RNA 3D Hub //

6FAI Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6FAI_0011/2/7:17No text annotation
homologous
HL_4V88_186
NA
HL_6FAI_0021/2/70:81No text annotation
homologous
HL_4V88_187
NA
HL_6FAI_0031/2/154:160GNRA related
homologous
HL_4V88_188
NA
HL_6FAI_0041/2/190:195No text annotation
homologous
HL_4V88_189
NA
HL_6FAI_0051/2/230:235UNCG
geometric
HL_5J7L_011
HL_34617.5
HL_6FAI_0061/2/243:250T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_6FAI_0071/2/276:279No text annotation
geometric
HL_5TBW_068
NA
HL_6FAI_0081/2/330:338GNRA related
homologous
HL_4V88_193
NA
HL_6FAI_0091/2/368:373GNRA
geometric
HL_5J7L_007
HL_37824.7
HL_6FAI_0101/2/393:404No text annotation
homologous
HL_4V88_195
NA
HL_6FAI_0111/2/414:419UNCG
homologous
HL_4V88_196
NA
HL_6FAI_0381/2/450:456No text annotation
homologous
HL_8P9A_201
HL_48417.5
HL_6FAI_0131/2/491:496No text annotation
HL_6FAI_0141/2/520:532No text annotation
homologous
HL_4V88_199
NA
HL_6FAI_0151/2/552:572No text annotation
geometric
HL_2ZZM_002
HL_13963.3
HL_6FAI_0161/2/716:722No text annotation
HL_6FAI_0171/2/764:772No text annotation
homologous
HL_4V88_203
NA
HL_6FAI_0181/2/777:783No text annotation
homologous
HL_4V88_204
NA
HL_6FAI_0191/2/829:843Pseudoknot geometry
homologous
HL_4V88_205
NA
HL_6FAI_0201/2/900:909No text annotation
homologous
HL_4V88_206
NA
HL_6FAI_0211/2/937:942GNRA
homologous
HL_4V88_207
NA
HL_6FAI_0221/2/997:1007No text annotation
HL_6FAI_0231/2/1055:1064No text annotation
homologous
HL_8P9A_212
HL_97917.2
HL_6FAI_0241/2/1084:1089GNRA
homologous
HL_4V88_210
NA
HL_6FAI_0251/2/1121:1126GNRA
homologous
HL_4V88_211
NA
HL_6FAI_0391/2/1238:1247No text annotation
HL_6FAI_0281/2/1296:1301GNRA
homologous
HL_4V88_214
NA
HL_6FAI_0291/2/1309:1316No text annotation
homologous
HL_4V88_215
NA
HL_6FAI_0301/2/1359:1364No text annotation
homologous
HL_4V88_216
NA
HL_6FAI_0311/2/1396:1402GNRA
homologous
HL_4V88_217
NA
HL_6FAI_0321/2/1501:1506GNRA
homologous
HL_4V88_218
NA
HL_6FAI_0331/2/1550:1561No text annotation
homologous
HL_4V88_219
NA
HL_6FAI_0341/2/1594:1602No text annotation
homologous
HL_4V88_220
NA
HL_6FAI_0351/2/1698:1703No text annotation
HL_6FAI_0361/2/1778:1783No text annotation

Problematic loops

#loop idProblemSequence
HL_6FAI_012No text annotation
HL_6FAI_026No text annotation
HL_6FAI_027No text annotation
HL_6FAI_037No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6FAI_0011/2/24:26,
1/2/600:601		Single bulged C
geometric
IL_1DQH_001
IL_61258.15
IL_6FAI_0021/2/35:37,
1/2/471:473		Isolated non-canonical cWW pair
geometric
IL_4V88_385
NA
IL_6FAI_0031/2/37:41,
1/2/466:471		Triple sheared related
homologous
IL_4V88_386
NA
IL_6FAI_0041/2/42:48,
1/2/431:433		No text annotation
homologous
IL_4V88_387
NA
IL_6FAI_0051/2/50:52,
1/2/428:429		Minor groove platform
homologous
IL_4V88_388
NA
IL_6FAI_0061/2/58:63,
1/2/87:89		No text annotation
homologous
IL_4V88_389
NA
IL_6FAI_0071/2/64:69,
1/2/82:86		No text annotation
homologous
IL_4V88_390
NA
IL_6FAI_0081/2/109:112,
1/2/302:305		Tandem non-canonical cWW pairs
homologous
IL_4V88_391
NA
IL_6FAI_0091/2/113:116,
1/2/300:301		Multiple bulged bases
homologous
IL_4V88_392
NA
IL_6FAI_0101/2/117:122,
1/2/295:299		No text annotation
homologous
IL_4V88_393
NA
IL_6FAI_0891/2/144:149,
1/2/165:171		tWH-tWH-tHW-tHW
geometric
IL_4LFB_009
IL_12745.1
IL_6FAI_0121/2/150:152,
1/2/162:164		Isolated cWH basepair
geometric
IL_6RA4_002
IL_10167.6
IL_6FAI_0131/2/186:189,
1/2/196:199		Double sheared
homologous
IL_4V88_396
NA
IL_6FAI_0141/2/204:206,
1/2/259:263		Major groove platform with extra cWW
homologous
IL_4V88_397
NA
IL_6FAI_0151/2/206:208,
1/2/257:259		Isolated non-canonical cWW pair
geometric
IL_4V88_398
NA
IL_6FAI_0161/2/265:267,
1/2/288:289		Single bulged A
homologous
IL_4V88_399
NA
IL_6FAI_0171/2/270:273,
1/2/283:285		No text annotation
homologous
IL_4V88_400
NA
IL_6FAI_0181/2/275:276,
1/2/279:281		Single bulged U
homologous
IL_4V88_401
NA
IL_6FAI_0191/2/311:316,
1/2/348:355		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_6FAI_0201/2/318:323,
1/2/345:346		No text annotation
geometric
IL_5Y58_001
IL_59877.1
IL_6FAI_0211/2/363:365,
1/2/376:381		No text annotation
homologous
IL_4V88_404
NA
IL_6FAI_0221/2/389:391,
1/2/406:408		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_6FAI_0231/2/411:413,
1/2/420:422		Isolated near basepair
homologous
IL_4V88_406
NA
IL_6FAI_0241/2/439:441,
1/2/463:464		Single bulged U
geometric
IL_4V88_407
NA
IL_6FAI_1001/2/443:447,
1/2/460:461		No text annotation
homologous
IL_8P9A_397
IL_03109.3
IL_6FAI_1011/2/447:448,
1/2/458:460		Single bulged G
homologous
IL_8P9A_398
IL_00225.13
IL_6FAI_0901/2/481:482,
1/2/505:507		Single bulged A
homologous
IL_8P9A_399
IL_31462.6
IL_6FAI_0271/2/514:516,
1/2/536:543		No text annotation
IL_6FAI_0281/2/517:518,
1/2/533:535		Minor groove platform
geometric
IL_4V88_412
NA
IL_6FAI_0291/2/518:520,
1/2/532:533		Minor groove platform
geometric
IL_4V88_412
NA
IL_6FAI_0301/2/550:551,
1/2/573:588		No text annotation
IL_6FAI_0311/2/616:622,
1/2/1104:1105		No text annotation
homologous
IL_4V88_416
NA
IL_6FAI_0321/2/624:626,
1/2/973:975		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_6FAI_0331/2/627:631,
1/2/968:972		tSH-tHW-tHS
homologous
IL_4V88_418
NA
IL_6FAI_0341/2/646:648,
1/2/686:688		Isolated non-canonical cWW pair
homologous
IL_4V88_419
NA
IL_6FAI_0911/2/646:651,
1/2/683:688		No text annotation
geometric
IL_5TBW_476
NA
IL_6FAI_0351/2/652:658,
1/2/676:682		No text annotation
IL_6FAI_0361/2/703:705,
1/2/733:735		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_87907.2
IL_6FAI_0921/2/703:708,
1/2/730:735		No text annotation
geometric
IL_6O5F_001
NA
IL_6FAI_0371/2/705:708,
1/2/730:733		Tandem non-canonical cWW pairs
geometric
IL_1D4R_001
IL_85033.2
IL_6FAI_0381/2/709:712,
1/2/726:729		No text annotation
IL_6FAI_1021/2/746:747,
1/2/802:805		No text annotation
homologous
IL_8CRE_428
IL_68140.4
IL_6FAI_0401/2/748:750,
1/2/799:801		Isolated non-canonical cWW pair
homologous
IL_4V88_424
NA
IL_6FAI_0411/2/751:759,
1/2/791:798		No text annotation
homologous
IL_8P9A_414
IL_59049.1
IL_6FAI_1031/2/819:822,
1/2/850:852		Isolated non-canonical cWW pair
homologous
IL_8P9A_415
IL_07785.1
IL_6FAI_1041/2/822:824,
1/2/848:850		Isolated cWH basepair
geometric
IL_8AF0_002
IL_10167.6
IL_6FAI_0431/2/865:866,
1/2/962:965		Major groove platform; stack outside cWW
homologous
IL_4V88_428
NA
IL_6FAI_1051/2/868:869,
1/2/958:960		Single bulged U
geometric
IL_8P9A_427
IL_89505.4
IL_6FAI_0451/2/871:874,
1/2/953:956		Tandem non-canonical cWW pairs
homologous
IL_4V88_430
NA
IL_6FAI_0461/2/874:878,
1/2/950:953		Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA
IL_6FAI_0471/2/885:888,
1/2/924:927		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_6FAI_0481/2/893:899,
1/2/910:919		Kink-turn related
homologous
IL_8C3A_440
NA
IL_6FAI_0491/2/985:990,
1/2/1014:1016		Other IL
homologous
IL_4V88_435
NA
IL_6FAI_0501/2/990:994,
1/2/1010:1014		tSH-tHW-tHS
geometric
IL_4V88_436
NA
IL_6FAI_0511/2/1034:1036,
1/2/1095:1101		No text annotation
homologous
IL_4V88_437
NA
IL_6FAI_0521/2/1041:1044,
1/2/1074:1077		Tandem non-canonical cWW pairs
homologous
IL_4V88_438
NA
IL_6FAI_0531/2/1051:1053,
1/2/1066:1067		Single bulged U
homologous
IL_4V88_439
NA
IL_6FAI_0541/2/1111:1118,
1/2/1129:1134		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_6FAI_0551/2/1149:1152,
1/2/1626:1628		Isolated non-canonical cWW pair
geometric
IL_4V88_470
NA
IL_6FAI_0561/2/1157:1160,
1/2/1617:1621		C-loop
homologous
IL_4V88_443
NA
IL_6FAI_0571/2/1173:1175,
1/2/1464:1466		Isolated non-canonical cWW pair
homologous
IL_4V88_444
NA
IL_6FAI_0581/2/1178:1179,
1/2/1459:1461		Minor groove platform
homologous
IL_4V88_445
NA
IL_6FAI_0591/2/1213:1215,
1/2/1448:1450		Isolated non-canonical cWW pair
homologous
IL_4V88_446
NA
IL_6FAI_0601/2/1224:1230,
1/2/1257:1259		No text annotation
IL_6FAI_0941/2/1224:1233,
1/2/1252:1259		No text annotation
homologous
IL_8P9A_470
IL_28304.1
IL_6FAI_0611/2/1230:1233,
1/2/1252:1257		No text annotation
IL_6FAI_0621/2/1234:1236,
1/2/1249:1251		Isolated non-canonical cWW pair
geometric
IL_4KNQ_003
IL_87907.2
IL_6FAI_0951/2/1268:1270,
1/2/1440:1441		No text annotation
IL_6FAI_0641/2/1273:1274,
1/2/1435:1437		No text annotation
IL_6FAI_0651/2/1276:1277,
1/2/1431:1433		Single bulged U
geometric
IL_4V88_407
NA
IL_6FAI_0661/2/1280:1281,
1/2/1426:1428		Single bulged A
geometric
IL_4V9F_064
IL_31462.6
IL_6FAI_0671/2/1290:1292,
1/2/1323:1325		Isolated cWH basepair
homologous
IL_4V88_453
NA
IL_6FAI_0681/2/1306:1308,
1/2/1317:1318		Minor groove platform
geometric
IL_5TBW_039
NA
IL_6FAI_0691/2/1339:1342,
1/2/1383:1385		Isolated non-canonical cWW pair
homologous
IL_4V88_455
NA
IL_6FAI_0701/2/1345:1348,
1/2/1377:1380		Minor groove platform
homologous
IL_4V88_456
NA
IL_6FAI_0711/2/1352:1354,
1/2/1369:1373		Isolated non-canonical cWW pair
homologous
IL_4V88_457
NA
IL_6FAI_0721/2/1389:1391,
1/2/1407:1412		Major groove platform; stack outside cWW
homologous
IL_4V88_458
NA
IL_6FAI_0731/2/1480:1487,
1/2/1519:1527		No text annotation
homologous
IL_4V88_459
NA
IL_6FAI_0741/2/1488:1494,
1/2/1513:1518		180 degree turn
homologous
IL_4V88_460
NA
IL_6FAI_0751/2/1495:1498,
1/2/1509:1512		Tandem non-canonical cWW pairs
homologous
IL_4V88_461
NA
IL_6FAI_0761/2/1540:1545,
1/2/1566:1571		No text annotation
homologous
IL_4V88_462
NA
IL_6FAI_0971/2/1637:1641,
1/2/1760:1767		No text annotation
IL_6FAI_0781/2/1642:1644,
1/2/1757:1759		Isolated non-canonical cWW pair
homologous
IL_4V88_465
NA
IL_6FAI_0791/2/1644:1647,
1/2/1753:1757		Tandem non-canonical cWW pairs
geometric
IL_2IL9_001
NA
IL_6FAI_0801/2/1650:1652,
1/2/1748:1750		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_6FAI_0981/2/1653:1656,
1/2/1745:1747		No text annotation
IL_6FAI_0821/2/1665:1667,
1/2/1734:1736		Isolated non-canonical cWW pair
homologous
IL_4V88_470
NA
IL_6FAI_0831/2/1669:1672,
1/2/1729:1732		Double sheared
homologous
IL_4V88_471
NA
IL_6FAI_0841/2/1672:1674,
1/2/1727:1729		Isolated non-canonical cWW pair
geometric
IL_4V88_472
NA
IL_6FAI_0851/2/1675:1678,
1/2/1723:1726		Tandem non-canonical cWW pairs
homologous
IL_4V88_473
NA
IL_6FAI_0861/2/1678:1682,
1/2/1719:1723		Triple sheared
geometric
IL_4V88_474
NA
IL_6FAI_0871/2/1688:1690,
1/2/1711:1713		Isolated cWH basepair
geometric
IL_3R1C_012
IL_10167.6
IL_6FAI_0881/2/1693:1695,
1/2/1706:1708		Isolated non-canonical cWW pair
geometric
IL_7A0S_014
IL_87907.2

Problematic loops

#loop idProblemSequence
IL_6FAI_011tWH-tWH-tHW-tHW
IL_6FAI_025C-loop with extra cWW pair
IL_6FAI_026No text annotation
IL_6FAI_039Major groove minor groove platform with extra cWW
IL_6FAI_042No text annotation
IL_6FAI_093Isolated non-canonical cWW pair
IL_6FAI_044Tandem non-canonical cWW pairs
IL_6FAI_063No text annotation
IL_6FAI_096Tandem non-canonical cWW pairs
IL_6FAI_077No text annotation
IL_6FAI_081No text annotation
IL_6FAI_099No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6FAI_0011/2/41:42,
1/2/433:439,
1/2/464:466		No text annotation
homologous
J3_8C3A_082
NA
J3_6FAI_0141/2/213:228,
1/2/237:243,
1/2/250:252		No text annotation
J3_6FAI_0021/2/633:635,
1/2/861:865,
1/2/965:966		No text annotation
geometric
J3_4V88_080
NA
J3_6FAI_0151/2/633:635,
1/2/861:866,
1/2/962:966		No text annotation
homologous
J3_8P9A_072
J3_17385.4
J3_6FAI_0031/2/760:763,
1/2/773:775,
1/2/785:790		No text annotation
homologous
J3_4V88_032
NA
J3_6FAI_0041/2/881:884,
1/2/928:936,
1/2/943:947		No text annotation
homologous
J3_4V88_033
NA
J3_6FAI_0051/2/1037:1039,
1/2/1079:1083,
1/2/1090:1094		No text annotation
homologous
J3_4V88_034
NA
J3_6FAI_0061/2/1161:1164,
1/2/1581:1587,
1/2/1609:1616		No text annotation
homologous
J3_4V88_035
NA
J3_6FAI_0071/2/1168:1171,
1/2/1468:1470,
1/2/1574:1577		No text annotation
homologous
J3_4V88_036
NA
J3_6FAI_0081/2/1180:1187,
1/2/1198:1209,
1/2/1454:1458		No text annotation
homologous
J3_8P9A_078
J3_83516.4
J3_6FAI_0091/2/1215:1220,
1/2/1263:1267,
1/2/1442:1448		No text annotation
J3_6FAI_0101/2/1283:1288,
1/2/1327:1332,
1/2/1419:1424		No text annotation
J3_6FAI_0111/2/1293:1294,
1/2/1303:1306,
1/2/1318:1322		No text annotation
homologous
J3_8C3A_085
NA
J3_6FAI_0121/2/1335:1338,
1/2/1386:1389,
1/2/1412:1416		No text annotation
J3_6FAI_0161/2/1335:1338,
1/2/1386:1391,
1/2/1407:1416		No text annotation
homologous
J3_8C3A_086
NA
J3_6FAI_0131/2/1470:1474,
1/2/1533:1540,
1/2/1571:1574		No text annotation
homologous
J3_4V88_041
NA
J4_6FAI_0011/2/99:107,
1/2/307:309,
1/2/357:361,
1/2/383:384		No text annotation
homologous
J4_8P9A_021
J4_15241.1
J4_6FAI_0021/2/622:624,
1/2/975:980,
1/2/1021:1032,
1/2/1103:1104		No text annotation
homologous
J4_8P9A_022
J4_61885.6
J5_6FAI_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_6FAI_0021/2/31:35,
1/2/473:479,
1/2/509:516,
1/2/536:546,
1/2/592:595		No text annotation
J5_6FAI_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_6FAI_0041/2/124:143,
1/2/172:182,
1/2/203:204,
1/2/263:265,
1/2/289:293		No text annotation
J5_6FAI_0051/2/124:143,
1/2/172:182,
1/2/203:204,
1/2/263:267,
1/2/288:293		No text annotation
J5_6FAI_0071/2/636:641,
1/2/693:698,
1/2/740:744,
1/2/807:817,
1/2/854:860		No text annotation

Problematic loops

#loop idProblemSequence
J5_6FAI_006No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.1647 s