RNA 3D Hub //

4D5L Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_4D5L_0011/1/7:17No text annotation
Not in a motif group		homologous
HL_4V88_186
HL_89881.2
HL_4D5L_0021/1/63:85No text annotation
Not in a motif group
HL_4D5L_0031/1/156:162Other HL
Not in a motif group		homologous
HL_4V88_188
HL_76539.7
HL_4D5L_0351/1/197:202No text annotation
Not in a motif group
HL_4D5L_0061/1/322:329T-loop with 1 bulged base
Not in a motif group		geometric
HL_5TBW_005
HL_23932.1
HL_4D5L_0071/1/377:387No text annotation
Not in a motif group		geometric
HL_4WSM_226
NA
HL_4D5L_0081/1/416:421No text annotation
Not in a motif group		homologous
HL_4V88_194
HL_50142.2
HL_4D5L_0091/1/441:452No text annotation
Not in a motif group		homologous
HL_4V88_195
HL_84288.1
HL_4D5L_0101/1/462:467UNCG
Not in a motif group		homologous
HL_4V88_196
HL_29960.2
HL_4D5L_0111/1/498:504No text annotation
Not in a motif group		geometric
HL_5NFV_001
HL_76539.7
HL_4D5L_0121/1/539:544No text annotation
Not in a motif group		geometric
HL_5NFV_001
HL_76539.7
HL_4D5L_0361/1/565:585No text annotation
Not in a motif group
HL_4D5L_0131/1/569:581No text annotation
Not in a motif group
HL_4D5L_0141/1/618:623Other HL
Not in a motif group		homologous
HL_4V88_200
HL_64107.1
HL_4D5L_0151/1/820:828No text annotation
Not in a motif group		homologous
HL_4V88_203
HL_46766.2
HL_4D5L_0161/1/833:841No text annotation
Not in a motif group		geometric
HL_5TBW_006
HL_33074.1
HL_4D5L_0171/1/884:902No text annotation
Not in a motif group
HL_4D5L_0181/1/957:966No text annotation
Not in a motif group		homologous
HL_4V88_206
HL_12326.2
HL_4D5L_0191/1/994:999Other HL
Not in a motif group		homologous
HL_4V88_207
HL_29031.1
HL_4D5L_0371/1/1052:1066No text annotation
Not in a motif group
HL_4D5L_0201/1/1054:1064No text annotation
Not in a motif group		homologous
HL_4V88_208
HL_12326.2
HL_4D5L_0381/1/1110:1123No text annotation
Not in a motif group
HL_4D5L_0211/1/1112:1121No text annotation
Not in a motif group
HL_4D5L_0221/1/1141:1146Other HL
Not in a motif group		homologous
HL_4V88_210
HL_85603.2
HL_4D5L_0231/1/1178:1183GNRA
Not in a motif group		homologous
HL_4V88_211
HL_85603.2
HL_4D5L_0241/1/1245:1254No text annotation
Not in a motif group		homologous
HL_4V88_212
HL_50779.1
HL_4D5L_0251/1/1294:1305No text annotation
Not in a motif group
HL_4D5L_0391/1/1352:1359No text annotation
Not in a motif group
HL_4D5L_0261/1/1353:1358GNRA
Not in a motif group		homologous
HL_4V88_214
HL_85603.2
HL_4D5L_0271/1/1366:1373No text annotation
Not in a motif group		homologous
HL_4V88_215
HL_71554.2
HL_4D5L_0281/1/1420:1427No text annotation
Not in a motif group
HL_4D5L_0401/1/1460:1466No text annotation
Not in a motif group
HL_4D5L_0301/1/1565:1570GNRA
Not in a motif group		homologous
HL_4V88_218
HL_85603.2
HL_4D5L_0311/1/1614:1625No text annotation
Not in a motif group
HL_4D5L_0321/1/1658:1666No text annotation
Not in a motif group		homologous
HL_4V88_220
HL_01927.1
HL_4D5L_0411/1/1761:1771No text annotation
Not in a motif group
HL_4D5L_0331/1/1763:1769GNRA
Not in a motif group		geometric
HL_3SUX_002
HL_85603.2
HL_4D5L_0341/1/1847:1852Other HL
Not in a motif group		homologous
HL_4V88_222
HL_29031.1

Problematic loops

#loop idProblemSequence
HL_4D5L_004No text annotation
HL_4D5L_005No text annotation
HL_4D5L_029No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_4D5L_0011/1/23:26,
1/1/648:651		Tandem non-canonical cWW pairs
Not in a motif group		geometric
IL_5C5W_001
IL_35199.1
IL_4D5L_0021/1/34:36,
1/1/519:521		UC cWW
Not in a motif group		homologous
IL_4V88_385
IL_64928.1
IL_4D5L_0831/1/34:40,
1/1/514:521		No text annotation
Not in a motif group
IL_4D5L_0031/1/36:40,
1/1/514:519		No text annotation
Not in a motif group		homologous
IL_4V88_386
IL_37842.1
IL_4D5L_0041/1/41:47,
1/1/479:481		No text annotation
Not in a motif group		homologous
IL_4V88_387
IL_33912.1
IL_4D5L_0051/1/49:51,
1/1/476:477		Minor groove platform
Not in a motif group		homologous
IL_4V88_388
IL_80097.3
IL_4D5L_0061/1/56:62,
1/1/86:89		No text annotation
Not in a motif group
IL_4D5L_0071/1/108:112,
1/1/349:353		No text annotation
Not in a motif group
IL_4D5L_0081/1/112:115,
1/1/348:349		Multiple bulged bases
Not in a motif group		homologous
IL_4V88_392
IL_44546.2
IL_4D5L_0841/1/116:121,
1/1/343:347		No text annotation
Not in a motif group
IL_4D5L_0101/1/146:151,
1/1/167:174		No text annotation
Not in a motif group
IL_4D5L_0111/1/152:154,
1/1/164:166		No text annotation
Not in a motif group		homologous
IL_4V88_395
IL_76636.1
IL_4D5L_0851/1/187:192,
1/1/207:212		No text annotation
Not in a motif group
IL_4D5L_0131/1/317:319,
1/1/332:333		No text annotation
Not in a motif group
IL_4D5L_0861/1/317:321,
1/1/330:333		No text annotation
Not in a motif group
IL_4D5L_0141/1/359:364,
1/1/396:403		Kink-turn with non-sequential stacking
Not in a motif group		homologous
IL_4V88_402
IL_45067.4
IL_4D5L_0151/1/366:371,
1/1/393:394		No text annotation
Not in a motif group		geometric
IL_4ERD_001
IL_24807.1
IL_4D5L_0161/1/411:413,
1/1/424:429		No text annotation
Not in a motif group
IL_4D5L_0171/1/437:439,
1/1/454:456		Isolated cWH basepair
Not in a motif group		homologous
IL_4V88_405
IL_27267.1
IL_4D5L_0181/1/459:461,
1/1/468:470		Isolated near basepair
Not in a motif group		homologous
IL_4V88_406
IL_64928.1
IL_4D5L_0191/1/487:489,
1/1/511:512		Single bulged U
Not in a motif group		homologous
IL_4V88_407
IL_83039.18
IL_4D5L_0201/1/491:495,
1/1/508:509		C-loop
Not in a motif group		geometric
IL_4LFB_015
IL_75255.1
IL_4D5L_0211/1/495:496,
1/1/506:508		Single bulged G
Not in a motif group		geometric
IL_5J7L_019
IL_00225.5
IL_4D5L_0221/1/530:531,
1/1/553:555		Single bulged A
Not in a motif group		homologous
IL_4V88_409
IL_37497.8
IL_4D5L_0231/1/535:539,
1/1/544:549		No text annotation
Not in a motif group
IL_4D5L_0241/1/565:569,
1/1/581:585		No text annotation
Not in a motif group
IL_4D5L_0251/1/599:608,
1/1/635:637		No text annotation
Not in a motif group		geometric
IL_4V88_470
IL_27267.1
IL_4D5L_0261/1/611:617,
1/1/624:632		No text annotation
Not in a motif group		homologous
IL_4V88_415
IL_54177.1
IL_4D5L_0271/1/663:665,
1/1/1162:1164		Isolated cWH basepair
Not in a motif group		geometric
IL_406D_002
IL_66171.1
IL_4D5L_0281/1/673:675,
1/1/1030:1032		No text annotation
Not in a motif group		homologous
IL_4V88_417
IL_64928.1
IL_4D5L_0291/1/676:680,
1/1/1025:1029		tSH-tHW-tHS
Not in a motif group		homologous
IL_4V88_418
IL_17136.3
IL_4D5L_0301/1/692:694,
1/1/738:739		No text annotation
Not in a motif group
IL_4D5L_0311/1/752:754,
1/1/790:791		No text annotation
Not in a motif group
IL_4D5L_0321/1/802:803,
1/1/860:863		Major groove minor groove platform; mini C-loop
Not in a motif group		homologous
IL_4V88_423
IL_09061.10
IL_4D5L_0331/1/804:807,
1/1/856:859		Tandem non-canonical cWW pairs
Not in a motif group		geometric
IL_7A0S_040
IL_58179.1
IL_4D5L_0341/1/807:815,
1/1/849:856		No text annotation
Not in a motif group		homologous
IL_4V88_425
IL_53064.1
IL_4D5L_0351/1/877:879,
1/1/907:909		Isolated cWH basepair
Not in a motif group		homologous
IL_4V88_427
NA
IL_4D5L_0361/1/922:923,
1/1/1019:1022		Major groove platform; stack outside cWW
Not in a motif group		geometric
IL_4V88_428
IL_50694.3
IL_4D5L_0871/1/924:926,
1/1/1015:1018		No text annotation
Not in a motif group
IL_4D5L_0371/1/925:927,
1/1/1014:1017		Isolated non-canonical cWW with bulges
Not in a motif group		geometric
IL_5J7L_009
IL_12554.1
IL_4D5L_0381/1/928:931,
1/1/1010:1013		Tandem non-canonical cWW pairs
Not in a motif group		geometric
IL_4V88_430
IL_32955.1
IL_4D5L_0391/1/931:935,
1/1/1007:1010		Tandem non-canonical cWW pairs
Not in a motif group		homologous
IL_4V88_431
IL_73915.1
IL_4D5L_0401/1/942:945,
1/1/981:984		Tandem non-canonical cWW pairs
Not in a motif group		homologous
IL_4V88_432
IL_32955.1
IL_4D5L_0411/1/950:956,
1/1/967:976		No text annotation
Not in a motif group		homologous
IL_8C3A_440
IL_22252.1
IL_4D5L_0421/1/1042:1047,
1/1/1071:1073		Other IL
Not in a motif group		homologous
IL_4V88_435
IL_22046.1
IL_4D5L_0431/1/1047:1051,
1/1/1067:1071		tSH-tHW-tHS
Not in a motif group		geometric
IL_4V88_436
IL_17136.3
IL_4D5L_0441/1/1091:1093,
1/1/1152:1158		No text annotation
Not in a motif group		homologous
IL_4V88_437
IL_62898.1
IL_4D5L_0451/1/1098:1101,
1/1/1131:1134		Tandem non-canonical cWW pairs
Not in a motif group		homologous
IL_4V88_438
IL_73915.1
IL_4D5L_0461/1/1101:1103,
1/1/1129:1131		No text annotation
Not in a motif group		geometric
IL_5UNE_009
IL_76636.1
IL_4D5L_0471/1/1108:1110,
1/1/1123:1124		Single bulged U
Not in a motif group		homologous
IL_4V88_439
IL_83039.18
IL_4D5L_0481/1/1168:1175,
1/1/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
Not in a motif group		homologous
IL_4V88_440
IL_14135.1
IL_4D5L_0881/1/1202:1204,
1/1/1694:1697		No text annotation
Not in a motif group
IL_4D5L_0501/1/1206:1210,
1/1/1689:1692		Tandem non-canonical cWW pairs
Not in a motif group		geometric
IL_1D4R_001
IL_73915.1
IL_4D5L_0891/1/1206:1213,
1/1/1686:1692		No text annotation
Not in a motif group
IL_4D5L_0511/1/1213:1217,
1/1/1681:1686		No text annotation
Not in a motif group
IL_4D5L_0901/1/1213:1218,
1/1/1680:1686		No text annotation
Not in a motif group
IL_4D5L_0521/1/1230:1232,
1/1/1526:1528		No text annotation
Not in a motif group		homologous
IL_4V88_444
IL_64928.1
IL_4D5L_0531/1/1235:1236,
1/1/1521:1523		Minor groove platform
Not in a motif group		homologous
IL_4V88_445
IL_23419.1
IL_4D5L_0911/1/1270:1272,
1/1/1510:1512		No text annotation
Not in a motif group
IL_4D5L_0921/1/1279:1290,
1/1/1309:1318		No text annotation
Not in a motif group
IL_4D5L_0551/1/1281:1290,
1/1/1309:1316		No text annotation
Not in a motif group
IL_4D5L_0931/1/1290:1293,
1/1/1306:1309		No text annotation
Not in a motif group
IL_4D5L_0561/1/1291:1293,
1/1/1306:1308		No text annotation
Not in a motif group		homologous
IL_4V88_448
IL_27844.3
IL_4D5L_0571/1/1325:1327,
1/1/1502:1503		Single bulged U
Not in a motif group		homologous
IL_4V88_449
IL_83039.18
IL_4D5L_0941/1/1329:1332,
1/1/1499:1500		No text annotation
Not in a motif group
IL_4D5L_0591/1/1333:1335,
1/1/1492:1498		Minor groove platform with extra cWW
Not in a motif group		homologous
IL_4V88_451
IL_97255.1
IL_4D5L_0601/1/1337:1338,
1/1/1488:1490		Single bulged A
Not in a motif group		homologous
IL_4V88_452
IL_37497.8
IL_4D5L_0611/1/1347:1349,
1/1/1380:1382		Isolated cWH basepair
Not in a motif group		homologous
IL_4V88_453
IL_27267.1
IL_4D5L_0621/1/1395:1397,
1/1/1448:1450		No text annotation
Not in a motif group		geometric
IL_5UNE_001
IL_76636.1
IL_4D5L_0631/1/1397:1399,
1/1/1447:1448		No text annotation
Not in a motif group
IL_4D5L_0951/1/1401:1405,
1/1/1441:1445		No text annotation
Not in a motif group
IL_4D5L_0651/1/1408:1413,
1/1/1433:1438		No text annotation
Not in a motif group
IL_4D5L_0961/1/1415:1418,
1/1/1429:1431		No text annotation
Not in a motif group
IL_4D5L_0671/1/1537:1539,
1/1/1594:1596		No text annotation
Not in a motif group		geometric
IL_6OL3_002
IL_64928.1
IL_4D5L_0971/1/1537:1540,
1/1/1593:1596		No text annotation
Not in a motif group
IL_4D5L_0981/1/1541:1550,
1/1/1582:1592		No text annotation
Not in a motif group
IL_4D5L_0681/1/1550:1558,
1/1/1577:1582		No text annotation
Not in a motif group
IL_4D5L_0691/1/1559:1562,
1/1/1573:1576		Tandem non-canonical cWW pairs
Not in a motif group		homologous
IL_4V88_461
IL_86432.1
IL_4D5L_0701/1/1604:1610,
1/1/1629:1635		No text annotation
Not in a motif group		homologous
IL_8C3A_469
NA
IL_4D5L_0711/1/1700:1702,
1/1/1833:1836		No text annotation
Not in a motif group		homologous
IL_4V88_463
IL_61438.1
IL_4D5L_0721/1/1702:1705,
1/1/1829:1833		No text annotation
Not in a motif group		geometric
IL_4V88_464
IL_65718.1
IL_4D5L_0731/1/1706:1708,
1/1/1826:1828		No text annotation
Not in a motif group		homologous
IL_4V88_465
IL_64928.1
IL_4D5L_0741/1/1708:1711,
1/1/1822:1826		Non canonical cWW and near pair
Not in a motif group		geometric
IL_4V88_466
IL_99772.1
IL_4D5L_0991/1/1714:1716,
1/1/1817:1819		No text annotation
Not in a motif group
IL_4D5L_0761/1/1717:1720,
1/1/1813:1816		Double sheared
Not in a motif group		geometric
IL_4V88_468
IL_09705.12
IL_4D5L_0771/1/1720:1722,
1/1/1812:1813		No text annotation
Not in a motif group
IL_4D5L_0781/1/1729:1731,
1/1/1803:1805		No text annotation
Not in a motif group		homologous
IL_4V88_470
IL_27267.1
IL_4D5L_0791/1/1733:1736,
1/1/1798:1801		Double sheared
Not in a motif group		homologous
IL_4V88_471
IL_09705.12
IL_4D5L_0801/1/1739:1742,
1/1/1792:1795		Tandem non-canonical cWW pairs
Not in a motif group		homologous
IL_4V88_473
IL_35199.1
IL_4D5L_1001/1/1742:1746,
1/1/1788:1792		No text annotation
Not in a motif group
IL_4D5L_1011/1/1748:1752,
1/1/1780:1786		No text annotation
Not in a motif group
IL_4D5L_0821/1/1750:1752,
1/1/1780:1784		No text annotation
Not in a motif group		homologous
IL_4V88_475
NA

Problematic loops

#loop idProblemSequence
IL_4D5L_009No text annotation
IL_4D5L_012No text annotation
IL_4D5L_049No text annotation
IL_4D5L_054Tandem non-canonical cWW pairs
IL_4D5L_058Tandem non-canonical cWW pairs
IL_4D5L_064No text annotation
IL_4D5L_066No text annotation
IL_4D5L_075Tandem non-canonical cWW pairs
IL_4D5L_081No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_4D5L_0011/1/40:41,
1/1/481:487,
1/1/512:514		No text annotation
Not in a motif group
J3_4D5L_0021/1/681:684,
1/1/918:922,
1/1/1022:1024		No text annotation
Not in a motif group
J3_4D5L_0031/1/816:819,
1/1/829:831,
1/1/843:848		No text annotation
Not in a motif group
J3_4D5L_0111/1/816:820,
1/1/828:831,
1/1/843:848		No text annotation
Not in a motif group
J3_4D5L_0041/1/938:941,
1/1/985:993,
1/1/1000:1004		No text annotation
Not in a motif group		homologous
J3_4V88_033
NA
J3_4D5L_0121/1/1094:1096,
1/1/1136:1140,
1/1/1147:1151		No text annotation
Not in a motif group
J3_4D5L_0061/1/1218:1221,
1/1/1645:1651,
1/1/1673:1680		No text annotation
Not in a motif group		homologous
J3_8C3A_038
NA
J3_4D5L_0071/1/1237:1245,
1/1/1254:1266,
1/1/1516:1520		No text annotation
Not in a motif group
J3_4D5L_0081/1/1272:1277,
1/1/1320:1324,
1/1/1504:1510		No text annotation
Not in a motif group
J3_4D5L_0091/1/1340:1345,
1/1/1384:1389,
1/1/1481:1486		No text annotation
Not in a motif group		homologous
J3_4V88_039
NA
J3_4D5L_0131/1/1340:1345,
1/1/1384:1390,
1/1/1480:1486		No text annotation
Not in a motif group
J3_4D5L_0101/1/1350:1351,
1/1/1360:1365,
1/1/1374:1379		No text annotation
Not in a motif group
J3_4D5L_0141/1/1391:1395,
1/1/1450:1456,
1/1/1470:1479		No text annotation
Not in a motif group
J4_4D5L_0011/1/98:106,
1/1/355:357,
1/1/405:410,
1/1/430:432		No text annotation
Not in a motif group
J4_4D5L_0021/1/665:673,
1/1/1032:1037,
1/1/1078:1089,
1/1/1160:1162		No text annotation
Not in a motif group
J4_4D5L_0031/1/1225:1228,
1/1/1530:1536,
1/1/1597:1610,
1/1/1629:1641		No text annotation
Not in a motif group
J5_4D5L_0011/1/30:34,
1/1/521:528,
1/1/557:565,
1/1/585:595,
1/1/641:644		No text annotation
Not in a motif group
J5_4D5L_0021/1/53:56,
1/1/89:96,
1/1/434:436,
1/1/457:459,
1/1/470:474		No text annotation
Not in a motif group
J5_4D5L_0031/1/123:146,
1/1/174:186,
1/1/213:220,
1/1/301:316,
1/1/334:341		No text annotation
Not in a motif group
J6_4D5L_0011/1/682:694,
1/1/738:750,
1/1/793:807,
1/1/856:877,
1/1/909:922,
1/1/1022:1023		No text annotation
Not in a motif group
J6_4D5L_0021/1/682:694,
1/1/738:750,
1/1/793:807,
1/1/856:877,
1/1/909:923,
1/1/1019:1023		No text annotation
Not in a motif group

Problematic loops

#loop idProblemSequence
J3_4D5L_005No text annotation

Coloring options:
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