9G8O Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9G8O_001 | 1/S2/7:17 | No text annotation | homologous HL_8C3A_192 NA | |
| HL_9G8O_002 | 1/S2/69:80 | No text annotation | geometric HL_361D_002 NA | |
| HL_9G8O_003 | 1/S2/156:162 | GNRA related | homologous HL_8C3A_194 NA | |
| HL_9G8O_005 | 1/S2/288:295 | No text annotation | geometric HL_5TBW_006 NA | |
| HL_9G8O_006 | 1/S2/322:329 | No text annotation | ||
| HL_9G8O_007 | 1/S2/377:387 | No text annotation | geometric HL_1KH6_003 HL_33487.1 | |
| HL_9G8O_008 | 1/S2/416:421 | GNRA variation | homologous HL_8C3A_200 NA | |
| HL_9G8O_009 | 1/S2/441:452 | No text annotation | homologous HL_8P9A_199 HL_86432.1 | |
| HL_9G8O_010 | 1/S2/462:467 | UNCG | homologous HL_8P9A_200 HL_61337.3 | |
| HL_9G8O_011 | 1/S2/498:504 | No text annotation | homologous HL_8C3A_203 NA | |
| HL_9G8O_012 | 1/S2/534:550 | No text annotation | ||
| HL_9G8O_013 | 1/S2/569:581 | No text annotation | homologous HL_8P9A_203 HL_68749.1 | |
| HL_9G8O_014 | 1/S2/618:623 | No text annotation | homologous HL_8P9A_204 HL_93535.2 | |
| HL_9G8O_015 | 1/S2/820:828 | No text annotation | homologous HL_8C3A_208 NA | |
| HL_9G8O_016 | 1/S2/833:841 | No text annotation | geometric HL_2Y8Y_001 HL_40612.1 | |
| HL_9G8O_037 | 1/S2/957:966 | No text annotation | homologous HL_8CRE_210 HL_38491.2 | |
| HL_9G8O_019 | 1/S2/994:999 | GNRA | homologous HL_8C3A_212 NA | |
| HL_9G8O_020 | 1/S2/1054:1064 | No text annotation | homologous HL_8P9A_211 HL_38491.2 | |
| HL_9G8O_021 | 1/S2/1112:1121 | No text annotation | ||
| HL_9G8O_022 | 1/S2/1141:1146 | GNRA | homologous HL_8P9A_213 HL_34789.4 | |
| HL_9G8O_023 | 1/S2/1178:1183 | GNRA | homologous HL_8C3A_216 NA | |
| HL_9G8O_024 | 1/S2/1245:1254 | No text annotation | homologous HL_8C3A_217 NA | |
| HL_9G8O_025 | 1/S2/1295:1304 | Anticodon loop related | homologous HL_8C3A_218 NA | |
| HL_9G8O_026 | 1/S2/1353:1358 | GNRA | homologous HL_8P9A_217 HL_34789.4 | |
| HL_9G8O_027 | 1/S2/1366:1373 | T-loop related | homologous HL_8P9A_218 HL_63894.2 | |
| HL_9G8O_028 | 1/S2/1460:1466 | No text annotation | homologous HL_8C3A_222 NA | |
| HL_9G8O_029 | 1/S2/1565:1570 | GNRA | homologous HL_8C3A_223 NA | |
| HL_9G8O_030 | 1/S2/1614:1625 | No text annotation | homologous HL_8C3A_224 NA | |
| HL_9G8O_031 | 1/S2/1658:1666 | No text annotation | homologous HL_8C3A_225 NA | |
| HL_9G8O_032 | 1/S2/1749:1785 | No text annotation | ||
| HL_9G8O_033 | 1/S2/1847:1852 | GNRA variation | homologous HL_8C3A_227 NA | |
| HL_9G8O_034 | 1/X/81:86 | No text annotation | geometric HL_8P9A_134 HL_27530.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9G8O_004 | No text annotation | ||
| HL_9G8O_036 | No text annotation | ||
| HL_9G8O_017 | No text annotation | ||
| HL_9G8O_018 | No text annotation | ||
| HL_9G8O_035 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9G8O_001 | 1/S2/23:25, 1/S2/649:651 | Isolated non-canonical cWW pair | geometric IL_4WF9_020 IL_01003.4 | |
| IL_9G8O_002 | 1/S2/26:28, 1/S2/646:648 | Isolated cWH basepair | geometric IL_2R1S_002 IL_10892.2 | |
| IL_9G8O_003 | 1/S2/34:36, 1/S2/519:521 | Isolated non-canonical cWW pair | homologous IL_8C3A_393 NA | |
| IL_9G8O_004 | 1/S2/37:40, 1/S2/514:518 | Double sheared | geometric IL_4WF9_016 IL_58355.2 | |
| IL_9G8O_005 | 1/S2/41:47, 1/S2/479:481 | No text annotation | geometric IL_8C3A_395 NA | |
| IL_9G8O_006 | 1/S2/49:51, 1/S2/476:477 | Minor groove platform | homologous IL_8C3A_396 NA | |
| IL_9G8O_007 | 1/S2/57:62, 1/S2/86:88 | No text annotation | homologous IL_8P9A_378 IL_61299.6 | |
| IL_9G8O_008 | 1/S2/63:69, 1/S2/80:85 | No text annotation | geometric IL_1M5K_001 IL_47352.2 | |
| IL_9G8O_009 | 1/S2/108:110, 1/S2/351:353 | Isolated non-canonical cWW pair | geometric IL_1ZX7_004 NA | |
| IL_9G8O_010 | 1/S2/110:112, 1/S2/349:351 | Isolated non-canonical cWW contact | geometric IL_5UNE_001 IL_87720.1 | |
| IL_9G8O_011 | 1/S2/112:115, 1/S2/348:349 | Multiple bulged bases | homologous IL_8C3A_400 NA | |
| IL_9G8O_012 | 1/S2/116:121, 1/S2/343:347 | No text annotation | homologous IL_8C3A_401 NA | |
| IL_9G8O_013 | 1/S2/145:151, 1/S2/167:174 | No text annotation | homologous IL_8C3A_402 NA | |
| IL_9G8O_088 | 1/S2/152:155, 1/S2/163:166 | No text annotation | homologous IL_8CRE_401 IL_65740.1 | |
| IL_9G8O_015 | 1/S2/188:192, 1/S2/207:211 | No text annotation | ||
| IL_9G8O_089 | 1/S2/317:320, 1/S2/331:333 | No text annotation | ||
| IL_9G8O_017 | 1/S2/359:364, 1/S2/396:403 | Kink-turn with non-sequential stacking | homologous IL_8C3A_410 NA | |
| IL_9G8O_018 | 1/S2/366:371, 1/S2/393:394 | No text annotation | homologous IL_8P9A_392 IL_01372.1 | |
| IL_9G8O_019 | 1/S2/411:413, 1/S2/424:429 | No text annotation | homologous IL_8P9A_393 IL_93336.1 | |
| IL_9G8O_020 | 1/S2/437:439, 1/S2/454:456 | Isolated cWH basepair | homologous IL_8C3A_413 NA | |
| IL_9G8O_021 | 1/S2/459:461, 1/S2/468:470 | Isolated non-canonical cWW pair | homologous IL_8C3A_414 NA | |
| IL_9G8O_022 | 1/S2/487:489, 1/S2/511:512 | Single bulged U | homologous IL_8C3A_415 NA | |
| IL_9G8O_023 | 1/S2/491:495, 1/S2/508:509 | C-loop | homologous IL_8C3A_416 NA | |
| IL_9G8O_024 | 1/S2/495:496, 1/S2/506:508 | Single bulged G | homologous IL_8P9A_398 IL_28408.2 | |
| IL_9G8O_090 | 1/S2/528:530, 1/S2/554:557 | Stack and bulge | geometric IL_2ET8_001 IL_53541.1 | |
| IL_9G8O_026 | 1/S2/563:565, 1/S2/585:592 | No text annotation | ||
| IL_9G8O_027 | 1/S2/566:569, 1/S2/581:584 | Tandem non-canonical cWW pairs | geometric IL_5C5W_003 NA | |
| IL_9G8O_028 | 1/S2/599:608, 1/S2/635:637 | Other IL | geometric IL_7A0S_092 IL_10892.2 | |
| IL_9G8O_029 | 1/S2/611:617, 1/S2/624:632 | No text annotation | homologous IL_8P9A_404 IL_52042.1 | |
| IL_9G8O_030 | 1/S2/663:665, 1/S2/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_01003.4 | |
| IL_9G8O_031 | 1/S2/665:671, 1/S2/1161:1162 | No text annotation | homologous IL_8C3A_426 NA | |
| IL_9G8O_032 | 1/S2/673:675, 1/S2/1030:1032 | Isolated non-canonical cWW pair | homologous IL_8C3A_427 NA | |
| IL_9G8O_033 | 1/S2/676:680, 1/S2/1025:1029 | tSH-tHW-tHS | homologous IL_8C3A_428 NA | |
| IL_9G8O_091 | 1/S2/802:803, 1/S2/860:863 | No text annotation | homologous IL_8CRE_428 IL_73108.2 | |
| IL_9G8O_035 | 1/S2/805:807, 1/S2/856:858 | Isolated non-canonical cWW pair | homologous IL_8P9A_413 IL_71625.3 | |
| IL_9G8O_092 | 1/S2/807:815, 1/S2/849:856 | No text annotation | homologous IL_8CRE_430 IL_59049.2 | |
| IL_9G8O_037 | 1/S2/874:879, 1/S2/907:911 | No text annotation | homologous IL_8P9A_416 NA | |
| IL_9G8O_038 | 1/S2/922:923, 1/S2/1019:1022 | Major groove platform; stack outside cWW | geometric IL_4V88_428 NA | |
| IL_9G8O_039 | 1/S2/925:927, 1/S2/1014:1017 | Isolated cWH basepair | homologous IL_8C3A_510 NA | |
| IL_9G8O_040 | 1/S2/928:931, 1/S2/1010:1013 | Tandem non-canonical cWW pairs | homologous IL_8P9A_419 IL_15225.2 | |
| IL_9G8O_041 | 1/S2/931:935, 1/S2/1007:1010 | Tandem non-canonical cWW pairs | homologous IL_8C3A_438 NA | |
| IL_9G8O_042 | 1/S2/942:945, 1/S2/981:984 | Tandem non-canonical cWW pairs | homologous IL_8P9A_421 IL_15225.2 | |
| IL_9G8O_043 | 1/S2/952:956, 1/S2/967:974 | Kink-turn | geometric IL_4V88_434 NA | |
| IL_9G8O_044 | 1/S2/1042:1051, 1/S2/1067:1073 | No text annotation | ||
| IL_9G8O_045 | 1/S2/1091:1093, 1/S2/1152:1158 | No text annotation | homologous IL_8P9A_425 IL_82706.2 | |
| IL_9G8O_046 | 1/S2/1098:1101, 1/S2/1131:1134 | Tandem non-canonical cWW pairs | homologous IL_8C3A_444 NA | |
| IL_9G8O_047 | 1/S2/1101:1103, 1/S2/1129:1131 | Stack and bulge | geometric IL_2ET8_001 IL_53541.1 | |
| IL_9G8O_048 | 1/S2/1108:1110, 1/S2/1123:1124 | Minor groove platform | geometric IL_4V88_412 NA | |
| IL_9G8O_049 | 1/S2/1168:1175, 1/S2/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_8P9A_428 IL_84044.1 | |
| IL_9G8O_050 | 1/S2/1203:1204, 1/S2/1694:1696 | Single bulged A | homologous IL_8C3A_447 NA | |
| IL_9G8O_051 | 1/S2/1206:1208, 1/S2/1691:1692 | Single bulged G | homologous IL_8C3A_448 NA | |
| IL_9G8O_052 | 1/S2/1230:1232, 1/S2/1526:1528 | Isolated non-canonical cWW pair | homologous IL_8P9A_432 IL_01003.4 | |
| IL_9G8O_053 | 1/S2/1235:1236, 1/S2/1521:1523 | Minor groove platform | homologous IL_8C3A_451 NA | |
| IL_9G8O_054 | 1/S2/1270:1272, 1/S2/1510:1512 | Isolated non-canonical cWW pair | homologous IL_8C3A_452 NA | |
| IL_9G8O_055 | 1/S2/1281:1290, 1/S2/1309:1316 | No text annotation | homologous IL_8P9A_470 IL_28304.1 | |
| IL_9G8O_056 | 1/S2/1291:1293, 1/S2/1306:1308 | No text annotation | homologous IL_8P9A_436 IL_38565.2 | |
| IL_9G8O_057 | 1/S2/1325:1327, 1/S2/1502:1503 | Single bulged U | homologous IL_8C3A_455 NA | |
| IL_9G8O_058 | 1/S2/1329:1333, 1/S2/1498:1500 | Isolated cWS basepair | geometric IL_4LFB_044 IL_82453.1 | |
| IL_9G8O_059 | 1/S2/1329:1335, 1/S2/1492:1500 | No text annotation | geometric IL_4V88_510 NA | |
| IL_9G8O_060 | 1/S2/1333:1335, 1/S2/1492:1498 | No text annotation | homologous IL_8P9A_440 IL_34117.1 | |
| IL_9G8O_061 | 1/S2/1337:1338, 1/S2/1488:1490 | Single bulged A | homologous IL_8C3A_458 NA | |
| IL_9G8O_062 | 1/S2/1347:1349, 1/S2/1380:1382 | Isolated cWH basepair | homologous IL_8P9A_442 IL_10892.2 | |
| IL_9G8O_063 | 1/S2/1363:1365, 1/S2/1374:1375 | Minor groove platform | homologous IL_8C3A_460 NA | |
| IL_9G8O_093 | 1/S2/1395:1400, 1/S2/1446:1450 | No text annotation | ||
| IL_9G8O_065 | 1/S2/1402:1405, 1/S2/1441:1444 | No text annotation | homologous IL_8C3A_462 NA | |
| IL_9G8O_066 | 1/S2/1408:1409, 1/S2/1432:1438 | Multiple bulged bases | geometric IL_8C3A_400 NA | |
| IL_9G8O_067 | 1/S2/1412:1413, 1/S2/1427:1429 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_9G8O_068 | 1/S2/1416:1417, 1/S2/1422:1424 | Single bulged C | geometric IL_5J7L_311 NA | |
| IL_9G8O_069 | 1/S2/1537:1539, 1/S2/1594:1596 | Isolated non-canonical cWW pair | geometric IL_4P3T_001 NA | |
| IL_9G8O_070 | 1/S2/1541:1550, 1/S2/1582:1592 | No text annotation | ||
| IL_9G8O_071 | 1/S2/1550:1558, 1/S2/1577:1582 | No text annotation | ||
| IL_9G8O_072 | 1/S2/1560:1562, 1/S2/1573:1575 | Isolated non-canonical cWW pair | homologous IL_8C3A_468 NA | |
| IL_9G8O_073 | 1/S2/1604:1610, 1/S2/1629:1635 | No text annotation | homologous IL_8C3A_469 NA | |
| IL_9G8O_074 | 1/S2/1700:1702, 1/S2/1833:1836 | No text annotation | homologous IL_8P9A_452 IL_18228.1 | |
| IL_9G8O_075 | 1/S2/1702:1705, 1/S2/1829:1833 | No text annotation | homologous IL_8C3A_471 NA | |
| IL_9G8O_076 | 1/S2/1706:1708, 1/S2/1826:1828 | Isolated non-canonical cWW pair | homologous IL_8C3A_472 NA | |
| IL_9G8O_077 | 1/S2/1708:1711, 1/S2/1822:1826 | No text annotation | ||
| IL_9G8O_078 | 1/S2/1713:1716, 1/S2/1817:1820 | No text annotation | geometric IL_7LYF_005 NA | |
| IL_9G8O_079 | 1/S2/1717:1720, 1/S2/1813:1816 | Double sheared | homologous IL_8P9A_457 IL_58355.2 | |
| IL_9G8O_082 | 1/S2/1733:1736, 1/S2/1798:1801 | Double sheared | homologous IL_8P9A_460 IL_58355.2 | |
| IL_9G8O_083 | 1/S2/1739:1741, 1/S2/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4E48_002 IL_01003.4 | |
| IL_9G8O_084 | 1/S2/1742:1746, 1/S2/1788:1792 | Triple sheared | homologous IL_8C3A_480 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9G8O_014 | Partly complementary | ||
| IL_9G8O_016 | No text annotation | ||
| IL_9G8O_025 | No text annotation | ||
| IL_9G8O_034 | Major groove minor groove platform with extra cWW | ||
| IL_9G8O_036 | No text annotation | ||
| IL_9G8O_064 | No text annotation | ||
| IL_9G8O_094 | Single bulged U | ||
| IL_9G8O_080 | No text annotation | ||
| IL_9G8O_081 | Tandem non-canonical cWW pairs | ||
| IL_9G8O_095 | Isolated non-canonical cWW pair | ||
| IL_9G8O_085 | No text annotation | ||
| IL_9G8O_096 | No text annotation | ||
| IL_9G8O_086 | Single stack bend | ||
| IL_9G8O_087 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9G8O_001 | 1/S2/40:41, 1/S2/481:487, 1/S2/512:514 | No text annotation | geometric J3_4V88_078 NA | |
| J3_9G8O_002 | 1/S2/40:47, 1/S2/479:487, 1/S2/512:514 | No text annotation | homologous J3_8P9A_069 J3_63856.1 | |
| J3_9G8O_003 | 1/S2/682:685, 1/S2/917:922, 1/S2/1022:1023 | No text annotation | ||
| J3_9G8O_004 | 1/S2/682:685, 1/S2/917:923, 1/S2/1019:1023 | No text annotation | ||
| J3_9G8O_005 | 1/S2/816:819, 1/S2/829:831, 1/S2/843:848 | No text annotation | homologous J3_8P9A_073 J3_97642.2 | |
| J3_9G8O_006 | 1/S2/938:941, 1/S2/985:993, 1/S2/1000:1004 | No text annotation | homologous J3_8P9A_074 J3_23895.1 | |
| J3_9G8O_007 | 1/S2/1094:1096, 1/S2/1136:1140, 1/S2/1147:1151 | No text annotation | ||
| J3_9G8O_008 | 1/S2/1214:1221, 1/S2/1645:1651, 1/S2/1673:1685 | No text annotation | ||
| J3_9G8O_009 | 1/S2/1225:1228, 1/S2/1530:1532, 1/S2/1638:1641 | No text annotation | homologous J3_8C3A_039 NA | |
| J3_9G8O_010 | 1/S2/1237:1244, 1/S2/1255:1266, 1/S2/1516:1520 | No text annotation | homologous J3_8C3A_040 NA | |
| J3_9G8O_011 | 1/S2/1272:1277, 1/S2/1320:1324, 1/S2/1504:1510 | No text annotation | homologous J3_8C3A_041 NA | |
| J3_9G8O_012 | 1/S2/1340:1345, 1/S2/1384:1389, 1/S2/1481:1486 | No text annotation | homologous J3_8P9A_080 J3_17077.1 | |
| J3_9G8O_013 | 1/S2/1350:1351, 1/S2/1360:1363, 1/S2/1375:1379 | No text annotation | homologous J3_8C3A_085 NA | |
| J3_9G8O_014 | 1/S2/1391:1395, 1/S2/1450:1456, 1/S2/1470:1479 | No text annotation | ||
| J3_9G8O_016 | 1/S2/1532:1536, 1/S2/1597:1604, 1/S2/1635:1638 | No text annotation | homologous J3_8CRE_086 J3_03192.1 | |
| J4_9G8O_001 | 1/S2/98:106, 1/S2/355:357, 1/S2/405:409, 1/S2/431:432 | No text annotation | homologous J4_8C3A_021 NA | |
| J4_9G8O_002 | 1/S2/671:673, 1/S2/1032:1037, 1/S2/1078:1089, 1/S2/1160:1161 | No text annotation | homologous J4_8P9A_022 J4_14595.1 | |
| J5_9G8O_001 | 1/S2/30:34, 1/S2/521:527, 1/S2/558:563, 1/S2/592:595, 1/S2/641:644 | No text annotation | homologous J5_8C3A_018 NA | |
| J5_9G8O_002 | 1/S2/53:56, 1/S2/89:96, 1/S2/434:436, 1/S2/457:459, 1/S2/470:474 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_9G8O_003 | 1/S2/123:145, 1/S2/174:187, 1/S2/212:219, 1/S2/302:314, 1/S2/336:341 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9G8O_015 | No text annotation |
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