RNA 3D Hub //

8CAS Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8CAS_0021/1/31:39tRNA anticodon loop
homologous
HL_6CFJ_107
HL_81376.3
HL_8CAS_0041/2/7:17No text annotation
homologous
HL_4V88_186
NA
HL_8CAS_0051/2/70:81No text annotation
HL_8CAS_0061/2/154:160GNRA related
homologous
HL_4V88_188
NA
HL_8CAS_0091/2/243:250T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_8CAS_0111/2/330:338GNRA related
homologous
HL_4V88_193
NA
HL_8CAS_0121/2/368:373No text annotation
homologous
HL_4V88_194
NA
HL_8CAS_0131/2/393:404No text annotation
homologous
HL_4V88_195
NA
HL_8CAS_0141/2/414:419UNCG
homologous
HL_4V88_196
NA
HL_8CAS_0151/2/450:456No text annotation
homologous
HL_4V88_197
NA
HL_8CAS_0171/2/520:532No text annotation
homologous
HL_4V88_199
NA
HL_8CAS_0181/2/569:574GNRA variation
homologous
HL_4V88_200
NA
HL_8CAS_0211/2/764:772No text annotation
homologous
HL_4V88_203
NA
HL_8CAS_0221/2/777:783No text annotation
homologous
HL_8P9A_207
HL_89167.2
HL_8CAS_0241/2/900:909No text annotation
homologous
HL_4V88_206
NA
HL_8CAS_0251/2/937:942GNRA
homologous
HL_4V88_207
NA
HL_8CAS_0261/2/997:1007No text annotation
homologous
HL_4V88_208
NA
HL_8CAS_0271/2/1055:1064No text annotation
homologous
HL_8P9A_212
HL_61768.1
HL_8CAS_0281/2/1084:1089GNRA
homologous
HL_4V88_210
NA
HL_8CAS_0291/2/1121:1126GNRA
homologous
HL_4V88_211
NA
HL_8CAS_0301/2/1188:1197No text annotation
homologous
HL_4V88_212
NA
HL_8CAS_0311/2/1238:1247Anticodon loop related
homologous
HL_4V88_213
NA
HL_8CAS_0321/2/1296:1301GNRA
homologous
HL_4V88_214
NA
HL_8CAS_0331/2/1309:1316No text annotation
homologous
HL_4V88_215
NA
HL_8CAS_0351/2/1396:1402GNRA
homologous
HL_4V88_217
NA
HL_8CAS_0361/2/1501:1506GNRA
homologous
HL_4V88_218
NA
HL_8CAS_0371/2/1550:1561No text annotation
homologous
HL_4V88_219
NA
HL_8CAS_0381/2/1594:1602No text annotation
homologous
HL_4V88_220
NA
HL_8CAS_0401/2/1778:1783GNRA variation
homologous
HL_4V88_222
NA

Problematic loops

#loop idProblemSequence
HL_8CAS_001tRNA D-loop
HL_8CAS_003No text annotation
HL_8CAS_007No text annotation
HL_8CAS_008No text annotation
HL_8CAS_010Mini UNCG
HL_8CAS_016No text annotation
HL_8CAS_019No text annotation
HL_8CAS_020No text annotation
HL_8CAS_023Pseudoknot geometry
HL_8CAS_041Pseudoknot geometry
HL_8CAS_034No text annotation
HL_8CAS_039Externally structured

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8CAS_0971/2/24:26,
1/2/600:601		Single bulged C
homologous
IL_8P9A_373
IL_05642.2
IL_8CAS_0021/2/35:37,
1/2/471:473		Isolated non-canonical cWW pair
homologous
IL_4V88_385
NA
IL_8CAS_0031/2/37:41,
1/2/466:471		Triple sheared related
geometric
IL_4V88_386
NA
IL_8CAS_0041/2/42:48,
1/2/431:433		No text annotation
homologous
IL_4V88_387
NA
IL_8CAS_0051/2/50:52,
1/2/428:429		Minor groove platform
homologous
IL_4V88_388
NA
IL_8CAS_0061/2/58:63,
1/2/87:89		No text annotation
homologous
IL_4V88_389
NA
IL_8CAS_0071/2/64:69,
1/2/82:86		No text annotation
homologous
IL_4V88_390
NA
IL_8CAS_0081/2/109:112,
1/2/302:305		Tandem non-canonical cWW pairs
homologous
IL_4V88_391
NA
IL_8CAS_0091/2/113:116,
1/2/300:301		Multiple bulged bases
homologous
IL_4V88_392
NA
IL_8CAS_0101/2/117:122,
1/2/295:299		No text annotation
homologous
IL_4V88_393
NA
IL_8CAS_0981/2/144:149,
1/2/165:171		tWH-tWH-tHW-tHW
geometric
IL_4LFB_009
IL_00680.1
IL_8CAS_0121/2/150:152,
1/2/162:164		Isolated cWH basepair
geometric
IL_6RA4_002
IL_10892.2
IL_8CAS_0131/2/186:189,
1/2/196:199		Double sheared
homologous
IL_4V88_396
NA
IL_8CAS_0141/2/204:206,
1/2/259:263		Major groove platform with extra cWW
geometric
IL_7RQB_022
NA
IL_8CAS_0151/2/206:208,
1/2/257:259		Isolated non-canonical cWW pair
homologous
IL_4V88_398
NA
IL_8CAS_0171/2/265:267,
1/2/288:289		Single bulged A
homologous
IL_4V88_399
NA
IL_8CAS_0181/2/270:273,
1/2/283:285		No text annotation
homologous
IL_4V88_400
NA
IL_8CAS_0201/2/311:316,
1/2/348:355		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_8CAS_0211/2/318:323,
1/2/345:346		No text annotation
homologous
IL_4V88_403
NA
IL_8CAS_0221/2/363:365,
1/2/376:381		No text annotation
homologous
IL_4V88_404
NA
IL_8CAS_0231/2/389:391,
1/2/406:408		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_8CAS_0241/2/411:413,
1/2/420:422		Isolated near basepair
homologous
IL_4V88_406
NA
IL_8CAS_0251/2/439:441,
1/2/463:464		Single bulged U
homologous
IL_4V88_407
NA
IL_8CAS_0261/2/443:447,
1/2/460:461		C-loop
geometric
IL_5J7L_018
NA
IL_8CAS_0271/2/447:448,
1/2/458:460		Single bulged G
geometric
IL_5J7L_019
NA
IL_8CAS_0281/2/481:482,
1/2/505:507		Single bulged A
homologous
IL_4V88_409
NA
IL_8CAS_0311/2/514:516,
1/2/536:543		No text annotation
IL_8CAS_0321/2/517:518,
1/2/533:535		Minor groove platform
geometric
IL_4LFB_004
IL_34520.3
IL_8CAS_0331/2/518:520,
1/2/532:533		Minor groove platform
geometric
IL_4V88_412
NA
IL_8CAS_0341/2/550:557,
1/2/587:588		SSU/LSU pseudoknot
geometric
IL_4V88_413
NA
IL_8CAS_0351/2/557:559,
1/2/586:587		Single bulged U
homologous
IL_4V88_414
NA
IL_8CAS_0361/2/562:568,
1/2/575:583		Kink-turn related
homologous
IL_4V88_415
NA
IL_8CAS_0371/2/616:622,
1/2/1104:1105		No text annotation
homologous
IL_4V88_416
NA
IL_8CAS_0381/2/624:626,
1/2/973:975		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_8CAS_0391/2/627:631,
1/2/968:972		tSH-tHW-tHS
homologous
IL_4V88_418
NA
IL_8CAS_0401/2/646:648,
1/2/686:688		Isolated non-canonical cWW pair
homologous
IL_4V88_419
NA
IL_8CAS_0411/2/746:747,
1/2/802:805		Major groove minor groove platform; mini C-loop
homologous
IL_4V88_423
NA
IL_8CAS_0421/2/748:750,
1/2/799:801		Isolated non-canonical cWW pair
homologous
IL_4V88_424
NA
IL_8CAS_0431/2/751:759,
1/2/791:798		No text annotation
homologous
IL_4V88_425
NA
IL_8CAS_0441/2/817:822,
1/2/850:854		No text annotation
IL_8CAS_0471/2/865:866,
1/2/962:965		Major groove platform; stack outside cWW
homologous
IL_4V88_428
NA
IL_8CAS_0481/2/868:870,
1/2/957:960		Isolated non-canonical cWW pair
geometric
IL_5UNE_004
IL_01003.3
IL_8CAS_0991/2/871:873,
1/2/954:956		Isolated non-canonical cWW pair
geometric
IL_2R8S_001
IL_01003.3
IL_8CAS_0501/2/874:878,
1/2/950:953		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_8CAS_0511/2/885:888,
1/2/924:927		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_8CAS_0521/2/893:895,
1/2/917:919		Isolated non-canonical cWW pair
geometric
IL_3U4M_001
IL_71625.2
IL_8CAS_0531/2/895:899,
1/2/910:917		Kink-turn
homologous
IL_4V88_434
NA
IL_8CAS_0541/2/985:990,
1/2/1014:1016		Other IL
geometric
IL_4V88_435
NA
IL_8CAS_0551/2/990:994,
1/2/1010:1014		tSH-tHW-tHS
homologous
IL_4V88_436
NA
IL_8CAS_0561/2/1034:1036,
1/2/1095:1101		No text annotation
homologous
IL_4V88_437
NA
IL_8CAS_0571/2/1041:1044,
1/2/1074:1077		Tandem non-canonical cWW pairs
homologous
IL_4V88_438
NA
IL_8CAS_0581/2/1051:1053,
1/2/1066:1067		Single bulged U
homologous
IL_4V88_439
NA
IL_8CAS_0591/2/1111:1118,
1/2/1129:1134		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_8CAS_0601/2/1146:1147,
1/2/1630:1632		Single bulged A
homologous
IL_4V88_441
NA
IL_8CAS_0611/2/1149:1151,
1/2/1627:1628		Single bulged G
homologous
IL_4V88_442
NA
IL_8CAS_0621/2/1157:1160,
1/2/1617:1621		C-loop
geometric
IL_1KOG_007
IL_63596.12
IL_8CAS_0631/2/1173:1175,
1/2/1464:1466		Isolated non-canonical cWW pair
homologous
IL_4V88_444
NA
IL_8CAS_0641/2/1178:1179,
1/2/1459:1461		Minor groove platform
homologous
IL_4V88_445
NA
IL_8CAS_0651/2/1213:1215,
1/2/1448:1450		Isolated non-canonical cWW pair
homologous
IL_4V88_446
NA
IL_8CAS_0691/2/1268:1270,
1/2/1440:1441		Single bulged U
homologous
IL_4V88_449
NA
IL_8CAS_1011/2/1272:1276,
1/2/1436:1438		Isolated cWS basepair
geometric
IL_4LFB_044
IL_82453.1
IL_8CAS_1021/2/1272:1278,
1/2/1430:1438		No text annotation
homologous
IL_8P9A_439
IL_99893.1
IL_8CAS_0711/2/1276:1278,
1/2/1430:1436		Minor groove platform with extra cWW
homologous
IL_4V88_451
NA
IL_8CAS_0721/2/1280:1281,
1/2/1426:1428		Single bulged A
homologous
IL_4V88_452
NA
IL_8CAS_0731/2/1290:1292,
1/2/1323:1325		Isolated cWH basepair
homologous
IL_4V88_453
NA
IL_8CAS_0741/2/1306:1308,
1/2/1317:1318		Minor groove platform
homologous
IL_4V88_454
NA
IL_8CAS_0751/2/1339:1342,
1/2/1383:1385		Isolated non-canonical cWW pair
homologous
IL_4V88_455
NA
IL_8CAS_0761/2/1345:1348,
1/2/1377:1380		Minor groove platform
homologous
IL_4V88_456
NA
IL_8CAS_0781/2/1389:1391,
1/2/1407:1412		No text annotation
homologous
IL_8C3A_465
NA
IL_8CAS_0791/2/1480:1487,
1/2/1519:1527		No text annotation
homologous
IL_4V88_459
NA
IL_8CAS_0801/2/1488:1494,
1/2/1513:1518		180 degree turn
homologous
IL_4V88_460
NA
IL_8CAS_0811/2/1495:1498,
1/2/1509:1512		Tandem non-canonical cWW pairs
homologous
IL_4V88_461
NA
IL_8CAS_0821/2/1540:1545,
1/2/1566:1571		No text annotation
geometric
IL_4V88_462
NA
IL_8CAS_0831/2/1636:1638,
1/2/1764:1767		No text annotation
geometric
IL_4V88_463
NA
IL_8CAS_0841/2/1638:1641,
1/2/1760:1764		No text annotation
homologous
IL_4V88_464
NA
IL_8CAS_0851/2/1642:1644,
1/2/1757:1759		Isolated non-canonical cWW pair
geometric
IL_1UN6_005
IL_01003.3
IL_8CAS_0861/2/1644:1647,
1/2/1753:1757		Tandem non-canonical cWW pairs
geometric
IL_5J7L_033
NA
IL_8CAS_0871/2/1650:1652,
1/2/1748:1750		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_8CAS_0881/2/1653:1656,
1/2/1744:1747		Double sheared
homologous
IL_4V88_468
NA
IL_8CAS_0911/2/1669:1672,
1/2/1729:1732		Double sheared
geometric
IL_4V88_471
NA
IL_8CAS_0921/2/1672:1674,
1/2/1727:1729		Isolated non-canonical cWW pair
homologous
IL_4V88_472
NA
IL_8CAS_0931/2/1675:1678,
1/2/1723:1726		Tandem non-canonical cWW pairs
homologous
IL_4V88_473
NA
IL_8CAS_0941/2/1678:1682,
1/2/1719:1723		Triple sheared
geometric
IL_4V88_474
NA

Problematic loops

#loop idProblemSequence
IL_8CAS_001Isolated non-canonical cWW pair
IL_8CAS_011tWH-tWH-tHW-tHW
IL_8CAS_016No text annotation
IL_8CAS_019Single bulged U
IL_8CAS_029Isolated non-canonical cWW pair
IL_8CAS_030No text annotation
IL_8CAS_045Isolated non-canonical cWW pair
IL_8CAS_046Isolated non-canonical cWW pair
IL_8CAS_049Tandem non-canonical cWW pairs
IL_8CAS_066No text annotation
IL_8CAS_100No text annotation
IL_8CAS_067No text annotation
IL_8CAS_068No text annotation
IL_8CAS_070tSH-tHW
IL_8CAS_077No text annotation
IL_8CAS_089Single bulged U
IL_8CAS_090Isolated non-canonical cWW pair
IL_8CAS_095Tandem non-canonical cWW pairs
IL_8CAS_103Isolated tWW contact
IL_8CAS_096Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8CAS_0111/2/41:42,
1/2/433:439,
1/2/464:466		No text annotation
geometric
J3_4V88_078
NA
J3_8CAS_0121/2/41:48,
1/2/431:439,
1/2/464:466		No text annotation
homologous
J3_8P9A_069
J3_63856.1
J3_8CAS_0131/2/213:228,
1/2/237:243,
1/2/250:252		No text annotation
J3_8CAS_0141/2/633:635,
1/2/861:865,
1/2/965:966		No text annotation
geometric
J3_4V88_080
NA
J3_8CAS_0151/2/633:635,
1/2/861:866,
1/2/962:966		No text annotation
homologous
J3_8P9A_072
J3_17385.5
J3_8CAS_0011/2/760:763,
1/2/773:775,
1/2/785:790		No text annotation
homologous
J3_4V88_032
NA
J3_8CAS_0021/2/881:884,
1/2/928:936,
1/2/943:947		No text annotation
homologous
J3_4V88_033
NA
J3_8CAS_0031/2/1037:1039,
1/2/1079:1083,
1/2/1090:1094		No text annotation
homologous
J3_4V88_034
NA
J3_8CAS_0041/2/1161:1164,
1/2/1581:1587,
1/2/1609:1616		No text annotation
homologous
J3_4V88_035
NA
J3_8CAS_0051/2/1168:1171,
1/2/1468:1470,
1/2/1574:1577		No text annotation
homologous
J3_8C3A_039
NA
J3_8CAS_0061/2/1180:1187,
1/2/1198:1209,
1/2/1454:1458		No text annotation
homologous
J3_8C3A_040
NA
J3_8CAS_0071/2/1215:1220,
1/2/1263:1267,
1/2/1442:1448		No text annotation
homologous
J3_8C3A_041
NA
J3_8CAS_0081/2/1283:1288,
1/2/1327:1332,
1/2/1419:1424		No text annotation
homologous
J3_4V88_039
NA
J3_8CAS_0161/2/1293:1294,
1/2/1303:1306,
1/2/1318:1322		No text annotation
homologous
J3_8C3A_085
NA
J3_8CAS_0091/2/1336:1338,
1/2/1386:1389,
1/2/1412:1415		No text annotation
homologous
J3_4V88_040
NA
J3_8CAS_0171/2/1336:1338,
1/2/1386:1391,
1/2/1407:1415		No text annotation
homologous
J3_8C3A_086
NA
J3_8CAS_0101/2/1470:1474,
1/2/1533:1540,
1/2/1571:1574		No text annotation
homologous
J3_4V88_041
NA
J4_8CAS_0021/2/99:107,
1/2/307:309,
1/2/357:361,
1/2/383:384		No text annotation
homologous
J4_8C3A_021
NA
J4_8CAS_0031/2/622:624,
1/2/975:980,
1/2/1021:1032,
1/2/1103:1104		No text annotation
homologous
J4_8P9A_022
J4_14595.1
J5_8CAS_0011/2/31:35,
1/2/473:479,
1/2/509:514,
1/2/543:546,
1/2/592:595		No text annotation
homologous
J5_8C3A_018
NA
J5_8CAS_0021/2/31:35,
1/2/473:479,
1/2/509:516,
1/2/536:546,
1/2/592:595		No text annotation
J5_8CAS_0031/2/54:57,
1/2/90:97,
1/2/386:388,
1/2/409:411,
1/2/422:426		No text annotation
homologous
J5_8C3A_020
NA
J5_8CAS_0051/2/636:641,
1/2/693:698,
1/2/740:744,
1/2/807:817,
1/2/854:860		No text annotation

Problematic loops

#loop idProblemSequence
J4_8CAS_001tRNA junction
J5_8CAS_004No text annotation

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