA oligo" EXACT []
xref: http://en.wikipedia.org/wiki/Glycerol_nucleic_acid "wiki"
is_a: SO:0001247 ! synthetic_oligo
relationship: has_quality SO:0001192 ! GNA
[Term]
id: SO:0001194
name: R_GNA
def: "An attribute describing a GNA sequence in the (R)-GNA enantiomer." [CHEBI:48016]
comment: Do not use this term for feature annotation. Use R_GNA_oligo (SO:0001195) instead.
synonym: "R GNA" EXACT []
is_a: SO:0001192 ! GNA
[Term]
id: SO:0001195
name: R_GNA_oligo
def: "An oligo composed of (R)-GNA residues." [RSC:cb]
synonym: "(R)-glycerol nucleic acid" EXACT []
synonym: "(R)-glycol nucleic acid" EXACT []
synonym: "R GNA oligo" EXACT []
is_a: SO:0001193 ! GNA_oligo
relationship: has_quality SO:0001194 ! R_GNA
[Term]
id: SO:0001196
name: S_GNA
def: "An attribute describing a GNA sequence in the (S)-GNA enantiomer." [CHEBI:48017]
comment: Do not use this term for feature annotation. Use S_GNA_oligo (SO:0001197) instead.
synonym: "S GNA" EXACT []
is_a: SO:0001192 ! GNA
[Term]
id: SO:0001197
name: S_GNA_oligo
def: "An oligo composed of (S)-GNA residues." [RSC:cb]
synonym: "(S)-glycerol nucleic acid" EXACT []
synonym: "(S)-glycol nucleic acid" EXACT []
synonym: "S GNA oligo" EXACT []
is_a: SO:0001193 ! GNA_oligo
relationship: has_quality SO:0001196 ! S_GNA
[Term]
id: SO:0001198
name: ds_DNA_viral_sequence
def: "A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA." [SO:ke]
synonym: "double stranded DNA virus" EXACT []
synonym: "ds DNA viral sequence" EXACT []
is_a: SO:0001041 ! viral_sequence
[Term]
id: SO:0001199
name: ss_RNA_viral_sequence
def: "A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA." [SO:ke]
synonym: "single strand RNA virus" EXACT []
synonym: "ss RNA viral sequence" EXACT []
is_a: SO:0001041 ! viral_sequence
[Term]
id: SO:0001200
name: negative_sense_ssRNA_viral_sequence
def: "A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation." [SO:ke]
synonym: "negative sense single stranded RNA virus" RELATED []
synonym: "negative sense ssRNA viral sequence" EXACT []
is_a: SO:0001199 ! ss_RNA_viral_sequence
[Term]
id: SO:0001201
name: positive_sense_ssRNA_viral_sequence
def: "A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host." [SO:ke]
synonym: "positive sense single stranded RNA virus" RELATED []
synonym: "positive sense ssRNA viral sequence" EXACT []
is_a: SO:0001199 ! ss_RNA_viral_sequence
[Term]
id: SO:0001202
name: ambisense_ssRNA_viral_sequence
def: "A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity." [SO:ke]
synonym: "ambisense single stranded RNA virus" EXACT []
synonym: "ambisense ssRNA viral sequence" EXACT []
is_a: SO:0001199 ! ss_RNA_viral_sequence
[Term]
id: SO:0001203
name: RNA_polymerase_promoter
def: "A region (DNA) to which RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "RNA polymerase promoter" EXACT []
is_a: SO:0000167 ! promoter
[Term]
id: SO:0001204
name: Phage_RNA_Polymerase_Promoter
def: "A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "Phage RNA Polymerase Promoter" EXACT []
is_a: SO:0001203 ! RNA_polymerase_promoter
[Term]
id: SO:0001205
name: SP6_RNA_Polymerase_Promoter
def: "A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "SP6 RNA Polymerase Promoter" EXACT []
is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter
[Term]
id: SO:0001206
name: T3_RNA_Polymerase_Promoter
def: "A DNA sequence to which the T3 RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "T3 RNA Polymerase Promoter" EXACT []
is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter
[Term]
id: SO:0001207
name: T7_RNA_Polymerase_Promoter
def: "A region (DNA) to which the T7 RNA polymerase binds, to begin transcription." [xenbase:jb]
synonym: "T7 RNA Polymerase Promoter" EXACT []
is_a: SO:0001204 ! Phage_RNA_Polymerase_Promoter
[Term]
id: SO:0001208
name: five_prime_EST
def: "An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]
synonym: "5' EST" EXACT []
synonym: "five prime EST" EXACT []
is_a: SO:0000345 ! EST
[Term]
id: SO:0001209
name: three_prime_EST
def: "An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs)." [http://www.ncbi.nlm.nih.gov/About/primer/est.html]
synonym: "3' EST" EXACT []
synonym: "three prime EST" EXACT []
is_a: SO:0000345 ! EST
[Term]
id: SO:0001210
name: translational_frameshift
def: "The region of mRNA (not divisible by 3 bases) that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]
synonym: "ribosomal frameshift" EXACT []
synonym: "translational frameshift" EXACT []
xref: http://en.wikipedia.org/wiki/Translational_frameshift "wiki"
is_a: SO:0000836 ! mRNA_region
[Term]
id: SO:0001211
name: plus_1_translational_frameshift
def: "The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]
synonym: "plus 1 ribosomal frameshift" EXACT []
synonym: "plus 1 translational frameshift" EXACT []
is_a: SO:0001210 ! translational_frameshift
[Term]
id: SO:0001212
name: plus_2_translational_frameshift
def: "The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different." [SO:ke]
synonym: "plus 2 ribosomal frameshift" EXACT []
synonym: "plus 2 translational frameshift" EXACT []
is_a: SO:0001210 ! translational_frameshift
[Term]
id: SO:0001213
name: group_III_intron
def: "Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile." [PMID:11377794]
comment: GO:0000374.
synonym: "group III intron" EXACT []
xref: http://en.wikipedia.org/wiki/Group_III_intron "wiki"
is_a: SO:0000588 ! autocatalytically_spliced_intron
[Term]
id: SO:0001214
name: noncoding_region_of_exon
def: "The maximal intersection of exon and UTR." [SO:ke]
comment: An exon either containing but not starting with a start codon or containing but not ending with a stop codon will be partially coding and partially non coding.
subset: SOFA
synonym: "noncoding region of exon" EXACT []
is_a: SO:0000852 ! exon_region
[Term]
id: SO:0001215
name: coding_region_of_exon
def: "The region of an exon that encodes for protein sequence." [SO:ke]
comment: An exon containing either a start or stop codon will be partially coding and partially non coding.
subset: SOFA
synonym: "coding region of exon" EXACT []
is_a: SO:0000852 ! exon_region
[Term]
id: SO:0001216
name: endonuclease_spliced_intron
def: "An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]
synonym: "endonuclease spliced intron" EXACT []
is_a: SO:0000188 ! intron
[Term]
id: SO:0001217
name: protein_coding_gene
synonym: "protein coding gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000010 ! protein_coding
[Term]
id: SO:0001218
name: transgenic_insertion
def: "An insertion that derives from another organism, via the use of recombinant DNA technology." [SO:bm]
synonym: "transgenic insertion" EXACT []
is_a: SO:0000667 ! insertion
relationship: has_quality SO:0000781 ! transgenic
[Term]
id: SO:0001219
name: retrogene
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000569 ! retrotransposed
[Term]
id: SO:0001220
name: silenced_by_RNA_interference
def: "An attribute describing an epigenetic process where a gene is inactivated by RNA interference." [RSC:cb]
comment: RNA interference is GO:0016246.
synonym: "silenced by RNA interference" EXACT []
is_a: SO:0000893 ! silenced
[Term]
id: SO:0001221
name: silenced_by_histone_modification
def: "An attribute describing an epigenetic process where a gene is inactivated by histone modification." [RSC:cb]
comment: Histone modification is GO:0016570.
synonym: "silenced by histone modification" EXACT []
is_a: SO:0000893 ! silenced
[Term]
id: SO:0001222
name: silenced_by_histone_methylation
def: "An attribute describing an epigenetic process where a gene is inactivated by histone methylation." [RSC:cb]
comment: Histone methylation is GO:0016571.
synonym: "silenced by histone methylation" EXACT []
is_a: SO:0001221 ! silenced_by_histone_modification
[Term]
id: SO:0001223
name: silenced_by_histone_deacetylation
def: "An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation." [RSC:cb]
comment: Histone deacetylation is GO:0016573.
synonym: "silenced by histone deacetylation" EXACT []
is_a: SO:0001221 ! silenced_by_histone_modification
[Term]
id: SO:0001224
name: gene_silenced_by_RNA_interference
def: "A gene that is silenced by RNA interference." [SO:xp]
synonym: "gene silenced by RNA interference" EXACT []
synonym: "RNA interference silenced gene" EXACT []
synonym: "RNAi silenced gene" EXACT []
is_a: SO:0000127 ! silenced_gene
relationship: has_quality SO:0001220 ! silenced_by_RNA_interference
[Term]
id: SO:0001225
name: gene_silenced_by_histone_modification
def: "A gene that is silenced by histone modification." [SO:xp]
synonym: "gene silenced by histone modification" EXACT []
is_a: SO:0000127 ! silenced_gene
relationship: has_quality SO:0001221 ! silenced_by_histone_modification
[Term]
id: SO:0001226
name: gene_silenced_by_histone_methylation
def: "A gene that is silenced by histone methylation." [SO:xp]
synonym: "gene silenced by histone methylation" EXACT []
is_a: SO:0001225 ! gene_silenced_by_histone_modification
relationship: has_quality SO:0001222 ! silenced_by_histone_methylation
[Term]
id: SO:0001227
name: gene_silenced_by_histone_deacetylation
def: "A gene that is silenced by histone deacetylation." [SO:xp]
synonym: "gene silenced by histone deacetylation" EXACT []
is_a: SO:0001225 ! gene_silenced_by_histone_modification
relationship: has_quality SO:0001223 ! silenced_by_histone_deacetylation
[Term]
id: SO:0001228
name: dihydrouridine
def: "A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring." [RSC:cb]
synonym: " D" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/Dihydrouridine "wiki"
xref: RNAMOD:051
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001229
name: pseudouridine
def: "A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position." [RSC:cb]
comment: The free molecule is CHEBI:17802.
synonym: " Y" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/Pseudouridine "wiki"
xref: RNAMOD:050
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001230
name: inosine
def: "A modified RNA base in which hypoxanthine is bound to the ribose ring." [http://library.med.utah.edu/RNAmods/, RSC:cb]
comment: The free molecule is CHEBI:17596.
synonym: "I" RELATED []
synonym: "RNAMOD:017" RELATED []
xref: http://en.wikipedia.org/wiki/Inosine "wiki"
is_a: SO:0000250 ! modified_RNA_base_feature
[Term]
id: SO:0001231
name: seven_methylguanine
def: "A modified RNA base in which guanine is methylated at the 7- position." [RSC:cb]
comment: The free molecule is CHEBI:2274.
synonym: "7-methylguanine" EXACT []
synonym: "seven methylguanine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature
[Term]
id: SO:0001232
name: ribothymidine
def: "A modified RNA base in which thymine is bound to the ribose ring." [RSC:cb]
comment: The free molecule is CHEBI:30832.
is_a: SO:0000250 ! modified_RNA_base_feature
[Term]
id: SO:0001233
name: methylinosine
def: "A modified RNA base in which methylhypoxanthine is bound to the ribose ring." [RSC:cb]
is_a: SO:0001274 ! modified_inosine
[Term]
id: SO:0001234
name: mobile
def: "An attribute describing a feature that has either intra-genome or intracellular mobility." [RSC:cb]
xref: http://en.wikipedia.org/wiki/Mobile "wiki"
is_a: SO:0000733 ! feature_attribute
[Term]
id: SO:0001235
name: replicon
def: "A region containing at least one unique origin of replication and a unique termination site." [ISBN:0716719207]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Replicon_(genetics) "wiki"
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0001236
name: base
def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Nucleobase "wiki"
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0001237
name: amino_acid
def: "A sequence feature that corresponds to a single amino acid residue in a polypeptide." [RSC:cb]
comment: Probably in the future this will cross reference to Chebi.
synonym: "amino acid" EXACT []
xref: http://en.wikipedia.org/wiki/Amino_acid "wiki"
is_a: SO:0001411 ! biological_region
relationship: part_of SO:0000104 ! polypeptide
[Term]
id: SO:0001238
name: major_TSS
synonym: "major transcription start site" EXACT []
synonym: "major TSS" EXACT []
is_a: SO:0000315 ! TSS
[Term]
id: SO:0001239
name: minor_TSS
synonym: "minor TSS" EXACT []
is_a: SO:0000315 ! TSS
[Term]
id: SO:0001240
name: TSS_region
def: "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw]
synonym: "TSS region" EXACT []
is_a: SO:0000842 ! gene_component_region
relationship: has_part SO:0000315 ! TSS
[Term]
id: SO:0001241
name: encodes_alternate_transcription_start_sites
synonym: "encodes alternate transcription start sites" EXACT []
is_a: SO:0000401 ! gene_attribute
[Term]
id: SO:0001243
name: miRNA_primary_transcript_region
def: "A part of an miRNA primary_transcript." [SO:ke]
synonym: "miRNA primary transcript region" EXACT []
is_a: SO:0000835 ! primary_transcript_region
[Term]
id: SO:0001244
name: pre_miRNA
def: "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke]
synonym: "pre-miRNA" EXACT []
is_a: SO:0001243 ! miRNA_primary_transcript_region
[Term]
id: SO:0001245
name: miRNA_stem
def: "The stem of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]
synonym: "miRNA stem" EXACT []
is_a: SO:0001243 ! miRNA_primary_transcript_region
relationship: part_of SO:0001244 ! pre_miRNA
[Term]
id: SO:0001246
name: miRNA_loop
def: "The loop of the hairpin loop formed by folding of the pre-miRNA." [SO:ke]
synonym: "miRNA loop" EXACT []
is_a: SO:0001243 ! miRNA_primary_transcript_region
relationship: part_of SO:0001244 ! pre_miRNA
[Term]
id: SO:0001247
name: synthetic_oligo
def: "An oligo composed of synthetic nucleotides." [SO:ke]
synonym: "synthetic oligo" EXACT []
is_a: SO:0000696 ! oligo
[Term]
id: SO:0001248
name: assembly
def: "A region of the genome of known length that is composed by ordering and aligning two or more different regions." [SO:ke]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Genome_assembly#Genome_assembly "wiki"
is_a: SO:0001410 ! experimental_feature
[Term]
id: SO:0001249
name: fragment_assembly
def: "A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths." [SO:ke]
synonym: "fragment assembly" EXACT []
synonym: "physical map" EXACT []
is_a: SO:0001248 ! assembly
[Term]
id: SO:0001250
name: fingerprint_map
def: "A fingerprint_map is a physical map composed of restriction fragments." [SO:ke]
synonym: "BACmap" EXACT []
synonym: "fingerprint map" EXACT []
synonym: "FPC" EXACT []
synonym: "FPCmap" EXACT []
synonym: "restriction map" EXACT []
is_a: SO:0001249 ! fragment_assembly
relationship: has_part SO:0000412 ! restriction_fragment
[Term]
id: SO:0001251
name: STS_map
def: "An STS map is a physical map organized by the unique STS landmarks." [SO:ke]
synonym: "STS map" EXACT []
is_a: SO:0001249 ! fragment_assembly
relationship: has_part SO:0000331 ! STS
[Term]
id: SO:0001252
name: RH_map
def: "A radiation hybrid map is a physical map." [SO:ke]
synonym: "radiation hybrid map" EXACT []
synonym: "RH map" EXACT []
is_a: SO:0001249 ! fragment_assembly
relationship: has_part SO:0000331 ! STS
[Term]
id: SO:0001253
name: sonicate_fragment
def: "A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments." [SO:ke]
synonym: "sonicate fragment" EXACT []
is_a: SO:0000143 ! assembly_component
[Term]
id: SO:0001254
name: polyploid
def: "A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number." [SO:ke]
xref: http://en.wikipedia.org/wiki/Polyploid "wiki"
is_a: SO:1000182 ! chromosome_number_variation
[Term]
id: SO:0001255
name: autopolyploid
def: "A polyploid where the multiple chromosome set was derived from the same organism." [SO:ke]
xref: http://en.wikipedia.org/wiki/Autopolyploid "wiki"
is_a: SO:0001254 ! polyploid
[Term]
id: SO:0001256
name: allopolyploid
def: "A polyploid where the multiple chromosome set was derived from a different organism." [SO:ke]
xref: http://en.wikipedia.org/wiki/Allopolyploid "wiki"
is_a: SO:0001254 ! polyploid
[Term]
id: SO:0001257
name: homing_endonuclease_binding_site
def: "The binding site (recognition site) of a homing endonuclease. The binding site is typically large." [SO:ke]
synonym: "homing endonuclease binding site" EXACT []
is_a: SO:0000059 ! nuclease_binding_site
[Term]
id: SO:0001258
name: octamer_motif
def: "A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors." [GOC:dh, PMID:3095662]
comment: Nature. 1986 Oct 16-22;323(6089):640-3.
synonym: "octamer motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000170 ! RNApol_II_promoter
[Term]
id: SO:0001259
name: apicoplast_chromosome
def: "A chromosome originating in an apicoplast." [SO:xp]
synonym: "apicoplast chromosome" EXACT []
is_a: SO:0000340 ! chromosome
relationship: has_origin SO:0000743 ! apicoplast_sequence
[Term]
id: SO:0001260
name: sequence_collection
def: "A collection of discontinuous sequences." [SO:ke]
synonym: "sequence collection" EXACT []
[Term]
id: SO:0001261
name: overlapping_feature_set
def: "A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature." [SO:ke]
comment: This feature was requested by Nicole, tracker id 1911479. It is required to gather evidence together for annotation. An example would be overlapping ESTs that support an mRNA.
synonym: "overlapping feature set" EXACT []
is_a: SO:0000703 ! experimental_result_region
[Term]
id: SO:0001262
name: overlapping_EST_set
def: "A continous experimental result region extending the length of multiple overlapping EST's." [SO:ke]
synonym: "overlapping EST set" EXACT []
is_a: SO:0001261 ! overlapping_feature_set
relationship: has_part SO:0000345 ! EST
[Term]
id: SO:0001263
name: ncRNA_gene
synonym: "ncRNA gen" EXACT []
synonym: "ncRNA gene" EXACT []
synonym: "non-coding RNA gene" RELATED []
is_a: SO:0000704 ! gene
[Term]
id: SO:0001264
name: gRNA_gene
synonym: "gRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
relationship: has_quality SO:0000979 ! gRNA_encoding
[Term]
id: SO:0001265
name: miRNA_gene
alt_id: SO:0001270
synonym: "miRNA gene" EXACT []
synonym: "stRNA gene" EXACT []
synonym: "stRNA_gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
relationship: has_quality SO:0000571 ! miRNA_encoding
relationship: has_quality SO:0000656 ! stRNA_encoding
[Term]
id: SO:0001266
name: scRNA_gene
synonym: "scRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
relationship: has_quality SO:0000575 ! scRNA_encoding
[Term]
id: SO:0001267
name: snoRNA_gene
synonym: "snoRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
relationship: has_quality SO:0000578 ! snoRNA_encoding
[Term]
id: SO:0001268
name: snRNA_gene
synonym: "snRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
relationship: has_quality SO:0001263 ! ncRNA_gene
[Term]
id: SO:0001269
name: SRP_RNA_gene
synonym: "SRP RNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
relationship: has_quality SO:0000642 ! SRP_RNA_encoding
[Term]
id: SO:0001271
name: tmRNA_gene
synonym: "tmRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
relationship: has_quality SO:0000659 ! tmRNA_encoding
[Term]
id: SO:0001272
name: tRNA_gene
synonym: "tRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
relationship: has_quality SO:0000663 ! tRNA_encoding
[Term]
id: SO:0001273
name: modified_adenosine
def: "A modified adenine is an adenine base feature that has been altered." [SO:ke]
synonym: "modified adenosine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature
[Term]
id: SO:0001274
name: modified_inosine
def: "A modified inosine is an inosine base feature that has been altered." [SO:ke]
synonym: "modified inosine" EXACT []
is_a: SO:0001230 ! inosine
[Term]
id: SO:0001275
name: modified_cytidine
def: "A modified cytidine is a cytidine base feature which has been altered." [SO:ke]
synonym: "modified cytidine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature
[Term]
id: SO:0001276
name: modified_guanosine
synonym: "modified guanosine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature
[Term]
id: SO:0001277
name: modified_uridine
synonym: "modified uridine" EXACT []
is_a: SO:0000250 ! modified_RNA_base_feature
[Term]
id: SO:0001278
name: one_methylinosine
def: "1-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methylinosine" EXACT []
synonym: "m1I" EXACT RNAMOD []
synonym: "one methylinosine" EXACT []
xref: RNAMOD:018
is_a: SO:0001274 ! modified_inosine
[Term]
id: SO:0001279
name: one_two_prime_O_dimethylinosine
def: "1,2'-O-dimethylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
synonym: "1,2'-O-dimethylinosine" EXACT []
synonym: "m'Im" EXACT RNAMOD []
synonym: "one two prime O dimethylinosine" EXACT []
xref: RNAMOD:019
is_a: SO:0001274 ! modified_inosine
[Term]
id: SO:0001280
name: two_prime_O_methylinosine
def: "2'-O-methylinosine is a modified inosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methylinosine" EXACT []
synonym: "Im" EXACT RNAMOD []
synonym: "two prime O methylinosine" EXACT []
xref: RNAMOD:081
is_a: SO:0001274 ! modified_inosine
[Term]
id: SO:0001281
name: three_methylcytidine
def: "3-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "3-methylcytidine" EXACT []
synonym: "m3C" EXACT RNAMOD []
synonym: "three methylcytidine" EXACT []
xref: RNAMOD:020
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001282
name: five_methylcytidine
def: "5-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methylcytidine" EXACT []
synonym: "five methylcytidine" EXACT []
synonym: "m5C" EXACT RNAMOD []
xref: RNAMOD:021
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001283
name: two_prime_O_methylcytidine
def: "2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methylcytidine" EXACT []
synonym: "Cm" EXACT RNAMOD []
synonym: "two prime O methylcytidine" EXACT []
xref: RNAMOD:022
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001284
name: two_thiocytidine
def: "2-thiocytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-thiocytidine" EXACT []
synonym: "s2C" EXACT RNAMOD []
synonym: "two thiocytidine" EXACT []
xref: RNAMOD:023
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001285
name: N4_acetylcytidine
def: "N4-acetylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "ac4C" EXACT RNAMOD []
synonym: "N4 acetylcytidine" EXACT []
synonym: "N4-acetylcytidine" EXACT []
xref: RNAMOD:024
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001286
name: five_formylcytidine
def: "5-formylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5-formylcytidine" EXACT []
synonym: "f5C" EXACT RNAMOD []
synonym: "five formylcytidine" EXACT []
xref: RNAMOD:025
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001287
name: five_two_prime_O_dimethylcytidine
def: "5,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5,2'-O-dimethylcytidine" EXACT []
synonym: "five two prime O dimethylcytidine" EXACT []
synonym: "m5Cm" EXACT RNAMOD []
xref: RNAMOD:026
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001288
name: N4_acetyl_2_prime_O_methylcytidine
def: "N4-acetyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "ac4Cm" EXACT RNAMOD []
synonym: "N4 acetyl 2 prime O methylcytidine" EXACT []
synonym: "N4-acetyl-2'-O-methylcytidine" EXACT []
xref: RNAMOD:027
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001289
name: lysidine
def: "Lysidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "k2C" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/Lysidine "wiki"
xref: RNAMOD:028
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001290
name: N4_methylcytidine
def: "N4-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "m4C" EXACT RNAMOD []
synonym: "N4 methylcytidine" EXACT []
synonym: "N4-methylcytidine" EXACT []
xref: RNAMOD:082
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001291
name: N4_2_prime_O_dimethylcytidine
def: "N4,2'-O-dimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "m4Cm" EXACT RNAMOD []
synonym: "N4 2 prime O dimethylcytidine" EXACT []
synonym: "N4,2'-O-dimethylcytidine" EXACT []
xref: RNAMOD:083
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001292
name: five_hydroxymethylcytidine
def: "5-hydroxymethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5-hydroxymethylcytidine" EXACT []
synonym: "five hydroxymethylcytidine" EXACT []
synonym: "hm5C" EXACT RNAMOD []
xref: RNAMOD:084
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001293
name: five_formyl_two_prime_O_methylcytidine
def: "5-formyl-2'-O-methylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "5-formyl-2'-O-methylcytidine" EXACT []
synonym: "f5Cm" EXACT RNAMOD []
synonym: "five formyl two prime O methylcytidine" EXACT []
xref: RNAMOD:095
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001294
name: N4_N4_2_prime_O_trimethylcytidine
def: "N4_N4_2_prime_O_trimethylcytidine is a modified cytidine." [http://library.med.utah.edu/RNAmods/]
synonym: "m42Cm" EXACT RNAMOD []
synonym: "N4,N4,2'-O-trimethylcytidine" EXACT []
xref: RNAMOD:107
is_a: SO:0001275 ! modified_cytidine
[Term]
id: SO:0001295
name: one_methyladenosine
def: "1_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methyladenosine" EXACT []
synonym: "m1A" EXACT RNAMOD []
synonym: "one methyladenosine" EXACT []
xref: RNAMOD:001
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001296
name: two_methyladenosine
def: "2_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methyladenosine" EXACT []
synonym: "m2A" EXACT RNAMOD []
synonym: "two methyladenosine" EXACT []
xref: RNAMOD:002
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001297
name: N6_methyladenosine
def: "N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m6A" EXACT RNAMOD []
synonym: "N6 methyladenosine" EXACT []
synonym: "N6-methyladenosine" EXACT []
xref: RNAMOD:003
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001298
name: two_prime_O_methyladenosine
def: "2prime_O_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methyladenosine" EXACT []
synonym: "Am" EXACT RNAMOD []
synonym: "two prime O methyladenosine" EXACT []
xref: RNAMOD:004
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001299
name: two_methylthio_N6_methyladenosine
def: "2_methylthio_N6_methyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-methyladenosine" EXACT []
synonym: "ms2m6A" EXACT RNAMOD []
synonym: "two methylthio N6 methyladenosine" EXACT []
xref: RNAMOD:005
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001300
name: N6_isopentenyladenosine
def: "N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "i6A" EXACT RNAMOD []
synonym: "N6 isopentenyladenosine" EXACT []
synonym: "N6-isopentenyladenosine" EXACT []
xref: RNAMOD:006
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001301
name: two_methylthio_N6_isopentenyladenosine
def: "2_methylthio_N6_isopentenyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-isopentenyladenosine" EXACT []
synonym: "ms2i6A" EXACT RNAMOD []
synonym: "two methylthio N6 isopentenyladenosine" EXACT []
xref: RNAMOD:007
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001302
name: N6_cis_hydroxyisopentenyl_adenosine
def: "N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "io6A" EXACT RNAMOD []
synonym: "N6 cis hydroxyisopentenyl adenosine" EXACT []
synonym: "N6-(cis-hydroxyisopentenyl)adenosine" EXACT []
xref: RNAMOD:008
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001303
name: two_methylthio_N6_cis_hydroxyisopentenyl_adenosine
def: "2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-(cis-hydroxyisopentenyl) adenosine" EXACT []
synonym: "ms2io6A" EXACT RNAMOD []
synonym: "two methylthio N6 cis hydroxyisopentenyl adenosine" EXACT []
xref: RNAMOD:009
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001304
name: N6_glycinylcarbamoyladenosine
def: "N6_glycinylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "g6A" EXACT RNAMOD []
synonym: "N6 glycinylcarbamoyladenosine" EXACT []
synonym: "N6-glycinylcarbamoyladenosine" EXACT []
xref: RNAMOD:010
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001305
name: N6_threonylcarbamoyladenosine
def: "N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "N6 threonylcarbamoyladenosine" EXACT []
synonym: "N6-threonylcarbamoyladenosine" EXACT []
synonym: "t6A" EXACT RNAMOD []
xref: RNAMOD:011
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001306
name: two_methylthio_N6_threonyl_carbamoyladenosine
def: "2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-threonyl carbamoyladenosine" EXACT []
synonym: "ms2t6A" EXACT RNAMOD []
synonym: "two methylthio N6 threonyl carbamoyladenosine" EXACT []
xref: RNAMOD:012
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001307
name: N6_methyl_N6_threonylcarbamoyladenosine
def: "N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m6t6A" EXACT RNAMOD []
synonym: "N6 methyl N6 threonylcarbamoyladenosine" EXACT []
synonym: "N6-methyl-N6-threonylcarbamoyladenosine" EXACT []
xref: RNAMOD:013
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001308
name: N6_hydroxynorvalylcarbamoyladenosine
def: "N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "hn6A" EXACT RNAMOD []
synonym: "N6 hydroxynorvalylcarbamoyladenosine" EXACT []
synonym: "N6-hydroxynorvalylcarbamoyladenosine" EXACT []
xref: RNAMOD:014
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001309
name: two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine
def: "2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2-methylthio-N6-hydroxynorvalyl carbamoyladenosine" EXACT []
synonym: "ms2hn6A" EXACT RNAMOD []
synonym: "two methylthio N6 hydroxynorvalyl carbamoyladenosine" EXACT []
xref: RNAMOD:015
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001310
name: two_prime_O_ribosyladenosine_phosphate
def: "2prime_O_ribosyladenosine_phosphate is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-ribosyladenosine (phosphate)" EXACT []
synonym: "Ar(p)" EXACT RNAMOD []
synonym: "two prime O ribosyladenosine phosphate" EXACT []
xref: RNAMOD:016
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001311
name: N6_N6_dimethyladenosine
def: "N6_N6_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m62A" EXACT RNAMOD []
synonym: "N6,N6-dimethyladenosine" EXACT []
xref: RNAMOD:080
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001312
name: N6_2_prime_O_dimethyladenosine
def: "N6_2prime_O_dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m6Am" EXACT RNAMOD []
synonym: "N6 2 prime O dimethyladenosine" EXACT []
synonym: "N6,2'-O-dimethyladenosine" EXACT []
xref: RNAMOD:088
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001313
name: N6_N6_2_prime_O_trimethyladenosine
def: "N6_N6_2prime_O_trimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "m62Am" EXACT RNAMOD []
synonym: "N6,N6,2'-O-trimethyladenosine" EXACT []
xref: RNAMOD:089
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001314
name: one_two_prime_O_dimethyladenosine
def: "1,2'-O-dimethyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "1,2'-O-dimethyladenosine" EXACT []
synonym: "m1Am" EXACT RNAMOD []
synonym: "one two prime O dimethyladenosine" EXACT []
xref: RNAMOD:097
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001315
name: N6_acetyladenosine
def: "N6_acetyladenosine is a modified adenosine." [http://library.med.utah.edu/RNAmods/]
synonym: "ac6A" EXACT RNAMOD []
synonym: "N6 acetyladenosine" EXACT []
synonym: "N6-acetyladenosine" EXACT []
xref: RNAMOD:102
is_a: SO:0001273 ! modified_adenosine
[Term]
id: SO:0001316
name: seven_deazaguanosine
def: "7-deazaguanosine is a modified guanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "7-deazaguanosine" RELATED []
synonym: "seven deazaguanosine" EXACT []
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001317
name: queuosine
def: "Queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: " Q" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/Queuosine "wiki"
xref: RNAMOD:043
is_a: SO:0001316 ! seven_deazaguanosine
[Term]
id: SO:0001318
name: epoxyqueuosine
def: "Epoxyqueuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "eQ" EXACT RNAMOD []
xref: RNAMOD:044
is_a: SO:0001316 ! seven_deazaguanosine
[Term]
id: SO:0001319
name: galactosyl_queuosine
def: "Galactosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "galactosyl queuosine" EXACT []
synonym: "galactosyl-queuosine" EXACT []
synonym: "galQ" EXACT RNAMOD []
xref: RNAMOD:045
is_a: SO:0001316 ! seven_deazaguanosine
[Term]
id: SO:0001320
name: mannosyl_queuosine
def: "Mannosyl_queuosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "mannosyl queuosine" EXACT []
synonym: "mannosyl-queuosine" EXACT []
synonym: "manQ" EXACT RNAMOD []
xref: RNAMOD:046
is_a: SO:0001316 ! seven_deazaguanosine
[Term]
id: SO:0001321
name: seven_cyano_seven_deazaguanosine
def: "7_cyano_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "7-cyano-7-deazaguanosine" EXACT []
synonym: "preQ0" EXACT RNAMOD []
synonym: "seven cyano seven deazaguanosine" EXACT []
xref: RNAMOD:047
is_a: SO:0001316 ! seven_deazaguanosine
[Term]
id: SO:0001322
name: seven_aminomethyl_seven_deazaguanosine
def: "7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "7-aminomethyl-7-deazaguanosine" EXACT []
synonym: "preQ1" EXACT RNAMOD []
synonym: "seven aminomethyl seven deazaguanosine" EXACT []
xref: RNAMOD:048
is_a: SO:0001316 ! seven_deazaguanosine
[Term]
id: SO:0001323
name: archaeosine
def: "Archaeosine is a modified 7-deazoguanosine." [http://library.med.utah.edu/RNAmods/]
synonym: "G+" EXACT RNAMOD []
xref: RNAMOD:049
is_a: SO:0001316 ! seven_deazaguanosine
[Term]
id: SO:0001324
name: one_methylguanosine
def: "1_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methylguanosine" EXACT []
synonym: "m1G" EXACT RNAMOD []
synonym: "one methylguanosine" EXACT []
xref: RNAMOD:029
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001325
name: N2_methylguanosine
def: "N2_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2G" EXACT RNAMOD []
synonym: "N2 methylguanosine" EXACT []
synonym: "N2-methylguanosine" EXACT []
xref: RNAMOD:030
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001326
name: seven_methylguanosine
def: "7_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "7-methylguanosine" EXACT []
synonym: "m7G" EXACT RNAMOD []
synonym: "seven methylguanosine" EXACT []
xref: RNAMOD:031
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001327
name: two_prime_O_methylguanosine
def: "2prime_O_methylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methylguanosine" EXACT []
synonym: "Gm" EXACT RNAMOD []
synonym: "two prime O methylguanosine" EXACT []
xref: RNAMOD:032
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001328
name: N2_N2_dimethylguanosine
def: "N2_N2_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m22G" EXACT RNAMOD []
synonym: "N2,N2-dimethylguanosine" EXACT []
xref: RNAMOD:033
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001329
name: N2_2_prime_O_dimethylguanosine
def: "N2_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2Gm" EXACT RNAMOD []
synonym: "N2 2 prime O dimethylguanosine" EXACT []
synonym: "N2,2'-O-dimethylguanosine" EXACT []
xref: RNAMOD:034
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001330
name: N2_N2_2_prime_O_trimethylguanosine
def: "N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m22Gmv" EXACT RNAMOD []
synonym: "N2,N2,2'-O-trimethylguanosine" EXACT []
xref: RNAMOD:035
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001331
name: two_prime_O_ribosylguanosine_phosphate
def: "2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-ribosylguanosine (phosphate)" EXACT []
synonym: "Gr(p)" EXACT RNAMOD []
synonym: "two prime O ribosylguanosine phosphate" EXACT []
xref: RNAMOD:036
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001332
name: wybutosine
def: "Wybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "yW" EXACT RNAMOD []
xref: RNAMOD:037
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001333
name: peroxywybutosine
def: "Peroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "o2yW" EXACT RNAMOD []
xref: RNAMOD:038
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001334
name: hydroxywybutosine
def: "Hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "OHyW" EXACT RNAMOD []
xref: RNAMOD:039
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001335
name: undermodified_hydroxywybutosine
def: "Undermodified_hydroxywybutosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "OHyW*" EXACT RNAMOD []
synonym: "undermodified hydroxywybutosine" EXACT []
xref: RNAMOD:040
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001336
name: wyosine
def: "Wyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "IMG" EXACT RNAMOD []
xref: RNAMOD:041
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001337
name: methylwyosine
def: "Methylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "mimG" EXACT RNAMOD []
xref: RNAMOD:042
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001338
name: N2_7_dimethylguanosine
def: "N2_7_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2,7G" EXACT RNAMOD []
synonym: "N2 7 dimethylguanosine" EXACT []
synonym: "N2,7-dimethylguanosine" EXACT []
xref: RNAMOD:090
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001339
name: N2_N2_7_trimethylguanosine
def: "N2_N2_7_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2,2,7G" EXACT RNAMOD []
synonym: "N2,N2,7-trimethylguanosine" EXACT []
xref: RNAMOD:091
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001340
name: one_two_prime_O_dimethylguanosine
def: "1_2prime_O_dimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "1,2'-O-dimethylguanosine" EXACT []
synonym: "m1Gm" EXACT RNAMOD []
synonym: "one two prime O dimethylguanosine" EXACT []
xref: RNAMOD:096
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001341
name: four_demethylwyosine
def: "4_demethylwyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "4-demethylwyosine" EXACT []
synonym: "four demethylwyosine" EXACT []
synonym: "imG-14" EXACT RNAMOD []
xref: RNAMOD:100
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001342
name: isowyosine
def: "Isowyosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "imG2" EXACT RNAMOD []
xref: RNAMOD:101
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001343
name: N2_7_2prirme_O_trimethylguanosine
def: "N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "m2,7Gm" EXACT RNAMOD []
synonym: "N2 7 2prirme O trimethylguanosine" EXACT []
synonym: "N2,7,2'-O-trimethylguanosine" EXACT []
xref: RNAMOD:106
is_a: SO:0001276 ! modified_guanosine
[Term]
id: SO:0001344
name: five_methyluridine
def: "5_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methyluridine" EXACT []
synonym: "five methyluridine" EXACT []
synonym: "m5U" EXACT RNAMOD []
xref: http://en.wikipedia.org/wiki/5-methyluridine "wiki"
xref: RNAMOD:052
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001345
name: two_prime_O_methyluridine
def: "2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methyluridine" EXACT []
synonym: "two prime O methyluridine" EXACT []
synonym: "Um" EXACT RNAMOD []
xref: RNAMOD:053
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001346
name: five_two_prime_O_dimethyluridine
def: "5_2_prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5,2'-O-dimethyluridine" EXACT []
synonym: "five two prime O dimethyluridine" EXACT []
synonym: "m5Um" EXACT RNAMOD []
xref: RNAMOD:054
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001347
name: one_methylpseudouridine
def: "1_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methylpseudouridine" EXACT []
synonym: "m1Y" EXACT RNAMOD []
synonym: "one methylpseudouridine" EXACT []
xref: RNAMOD:055
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001348
name: two_prime_O_methylpseudouridine
def: "2prime_O_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2'-O-methylpseudouridine" EXACT []
synonym: "two prime O methylpseudouridine" EXACT []
synonym: "Ym" EXACT RNAMOD []
xref: RNAMOD:056
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001349
name: two_thiouridine
def: "2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2-thiouridine" EXACT []
synonym: "s2U" EXACT RNAMOD []
synonym: "two thiouridine" EXACT []
xref: RNAMOD:057
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001350
name: four_thiouridine
def: "4_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "4-thiouridine" EXACT []
synonym: "four thiouridine" EXACT []
synonym: "s4U" EXACT RNAMOD []
xref: RNAMOD:058
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001351
name: five_methyl_2_thiouridine
def: "5_methyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methyl-2-thiouridine" EXACT []
synonym: "five methyl 2 thiouridine" EXACT []
synonym: "m5s2U" EXACT RNAMOD []
xref: RNAMOD:059
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001352
name: two_thio_two_prime_O_methyluridine
def: "2_thio_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "2-thio-2'-O-methyluridine" EXACT []
synonym: "s2Um" EXACT RNAMOD []
synonym: "two thio two prime O methyluridine" EXACT []
xref: RNAMOD:060
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001353
name: three_three_amino_three_carboxypropyl_uridine
def: "3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "3-(3-amino-3-carboxypropyl)uridine" EXACT []
synonym: "acp3U" EXACT RNAMOD []
xref: RNAMOD:061
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001354
name: five_hydroxyuridine
def: "5_hydroxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-hydroxyuridine" EXACT []
synonym: "five hydroxyuridine" EXACT []
synonym: "ho5U" EXACT RNAMOD []
xref: RNAMOD:060
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001355
name: five_methoxyuridine
def: "5_methoxyuridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methoxyuridine" EXACT []
synonym: "five methoxyuridine" EXACT []
synonym: "mo5U" EXACT RNAMOD []
xref: RNAMOD:063
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001356
name: uridine_five_oxyacetic_acid
def: "Uridine_5_oxyacetic_acid is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "cmo5U" EXACT RNAMOD []
synonym: "uridine 5-oxyacetic acid" EXACT []
synonym: "uridine five oxyacetic acid" EXACT []
xref: RNAMOD:064
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001357
name: uridine_five_oxyacetic_acid_methyl_ester
def: "Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "mcmo5U" EXACT RNAMOD []
synonym: "uridine 5-oxyacetic acid methyl ester" EXACT []
synonym: "uridine five oxyacetic acid methyl ester" EXACT []
xref: RNAMOD:065
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001358
name: five_carboxyhydroxymethyl_uridine
def: "5_carboxyhydroxymethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(carboxyhydroxymethyl)uridine" EXACT []
synonym: "chm5U" EXACT RNAMOD []
synonym: "five carboxyhydroxymethyl uridine" EXACT []
xref: RNAMOD:066
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001359
name: five_carboxyhydroxymethyl_uridine_methyl_ester
def: "5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(carboxyhydroxymethyl)uridine methyl ester" EXACT []
synonym: "five carboxyhydroxymethyl uridine methyl ester" EXACT []
synonym: "mchm5U" EXACT RNAMOD []
xref: RNAMOD:067
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001360
name: five_methoxycarbonylmethyluridine
def: "Five_methoxycarbonylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methoxycarbonylmethyluridine" EXACT []
synonym: "five methoxycarbonylmethyluridine" EXACT []
synonym: "mcm5U" EXACT RNAMOD []
xref: RNAMOD:068
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001361
name: five_methoxycarbonylmethyl_two_prime_O_methyluridine
def: "Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methoxycarbonylmethyl-2'-O-methyluridine" EXACT []
synonym: "five methoxycarbonylmethyl two prime O methyluridine" EXACT []
synonym: "mcm5Um" EXACT RNAMOD []
xref: RNAMOD:069
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001362
name: five_methoxycarbonylmethyl_two_thiouridine
def: "5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methoxycarbonylmethyl-2-thiouridine" EXACT []
synonym: "five methoxycarbonylmethyl two thiouridine" EXACT []
synonym: "mcm5s2U" EXACT RNAMOD []
xref: RNAMOD:070
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001363
name: five_aminomethyl_two_thiouridine
def: "5_aminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-aminomethyl-2-thiouridine" EXACT []
synonym: "five aminomethyl two thiouridine" EXACT []
synonym: "nm5s2U" EXACT RNAMOD []
xref: RNAMOD:071
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001364
name: five_methylaminomethyluridine
def: "5_methylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methylaminomethyluridine" EXACT []
synonym: "five methylaminomethyluridine" EXACT []
synonym: "mnm5U" EXACT RNAMOD []
xref: RNAMOD:072
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001365
name: five_methylaminomethyl_two_thiouridine
def: "5_methylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methylaminomethyl-2-thiouridine" EXACT []
synonym: "five methylaminomethyl two thiouridine" EXACT []
synonym: "mnm5s2U" EXACT RNAMOD []
xref: RNAMOD:073
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001366
name: five_methylaminomethyl_two_selenouridine
def: "5_methylaminomethyl_2_selenouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methylaminomethyl-2-selenouridine" EXACT []
synonym: "five methylaminomethyl two selenouridine" EXACT []
synonym: "mnm5se2U" EXACT RNAMOD []
xref: RNAMOD:074
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001367
name: five_carbamoylmethyluridine
def: "5_carbamoylmethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carbamoylmethyluridine" EXACT []
synonym: "five carbamoylmethyluridine" EXACT []
synonym: "ncm5U" EXACT RNAMOD []
xref: RNAMOD:075
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001368
name: five_carbamoylmethyl_two_prime_O_methyluridine
def: "5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carbamoylmethyl-2'-O-methyluridine" EXACT []
synonym: "five carbamoylmethyl two prime O methyluridine" EXACT []
synonym: "ncm5Um" EXACT RNAMOD []
xref: RNAMOD:076
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001369
name: five_carboxymethylaminomethyluridine
def: "5_carboxymethylaminomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carboxymethylaminomethyluridine" EXACT []
synonym: "cmnm5U" EXACT RNAMOD []
synonym: "five carboxymethylaminomethyluridine" EXACT []
xref: RNAMOD:077
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001370
name: five_carboxymethylaminomethyl_two_prime_O_methyluridine
def: "5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carboxymethylaminomethyl- 2'-O-methyluridine" EXACT []
synonym: "cmnm5Um" EXACT RNAMOD []
synonym: "five carboxymethylaminomethyl two prime O methyluridine" EXACT []
xref: RNAMOD:078
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001371
name: five_carboxymethylaminomethyl_two_thiouridine
def: "5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carboxymethylaminomethyl-2-thiouridine" EXACT []
synonym: "cmnm5s2U" EXACT RNAMOD []
synonym: "five carboxymethylaminomethyl two thiouridine" EXACT []
xref: RNAMOD:079
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001372
name: three_methyluridine
def: "3_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "3-methyluridine" EXACT []
synonym: "m3U" EXACT RNAMOD []
synonym: "three methyluridine" EXACT []
xref: RNAMOD:085
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001373
name: one_methyl_three_three_amino_three_carboxypropyl_pseudouridine
def: "1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "1-methyl-3-(3-amino-3-carboxypropyl) pseudouridine" EXACT []
synonym: "m1acp3Y" EXACT RNAMOD []
xref: RNAMOD:086
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001374
name: five_carboxymethyluridine
def: "5_carboxymethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-carboxymethyluridine" EXACT []
synonym: "cm5U" EXACT RNAMOD []
synonym: "five carboxymethyluridine" EXACT []
xref: RNAMOD:087
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001375
name: three_two_prime_O_dimethyluridine
def: "3_2prime_O_dimethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "3,2'-O-dimethyluridine" EXACT []
synonym: "m3Um" EXACT RNAMOD []
synonym: "three two prime O dimethyluridine" EXACT []
xref: RNAMOD:092
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001376
name: five_methyldihydrouridine
def: "5_methyldihydrouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-methyldihydrouridine" EXACT []
synonym: "five methyldihydrouridine" EXACT []
synonym: "m5D" EXACT RNAMOD []
xref: RNAMOD:093
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001377
name: three_methylpseudouridine
def: "3_methylpseudouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "3-methylpseudouridine" EXACT []
synonym: "m3Y" EXACT RNAMOD []
synonym: "three methylpseudouridine" EXACT []
xref: RNAMOD:094
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001378
name: five_taurinomethyluridine
def: "5_taurinomethyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-taurinomethyluridine" EXACT []
synonym: "five taurinomethyluridine" EXACT []
synonym: "tm5U" EXACT RNAMOD []
xref: RNAMOD:098
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001379
name: five_taurinomethyl_two_thiouridine
def: "5_taurinomethyl_2_thiouridineis a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-taurinomethyl-2-thiouridine" EXACT []
synonym: "five taurinomethyl two thiouridine" EXACT []
synonym: "tm5s2U" EXACT RNAMOD []
xref: RNAMOD:099
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001380
name: five_isopentenylaminomethyl_uridine
def: "5_isopentenylaminomethyl_uridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(isopentenylaminomethyl)uridine" EXACT []
synonym: "five isopentenylaminomethyl uridine" EXACT []
synonym: "inm5U" EXACT RNAMOD []
xref: RNAMOD:103
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001381
name: five_isopentenylaminomethyl_two_thiouridine
def: "5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(isopentenylaminomethyl)- 2-thiouridine" EXACT []
synonym: "five isopentenylaminomethyl two thiouridine" EXACT []
synonym: "inm5s2U" EXACT RNAMOD []
xref: RNAMOD:104
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001382
name: five_isopentenylaminomethyl_two_prime_O_methyluridine
def: "5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature." [http://library.med.utah.edu/RNAmods/]
synonym: "5-(isopentenylaminomethyl)- 2'-O-methyluridine" EXACT []
synonym: "five isopentenylaminomethyl two prime O methyluridine" EXACT []
synonym: "inm5Um" EXACT RNAMOD []
xref: RNAMOD:105
is_a: SO:0001277 ! modified_uridine
[Term]
id: SO:0001383
name: histone_binding_site
def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone." [SO:ke]
synonym: "histone binding site" EXACT []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site
[Term]
id: SO:0001384
name: CDS_fragment
synonym: "CDS fragment" EXACT []
synonym: "incomplete CDS" EXACT []
is_a: SO:0000316 ! CDS
relationship: has_quality SO:0000731 ! fragmentary
[Term]
id: SO:0001385
name: modified_amino_acid_feature
def: "A post translationally modified amino acid feature." [SO:ke]
synonym: "modified amino acid feature" EXACT []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001386
name: modified_glycine
def: "A post translationally modified glycine amino acid feature." [SO:ke]
synonym: "ModGly" EXACT AAMOD []
synonym: "modified glycine" EXACT []
xref: MOD:00908
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001387
name: modified_L_alanine
def: "A post translationally modified alanine amino acid feature." [SO:ke]
synonym: "ModAla" EXACT AAMOD []
synonym: "modified L alanine" EXACT []
synonym: "modified L-alanine" EXACT []
xref: MOD:00901
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001388
name: modified_L_asparagine
def: "A post translationally modified asparagine amino acid feature." [SO:ke]
synonym: "ModAsn" EXACT AAMOD []
synonym: "modified L asparagine" EXACT []
synonym: "modified L-asparagine" EXACT []
xref: MOD:00903
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001389
name: modified_L_aspartic_acid
def: "A post translationally modified aspartic acid amino acid feature." [SO:ke]
synonym: "ModAsp" EXACT AAMOD []
synonym: "modified L aspartic acid" EXACT []
synonym: "modified L-aspartic acid" EXACT []
xref: MOD:00904
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001390
name: modified_L_cysteine
def: "A post translationally modified cysteine amino acid feature." [SO:ke]
synonym: "ModCys" EXACT AAMOD []
synonym: "modified L cysteine" EXACT []
synonym: "modified L-cysteine" EXACT []
xref: MOD:00905
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001391
name: modified_L_glutamic_acid
synonym: "ModGlu" EXACT AAMOD []
synonym: "modified L glutamic acid" EXACT []
synonym: "modified L-glutamic acid" EXACT []
xref: MOD:00906
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001392
name: modified_L_threonine
def: "A post translationally modified threonine amino acid feature." [SO:ke]
synonym: "modified L threonine" EXACT []
synonym: "modified L-threonine" EXACT []
synonym: "ModThr" EXACT AAMOD []
xref: MOD:00917
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001393
name: modified_L_tryptophan
def: "A post translationally modified tryptophan amino acid feature." [SO:ke]
synonym: "modified L tryptophan" EXACT []
synonym: "modified L-tryptophan" EXACT []
synonym: "ModTrp" EXACT AAMOD []
xref: MOD:00918
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001394
name: modified_L_glutamine
def: "A post translationally modified glutamine amino acid feature." [SO:ke]
synonym: "ModGln" EXACT []
synonym: "modified L glutamine" EXACT []
synonym: "modified L-glutamine" EXACT []
xref: MOD:00907
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001395
name: modified_L_methionine
def: "A post translationally modified methionine amino acid feature." [SO:ke]
synonym: "modified L methionine" EXACT []
synonym: "modified L-methionine" EXACT []
synonym: "ModMet" EXACT AAMOD []
xref: MOD:00913
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001396
name: modified_L_isoleucine
def: "A post translationally modified isoleucine amino acid feature." [SO:ke]
synonym: "modified L isoleucine" EXACT []
synonym: "modified L-isoleucine" EXACT []
synonym: "ModIle" EXACT AAMOD []
xref: MOD:00910
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001397
name: modified_L_phenylalanine
def: "A post translationally modified phenylalanine amino acid feature." [SO:ke]
synonym: "modified L phenylalanine" EXACT []
synonym: "modified L-phenylalanine" EXACT []
synonym: "ModPhe" EXACT AAMOD []
xref: MOD:00914
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001398
name: modified_L_histidine
def: "A post translationally modified histidine amino acid feature." [SO:ke]
synonym: "ModHis" EXACT []
synonym: "modified L histidine" EXACT []
synonym: "modified L-histidine" EXACT []
xref: MOD:00909
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001399
name: modified_L_serine
def: "A post translationally modified serine amino acid feature." [SO:ke]
synonym: "modified L serine" EXACT []
synonym: "modified L-serine" EXACT []
synonym: "MosSer" EXACT AAMOD []
xref: MOD:00916 "http://www.psidev.info/index.php?q=node/104"
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001400
name: modified_L_lysine
def: "A post translationally modified lysine amino acid feature." [SO:ke]
synonym: "modified L lysine" EXACT []
synonym: "modified L-lysine" EXACT []
synonym: "ModLys" EXACT AAMOD []
xref: MOD:00912
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001401
name: modified_L_leucine
def: "A post translationally modified leucine amino acid feature." [SO:ke]
synonym: "modified L leucine" EXACT []
synonym: "modified L-leucine " EXACT []
synonym: "ModLeu" EXACT AAMOD []
xref: MOD:00911
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001402
name: modified_L_selenocysteine
def: "A post translationally modified selenocysteine amino acid feature." [SO:ke]
synonym: "modified L selenocysteine" EXACT []
synonym: "modified L-selenocysteine" EXACT []
xref: MOD:01158
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001403
name: modified_L_valine
def: "A post translationally modified valine amino acid feature." [SO:ke]
synonym: "modified L valine" EXACT []
synonym: "modified L-valine" EXACT []
synonym: "ModVal" EXACT AAMOD []
xref: MOD:00920
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001404
name: modified_L_proline
def: "A post translationally modified proline amino acid feature." [SO:ke]
synonym: "modified L proline" EXACT []
synonym: "modified L-proline " EXACT []
synonym: "ModPro" EXACT AAMOD []
xref: MOD:00915
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001405
name: modified_L_tyrosine
def: "A post translationally modified tyrosine amino acid feature." [SO:ke]
synonym: "modified L tyrosine" EXACT []
synonym: "modified L-tyrosine" EXACT []
synonym: "ModTry" EXACT AAMOD []
xref: MOD:00919
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001406
name: modified_L_arginine
def: "A post translationally modified arginine amino acid feature." [SO:ke]
synonym: "ModArg" EXACT AAMOD []
synonym: "modified L arginine" EXACT []
synonym: "modified L-arginine" EXACT []
xref: MOD:00902
is_a: SO:0001385 ! modified_amino_acid_feature
[Term]
id: SO:0001407
name: peptidyl
def: "An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds." [SO:ke]
is_a: SO:0000443 ! polymer_attribute
[Term]
id: SO:0001408
name: cleaved_for_gpi_anchor_region
def: "The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor." [EBI:rh]
synonym: "cleaved for gpi anchor region" EXACT []
is_a: SO:0100011 ! cleaved_peptide_region
[Term]
id: SO:0001409
name: biomaterial_region
def: "A region which is intended for use in an experiment." [SO:cb]
subset: SOFA
synonym: "biomaterial region" EXACT []
is_a: SO:0000001 ! region
[Term]
id: SO:0001410
name: experimental_feature
def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb]
subset: SOFA
synonym: "analysis feature" RELATED []
synonym: "experimental output artefact" EXACT []
synonym: "experimental_output_artefact" EXACT []
is_a: SO:0000001 ! region
[Term]
id: SO:0001411
name: biological_region
def: "A region defined by its disposition to be involved in a biological process." [SO:cb]
subset: SOFA
synonym: "biological region" EXACT []
is_a: SO:0000001 ! region
[Term]
id: SO:0001412
name: topologically_defined_region
def: "A region that is defined according to its relations with other regions within the same sequence." [SO:cb]
subset: SOFA
synonym: "topologically defined region" EXACT []
is_a: SO:0000001 ! region
[Term]
id: SO:0001413
name: translocation_breakpoint
def: "The point within a chromosome where a translocation begins or ends." [SO:cb]
synonym: "translocation breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint
[Term]
id: SO:0001414
name: insertion_breakpoint
def: "The point within a chromosome where a insertion begins or ends." [SO:cb]
synonym: "insertion breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint
[Term]
id: SO:0001415
name: deletion_breakpoint
def: "The point within a chromosome where a deletion begins or ends." [SO:cb]
synonym: "deletion breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint
[Term]
id: SO:0001416
name: five_prime_flanking_region
def: "A flanking region located five prime of a specific region." [SO:chado]
synonym: "5' flanking region" RELATED []
synonym: "five prime flanking region" EXACT []
is_a: SO:0000239 ! flanking_region
[Term]
id: SO:0001417
name: three_prime_flanking_region
def: "A flanking region located three prime of a specific region." [SO:chado]
synonym: "3' flanking region" RELATED []
synonym: "three prime flanking region" EXACT []
is_a: SO:0000239 ! flanking_region
[Term]
id: SO:0001418
name: transcribed_fragment
def: "An experimental region, defined by a tiling array experiment to be transcribed at some level." [SO:ke]
comment: Term requested by the MODencode group.
synonym: "transcribed fragment" EXACT []
synonym: "transfrag" RELATED []
is_a: SO:0001410 ! experimental_feature
[Term]
id: SO:0001419
name: cis_splice_site
def: "Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron." [SO:cjm, SO:ke]
subset: SOFA
synonym: "cis splice site" EXACT []
is_a: SO:0000162 ! splice_site
[Term]
id: SO:0001420
name: trans_splice_site
def: "Primary transcript region bordering trans-splice junction." [SO:ke]
subset: SOFA
synonym: "trans splice site" EXACT []
is_a: SO:0000162 ! splice_site
[Term]
id: SO:0001421
name: splice_junction
def: "The boundary between an intron and an exon." [SO:ke]
synonym: "splice boundary" EXACT []
synonym: "splice junction" EXACT []
is_a: SO:0000699 ! junction
[Term]
id: SO:0001422
name: conformational_switch
def: "A region of a polypeptide, involved in the transition from one conformational state to another." [SO:ke]
comment: MM Young, K Kirshenbaum, KA Dill & S Highsmith. Predicting conformational switches in proteins. Protein Science, 1999, 8, 1752-64. K. Kirshenbaum, M.M. Young and S. Highsmith. Predicting Allosteric Switches in Myosins. Protein Science 8(9):1806-1815. 1999.
synonym: "polypeptide conformational switch" EXACT []
is_a: SO:0100001 ! biochemical_region_of_peptide
[Term]
id: SO:0001423
name: dye_terminator_read
def: "A read produced by the dye terminator method of sequencing." [SO:ke]
synonym: "dye terminator read" RELATED []
is_a: SO:0000150 ! read
[Term]
id: SO:0001424
name: pyrosequenced_read
def: "A read produced by pyrosequencing technology." [SO:ke]
comment: An example is a read produced by Roche 454 technology.
synonym: "pyorsequenced read" RELATED []
is_a: SO:0000150 ! read
[Term]
id: SO:0001425
name: ligation_based_read
def: "A read produced by ligation based sequencing technologies." [SO:ke]
comment: An example of this kind of read is one produced by ABI SOLiD.
synonym: "ligation based read" RELATED []
is_a: SO:0000150 ! read
[Term]
id: SO:0001426
name: polymerase_synthesis_read
def: "A read produced by the polymerase based sequence by synthesis method." [SO:ke]
comment: An example is a read produced by Illumina technology.
synonym: "polymerase synthesis read" RELATED []
is_a: SO:0000150 ! read
[Term]
id: SO:0001427
name: cis_regulatory_frameshift_element
def: "A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence." [RFAM:jd]
synonym: "cis regulatory frameshift element" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
[Term]
id: SO:0001428
name: expressed_sequence_assembly
def: "A sequence assembly derived from expressed sequences." [SO:ke]
comment: From tracker [ 2372385 ] expressed_sequence_assembly.
synonym: "expressed sequence assembly" EXACT []
is_a: SO:0000353 ! sequence_assembly
[Term]
id: SO:0001429
name: DNA_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with DNA." [SO:ke]
synonym: "DNA binding site" EXACT []
is_a: SO:0001655 ! nucleotide_binding_site
[Term]
id: SO:0001431
name: cryptic_gene
def: "A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning." [SO:ke]
synonym: "cryptic gene" EXACT []
is_a: SO:0000704 ! gene
relationship: has_quality SO:0000976 ! cryptic
[Term]
id: SO:0001432
name: sequence_variant_affecting_polyadenylation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting polyadenylation" RELATED []
synonym: "sequence variant affecting polyadenylation" EXACT []
is_obsolete: true
replaced_by: SO:0001545
[Term]
id: SO:0001433
name: three_prime_RACE_clone
def: "A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host." [modENCODE:nlw]
synonym: "3' RACE clone" RELATED []
is_a: SO:0000317 ! cDNA_clone
[Term]
id: SO:0001434
name: cassette_pseudogene
def: "A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy." [SO:ke]
comment: Requested by the Trypanosome community.
synonym: "cassette pseudogene" EXACT []
synonym: "cassette type psedogene" RELATED []
is_a: SO:0001760 ! non_processed_pseudogene
[Term]
id: SO:0001435
name: alanine
comment: A place holder for a cross product with chebi.
synonym: "A" EXACT aa1 []
synonym: "Ala" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001436
name: valine
comment: A place holder for a cross product with chebi.
synonym: "V" EXACT aa1 []
synonym: "Val" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001437
name: leucine
comment: A place holder for a cross product with chebi.
synonym: "L" EXACT aa1 []
synonym: "Leu" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001438
name: isoleucine
comment: A place holder for a cross product with chebi.
synonym: "I" EXACT aa1 []
synonym: "Ile" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001439
name: proline
comment: A place holder for a cross product with chebi.
synonym: "P" EXACT aa1 []
synonym: "Pro" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001440
name: tryptophan
comment: A place holder for a cross product with chebi.
synonym: "Trp" EXACT aa3 []
synonym: "W" EXACT aa1 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001441
name: phenylalanine
comment: A place holder for a cross product with chebi.
synonym: "F" EXACT aa1 []
synonym: "Phe" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001442
name: methionine
comment: A place holder for a cross product with chebi.
synonym: "M" EXACT aa1 []
synonym: "Met" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001443
name: glycine
comment: A place holder for a cross product with chebi.
synonym: "G" EXACT aa1 []
synonym: "Gly" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001444
name: serine
comment: A place holder for a cross product with chebi.
synonym: "S" EXACT aa1 []
synonym: "Ser" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001445
name: threonine
comment: A place holder for a cross product with chebi.
synonym: "T" EXACT aa1 []
synonym: "Thr" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001446
name: tyrosine
comment: A place holder for a cross product with chebi.
synonym: "Tyr" EXACT aa3 []
synonym: "Y" EXACT aa1 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001447
name: cysteine
comment: A place holder for a cross product with chebi.
synonym: "C" EXACT aa1 []
synonym: "Cys" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001448
name: glutamine
comment: A place holder for a cross product with chebi.
synonym: "Gln" EXACT aa3 []
synonym: "Q" EXACT aa1 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001449
name: asparagine
comment: A place holder for a cross product with chebi.
synonym: "Asn" EXACT aa3 []
synonym: "N" EXACT aa1 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001450
name: lysine
comment: A place holder for a cross product with chebi.
synonym: "K" EXACT aa1 []
synonym: "Lys" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001451
name: arginine
comment: A place holder for a cross product with chebi.
synonym: "Arg" EXACT aa3 []
synonym: "R" EXACT aa1 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001452
name: histidine
comment: A place holder for a cross product with chebi.
synonym: "H" EXACT aa1 []
synonym: "His" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001453
name: aspartic_acid
comment: A place holder for a cross product with chebi.
synonym: "Asp" EXACT aa3 []
synonym: "aspartic acid" EXACT []
synonym: "D" EXACT aa1 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001454
name: glutamic_acid
comment: A place holder for a cross product with chebi.
synonym: "E" EXACT aa1 []
synonym: "Glu" EXACT aa3 []
synonym: "glutamic acid" EXACT []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001455
name: selenocysteine
comment: A place holder for a cross product with chebi.
synonym: "Sec" EXACT aa3 []
synonym: "U" EXACT aa1 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001456
name: pyrrolysine
comment: A place holder for a cross product with chebi.
synonym: "O" EXACT aa1 []
synonym: "Pyl" EXACT aa3 []
is_a: SO:0001237 ! amino_acid
[Term]
id: SO:0001457
name: transcribed_cluster
def: "A region defined by a set of transcribed sequences from the same gene or expressed pseudogene." [SO:ke]
comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
synonym: "transcribed cluster" EXACT []
synonym: "unigene cluster" RELATED []
is_a: SO:0001410 ! experimental_feature
relationship: has_part SO:0000695 ! reagent
[Term]
id: SO:0001458
name: unigene_cluster
def: "A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene." [SO:ke]
comment: This term was requested by Jeff Bowes, using the tracker, ID = 2594157.
synonym: "unigene cluster" RELATED []
is_a: SO:0001457 ! transcribed_cluster
[Term]
id: SO:0001459
name: CRISPR
def: "Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences." [RFAM:jd]
synonym: "Clustered_Regularly_Interspaced_Short_Palindromic_Repeat" EXACT []
synonym: "CRISPR element" EXACT []
xref: http:en.wikipedia.org/wiki/CRISPR
is_a: SO:0000314 ! direct_repeat
[Term]
id: SO:0001460
name: insulator_binding_site
def: "A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
comment: See tracker ID 2060908.
synonym: "insulator binding site" RELATED []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site
relationship: part_of SO:0000627 ! insulator
[Term]
id: SO:0001461
name: enhancer_binding_site
def: "A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
synonym: "enhancer binding site" RELATED []
is_a: SO:0001654 ! nucleotide_to_protein_binding_site
relationship: part_of SO:0000165 ! enhancer
[Term]
id: SO:0001462
name: contig_collection
def: "A collection of contigs." [SO:ke]
comment: See tracker ID: 2138359.
synonym: "contig collection" EXACT []
is_a: SO:0001085 ! sequence_conflict
is_a: SO:0001260 ! sequence_collection
relationship: has_part SO:0000149 ! contig
[Term]
id: SO:0001463
name: lincRNA
def: "A multiexonic non-coding RNA transcribed by RNA polymerase II." [PMID:19182780, SO:ke]
synonym: "large intervening non-coding RNA" EXACT []
synonym: "long intergenic non-coding RNA" EXACT []
is_a: SO:0001877 ! lnc_RNA
[Term]
id: SO:0001464
name: UST
def: "An EST spanning part or all of the untranslated regions of a protein-coding transcript." [SO:nlw]
synonym: "UTR sequence tag" EXACT []
is_a: SO:0000345 ! EST
[Term]
id: SO:0001465
name: three_prime_UST
def: "A UST located in the 3'UTR of a protein-coding transcript." [SO:nlw]
synonym: "3' UST" RELATED []
is_a: SO:0001464 ! UST
[Term]
id: SO:0001466
name: five_prime_UST
def: "An UST located in the 5'UTR of a protein-coding transcript." [SO:nlw]
synonym: "5' UST" RELATED []
is_a: SO:0001464 ! UST
[Term]
id: SO:0001467
name: RST
def: "A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long." [SO:nlw]
synonym: "RACE sequence tag" EXACT []
is_a: SO:0000345 ! EST
[Term]
id: SO:0001468
name: three_prime_RST
def: "A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long." [SO:nlw]
synonym: "3' RST" EXACT []
is_a: SO:0001467 ! RST
[Term]
id: SO:0001469
name: five_prime_RST
def: "A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long." [SO:nlw]
synonym: "5' RST" RELATED []
is_a: SO:0001467 ! RST
[Term]
id: SO:0001470
name: UST_match
def: "A match against an UST sequence." [SO:nlw]
synonym: "UST match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match
[Term]
id: SO:0001471
name: RST_match
def: "A match against an RST sequence." [SO:nlw]
synonym: "RST match" EXACT []
is_a: SO:0000102 ! expressed_sequence_match
[Term]
id: SO:0001472
name: primer_match
def: "A nucleotide match to a primer sequence." [SO:nlw]
synonym: "primer match" EXACT []
is_a: SO:0000347 ! nucleotide_match
[Term]
id: SO:0001473
name: miRNA_antiguide
def: "A region of the pri miRNA that base pairs with the guide to form the hairpin." [SO:ke]
synonym: "miRNA antiguide " EXACT []
synonym: "miRNA passenger strand" EXACT []
synonym: "miRNA star" EXACT []
is_a: SO:0001243 ! miRNA_primary_transcript_region
created_by: kareneilbeck
creation_date: 2009-05-27T03:35:43Z
[Term]
id: SO:0001474
name: trans_splice_junction
def: "The boundary between the spliced leader and the first exon of the mRNA." [SO:ke]
synonym: "trans-splice junction" EXACT []
is_a: SO:0000699 ! junction
created_by: kareneilbeck
creation_date: 2009-07-13T04:50:49Z
[Term]
id: SO:0001475
name: outron
def: "A region of a primary transcript, that is removed via trans splicing." [PMID:16401417, SO:ke]
is_a: SO:0000835 ! primary_transcript_region
created_by: kareneilbeck
creation_date: 2009-07-14T11:36:08Z
[Term]
id: SO:0001476
name: natural_plasmid
def: "A plasmid that occurs naturally." [SO:xp]
synonym: "natural plasmid" EXACT []
is_a: SO:0000155 ! plasmid
is_a: SO:0001038 ! extrachromosomal_mobile_genetic_element
relationship: has_quality SO:0000782 ! natural
created_by: kareneilbeck
creation_date: 2009-09-01T03:43:06Z
[Term]
id: SO:0001477
name: gene_trap_construct
def: "A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker." [ZFIN:dh]
synonym: "gene trap construct" EXACT []
is_a: SO:0000637 ! engineered_plasmid
created_by: kareneilbeck
creation_date: 2009-09-01T03:49:09Z
[Term]
id: SO:0001478
name: promoter_trap_construct
def: "A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic." [ZFIN:dh]
synonym: "promoter trap construct" EXACT []
is_a: SO:0000637 ! engineered_plasmid
created_by: kareneilbeck
creation_date: 2009-09-01T03:52:01Z
[Term]
id: SO:0001479
name: enhancer_trap_construct
def: "An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic." [ZFIN:dh]
synonym: "enhancer trap construct" EXACT []
is_a: SO:0000637 ! engineered_plasmid
created_by: kareneilbeck
creation_date: 2009-09-01T03:53:26Z
[Term]
id: SO:0001480
name: PAC_end
def: "A region of sequence from the end of a PAC clone that may provide a highly specific marker." [ZFIN:mh]
synonym: "PAC end" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000154 ! PAC
created_by: kareneilbeck
creation_date: 2009-09-09T05:18:12Z
[Term]
id: SO:0001481
name: RAPD
def: "RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers." [ZFIN:mh]
synonym: "Random Amplification Polymorphic DNA" EXACT []
is_a: SO:0000006 ! PCR_product
created_by: kareneilbeck
creation_date: 2009-09-09T05:26:10Z
[Term]
id: SO:0001482
name: shadow_enhancer
synonym: "shadow enhancer" EXACT []
is_a: SO:0000165 ! enhancer
created_by: kareneilbeck
creation_date: 2009-09-09T05:29:29Z
[Term]
id: SO:0001483
name: SNV
def: "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist." [SO:bm]
subset: SOFA
synonym: "single nucleotide variant" EXACT []
is_a: SO:1000002 ! substitution
created_by: kareneilbeck
creation_date: 2009-10-08T11:37:49Z
[Term]
id: SO:0001484
name: X_element_combinatorial_repeat
def: "An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element." [http://www.yeastgenome.org/help/glossary.html]
comment: X element combinatorial repeats contain Tbf1p binding sites,\nand possible functions include a role in telomerase-independent telomere\nmaintenance via recombination or as a barrier against transcriptional\nsilencing. These are usually present as a combination of one or more of\nseveral types of smaller elements (designated A, B, C, or D). This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
synonym: "X element combinatorial repeat" EXACT []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000624 ! telomere
created_by: kareneilbeck
creation_date: 2009-11-10T11:03:37Z
[Term]
id: SO:0001485
name: Y_prime_element
def: "A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies." [http:http://www.yeastgenome.org/help/glossary.html]
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747.
synonym: "Y' element" EXACT []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000624 ! telomere
created_by: kareneilbeck
creation_date: 2009-11-10T12:08:57Z
[Term]
id: SO:0001486
name: standard_draft
def: "The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete." [DOI:10.1126]
synonym: "standard draft" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T12:48:32Z
[Term]
id: SO:0001487
name: high_quality_draft
def: "The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome." [DOI:10.1126]
synonym: "high quality draft" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T12:52:36Z
[Term]
id: SO:0001488
name: improved_high_quality_draft
def: "The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution." [DOI:10.1126]
synonym: "improved high quality draft" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T12:54:35Z
[Term]
id: SO:0001489
name: annotation_directed_improved_draft
def: "The status of a whole genome sequence,where annotation, and verification of coding regions has occurred." [DOI:10.1126]
synonym: "annotation directed improvement" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T12:57:10Z
[Term]
id: SO:0001490
name: noncontiguous_finished
def: "The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions." [DOI:10.1126]
synonym: "non contiguous finished" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T01:01:07Z
[Term]
id: SO:0001491
name: finished_genome
def: "The status of a whole genome sequence, with less than 1 error per 100,000 base pairs." [DOI:10.1126]
synonym: "finished" EXACT []
synonym: "finished genome" EXACT []
is_a: SO:0001499 ! whole_genome_sequence_status
created_by: kareneilbeck
creation_date: 2009-10-23T01:04:43Z
[Term]
id: SO:0001492
name: intronic_regulatory_region
def: "A regulatory region that is part of an intron." [SO:ke]
synonym: "intronic regulatory region" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
relationship: part_of SO:0000188 ! intron
created_by: kareneilbeck
creation_date: 2009-11-08T02:48:02Z
[Term]
id: SO:0001493
name: centromere_DNA_Element_I
def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p)." [PMID:11222754]
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
synonym: "CDEI" EXACT []
synonym: "Centromere DNA Element I" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0001794 ! point_centromere
created_by: kareneilbeck
creation_date: 2009-11-09T05:47:23Z
[Term]
id: SO:0001494
name: centromere_DNA_Element_II
def: "A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length." [PMID:11222754]
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
synonym: "CDEII" EXACT []
synonym: "centromere DNA Element II" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0001794 ! point_centromere
created_by: kareneilbeck
creation_date: 2009-11-09T05:51:26Z
[Term]
id: SO:0001495
name: centromere_DNA_Element_III
def: "A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex." [PMID:11222754]
comment: This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880699.
synonym: "CDEIII" EXACT []
synonym: "centromere DNA Element III" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0001794 ! point_centromere
created_by: kareneilbeck
creation_date: 2009-11-09T05:54:47Z
[Term]
id: SO:0001496
name: telomeric_repeat
def: "The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n." [PMID:8720065]
comment: The repeats are maintained by telomerase and there is generally 300 (+/-) 75 bp of TG(1-3) at a given end. Telomeric repeats function in completing chromosome replication and protecting the ends from degradation and end-to-end fusions. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880739.
synonym: "telomeric repeat" EXACT []
is_a: SO:0000657 ! repeat_region
relationship: part_of SO:0000624 ! telomere
created_by: kareneilbeck
creation_date: 2009-11-09T06:00:42Z
[Term]
id: SO:0001497
name: X_element
def: "The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site." [http://www.yeastgenome.org/help/glossary.html#xelemcoresequence, PMID:7785338, PMID:8005434]
comment: Possible functions include roles in chromosomal segregation,\nmaintenance of chromosome stability, recombinational sequestering, or as a\nbarrier to transcriptional silencing. This term was requested 2009-10-16 by Michel Dumontier, tracker id 2880747. \n\nFrom Janos Demeter: The only region shared by all chromosome ends, the X element core sequence is a small conserved element (~475 bp) that contains an ARS sequence and in most cases an Abf1p binding site. Between these is a GC-rich region nearly identical to the meiosis-specific regulatory sequence URS1.
synonym: "X element" RELATED []
synonym: "X element core sequence" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0000624 ! telomere
created_by: kareneilbeck
creation_date: 2009-11-10T10:56:54Z
[Term]
id: SO:0001498
name: YAC_end
def: "A region of sequence from the end of a YAC clone that may provide a highly specific marker." [SO:ke]
synonym: "YAC end" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000152 ! YAC
created_by: kareneilbeck
creation_date: 2009-11-19T11:07:18Z
[Term]
id: SO:0001499
name: whole_genome_sequence_status
def: "The status of whole genome sequence." [DOI:10.1126]
comment: This terms and children were added to SO in response to tracker request by Patrick Chain. The paper Genome Project Standards in a New Era of Sequencing. Science October 9th 2009, addresses these terms.
synonym: "whole genome sequence status" EXACT []
is_a: SO:0000905 ! status
created_by: kareneilbeck
creation_date: 2009-10-23T12:47:47Z
[Term]
id: SO:0001500
name: heritable_phenotypic_marker
def: "A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus." [JAX:hdene]
synonym: "heritable phenotypic marker" EXACT []
synonym: "phenotypic marker" EXACT []
is_a: SO:0001645 ! genetic_marker
created_by: kareneilbeck
creation_date: 2009-12-07T01:50:55Z
[Term]
id: SO:0001501
name: peptide_collection
def: "A collection of peptide sequences." [BBOP:nlw]
comment: Term requested via tracker ID: 2910829.
synonym: "peptide collection" EXACT []
synonym: "peptide set" EXACT []
is_a: SO:0001260 ! sequence_collection
relationship: has_part SO:0000104 ! polypeptide
created_by: kareneilbeck
creation_date: 2009-12-11T10:58:58Z
[Term]
id: SO:0001502
name: high_identity_region
def: "An experimental feature with high sequence identity to another sequence." [SO:ke]
comment: Requested by tracker ID: 2902685.
synonym: "high identity region" EXACT []
is_a: SO:0001410 ! experimental_feature
created_by: kareneilbeck
creation_date: 2009-12-11T11:06:05Z
[Term]
id: SO:0001503
name: processed_transcript
def: "A transcript for which no open reading frame has been identified and for which no other function has been determined." [MGI:hdeen]
comment: Ensembl and Vega also use this term name. Requested by Howard Deen of MGI.
synonym: "processed transcript" EXACT []
is_a: SO:0000673 ! transcript
created_by: kareneilbeck
creation_date: 2009-12-21T05:37:14Z
[Term]
id: SO:0001504
name: assortment_derived_variation
def: "A chromosome variation derived from an event during meiosis." [SO:ke]
synonym: "assortment derived variation" RELATED []
is_a: SO:0000240 ! chromosome_variation
created_by: kareneilbeck
creation_date: 2010-03-02T05:03:18Z
[Term]
id: SO:0001505
name: reference_genome
def: "A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly." [SO:ke]
synonym: "reference genome" RELATED []
is_a: SO:0001026 ! genome
created_by: kareneilbeck
creation_date: 2010-03-03T02:10:03Z
[Term]
id: SO:0001506
name: variant_genome
def: "A collection of sequences (often chromosomes) of an individual." [SO:ke]
synonym: "variant genome" RELATED []
is_a: SO:0001026 ! genome
created_by: kareneilbeck
creation_date: 2010-03-03T02:11:25Z
[Term]
id: SO:0001507
name: variant_collection
def: "A collection of one or more sequences of an individual." [SO:ke]
synonym: "variant collection" RELATED []
is_a: SO:0001260 ! sequence_collection
relationship: has_part SO:0001059 ! sequence_alteration
created_by: kareneilbeck
creation_date: 2010-03-03T02:13:28Z
[Term]
id: SO:0001508
name: alteration_attribute
synonym: "alteration attribute" EXACT []
is_a: SO:0000733 ! feature_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:53:23Z
[Term]
id: SO:0001509
name: chromosomal_variation_attribute
synonym: "chromosomal variation attribute" EXACT []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:54:30Z
[Term]
id: SO:0001510
name: intrachromosomal
is_a: SO:0001509 ! chromosomal_variation_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:55:25Z
[Term]
id: SO:0001511
name: interchromosomal
is_a: SO:0001509 ! chromosomal_variation_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:55:43Z
[Term]
id: SO:0001512
name: insertion_attribute
def: "A quality of a chromosomal insertion,." [SO:ke]
synonym: "insertion attribute" EXACT []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:55:56Z
[Term]
id: SO:0001513
name: tandem
is_a: SO:0001512 ! insertion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:56:37Z
[Term]
id: SO:0001514
name: direct
def: "A quality of an insertion where the insert is not in a cytologically inverted orientation." [SO:ke]
is_a: SO:0001512 ! insertion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:56:49Z
[Term]
id: SO:0001515
name: inverted
def: "A quality of an insertion where the insert is in a cytologically inverted orientation." [SO:ke]
is_a: SO:0001512 ! insertion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:57:40Z
[Term]
id: SO:0001516
name: free
def: "The quality of a duplication where the new region exists independently of the original." [SO:ke]
is_a: SO:0001523 ! duplication_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:57:51Z
[Term]
id: SO:0001517
name: inversion_attribute
synonym: "inversion attribute" EXACT []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:58:10Z
[Term]
id: SO:0001518
name: pericentric
is_a: SO:0001517 ! inversion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:58:24Z
[Term]
id: SO:0001519
name: paracentric
is_a: SO:0001517 ! inversion_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:58:35Z
[Term]
id: SO:0001520
name: translocaton_attribute
synonym: "translocation attribute" EXACT []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:58:47Z
[Term]
id: SO:0001521
name: reciprocal
is_a: SO:0001520 ! translocaton_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:59:34Z
[Term]
id: SO:0001522
name: insertional
is_a: SO:0001520 ! translocaton_attribute
created_by: kareneilbeck
creation_date: 2010-03-04T02:59:51Z
[Term]
id: SO:0001523
name: duplication_attribute
synonym: "duplication attribute" RELATED []
is_a: SO:0001508 ! alteration_attribute
created_by: kareneilbeck
creation_date: 2010-03-05T01:56:33Z
[Term]
id: SO:0001524
name: chromosomally_aberrant_genome
synonym: "chromosomally aberrant genome" RELATED []
is_a: SO:0001506 ! variant_genome
created_by: kareneilbeck
creation_date: 2010-03-05T02:21:00Z
[Term]
id: SO:0001525
name: assembly_error_correction
def: "A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake." [SO:ke]
synonym: "assembly error correction" RELATED []
is_a: SO:0000413 ! sequence_difference
created_by: kareneilbeck
creation_date: 2010-03-09T02:16:31Z
[Term]
id: SO:0001526
name: base_call_error_correction
def: "A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake." [SO:ke]
synonym: "base call error correction" RELATED []
is_a: SO:0000413 ! sequence_difference
created_by: kareneilbeck
creation_date: 2010-03-09T02:18:07Z
[Term]
id: SO:0001527
name: peptide_localization_signal
def: "A region of peptide sequence used to target the polypeptide molecule to a specific organelle." [SO:ke]
subset: SOFA
synonym: "localization signal" RELATED []
synonym: "peptide localization signal" EXACT []
is_a: SO:0000839 ! polypeptide_region
created_by: kareneilbeck
creation_date: 2010-03-11T02:15:05Z
[Term]
id: SO:0001528
name: nuclear_localization_signal
def: "A polypeptide region that targets a polypeptide to the nucleus." [SO:ke]
synonym: "NLS" EXACT []
xref: http://en.wikipedia.org/wiki/Nuclear_localization_signal "wikipedia"
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T02:16:38Z
[Term]
id: SO:0001529
name: endosomal_localization_signal
def: "A polypeptide region that targets a polypeptide to the endosome." [SO:ke]
synonym: "endosomal localization signal" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T02:20:58Z
[Term]
id: SO:0001530
name: lysosomal_localization_signal
def: "A polypeptide region that targets a polypeptide to the lysosome." [SO:ke]
synonym: "lysosomal localization signal" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T02:24:10Z
[Term]
id: SO:0001531
name: nuclear_export_signal
def: "A polypeptide region that targets a polypeptide to he cytoplasm." [SO:ke]
synonym: "NES" EXACT []
synonym: "nuclear export signal" EXACT []
xref: http://en.wikipedia.org/wiki/Nuclear_export_signal
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T02:25:25Z
[Term]
id: SO:0001532
name: recombination_signal_sequence
def: "A region recognized by a recombinase." [SO:ke]
synonym: "recombination signal sequence" RELATED []
xref: http://en.wikipedia.org/wiki/Recombination_Signal_Sequences "wikipedia"
is_a: SO:0000299 ! specific_recombination_site
created_by: kareneilbeck
creation_date: 2010-03-11T03:16:47Z
[Term]
id: SO:0001533
name: cryptic_splice_site
def: "A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error." [SO:ke]
synonym: "cryptic splice signal" RELATED []
synonym: "cryptic splice site" EXACT []
is_a: SO:0000162 ! splice_site
created_by: kareneilbeck
creation_date: 2010-03-11T03:25:06Z
[Term]
id: SO:0001534
name: nuclear_rim_localization_signal
def: "A polypeptide region that targets a polypeptide to the nuclear rim." [SO:ke]
synonym: "nuclear rim localization signal" RELATED []
xref: PMID:16027110
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2010-03-11T03:31:30Z
[Term]
id: SO:0001535
name: p_element
def: "A P_element is a DNA transposon responsible for hybrid dysgenesis." [SO:ke]
synonym: "P element" RELATED []
is_a: SO:0000182 ! DNA_transposon
created_by: kareneilbeck
creation_date: 2010-03-12T03:40:33Z
[Term]
id: SO:0001536
name: functional_variant
def: "A sequence variant in which the function of a gene product is altered with respect to a reference." [SO:ke]
synonym: "functional variant" EXACT []
is_a: SO:0001060 ! sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:30:25Z
[Term]
id: SO:0001537
name: structural_variant
def: "A sequence variant that changes one or more sequence features." [SO:ke]
synonym: "structural variant" RELATED []
is_a: SO:0001060 ! sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:31:01Z
[Term]
id: SO:0001538
name: transcript_function_variant
def: "A sequence variant which alters the functioning of a transcript with respect to a reference sequence." [SO:ke]
synonym: "transcript function variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:32:58Z
[Term]
id: SO:0001539
name: translational_product_function_variant
def: "A sequence variant that affects the functioning of a translational product with respect to a reference sequence." [SO:ke]
synonym: "translational product variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:46:15Z
[Term]
id: SO:0001540
name: level_of_transcript_variant
def: "A sequence variant which alters the level of a transcript." [SO:ke]
synonym: "level of transcript variant" EXACT []
is_a: SO:0001538 ! transcript_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:47:07Z
[Term]
id: SO:0001541
name: decreased_transcript_level_variant
def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]
synonym: "decreased transcript level" EXACT []
is_a: SO:0001540 ! level_of_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:47:47Z
[Term]
id: SO:0001542
name: increased_transcript_level_variant
def: "A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence." [SO:ke]
synonym: "increased transcript level variant" EXACT []
is_a: SO:0001540 ! level_of_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:48:17Z
[Term]
id: SO:0001543
name: transcript_processing_variant
def: "A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence." [SO:ke]
synonym: "transcript processing variant" EXACT []
is_a: SO:0001538 ! transcript_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:48:48Z
[Term]
id: SO:0001544
name: editing_variant
def: "A transcript processing variant whereby the process of editing is disrupted with respect to the reference." [SO:ke]
synonym: "editing variant" EXACT []
is_a: SO:0001543 ! transcript_processing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:49:25Z
[Term]
id: SO:0001545
name: polyadenylation_variant
def: "A sequence variant that changes polyadenylation with respect to a reference sequence." [SO:ke]
synonym: "polyadenylation variant" EXACT []
is_a: SO:0001543 ! transcript_processing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:49:40Z
[Term]
id: SO:0001546
name: transcript_stability_variant
def: "A variant that changes the stability of a transcript with respect to a reference sequence." [SO:ke]
synonym: "transcript stability variant" EXACT []
is_a: SO:0001538 ! transcript_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:50:01Z
[Term]
id: SO:0001547
name: decreased_transcript_stability_variant
def: "A sequence variant that decreases transcript stability with respect to a reference sequence." [SO:ke]
synonym: "decrease transcript stability variant" EXACT []
is_a: SO:0001546 ! transcript_stability_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:50:23Z
[Term]
id: SO:0001548
name: increased_transcript_stability_variant
def: "A sequence variant that increases transcript stability with respect to a reference sequence." [SO:ke]
synonym: "increased transcript stability variant" EXACT []
is_a: SO:0001546 ! transcript_stability_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:50:39Z
[Term]
id: SO:0001549
name: transcription_variant
def: "A variant that changes alters the transcription of a transcript with respect to a reference sequence." [SO:ke]
synonym: "transcription variant" EXACT []
is_a: SO:0001538 ! transcript_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:51:26Z
[Term]
id: SO:0001550
name: rate_of_transcription_variant
def: "A sequence variant that changes the rate of transcription with respect to a reference sequence." [SO:ke]
synonym: "rate of transcription variant" EXACT []
is_a: SO:0001549 ! transcription_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:51:50Z
[Term]
id: SO:0001551
name: increased_transcription_rate_variant
def: "A sequence variant that increases the rate of transcription with respect to a reference sequence." [SO:ke]
synonym: "increased transcription rate variant" EXACT []
is_a: SO:0001550 ! rate_of_transcription_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:52:17Z
[Term]
id: SO:0001552
name: decreased_transcription_rate_variant
def: "A sequence variant that decreases the rate of transcription with respect to a reference sequence." [SO:ke]
synonym: "decreased transcription rate variant" EXACT []
is_a: SO:0001550 ! rate_of_transcription_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:52:43Z
[Term]
id: SO:0001553
name: translational_product_level_variant
def: "A functional variant that changes the translational product level with respect to a reference sequence." [SO:ke]
synonym: "translational product level variant" EXACT []
is_a: SO:0001539 ! translational_product_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:53:32Z
[Term]
id: SO:0001554
name: polypeptide_function_variant
def: "A sequence variant which changes polypeptide functioning with respect to a reference sequence." [SO:ke]
synonym: "polypeptide function variant" EXACT []
is_a: SO:0001539 ! translational_product_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:53:54Z
[Term]
id: SO:0001555
name: decreased_translational_product_level
def: "A sequence variant which decreases the translational product level with respect to a reference sequence." [SO:ke]
synonym: "decrease translational product level" EXACT []
is_a: SO:0001553 ! translational_product_level_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:54:25Z
[Term]
id: SO:0001556
name: increased_translational_product_level
def: "A sequence variant which increases the translational product level with respect to a reference sequence." [SO:ke]
synonym: "increase translational product level" EXACT []
is_a: SO:0001553 ! translational_product_level_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:55:25Z
[Term]
id: SO:0001557
name: polypeptide_gain_of_function_variant
def: "A sequence variant which causes gain of polypeptide function with respect to a reference sequence." [SO:ke]
synonym: "polypeptide gain of function variant" EXACT []
is_a: SO:0001554 ! polypeptide_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:56:12Z
[Term]
id: SO:0001558
name: polypeptide_localization_variant
def: "A sequence variant which changes the localization of a polypeptide with respect to a reference sequence." [SO:ke]
synonym: "polypeptide localization variant" EXACT []
is_a: SO:0001554 ! polypeptide_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:56:37Z
[Term]
id: SO:0001559
name: polypeptide_loss_of_function_variant
def: "A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence." [SO:ke]
synonym: "polypeptide loss of function variant" EXACT []
is_a: SO:0001554 ! polypeptide_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:56:58Z
[Term]
id: SO:0001560
name: inactive_ligand_binding_site
def: "A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence." [SO:ke]
synonym: "inactive ligand binding site" EXACT []
is_a: SO:0001559 ! polypeptide_loss_of_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:58:00Z
[Term]
id: SO:0001561
name: polypeptide_partial_loss_of_function
def: "A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence." [SO:ke]
synonym: "polypeptide partial loss of function" EXACT []
is_a: SO:0001559 ! polypeptide_loss_of_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:58:32Z
[Term]
id: SO:0001562
name: polypeptide_post_translational_processing_variant
def: "A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence." [SO:ke]
synonym: "polypeptide post translational processing variant" EXACT []
is_a: SO:0001554 ! polypeptide_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T11:59:06Z
[Term]
id: SO:0001563
name: copy_number_change
def: "A sequence variant where copies of a feature (CNV) are either increased or decreased." [SO:ke]
synonym: "copy number change" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:27:33Z
[Term]
id: SO:0001564
name: gene_variant
def: "A sequence variant where the structure of the gene is changed." [SO:ke]
synonym: "gene structure variant" EXACT []
synonym: "snpEff:GENE" EXACT VAR []
synonym: "VAAST:gene_variant" EXACT VAR []
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:28:01Z
[Term]
id: SO:0001565
name: gene_fusion
def: "A sequence variant whereby a two genes have become joined." [SO:ke]
synonym: "gene fusion" EXACT []
is_a: SO:0001564 ! gene_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:28:28Z
[Term]
id: SO:0001566
name: regulatory_region_variant
def: "A sequence variant located within a regulatory region." [SO:ke]
comment: EBI term: Regulatory region variations - In regulatory region annotated by Ensembl.
synonym: "regulatory region variant" EXACT []
synonym: "regulatory_region_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:28:48Z
[Term]
id: SO:0001567
name: stop_retained_variant
def: "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains." [SO:ke]
synonym: "snpEff:SYNONYMOUS_STOP" EXACT VAR []
synonym: "stop retained variant" EXACT []
synonym: "VAAST:stop_retained" EXACT VAR []
is_a: SO:0001590 ! terminator_codon_variant
is_a: SO:0001819 ! synonymous_variant
created_by: kareneilbeck
creation_date: 2010-04-19T05:02:30Z
[Term]
id: SO:0001568
name: splicing_variant
def: "A sequence variant that changes the process of splicing." [SO:ke]
synonym: "splicing variant" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:29:22Z
[Term]
id: SO:0001569
name: cryptic_splice_site_variant
def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "cryptic splice site activation" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:29:41Z
[Term]
id: SO:0001570
name: cryptic_splice_acceptor
def: "A sequence variant whereby a new splice site is created due to the activation of a new acceptor." [SO:ke]
synonym: "cryptic splice acceptor" EXACT []
is_a: SO:0001569 ! cryptic_splice_site_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:30:11Z
[Term]
id: SO:0001571
name: cryptic_splice_donor
def: "A sequence variant whereby a new splice site is created due to the activation of a new donor." [SO:ke]
synonym: "cryptic splice donor" EXACT []
is_a: SO:0001569 ! cryptic_splice_site_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:30:35Z
[Term]
id: SO:0001572
name: exon_loss_variant
def: "A sequence variant whereby an exon is lost from the transcript." [SO:ke]
synonym: "exon loss" EXACT []
synonym: "snpEff:EXON_DELETED" EXACT VAR []
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:31:09Z
[Term]
id: SO:0001573
name: intron_gain_variant
def: "A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "intron gain" EXACT []
synonym: "intron gain variant" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:31:25Z
[Term]
id: SO:0001574
name: splice_acceptor_variant
def: "A splice variant that changes the 2 base region at the 3' end of an intron." [SO:ke]
synonym: "snpEff:SPLICE_SITE_ACCEPTOR" EXACT VAR []
synonym: "splice acceptor variant" EXACT []
synonym: "VAAST:splice_acceptor_variant" EXACT VAR []
is_a: SO:0001629 ! splice_site_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:31:52Z
[Term]
id: SO:0001575
name: splice_donor_variant
def: "A splice variant that changes the 2 base pair region at the 5' end of an intron." [SO:ke]
synonym: "snpEff:SPLICE_SITE_DONOR" EXACT VAR []
synonym: "splice donor variant" EXACT []
synonym: "VAAST:splice_donor_variant" EXACT VAR []
is_a: SO:0001629 ! splice_site_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:32:10Z
[Term]
id: SO:0001576
name: transcript_variant
def: "A sequence variant that changes the structure of the transcript." [SO:ke]
synonym: "snpEff:TRANSCRIPT" EXACT VAR []
synonym: "transcript variant" EXACT []
synonym: "VAAST:transcript_variant" EXACT VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001564 ! gene_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:32:41Z
[Term]
id: SO:0001577
name: complex_transcript_variant
def: "A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border." [http://ensembl.org/info/docs/variation/index.html]
comment: EBI term: Complex InDel - Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border.
synonym: "complex transcript variant" EXACT []
synonym: "complex_indel" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "complext change in transcript" EXACT []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:33:03Z
[Term]
id: SO:0001578
name: stop_lost
def: "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript." [SO:ke]
comment: EBI term: Stop lost - In coding sequence, resulting in the loss of a stop codon.
synonym: "ANNOVAR:stoploss" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "snpEff:STOP_LOST" EXACT VAR []
synonym: "stop codon lost" EXACT []
synonym: "stop lost" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "VAAST:stop_lost" EXACT VAR []
is_a: SO:0001590 ! terminator_codon_variant
is_a: SO:0001907 ! feature_elongation
is_a: SO:0001992 ! nonsynonymous_variant
created_by: kareneilbeck
creation_date: 2010-03-23T03:46:42Z
[Term]
id: SO:0001579
name: transcript_sequence_variant
synonym: "transcript sequence variant" EXACT []
is_obsolete: true
[Term]
id: SO:0001580
name: coding_sequence_variant
alt_id: SO:0001581
def: "A sequence variant that changes the coding sequence." [SO:ke]
synonym: "coding sequence variant" EXACT []
synonym: "coding variant" EXACT []
synonym: "codon variant" EXACT []
synonym: "codon_variant" EXACT []
synonym: "snpEff:CDS" EXACT VAR []
synonym: "snpEff:CODON_CHANGE" RELATED VAR []
synonym: "VAAST:coding_sequence_variant" EXACT VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001791 ! exon_variant
is_a: SO:0001968 ! coding_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:34:36Z
[Term]
id: SO:0001582
name: initiator_codon_variant
def: "A codon variant that changes at least one base of the first codon of a transcript." [SO:ke]
comment: This is being used to annotate changes to the first codon of a transcript, when the first annotated codon is not to methionine. A variant is predicted to change the first amino acid of a translation irrespective of the fact that the underlying codon is an AUG. As such for transcripts with an incomplete CDS (sequence does not start with an AUG), it is still called.
synonym: "initiatior codon variant" EXACT []
synonym: "initiator codon change" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
xref: loinc:LA6695-6 "Initiating Methionine"
is_a: SO:0001580 ! coding_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:35:18Z
[Term]
id: SO:0001583
name: missense_variant
alt_id: SO:0001584
alt_id: SO:0001783
def: "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved." [EBI:fc, EBI:gr, SO:ke]
comment: EBI term: Non-synonymous SNPs. SNPs that are located in the coding sequence and result in an amino acid change in the encoded peptide sequence. A change that causes a non_synonymous_codon can be more than 3 bases - for example 4 base substitution.
synonym: "ANNOVAR:nonsynonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "missense" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "missense codon" EXACT []
synonym: "snpEff:NON_SYSNONYMOUS_CODING" EXACT VAR []
synonym: "VAAST:non_synonymous_codon" RELATED VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
xref: http://en.wikipedia.org/wiki/Missense_mutation
xref: loinc:LA6698-0 "Missense"
is_a: SO:0001992 ! nonsynonymous_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:35:49Z
[Term]
id: SO:0001585
name: conservative_missense_variant
def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious." [SO:ke]
synonym: "conservative missense codon" EXACT []
synonym: "conservative missense variant" EXACT []
synonym: "neutral missense codon" RELATED []
synonym: "quiet missense codon" RELATED []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001583 ! missense_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:36:40Z
[Term]
id: SO:0001586
name: non_conservative_missense_variant
def: "A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties." [SO:ke]
synonym: "non conservative missense codon" EXACT []
synonym: "non conservative missense variant" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001583 ! missense_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:37:16Z
[Term]
id: SO:0001587
name: stop_gained
def: "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript." [SO:ke]
comment: EBI term: Stop gained - In coding sequence, resulting in the gain of a stop codon (i.e. leading to a shortened peptide sequence).
synonym: "ANNOVAR:stopgain" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "nonsense" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "nonsense codon" EXACT []
synonym: "snpEFF:STOP_GAINED" EXACT VAR []
synonym: "stop codon gained" RELATED []
synonym: "stop gained" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "VAAST:stop_gained" EXACT VAR []
xref: loinc:LA6699-8 "Nonsense"
is_a: SO:0001906 ! feature_truncation
is_a: SO:0001992 ! nonsynonymous_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:37:52Z
[Term]
id: SO:0001589
name: frameshift_variant
def: "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]
comment: EBI term:Frameshift variations - In coding sequence, resulting in a frameshift.
synonym: "ANNOVAR:frameshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "frameshift variant" EXACT []
synonym: "frameshift_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "frameshift_coding" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "snpEff:FRAME_SHIFT" EXACT VAR []
synonym: "VAAST:frameshift_variant" EXACT VAR []
xref: loinc:LA6694-9 "Frameshift"
is_a: SO:0001818 ! protein_altering_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:40:19Z
[Term]
id: SO:0001590
name: terminator_codon_variant
alt_id: SO:0001625
def: "A sequence variant whereby at least one of the bases in the terminator codon is changed." [SO:ke]
comment: The terminal codon may be the terminator, or in an incomplete transcript the last available codon.
synonym: "terminal codon variant" EXACT []
synonym: "terminal_codon_variant" EXACT []
synonym: "terminator codon variant" EXACT []
xref: loinc:LA6700-2 "Stop Codon Mutation"
is_a: SO:0001580 ! coding_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:40:37Z
[Term]
id: SO:0001591
name: frame_restoring_variant
def: "A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]
synonym: "frame restoring variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:41:09Z
[Term]
id: SO:0001592
name: minus_1_frameshift_variant
def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]
synonym: "-1 frameshift variant" EXACT []
synonym: "minus 1 frameshift variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:41:30Z
[Term]
id: SO:0001593
name: minus_2_frameshift_variant
synonym: "-2 frameshift variant" EXACT []
synonym: "minus 2 frameshift variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:41:52Z
[Term]
id: SO:0001594
name: plus_1_frameshift_variant
def: "A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward." [http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.08.120174.001535]
synonym: "+1 frameshift variant" EXACT []
synonym: "plus 1 frameshift variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:42:06Z
[Term]
id: SO:0001595
name: plus_2_frameshift_variant
synonym: "+2 frameshift variant" EXACT []
synonym: "plus 2 frameshift variant" EXACT []
is_a: SO:0001589 ! frameshift_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:42:23Z
[Term]
id: SO:0001596
name: transcript_secondary_structure_variant
def: "A sequence variant within a transcript that changes the secondary structure of the RNA product." [SO:ke]
synonym: "transcript secondary structure variant" EXACT []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:43:18Z
[Term]
id: SO:0001597
name: compensatory_transcript_secondary_structure_variant
def: "A secondary structure variant that compensate for the change made by a previous variant." [SO:ke]
synonym: "compensatory transcript secondary structure variant" EXACT []
is_a: SO:0001596 ! transcript_secondary_structure_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:43:54Z
[Term]
id: SO:0001598
name: translational_product_structure_variant
def: "A sequence variant within the transcript that changes the structure of the translational product." [SO:ke]
synonym: "translational product structure variant" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001564 ! gene_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:44:17Z
[Term]
id: SO:0001599
name: 3D_polypeptide_structure_variant
def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke]
synonym: "3D polypeptide structure variant" EXACT []
is_a: SO:0001539 ! translational_product_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:44:46Z
[Term]
id: SO:0001600
name: complex_3D_structural_variant
def: "A sequence variant that changes the resulting polypeptide structure." [SO:ke]
synonym: "complex 3D structural variant" EXACT []
is_a: SO:0001599 ! 3D_polypeptide_structure_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:45:13Z
[Term]
id: SO:0001601
name: conformational_change_variant
def: "A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence." [SO:ke]
synonym: "conformational change variant" EXACT []
is_a: SO:0001599 ! 3D_polypeptide_structure_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:45:48Z
[Term]
id: SO:0001602
name: complex_change_of_translational_product_variant
synonym: "complex change of translational product variant" EXACT []
is_a: SO:0001539 ! translational_product_function_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:46:54Z
[Term]
id: SO:0001603
name: polypeptide_sequence_variant
def: "A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence." [SO:ke]
synonym: "polypeptide sequence variant" EXACT []
is_a: SO:0001598 ! translational_product_structure_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:47:13Z
[Term]
id: SO:0001604
name: amino_acid_deletion
def: "A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide." [SO:ke]
synonym: "amino acid deletion" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:47:36Z
[Term]
id: SO:0001605
name: amino_acid_insertion
def: "A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide." [SO:ke]
synonym: "amino acid insertion" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:47:56Z
[Term]
id: SO:0001606
name: amino_acid_substitution
def: "A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide." [SO:ke]
synonym: "amino acid substitution" EXACT []
synonym: "VAAST:amino_acid_substitution" EXACT VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:48:17Z
[Term]
id: SO:0001607
name: conservative_amino_acid_substitution
def: "A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide." [SO:ke]
synonym: "conservative amino acid substitution" EXACT []
is_a: SO:0001606 ! amino_acid_substitution
created_by: kareneilbeck
creation_date: 2010-03-22T02:48:57Z
[Term]
id: SO:0001608
name: non_conservative_amino_acid_substitution
def: "A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide." [SO:ke]
synonym: "non conservative amino acid substitution" EXACT []
is_a: SO:0001606 ! amino_acid_substitution
created_by: kareneilbeck
creation_date: 2010-03-22T02:49:23Z
[Term]
id: SO:0001609
name: elongated_polypeptide
def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence." [SO:ke]
synonym: "elongated polypeptide" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:49:52Z
[Term]
id: SO:0001610
name: elongated_polypeptide_C_terminal
def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
synonym: "elongated polypeptide C terminal" EXACT []
is_a: SO:0001609 ! elongated_polypeptide
created_by: kareneilbeck
creation_date: 2010-03-22T02:50:20Z
[Term]
id: SO:0001611
name: elongated_polypeptide_N_terminal
def: "A sequence variant with in the CDS that causes elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
synonym: "elongated polypeptide N terminal" EXACT []
is_a: SO:0001609 ! elongated_polypeptide
created_by: kareneilbeck
creation_date: 2010-03-22T02:50:31Z
[Term]
id: SO:0001612
name: elongated_in_frame_polypeptide_C_terminal
def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
synonym: "elongated in frame polypeptide C terminal" EXACT []
is_a: SO:0001610 ! elongated_polypeptide_C_terminal
created_by: kareneilbeck
creation_date: 2010-03-22T02:51:05Z
[Term]
id: SO:0001613
name: elongated_out_of_frame_polypeptide_C_terminal
def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus." [SO:ke]
synonym: "elongated polypeptide out of frame C terminal" EXACT []
is_a: SO:0001610 ! elongated_polypeptide_C_terminal
created_by: kareneilbeck
creation_date: 2010-03-22T02:51:20Z
[Term]
id: SO:0001614
name: elongated_in_frame_polypeptide_N_terminal_elongation
def: "A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
synonym: "elongated in frame polypeptide N terminal" EXACT []
is_a: SO:0001611 ! elongated_polypeptide_N_terminal
created_by: kareneilbeck
creation_date: 2010-03-22T02:51:49Z
[Term]
id: SO:0001615
name: elongated_out_of_frame_polypeptide_N_terminal
def: "A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus." [SO:ke]
synonym: "elongated out of frame N terminal" EXACT []
is_a: SO:0001611 ! elongated_polypeptide_N_terminal
created_by: kareneilbeck
creation_date: 2010-03-22T02:52:05Z
[Term]
id: SO:0001616
name: polypeptide_fusion
def: "A sequence variant that causes a fusion of two polypeptide sequences." [SO:ke]
synonym: "polypeptide fusion" EXACT []
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:52:43Z
[Term]
id: SO:0001617
name: polypeptide_truncation
def: "A sequence variant of the CD that causes a truncation of the resulting polypeptide." [SO:ke]
synonym: "polypeptide truncation" EXACT []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
is_a: SO:0001603 ! polypeptide_sequence_variant
created_by: kareneilbeck
creation_date: 2010-03-22T02:53:07Z
[Term]
id: SO:0001618
name: inactive_catalytic_site
def: "A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence." [SO:ke]
synonym: "inactive catalytic site" EXACT []
is_a: SO:0001560 ! inactive_ligand_binding_site
created_by: kareneilbeck
creation_date: 2010-03-22T03:06:14Z
[Term]
id: SO:0001619
name: non_coding_transcript_variant
def: "A transcript variant of a non coding RNA gene." [SO:ke]
comment: Within non-coding gene - Located within a gene that does not code for a protein.
synonym: "ANNOVAR:ncRNA" RELATED VAR [http:http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "nc transcript variant" EXACT []
synonym: "non coding transcript variant" EXACT []
synonym: "within_non_coding_gene" EXACT dbsnp [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:16:23Z
[Term]
id: SO:0001620
name: mature_miRNA_variant
def: "A transcript variant located with the sequence of the mature miRNA." [SO:ke]
comment: EBI term: Within mature miRNA - Located within a microRNA.
synonym: "mature miRNA variant" EXACT []
synonym: "within_mature_miRNA" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001619 ! non_coding_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:16:58Z
[Term]
id: SO:0001621
name: NMD_transcript_variant
def: "A variant in a transcript that is the target of NMD." [SO:ke]
synonym: "NMD transcript variant" EXACT []
synonym: "NMD_transcript" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:20:40Z
[Term]
id: SO:0001622
name: UTR_variant
def: "A transcript variant that is located within the UTR." [SO:ke]
synonym: "UTR variant" EXACT []
synonym: "UTR_" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001791 ! exon_variant
is_a: SO:0001968 ! coding_transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:22:58Z
[Term]
id: SO:0001623
name: 5_prime_UTR_variant
def: "A UTR variant of the 5' UTR." [SO:ke]
comment: EBI term: 5prime UTR variations - In 5prime UTR (untranslated region).
synonym: "5'UTR variant" EXACT []
synonym: "5PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "ANNOVAR:UTR5" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "five prime UTR variant" EXACT []
synonym: "snpEff:UTR_5_PRIME" EXACT VAR []
synonym: "untranslated-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "VAAST:five_prime_UTR_variant" EXACT VAR []
is_a: SO:0001622 ! UTR_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:23:29Z
[Term]
id: SO:0001624
name: 3_prime_UTR_variant
def: "A UTR variant of the 3' UTR." [SO:ke]
comment: EBI term 3prime UTR variations - In 3prime UTR.
synonym: "3'UTR variant" EXACT []
synonym: "3PRIME_UTR" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "ANNOVAR:UTR3" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "snpEff:UTR_3_PRIME" EXACT VAR []
synonym: "three prime UTR variant" EXACT []
synonym: "untranslated-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "VAAST:three_prime_UTR_variant" EXACT VAR []
is_a: SO:0001622 ! UTR_variant
created_by: kareneilbeck
creation_date: 2010-03-23T11:23:54Z
[Term]
id: SO:0001626
name: incomplete_terminal_codon_variant
def: "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed." [SO:ke]
comment: EBI term: Partial codon - Located within the final, incomplete codon of a transcript with a shortened coding sequence where the end is unknown.
synonym: "incomplete terminal codon variant" EXACT []
synonym: "partial_codon" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001590 ! terminator_codon_variant
is_a: SO:0001650 ! inframe_variant
created_by: kareneilbeck
creation_date: 2010-03-23T03:51:15Z
[Term]
id: SO:0001627
name: intron_variant
def: "A transcript variant occurring within an intron." [SO:ke]
comment: EBI term: Intronic variations - In intron.
synonym: "ANNOVAR:intronic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "intron variant" EXACT []
synonym: "intron_" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "intronic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "snpEff:INTRON" EXACT VAR []
synonym: "VAAST:intron_variant" EXACT VAR []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2010-03-23T03:52:38Z
[Term]
id: SO:0001628
name: intergenic_variant
def: "A sequence variant located in the intergenic region, between genes." [SO:ke]
comment: EBI term Intergenic variations - More than 5 kb either upstream or downstream of a transcript.
synonym: "ANNOVAR:intergenic" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "intergenic" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "intergenic variant" EXACT []
synonym: "snpEff:INTERGENIC" EXACT VAR []
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2010-03-23T05:07:37Z
[Term]
id: SO:0001629
name: splice_site_variant
def: "A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript." [http://ensembl.org/info/docs/variation/index.html]
comment: EBI term - essential splice site - In the first 2 or the last 2 base pairs of an intron. The 5th base is on the donor (5') side of the intron. Updated to b in line with Cancer Genome Project at the Sanger.
synonym: "essential_splice_site" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "splice site variant" EXACT []
is_a: SO:0001568 ! splicing_variant
is_a: SO:0001627 ! intron_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:42:00Z
[Term]
id: SO:0001630
name: splice_region_variant
def: "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [http://ensembl.org/info/docs/variation/index.html]
comment: EBI term: splice site - 1-3 bps into an exon or 3-8 bps into an intron.
synonym: "ANNOVAR:splicing" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "splice region variant" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "VAAST:splice_region_variant" EXACT VAR []
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:46:02Z
[Term]
id: SO:0001631
name: upstream_gene_variant
def: "A sequence variant located 5' of a gene." [SO:ke]
comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
synonym: "ANNOVAR:upstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "snpEff:UPSTREAM" EXACT VAR []
synonym: "upstream gene variant" EXACT []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:49:13Z
[Term]
id: SO:0001632
name: downstream_gene_variant
def: "A sequence variant located 3' of a gene." [SO:ke]
comment: Different groups annotate up and downstream to different lengths. The subtypes are specific and are backed up with cross references.
synonym: "ANNOVAR:downstream" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "downstream gene variant" EXACT []
synonym: "snpEff:DOWNSTREAM" EXACT VAR []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:49:38Z
[Term]
id: SO:0001633
name: 5KB_downstream_variant
def: "A sequence variant located within 5 KB of the end of a gene." [SO:ke]
comment: EBI term Downstream variations - Within 5 kb downstream of the 3prime end of a transcript.
synonym: "5KB downstream variant" EXACT []
synonym: "downstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
synonym: "within 5KB downstream" RELATED []
is_a: SO:0001632 ! downstream_gene_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:50:16Z
[Term]
id: SO:0001634
name: 500B_downstream_variant
def: "A sequence variant located within a half KB of the end of a gene." [SO:ke]
synonym: "500B downstream variant" EXACT []
synonym: "near-gene-3" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
is_a: SO:0001633 ! 5KB_downstream_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:50:42Z
[Term]
id: SO:0001635
name: 5KB_upstream_variant
def: "A sequence variant located within 5KB 5' of a gene." [SO:ke]
comment: EBI term Upstream variations - Within 5 kb upstream of the 5prime end of a transcript.
synonym: "5kb upstream variant" EXACT []
synonym: "upstream" EXACT ebi_variants [http://ensembl.org/info/docs/variation/index.html]
is_a: SO:0001631 ! upstream_gene_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:51:06Z
[Term]
id: SO:0001636
name: 2KB_upstream_variant
def: "A sequence variant located within 2KB 5' of a gene." [SO:ke]
synonym: "2KB upstream variant" EXACT []
synonym: "near-gene-5" EXACT dbsnp [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
is_a: SO:0001635 ! 5KB_upstream_variant
created_by: kareneilbeck
creation_date: 2010-03-24T09:51:22Z
[Term]
id: SO:0001637
name: rRNA_gene
def: "A gene that encodes for ribosomal RNA." [SO:ke]
synonym: "rDNA" EXACT []
synonym: "rRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:10:32Z
[Term]
id: SO:0001638
name: piRNA_gene
def: "A gene that encodes for an piwi associated RNA." [SO:ke]
synonym: "piRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:11:36Z
[Term]
id: SO:0001639
name: RNase_P_RNA_gene
def: "A gene that encodes an RNase P RNA." [SO:ke]
synonym: "RNase P RNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:13:23Z
[Term]
id: SO:0001640
name: RNase_MRP_RNA_gene
def: "A gene that encodes a RNase_MRP_RNA." [SO:ke]
synonym: "RNase MRP RNA gene" RELATED []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:13:58Z
[Term]
id: SO:0001641
name: lincRNA_gene
def: "A gene that encodes large intervening non-coding RNA." [SO:ke]
synonym: "lincRNA gene" EXACT []
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-04-21T10:14:24Z
[Term]
id: SO:0001642
name: mathematically_defined_repeat
def: "A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness." [SO:jestill]
comment: Mathematically defined repeat regions are determined without regard to the biological origin of the repetitive region. The repeat units of a MDR are the overlapping oligomers of size k that were used to for the query. Tools that can annotate mathematically defined repeats include Tallymer (Kurtz et al 2008, BMC Genomics: 517) and RePS (Wang et al, Genome Res 12(5): 824-831.).
synonym: "mathematically defined repeat" EXACT []
is_a: SO:0001410 ! experimental_feature
created_by: kareneilbeck
creation_date: 2010-05-03T11:50:14Z
[Term]
id: SO:0001643
name: telomerase_RNA_gene
def: "A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase." [SO:ke]
synonym: "Telomerase RNA component" EXACT []
synonym: "telomerase RNA gene" EXACT []
synonym: "TERC" EXACT []
xref: http:http://en.wikipedia.org/wiki/Telomerase_RNA_component "wikipedia"
is_a: SO:0001263 ! ncRNA_gene
created_by: kareneilbeck
creation_date: 2010-05-18T05:26:38Z
[Term]
id: SO:0001644
name: targeting_vector
def: "An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications." [MGD:tm, PMID:10354467]
synonym: "targeting vector" RELATED []
is_a: SO:0000440 ! vector_replicon
is_a: SO:0000804 ! engineered_region
relationship: has_part SO:0000853 ! homologous_region
relationship: has_quality SO:0000783 ! engineered
created_by: kareneilbeck
creation_date: 2010-05-28T02:05:25Z
[Term]
id: SO:0001645
name: genetic_marker
def: "A measurable sequence feature that varies within a population." [SO:db]
synonym: "genetic marker" RELATED []
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2010-05-28T02:33:07Z
[Term]
id: SO:0001646
name: DArT_marker
def: "A genetic marker, discovered using Diversity Arrays Technology (DArT) technology." [SO:ke]
synonym: "DArT marker" EXACT []
is_a: SO:0001645 ! genetic_marker
created_by: kareneilbeck
creation_date: 2010-05-28T02:34:43Z
[Term]
id: SO:0001647
name: kozak_sequence
def: "A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence." [SO:ke]
subset: SOFA
synonym: "kozak consensus" EXACT []
synonym: "kozak consensus sequence" EXACT []
synonym: "kozak sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Kozak_consensus_sequence "wikipedia"
is_a: SO:0000139 ! ribosome_entry_site
created_by: kareneilbeck
creation_date: 2010-06-07T03:12:20Z
[Term]
id: SO:0001648
name: nested_transposon
def: "A transposon that is disrupted by the insertion of another element." [SO:ke]
synonym: "nested transposon" EXACT []
is_a: SO:0000101 ! transposable_element
created_by: kareneilbeck
creation_date: 2010-06-23T03:22:57Z
[Term]
id: SO:0001649
name: nested_repeat
def: "A repeat that is disrupted by the insertion of another element." [SO:ke]
synonym: "nested repeat" RELATED []
is_a: SO:0000657 ! repeat_region
created_by: kareneilbeck
creation_date: 2010-06-23T03:24:55Z
[Term]
id: SO:0001650
name: inframe_variant
def: "A sequence variant which does not cause a disruption of the translational reading frame." [SO:ke]
synonym: "ANNOVAR:nonframeshift block substitution" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "cds-indel" EXACT dbsnp []
synonym: "inframe variant" EXACT []
synonym: "VAAST:inframe_variant" EXACT VAR []
is_a: SO:0001818 ! protein_altering_variant
created_by: kareneilbeck
creation_date: 2010-07-19T01:24:44Z
[Term]
id: SO:0001653
name: retinoic_acid_responsive_element
def: "A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind." [PMID:11327309, PMID:19917671]
synonym: "RARE" EXACT []
synonym: "retinoic acid responsive element" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000167 ! promoter
created_by: kareneilbeck
creation_date: 2010-08-03T10:46:12Z
[Term]
id: SO:0001654
name: nucleotide_to_protein_binding_site
def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke]
subset: SOFA
synonym: "nucleotide to protein binding site" RELATED []
is_a: SO:0000410 ! protein_binding_site
created_by: kareneilbeck
creation_date: 2010-08-03T12:26:05Z
[Term]
id: SO:0001655
name: nucleotide_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues." [SO:cb]
comment: See GO:0000166 : nucleotide binding.
synonym: "np_bind" EXACT BS [uniprot:feature]
synonym: "nucleotide binding site" EXACT []
is_a: SO:0000409 ! binding_site
created_by: kareneilbeck
creation_date: 2010-08-03T12:30:04Z
[Term]
id: SO:0001656
name: metal_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with metal ions." [SO:cb]
comment: See GO:0046872 : metal ion binding.
synonym: "metal binding site" RELATED []
is_a: SO:0000409 ! binding_site
created_by: kareneilbeck
creation_date: 2010-08-03T12:31:42Z
[Term]
id: SO:0001657
name: ligand_binding_site
def: "A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone." [SO:ke]
synonym: "ligand binding site" EXACT []
is_a: SO:0000409 ! binding_site
created_by: kareneilbeck
creation_date: 2010-08-03T12:32:58Z
[Term]
id: SO:0001658
name: nested_tandem_repeat
def: "An NTR is a nested repeat of two distinct tandem motifs interspersed with each other." [SO:AF]
comment: Tracker ID: 3052459.
synonym: "nested tandem repeat" EXACT []
synonym: "NTR" EXACT []
is_a: SO:0001649 ! nested_repeat
created_by: kareneilbeck
creation_date: 2010-08-26T09:36:16Z
[Term]
id: SO:0001659
name: promoter_element
synonym: "promoter element" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: overlaps SO:0000235 ! TF_binding_site
created_by: kareneilbeck
creation_date: 2010-10-01T11:48:32Z
[Term]
id: SO:0001660
name: core_promoter_element
synonym: "core promoter element" EXACT []
synonym: "general transcription factor binding site" RELATED []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2010-10-01T11:49:03Z
[Term]
id: SO:0001661
name: RNA_polymerase_II_TATA_box
def: "A TATA box core promoter of a gene transcribed by RNA polymerase II." [PMID:16858867]
synonym: "RNA polymerase II TATA box" EXACT []
is_a: SO:0000174 ! TATA_box
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T02:42:12Z
[Term]
id: SO:0001662
name: RNA_polymerase_III_TATA_box
def: "A TATA box core promoter of a gene transcribed by RNA polymerase III." [SO:ke]
synonym: "RNA polymerase III TATA box" EXACT []
is_a: SO:0000174 ! TATA_box
relationship: part_of SO:0000171 ! RNApol_III_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T02:43:16Z
[Term]
id: SO:0001663
name: BREd_motif
def: "A core TRNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G)." [PMID:16858867]
synonym: "BREd" EXACT []
synonym: "BREd motif" RELATED []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T02:49:55Z
[Term]
id: SO:0001664
name: DCE
def: "A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII." [PMID:16858867]
synonym: "downstream core element" RELATED []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0001669 ! RNApol_II_core_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T02:56:41Z
[Term]
id: SO:0001665
name: DCE_SI
def: "A sub element of the DCE core promoter element, with consensus sequence CTTC." [PMID:16858867, SO:ke]
synonym: "DCE SI" RELATED []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001664 ! DCE
created_by: kareneilbeck
creation_date: 2010-10-01T03:00:10Z
[Term]
id: SO:0001666
name: DCE_SII
def: "A sub element of the DCE core promoter element with consensus sequence CTGT." [PMID:16858867, SO:ke]
synonym: "DCE SII" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001664 ! DCE
created_by: kareneilbeck
creation_date: 2010-10-01T03:00:30Z
[Term]
id: SO:0001667
name: DCE_SIII
def: "A sub element of the DCE core promoter element with consensus sequence AGC." [PMID:16858867, SO:ke]
synonym: "DCE SIII" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001664 ! DCE
created_by: kareneilbeck
creation_date: 2010-10-01T03:00:44Z
[Term]
id: SO:0001668
name: proximal_promoter_element
def: "DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor)." [PMID:12515390, PMID:9679020, SO:ml]
synonym: "proximal promoter element" RELATED []
synonym: "specific transcription factor binding site" RELATED []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2010-10-01T03:10:23Z
[Term]
id: SO:0001669
name: RNApol_II_core_promoter
def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867]
synonym: "RNApol II core promoter" EXACT []
is_a: SO:0000170 ! RNApol_II_promoter
created_by: kareneilbeck
creation_date: 2010-10-01T03:13:41Z
[Term]
id: SO:0001670
name: distal_promoter_element
synonym: "distal promoter element" RELATED []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2010-10-01T03:21:08Z
[Term]
id: SO:0001671
name: bacterial_RNApol_promoter_sigma_70
synonym: "bacterial RNA polymerase promoter sigma 70" EXACT []
is_a: SO:0000613 ! bacterial_RNApol_promoter
created_by: kareneilbeck
creation_date: 2010-10-06T01:41:34Z
[Term]
id: SO:0001672
name: bacterial_RNApol_promoter_sigma54
synonym: "bacterial RNA polymerase promoter sigma54" EXACT []
is_a: SO:0000613 ! bacterial_RNApol_promoter
created_by: kareneilbeck
creation_date: 2010-10-06T01:42:37Z
[Term]
id: SO:0001673
name: minus_12_signal
def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]
synonym: "minus 12 signal" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54
created_by: kareneilbeck
creation_date: 2010-10-06T01:44:57Z
[Term]
id: SO:0001674
name: minus_24_signal
def: "A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54." [PMID:18331472]
synonym: "minus 24 signal" RELATED []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001672 ! bacterial_RNApol_promoter_sigma54
created_by: kareneilbeck
creation_date: 2010-10-06T01:45:24Z
[Term]
id: SO:0001675
name: A_box_type_1
def: "An A box within an RNA polymerase III type 1 promoter." [SO:ke]
comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
synonym: "A box type 1" RELATED []
is_a: SO:0000619 ! A_box
relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
created_by: kareneilbeck
creation_date: 2010-10-06T05:43:43Z
[Term]
id: SO:0001676
name: A_box_type_2
def: "An A box within an RNA polymerase III type 2 promoter." [SO:ke]
comment: The A box can be found in the promoters of type 1 and type 2 (pol III) so sub-typing here allows the part of relationship of the subtypes to remain true.
synonym: "A box type 2" RELATED []
is_a: SO:0000619 ! A_box
relationship: part_of SO:0000618 ! RNApol_III_promoter_type_2
created_by: kareneilbeck
creation_date: 2010-10-06T05:44:18Z
[Term]
id: SO:0001677
name: intermediate_element
def: "A core promoter region of RNA polymerase III type 1 promoters." [PMID:12381659]
synonym: "IE" EXACT []
synonym: "intermediate element" RELATED []
is_a: SO:0001660 ! core_promoter_element
relationship: part_of SO:0000617 ! RNApol_III_promoter_type_1
created_by: kareneilbeck
creation_date: 2010-10-06T05:52:03Z
[Term]
id: SO:0001678
name: regulatory_promoter_element
def: "A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region." [PMID:12381659]
synonym: "regulatory promoter element" RELATED []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2010-10-07T04:39:48Z
[Term]
id: SO:0001679
name: transcription_regulatory_region
def: "A regulatory region that is involved in the control of the process of transcription." [SO:ke]
subset: SOFA
synonym: "transcription regulatory region" EXACT []
is_a: SO:0005836 ! regulatory_region
created_by: kareneilbeck
creation_date: 2010-10-12T03:49:35Z
[Term]
id: SO:0001680
name: translation_regulatory_region
def: "A regulatory region that is involved in the control of the process of translation." [SO:ke]
synonym: "translation regulatory region" EXACT []
is_a: SO:0005836 ! regulatory_region
created_by: kareneilbeck
creation_date: 2010-10-12T03:52:45Z
[Term]
id: SO:0001681
name: recombination_regulatory_region
def: "A regulatory region that is involved in the control of the process of recombination." [SO:ke]
synonym: "recombination regulatory region" EXACT []
is_a: SO:0005836 ! regulatory_region
created_by: kareneilbeck
creation_date: 2010-10-12T03:53:35Z
[Term]
id: SO:0001682
name: replication_regulatory_region
def: "A regulatory region that is involved in the control of the process of nucleotide replication." [SO:ke]
synonym: "replication regulatory region" RELATED []
is_a: SO:0005836 ! regulatory_region
created_by: kareneilbeck
creation_date: 2010-10-12T03:54:09Z
[Term]
id: SO:0001683
name: sequence_motif
def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif]
subset: SOFA
synonym: "sequence motif" RELATED []
xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia"
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2010-10-14T04:13:22Z
[Term]
id: SO:0001684
name: experimental_feature_attribute
def: "An attribute of an experimentally derived feature." [SO:ke]
synonym: "experimental feature attribute" RELATED []
is_a: SO:0000733 ! feature_attribute
created_by: kareneilbeck
creation_date: 2010-10-28T02:22:23Z
[Term]
id: SO:0001685
name: score
def: "The score of an experimentally derived feature such as a p-value." [SO:ke]
is_a: SO:0001684 ! experimental_feature_attribute
created_by: kareneilbeck
creation_date: 2010-10-28T02:23:16Z
[Term]
id: SO:0001686
name: quality_value
def: "An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score." [SO:ke]
synonym: "quality value" RELATED []
is_a: SO:0001684 ! experimental_feature_attribute
created_by: kareneilbeck
creation_date: 2010-10-28T02:24:11Z
[Term]
id: SO:0001687
name: restriction_enzyme_recognition_site
def: "The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site." [SO:ke]
synonym: "restriction endonuclease recognition site" EXACT []
synonym: "restriction enzyme recognition site" EXACT []
is_a: SO:0001954 ! restriction_enzyme_region
created_by: kareneilbeck
creation_date: 2010-10-29T12:29:57Z
[Term]
id: SO:0001688
name: restriction_enzyme_cleavage_junction
def: "The boundary at which a restriction enzyme breaks the nucleotide sequence." [SO:ke]
synonym: "restriction enzyme cleavage junction" EXACT []
is_a: SO:0000699 ! junction
created_by: kareneilbeck
creation_date: 2010-10-29T12:35:02Z
[Term]
id: SO:0001689
name: five_prime_restriction_enzyme_junction
def: "The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence." [SO:ke]
synonym: "5' restriction enzyme junction" EXACT []
is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site
relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:36:24Z
[Term]
id: SO:0001690
name: three_prime_restriction_enzyme_junction
synonym: "3' restriction enzyme junction" EXACT []
is_a: SO:0001694 ! single_strand_restriction_enzyme_cleavage_site
relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:37:52Z
[Term]
id: SO:0001691
name: blunt_end_restriction_enzyme_cleavage_site
synonym: "blunt end restriction enzyme cleavage site" EXACT []
is_a: SO:0001687 ! restriction_enzyme_recognition_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:39:53Z
[Term]
id: SO:0001692
name: sticky_end_restriction_enzyme_cleavage_site
synonym: "sticky end restriction enzyme cleavage site" RELATED []
is_a: SO:0001687 ! restriction_enzyme_recognition_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:40:50Z
[Term]
id: SO:0001693
name: blunt_end_restriction_enzyme_cleavage_junction
def: "A restriction enzyme cleavage site where both strands are cut at the same position." [SO:ke]
synonym: "blunt end restriction enzyme cleavage site" RELATED []
is_a: SO:0001688 ! restriction_enzyme_cleavage_junction
relationship: part_of SO:0001691 ! blunt_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:43:14Z
[Term]
id: SO:0001694
name: single_strand_restriction_enzyme_cleavage_site
def: "A restriction enzyme cleavage site whereby only one strand is cut." [SO:ke]
synonym: "single strand restriction enzyme cleavage site" RELATED []
is_a: SO:0001688 ! restriction_enzyme_cleavage_junction
created_by: kareneilbeck
creation_date: 2010-10-29T12:44:48Z
[Term]
id: SO:0001695
name: restriction_enzyme_single_strand_overhang
def: "A terminal region of DNA sequence where the end of the region is not blunt ended." [SO:ke]
synonym: "single strand overhang" EXACT []
synonym: "sticky end" RELATED []
is_a: SO:0001954 ! restriction_enzyme_region
relationship: part_of SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2010-10-29T12:48:35Z
[Term]
id: SO:0001696
name: experimentally_defined_binding_region
def: "A region that has been implicated in binding although the exact coordinates of binding may be unknown." [SO:ke]
synonym: "experimentally defined binding region" RELATED []
is_a: SO:0001410 ! experimental_feature
created_by: kareneilbeck
creation_date: 2010-11-02T11:39:59Z
[Term]
id: SO:0001697
name: ChIP_seq_region
def: "A region of sequence identified by CHiP seq technology to contain a protein binding site." [SO:ke]
synonym: "ChIP seq region" RELATED []
is_a: SO:0001696 ! experimentally_defined_binding_region
relationship: contains SO:0000410 ! protein_binding_site
created_by: kareneilbeck
creation_date: 2010-11-02T11:43:07Z
[Term]
id: SO:0001698
name: ASPE_primer
def: "\"A primer containing an SNV at the 3' end for accurate genotyping." [http://www.ncbi.nlm.nih.gov/pubmed/11252801]
synonym: "allele specific primer extension primer" EXACT []
synonym: "ASPE primer" EXACT []
is_a: SO:0000112 ! primer
created_by: kareneilbeck
creation_date: 2010-11-11T03:25:21Z
[Term]
id: SO:0001699
name: dCAPS_primer
def: "A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site." [http://www.ncbi.nlm.nih.gov/pubmed/9628033]
synonym: "dCAPS primer" EXACT []
synonym: "derived cleaved amplified polymorphic primer" EXACT []
is_a: SO:0000112 ! primer
created_by: kareneilbeck
creation_date: 2010-11-11T03:27:09Z
[Term]
id: SO:0001700
name: histone_modification
def: "Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation." [http:en.wikipedia.org/wiki/Histone]
synonym: "histone modification" EXACT []
synonym: "histone modification site" RELATED []
is_a: SO:0001089 ! post_translationally_modified_region
is_a: SO:0001720 ! epigenetically_modified_region
relationship: has_quality SO:0000133 ! epigenetically_modified
created_by: kareneilbeck
creation_date: 2010-03-31T10:22:08Z
[Term]
id: SO:0001701
name: histone_methylation_site
def: "A histone modification site where the modification is the methylation of the residue." [SO:ke]
synonym: "histone methylation" EXACT []
synonym: "histone methylation site" EXACT []
is_a: SO:0001700 ! histone_modification
created_by: kareneilbeck
creation_date: 2010-03-31T10:23:02Z
[Term]
id: SO:0001702
name: histone_acetylation_site
def: "A histone modification where the modification is the acylation of the residue." [SO:ke]
synonym: "histone acetylation" EXACT []
synonym: "histone acetylation site" EXACT []
is_a: SO:0001700 ! histone_modification
created_by: kareneilbeck
creation_date: 2010-03-31T10:23:27Z
[Term]
id: SO:0001703
name: H3K9_acetylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K9 acetylation site" EXACT []
synonym: "H3K9Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:25:05Z
[Term]
id: SO:0001704
name: H3K14_acetylation_site
def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K14 acetylation site" EXACT []
synonym: "H3K14Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:25:53Z
[Term]
id: SO:0001705
name: H3K4_monomethylation_site
def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K4 mono-methylation site" EXACT []
synonym: "H3K4me1" RELATED []
is_a: SO:0001734 ! H3K4_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:28:14Z
[Term]
id: SO:0001706
name: H3K4_trimethylation
def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K4 tri-methylation" EXACT []
synonym: "H3K4me3" RELATED []
is_a: SO:0001734 ! H3K4_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:29:12Z
[Term]
id: SO:0001707
name: H3K9_trimethylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K9 tri-methylation site" EXACT []
synonym: "H3K9Me3" RELATED []
is_a: SO:0001736 ! H3K9_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:30:34Z
[Term]
id: SO:0001708
name: H3K27_monomethylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H2K27 mono-methylation site" EXACT []
synonym: "H2K27Me1" RELATED []
is_a: SO:0001732 ! H3K27_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:31:54Z
[Term]
id: SO:0001709
name: H3K27_trimethylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K27 tri-methylation site" EXACT []
synonym: "H3K27Me3" RELATED []
is_a: SO:0001732 ! H3K27_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:32:41Z
[Term]
id: SO:0001710
name: H3K79_monomethylation_site
def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K79 mono-methylation site" EXACT []
synonym: "H3K79me1" RELATED []
is_a: SO:0001735 ! H3K79_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:33:42Z
[Term]
id: SO:0001711
name: H3K79_dimethylation_site
def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K79 di-methylation site" EXACT []
synonym: "H3K79Me2" RELATED []
is_a: SO:0001735 ! H3K79_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:34:39Z
[Term]
id: SO:0001712
name: H3K79_trimethylation_site
def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H3K79 tri-methylation site" EXACT []
synonym: "H3K79Me3" RELATED []
is_a: SO:0001735 ! H3K79_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:35:30Z
[Term]
id: SO:0001713
name: H4K20_monomethylation_site
def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H4K20 mono-methylation site" EXACT []
synonym: "H4K20Me1" RELATED []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:36:43Z
[Term]
id: SO:0001714
name: H2BK5_monomethylation_site
def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated." [http://en.wikipedia.org/wiki/Histone]
synonym: "H2BK5 mono-methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-03-31T10:38:12Z
[Term]
id: SO:0001715
name: ISRE
def: "An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding." [http://genesdev.cshlp.org/content/2/4/383.abstrac]
comment: Term requested via tracker (2981725) by Alan Ruttenberg, April 2010. It has been described as both an enhancer and a promoter, so the parent is the more general term.
synonym: "interferon stimulated response element" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
created_by: kareneilbeck
creation_date: 2010-04-05T11:15:08Z
[Term]
id: SO:0001716
name: histone_ubiqitination_site
def: "A histone modification site where ubiquitin may be added." [SO:ke]
synonym: "histone ubiquitination site" RELATED []
is_a: SO:0001700 ! histone_modification
created_by: kareneilbeck
creation_date: 2010-04-13T10:12:18Z
[Term]
id: SO:0001717
name: H2B_ubiquitination_site
def: "A histone modification site on H2B where ubiquitin may be added." [SO:ke]
synonym: "H2BUbiq" RELATED []
is_a: SO:0001716 ! histone_ubiqitination_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:13:28Z
[Term]
id: SO:0001718
name: H3K18_acetylation_site
def: "A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
synonym: "H3K18 acetylation site" EXACT []
synonym: "H3K18Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:39:35Z
[Term]
id: SO:0001719
name: H3K23_acylation_site
def: "A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
synonym: "H3K23 acylation site" RELATED []
synonym: "H3K23Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:42:45Z
[Term]
id: SO:0001720
name: epigenetically_modified_region
def: "A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence." [http://en.wikipedia.org/wiki/Epigenetics, SO:ke]
subset: SOFA
synonym: "epigenetically modified region" RELATED []
is_a: SO:0001411 ! biological_region
relationship: has_quality SO:0000133 ! epigenetically_modified
created_by: kareneilbeck
creation_date: 2010-03-27T12:02:29Z
[Term]
id: SO:0001721
name: H3K27_acylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated." [SO:ke]
synonym: "H3K27 acylation site" EXACT []
synonym: "H3K27Ac" RELATED []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:44:09Z
[Term]
id: SO:0001722
name: H3K36_monomethylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]
synonym: "H3K36 mono-methylation site" EXACT []
synonym: "H3K36<Me1" RELATED []
is_a: SO:0001733 ! H3K36_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:46:32Z
[Term]
id: SO:0001723
name: H3K36_dimethylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated." [SO:ke]
synonym: "H3K36 di-methylation site" EXACT []
synonym: "H3K36Me2" RELATED []
is_a: SO:0001733 ! H3K36_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T10:59:35Z
[Term]
id: SO:0001724
name: H3K36_trimethylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated." [SO:ke]
synonym: "H3K36 tri-methylation site" EXACT []
synonym: "H3K36Me3" RELATED []
is_a: SO:0001733 ! H3K36_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:01:58Z
[Term]
id: SO:0001725
name: H3K4_dimethylation_site
def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]
synonym: "H3K4 di-methylation site" EXACT []
synonym: "H3K4Me2" RELATED []
is_a: SO:0001734 ! H3K4_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:03:15Z
[Term]
id: SO:0001726
name: H3K27_dimethylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated." [SO:ke]
synonym: "H3K27 di-methylation site" EXACT []
synonym: "H3K27Me2" RELATED []
is_a: SO:0001732 ! H3K27_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T01:45:41Z
[Term]
id: SO:0001727
name: H3K9_monomethylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated." [SO:ke]
synonym: "H3K9 mono-methylation site" EXACT []
synonym: "H3K9Me1" RELATED []
is_a: SO:0001736 ! H3K9_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:06:17Z
[Term]
id: SO:0001728
name: H3K9_dimethylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated." [SO:ke]
synonym: "H3K9 di-methylation site" EXACT []
synonym: "H3K9Me2" RELATED []
is_a: SO:0001736 ! H3K9_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:08:19Z
[Term]
id: SO:0001729
name: H4K16_acylation_site
def: "A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
synonym: "H4K16 acylation_site" RELATED []
synonym: "H4K16Ac" RELATED []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:09:41Z
[Term]
id: SO:0001730
name: H4K5_acylation_site
def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:ke]
synonym: "H4K5 acylation site" RELATED []
synonym: "H4K5Ac" RELATED []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:13:00Z
[Term]
id: SO:0001731
name: H4K8_acylation_site
def: "A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acylated." [SO:KE]
synonym: "H4K8 acylation site" RELATED []
synonym: "H4K8Ac" RELATED []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:14:24Z
[Term]
id: SO:0001732
name: H3K27_methylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
synonym: "H3K27 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:26:22Z
[Term]
id: SO:0001733
name: H3K36_methylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
synonym: "H3K36 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:27:28Z
[Term]
id: SO:0001734
name: H3K4_methylation_site
def: "A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated." [SO:ke]
synonym: "H3K4 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:28:14Z
[Term]
id: SO:0001735
name: H3K79_methylation_site
def: "A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
synonym: "H3K79 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:29:16Z
[Term]
id: SO:0001736
name: H3K9_methylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated." [SO:ke]
synonym: "H3K9 methylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2010-04-13T11:31:37Z
[Term]
id: SO:0001737
name: histone_acylation_region
def: "A histone modification, whereby the histone protein is acylated at multiple sites in a region." [SO:ke]
synonym: "histone acylation region" RELATED []
is_a: SO:0001700 ! histone_modification
created_by: kareneilbeck
creation_date: 2010-04-13T01:58:21Z
[Term]
id: SO:0001738
name: H4K_acylation_region
def: "A region of the H4 histone whereby multiple lysines are acylated." [SO:ke]
synonym: "H4K acylation region" EXACT []
synonym: "H4KAc" RELATED []
is_a: SO:0001737 ! histone_acylation_region
created_by: kareneilbeck
creation_date: 2010-04-13T02:00:06Z
[Term]
id: SO:0001739
name: gene_with_non_canonical_start_codon
def: "A gene with a start codon other than AUG." [SO:xp]
comment: Requested by flybase, Dec 2010.
synonym: "gene with non canonical start codon" EXACT []
is_a: SO:0000704 ! gene
relationship: contains SO:0000680 ! non_canonical_start_codon
created_by: kareneilbeck
creation_date: 2011-01-10T01:30:31Z
[Term]
id: SO:0001740
name: gene_with_start_codon_CUG
def: "A gene with a translational start codon of CUG." [SO:mc]
comment: Requested by flybase, Dec 2010.
synonym: "gene with start codon CUG" EXACT []
is_a: SO:0001739 ! gene_with_non_canonical_start_codon
created_by: kareneilbeck
creation_date: 2011-01-10T01:32:35Z
[Term]
id: SO:0001741
name: pseudogenic_gene_segment
def: "A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product." [SO:hd]
synonym: "pseudogenic gene segment" EXACT []
is_a: SO:3000000 ! gene_segment
created_by: batchelorc
creation_date: 2011-02-15T05:07:52Z
[Term]
id: SO:0001742
name: copy_number_gain
def: "A sequence alteration whereby the copy number of a given regions is greater than the reference sequence." [SO:ke]
subset: DBVAR
synonym: "copy number gain" EXACT []
synonym: "gain" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
is_a: SO:0001019 ! copy_number_variation
created_by: kareneilbeck
creation_date: 2011-02-28T01:54:09Z
[Term]
id: SO:0001743
name: copy_number_loss
def: "A sequence alteration whereby the copy number of a given region is less than the reference sequence." [SO:ke]
subset: DBVAR
synonym: "copy number loss" EXACT []
synonym: "loss" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
is_a: SO:0001019 ! copy_number_variation
created_by: kareneilbeck
creation_date: 2011-02-28T01:55:02Z
[Term]
id: SO:0001744
name: UPD
def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent." [SO:BM]
subset: DBVAR
synonym: "uniparental disomy" EXACT []
synonym: "UPD" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
xref: http:http://en.wikipedia.org/wiki/Uniparental_disomy "wikipedia"
is_a: SO:0001059 ! sequence_alteration
created_by: kareneilbeck
creation_date: 2011-02-28T02:01:05Z
[Term]
id: SO:0001745
name: maternal_uniparental_disomy
def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father." [SO:bm]
synonym: "maternal uniparental disomy" EXACT []
is_a: SO:0001744 ! UPD
created_by: kareneilbeck
creation_date: 2011-02-28T02:03:01Z
[Term]
id: SO:0001746
name: paternal_uniparental_disomy
def: "Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother." [SO:bm]
synonym: "paternal uniparental disomy" EXACT []
is_a: SO:0001744 ! UPD
created_by: kareneilbeck
creation_date: 2011-02-28T02:03:30Z
[Term]
id: SO:0001747
name: open_chromatin_region
def: "A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA." [SO:cb]
comment: Requested by John Calley 3125900.
synonym: "open chromatin region" EXACT []
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2011-02-28T02:21:52Z
[Term]
id: SO:0001748
name: SL3_acceptor_site
def: "A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL3 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T02:58:40Z
[Term]
id: SO:0001749
name: SL4_acceptor_site
def: "A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL4 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:08:47Z
[Term]
id: SO:0001750
name: SL5_acceptor_site
def: "A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL5 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:09:36Z
[Term]
id: SO:0001751
name: SL6_acceptor_site
def: "A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL6 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:10:14Z
[Term]
id: SO:0001752
name: SL7_acceptor_site
def: "A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL37 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:13:20Z
[Term]
id: SO:0001753
name: SL8_acceptor_site
def: "A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL8 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:15:26Z
[Term]
id: SO:0001754
name: SL9_acceptor_site
def: "A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL9 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:15:57Z
[Term]
id: SO:0001755
name: SL10_acceptor_site
def: "A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL10 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:16:31Z
[Term]
id: SO:0001756
name: SL11_acceptor_site
def: "A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL11 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:16:54Z
[Term]
id: SO:0001757
name: SL12_acceptor_site
def: "A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts." [SO:nlw]
synonym: "SL12 acceptor site" EXACT []
is_a: SO:0000709 ! SL2_acceptor_site
created_by: kareneilbeck
creation_date: 2011-02-28T03:17:23Z
[Term]
id: SO:0001758
name: duplicated_pseudogene
def: "A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence." [http://en.wikipedia.org/wiki/Pseudogene]
synonym: "duplicated pseudogene" RELATED []
is_a: SO:0001760 ! non_processed_pseudogene
created_by: kareneilbeck
creation_date: 2011-03-09T09:58:04Z
[Term]
id: SO:0001759
name: unitary_pseudogene
def: "A pseudogene, deactivated from original state by mutation, fixed in a population." [http://en.wikipedia.org/wiki/Pseudogene, SO:ke]
comment: This is different from a non processed pseudogene because the gene was not duplicated. An example is the L-gulono-lactone oxidase pseudogene in primates.
synonym: "disabled gene" RELATED []
synonym: "unitary pseudogene" RELATED []
is_a: SO:0001760 ! non_processed_pseudogene
created_by: kareneilbeck
creation_date: 2011-03-09T10:04:04Z
[Term]
id: SO:0001760
name: non_processed_pseudogene
def: "A pseudogene that arose from a means other than retrotransposition." [SO:ke]
synonym: "non processed pseudogene" RELATED []
is_a: SO:0000336 ! pseudogene
created_by: kareneilbeck
creation_date: 2011-03-09T10:54:47Z
[Term]
id: SO:0001761
name: variant_quality
def: "A dependent entity that inheres in a bearer, a sequence variant." [PMID:17597783, SO:ke]
synonym: "variant quality" EXACT []
is_a: SO:0000400 ! sequence_attribute
created_by: kareneilbeck
creation_date: 2011-03-15T03:40:35Z
[Term]
id: SO:0001762
name: variant_origin
def: "A quality inhering in a variant by virtue of its origin." [PMID:17597783, SO:ke]
synonym: "variant origin" EXACT []
is_a: SO:0001761 ! variant_quality
created_by: kareneilbeck
creation_date: 2011-03-15T03:42:13Z
[Term]
id: SO:0001763
name: variant_frequency
def: "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [PMID:17597783, SO:ke]
synonym: "variant frequency" EXACT []
is_a: SO:0001761 ! variant_quality
created_by: kareneilbeck
creation_date: 2011-03-15T03:44:39Z
[Term]
id: SO:0001764
name: unique_variant
def: "A physical quality which inheres to the variant by virtue of the number instances of the variant within a population." [SO:ke]
synonym: "unique variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:47:20Z
[Term]
id: SO:0001765
name: rare_variant
synonym: "rare variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:48:29Z
[Term]
id: SO:0001766
name: polymorphic_variant
synonym: "polymorphic variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:48:51Z
[Term]
id: SO:0001767
name: common_variant
synonym: "common variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:50:36Z
[Term]
id: SO:0001768
name: fixed_variant
synonym: "fixed variant" EXACT []
is_a: SO:0001763 ! variant_frequency
created_by: kareneilbeck
creation_date: 2011-03-15T03:50:53Z
[Term]
id: SO:0001769
name: variant_phenotype
def: "A quality inhering in a variant by virtue of its phenotype." [PMID:17597783, SO:ke]
synonym: "variant phenotype" EXACT []
is_a: SO:0001761 ! variant_quality
created_by: kareneilbeck
creation_date: 2011-03-15T03:53:15Z
[Term]
id: SO:0001770
name: benign_variant
synonym: "benign variant" EXACT []
is_a: SO:0001769 ! variant_phenotype
created_by: kareneilbeck
creation_date: 2011-03-15T03:55:40Z
[Term]
id: SO:0001771
name: disease_associated_variant
synonym: "disease associated variant" EXACT []
is_a: SO:0001769 ! variant_phenotype
created_by: kareneilbeck
creation_date: 2011-03-15T04:05:16Z
[Term]
id: SO:0001772
name: disease_causing_variant
synonym: "disease causing variant" EXACT []
is_a: SO:0001769 ! variant_phenotype
created_by: kareneilbeck
creation_date: 2011-03-15T04:05:46Z
[Term]
id: SO:0001773
name: lethal_variant
synonym: "lethal variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2011-03-15T04:06:22Z
[Term]
id: SO:0001774
name: quantitative_variant
synonym: "quantitative variant" EXACT []
is_a: SO:0001769 ! variant_phenotype
created_by: kareneilbeck
creation_date: 2011-03-15T04:28:13Z
[Term]
id: SO:0001775
name: maternal_variant
synonym: "maternal variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:30:23Z
[Term]
id: SO:0001776
name: paternal_variant
synonym: "paternal variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:30:47Z
[Term]
id: SO:0001777
name: somatic_variant
synonym: "somatic variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:31:12Z
[Term]
id: SO:0001778
name: germline_variant
synonym: "germline variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:31:46Z
[Term]
id: SO:0001779
name: pedigree_specific_variant
synonym: "pedigree specific variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:32:18Z
[Term]
id: SO:0001780
name: population_specific_variant
synonym: "population specific variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:33:05Z
[Term]
id: SO:0001781
name: de_novo_variant
synonym: "de novo variant" EXACT []
is_a: SO:0001762 ! variant_origin
created_by: kareneilbeck
creation_date: 2011-03-15T04:33:34Z
[Term]
id: SO:0001782
name: TF_binding_site_variant
def: "A sequence variant located within a transcription factor binding site." [EBI:fc]
synonym: "TF binding site variant" EXACT []
is_a: SO:0001566 ! regulatory_region_variant
created_by: kareneilbeck
creation_date: 2011-03-17T10:59:20Z
[Term]
id: SO:0001784
name: complex_structural_alteration
alt_id: SO:1000146
def: "A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints." [FB:reference_manual, NCBI:th, SO:ke]
subset: DBVAR
synonym: "complex" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "complex chromosomal mutation" EXACT []
synonym: "complex_chromosomal_mutation" EXACT []
is_a: SO:0001785 ! structural_alteration
is_a: SO:1000183 ! chromosome_structure_variation
created_by: kareneilbeck
creation_date: 2011-03-23T03:21:19Z
[Term]
id: SO:0001785
name: structural_alteration
subset: DBVAR
synonym: "structural alteration" EXACT []
is_a: SO:0001059 ! sequence_alteration
created_by: kareneilbeck
creation_date: 2011-03-25T02:27:41Z
[Term]
id: SO:0001786
name: loss_of_heterozygosity
def: "A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene." [SO:ke]
subset: DBVAR
synonym: "LOH" EXACT []
synonym: "loss of heterozygosity" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2011-03-25T02:32:58Z
[Term]
id: SO:0001787
name: splice_donor_5th_base_variant
def: "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript." [EBI:gr]
synonym: "splice donor 5th base variant" EXACT []
is_a: SO:0001629 ! splice_site_variant
created_by: kareneilbeck
creation_date: 2011-04-05T04:16:28Z
[Term]
id: SO:0001788
name: U_box
def: "An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription." [PMID:10556309, PMID:11577982, PMID:9649446]
synonym: "U-box" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0000186 ! LTR_retrotransposon
created_by: kareneilbeck
creation_date: 2011-04-08T10:39:14Z
[Term]
id: SO:0001789
name: mating_type_region
def: "A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type." [SO:ke]
synonym: "mating type region" EXACT []
xref: http://en.wikipedia.org/wiki/Mating-type_region
is_a: SO:0005855 ! gene_group
created_by: kareneilbeck
creation_date: 2011-04-08T11:14:07Z
[Term]
id: SO:0001790
name: paired_end_fragment
def: "An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair)." [SO:ke]
subset: SOFA
synonym: "paired end fragment" EXACT []
is_a: SO:0000143 ! assembly_component
created_by: kareneilbeck
creation_date: 2011-04-14T01:48:20Z
[Term]
id: SO:0001791
name: exon_variant
def: "A sequence variant that changes exon sequence." [SO:ke]
synonym: "ANNOVAR:exonic" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "exon variant" EXACT []
synonym: "snpEff:EXON" EXACT VAR []
synonym: "VAAST:exon_variant" EXACT VAR []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2011-05-06T01:51:17Z
[Term]
id: SO:0001792
name: non_coding_transcript_exon_variant
def: "A sequence variant that changes non-coding exon sequence in a non-coding transcript." [EBI:fc, SO:ke]
synonym: "non coding transcript exon variant" EXACT []
is_a: SO:0001619 ! non_coding_transcript_variant
is_a: SO:0001791 ! exon_variant
created_by: kareneilbeck
creation_date: 2011-05-06T01:51:59Z
[Term]
id: SO:0001793
name: clone_end
def: "A read from an end of the clone sequence." [SO:ke]
synonym: "clone end" EXACT []
is_a: SO:0000150 ! read
relationship: part_of SO:0000151 ! clone
created_by: kareneilbeck
creation_date: 2011-05-13T11:32:27Z
[Term]
id: SO:0001794
name: point_centromere
def: "A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae." [PMID:7502067, SO:vw]
synonym: "point centromere" EXACT []
is_a: SO:0000577 ! centromere
created_by: kareneilbeck
creation_date: 2011-05-31T12:42:35Z
[Term]
id: SO:0001795
name: regional_centromere
def: "A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions." [PMID:7502067, SO:vw]
synonym: "regional centromere" EXACT []
is_a: SO:0000577 ! centromere
created_by: kareneilbeck
creation_date: 2011-05-31T12:43:07Z
[Term]
id: SO:0001796
name: regional_centromere_central_core
def: "A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw]
synonym: "regional centromere central core" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: part_of SO:0001795 ! regional_centromere
created_by: kareneilbeck
creation_date: 2011-05-31T12:56:30Z
[Term]
id: SO:0001797
name: centromeric_repeat
def: "A repeat region found within the modular centromere." [SO:ke]
synonym: "centromeric repeat" EXACT []
is_a: SO:0000657 ! repeat_region
created_by: kareneilbeck
creation_date: 2011-05-31T12:59:27Z
[Term]
id: SO:0001798
name: regional_centromere_inner_repeat_region
def: "The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm." [SO:vw]
synonym: "lmr repeat" EXACT []
synonym: "lmr1L" EXACT []
synonym: "lmr1R" EXACT []
synonym: "regional centromere inner repeat region" EXACT []
is_a: SO:0001797 ! centromeric_repeat
relationship: part_of SO:0001796 ! regional_centromere_central_core
created_by: kareneilbeck
creation_date: 2011-05-31T01:01:08Z
[Term]
id: SO:0001799
name: regional_centromere_outer_repeat_region
def: "The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms." [SO:vw]
synonym: "regional centromere outer repeat region" EXACT []
is_a: SO:0001797 ! centromeric_repeat
relationship: part_of SO:0001795 ! regional_centromere
created_by: kareneilbeck
creation_date: 2011-05-31T01:03:23Z
[Term]
id: SO:0001800
name: tasiRNA
def: "The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene." [PMID:16145017]
synonym: "trans acting small interfering RNA" RELATED []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0001801 ! tasiRNA_primary_transcript
created_by: kareneilbeck
creation_date: 2011-05-31T03:24:06Z
[Term]
id: SO:0001801
name: tasiRNA_primary_transcript
def: "A primary transcript encoding a tasiRNA." [PMID:16145017]
synonym: "tasiRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2011-05-31T03:27:35Z
[Term]
id: SO:0001802
name: increased_polyadenylation_variant
def: "A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference." [SO:ke]
comment: Term requested by M. Dumontier, June 1 2011.
synonym: "increased polyadenylation variant" EXACT []
is_a: SO:0001545 ! polyadenylation_variant
created_by: kareneilbeck
creation_date: 2011-06-01T10:53:12Z
[Term]
id: SO:0001803
name: decreased_polyadenylation_variant
def: "A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference." [SO:ke]
comment: Term requested by M. Dumontier, June 1 2011.
synonym: "decreased polyadenylation variant" EXACT []
is_a: SO:0001545 ! polyadenylation_variant
created_by: kareneilbeck
creation_date: 2011-06-01T10:53:40Z
[Term]
id: SO:0001804
name: DDB_box
def: "A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases." [PMID:18794354, PMID:19818632]
comment: Note: PMID:18794354 describes the DDB box, and has lots of alignments, but doesn't actually come out with a consensus sequence.
synonym: "DDB box" EXACT []
synonym: "DDB-box" EXACT []
is_a: SO:0001093 ! protein_protein_contact
created_by: kareneilbeck
creation_date: 2011-06-17T12:10:44Z
[Term]
id: SO:0001805
name: destruction_box
def: "A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN." [PMID:12208841, PMID:1842691]
synonym: "D-box" EXACT []
synonym: "destruction box" EXACT []
is_a: SO:0100017 ! polypeptide_conserved_motif
created_by: kareneilbeck
creation_date: 2011-06-17T12:16:02Z
[Term]
id: SO:0001806
name: ER_retention_signal
def: "A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL." [doi:10.1093/jxb/50.331.157, PMID:2077689]
synonym: "endoplasmic reticulum retention signal" EXACT []
synonym: "ER retention signal" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2011-06-17T12:19:49Z
[Term]
id: SO:0001807
name: KEN_box
def: "A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN." [PMID:10733526, PMID:1220884, PMID:18426916]
synonym: "KEN box" EXACT []
is_a: SO:0100017 ! polypeptide_conserved_motif
created_by: kareneilbeck
creation_date: 2011-06-17T12:24:14Z
[Term]
id: SO:0001808
name: mitochondrial_targeting_signal
def: "A polypeptide region that targets a polypeptide to the mitochondrion." [PomBase:mah]
synonym: "mitochondrial signal sequence" EXACT []
synonym: "mitochondrial targeting signal" EXACT []
synonym: "MTS" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2011-06-17T12:26:35Z
[Term]
id: SO:0001809
name: signal_anchor
def: "A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane." [http://www.cbs.dtu.dk/services/SignalP/background/biobackground.php]
synonym: "signal anchor" EXACT []
synonym: "uncleaved signal peptide" EXACT []
is_a: SO:0000418 ! signal_peptide
created_by: kareneilbeck
creation_date: 2011-06-17T12:28:53Z
[Term]
id: SO:0001810
name: PIP_box
def: "A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains." [PMID:9631646]
synonym: "PIP box" EXACT []
is_a: SO:0001093 ! protein_protein_contact
created_by: kareneilbeck
creation_date: 2011-06-17T12:33:25Z
[Term]
id: SO:0001811
name: phosphorylation_site
def: "A post-translationally modified region in which residues of the protein are modified by phosphorylation." [PomBase:mah]
synonym: "phosphorylation site" EXACT []
is_a: SO:0001089 ! post_translationally_modified_region
created_by: kareneilbeck
creation_date: 2011-06-17T12:36:20Z
[Term]
id: SO:0001812
name: transmembrane_helix
def: "A region that traverses the lipid bilayer and adopts a helical secondary structure." [PomBase:mah]
synonym: "transmembrane helix" EXACT []
is_a: SO:0001114 ! peptide_helix
relationship: part_of SO:0001077 ! transmembrane_polypeptide_region
created_by: kareneilbeck
creation_date: 2011-06-17T12:39:46Z
[Term]
id: SO:0001813
name: vacuolar_sorting_signal
def: "A polypeptide region that targets a polypeptide to the vacuole." [PomBase:mah]
synonym: "vacuolar sorting signal" EXACT []
is_a: SO:0001527 ! peptide_localization_signal
created_by: kareneilbeck
creation_date: 2011-06-17T12:42:48Z
[Term]
id: SO:0001814
name: coding_variant_quality
synonym: "coding variant quality" EXACT []
is_a: SO:0001761 ! variant_quality
created_by: kareneilbeck
creation_date: 2011-06-24T03:32:25Z
[Term]
id: SO:0001815
name: synonymous
is_a: SO:0001814 ! coding_variant_quality
created_by: kareneilbeck
creation_date: 2011-06-24T03:33:16Z
[Term]
id: SO:0001816
name: non_synonymous
synonym: "non synonymous" RELATED []
is_a: SO:0001814 ! coding_variant_quality
created_by: kareneilbeck
creation_date: 2011-06-24T03:33:36Z
[Term]
id: SO:0001817
name: inframe
def: "An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3." [SO:ke]
is_a: SO:0000863 ! mRNA_attribute
created_by: kareneilbeck
creation_date: 2011-06-24T03:34:03Z
[Term]
id: SO:0001818
name: protein_altering_variant
def: "A sequence_variant which is predicted to change the protein encoded in the coding sequence." [EBI:gr]
synonym: "protein altering variant" EXACT []
is_a: SO:0001580 ! coding_sequence_variant
created_by: kareneilbeck
creation_date: 2011-06-24T03:38:02Z
[Term]
id: SO:0001819
name: synonymous_variant
alt_id: SO:0001588
def: "A sequence variant where there is no resulting change to the encoded amino acid." [SO:ke]
comment: EBI term: Synonymous SNPs - In coding sequence, not resulting in an amino acid change (i.e. silent mutation).\nThis term is sometimes used synonomously with the more general term 'silent mutation', although a silent mutation may occur in non coding sequence. The best practice is to annotate to the most specific term.
synonym: "ANNOVAR:synonymous SNV" RELATED VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "coding-synon" EXACT [ftp://ftp.ncbi.nih.gov/snp/specs/docsum_3.1.xsd]
synonym: "silent mutation" RELATED []
synonym: "silent substitution" RELATED []
synonym: "silent_mutation" RELATED []
synonym: "snpEff:SYNONYMOUS_CODING" EXACT VAR []
synonym: "synonymous codon" EXACT []
synonym: "synonymous_coding" EXACT []
synonym: "synonymous_codon" EXACT []
synonym: "VAAST:synonymous_codon" EXACT VAR []
xref: EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html
xref: http://en.wikipedia.org/wiki/Silent_mutation "wiki"
xref: http://en.wikipedia.org/wiki/Synonymous_mutation
is_a: SO:0001580 ! coding_sequence_variant
created_by: kareneilbeck
creation_date: 2011-06-24T03:38:30Z
[Term]
id: SO:0001820
name: inframe_indel
def: "A coding sequence variant where the change does not alter the frame of the transcript." [SO:ke]
synonym: "inframe change in CDS length" EXACT []
synonym: "inframe indel" EXACT []
is_a: SO:0001650 ! inframe_variant
created_by: kareneilbeck
creation_date: 2011-06-27T11:25:33Z
[Term]
id: SO:0001821
name: inframe_insertion
alt_id: SO:0001651
def: "An inframe non synonymous variant that inserts bases into in the coding sequence." [EBI:gr]
synonym: "ANNOVAR:nonframeshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "inframe codon gain" RELATED []
synonym: "inframe increase in CDS length" EXACT []
synonym: "inframe insertion" EXACT []
synonym: "inframe_codon_gain" EXACT []
synonym: "snpEFF:CODON_INSERTION" EXACT VAR []
is_a: SO:0001820 ! inframe_indel
is_a: SO:0001908 ! internal_feature_elongation
created_by: kareneilbeck
creation_date: 2011-06-27T11:26:22Z
[Term]
id: SO:0001822
name: inframe_deletion
alt_id: SO:0001652
def: "An inframe non synonymous variant that deletes bases from the coding sequence." [EBI:gr]
synonym: "ANNOVAR:nonframeshift deletion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "inframe codon loss" RELATED []
synonym: "inframe decrease in CDS length" EXACT []
synonym: "inframe deletion" RELATED []
synonym: "inframe_codon_loss" EXACT []
synonym: "snpEff:CODON_DELETION" RELATED VAR []
is_a: SO:0001820 ! inframe_indel
is_a: SO:0001906 ! feature_truncation
created_by: kareneilbeck
creation_date: 2011-06-27T11:27:10Z
[Term]
id: SO:0001823
name: conservative_inframe_insertion
def: "An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons." [EBI:gr]
synonym: "conservative increase in CDS length" EXACT []
synonym: "conservative inframe insertion" EXACT []
is_a: SO:0001821 ! inframe_insertion
created_by: kareneilbeck
creation_date: 2011-06-27T11:28:02Z
[Term]
id: SO:0001824
name: disruptive_inframe_insertion
def: "An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon." [EBI:gr]
synonym: "disruptive increase in CDS length" EXACT []
synonym: "disruptive inframe insertion" EXACT []
synonym: "snpEff:CODON_CHANGE_PLUS_CODON_INSERTION" EXACT VAR []
is_a: SO:0001821 ! inframe_insertion
created_by: kareneilbeck
creation_date: 2011-06-27T11:28:37Z
[Term]
id: SO:0001825
name: conservative_inframe_deletion
def: "An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons." [EBI:gr]
synonym: "conservative decrease in CDS length" RELATED []
synonym: "conservative inframe deletion" EXACT []
is_a: SO:0001822 ! inframe_deletion
created_by: kareneilbeck
creation_date: 2011-06-27T11:30:43Z
[Term]
id: SO:0001826
name: disruptive_inframe_deletion
def: "An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon." [EBI:gr]
synonym: "disruptive decrease in CDS length" EXACT []
synonym: "disruptive inframe deletion" EXACT []
synonym: "snpEff:CODON_CHANGE_PLUS_CODON_DELETION" EXACT VAR []
is_a: SO:0001822 ! inframe_deletion
created_by: kareneilbeck
creation_date: 2011-06-27T11:31:31Z
[Term]
id: SO:0001827
name: mRNA_read
def: "A sequencer read of an mRNA substrate." [SO:ke]
comment: Requested by Bayer Cropscience June, 2011.
synonym: "mRNA read" EXACT []
is_a: SO:0000150 ! read
created_by: kareneilbeck
creation_date: 2011-06-28T04:04:32Z
[Term]
id: SO:0001828
name: genomic_DNA_read
def: "A sequencer read of a genomic DNA substrate." [SO:ke]
synonym: "genomic DNA read" EXACT []
is_a: SO:0000150 ! read
created_by: kareneilbeck
creation_date: 2011-06-28T04:06:10Z
[Term]
id: SO:0001829
name: mRNA_contig
def: "A contig composed of mRNA_reads." [SO:ke]
comment: Requested by Bayer Cropscience June, 2011.
synonym: "mRNA contig" RELATED []
is_a: SO:0000149 ! contig
created_by: kareneilbeck
creation_date: 2011-06-28T04:07:09Z
[Term]
id: SO:0001830
name: AFLP_fragment
def: "A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments." [GMOD:ea]
comment: Requested by Bayer Cropscience June, 2011.
synonym: "AFLP" EXACT []
synonym: "AFLP fragment" EXACT []
synonym: "AFLP-PCR" EXACT []
synonym: "amplified fragment length polymorphism" EXACT []
synonym: "amplified fragment length polymorphism PCR" EXACT []
xref: http://en.wikipedia.org/wiki/Amplified_fragment_length_polymorphism "wiki"
is_a: SO:0000006 ! PCR_product
created_by: kareneilbeck
creation_date: 2011-07-14T12:12:35Z
[Term]
id: SO:0001831
name: protein_hmm_match
def: "A match to a protein HMM such as pfam." [SO:ke]
synonym: "protein hmm match" EXACT []
is_a: SO:0000349 ! protein_match
created_by: kareneilbeck
creation_date: 2011-08-11T03:20:27Z
[Term]
id: SO:0001832
name: immunoglobulin_region
def: "A region of immunoglobulin sequence, either constant or variable." [SO:ke]
synonym: "immunoglobulin region" EXACT []
is_a: SO:0000839 ! polypeptide_region
created_by: kareneilbeck
creation_date: 2011-09-01T03:27:20Z
[Term]
id: SO:0001833
name: V_region
def: "The variable region of an immunoglobulin polypeptide sequence." [SO:ke]
synonym: "V region" EXACT []
is_a: SO:0001832 ! immunoglobulin_region
created_by: kareneilbeck
creation_date: 2011-09-01T03:28:40Z
[Term]
id: SO:0001834
name: C_region
def: "The constant region of an immunoglobulin polypeptide sequence." [SO:ke]
synonym: "C region" EXACT []
is_a: SO:0001832 ! immunoglobulin_region
created_by: kareneilbeck
creation_date: 2011-09-01T03:29:41Z
[Term]
id: SO:0001835
name: N_region
def: "Extra nucleotides inserted between rearranged immunoglobulin segments." [SO:ke]
synonym: "N-region" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
created_by: kareneilbeck
creation_date: 2011-09-01T03:50:16Z
[Term]
id: SO:0001836
name: S_region
def: "The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell." [SO:ke]
synonym: "S region" EXACT []
is_a: SO:0000301 ! vertebrate_immune_system_gene_recombination_feature
created_by: kareneilbeck
creation_date: 2011-09-01T03:52:05Z
[Term]
id: SO:0001837
name: mobile_element_insertion
def: "A kind of insertion where the inserted sequence is a mobile element." [EBI:dvga]
comment: Requested by the EBI.
synonym: "mobile element insertion" EXACT []
is_a: SO:0000667 ! insertion
relationship: contains SO:0001037 ! mobile_genetic_element
created_by: kareneilbeck
creation_date: 2011-10-04T12:36:52Z
[Term]
id: SO:0001838
name: novel_sequence_insertion
def: "An insertion the sequence of which cannot be mapped to the reference genome." [NCBI:th]
comment: Requested by the NCBI.
synonym: "novel sequence insertion" EXACT []
is_a: SO:0000667 ! insertion
created_by: kareneilbeck
creation_date: 2011-10-04T01:14:50Z
[Term]
id: SO:0001839
name: CSL_response_element
def: "A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors." [PMID:19101542]
synonym: "CSL response element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T03:37:43Z
[Term]
id: SO:0001840
name: GATA_box
def: "A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G)." [PMID:8321208]
synonym: "GATA box" EXACT []
synonym: "GATA element" RELATED []
is_a: SO:0001660 ! core_promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T03:42:05Z
[Term]
id: SO:0001841
name: polymorphic_pseudogene
def: "Pseudogene owing to a SNP/DIP but in other individuals/haplotypes/strains the gene is translated." [JAX:hd]
comment: This terms is used by Ensembl and Vega.
synonym: "polymorphic psuedogene" EXACT []
is_a: SO:0000336 ! pseudogene
created_by: kareneilbeck
creation_date: 2011-10-07T03:46:57Z
[Term]
id: SO:0001842
name: AP_1_binding_site
def: "A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors." [PMID:1899230, PMID:3034432, PMID:3125983]
synonym: "AP-1 binding site" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T03:54:52Z
[Term]
id: SO:0001843
name: CRE
def: "A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors." [PMID:11483355, PMID:11483993]
synonym: "ATF/CRE site" EXACT [PMID:11483993]
synonym: "cyclic AMP response element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T03:58:48Z
[Term]
id: SO:0001844
name: CuRE
def: "A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast)." [PMID:10593913, PMID:9188496, PMID:9211922]
synonym: "copper-response element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:02:51Z
[Term]
id: SO:0001845
name: DRE
def: "A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis." [PMID:11073995, PMID:8668127]
synonym: "DNA damage response element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:17:25Z
[Term]
id: SO:0001846
name: FLEX_element
def: "A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:10747048, PMID:14871934]
synonym: "FLEX element" RELATED []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:20:01Z
[Term]
id: SO:0001847
name: forkhead_motif
def: "A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain." [PMID:15195092]
synonym: "forkhead motif" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:22:06Z
[Term]
id: SO:0001848
name: homol_D_box
def: "A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence." [PMID:7501449, PMID:8458332]
synonym: "homol D box" EXACT []
is_a: SO:0001660 ! core_promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:24:14Z
[Term]
id: SO:0001849
name: homol_E_box
def: "A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence." [PMID:7501449]
synonym: "homol E box" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:26:09Z
[Term]
id: SO:0001850
name: HSE
def: "A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF." [PMID:17347150, PMID:8689565]
synonym: "heat shock element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:29:10Z
[Term]
id: SO:0001851
name: iron_repressed_GATA_element
def: "A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron." [PMID:11956219, PMID:17211681]
comment: The synonym IDP (GATA) is found in an annotation but un-traced as far as literature goes.
synonym: "IDP (GATA)" EXACT []
synonym: "iron repressed GATA element" EXACT []
is_a: SO:0001840 ! GATA_box
created_by: kareneilbeck
creation_date: 2011-10-07T04:32:42Z
[Term]
id: SO:0001852
name: mating_type_M_box
def: "A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc." [PMID:9233811]
comment: Note that this should not be confused with the M-box that has consensus sequence CATGTG and is bound by bHLH transcription factors such as MITF.
synonym: "mating type M-box" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-07T04:39:43Z
[Term]
id: SO:0001853
name: androgen_response_element
def: "A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen." [PMID:21796522]
synonym: "androgen response element" EXACT []
synonym: "ARE" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2011-10-10T04:52:44Z
[Term]
id: SO:0001854
name: smFISH_probe
def: "A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment." [PMID:18806792]
synonym: "single molecule fish probe" EXACT []
synonym: "smFISH probe" RELATED []
is_a: SO:0000051 ! probe
created_by: kareneilbeck
creation_date: 2011-10-10T05:00:30Z
[Term]
id: SO:0001855
name: MCB
def: "A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle." [PMID:16285853]
synonym: "MluI cell cycle box" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-10T05:09:45Z
[Term]
id: SO:0001856
name: CCAAT_motif
def: "A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels." [PMID:16963626]
synonym: "CCAAT motif" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-10T05:13:54Z
[Term]
id: SO:0001857
name: Ace2_UAS
def: "A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2." [PMID:16678171]
synonym: "Ace2 upstream activating sequence" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-10T05:19:10Z
[Term]
id: SO:0001858
name: TR_box
def: "A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis." [PMID:1657709]
synonym: "TR box" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-10T05:22:13Z
[Term]
id: SO:0001859
name: STREP_motif
def: "A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2." [PMID:11739717]
synonym: "STREP motif" RELATED []
synonym: "stress-starvation response element of Schizosaccharomyces pombe" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-14T10:25:02Z
[Term]
id: SO:0001860
name: rDNA_intergenic_spacer_element
def: "A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1)." [PMID:9016645]
synonym: "rDIS" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2011-10-19T11:23:09Z
[Term]
id: SO:0001861
name: sterol_regulatory_element
def: "A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs." [GO:mah, PMID:11111080, PMID:16537923]
synonym: "SRE" BROAD [GO:mah]
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-19T03:02:05Z
[Term]
id: SO:0001862
name: GT_dinucleotide_repeat
def: "A dinucleotide repeat region composed of GT repeating elements." [SO:ke]
comment: paper:PMID:16043634.
synonym: "d(GT)n" EXACT []
is_a: SO:0000290 ! dinucleotide_repeat_microsatellite_feature
created_by: kareneilbeck
creation_date: 2011-10-19T03:54:37Z
[Term]
id: SO:0001863
name: GTT_trinucleotide_repeat
def: "A trinucleotide repeat region composed of GTT repeating elements." [SO:ke]
synonym: "d(GTT)" EXACT []
is_a: SO:0000291 ! trinucleotide_repeat_microsatellite_feature
created_by: kareneilbeck
creation_date: 2011-10-19T03:56:54Z
[Term]
id: SO:0001864
name: Sap1_recognition_motif
def: "A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats." [PMID:16166653, PMID:7651412]
synonym: "Sap1 recognitions site" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2011-10-19T04:24:16Z
[Term]
id: SO:0001865
name: CDRE_motif
def: "An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA." [PMID:16928959]
synonym: "calcineurin-dependent response element" EXACT [PMID:16928959]
synonym: "CDRE motif" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2011-10-20T10:12:19Z
[Term]
id: SO:0001866
name: BAC_read_contig
def: "A contig of BAC reads." [GMOD:ea]
comment: Requested by Bayer Cropscience December, 2011.
synonym: "BAC read contig" EXACT []
is_a: SO:0000149 ! contig
relationship: has_origin SO:0000153 ! BAC
relationship: part_of SO:0000153 ! BAC
created_by: kareneilbeck
creation_date: 2012-01-17T02:45:04Z
[Term]
id: SO:0001867
name: candidate_gene
def: "A gene suspected of being involved in the expression of a trait." [GMOD:ea]
comment: Requested by Bayer Cropscience December, 2011.
synonym: "candidate gene" EXACT []
synonym: "target gene" EXACT []
is_a: SO:0000704 ! gene
created_by: kareneilbeck
creation_date: 2012-01-17T02:53:03Z
[Term]
id: SO:0001868
name: positional_candidate_gene
def: "A candidate gene whose association with a trait is based on the gene's location on a chromosome." [GMOD:ea]
comment: Requested by Bayer Cropscience December, 2011.
synonym: "positional candidate gene" EXACT []
synonym: "positional target gene" RELATED []
is_a: SO:0001867 ! candidate_gene
created_by: kareneilbeck
creation_date: 2012-01-17T02:54:42Z
[Term]
id: SO:0001869
name: functional_candidate_gene
def: "A candidate gene whose function has something in common biologically with the trait under investigation." [GMOD:ea]
comment: Requested by Bayer Cropscience December, 2011.
synonym: "functional candidate gene" EXACT []
synonym: "functional target gene" EXACT []
is_a: SO:0001867 ! candidate_gene
created_by: kareneilbeck
creation_date: 2012-01-17T02:57:30Z
[Term]
id: SO:0001870
name: enhancerRNA
def: "A short ncRNA that is transcribed from an enhancer. May have a regulatory function." [doi:10.1038/465173a, SO:cjm]
synonym: "eRNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: transcribed_from SO:0000165 ! enhancer
created_by: kareneilbeck
creation_date: 2012-01-17T03:09:35Z
[Term]
id: SO:0001871
name: PCB
def: "A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle." [GO:mah, PMID:12411492]
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2012-01-17T03:14:02Z
[Term]
id: SO:0001872
name: rearrangement_region
def: "A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome." [NCBI:th, PMID:18564416]
comment: NCBI definition: An orphan rearrangement between chromosomal location observed in isolation.
synonym: "rearrangement region" EXACT []
is_a: SO:0001411 ! biological_region
is_a: SO:0001785 ! structural_alteration
created_by: kareneilbeck
creation_date: 2012-02-03T04:38:35Z
[Term]
id: SO:0001873
name: interchromosomal_breakpoint
def: "A rearrangement breakpoint between two different chromosomes." [NCBI:th]
synonym: "interchromosomal breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint
created_by: kareneilbeck
creation_date: 2012-02-03T04:43:45Z
[Term]
id: SO:0001874
name: intrachromosomal_breakpoint
def: "A rearrangement breakpoint within the same chromosome." [NCBI:th]
synonym: "intrachromosomal breakpoint" EXACT []
is_a: SO:0001021 ! chromosome_breakpoint
created_by: kareneilbeck
creation_date: 2012-02-03T04:44:53Z
[Term]
id: SO:0001875
name: unassigned_supercontig
def: "A supercontig that is not been assigned to any ultracontig during a genome assembly project." [GMOD:ea]
comment: Requested by Bayer Cropscience January, 2012.
synonym: "unassigned scaffold" RELATED []
synonym: "unassigned supercontig" EXACT []
is_a: SO:0000148 ! supercontig
created_by: kareneilbeck
creation_date: 2012-02-14T05:02:20Z
[Term]
id: SO:0001876
name: partial_genomic_sequence_assembly
def: "A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's." [GMOD:ea]
comment: Requested by Bayer Cropscience January, 2012.
synonym: "partial genomic sequence assembly" EXACT []
synonym: "pseudomolecule" BROAD []
synonym: "sequence assembly with N-gaps" EXACT []
is_a: SO:0000353 ! sequence_assembly
created_by: kareneilbeck
creation_date: 2012-02-14T05:05:32Z
[Term]
id: SO:0001877
name: lnc_RNA
def: "A non-coding RNA over 200nucleotides in length." [HGNC:mw]
synonym: "long non-coding RNA" EXACT []
is_a: SO:0000655 ! ncRNA
created_by: kareneilbeck
creation_date: 2012-02-14T05:18:01Z
[Term]
id: SO:0001878
name: feature_variant
def: "A sequence variant that falls entirely or partially within a genomic feature." [EBI:fc, SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature alteration" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:27:27Z
[Term]
id: SO:0001879
name: feature_ablation
def: "A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature ablation" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:36:48Z
[Term]
id: SO:0001880
name: feature_amplification
def: "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature amplification" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:37:48Z
[Term]
id: SO:0001881
name: feature_translocation
def: "A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature translocation" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:38:52Z
[Term]
id: SO:0001882
name: feature_fusion
def: "A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "feature fusion" EXACT []
is_a: SO:0001537 ! structural_variant
created_by: kareneilbeck
creation_date: 2012-04-03T11:39:20Z
[Term]
id: SO:0001883
name: transcript_translocation
def: "A feature translocation where the region contains a transcript." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript translocation" EXACT []
is_a: SO:0001881 ! feature_translocation
created_by: kareneilbeck
creation_date: 2012-04-03T12:29:52Z
[Term]
id: SO:0001884
name: regulatory_region_translocation
def: "A feature translocation where the region contains a regulatory region." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "regulatory region translocation" EXACT []
is_a: SO:0001881 ! feature_translocation
created_by: kareneilbeck
creation_date: 2012-04-03T12:31:04Z
[Term]
id: SO:0001885
name: TFBS_translocation
def: "A feature translocation where the region contains a transcription factor binding site." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "TFBS binding site translocation" EXACT []
synonym: "transcription factor binding site translocation" EXACT []
is_a: SO:0001884 ! regulatory_region_translocation
created_by: kareneilbeck
creation_date: 2012-04-03T12:31:15Z
[Term]
id: SO:0001886
name: transcript_fusion
def: "A feature fusion where the deletion brings together transcript regions." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript fusion" EXACT []
is_a: SO:0001882 ! feature_fusion
created_by: kareneilbeck
creation_date: 2012-04-03T12:34:56Z
[Term]
id: SO:0001887
name: regulatory_region_fusion
def: "A feature fusion where the deletion brings together regulatory regions." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "regulatory region fusion" EXACT []
is_a: SO:0001882 ! feature_fusion
created_by: kareneilbeck
creation_date: 2012-04-03T12:35:58Z
[Term]
id: SO:0001888
name: TFBS_fusion
def: "A fusion where the deletion brings together transcription factor binding sites." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "TFBS fusion " EXACT []
synonym: "transcription factor binding site fusion" EXACT []
is_a: SO:0001887 ! regulatory_region_fusion
created_by: kareneilbeck
creation_date: 2012-04-03T12:36:42Z
[Term]
id: SO:0001889
name: transcript_amplification
def: "A feature amplification of a region containing a transcript." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript amplification" EXACT []
is_a: SO:0001880 ! feature_amplification
created_by: kareneilbeck
creation_date: 2012-04-03T12:39:23Z
[Term]
id: SO:0001890
name: transcript_regulatory_region_fusion
def: "A feature fusion where the deletion brings together a regulatory region and a transcript region." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript regulatory region fusion" EXACT []
is_a: SO:0001882 ! feature_fusion
created_by: kareneilbeck
creation_date: 2012-04-03T12:40:17Z
[Term]
id: SO:0001891
name: regulatory_region_amplification
def: "A feature amplification of a region containing a regulatory region." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "regulatory region amplification" EXACT []
is_a: SO:0001880 ! feature_amplification
created_by: kareneilbeck
creation_date: 2012-04-03T12:41:28Z
[Term]
id: SO:0001892
name: TFBS_amplification
def: "A feature amplification of a region containing a transcription factor binding site." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "TFBS amplification " EXACT []
synonym: "transcription factor binding site amplification" EXACT []
is_a: SO:0001891 ! regulatory_region_amplification
created_by: kareneilbeck
creation_date: 2012-04-03T12:42:48Z
[Term]
id: SO:0001893
name: transcript_ablation
def: "A feature ablation whereby the deleted region includes a transcript feature." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "transcript ablation" EXACT []
is_a: SO:0001879 ! feature_ablation
created_by: kareneilbeck
creation_date: 2012-04-03T12:44:19Z
[Term]
id: SO:0001894
name: regulatory_region_ablation
def: "A feature ablation whereby the deleted region includes a regulatory region." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "regulatory region ablation" EXACT []
is_a: SO:0001879 ! feature_ablation
created_by: kareneilbeck
creation_date: 2012-04-03T12:45:13Z
[Term]
id: SO:0001895
name: TFBS_ablation
def: "A feature ablation whereby the deleted region includes a transcription factor binding site." [SO:ke]
comment: Created in conjunction with the EBI.
synonym: "TFBS ablation" EXACT []
synonym: "transcription factor binding site ablation" EXACT []
is_a: SO:0001894 ! regulatory_region_ablation
created_by: kareneilbeck
creation_date: 2012-04-03T12:45:56Z
[Term]
id: SO:0001896
name: transposable_element_CDS
def: "A CDS that is part of a transposable element." [SO:ke]
synonym: "transposable element CDS" EXACT []
is_a: SO:0000316 ! CDS
relationship: part_of SO:0000101 ! transposable_element
created_by: kareneilbeck
creation_date: 2012-04-05T01:57:04Z
[Term]
id: SO:0001897
name: transposable_element_pseudogene
def: "A pseudogene contained within a transposable element." [SO:ke]
synonym: "transposable element pseudogene" EXACT []
is_a: SO:0000336 ! pseudogene
relationship: part_of SO:0000101 ! transposable_element
created_by: kareneilbeck
creation_date: 2012-04-05T04:09:45Z
[Term]
id: SO:0001898
name: dg_repeat
def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]
comment: For the S. pombe project - requested by Val Wood.
synonym: "dg repeat" EXACT []
is_a: SO:0001797 ! centromeric_repeat
relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region
created_by: kareneilbeck
creation_date: 2012-04-06T11:48:48Z
[Term]
id: SO:0001899
name: dh_repeat
def: "A repeat region which is part of the regional centromere outer repeat region." [PMID:16407326, SO:vw]
comment: For the S. pombe project - requested by Val Wood.
synonym: "dh repeat" EXACT []
is_a: SO:0001797 ! centromeric_repeat
relationship: part_of SO:0001799 ! regional_centromere_outer_repeat_region
created_by: kareneilbeck
creation_date: 2012-04-06T11:50:07Z
[Term]
id: SO:0001900
name: M26_binding_site
def: "A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components." [PMID:15448137]
synonym: "m26 site" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2012-04-06T12:02:10Z
[Term]
id: SO:0001901
name: AACCCT_box
def: "A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site." [PMID:17452352, PMID:4092687]
synonym: "AACCCT box" EXACT []
is_a: SO:0001660 ! core_promoter_element
created_by: kareneilbeck
creation_date: 2012-04-06T12:05:24Z
[Term]
id: SO:0001902
name: splice_region
def: "A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron." [SO:bm]
synonym: "splice region" RELATED []
is_a: SO:0000835 ! primary_transcript_region
relationship: part_of SO:0000185 ! primary_transcript
created_by: kareneilbeck
creation_date: 2012-04-06T12:23:32Z
[Term]
id: SO:0001903
name: intronic_lncRNA
def: "A lnc_RNA totally contained within an intron." [PMID:19071207, SO:ke]
synonym: "intronic lncRNA" EXACT []
is_a: SO:0001877 ! lnc_RNA
created_by: kareneilbeck
creation_date: 2012-04-06T04:34:17Z
[Term]
id: SO:0001904
name: antisense_lncRNA
def: "Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA." [PMID:19638999]
synonym: "antisense lncRNA" RELATED []
synonym: "natural antisense transcript" EXACT []
is_a: SO:0001877 ! lnc_RNA
created_by: kareneilbeck
creation_date: 2012-04-06T04:36:44Z
[Term]
id: SO:0001905
name: regional_centromere_outer_repeat_transcript
def: "A transcript that is transcribed from the outer repeat region of a regional centromere." [PomBase:mah]
synonym: "centromere outer repeat transcript" EXACT []
synonym: "regional centromere outer repeat region transcript" EXACT []
synonym: "regional_centromere_outer_repeat_region_transcript" EXACT []
is_a: SO:0000185 ! primary_transcript
relationship: derives_from SO:0001799 ! regional_centromere_outer_repeat_region
created_by: kareneilbeck
creation_date: 2012-04-11T04:54:22Z
[Term]
id: SO:0001906
name: feature_truncation
def: "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence." [SO:ke]
synonym: "feature truncation" EXACT []
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2012-04-12T05:05:28Z
[Term]
id: SO:0001907
name: feature_elongation
def: "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence." [SO:ke]
synonym: "feature elongation" EXACT []
is_a: SO:0001878 ! feature_variant
created_by: kareneilbeck
creation_date: 2012-04-12T05:05:56Z
[Term]
id: SO:0001908
name: internal_feature_elongation
def: "A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence." [SO:ke]
synonym: "internal feature elongation" EXACT []
is_a: SO:0001907 ! feature_elongation
created_by: kareneilbeck
creation_date: 2012-04-12T05:06:20Z
[Term]
id: SO:0001909
name: frameshift_elongation
def: "A frameshift variant that causes the translational reading frame to be extended relative to the reference feature." [SO:ke]
synonym: "ANNOVAR:frameshift insertion" EXACT VAR [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "frameshift elongation" EXACT []
is_a: SO:0001589 ! frameshift_variant
is_a: SO:0001908 ! internal_feature_elongation
created_by: kareneilbeck
creation_date: 2012-04-12T05:10:05Z
[Term]
id: SO:0001910
name: frameshift_truncation
def: "A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature." [SO:ke]
synonym: "ANNOVAR:frameshit deletion" EXACT ebi_variants [http://www.openbioinformatics.org/annovar/annovar_download.html]
synonym: "frameshft truncation" EXACT []
is_a: SO:0001589 ! frameshift_variant
is_a: SO:0001906 ! feature_truncation
created_by: kareneilbeck
creation_date: 2012-04-12T05:10:45Z
[Term]
id: SO:0001911
name: copy_number_increase
def: "A sequence variant where copies of a feature are increased relative to the reference." [SO:ke]
synonym: "copy number increase" EXACT []
is_a: SO:0001563 ! copy_number_change
created_by: kareneilbeck
creation_date: 2012-04-13T11:26:32Z
[Term]
id: SO:0001912
name: copy_number_decrease
def: "A sequence variant where copies of a feature are decreased relative to the reference." [SO:ke]
is_a: SO:0001563 ! copy_number_change
created_by: kareneilbeck
creation_date: 2012-04-13T11:27:52Z
[Term]
id: SO:0001913
name: bacterial_RNApol_promoter_sigma_ecf
def: "A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation." [Invitrogen:kc]
comment: Requested by Kevin Clancy - invitrogen -May 2012.
synonym: "bacterial RNApol promoter sigma ecf " EXACT []
is_a: SO:0000613 ! bacterial_RNApol_promoter
created_by: kareneilbeck
creation_date: 2012-06-11T02:41:33Z
[Term]
id: SO:0001914
name: rDNA_replication_fork_barrier
def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529]
comment: Requested by Midori - June 2012.
synonym: "DNA spacer replication fork barrier" EXACT []
synonym: "rDNA replication fork barrier" EXACT []
synonym: "RFB" EXACT []
synonym: "RTS1 barrier" EXACT []
synonym: "RTS1 element" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2012-06-11T02:55:02Z
[Term]
id: SO:0001915
name: transcription_start_cluster
def: "A region defined by a cluster of experimentally determined transcription starting sites." [PMID:19624849, PMID:21372179, SO:andrewgibson]
synonym: "transcriptional initiation cluster" EXACT []
synonym: "transcriptional start site cluster" EXACT []
synonym: "TSC" EXACT []
synonym: "TSS cluster" EXACT []
is_a: SO:0001410 ! experimental_feature
created_by: kareneilbeck
creation_date: 2012-10-17T12:09:50Z
[Term]
id: SO:0001916
name: CAGE_tag
def: "A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites." [SO:andrewgibson]
synonym: "CAGE tag" EXACT []
is_a: SO:0000324 ! tag
created_by: kareneilbeck
creation_date: 2012-10-17T12:36:58Z
[Term]
id: SO:0001917
name: CAGE_cluster
def: "A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region." [PMID:16645617, SO:andrewgibson]
synonym: "CAGE cluster" EXACT []
synonym: "CAGE peak" EXACT []
synonym: "CAGE_peak" EXACT []
is_a: SO:0001915 ! transcription_start_cluster
created_by: kareneilbeck
creation_date: 2012-10-17T12:42:03Z
[Term]
id: SO:0001918
name: 5_methylcytosine
def: "A cytosine methylated at the 5 carbon." [SO:rtapella]
synonym: "5 methylcytosine" EXACT []
synonym: "5-mC" EXACT []
synonym: "m-5C" EXACT []
synonym: "m5c" EXACT []
xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0000114 ! methylated_cytosine
created_by: kareneilbeck
creation_date: 2012-10-17T12:46:10Z
[Term]
id: SO:0001919
name: 4_methylcytosine
def: "A cytosine methylated at the 4 nitrogen." [SO:rtapella]
synonym: "4-mC" EXACT []
synonym: "4-methylcytosine" EXACT []
synonym: "m-4C" EXACT []
synonym: "m4c" EXACT []
synonym: "N4 methylcytosine" EXACT []
synonym: "N4-methylcytosine" EXACT []
synonym: "N4_methylcytosine" EXACT []
xref: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html#7.4.2
xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0000114 ! methylated_cytosine
created_by: kareneilbeck
creation_date: 2012-10-17T12:50:40Z
[Term]
id: SO:0001920
name: N6_methyladenine
def: "An adenine methylated at the 6 nitrogen." [SO:rtapella]
synonym: "6-mA" EXACT []
synonym: "6-methyladenine" EXACT []
synonym: "6mA" EXACT []
synonym: "m-6A" EXACT []
synonym: "m6a" EXACT []
synonym: "N6-methyladenine" EXACT []
xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0000161 ! methylated_adenine
created_by: kareneilbeck
creation_date: 2012-10-17T12:54:23Z
[Term]
id: SO:0001921
name: mitochondrial_contig
def: "A contig of mitochondria derived sequences." [GMOD:ea]
comment: Requested by Bayer Cropscience, October, 2012.
synonym: "mitochondrial contig" EXACT []
is_a: SO:0000149 ! contig
relationship: has_origin SO:0000737 ! mitochondrial_sequence
created_by: kareneilbeck
creation_date: 2012-10-31T12:34:38Z
[Term]
id: SO:0001922
name: mitochondrial_supercontig
def: "A scaffold composed of mitochondrial contigs." [GMOD:ea]
synonym: "mitochondrial scaffold" EXACT []
synonym: "mitochondrial supercontig" EXACT []
synonym: "mitochondrial_scaffold" EXACT []
is_a: SO:0000148 ! supercontig
created_by: kareneilbeck
creation_date: 2012-10-31T12:42:45Z
[Term]
id: SO:0001923
name: TERRA
def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long." [PMID:22139915]
comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
synonym: "telomeric repeat containing RNA" RELATED []
is_a: SO:0001927 ! telomeric_transcript
created_by: kareneilbeck
creation_date: 2012-10-31T01:06:40Z
[Term]
id: SO:0001924
name: ARRET
def: "A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats." [PMID:2139915]
comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
is_a: SO:0001927 ! telomeric_transcript
created_by: kareneilbeck
creation_date: 2012-10-31T01:11:49Z
[Term]
id: SO:0001925
name: ARIA
def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats." [PMID:22139915]
comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
is_a: SO:0001927 ! telomeric_transcript
created_by: kareneilbeck
creation_date: 2012-10-31T01:24:37Z
[Term]
id: SO:0001926
name: anti_ARRET
def: "A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts." [PMID:22139915]
comment: Telomeric transcription has been documented in mammals, birds, fish, plants and yeast. Requested by Antonia Lock, October 2012.
synonym: "anti-ARRET" EXACT []
is_a: SO:0001927 ! telomeric_transcript
created_by: kareneilbeck
creation_date: 2012-10-31T01:40:22Z
[Term]
id: SO:0001927
name: telomeric_transcript
def: "A non-coding transcript derived from the transcript of the telomere." [PMID:22139915]
synonym: "telomeric transcript" EXACT []
is_a: SO:0000655 ! ncRNA
created_by: kareneilbeck
creation_date: 2012-10-31T01:42:15Z
[Term]
id: SO:0001928
name: distal_duplication
def: "A duplication of the distal region of a chromosome." [SO:bm]
comment: This term is used by Complete Genomics in the structural variant analysis files.
synonym: "distal duplication" EXACT []
is_a: SO:1000035 ! duplication
created_by: kareneilbeck
creation_date: 2012-10-31T01:56:44Z
[Term]
id: SO:0001929
name: mitochondrial_DNA_read
def: "A sequencer read of a mitochondrial DNA sample." [GMOD:ea]
comment: Requested by Bayer Cropscience, October, 2012.
synonym: "mitochondrial DNA read" EXACT []
is_a: SO:0000150 ! read
relationship: has_origin SO:0001032 ! mitochondrial_DNA
created_by: kareneilbeck
creation_date: 2012-11-14T04:39:56Z
[Term]
id: SO:0001930
name: chloroplast_DNA_read
def: "A sequencer read of a chloroplast DNA sample." [GMOD:ea]
comment: Requested by Bayer Cropscience, October, 2012.
synonym: "chloroplast DNA read" EXACT []
is_a: SO:0000150 ! read
relationship: has_origin SO:0001033 ! chloroplast_DNA
created_by: kareneilbeck
creation_date: 2012-11-14T04:43:45Z
[Term]
id: SO:0001931
name: consensus_gDNA
def: "Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input." [GMOD:ea]
comment: Requested by Bayer Cropscience November, 2012.
synonym: "consensus gDNA" EXACT []
synonym: "consensus genomic DNA" EXACT []
is_a: SO:0000994 ! consensus_region
created_by: kareneilbeck
creation_date: 2012-11-28T12:53:14Z
[Term]
id: SO:0001932
name: restriction_enzyme_five_prime_single_strand_overhang
def: "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end." [SO:ke]
synonym: "restriction enzyme five prime single strand overhang" EXACT []
is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang
created_by: kareneilbeck
creation_date: 2013-03-06T09:50:44Z
[Term]
id: SO:0001933
name: restriction_enzyme_three_prime_single_strand_overhang
def: "A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end." [SO:ke]
synonym: "restriction enzyme three prime single strand overhang" EXACT []
is_a: SO:0001695 ! restriction_enzyme_single_strand_overhang
created_by: kareneilbeck
creation_date: 2013-03-06T09:52:14Z
[Term]
id: SO:0001934
name: monomeric_repeat
def: "A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem." [SO:ke]
synonym: "monomeric repeat" EXACT []
is_a: SO:0000705 ! tandem_repeat
created_by: kareneilbeck
creation_date: 2013-03-06T09:59:15Z
[Term]
id: SO:0001935
name: H3K20_trimethylation_site
def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated." [EBI:nj]
synonym: "H3K20 trimethylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:13:48Z
[Term]
id: SO:0001936
name: H3K36_acetylation_site
def: "A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acylated." [EBI:nj]
synonym: "H3K36 acetylation site" EXACT []
synonym: "H3K36ac" EXACT []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:16:55Z
[Term]
id: SO:0001937
name: H2BK12_acetylation_site
def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is methylated." [EBI:nj]
synonym: "H2BK12 acetylation site" EXACT []
synonym: "H2BK12ac" RELATED []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:19:13Z
[Term]
id: SO:0001938
name: H2AK5_acetylation_site
def: "A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
synonym: "H2AK5 acetylation site" EXACT []
synonym: "H2AK5ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:20:57Z
[Term]
id: SO:0001939
name: H4K12_acetylation_site
def: "A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
synonym: "H4K12 acetylation site" EXACT []
synonym: "H4K12ac" EXACT []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:26:15Z
[Term]
id: SO:0001940
name: H2BK120_acetylation_site
def: "A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
synonym: "H2BK120 acetylation site" EXACT []
synonym: "H2BK120ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:28:38Z
[Term]
id: SO:0001941
name: H4K91_acetylation_site
def: "A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated." [EBI:nj]
synonym: "H4K91 acetylation site" EXACT []
is_a: SO:0001972 ! histone_4_acylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:41:04Z
[Term]
id: SO:0001942
name: H2BK20_acetylation_site
def: "A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
synonym: "H2BK20 acetylation site" RELATED []
synonym: "H2BK20ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:44:31Z
[Term]
id: SO:0001943
name: H3K4ac_acetylation_site
def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
synonym: "H3K4ac" EXACT []
synonym: "H3K4ac acetylation site" EXACT []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:46:32Z
[Term]
id: SO:0001944
name: H2AK9_acetylation_site
def: "A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated." [EBI:nj]
synonym: "H2AK9 acetylation site" EXACT []
synonym: "H2AK9ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:48:11Z
[Term]
id: SO:0001945
name: H3K56_acetylation_site
def: "A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated." [EBI:nj]
synonym: "H3K56 acetylation site" EXACT []
synonym: "H3K56ac" EXACT []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:51:14Z
[Term]
id: SO:0001946
name: H2BK15_acetylation_site
def: "A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated." [EBI:nj]
synonym: "H2BK15 acetylation site" EXACT []
synonym: "H2BK15ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:53:23Z
[Term]
id: SO:0001947
name: H3R2_monomethylation_site
def: "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated." [EBI:nj]
synonym: " H3R2me1" EXACT []
synonym: "H3R2 monomethylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:57:13Z
[Term]
id: SO:0001948
name: H3R2_dimethylation_site
def: "A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated." [EBI:nj]
synonym: "H3R2 dimethylation site" EXACT []
synonym: "H3R2me2" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T10:59:17Z
[Term]
id: SO:0001949
name: H4R3_dimethylation_site
def: "A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated." [EBI:nj]
synonym: "H4R3 dimethylation site" EXACT []
synonym: "H4R3me2" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T11:01:27Z
[Term]
id: SO:0001950
name: H4K4_trimethylation_site
def: "A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated." [EBI:nj]
synonym: " H4K4me3" EXACT []
synonym: "H4K4 trimethylation site" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T11:03:29Z
[Term]
id: SO:0001951
name: H3K23_dimethylation_site
def: "A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated." [EBI:nj]
synonym: "H3K23 dimethylation site" EXACT []
synonym: "H3K23me2" EXACT []
is_a: SO:0001701 ! histone_methylation_site
created_by: kareneilbeck
creation_date: 2013-03-06T11:05:33Z
[Term]
id: SO:0001952
name: promoter_flanking_region
def: "A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites." [EBI:nj]
synonym: "promoter flanking region" EXACT []
is_a: SO:0001055 ! transcriptional_cis_regulatory_region
created_by: kareneilbeck
creation_date: 2013-03-06T11:36:25Z
[Term]
id: SO:0001953
name: restriction_enzyme_assembly_scar
def: "A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends." [SO:ke]
is_a: SO:0001954 ! restriction_enzyme_region
created_by: kareneilbeck
creation_date: 2013-03-06T03:18:11Z
[Term]
id: SO:0001954
name: restriction_enzyme_region
def: "A region related to restriction enzyme function." [SO:ke]
comment: Not a great term for annotation, but used to classify the various regions related to restriction enzymes.
synonym: "restriction enzyme region" RELATED []
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2013-03-06T03:23:34Z
[Term]
id: SO:0001955
name: protein_stability_element
def: "A polypeptide region that proves structure in a protein that affects the stability of the protein." [SO:ke]
synonym: "protein stability element" RELATED []
is_a: SO:0000839 ! polypeptide_region
created_by: kareneilbeck
creation_date: 2013-03-06T03:32:47Z
[Term]
id: SO:0001956
name: protease_site
def: "A polypeptide_region that codes for a protease cleavage site." [SO:ke]
synonym: "protease site" EXACT []
is_a: SO:0000839 ! polypeptide_region
created_by: kareneilbeck
creation_date: 2013-03-06T03:36:28Z
[Term]
id: SO:0001957
name: RNA_stability_element
def: "RNA secondary structure that affects the stability of an RNA molecule." [SO:ke]
synonym: "rna stability element" RELATED []
created_by: kareneilbeck
creation_date: 2013-03-06T03:38:35Z
is_obsolete: true
[Term]
id: SO:0001958
name: lariat_intron
def: "A kind of intron whereby the excision is driven by lariat formation." [SO:ke]
comment: Requested by PomBase 3604508.
synonym: "lariat intron" EXACT []
is_a: SO:0000188 ! intron
created_by: kareneilbeck
creation_date: 2013-03-07T10:58:40Z
[Term]
id: SO:0001959
name: TCT_motif
def: "A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator." [PMID:20801935, SO:myl]
synonym: "polypyrimidine initiator" EXACT []
synonym: "TCT element" EXACT []
is_a: SO:0001660 ! core_promoter_element
created_by: kareneilbeck
creation_date: 2013-05-17T04:38:48Z
[Term]
id: SO:0001960
name: 5_hydroxymethylcytosine
def: "A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon." [SO:ke]
synonym: "5-hmC" EXACT []
synonym: "5-hydroxymethylcytosine" EXACT []
xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0000114 ! methylated_cytosine
created_by: kareneilbeck
creation_date: 2013-05-17T05:05:31Z
[Term]
id: SO:0001961
name: 5_formylcytosine
def: "A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon." [SO:ke]
synonym: "5-fC" EXACT []
synonym: "5-formylcytosine" EXACT []
xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0001963 ! modified_cytosine
created_by: kareneilbeck
creation_date: 2013-05-17T05:06:13Z
[Term]
id: SO:0001962
name: modified_adenine
def: "A modified adenine DNA base feature." [SO:ke]
is_a: SO:0000305 ! modified_DNA_base
created_by: kareneilbeck
creation_date: 2013-05-20T01:22:30Z
[Term]
id: SO:0001963
name: modified_cytosine
def: "A modified cytosine DNA base feature." [SO:ke]
is_a: SO:0000305 ! modified_DNA_base
created_by: kareneilbeck
creation_date: 2013-05-20T01:23:47Z
[Term]
id: SO:0001964
name: modified_guanine
def: "A modified guanine DNA base feature." [SO:ke]
is_a: SO:0000305 ! modified_DNA_base
created_by: kareneilbeck
creation_date: 2013-05-20T01:25:31Z
[Term]
id: SO:0001965
name: 8_oxoguanine
def: "A modified DNA guanine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
synonym: "8-oxoG" EXACT []
synonym: "8-oxoguanine" EXACT []
xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0001964 ! modified_guanine
created_by: kareneilbeck
creation_date: 2013-05-20T01:27:51Z
[Term]
id: SO:0001966
name: 5_carboxylcytosine
def: "A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon." [SO:ke]
synonym: "5-caC" EXACT []
synonym: "5-carboxycytosine" EXACT []
xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0001963 ! modified_cytosine
created_by: kareneilbeck
creation_date: 2013-05-20T01:30:01Z
[Term]
id: SO:0001967
name: 8_oxoadenine
def: "A modified DNA adenine base,at the 8 carbon, often the product of DNA damage." [SO:ke]
synonym: "8-oxoA" EXACT []
synonym: "8-oxoadenine" EXACT []
xref: http:http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
is_a: SO:0001962 ! modified_adenine
created_by: kareneilbeck
creation_date: 2013-05-20T01:31:05Z
[Term]
id: SO:0001968
name: coding_transcript_variant
def: "A transcript variant of a protein coding gene." [SO:ke]
synonym: "coding transcript variant" EXACT []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2013-05-22T04:34:49Z
[Term]
id: SO:0001969
name: coding_transcript_intron_variant
def: "A transcript variant occurring within an intron of a coding transcript." [SO:ke]
synonym: "coding sequence intron variant" EXACT []
is_a: SO:0001627 ! intron_variant
is_a: SO:0001968 ! coding_transcript_variant
created_by: kareneilbeck
creation_date: 2013-05-23T10:54:17Z
[Term]
id: SO:0001970
name: non_coding_transcript_intron_variant
def: "A transcript variant occurring within an intron of a non coding transcript." [SO:ke]
synonym: "non coding transcript intron variant" EXACT []
is_a: SO:0001619 ! non_coding_transcript_variant
is_a: SO:0001627 ! intron_variant
created_by: kareneilbeck
creation_date: 2013-05-23T10:55:03Z
[Term]
id: SO:0001971
name: zinc_finger_binding_site
synonym: "zinc finger binding site" EXACT []
synonym: "zinc_fing" EXACT BS [unirot:features]
is_a: SO:0001429 ! DNA_binding_site
created_by: kareneilbeck
creation_date: 2013-07-29T04:41:53Z
[Term]
id: SO:0001972
name: histone_4_acylation_site
def: "A histone 4 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
synonym: "H4ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-07-30T10:43:04Z
[Term]
id: SO:0001973
name: histone_3_acetylation_site
def: "A histone 3 modification where the modification is the acylation of the residue." [EBI:nj, SO:ke]
synonym: "H3ac" EXACT []
is_a: SO:0001702 ! histone_acetylation_site
created_by: kareneilbeck
creation_date: 2013-07-30T10:46:42Z
[Term]
id: SO:0001974
name: CTCF_binding_site
def: "A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor." [EBI:nj]
synonym: "CCCTF binding site" EXACT []
synonym: "CTCF binding site" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2013-07-30T10:59:11Z
[Term]
id: SO:0001975
name: five_prime_sticky_end_restriction_enzyme_cleavage_site
def: "A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs." [SO:ke]
comment: Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
synonym: "five prime sticky end restriction enzyme cleavage site" EXACT []
is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2013-07-30T11:32:16Z
[Term]
id: SO:0001976
name: three_prime_sticky_end_restriction_enzyme_cleavage_site
def: "A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs." [SO:ke]
comment: Requested by Jackie Quinn. The sticky restriction sites are different from junctions because they include the sequence that is cut, inclusive of the five prime junction and the three prime junction.
synonym: "three prime sticky end restriction enzyme cleavage site" EXACT []
is_a: SO:0001692 ! sticky_end_restriction_enzyme_cleavage_site
created_by: kareneilbeck
creation_date: 2013-07-30T11:37:19Z
[Term]
id: SO:0001977
name: ribonuclease_site
def: "A region of a transcript encoding the cleavage site for a ribonuclease enzyme." [SO:ke]
synonym: "ribonuclease site" EXACT []
is_a: SO:0000833 ! transcript_region
created_by: kareneilbeck
creation_date: 2013-07-30T11:41:06Z
[Term]
id: SO:0001978
name: signature
def: "A region of sequence where developer information is encoded." [SO:ke]
comment: Requested by Jackie Quinn for use in synthetic biology.
synonym: "DNA signature" EXACT []
is_a: SO:0000804 ! engineered_region
created_by: kareneilbeck
creation_date: 2013-07-30T11:49:22Z
[Term]
id: SO:0001979
name: RNA_stability_element
def: "A motif that affects the stability of RNA." [PMID:22495308, SO:ke]
synonym: "RNA stability element" EXACT []
is_a: SO:0000715 ! RNA_motif
created_by: kareneilbeck
creation_date: 2013-07-30T03:33:53Z
[Term]
id: SO:0001980
name: G_box
def: "A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a." [PMID:19249238, PMID:8571452, SO:ml]
comment: A plant specific region.
synonym: "G-box" EXACT []
synonym: "GBF binding sequence" EXACT []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2013-07-30T04:00:50Z
[Term]
id: SO:0001981
name: L_box
def: "An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants." [PMID:17381552, PMID:2902624, SO:ml]
synonym: "L-box" EXACT []
synonym: "L-box promoter element" EXACT []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2013-07-30T04:12:19Z
[Term]
id: SO:0001982
name: I-box
def: "A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core)." [PMID:2347304, PMID:2902624, SO:ml]
synonym: "I-box promoter motif" EXACT []
is_a: SO:0001678 ! regulatory_promoter_element
created_by: kareneilbeck
creation_date: 2013-07-30T04:17:55Z
[Term]
id: SO:0001983
name: 5_prime_UTR_premature_start_codon_variant
def: "A 5' UTR variant where a premature start codon is introduced, moved or lost." [SANGER:am]
comment: Requested by Andy Menzies at the Sanger. This isn't necessarily a protein coding change. A premature start codon can effect the production of a mature protein product by providing a competing translation start point. Some genes balance their expression this way, eg THPO requires the presence of a premature start to limit expression, its loss leads to Familial thrombocythemia.
synonym: "5' UTR premature start codon variant" EXACT []
synonym: "snpEff:START_GAINED" EXACT VAR []
is_a: SO:0001623 ! 5_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2013-07-30T04:36:25Z
[Term]
id: SO:0001984
name: silent_mating_type_cassette_array
def: "A gene cassette array that corresponds to a silenced version of a mating type region." [PomBase:mah]
synonym: "silent mating-type cassette" RELATED []
is_a: SO:0005854 ! gene_cassette_array
created_by: kareneilbeck
creation_date: 2013-07-31T02:40:38Z
[Term]
id: SO:0001985
name: Okazaki_fragment
def: "Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication." [ISBN:0805350152]
comment: Requested by Midori Harris, 2013.
synonym: "Okazaki fragment" EXACT []
is_a: SO:0001411 ! biological_region
created_by: kareneilbeck
creation_date: 2013-07-31T02:57:55Z
[Term]
id: SO:0001986
name: upstream_transcript_variant
def: "A feature variant, where the alteration occurs upstream of the transcript TSS." [EBI:gr]
comment: Requested by Graham Ritchie, EBI/Sanger.
synonym: "upstream transcript variant" EXACT []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:46:14Z
[Term]
id: SO:0001987
name: downstream_transcript_variant
comment: Requested by Graham Ritchie, EBI/Sanger.
synonym: "downstream transcript variant" EXACT []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:47:51Z
[Term]
id: SO:0001988
name: 5_prime_UTR_premature_start_codon_gain_variant
def: "A 5' UTR variant where a premature start codon is gained." [Sanger:am]
synonym: "5 prime UTR premature start codon gain variant" EXACT []
is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:53:06Z
[Term]
id: SO:0001989
name: 5_prime_UTR_premature_start_codon_loss_variant
def: "A 5' UTR variant where a premature start codon is lost." [SANGER:am]
is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:56:48Z
[Term]
id: SO:0001990
name: five_prime_UTR_premature_start_codon_location_variant
def: "A 5' UTR variant where a premature start codon is moved." [SANGER:am]
is_a: SO:0001983 ! 5_prime_UTR_premature_start_codon_variant
created_by: kareneilbeck
creation_date: 2013-07-31T03:57:47Z
[Term]
id: SO:0001991
name: consensus_AFLP_fragment
def: "A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input." [GMOD:ea]
comment: Requested by Bayer Cropscience September, 2013.
synonym: "consensus AFLP fragment" EXACT []
synonym: "consensus amplified fragment length polymorphism fragment" EXACT []
is_a: SO:0000994 ! consensus_region
created_by: kareneilbeck
creation_date: 2013-09-24T10:43:41Z
[Term]
id: SO:0001992
name: nonsynonymous_variant
def: "A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change." [SO:ke]
synonym: "non_synonymous_coding" EXACT [http://ensembl.org/info/docs/variation/index.html]
synonym: "nonsynonymous variant" EXACT []
is_a: SO:0001650 ! inframe_variant
created_by: kareneilbeck
creation_date: 2013-10-16T11:47:51Z
[Term]
id: SO:0001993
name: extended_cis_splice_site
def: "Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after." [SANGER:am]
comment: Added by Andy Menzies (Sanger).
synonym: "extended cis splice site" EXACT []
is_a: SO:0001419 ! cis_splice_site
created_by: kareneilbeck
creation_date: 2014-01-04T06:20:00Z
[Term]
id: SO:0001994
name: intron_base_5
def: "Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron." [SANGER:am]
synonym: "intron base 5" EXACT []
is_a: SO:0001014 ! intron_domain
relationship: part_of SO:0001993 ! extended_cis_splice_site
created_by: kareneilbeck
creation_date: 2014-01-04T06:26:02Z
[Term]
id: SO:0001995
name: extended_intronic_splice_region_variant
def: "A sequence variant occurring in the intron, within 10 bases of exon." [sanger:am]
comment: Added by Andy Menzies (Sanger).
synonym: "extended intronic splice region variant" EXACT []
is_a: SO:0001568 ! splicing_variant
created_by: kareneilbeck
creation_date: 2014-01-04T06:37:27Z
[Term]
id: SO:0001996
name: extended_intronic_splice_region
def: "Region of intronic sequence within 10 bases of an exon." [SANGER:am]
synonym: "extended intronic splice region " EXACT []
is_a: SO:0001014 ! intron_domain
created_by: kareneilbeck
creation_date: 2014-01-04T06:41:23Z
[Term]
id: SO:0001997
name: subtelomere
def: "A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed." [POMBE:al]
is_a: SO:0000628 ! chromosomal_structural_element
created_by: kareneilbeck
creation_date: 2014-01-05T07:02:01Z
[Term]
id: SO:0001998
name: sgRNA
def: "A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method." [PMID:23934893]
synonym: "gRNA" RELATED []
synonym: "guide RNA" RELATED []
synonym: "small guide RNA" EXACT []
is_a: SO:0000696 ! oligo
created_by: kareneilbeck
creation_date: 2014-01-05T07:25:08Z
[Term]
id: SO:0001999
name: mating_type_region_motif
def: "DNA motif that is a component of a mating type region." [SO:ke]
synonym: "mating type region motif" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0001789 ! mating_type_region
created_by: kareneilbeck
creation_date: 2014-01-05T07:30:17Z
[Term]
id: SO:0002001
name: Y_region
def: "A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha)." [SGD:jd]
comment: Requested by Janos Demeter, SGD.
synonym: "Y-region" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-01-05T07:33:30Z
[Term]
id: SO:0002002
name: Z1_region
def: "A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR)." [SGD:jd]
comment: Requested by Janos Demeter, SGD.
synonym: "Z1-region" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-01-05T07:34:59Z
[Term]
id: SO:0002003
name: Z2_region
def: "A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR)." [SGD:jd]
comment: Requested by Janos Demeter, SGD.
synonym: "Z2-segment" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-01-05T07:36:45Z
[Term]
id: SO:0002004
name: ARS_consensus_sequence
def: "The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS." [SGD:jd]
synonym: "ACS" EXACT []
synonym: "ARS consensus sequence" EXACT []
is_a: SO:0000713 ! DNA_motif
relationship: part_of SO:0000436 ! ARS
created_by: kareneilbeck
creation_date: 2014-01-05T07:47:48Z
[Term]
id: SO:0002005
name: DSR_motif
def: "The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome." [PMID:22645662]
comment: Requested by Antonia Locke, (Pombe).
synonym: "DSR motif" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2014-01-05T07:51:27Z
[Term]
id: SO:0002006
name: zinc_repressed_element
def: "A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc." [PMID:24003116, POMBE:mh]
comment: This element is bound by Loz1 in S. pombe. The paper does not name the element. This term was requested by Midoris Harris, for Pombe.
synonym: "zinc repressed element" EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2014-01-05T09:23:27Z
[Term]
id: SO:0002007
name: MNV
def: "An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence." [NCBI:th]
synonym: "multiple nucleotide substitution" EXACT []
synonym: "multiple nucleotide variant" EXACT []
is_a: SO:1000002 ! substitution
created_by: kareneilbeck
creation_date: 2014-01-13T03:48:40Z
[Term]
id: SO:0002008
name: rare_amino_acid_variant
def: "A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid." [SO:ke]
comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
synonym: "rare amino acid variant" EXACT []
is_a: SO:0001586 ! non_conservative_missense_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:24:01Z
[Term]
id: SO:0002009
name: selenocysteine_loss
def: "A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid." [SO:ke]
comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
synonym: "selenocysteine loss" EXACT []
is_a: SO:0002008 ! rare_amino_acid_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:29:44Z
[Term]
id: SO:0002010
name: pyrrolysine_loss
def: "A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid." [SO:ke]
comment: Request from Uma Devi Paila, UVA. Variants in the sites of rare amino acids e.g. Selenocysteine. These are important impact terms since a loss of such rare amino acids may lead to a loss of function.
synonym: "pyrrolysine loss" EXACT []
is_a: SO:0002008 ! rare_amino_acid_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:30:16Z
[Term]
id: SO:0002011
name: intragenic_variant
def: "A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence." [SO:ke]
comment: Requested by Pablo Cingolani, for use in SnpEff.
synonym: "intragenic variant" EXACT []
synonym: "snpEff:INTRAGENIC" EXACT VAR []
is_a: SO:0001576 ! transcript_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:33:13Z
[Term]
id: SO:0002012
name: start_lost
def: "A codon variant that changes at least one base of the canonical start codon." [SO:ke]
comment: Request from Uma Devi Paila, UVA. This term should not be applied to incomplete transcripts.
synonym: "snpEff:START_LOST" EXACT VAR []
is_a: SO:0001582 ! initiator_codon_variant
is_a: SO:0001992 ! nonsynonymous_variant
created_by: kareneilbeck
creation_date: 2014-03-24T02:41:28Z
[Term]
id: SO:0002013
name: 5_prime_UTR_truncation
def: "A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence." [SO:ke]
synonym: "5 prime UTR truncation" EXACT []
synonym: "snpEff:UTR_5_DELETED" EXACT VAR []
is_a: SO:0001623 ! 5_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2014-03-25T10:46:42Z
[Term]
id: SO:0002014
name: 5_prime_UTR_elongation
def: "A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence." [SO:ke]
synonym: "5 prime UTR elongation" EXACT []
is_a: SO:0001623 ! 5_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2014-03-25T10:48:26Z
[Term]
id: SO:0002015
name: 3_prime_UTR_truncation
def: "A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence." [SO:ke]
synonym: "3 prime UTR truncation" EXACT []
synonym: "snpEff:UTR_3_DELETED" EXACT VAR []
is_a: SO:0001624 ! 3_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2014-03-25T10:54:50Z
[Term]
id: SO:0002016
name: 3_prime_UTR_elongation
def: "A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence." [SO:ke]
synonym: "3 prime UTR elongation" EXACT []
is_a: SO:0001624 ! 3_prime_UTR_variant
created_by: kareneilbeck
creation_date: 2014-03-25T10:55:33Z
[Term]
id: SO:0002017
name: conserved_intergenic_variant
def: "A sequence variant located in a conserved intergenic region, between genes." [SO:ke]
comment: Requested by Uma Paila (UVA) for snpEff.
synonym: "conserved intergenic variant" EXACT []
synonym: "snpEff:INTERGENIC_CONSERVED" EXACT VAR []
is_a: SO:0001628 ! intergenic_variant
created_by: kareneilbeck
creation_date: 2014-03-25T02:54:39Z
[Term]
id: SO:0002018
name: conserved_intron_variant
def: "A transcript variant occurring within a conserved region of an intron." [SO:ke]
comment: Requested by Uma Paila (UVA) for snpEff.
synonym: "conserved intron variant" EXACT []
synonym: "snpEff:INTRON_CONSERVED" EXACT VAR []
is_a: SO:0001627 ! intron_variant
created_by: kareneilbeck
creation_date: 2014-03-25T02:58:41Z
[Term]
id: SO:0002019
name: start_retained_variant
def: "A sequence variant where at least one base in the start codon is changed, but the start remains." [SO:ke]
comment: Requested by Uma Paila as this term is annotated by snpEff. This would be used for non_AUG start codon annotation.
is_a: SO:0001582 ! initiator_codon_variant
is_a: SO:0001819 ! synonymous_variant
created_by: kareneilbeck
creation_date: 2014-03-28T10:08:41Z
[Term]
id: SO:0002020
name: boundary_element
def: "Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions." [PMID:24013502]
comment: Requested by Antonia Lock.
synonym: "boundary element" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2014-05-30T14:45:37Z
[Term]
id: SO:0002021
name: mating_type_region_replication_fork_barrier
def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:17614787]
comment: Requested by Midori Harris.
synonym: "mating type region replication fork barrier" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2014-05-30T14:57:26Z
[Term]
id: SO:0002022
name: priRNA
def: "A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts." [PMID:20178743, PMID:24095277, PomBase:al]
synonym: "primal small RNA" EXACT []
is_a: SO:0000655 ! ncRNA
created_by: kareneilbeck
creation_date: 2014-05-30T15:01:24Z
[Term]
id: SO:0002023
name: multiplexing_sequence_identifier
def: "A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library." [OBO:prs, PMID:22574170]
synonym: "multiplexing sequence identifier" EXACT []
is_a: SO:0000324 ! tag
created_by: kareneilbeck
creation_date: 2014-05-30T15:13:16Z
[Term]
id: SO:0002024
name: W_region
alt_id: SO:0002000
def: "The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR." [SGD:jd]
comment: MERGED COMMENT:\nTARGET COMMENT: Requested by Janos Demeter, SGD.\n--------------------\nSOURCE COMMENT: Requested by Janos Demeter, SGD.
synonym: "W-region" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-07-11T13:20:08Z
[Term]
id: SO:0002025
name: cis_acting_homologous_chromosome_pairing_region
def: "A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I." [PMID:22582262, PMID:23117617, PMID:24173580, PomBase:vw]
comment: Comment: An example of this is the Sme2 locus in fission yeast S. pombe, where is coincident with an ribonuclear complex termed the "Mei2 dot". This term was Requested by Val Wood, PomBase.
synonym: "cis-acting homologous chromosome pairing region" EXACT []
is_a: SO:0000713 ! DNA_motif
created_by: kareneilbeck
creation_date: 2014-07-14T11:40:34Z
[Term]
id: SO:0002026
name: intein_encoding_region
def: "The nucleotide sequence which encodes the intein portion of the precursor gene." [PMID:8165123]
comment: Requested by Janos Demeter 2014.
is_a: SO:0000842 ! gene_component_region
created_by: kareneilbeck
creation_date: 2014-07-14T11:53:21Z
[Term]
id: SO:0002027
name: uORF
def: "A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation." [PMID:12890013, PMID:16153175, POMBASE:mah]
synonym: "upstream ORF" EXACT []
is_a: SO:0000236 ! ORF
created_by: kareneilbeck
creation_date: 2014-07-14T11:59:23Z
[Term]
id: SO:0002028
name: sORF
def: "An open reading frame that encodes a peptide of less than 100 amino acids." [PMID:23970561, PMID:24705786, POMBASE:mah]
synonym: "small ORF" EXACT []
synonym: "smORF" EXACT []
is_a: SO:0000236 ! ORF
created_by: kareneilbeck
creation_date: 2014-07-14T12:02:33Z
[Term]
id: SO:0002029
name: tnaORF
def: "A translated ORF encoded entirely within the antisense strand of a known protein coding gene." [POMBASE:vw]
synonym: "translated nested antisense gene" EXACT []
is_a: SO:0000236 ! ORF
created_by: kareneilbeck
creation_date: 2014-07-14T12:04:32Z
[Term]
id: SO:0002030
name: X_region
def: "One of two segments of homology found at all three mating loci (HML, MAT and HMR)." [SGD:jd]
synonym: "x-region" EXACT []
is_a: SO:0001999 ! mating_type_region_motif
created_by: kareneilbeck
creation_date: 2014-07-14T18:43:21Z
[Term]
id: SO:0002031
name: shRNA
def: "A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference." [PMID:6699500, SO:ke]
synonym: "short hairpin RNA" EXACT []
synonym: "small hairpin RNA" EXACT []
xref: http:http:en.wikipedia.org/wiki/Small_hairpin_RNA "wikipedia"
is_a: SO:0000655 ! ncRNA
created_by: kareneilbeck
creation_date: 2014-10-23T09:16:29Z
[Term]
id: SO:0002032
name: moR
def: "A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA." [SO:ke]
comment: MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015.
synonym: "microRNA-offset RNA" EXACT []
is_a: SO:0000370 ! small_regulatory_ncRNA
relationship: part_of SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T13:57:43Z
[Term]
id: SO:0002033
name: loR
def: "A short, non coding transcript of loop-derived sequences encoded in precursor miRNA." [SO:ke]
comment: MoRs are generated from miR hairpins that are longer and can produce two functional miR per strand. They are called moRs because they are not located next to the loop and thus their biogenesis process is a little different, but functionally, they are supposed to act like miRs. It is the same for loRs that are the loop fragments, they are generated differently than miRs or moRs but if loaded into the risc they are supposed to act the same way miRs do.\nRequested by Thomas Desvignes, Jan 2015.
synonym: "loop-origin miRs" EXACT []
is_a: SO:0000370 ! small_regulatory_ncRNA
relationship: part_of SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T14:02:02Z
[Term]
id: SO:0002034
name: miR_encoding_snoRNA_primary_transcript
def: "A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:02:13Z
[Term]
id: SO:0002035
name: lncRNA_primary_transcript
def: "A primary transcript encoding a lncRNA." [SO:ke]
synonym: "lncRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2015-01-09T15:23:03Z
[Term]
id: SO:0002036
name: miR_encoding_lncRNA_primary_transcript
def: "A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding lncRNA primary transcript" EXACT []
is_a: SO:0002035 ! lncRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:23:48Z
[Term]
id: SO:0002037
name: miR_encoding_tRNA_primary_transcript
def: "A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:28:23Z
[Term]
id: SO:0002038
name: shRNA_primary_transcript
def: "A primary transcript encoding an shRNA." [SO:ke]
synonym: "shRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2015-01-09T15:30:43Z
[Term]
id: SO:0002039
name: miR_encoding_shRNA_primary_transcript
def: "A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding shRNA primary transcript" EXACT []
is_a: SO:0002038 ! shRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:32:00Z
[Term]
id: SO:0002040
name: vaultRNA_primary_transcript
def: "A primary transcript encoding a vaultRNA." [SO:ke]
synonym: "vaultRNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2015-01-09T15:33:33Z
[Term]
id: SO:0002041
name: miR_encoding_vaultRNA_primary_transcript
def: "A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding vaultRNA primary transcript" EXACT []
is_a: SO:0002040 ! vaultRNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:34:32Z
[Term]
id: SO:0002042
name: Y_RNA_primary_transcript
def: "A primary transcript encoding a Y-RNA." [SO:ke]
synonym: "Y-RNA primary transcript" EXACT []
is_a: SO:0000483 ! nc_primary_transcript
created_by: kareneilbeck
creation_date: 2015-01-09T15:36:51Z
[Term]
id: SO:0002043
name: miR_encoding_Y_RNA_primary_transcript
def: "A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA." [SO:ke]
synonym: "miR encoding Y-RNA primary transcript" EXACT []
is_a: SO:0002042 ! Y_RNA_primary_transcript
relationship: has_part SO:0001244 ! pre_miRNA
created_by: kareneilbeck
creation_date: 2015-01-09T15:37:46Z
[Term]
id: SO:0002044
name: TCS_element
def: "A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT." [PMID:1489142, PMID:20118212, SO:ke]
comment: Requested by Rama - SGD.
synonym: "TCS element" EXACT []
synonym: "TEA Consensus Sequence " EXACT []
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2015-02-09T15:02:53Z
[Term]
id: SO:0002045
name: pheromone_response_element
def: "A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)]." [PMID:1489142, SO:ke]
comment: Requested by Rama, SGD.
synonym: "pheromone response element" EXACT []
synonym: "PRE" EXACT []
is_a: SO:0000235 ! TF_binding_site
is_a: SO:0001659 ! promoter_element
created_by: kareneilbeck
creation_date: 2015-02-09T15:05:43Z
[Term]
id: SO:0002046
name: FRE
def: "A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae." [PMID:1489142, SO:ke]
comment: Requested by Rama, SGD.
synonym: "filamentation and invasion response element" EXACT []
is_a: SO:0001461 ! enhancer_binding_site
created_by: kareneilbeck
creation_date: 2015-02-09T15:09:47Z
[Term]
id: SO:0002047
name: transcription_pause_site
def: "Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli." [PMID:24789973, SO:ke]
synonym: "transcription pause site" EXACT []
is_a: SO:0001679 ! transcription_regulatory_region
created_by: kareneilbeck
creation_date: 2015-02-09T15:32:52Z
[Term]
id: SO:0002048
name: disabled_reading_frame
def: "A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons)." [SGD:se]
synonym: "disabled ORF" EXACT []
synonym: "disabled_reading frame" RELATED []
synonym: "dORF" EXACT []
is_a: SO:0000717 ! reading_frame
created_by: kareneilbeck
creation_date: 2015-02-09T16:15:46Z
[Term]
id: SO:0002049
name: H3K27_acetylation_site
def: "A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated." [SO:rs]
comment: Requested by: Sagar Jain, Richard Scheuermann.
synonym: "H3K27 acetylation site" EXACT []
is_a: SO:0001973 ! histone_3_acetylation_site
created_by: kareneilbeck
creation_date: 2015-05-14T10:17:11Z
[Term]
id: SO:0002050
name: constitutive_promoter
def: "A promoter that allows for continual transcription of gene." [SO:ke]
synonym: "constitutive promoter" EXACT []
is_a: SO:0000167 ! promoter
created_by: kareneilbeck
creation_date: 2015-05-14T10:39:09Z
[Term]
id: SO:0002051
name: inducible_promoter
def: "A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors." [SO:ke]
synonym: "inducible promoter" EXACT []
is_a: SO:0000167 ! promoter
created_by: kareneilbeck
creation_date: 2015-05-14T10:39:56Z
[Term]
id: SO:0002052
name: dominant_negative_variant
def: "A variant where the mutated gene product adversely affects the other (wild type) gene product." [SO:ke]
comment: Requested by Deanna Church.
synonym: "dominant negative" EXACT []
synonym: "dominant negative variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2015-05-14T11:16:28Z
[Term]
id: SO:0002053
name: gain_of_function_variant
def: "A sequence variant whereby new or enhanced function is conferred on the gene product." [SO:ke]
synonym: "gain of function variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2015-05-14T11:20:47Z
[Term]
id: SO:0002054
name: loss_of_function_variant
def: "A sequence variant whereby the gene product has diminished or abolished function." [SO:ke]
synonym: "loss of function variant" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2015-05-14T11:21:29Z
[Term]
id: SO:0002055
name: null_mutation
def: "A variant whereby the gene product is not functional or the gene product is not produced." [SO:ke]
synonym: "null mutation" EXACT []
is_a: SO:0001536 ! functional_variant
created_by: kareneilbeck
creation_date: 2015-05-14T11:21:57Z
[Term]
id: SO:0002056
name: intronic_splicing_silencer
def: "An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke]
comment: Requested by Javier Diez Perez.
synonym: "intronic splicing silencer" EXACT []
synonym: "ISS" EXACT []
is_a: SO:0000625 ! silencer
relationship: part_of SO:0000188 ! intron
created_by: kareneilbeck
creation_date: 2015-05-14T12:24:10Z
[Term]
id: SO:0002057
name: intronic_splicing_enhancer
synonym: "ISE" EXACT []
created_by: kareneilbeck
creation_date: 2015-05-14T12:28:31Z
is_obsolete: true
[Term]
id: SO:0002058
name: exonic_splicing_silencer
def: "An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control." [PMID:23241926, SO:ke]
comment: Requested by Javier Diez Perez.
synonym: "ESS" EXACT []
synonym: "exonic splicing silencer" EXACT []
is_a: SO:0000625 ! silencer
is_a: SO:0000852 ! exon_region
created_by: kareneilbeck
creation_date: 2015-05-14T12:42:12Z
[Term]
id: SO:0002059
name: recombination_enhancer
def: "A regulatory_region that promotes or induces the process of recombination." [PMID:8861911, SGD:se]
synonym: "recombination enhancer" EXACT []
is_a: SO:0001681 ! recombination_regulatory_region
created_by: kareneilbeck
creation_date: 2015-05-14T13:08:58Z
[Term]
id: SO:0002060
name: interchomosomal_translocation
def: "A translocation where the regions involved are from different chromosomes." [NCBI:th]
is_a: SO:1000044 ! chromosomal_translocation
created_by: kareneilbeck
creation_date: 2015-06-18T11:10:30Z
[Term]
id: SO:0002061
name: intrachomosomal_translocation
def: "A translocation where the regions involved are from the same chromosome." [NCBI:th]
is_a: SO:1000044 ! chromosomal_translocation
created_by: kareneilbeck
creation_date: 2015-06-18T11:10:51Z
[Term]
id: SO:0002062
name: complex_chromosomal_rearrangement
def: "A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis." [NCBI:th]
synonym: "complex chromosomal rearrangement" EXACT []
is_a: SO:0001784 ! complex_structural_alteration
created_by: kareneilbeck
creation_date: 2015-06-18T11:24:55Z
[Term]
id: SO:0002063
name: alu_insertion
def: "An insertion of sequence from the Alu family of mobile elements." [NCBI:th]
synonym: "alu insertion" EXACT []
is_a: SO:0001837 ! mobile_element_insertion
created_by: kareneilbeck
creation_date: 2015-06-18T11:30:36Z
[Term]
id: SO:0002064
name: LINE1_insertion
def: "An insertion from the Line1 family of mobile elements." [NCBI:th]
synonym: "line1 insertion" RELATED []
is_a: SO:0001837 ! mobile_element_insertion
created_by: kareneilbeck
creation_date: 2015-06-18T11:34:44Z
[Term]
id: SO:0002065
name: SVA_insertion
def: "An insertion of sequence from the SVA family of mobile elements." [NCBI:th]
is_a: SO:0001837 ! mobile_element_insertion
created_by: kareneilbeck
creation_date: 2015-06-18T11:36:12Z
[Term]
id: SO:0005836
name: regulatory_region
def: "A region of sequence that is involved in the control of a biological process." [SO:ke]
subset: SOFA
synonym: "regulatory region" EXACT []
xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki"
is_a: SO:0000831 ! gene_member_region
[Term]
id: SO:0005837
name: U14_snoRNA_primary_transcript
def: "The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA." [PMID:2251119]
synonym: "4.5S snRNA primary transcript" EXACT []
synonym: "U14 snoRNA primary transcript" EXACT []
is_a: SO:0000232 ! snoRNA_primary_transcript
[Term]
id: SO:0005841
name: methylation_guide_snoRNA
def: "A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue." [GOC:mah, PMID:12457565]
comment: Has RNA 2'-O-ribose methylation guide activity (GO:0030561).
synonym: "methylation guide snoRNA" EXACT []
is_a: SO:0000593 ! C_D_box_snoRNA
relationship: derives_from SO:0000580 ! methylation_guide_snoRNA_primary_transcript
[Term]
id: SO:0005843
name: rRNA_cleavage_RNA
def: "An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules." [GOC:kgc]
synonym: "rRNA cleavage RNA" EXACT []
is_a: SO:0000655 ! ncRNA
relationship: derives_from SO:0000582 ! rRNA_cleavage_snoRNA_primary_transcript
[Term]
id: SO:0005845
name: exon_of_single_exon_gene
def: "An exon that is the only exon in a gene." [RSC:cb]
synonym: "exon of single exon gene" EXACT []
synonym: "single_exon" RELATED []
synonym: "singleton exon" EXACT []
is_a: SO:0000147 ! exon
[Term]
id: SO:0005847
name: cassette_array_member
synonym: "cassette array member" EXACT []
is_a: SO:0005848 ! gene_cassette_member
[Term]
id: SO:0005848
name: gene_cassette_member
synonym: "gene cassette member" EXACT []
is_a: SO:0000081 ! gene_array_member
[Term]
id: SO:0005849
name: gene_subarray_member
synonym: "gene subarray member" EXACT []
is_a: SO:0000081 ! gene_array_member
[Term]
id: SO:0005850
name: primer_binding_site
def: "Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription." [http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html]
synonym: "primer binding site" EXACT []
xref: http://en.wikipedia.org/wiki/Primer_binding_site "wiki"
is_a: SO:0001655 ! nucleotide_binding_site
relationship: part_of SO:0000186 ! LTR_retrotransposon
[Term]
id: SO:0005851
name: gene_array
def: "An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so." [SO:ma]
comment: This would include, for example, a cluster of genes each encoding the major ribosomal RNAs and a cluster of histone gene subarrays.
synonym: "gene array" EXACT []
is_a: SO:0005855 ! gene_group
[Term]
id: SO:0005852
name: gene_subarray
def: "A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function." [SO:ma]
comment: This would include, for example, a cluster of genes encoding different histones.
synonym: "gene subarray" EXACT []
is_a: SO:0005855 ! gene_group
[Term]
id: SO:0005853
name: gene_cassette
def: "A gene that can be substituted for a related gene at a different site in the genome." [SGD:se]
comment: This would include, for example, the mating type gene cassettes of S. cerevisiae. Gene cassettes usually exist as linear sequences as part of a larger DNA molecule, such as a chromosome or plasmid.
synonym: "gene cassette" EXACT []
xref: http://en.wikipedia.org/wiki/Gene_cassette "wiki"
is_a: SO:0000704 ! gene
[Term]
id: SO:0005854
name: gene_cassette_array
def: "An array of non-functional genes whose members, when captured by recombination form functional genes." [SO:ma]
comment: This would include, for example, the arrays of non-functional VSG genes of Trypanosomes.
synonym: "gene cassette array" EXACT []
is_a: SO:0005855 ! gene_group
relationship: has_part SO:0005853 ! gene_cassette
[Term]
id: SO:0005855
name: gene_group
def: "A collection of related genes." [SO:ma]
subset: SOFA
synonym: "gene group" EXACT []
is_a: SO:0001411 ! biological_region
[Term]
id: SO:0005856
name: selenocysteine_tRNA_primary_transcript
def: "A primary transcript encoding seryl tRNA (SO:000269)." [SO:ke]
synonym: "selenocysteine tRNA primary transcript" EXACT []
is_a: SO:0000210 ! tRNA_primary_transcript
[Term]
id: SO:0005857
name: selenocysteinyl_tRNA
def: "A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region." [SO:ke]
synonym: "selenocysteinyl tRNA" EXACT []
synonym: "selenocysteinyl-transfer ribonucleic acid" EXACT []
synonym: "selenocysteinyl-transfer RNA" EXACT []
is_a: SO:0000253 ! tRNA
relationship: derives_from SO:0005856 ! selenocysteine_tRNA_primary_transcript
[Term]
id: SO:0005858
name: syntenic_region
def: "A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species." [http://www.informatics.jax.org/silverbook/glossary.shtml]
synonym: "syntenic region" EXACT []
is_a: SO:0000330 ! conserved_region
relationship: has_quality SO:0000860 ! syntenic
[Term]
id: SO:0100001
name: biochemical_region_of_peptide
def: "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "biochemical motif" EXACT []
synonym: "biochemical region of peptide" EXACT []
synonym: "biochemical_region" RELATED []
is_a: SO:0001067 ! polypeptide_motif
[Term]
id: SO:0100002
name: molecular_contact_region
def: "A region that is involved a contact with another molecule." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "molecular contact region" RELATED []
is_a: SO:0100001 ! biochemical_region_of_peptide
[Term]
id: SO:0100003
name: intrinsically_unstructured_polypeptide_region
def: "A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]
subset: biosapiens
synonym: "disordered region" RELATED BS []
synonym: "intrinsically unstructured polypeptide region" EXACT []
is_a: SO:0001070 ! polypeptide_structural_region
[Term]
id: SO:0100004
name: catmat_left_handed_three
def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-3l" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0100005
name: catmat_left_handed_four
def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-4l" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0100006
name: catmat_right_handed_three
def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-3r" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0100007
name: catmat_right_handed_four
def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-4r" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0100008
name: alpha_beta_motif
def: "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "alpha beta motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0100009
name: lipoprotein_signal_peptide
def: "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]
subset: biosapiens
synonym: "lipoprotein signal peptide" EXACT []
synonym: "prokaryotic membrane lipoprotein lipid attachment site" EXACT []
is_a: SO:0100011 ! cleaved_peptide_region
[Term]
id: SO:0100010
name: no_output
def: "An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]
subset: biosapiens
synonym: "no output" EXACT BS []
is_a: SO:0000703 ! experimental_result_region
[Term]
id: SO:0100011
name: cleaved_peptide_region
def: "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]
comment: Range.
subset: biosapiens
subset: SOFA
synonym: "cleaved peptide region" EXACT []
is_a: SO:0000839 ! polypeptide_region
relationship: part_of SO:0001063 ! immature_peptide_region
[Term]
id: SO:0100012
name: peptide_coil
def: "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]
subset: biosapiens
synonym: "coil" RELATED BS []
synonym: "peptide coil" EXACT []
synonym: "random coil" RELATED BS []
is_a: SO:0001078 ! polypeptide_secondary_structure
[Term]
id: SO:0100013
name: hydrophobic_region_of_peptide
def: "Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "hydropathic" RELATED []
synonym: "hydrophobic region of peptide" RELATED []
synonym: "hydrophobic_region" EXACT []
synonym: "hydrophobicity" RELATED []
is_a: SO:0000839 ! polypeptide_region
[Term]
id: SO:0100014
name: n_terminal_region
def: "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]
subset: biosapiens
synonym: "N-region" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0000418 ! signal_peptide
[Term]
id: SO:0100015
name: c_terminal_region
def: "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]
subset: biosapiens
synonym: "C-region" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0000418 ! signal_peptide
[Term]
id: SO:0100016
name: central_hydrophobic_region_of_signal_peptide
def: "The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]
subset: biosapiens
synonym: "central hydrophobic region of signal peptide" EXACT []
synonym: "central_hydrophobic_region" RELATED []
synonym: "H-region" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0000418 ! signal_peptide
[Term]
id: SO:0100017
name: polypeptide_conserved_motif
def: "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]
subset: biosapiens
synonym: "motif" RELATED []
is_a: SO:0001067 ! polypeptide_motif
[Term]
id: SO:0100018
name: polypeptide_binding_motif
def: "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]
subset: biosapiens
synonym: "binding" RELATED [uniprot:feature_type]
synonym: "polypeptide binding motif" EXACT []
is_a: SO:0100001 ! biochemical_region_of_peptide
[Term]
id: SO:0100019
name: polypeptide_catalytic_motif
def: "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]
subset: biosapiens
synonym: "catalytic_motif" RELATED []
synonym: "polypeptide catalytic motif" EXACT []
is_a: SO:0100001 ! biochemical_region_of_peptide
[Term]
id: SO:0100020
name: polypeptide_DNA_contact
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]
subset: biosapiens
synonym: "DNA_bind" EXACT BS [uniprot:feature]
synonym: "polypeptide DNA contact" EXACT []
is_a: SO:0001429 ! DNA_binding_site
is_a: SO:0100002 ! molecular_contact_region
[Term]
id: SO:0100021
name: polypeptide_conserved_region
def: "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]
subset: biosapiens
synonym: "polypeptide conserved region" EXACT []
is_a: SO:0000839 ! polypeptide_region
[Term]
id: SO:1000002
name: substitution
def: "A sequence alteration where the length of the change in the variant is the same as that of the reference." [SO:ke]
subset: SOFA
xref: loinc:LA6690-7 "Substitution"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region
[Term]
id: SO:1000005
name: complex_substitution
def: "When no simple or well defined DNA mutation event describes the observed DNA change, the keyword \"complex\" should be used. Usually there are multiple equally plausible explanations for the change." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: SOFA
synonym: "complex substitution" EXACT []
is_a: SO:1000002 ! substitution
[Term]
id: SO:1000008
name: point_mutation
def: "A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence." [SO:immuno_workshop]
subset: SOFA
synonym: "point mutation" EXACT []
xref: http://en.wikipedia.org/wiki/Point_mutation "wiki"
is_a: SO:0001483 ! SNV
[Term]
id: SO:1000009
name: transition
def: "Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
is_a: SO:0001483 ! SNV
[Term]
id: SO:1000010
name: pyrimidine_transition
def: "A substitution of a pyrimidine, C or T, for another pyrimidine." [SO:ke]
synonym: "pyrimidine transition" EXACT []
is_a: SO:1000009 ! transition
[Term]
id: SO:1000011
name: C_to_T_transition
def: "A transition of a cytidine to a thymine." [SO:ke]
synonym: "C to T transition" EXACT []
is_a: SO:1000010 ! pyrimidine_transition
[Term]
id: SO:1000012
name: C_to_T_transition_at_pCpG_site
def: "The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
synonym: "C to T transition at pCpG site" EXACT []
is_a: SO:1000011 ! C_to_T_transition
[Term]
id: SO:1000013
name: T_to_C_transition
synonym: "T to C transition" EXACT []
is_a: SO:1000010 ! pyrimidine_transition
[Term]
id: SO:1000014
name: purine_transition
def: "A substitution of a purine, A or G, for another purine." [SO:ke]
synonym: "purine transition" EXACT []
is_a: SO:1000009 ! transition
[Term]
id: SO:1000015
name: A_to_G_transition
def: "A transition of an adenine to a guanine." [SO:ke]
synonym: "A to G transition" EXACT []
is_a: SO:1000014 ! purine_transition
[Term]
id: SO:1000016
name: G_to_A_transition
def: "A transition of a guanine to an adenine." [SO:ke]
synonym: "G to A transition" EXACT []
is_a: SO:1000014 ! purine_transition
[Term]
id: SO:1000017
name: transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
xref: http://en.wikipedia.org/wiki/Transversion "wiki"
is_a: SO:0001483 ! SNV
[Term]
id: SO:1000018
name: pyrimidine_to_purine_transversion
def: "Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G." [SO:ke]
synonym: "pyrimidine to purine transversion" EXACT []
is_a: SO:1000017 ! transversion
[Term]
id: SO:1000019
name: C_to_A_transversion
def: "A transversion from cytidine to adenine." [SO:ke]
synonym: "C to A transversion" EXACT []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion
[Term]
id: SO:1000020
name: C_to_G_transversion
synonym: "C to G transversion" EXACT []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion
[Term]
id: SO:1000021
name: T_to_A_transversion
def: "A transversion from T to A." [SO:ke]
synonym: "T to A transversion" EXACT []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion
[Term]
id: SO:1000022
name: T_to_G_transversion
def: "A transversion from T to G." [SO:ke]
synonym: "T to G transversion" EXACT []
is_a: SO:1000018 ! pyrimidine_to_purine_transversion
[Term]
id: SO:1000023
name: purine_to_pyrimidine_transversion
def: "Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T." [SO:ke]
synonym: "purine to pyrimidine transversion" EXACT []
is_a: SO:1000017 ! transversion
[Term]
id: SO:1000024
name: A_to_C_transversion
def: "A transversion from adenine to cytidine." [SO:ke]
synonym: "A to C transversion" EXACT []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion
[Term]
id: SO:1000025
name: A_to_T_transversion
def: "A transversion from adenine to thymine." [SO:ke]
synonym: "A to T transversion" EXACT []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion
[Term]
id: SO:1000026
name: G_to_C_transversion
def: "A transversion from guanine to cytidine." [SO:ke]
synonym: "G to C transversion" EXACT []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion
[Term]
id: SO:1000027
name: G_to_T_transversion
def: "A transversion from guanine to thymine." [SO:ke]
synonym: "G to T transversion" EXACT []
is_a: SO:1000023 ! purine_to_pyrimidine_transversion
[Term]
id: SO:1000028
name: intrachromosomal_mutation
def: "A chromosomal structure variation within a single chromosome." [SO:ke]
synonym: "intrachromosomal mutation" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation
relationship: has_quality SO:0001510 ! intrachromosomal
[Term]
id: SO:1000029
name: chromosomal_deletion
def: "An incomplete chromosome." [SO:ke]
synonym: "(bacteria)&Dgr;" RELATED []
synonym: "(Drosophila)Df" RELATED []
synonym: "(fungi)D" RELATED []
synonym: "chromosomal deletion" EXACT []
synonym: "deficiency" EXACT []
xref: http://en.wikipedia.org/wiki/Chromosomal_deletion "wiki"
is_a: SO:1000028 ! intrachromosomal_mutation
relationship: has_part SO:0000159 ! deletion
[Term]
id: SO:1000030
name: chromosomal_inversion
def: "An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type." [SO:ke]
synonym: "(bacteria)IN" RELATED []
synonym: "(Drosophila)In" RELATED []
synonym: "(fungi)In" RELATED []
synonym: "chromosomal inversion" EXACT []
xref: http://en.wikipedia.org/wiki/Chromosomal_inversion "wiki"
is_a: SO:1000028 ! intrachromosomal_mutation
relationship: has_part SO:1000036 ! inversion
[Term]
id: SO:1000031
name: interchromosomal_mutation
def: "A chromosomal structure variation whereby more than one chromosome is involved." [SO:ke]
synonym: "interchromosomal mutation" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation
relationship: has_quality SO:0001511 ! interchromosomal
[Term]
id: SO:1000032
name: indel
def: "A sequence alteration which included an insertion and a deletion, affecting 2 or more bases." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, http:http://www.hgvs.org/mutnomen/recs-DNA.html#indel]
comment: Indels can have a different number of bases than the corresponding reference sequence.
xref: http://en.wikipedia.org/wiki/Indel "wiki"
xref: loinc:LA9659-9 "Insertion and Deletion"
is_a: SO:0001059 ! sequence_alteration
[Term]
id: SO:1000035
name: duplication
def: "An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html, NCBI:th]
synonym: "nucleotide duplication" EXACT []
synonym: "nucleotide_duplication" RELATED []
xref: loinc:LA6686-5 "Duplication"
is_a: SO:0000667 ! insertion
[Term]
id: SO:1000036
name: inversion
def: "A continuous nucleotide sequence is inverted in the same position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
subset: DBVAR
subset: SOFA
synonym: "inversion" EXACT dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
xref: loinc:LA6689-9 "Inversion"
is_a: SO:0001059 ! sequence_alteration
is_a: SO:0001411 ! biological_region
[Term]
id: SO:1000037
name: chromosomal_duplication
def: "An extra chromosome." [SO:ke]
synonym: "(Drosophila)Dp" RELATED []
synonym: "(fungi)Dp" RELATED []
synonym: "chromosomal duplication" EXACT []
xref: http://en.wikipedia.org/wiki/Chromosomal_duplication "wiki"
is_a: SO:1000183 ! chromosome_structure_variation
[Term]
id: SO:1000038
name: intrachromosomal_duplication
def: "A duplication that occurred within a chromosome." [SO:ke]
synonym: "intrachromosomal duplication" EXACT []
is_a: SO:1000028 ! intrachromosomal_mutation
is_a: SO:1000037 ! chromosomal_duplication
relationship: has_part SO:1000035 ! duplication
[Term]
id: SO:1000039
name: direct_tandem_duplication
def: "A tandem duplication where the individual regions are in the same orientation." [SO:ke]
synonym: "direct tandem duplication" EXACT []
is_a: SO:1000173 ! tandem_duplication
[Term]
id: SO:1000040
name: inverted_tandem_duplication
def: "A tandem duplication where the individual regions are not in the same orientation." [SO:ke]
synonym: "inverted tandem duplication" EXACT []
synonym: "mirror duplication" RELATED []
is_a: SO:1000173 ! tandem_duplication
[Term]
id: SO:1000041
name: intrachromosomal_transposition
def: "A chromosome structure variation whereby a transposition occurred within a chromosome." [SO:ke]
synonym: "(Drosophila)Tp" RELATED []
synonym: "intrachromosomal transposition" EXACT []
is_a: SO:0000453 ! chromosomal_transposition
is_a: SO:1000038 ! intrachromosomal_duplication
relationship: has_part SO:0000199 ! translocation
relationship: has_part SO:1000035 ! duplication
[Term]
id: SO:1000042
name: compound_chromosome
def: "A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms." [SO:ke]
synonym: "compound chromosome" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation
[Term]
id: SO:1000043
name: Robertsonian_fusion
def: "A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere." [http://en.wikipedia.org/wiki/Robertsonian_translocation]
synonym: "centric-fusion translocations" EXACT []
synonym: "Robertsonian fusion" EXACT []
synonym: "whole-arm translocations" EXACT []
xref: http://en.wikipedia.org/wiki/Robertsonian_fusion "wiki"
is_a: SO:1000044 ! chromosomal_translocation
[Term]
id: SO:1000044
name: chromosomal_translocation
def: "An interchromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations." [FB:reference_manual]
synonym: "(Drosophila)T" RELATED []
synonym: "(fungi)T" RELATED []
synonym: "chromosomal translocation" EXACT []
xref: http://en.wikipedia.org/wiki/Chromosomal_translocation "wiki"
is_a: SO:0000199 ! translocation
is_a: SO:1000031 ! interchromosomal_mutation
[Term]
id: SO:1000045
name: ring_chromosome
def: "A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome." [http://en.wikipedia.org/wiki/Ring_chromosome]
synonym: "(Drosophila)R" RELATED []
synonym: "(fungi)C" RELATED []
synonym: "ring chromosome" EXACT []
xref: http://en.wikipedia.org/wiki/Ring_chromosome "wiki"
is_a: SO:1000028 ! intrachromosomal_mutation
relationship: has_quality SO:0000988 ! circular
[Term]
id: SO:1000046
name: pericentric_inversion
def: "A chromosomal inversion that includes the centromere." [FB:reference_manual]
synonym: "pericentric inversion" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
relationship: has_quality SO:0001518 ! pericentric
[Term]
id: SO:1000047
name: paracentric_inversion
def: "A chromosomal inversion that does not include the centromere." [FB:reference_manual]
synonym: "paracentric inversion" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
relationship: has_quality SO:0001519 ! paracentric
[Term]
id: SO:1000048
name: reciprocal_chromosomal_translocation
def: "A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged." [FB:reference_manual]
synonym: "reciprocal chromosomal translocation" EXACT []
is_a: SO:1000044 ! chromosomal_translocation
[Term]
id: SO:1000049
name: sequence_variation_affecting_transcript
alt_id: SO:1000177
alt_id: SO:1000179
def: "Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript" EXACT []
synonym: "mutation causing partially characterised change in transcript" RELATED []
synonym: "mutation causing uncharacterised change in transcript" RELATED []
synonym: "sequence variant causing partially characterised change in transcript" EXACT []
synonym: "sequence variant causing uncharacterised change in transcript" EXACT []
synonym: "sequence variation affecting transcript" EXACT []
synonym: "sequence_variant_causing_partially_characterised_change_in_transcript" EXACT []
synonym: "sequence_variant_causing_uncharacterised_change_in_transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001576
[Term]
id: SO:1000050
name: sequence_variant_causing_no_change_in_transcript
def: "No effect on the state of the RNA." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is not change, it is not a good ontological term.
synonym: "mutation causing no change in transcript" RELATED []
synonym: "sequence variant causing no change in transcript" EXACT []
is_obsolete: true
[Term]
id: SO:1000054
name: sequence_variation_affecting_coding_sequence
def: "Any of the amino acid coding triplets of a gene are affected by the DNA mutation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting coding sequence" EXACT []
synonym: "sequence variation affecting coding sequence" RELATED []
is_obsolete: true
replaced_by: SO:0001580
[Term]
id: SO:1000055
name: sequence_variant_causing_initiator_codon_change_in_transcript
def: "The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing initiator codon change in transcript" RELATED []
synonym: "sequence variant causing initiator codon change in transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001582
[Term]
id: SO:1000056
name: sequence_variant_causing_amino_acid_coding_codon_change_in_transcript
def: "The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutaton causing amino acid coding codon change in transcript" RELATED []
synonym: "sequence variant causing amino acid coding codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001606
[Term]
id: SO:1000057
name: sequence_variant_causing_synonymous_codon_change_in_transcript
def: "The changed codon has the same translation product as the original codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing synonymous codon change in transcript" RELATED []
synonym: "sequence variant causing synonymous codon change in transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001819
[Term]
id: SO:1000058
name: sequence_variant_causing_non_synonymous_codon_change_in_transcript
def: "A DNA point mutation that causes a substitution of an amino acid by an other." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing non synonymous codon change in transcript" RELATED []
synonym: "non-synonymous codon change in transcript" EXACT []
synonym: "sequence variant causing non synonymous codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001583
[Term]
id: SO:1000059
name: sequence_variant_causing_missense_codon_change_in_transcript
def: "The nucleotide change in the codon leads to a new codon coding for a new amino acid." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing missense codon change in transcript" RELATED []
synonym: "sequence variant causing missense codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001583
[Term]
id: SO:1000060
name: sequence_variant_causing_conservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
synonym: "mutation causing conservative missense codon change in transcript" RELATED []
synonym: "sequence variant causing conservative missense codon change in transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001585
[Term]
id: SO:1000061
name: sequence_variant_causing_nonconservative_missense_codon_change_in_transcript
def: "The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: The exact rules need to be stated, a common set of rules can be derived from e.g. BLOSUM62 amino acid distance matrix.
synonym: "mutation causing nonconservative missense codon change in transcript" RELATED []
synonym: "sequence variant causing nonconservative missense codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001586
[Term]
id: SO:1000062
name: sequence_variant_causing_nonsense_codon_change_in_transcript
def: "The nucleotide change in the codon triplet creates a terminator codon." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing nonsense codon change in transcript" RELATED []
synonym: "sequence variant causing nonsense codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001587
[Term]
id: SO:1000063
name: sequence_variant_causing_terminator_codon_change_in_transcript
def: "The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing terminator codon change in transcript" RELATED []
synonym: "sequence variant causing terminator codon change in transcript" EXACT []
is_obsolete: true
consider: SO:0001590
[Term]
id: SO:1000064
name: sequence_variation_affecting_reading_frame
def: "An umbrella term for terms describing an effect of a sequence variation on the frame of translation." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting reading frame" EXACT []
synonym: "sequence variation affecting reading frame" RELATED []
is_obsolete: true
[Term]
id: SO:1000065
name: frameshift_sequence_variation
def: "A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three." [SO:ke]
synonym: "frameshift mutation" EXACT []
synonym: "frameshift sequence variation" RELATED []
synonym: "out of frame mutation" RELATED []
xref: http://en.wikipedia.org/wiki/Frameshift_mutation "wiki"
is_obsolete: true
[Term]
id: SO:1000066
name: sequence_variant_causing_plus_1_frameshift_mutation
def: "A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "plus 1 frameshift mutation" EXACT []
synonym: "sequence variant causing plus 1 frameshift mutation" EXACT []
is_obsolete: true
replaced_by: SO:0001594
[Term]
id: SO:1000067
name: sequence_variant_causing_minus_1_frameshift
def: "A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "minus 1 frameshift mutation" EXACT []
synonym: "sequence variant causing minus 1 frameshift" EXACT []
is_obsolete: true
replaced_by: SO:0001592
[Term]
id: SO:1000068
name: sequence_variant_causing_plus_2_frameshift
def: "A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "plus 2 frameshift mutation" EXACT []
synonym: "sequence variant causing plus 2 frameshift" EXACT []
is_obsolete: true
replaced_by: SO:0001595
[Term]
id: SO:1000069
name: sequence_variant_causing_minus_2_frameshift
def: "A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "minus 2 frameshift mutation" EXACT []
synonym: "sequence variant causing minus 2 frameshift" EXACT []
is_obsolete: true
replaced_by: SO:0001593
[Term]
id: SO:1000070
name: sequence_variant_affecting_transcript_processing
def: "Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript processing" RELATED []
synonym: "sequence variant affecting transcript processing" EXACT []
is_obsolete: true
replaced_by: SO:0001543
[Term]
id: SO:1000071
name: sequence_variant_affecting_splicing
def: "A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting splicing" RELATED []
synonym: "sequence variant affecting splicing" EXACT []
is_obsolete: true
replaced_by: SO:0001568
[Term]
id: SO:1000072
name: sequence_variant_affecting_splice_donor
def: "A sequence_variant_effect that changes the splice donor sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting splice donor" RELATED []
synonym: "sequence variant affecting splice donor" RELATED []
synonym: "splice donor mutation" EXACT []
is_obsolete: true
replaced_by: SO:0001575
[Term]
id: SO:1000073
name: sequence_variant_affecting_splice_acceptor
def: "A sequence_variant_effect that changes the splice acceptor sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting splicing" RELATED []
synonym: "sequence variant affecting splice acceptor" RELATED []
synonym: "splice acceptor mutation" EXACT []
is_obsolete: true
replaced_by: SO:0001574
[Term]
id: SO:1000074
name: sequence_variant_causing_cryptic_splice_activation
def: "A sequence variant causing a new (functional) splice site." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: A cryptic splice site is only used when the natural splice site has been disrupted by a sequence alteration.
synonym: "cryptic splice activator sequence variant" EXACT []
synonym: "mutation causing cryptic splice activator" RELATED []
synonym: "sequence variant causing cryptic splice activator" EXACT []
is_obsolete: true
replaced_by: SO:0001569
[Term]
id: SO:1000075
name: sequence_variant_affecting_editing
def: "Sequence variant affects the editing of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting editing" RELATED []
synonym: "sequence variant affecting editing" EXACT []
is_obsolete: true
replaced_by: SO:0001544
[Term]
id: SO:1000076
name: sequence_variant_affecting_transcription
def: "Mutation affects the process of transcription, its initiation, progression or termination." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcription" RELATED []
synonym: "sequence variant affecting transcription" EXACT []
is_obsolete: true
replaced_by: SO:0001549
[Term]
id: SO:1000078
name: sequence_variant_decreasing_rate_of_transcription
def: "A sequence variation that decreases the rate a which transcription of the sequence occurs." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation decreasing rate of transcription" RELATED []
synonym: "sequence variation decreasing rate of transcription" EXACT []
is_obsolete: true
[Term]
id: SO:1000079
name: sequence_variation_affecting_transcript_sequence
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript sequence" EXACT []
synonym: "sequence variation affecting transcript sequence" EXACT []
is_obsolete: true
[Term]
id: SO:1000080
name: sequence_variant_increasing_rate_of_transcription
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation increasing rate of transcription" RELATED []
synonym: "sequence variation increasing rate of transcription" EXACT []
is_obsolete: true
[Term]
id: SO:1000081
name: sequence_variant_affecting_rate_of_transcription
def: "A mutation that alters the rate a which transcription of the sequence occurs." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting rate of transcription" RELATED []
synonym: "sequence variant affecting rate of transcription" EXACT []
is_obsolete: true
replaced_by: SO:0001550
[Term]
id: SO:1000082
name: sequence variant_affecting_transcript_stability
def: "Sequence variant affects the stability of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript stability" RELATED []
synonym: "sequence variant affecting transcript stability" EXACT []
is_obsolete: true
replaced_by: SO:0001546
[Term]
id: SO:1000083
name: sequence_variant_increasing_transcript_stability
def: "Sequence variant increases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation increasing transcript stability" RELATED []
synonym: "sequence variant increasing transcript stability" EXACT []
is_obsolete: true
[Term]
id: SO:1000084
name: sequence_variant_decreasing_transcript_stability
def: "Sequence variant decreases the stability (half-life) of the transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation decreasing transcript stability" RELATED []
synonym: "sequence variant decreasing transcript stability" EXACT []
is_obsolete: true
[Term]
id: SO:1000085
name: sequence_variation_affecting_level_of_transcript
def: "A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting level of transcript" RELATED []
synonym: "sequence variation affecting level of transcript" EXACT []
is_obsolete: true
replaced_by: SO:0001540
[Term]
id: SO:1000086
name: sequence_variation_decreasing_level_of_transcript
def: "A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation decreasing level of transcript" EXACT []
synonym: "sequence variation decreasing level of transcript" RELATED []
is_obsolete: true
[Term]
id: SO:1000087
name: sequence_variation_increasing_level_of_transcript
def: "A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation increasing level of transcript" EXACT []
synonym: "sequence variation increasing level of transcript" EXACT []
is_obsolete: true
[Term]
id: SO:1000088
name: sequence_variant_affecting_translational_product
alt_id: SO:1000090
alt_id: SO:1000091
def: "A sequence variant causing a change in primary translation product of a transcript." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting translational product" RELATED []
synonym: "mutation causing partially characterised change of translational product" RELATED []
synonym: "mutation causing uncharacterised change of translational product" RELATED []
synonym: "sequence variant affecting translational product" EXACT []
synonym: "sequence variant causing partially characterised change of translational product" EXACT []
synonym: "sequence variant causing uncharacterised change of translational product" EXACT []
synonym: "sequence_variant_causing_partially_characterised_change_of_translational_product" EXACT []
synonym: "sequence_variant_causing_uncharacterised_change_of_translational_product" EXACT []
is_obsolete: true
replaced_by: SO:0001553
[Term]
id: SO:1000089
name: sequence_variant_causing_no_change_of_translational_product
def: "The sequence variant at RNA level does not lead to any change in polypeptide." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also, as there is no change, this is not a good ontological term.
synonym: "mutation causing no change of translational product" RELATED []
synonym: "sequence variant causing no change of translational product" EXACT []
is_obsolete: true
[Term]
id: SO:1000092
name: sequence_variant_causing_complex_change_of_translational_product
def: "Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing complex change of translational product" RELATED []
synonym: "sequence variant causing complex change of translational product" EXACT []
is_obsolete: true
consider: SO:0001539
[Term]
id: SO:1000093
name: sequence_variant_causing_amino_acid_substitution
def: "The replacement of a single amino acid by another." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing amino acid substitution" RELATED []
synonym: "sequence variant causing amino acid substitution" EXACT []
is_obsolete: true
replaced_by: SO:0001606
[Term]
id: SO:1000094
name: sequence_variant_causing_conservative_amino_acid_substitution
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing conservative amino acid substitution" RELATED []
synonym: "sequence variant causing conservative amino acid substitution" EXACT []
is_obsolete: true
replaced_by: SO:0001607
[Term]
id: SO:1000095
name: sequence_variant_causing_nonconservative_amino_acid_substitution
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing nonconservative amino acid substitution" RELATED []
synonym: "sequence variant causing nonconservative amino acid substitution" EXACT []
is_obsolete: true
replaced_by: SO:0001607
[Term]
id: SO:1000096
name: sequence_variant_causing_amino_acid_insertion
def: "The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing amino acid insertion" RELATED []
synonym: "sequence variant causing amino acid insertion" EXACT []
is_obsolete: true
replaced_by: SO:0001605
[Term]
id: SO:1000097
name: sequence_variant_causing_amino_acid_deletion
def: "The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing amino acid deletion" RELATED []
synonym: "sequence variant causing amino acid deletion" EXACT []
is_obsolete: true
consider: SO:0001825
[Term]
id: SO:1000098
name: sequence_variant_causing_polypeptide_truncation
def: "The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide truncation" RELATED []
synonym: "sequence variant causing polypeptide truncation" EXACT []
is_obsolete: true
replaced_by: SO:0001587
[Term]
id: SO:1000099
name: sequence_variant_causing_polypeptide_elongation
def: "The extension of the translational product at either (or both) the N-terminus and/or the C-terminus." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide elongation" RELATED []
synonym: "sequence variant causing polypeptide elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001609
[Term]
id: SO:1000100
name: mutation_causing_polypeptide_N_terminal_elongation
def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide N terminal elongation" EXACT []
synonym: "polypeptide N-terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001611
[Term]
id: SO:1000101
name: mutation_causing_polypeptide_C_terminal_elongation
def: "." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide C terminal elongation" EXACT []
synonym: "polypeptide C-terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001610
[Term]
id: SO:1000102
name: sequence_variant_affecting_level_of_translational_product
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting level of translational product" RELATED []
synonym: "sequence variant affecting level of translational product" EXACT []
is_obsolete: true
replaced_by: SO:0001553
[Term]
id: SO:1000103
name: sequence_variant_decreasing_level_of_translation_product
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutationdecreasing level of translation product" RELATED []
synonym: "sequence variant decreasing level of translation product" EXACT []
is_obsolete: true
replaced_by: SO:0001555
[Term]
id: SO:1000104
name: sequence_variant_increasing_level_of_translation_product
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutationt increasing level of translation product" RELATED []
synonym: "sequence variant increasing level of translation product" EXACT []
is_obsolete: true
[Term]
id: SO:1000105
name: sequence_variant_affecting_polypeptide_amino_acid_sequence
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting polypeptide amino acid sequence" RELATED []
synonym: "sequence variant affecting polypeptide amino acid sequence" EXACT []
is_obsolete: true
replaced_by: SO:0001603
[Term]
id: SO:1000106
name: mutation_causing_inframe_polypeptide_N_terminal_elongation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "inframe polypeptide N-terminal elongation" EXACT []
synonym: "mutation causing inframe polypeptide N terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001614
[Term]
id: SO:1000107
name: mutation_causing_out_of_frame_polypeptide_N_terminal_elongation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing out of frame polypeptide N terminal elongation" EXACT []
synonym: "out of frame polypeptide N-terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001615
[Term]
id: SO:1000108
name: mutaton_causing_inframe_polypeptide_C_terminal_elongation
synonym: "inframe_polypeptide C-terminal elongation" EXACT []
synonym: "mutaton causing inframe polypeptide C terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001612
[Term]
id: SO:1000109
name: mutation_causing_out_of_frame_polypeptide_C_terminal_elongation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing out of frame polypeptide C terminal elongation" EXACT []
synonym: "out of frame polypeptide C-terminal elongation" EXACT []
is_obsolete: true
replaced_by: SO:0001613
[Term]
id: SO:1000110
name: frame_restoring_sequence_variant
def: "A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame." [SO:ke]
synonym: "frame restoring mutation" EXACT []
synonym: "frame restoring sequence variant" EXACT []
is_obsolete: true
[Term]
id: SO:1000111
name: sequence_variant_affecting_3D_structure_of_polypeptide
alt_id: SO:1000113
alt_id: SO:1000114
def: "A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting 3D structure of polypeptide" RELATED []
synonym: "mutation causing partially characterised 3D structural change" RELATED []
synonym: "mutation causing uncharacterised 3D structural change" RELATED []
synonym: "sequence variant affecting 3D structure of polypeptide" EXACT []
synonym: "sequence variant affecting 3D-structure of polypeptide" EXACT []
synonym: "sequence variant causing partially characterised 3D structural change" EXACT []
synonym: "sequence variant causing uncharacterised 3D structural change" EXACT []
synonym: "sequence_variant_causing_partially_characterised_3D_structural_change" EXACT []
synonym: "sequence_variant_causing_uncharacterised_3D_structural_change" EXACT []
is_obsolete: true
replaced_by: SO:0001599
[Term]
id: SO:1000112
name: sequence_variant_causing_no_3D_structural_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect. Also as there is no effect, it is not a good term.
synonym: "mutation causing no 3D structural change" RELATED []
synonym: "sequence variant causing no 3D structural change" EXACT []
is_obsolete: true
[Term]
id: SO:1000115
name: sequence_variant_causing_complex_3D_structural_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing complex 3D structural change" RELATED []
synonym: "sequence variant causing complex 3D structural change" EXACT []
is_obsolete: true
replaced_by: SO:0001600
[Term]
id: SO:1000116
name: sequence_variant_causing_conformational_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing conformational change" RELATED []
synonym: "sequence variant causing conformational change" EXACT []
is_obsolete: true
replaced_by: SO:0001601
[Term]
id: SO:1000117
name: sequence_variant_affecting_polypeptide_function
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting polypeptide function" RELATED []
synonym: "sequence variant affecting polypeptide function" EXACT []
is_obsolete: true
replaced_by: SO:0001554
[Term]
id: SO:1000118
name: sequence_variant_causing_loss_of_function_of_polypeptide
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "loss of function of polypeptide" RELATED []
synonym: "mutation causing loss of function of polypeptide" RELATED []
synonym: "sequence variant causing loss of function of polypeptide" EXACT []
is_obsolete: true
replaced_by: SO:0001559
[Term]
id: SO:1000119
name: sequence_variant_causing_inactive_ligand_binding_site
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing inactive ligand binding site" RELATED []
synonym: "sequence variant causing inactive ligand binding site" EXACT []
is_obsolete: true
replaced_by: SO:0001560
[Term]
id: SO:1000120
name: sequence_variant_causing_inactive_catalytic_site
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing inactive catalytic site" RELATED []
synonym: "sequence variant causing inactive catalytic site" EXACT []
is_obsolete: true
replaced_by: SO:0001618
[Term]
id: SO:1000121
name: sequence_variant_causing_polypeptide_localization_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide localization change" RELATED []
synonym: "sequence variant causing polypeptide localization change" EXACT []
is_obsolete: true
replaced_by: SO:0001558
[Term]
id: SO:1000122
name: sequence_variant_causing_polypeptide_post_translational_processing_change
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide post translational processing change" RELATED []
synonym: "polypeptide post-translational processing affected" EXACT []
synonym: "sequence variant causing polypeptide post translational processing change" EXACT []
is_obsolete: true
replaced_by: SO:0001562
[Term]
id: SO:1000123
name: polypeptide_post_translational_processing_affected
synonym: "polypeptide_post-translational_processing_affected" RELATED []
is_obsolete: true
[Term]
id: SO:1000124
name: sequence_variant_causing_partial_loss_of_function_of_polypeptide
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing partial loss of function of polypeptide" RELATED []
synonym: "partial loss of function of polypeptide" EXACT []
synonym: "sequence variant causing partial loss of function of polypeptide" EXACT []
is_obsolete: true
replaced_by: SO:0001561
[Term]
id: SO:1000125
name: sequence_variant_causing_gain_of_function_of_polypeptide
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "gain of function of polypeptide" EXACT []
synonym: "mutation causing gain of function of polypeptide" RELATED []
synonym: "sequence variant causing gain of function of polypeptide" EXACT []
is_obsolete: true
replaced_by: SO:0001557
[Term]
id: SO:1000126
name: sequence_variant_affecting_transcript_secondary_structure
def: "A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting transcript secondary structure" RELATED []
synonym: "sequence variant affecting transcript secondary structure" EXACT []
is_obsolete: true
replaced_by: SO:0001596
[Term]
id: SO:1000127
name: sequence_variant_causing_compensatory_transcript_secondary_structure_mutation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing compensatory transcript secondary structure mutation" RELATED []
synonym: "sequence variant causing compensatory transcript secondary structure mutation" EXACT []
is_obsolete: true
replaced_by: SO:0001597
[Term]
id: SO:1000132
name: sequence_variant_effect
def: "The effect of a change in nucleotide sequence." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.\nUpdated after discussion with Peter Taschner - Feb 09.
synonym: "sequence variant effect" RELATED []
is_obsolete: true
[Term]
id: SO:1000134
name: sequence_variant_causing_polypeptide_fusion
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing polypeptide fusion" RELATED []
synonym: "sequence variant causing polypeptide fusion" EXACT []
is_obsolete: true
replaced_by: SO:0001616
[Term]
id: SO:1000136
name: autosynaptic_chromosome
def: "An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome." [PMID:6804304]
synonym: "(Drosophila)A" RELATED []
synonym: "autosynaptic chromosome" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation
[Term]
id: SO:1000138
name: homo_compound_chromosome
def: "A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved." [SO:ke]
synonym: "homo compound chromosome" EXACT []
synonym: "homo-compound chromosome" EXACT []
is_a: SO:1000042 ! compound_chromosome
[Term]
id: SO:1000140
name: hetero_compound_chromosome
def: "A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them." [FB:reference_manual, SO:ke]
synonym: "hetero compound chromosome" EXACT []
synonym: "hetero-compound chromosome" EXACT []
is_a: SO:1000042 ! compound_chromosome
[Term]
id: SO:1000141
name: chromosome_fission
def: "A chromosome that occurred by the division of a larger chromosome." [SO:ke]
synonym: "chromosome fission" EXACT []
is_a: SO:1000028 ! intrachromosomal_mutation
[Term]
id: SO:1000142
name: dexstrosynaptic_chromosome
def: "An autosynaptic chromosome carrying the two right (D = dextro) telomeres." [FB:manual]
synonym: "dexstrosynaptic chromosome" EXACT []
is_a: SO:1000136 ! autosynaptic_chromosome
[Term]
id: SO:1000143
name: laevosynaptic_chromosome
def: "LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres." [FB:manual]
synonym: "laevosynaptic chromosome" EXACT []
is_a: SO:1000136 ! autosynaptic_chromosome
[Term]
id: SO:1000144
name: free_duplication
def: "A chromosome structure variation whereby the duplicated sequences are carried as a free centric element." [FB:reference_manual]
synonym: "free duplication" EXACT []
is_a: SO:1000037 ! chromosomal_duplication
[Term]
id: SO:1000145
name: free_ring_duplication
def: "A ring chromosome which is a copy of another chromosome." [SO:ke]
synonym: "(Drosophila)R" RELATED []
synonym: "free ring duplication" EXACT []
is_a: SO:1000045 ! ring_chromosome
is_a: SO:1000144 ! free_duplication
relationship: has_quality SO:0001516 ! free
[Term]
id: SO:1000147
name: deficient_translocation
def: "A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining." [FB:reference_manual]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfT" RELATED []
synonym: "deficient translocation" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000044 ! chromosomal_translocation
relationship: has_part SO:0000159 ! deletion
[Term]
id: SO:1000148
name: inversion_cum_translocation
def: "A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break." [FB:reference_manual]
synonym: "(Drosophila)InT" RELATED []
synonym: "(Drosophila)T" RELATED []
synonym: "inversion cum translocation" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
is_a: SO:1000044 ! chromosomal_translocation
relationship: has_part SO:1000036 ! inversion
[Term]
id: SO:1000149
name: bipartite_duplication
def: "An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break." [FB:reference_manual]
synonym: "(Drosophila)bDp" RELATED []
synonym: "bipartite duplication" EXACT []
is_a: SO:1000031 ! interchromosomal_mutation
is_a: SO:1000038 ! intrachromosomal_duplication
[Term]
id: SO:1000150
name: cyclic_translocation
def: "A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third." [FB:reference_manual]
synonym: "cyclic translocation" EXACT []
is_a: SO:0002060 ! interchomosomal_translocation
[Term]
id: SO:1000151
name: bipartite_inversion
def: "A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed)." [FB:reference_manual]
synonym: "(Drosophila)bIn" RELATED []
synonym: "bipartite inversion" EXACT []
is_a: SO:1000030 ! chromosomal_inversion
[Term]
id: SO:1000152
name: uninverted_insertional_duplication
def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)eDp" RELATED []
synonym: "uninverted insertional duplication" EXACT []
is_a: SO:1000154 ! insertional_duplication
[Term]
id: SO:1000153
name: inverted_insertional_duplication
def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)iDp" RELATED []
synonym: "inverted insertional duplication" EXACT []
is_a: SO:1000154 ! insertional_duplication
[Term]
id: SO:1000154
name: insertional_duplication
def: "A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication)." [SO:ke]
synonym: "(Drosophila)Dpp" RELATED []
synonym: "insertional duplication" EXACT []
is_a: SO:1000037 ! chromosomal_duplication
[Term]
id: SO:1000155
name: interchromosomal_transposition
def: "A chromosome structure variation whereby a transposition occurred between chromosomes." [SO:ke]
synonym: "(Drosophila)Tp" RELATED []
synonym: "interchromosomal transposition" EXACT []
is_a: SO:0000453 ! chromosomal_transposition
is_a: SO:1000031 ! interchromosomal_mutation
[Term]
id: SO:1000156
name: inverted_interchromosomal_transposition
def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment." [FB:reference_manual]
synonym: "(Drosophila)iTp" RELATED []
synonym: "inverted interchromosomal transposition" EXACT []
is_a: SO:1000155 ! interchromosomal_transposition
[Term]
id: SO:1000157
name: uninverted_interchromosomal_transposition
def: "An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)eTp" RELATED []
synonym: "uninverted interchromosomal transposition" EXACT []
is_a: SO:1000155 ! interchromosomal_transposition
[Term]
id: SO:1000158
name: inverted_intrachromosomal_transposition
def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)iTp" RELATED []
synonym: "inverted intrachromosomal transposition" EXACT []
is_a: SO:1000148 ! inversion_cum_translocation
relationship: has_part SO:1000036 ! inversion
[Term]
id: SO:1000159
name: uninverted_intrachromosomal_transposition
def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments." [FB:reference_manual]
synonym: "(Drosophila)eTp" RELATED []
synonym: "uninverted intrachromosomal transposition" EXACT []
is_a: SO:1000041 ! intrachromosomal_transposition
relationship: has_part SO:0001514 ! direct
[Term]
id: SO:1000160
name: unoriented_insertional_duplication
def: "An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]
comment: Flag - unknown in the definition.
synonym: "(Drosophila)uDp" RELATED []
synonym: "unoriented insertional duplication" EXACT []
is_a: SO:1000154 ! insertional_duplication
[Term]
id: SO:1000161
name: unoriented_interchromosomal_transposition
def: "An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]
comment: FLAG - term describes an unknown.
synonym: "(Drosophila)uTp" RELATED []
synonym: "unorientated interchromosomal transposition" EXACT []
is_a: SO:1000155 ! interchromosomal_transposition
[Term]
id: SO:1000162
name: unoriented_intrachromosomal_transposition
def: "An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded." [FB:reference_manual]
comment: FLAG - definition describes an unknown.
synonym: "(Drosophila)uTp" RELATED []
synonym: "unorientated intrachromosomal transposition" EXACT []
is_a: SO:1000041 ! intrachromosomal_transposition
[Term]
id: SO:1000170
name: uncharacterized_chromosomal_mutation
synonym: "uncharacterized chromosomal mutation" EXACT []
is_a: SO:1000183 ! chromosome_structure_variation
[Term]
id: SO:1000171
name: deficient_inversion
def: "A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted." [FB:reference_manual, SO:ke]
synonym: "(Drosophila)Df" RELATED []
synonym: "(Drosophila)DfIn" RELATED []
synonym: "deficient inversion" EXACT []
is_a: SO:1000029 ! chromosomal_deletion
is_a: SO:1000030 ! chromosomal_inversion
relationship: has_part SO:0000159 ! deletion
relationship: has_part SO:1000036 ! inversion
[Term]
id: SO:1000173
name: tandem_duplication
def: "A duplication consisting of 2 identical adjacent regions." [SO:ke]
subset: DBVAR
synonym: "erverted" RELATED dbvar [http://www.ncbi.nlm.nih.gov/dbvar/]
synonym: "tandem duplication" EXACT []
is_a: SO:1000035 ! duplication
[Term]
id: SO:1000175
name: partially_characterized_chromosomal_mutation
synonym: "partially characterized chromosomal mutation" EXACT []
is_a: SO:1000170 ! uncharacterized_chromosomal_mutation
[Term]
id: SO:1000180
name: sequence_variant_affecting_gene_structure
def: "A sequence_variant_effect that changes the gene structure." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation affecting gene structure" RELATED []
synonym: "sequence variant affecting gene structure" EXACT []
is_obsolete: true
replaced_by: SO:0001564
[Term]
id: SO:1000181
name: sequence_variant_causing_gene_fusion
def: "A sequence_variant_effect that changes the gene structure by causing a fusion to another gene." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causing gene fusion" RELATED []
synonym: "sequence variant causing gene fusion" EXACT []
is_obsolete: true
replaced_by: SO:0001565
[Term]
id: SO:1000182
name: chromosome_number_variation
def: "A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number." [SO:ke]
synonym: "chromosome number variation" EXACT []
is_a: SO:0000240 ! chromosome_variation
[Term]
id: SO:1000183
name: chromosome_structure_variation
synonym: "chromosome structure variation" EXACT []
is_a: SO:0000240 ! chromosome_variation
[Term]
id: SO:1000184
name: sequence_variant_causes_exon_loss
def: "A sequence variant affecting splicing and causes an exon loss." [SO:ke]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causes exon loss" RELATED []
synonym: "sequence variant causes exon loss" EXACT []
is_obsolete: true
[Term]
id: SO:1000185
name: sequence_variant_causes_intron_gain
def: "A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072)." [EBI:www.ebi.ac.uk/mutations/recommendations/mutevent.html]
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "mutation causes intron gain" RELATED []
synonym: "sequence variant causes intron gain" EXACT []
is_obsolete: true
[Term]
id: SO:1000186
name: sequence_variant_causing_cryptic_splice_donor_activation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "sequence variant causing cryptic splice donor activation" EXACT []
is_obsolete: true
replaced_by: SO:0001571
[Term]
id: SO:1001186
name: sequence_variant_causing_cryptic_splice_acceptor_activation
comment: OBSOLETE: This term was deleted as it conflated more than one term. The alteration is separate from the effect.
synonym: "sequence variant causing cryptic splice acceptor activation" EXACT []
is_obsolete: true
replaced_by: SO:0001570
[Term]
id: SO:1001187
name: alternatively_spliced_transcript
def: "A transcript that is alternatively spliced." [SO:xp]
synonym: "alternatively spliced transcript" EXACT []
is_a: SO:0000673 ! transcript
relationship: has_quality SO:0000877 ! alternatively_spliced
[Term]
id: SO:1001188
name: encodes_1_polypeptide
def: "A gene that is alternately spliced, but encodes only one polypeptide." [SO:ke]
synonym: "encodes 1 polypeptide" EXACT []
is_a: SO:0000463 ! encodes_alternately_spliced_transcripts
[Term]
id: SO:1001189
name: encodes_greater_than_1_polypeptide
def: "A gene that is alternately spliced, and encodes more than one polypeptide." [SO:ke]
synonym: "encodes greater than 1 polypeptide" EXACT []
is_a: SO:0000463 ! encodes_alternately_spliced_transcripts
[Term]
id: SO:1001190
name: encodes_different_polypeptides_different_stop
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons." [SO:ke]
synonym: "encodes different polypeptides different stop" EXACT []
is_a: SO:1001195 ! encodes_overlapping_peptides
[Term]
id: SO:1001191
name: encodes_overlapping_peptides_different_start
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons." [SO:ke]
synonym: "encodes overlapping peptides different start" EXACT []
is_a: SO:1001195 ! encodes_overlapping_peptides
[Term]
id: SO:1001192
name: encodes_disjoint_polypeptides
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences." [SO:ke]
synonym: "encodes disjoint polypeptides" EXACT []
is_a: SO:1001189 ! encodes_greater_than_1_polypeptide
[Term]
id: SO:1001193
name: encodes_overlapping_polypeptides_different_start_and_stop
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons." [SO:ke]
synonym: "encodes overlapping polypeptides different start and stop" EXACT []
is_a: SO:1001195 ! encodes_overlapping_peptides
[Term]
id: SO:1001194
name: alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping
is_obsolete: true
[Term]
id: SO:1001195
name: encodes_overlapping_peptides
def: "A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences." [SO:ke]
synonym: "encodes overlapping peptides" EXACT []
is_a: SO:1001189 ! encodes_greater_than_1_polypeptide
[Term]
id: SO:1001196
name: cryptogene
def: "A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence." [SO:ma]
is_a: SO:0000654 ! maxicircle_gene
is_a: SO:0001431 ! cryptic_gene
relationship: has_quality SO:0000976 ! cryptic
[Term]
id: SO:1001197
name: dicistronic_primary_transcript
def: "A primary transcript that has the quality dicistronic." [SO:xp]
synonym: "dicistronic primary transcript" EXACT []
is_a: SO:0000079 ! dicistronic_transcript
is_a: SO:0000631 ! polycistronic_primary_transcript
relationship: has_quality SO:0000879 ! dicistronic
[Term]
id: SO:1001217
name: member_of_regulon
synonym: "member of regulon" EXACT []
is_a: SO:0000081 ! gene_array_member
[Term]
id: SO:1001244
name: alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping
synonym: "alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non-overlapping" RELATED []
is_obsolete: true
[Term]
id: SO:1001246
name: CDS_independently_known
def: "A CDS with the evidence status of being independently known." [SO:xp]
synonym: "CDS independently known" EXACT []
is_a: SO:0000316 ! CDS
relationship: has_quality SO:0000906 ! independently_known
[Term]
id: SO:1001247
name: orphan_CDS
def: "A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence." [SO:ma]
synonym: "orphan CDS" EXACT []
is_a: SO:1001254 ! CDS_predicted
relationship: has_origin SO:0000910 ! orphan
[Term]
id: SO:1001249
name: CDS_supported_by_domain_match_data
def: "A CDS that is supported by domain similarity." [SO:xp]
synonym: "CDS supported by domain match data" EXACT []
is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
relationship: has_quality SO:0000908 ! supported_by_domain_match
[Term]
id: SO:1001251
name: CDS_supported_by_sequence_similarity_data
def: "A CDS that is supported by sequence similarity data." [SO:xp]
synonym: "CDS supported by sequence similarity data" EXACT []
is_a: SO:1001254 ! CDS_predicted
relationship: has_quality SO:0000907 ! supported_by_sequence_similarity
[Term]
id: SO:1001254
name: CDS_predicted
def: "A CDS that is predicted." [SO:ke]
synonym: "CDS predicted" EXACT []
is_a: SO:0000316 ! CDS
relationship: has_quality SO:0000732 ! predicted
[Term]
id: SO:1001255
name: status_of_coding_sequence
is_obsolete: true
[Term]
id: SO:1001259
name: CDS_supported_by_EST_or_cDNA_data
def: "A CDS that is supported by similarity to EST or cDNA data." [SO:xp]
synonym: "CDS supported by EST or cDNA data" EXACT []
is_a: SO:1001251 ! CDS_supported_by_sequence_similarity_data
relationship: has_quality SO:0000909 ! supported_by_EST_or_cDNA
[Term]
id: SO:1001260
name: internal_Shine_Dalgarno_sequence
def: "A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria." [PMID:12519954, SO:ke]
synonym: "internal Shine Dalgarno sequence" EXACT []
synonym: "internal Shine-Dalgarno sequence" EXACT []
is_a: SO:0000243 ! internal_ribosome_entry_site
is_a: SO:1001268 ! recoding_stimulatory_region
[Term]
id: SO:1001261
name: recoded_mRNA
def: "The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
synonym: "recoded mRNA" EXACT []
is_a: SO:0000234 ! mRNA
relationship: has_quality SO:0000881 ! recoded
[Term]
id: SO:1001262
name: minus_1_translationally_frameshifted
def: "An attribute describing a translational frameshift of -1." [SO:ke]
synonym: "minus 1 translationally frameshifted" EXACT []
is_a: SO:0000887 ! translationally_frameshifted
[Term]
id: SO:1001263
name: plus_1_translationally_frameshifted
def: "An attribute describing a translational frameshift of +1." [SO:ke]
synonym: "plus 1 translationally frameshifted" EXACT []
is_a: SO:0000887 ! translationally_frameshifted
[Term]
id: SO:1001264
name: mRNA_recoded_by_translational_bypass
def: "A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8811194&dopt=Abstract]
synonym: "mRNA recoded by translational bypass" EXACT []
is_a: SO:1001261 ! recoded_mRNA
relationship: has_quality SO:0000886 ! recoded_by_translational_bypass
[Term]
id: SO:1001265
name: mRNA_recoded_by_codon_redefinition
def: "A recoded_mRNA that was modified by an alteration of codon meaning." [SO:ma]
synonym: "mRNA recoded by codon redefinition" EXACT []
is_a: SO:1001261 ! recoded_mRNA
relationship: has_quality SO:0000882 ! codon_redefined
[Term]
id: SO:1001266
name: stop_codon_redefinition_as_selenocysteine
is_obsolete: true
[Term]
id: SO:1001267
name: stop_codon_readthrough
is_obsolete: true
[Term]
id: SO:1001268
name: recoding_stimulatory_region
def: "A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA." [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=12519954&dopt=Abstract]
synonym: "recoding stimulatory region" EXACT []
synonym: "recoding stimulatory signal" EXACT []
is_a: SO:0000836 ! mRNA_region
[Term]
id: SO:1001269
name: four_bp_start_codon
def: "A non-canonical start codon with 4 base pairs." [SO:ke]
synonym: "4bp start codon" EXACT []
synonym: "four bp start codon" EXACT []
is_a: SO:0000680 ! non_canonical_start_codon
[Term]
id: SO:1001270
name: stop_codon_redefinition_as_pyrrolysine
is_obsolete: true
[Term]
id: SO:1001271
name: archaeal_intron
def: "An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease." [PMID:9301331, SO:ma]
comment: Intron characteristic of tRNA genes; splices by an endonuclease-ligase mediated mechanism.
synonym: "archaeal intron" EXACT []
is_a: SO:0001216 ! endonuclease_spliced_intron
[Term]
id: SO:1001272
name: tRNA_intron
def: "An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification." [SO:ke]
comment: Could be a cross product with Gene ontology, GO:0006388.
synonym: "pre-tRNA intron" EXACT []
synonym: "tRNA intron" EXACT []
is_a: SO:0001216 ! endonuclease_spliced_intron
[Term]
id: SO:1001273
name: CTG_start_codon
def: "A non-canonical start codon of sequence CTG." [SO:ke]
synonym: "CTG start codon" EXACT []
is_a: SO:0000680 ! non_canonical_start_codon
[Term]
id: SO:1001274
name: SECIS_element
def: "The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes." [http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00031]
synonym: "SECIS element" EXACT []
xref: http://en.wikipedia.org/wiki/SECIS_element "wiki"
is_a: SO:1001268 ! recoding_stimulatory_region
[Term]
id: SO:1001275
name: retron
def: "Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes." [SO:ma]
is_a: SO:0001411 ! biological_region
[Term]
id: SO:1001277
name: three_prime_recoding_site
def: "The recoding stimulatory signal located downstream of the recoding site." [SO:ke]
synonym: "three prime recoding site" EXACT []
is_a: SO:1001268 ! recoding_stimulatory_region
[Term]
id: SO:1001279
name: three_prime_stem_loop_structure
def: "A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region." [PMID:12519954, SO:ke]
synonym: "three prime stem loop structure" EXACT []
is_a: SO:1001277 ! three_prime_recoding_site
[Term]
id: SO:1001280
name: five_prime_recoding_site
def: "The recoding stimulatory signal located upstream of the recoding site." [SO:ke]
synonym: "five prime recoding site" EXACT []
is_a: SO:1001268 ! recoding_stimulatory_region
[Term]
id: SO:1001281
name: flanking_three_prime_quadruplet_recoding_signal
def: "Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons." [PMID:12519954, SO:ke]
synonym: "flanking three prime quadruplet recoding signal" EXACT []
is_a: SO:1001277 ! three_prime_recoding_site
[Term]
id: SO:1001282
name: UAG_stop_codon_signal
def: "A stop codon signal for a UAG stop codon redefinition." [SO:ke]
synonym: "UAG stop codon signal" EXACT []
is_a: SO:1001288 ! stop_codon_signal
[Term]
id: SO:1001283
name: UAA_stop_codon_signal
def: "A stop codon signal for a UAA stop codon redefinition." [SO:ke]
synonym: "UAA stop codon signal" EXACT []
is_a: SO:1001288 ! stop_codon_signal
[Term]
id: SO:1001284
name: regulon
def: "A group of genes, whether linked as a cluster or not, that respond to a common regulatory signal." [ISBN:0198506732]
subset: SOFA
xref: http://en.wikipedia.org/wiki/Regulon "wiki"
is_a: SO:0005855 ! gene_group
[Term]
id: SO:1001285
name: UGA_stop_codon_signal
def: "A stop codon signal for a UGA stop codon redefinition." [SO:ke]
synonym: "UGA stop codon signal" EXACT []
is_a: SO:1001288 ! stop_codon_signal
[Term]
id: SO:1001286
name: three_prime_repeat_recoding_signal
def: "A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements." [PMID:12519954, SO:ke]
synonym: "three prime repeat recoding signal" EXACT []
is_a: SO:1001277 ! three_prime_recoding_site
[Term]
id: SO:1001287
name: distant_three_prime_recoding_signal
def: "A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon." [http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=8709208&dopt=Abstract]
synonym: "distant three prime recoding signal" EXACT []
is_a: SO:1001277 ! three_prime_recoding_site
[Term]
id: SO:1001288
name: stop_codon_signal
def: "A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding." [PMID:12519954, SO:ke]
comment: This term does not include the stop codons that are redefined. An example would be a stop codon that partially overlapped a frame shifting site would be an example stimulatory signal.
synonym: "stop codon signal" EXACT []
is_a: SO:1001268 ! recoding_stimulatory_region
[Term]
id: SO:2000061
name: databank_entry
def: "The sequence referred to by an entry in a databank such as GenBank or SwissProt." [SO:ke]
subset: SOFA
synonym: "accession" RELATED []
synonym: "databank entry" EXACT []
is_a: SO:0000695 ! reagent
[Term]
id: SO:3000000
name: gene_segment
def: "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add]
comment: Requested by tracker 2021594, July 2008, by Alex.
synonym: "gene segment" EXACT []
is_a: SO:0000842 ! gene_component_region
[Typedef]
id: adjacent_to
name: adjacent_to
def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap." [PMID:20226267, SO:ke]
subset: SOFA
[Typedef]
id: associated_with
name: associated_with
comment: This relationship is vague and up for discussion.
[Typedef]
id: complete_evidence_for_feature
name: complete_evidence_for_feature
def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke]
comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
is_transitive: true
is_a: evidence_for_feature ! evidence_for_feature
[Typedef]
id: connects_on
name: connects_on
def: "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z." [PMID:20226267]
comment: Example: A splice_junction connects_on exon, exon, mature_transcript.
created_by: kareneilbeck
creation_date: 2010-10-14T01:38:51Z
[Typedef]
id: contained_by
name: contained_by
def: "X contained_by Y iff X starts after start of Y and X ends before end of Y." [PMID:20226267]
comment: The inverse is contains. Example: intein contained_by immature_peptide_region.
is_transitive: true
created_by: kareneilbeck
creation_date: 2010-10-14T01:26:16Z
[Typedef]
id: contains
name: contains
def: "The inverse of contained_by." [PMID:20226267]
comment: Example: pre_miRNA contains miRNA_loop.
is_transitive: true
created_by: kareneilbeck
creation_date: 2010-10-14T01:32:15Z
[Typedef]
id: derives_from
name: derives_from
subset: SOFA
is_transitive: true
[Typedef]
id: disconnected_from
name: disconnected_from
def: "X is disconnected_from Y iff it is not the case that X overlaps Y." [PMID:20226267]
created_by: kareneilbeck
creation_date: 2010-10-14T01:42:10Z
[Typedef]
id: edited_from
name: edited_from
created_by: kareneilbeck
creation_date: 2009-08-19T02:19:45Z
[Typedef]
id: edited_to
name: edited_to
created_by: kareneilbeck
creation_date: 2009-08-19T02:19:11Z
[Typedef]
id: evidence_for_feature
name: evidence_for_feature
def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke]
comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
is_transitive: true
[Typedef]
id: exemplar_of
name: exemplar_of
def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke]
comment: Tracker id: 2594157.
[Typedef]
id: finished_by
name: finished_by
def: "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." [PMID:20226267]
comment: Example CDS finished_by stop_codon.
created_by: kareneilbeck
creation_date: 2010-10-14T01:45:45Z
[Typedef]
id: finishes
name: finishes
def: "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." [PMID:20226267]
comment: Example: stop_codon finishes CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T02:17:53Z
[Typedef]
id: gained
name: gained
def: "X gained Y if X is a variant_of X' and Y part of X but not X'." [SO:ke]
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence.
created_by: kareneilbeck
creation_date: 2011-06-28T12:51:10Z
[Typedef]
id: genome_of
name: genome_of
[Typedef]
id: guided_by
name: guided_by
created_by: kareneilbeck
creation_date: 2009-08-19T02:27:04Z
[Typedef]
id: guides
name: guides
created_by: kareneilbeck
creation_date: 2009-08-19T02:27:24Z
[Typedef]
id: has_integral_part
name: has_integral_part
def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: mRNA has_integral_part CDS.
is_a: has_part ! has_part
created_by: kareneilbeck
creation_date: 2009-08-19T12:01:46Z
[Typedef]
id: has_origin
name: has_origin
[Typedef]
id: has_part
name: has_part
def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: operon has_part gene.
[Typedef]
id: has_quality
name: has_quality
comment: The relationship between a feature and an attribute.
[Typedef]
id: homologous_to
name: homologous_to
subset: SOFA
is_symmetric: true
is_a: similar_to ! similar_to
[Typedef]
id: integral_part_of
name: integral_part_of
def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: exon integral_part_of transcript.
is_a: part_of ! part_of
created_by: kareneilbeck
creation_date: 2009-08-19T12:03:28Z
[Typedef]
id: is_consecutive_sequence_of
name: is_consecutive_sequence_of
def: "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical)." [PMID:20226267]
comment: Example: region is consecutive_sequence of base.
created_by: kareneilbeck
creation_date: 2010-10-14T02:19:48Z
[Typedef]
id: lost
name: lost
def: "X lost Y if X is a variant_of X' and Y part of X' but not X." [SO:ke]
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence.
created_by: kareneilbeck
creation_date: 2011-06-28T12:53:16Z
[Typedef]
id: maximally_overlaps
name: maximally_overlaps
def: "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." [PMID:20226267]
comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
created_by: kareneilbeck
creation_date: 2010-10-14T01:34:48Z
[Typedef]
id: member_of
name: member_of
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
subset: SOFA
is_transitive: true
is_a: part_of ! part_of
[Typedef]
id: non_functional_homolog_of
name: non_functional_homolog_of
def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
subset: SOFA
is_a: homologous_to ! homologous_to
[Typedef]
id: orthologous_to
name: orthologous_to
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to
[Typedef]
id: overlaps
name: overlaps
def: "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." [PMID:20226267]
comment: Example: coding_exon overlaps CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T01:33:15Z
[Typedef]
id: paralogous_to
name: paralogous_to
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to
[Typedef]
id: part_of
name: part_of
def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: amino_acid part_of polypeptide.
subset: SOFA
is_transitive: true
[Typedef]
id: partial_evidence_for_feature
name: partial_evidence_for_feature
def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke]
is_a: evidence_for_feature ! evidence_for_feature
[Typedef]
id: position_of
name: position_of
[Typedef]
id: processed_from
name: processed_from
def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: miRNA processed_from miRNA_primary_transcript.
created_by: kareneilbeck
creation_date: 2009-08-19T12:14:00Z
[Typedef]
id: processed_into
name: processed_into
def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: miRNA_primary_transcript processed into miRNA.
created_by: kareneilbeck
creation_date: 2009-08-19T12:15:02Z
[Typedef]
id: recombined_from
name: recombined_from
created_by: kareneilbeck
creation_date: 2009-08-19T02:21:03Z
[Typedef]
id: recombined_to
name: recombined_to
created_by: kareneilbeck
creation_date: 2009-08-19T02:20:07Z
[Typedef]
id: sequence_of
name: sequence_of
[Typedef]
id: similar_to
name: similar_to
subset: SOFA
is_symmetric: true
[Typedef]
id: started_by
name: started_by
def: "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." [PMID:20226267]
comment: Example: CDS started_by start_codon.
created_by: kareneilbeck
creation_date: 2010-10-14T01:43:55Z
[Typedef]
id: starts
name: starts
def: "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." [PMID:20226267]
comment: Example: start_codon starts CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T01:47:53Z
[Typedef]
id: trans_spliced_from
name: trans_spliced_from
created_by: kareneilbeck
creation_date: 2009-08-19T02:22:14Z
[Typedef]
id: trans_spliced_to
name: trans_spliced_to
created_by: kareneilbeck
creation_date: 2009-08-19T02:22:00Z
[Typedef]
id: transcribed_from
name: transcribed_from
def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: primary_transcript transcribed_from gene.
created_by: kareneilbeck
creation_date: 2009-08-19T12:05:39Z
[Typedef]
id: transcribed_to
name: transcribed_to
def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: gene transcribed_to primary_transcript.
created_by: kareneilbeck
creation_date: 2009-08-19T12:08:24Z
[Typedef]
id: translates_to
name: translates_to
def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: codon translates_to amino_acid.
created_by: kareneilbeck
creation_date: 2009-08-19T12:11:53Z
[Typedef]
id: translation_of
name: translation_of
def: "X is translation of Y if Y is translated by ribosome to create X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: Polypeptide translation_of CDS.
created_by: kareneilbeck
creation_date: 2009-08-19T12:09:59Z
[Typedef]
id: variant_of
name: variant_of
def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop]
comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.
|