RNA 3D Hub //

7A09 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7A09_0011/2/7:17No text annotation
homologous
HL_4V88_186
NA
HL_7A09_0021/2/69:80No text annotation
geometric
HL_361D_002
HL_13963.3
HL_7A09_0031/2/156:162GNRA related
homologous
HL_4V88_188
NA
HL_7A09_0041/2/195:204No text annotation
geometric
HL_2Y8W_001
HL_81100.2
HL_7A09_0051/2/288:295T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_7A09_0061/2/320:331No text annotation
geometric
HL_7KI3_001
HL_75660.5
HL_7A09_0071/2/377:387No text annotation
HL_7A09_0081/2/414:423No text annotation
geometric
HL_5TBW_015
NA
HL_7A09_0091/2/441:452No text annotation
homologous
HL_4V88_195
NA
HL_7A09_0101/2/462:467UNCG
homologous
HL_4V88_196
NA
HL_7A09_0111/2/498:504No text annotation
homologous
HL_4V88_197
NA
HL_7A09_0121/2/535:549No text annotation
HL_7A09_0131/2/569:581No text annotation
homologous
HL_4V88_199
NA
HL_7A09_0141/2/618:623GNRA variation
homologous
HL_4V88_200
NA
HL_7A09_0151/2/711:716GNRA
geometric
HL_7A0S_047
HL_37824.8
HL_7A09_0161/2/820:828No text annotation
homologous
HL_4V88_203
NA
HL_7A09_0171/2/833:841No text annotation
geometric
HL_8C3A_054
NA
HL_7A09_0181/2/882:904No text annotation
HL_7A09_0191/2/957:966No text annotation
homologous
HL_4V88_206
NA
HL_7A09_0201/2/994:999GNRA
homologous
HL_4V88_207
NA
HL_7A09_0211/2/1054:1064No text annotation
homologous
HL_4V88_208
NA
HL_7A09_0221/2/1113:1120No text annotation
HL_7A09_0231/2/1141:1146GNRA
homologous
HL_4V88_210
NA
HL_7A09_0241/2/1178:1183GNRA
homologous
HL_4V88_211
NA
HL_7A09_0251/2/1245:1254No text annotation
homologous
HL_4V88_212
NA
HL_7A09_0261/2/1295:1304Anticodon loop related
homologous
HL_4V88_213
NA
HL_7A09_0271/2/1353:1358GNRA
homologous
HL_4V88_214
NA
HL_7A09_0281/2/1366:1373No text annotation
homologous
HL_4V88_215
NA
HL_7A09_0291/2/1415:1425No text annotation
HL_7A09_0301/2/1460:1466GNRA related
geometric
HL_5J7L_179
HL_04783.2
HL_7A09_0311/2/1565:1570GNRA
homologous
HL_4V88_218
NA
HL_7A09_0321/2/1614:1625No text annotation
homologous
HL_4V88_219
NA
HL_7A09_0331/2/1658:1666No text annotation
homologous
HL_4V88_220
NA
HL_7A09_0401/2/1752:1780No text annotation
HL_7A09_0341/2/1760:1774No text annotation
HL_7A09_0351/2/1847:1852GNRA variation
homologous
HL_4V88_222
NA
HL_7A09_0361/f/13:22No text annotation
homologous
HL_3WFS_001
NA
HL_7A09_0371/f/31:39tRNA anticodon loop
homologous
HL_4TUE_034
HL_06059.7
HL_7A09_0381/f/53:61T-loop with 2 stacked bulged bases
homologous
HL_1QU2_003
HL_28252.9

Problematic loops

#loop idProblemSequence
HL_7A09_039No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7A09_0011/2/23:25,
1/2/649:651		Isolated non-canonical cWW pair
geometric
IL_3MEI_002
IL_87907.2
IL_7A09_0021/2/34:36,
1/2/519:521		Isolated non-canonical cWW pair
homologous
IL_4V88_385
NA
IL_7A09_0031/2/37:40,
1/2/514:518		Double sheared
geometric
IL_4WF9_016
IL_09705.15
IL_7A09_0041/2/41:47,
1/2/479:481		No text annotation
geometric
IL_4V88_387
NA
IL_7A09_0051/2/49:51,
1/2/476:477		Minor groove platform
homologous
IL_4V88_388
NA
IL_7A09_0061/2/57:62,
1/2/86:88		No text annotation
homologous
IL_4V88_389
NA
IL_7A09_0071/2/63:68,
1/2/81:85		No text annotation
homologous
IL_4V88_390
NA
IL_7A09_0081/2/108:110,
1/2/351:353		Isolated non-canonical cWW pair
geometric
IL_1T0E_002
IL_28037.2
IL_7A09_0091/2/110:112,
1/2/349:351		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_87907.2
IL_7A09_0101/2/112:115,
1/2/348:349		Multiple bulged bases
homologous
IL_4V88_392
NA
IL_7A09_0111/2/116:121,
1/2/343:347		No text annotation
IL_7A09_0121/2/123:124,
1/2/339:341		Minor groove platform
geometric
IL_4V88_388
NA
IL_7A09_0131/2/130:144,
1/2/175:182		No text annotation
IL_7A09_0141/2/145:151,
1/2/167:174		tWH-tWH-tHW-tHW
homologous
IL_4V88_394
NA
IL_7A09_0151/2/152:154,
1/2/164:166		Isolated cWH basepair
geometric
IL_3CZW_001
IL_10167.6
IL_7A09_0161/2/188:192,
1/2/207:211		Double sheared with non-canonical cWW
geometric
IL_5J7L_274
IL_17948.2
IL_7A09_0171/2/216:219,
1/2/302:309		No text annotation
IL_7A09_0181/2/219:221,
1/2/300:302		Isolated non-canonical cWW pair
geometric
IL_4WF9_020
IL_87907.2
IL_7A09_0191/2/223:288,
1/2/295:298		No text annotation
IL_7A09_0201/2/312:314,
1/2/336:337		Single bulged A
homologous
IL_4V88_399
NA
IL_7A09_0211/2/317:319,
1/2/332:333		Single stack bend
geometric
IL_5TBW_009
NA
IL_7A09_0951/2/359:364,
1/2/396:403		Kink-turn with non-sequential stacking
homologous
IL_8C3A_410
NA
IL_7A09_0231/2/366:371,
1/2/393:394		No text annotation
geometric
IL_5Y58_001
IL_59877.1
IL_7A09_0241/2/411:413,
1/2/424:429		No text annotation
homologous
IL_4V88_404
NA
IL_7A09_0251/2/437:439,
1/2/454:456		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_7A09_0261/2/459:461,
1/2/468:470		Isolated near basepair
homologous
IL_4V88_406
NA
IL_7A09_0271/2/487:489,
1/2/511:512		Single bulged U
geometric
IL_4LFB_014
IL_89505.4
IL_7A09_0281/2/491:495,
1/2/508:509		C-loop
geometric
IL_5J7L_018
IL_03109.3
IL_7A09_0291/2/495:496,
1/2/506:508		Single bulged G
geometric
IL_5J7L_019
IL_00225.14
IL_7A09_0301/2/529:530,
1/2/554:556		Single bulged A
homologous
IL_4V88_409
NA
IL_7A09_0311/2/563:565,
1/2/585:592		No text annotation
homologous
IL_8C3A_420
NA
IL_7A09_0971/2/566:569,
1/2/581:584		Tandem non-canonical cWW pairs
geometric
IL_402D_001
IL_77658.1
IL_7A09_0331/2/599:606,
1/2/636:637		SSU/LSU pseudoknot
homologous
IL_4V88_413
NA
IL_7A09_0341/2/606:608,
1/2/635:636		Single bulged U
geometric
IL_4V88_414
NA
IL_7A09_0351/2/611:617,
1/2/624:632		Kink-turn related
homologous
IL_4V88_415
NA
IL_7A09_0361/2/663:665,
1/2/1162:1164		Isolated non-canonical cWW pair
geometric
IL_1Y27_001
IL_87907.2
IL_7A09_0981/2/663:671,
1/2/1161:1164		No text annotation
IL_7A09_0371/2/665:671,
1/2/1161:1162		No text annotation
homologous
IL_4V88_416
NA
IL_7A09_0381/2/673:675,
1/2/1030:1032		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_7A09_0391/2/676:680,
1/2/1025:1029		tSH-tHW-tHS
homologous
IL_4V88_418
NA
IL_7A09_1001/2/692:694,
1/2/736:738		Isolated non-canonical cWW pair
geometric
IL_6CZR_118
NA
IL_7A09_1011/2/694:696,
1/2/734:736		No text annotation
homologous
IL_8P9A_408
IL_44465.1
IL_7A09_0411/2/706:708,
1/2/719:724		No text annotation
IL_7A09_0421/2/801:803,
1/2/860:864		No text annotation
IL_7A09_0431/2/805:807,
1/2/856:858		Isolated non-canonical cWW pair
homologous
IL_4V88_424
NA
IL_7A09_0441/2/807:815,
1/2/849:856		No text annotation
geometric
IL_4V88_425
NA
IL_7A09_0451/2/874:876,
1/2/910:912		Isolated non-canonical cWW pair
geometric
IL_5CCB_001
IL_87907.2
IL_7A09_0461/2/877:879,
1/2/907:909		Isolated non-canonical cWW pair
geometric
IL_5ED1_002
IL_87907.2
IL_7A09_0471/2/922:923,
1/2/1019:1022		Major groove platform; stack outside cWW
homologous
IL_4V88_428
NA
IL_7A09_1151/2/925:926,
1/2/1015:1017		Single bulged U
geometric
IL_2PJP_001
IL_89505.4
IL_7A09_0491/2/928:931,
1/2/1010:1013		Tandem non-canonical cWW pairs
homologous
IL_4V88_430
NA
IL_7A09_0501/2/931:935,
1/2/1007:1010		Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA
IL_7A09_0511/2/942:945,
1/2/981:984		Tandem non-canonical cWW pairs
homologous
IL_4V88_432
NA
IL_7A09_0521/2/951:956,
1/2/967:975		No text annotation
IL_7A09_0531/2/1041:1047,
1/2/1071:1074		No text annotation
IL_7A09_0541/2/1047:1051,
1/2/1067:1071		tSH-tHW-tHS
homologous
IL_4V88_436
NA
IL_7A09_1161/2/1091:1093,
1/2/1152:1158		No text annotation
homologous
IL_8P9A_425
IL_82706.1
IL_7A09_0561/2/1098:1103,
1/2/1129:1134		No text annotation
geometric
IL_6O5F_001
NA
IL_7A09_0571/2/1108:1110,
1/2/1123:1124		Minor groove platform
geometric
IL_4V88_412
NA
IL_7A09_0581/2/1168:1175,
1/2/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_7A09_1061/2/1203:1204,
1/2/1694:1696		Single bulged A
homologous
IL_8C3A_447
NA
IL_7A09_0601/2/1206:1208,
1/2/1691:1692		Single bulged G
homologous
IL_4V88_442
NA
IL_7A09_0611/2/1214:1217,
1/2/1681:1685		C-loop
geometric
IL_1KOG_007
IL_63596.11
IL_7A09_0621/2/1230:1232,
1/2/1526:1528		Isolated non-canonical cWW pair
homologous
IL_4V88_444
NA
IL_7A09_0631/2/1235:1236,
1/2/1521:1523		Minor groove platform
homologous
IL_4V88_445
NA
IL_7A09_0641/2/1270:1272,
1/2/1510:1512		Isolated non-canonical cWW pair
geometric
IL_5MWI_006
NA
IL_7A09_0651/2/1281:1290,
1/2/1309:1316		No text annotation
homologous
IL_8P9A_470
IL_28304.1
IL_7A09_0661/2/1291:1294,
1/2/1305:1308		No text annotation
IL_7A09_0671/2/1325:1327,
1/2/1502:1503		Single bulged U
homologous
IL_4V88_449
NA
IL_7A09_0681/2/1329:1333,
1/2/1498:1500		Isolated cWS basepair
homologous
IL_4V88_450
NA
IL_7A09_1171/2/1329:1335,
1/2/1492:1500		No text annotation
homologous
IL_8P9A_439
IL_86012.1
IL_7A09_0691/2/1333:1335,
1/2/1492:1498		Minor groove platform with extra cWW
geometric
IL_4V88_451
NA
IL_7A09_0701/2/1337:1338,
1/2/1488:1490		Single bulged A
homologous
IL_4V88_452
NA
IL_7A09_1181/2/1347:1349,
1/2/1380:1382		Isolated cWH basepair
homologous
IL_8P9A_442
IL_10167.6
IL_7A09_0721/2/1363:1365,
1/2/1374:1375		Minor groove platform
homologous
IL_4V88_454
NA
IL_7A09_0731/2/1395:1399,
1/2/1447:1450		Tandem non-canonical cWW pairs
geometric
IL_5EW4_002
IL_85033.2
IL_7A09_1191/2/1402:1405,
1/2/1441:1444		No text annotation
homologous
IL_8CRE_481
IL_78800.1
IL_7A09_1201/2/1412:1413,
1/2/1427:1429		Single bulged G
geometric
IL_2IZN_001
IL_00225.14
IL_7A09_0761/2/1537:1539,
1/2/1594:1596		Isolated non-canonical cWW pair
geometric
IL_4WF9_017
IL_07785.1
IL_7A09_1111/2/1541:1550,
1/2/1582:1592		No text annotation
IL_7A09_0771/2/1550:1558,
1/2/1577:1582		No text annotation
IL_7A09_0781/2/1560:1562,
1/2/1573:1575		Stack and bulge
geometric
IL_2ET8_001
IL_31737.3
IL_7A09_0791/2/1604:1610,
1/2/1629:1635		No text annotation
homologous
IL_8C3A_469
NA
IL_7A09_0801/2/1700:1702,
1/2/1833:1836		No text annotation
homologous
IL_4V88_463
NA
IL_7A09_0811/2/1702:1705,
1/2/1829:1833		No text annotation
geometric
IL_4V88_464
NA
IL_7A09_0821/2/1706:1708,
1/2/1826:1828		Isolated non-canonical cWW pair
homologous
IL_4V88_465
NA
IL_7A09_1121/2/1706:1713,
1/2/1820:1828		No text annotation
IL_7A09_0831/2/1708:1713,
1/2/1820:1826		No text annotation
IL_7A09_0841/2/1714:1716,
1/2/1817:1819		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_7A09_0851/2/1717:1720,
1/2/1813:1816		Double sheared
geometric
IL_4V88_468
NA
IL_7A09_0861/2/1720:1722,
1/2/1812:1813		No text annotation
IL_7A09_0871/2/1729:1731,
1/2/1803:1805		Isolated non-canonical cWW pair
homologous
IL_4V88_470
NA
IL_7A09_0881/2/1733:1736,
1/2/1798:1801		Double sheared
homologous
IL_4V88_471
NA
IL_7A09_0891/2/1739:1741,
1/2/1793:1795		Isolated non-canonical cWW pair
geometric
IL_4E48_002
IL_87907.2
IL_7A09_0901/2/1742:1746,
1/2/1788:1792		Triple sheared
homologous
IL_4V88_474
NA
IL_7A09_1211/2/1748:1752,
1/2/1780:1786		No text annotation
IL_7A09_0911/2/1749:1751,
1/2/1782:1785		No text annotation
homologous
IL_4V88_475
NA
IL_7A09_0921/2/1751:1752,
1/2/1780:1782		Single stack bend
geometric
IL_5TBW_375
NA
IL_7A09_0931/2/1752:1760,
1/2/1774:1780		No text annotation

Problematic loops

#loop idProblemSequence
IL_7A09_094No text annotation
IL_7A09_022No text annotation
IL_7A09_096No text annotation
IL_7A09_032No text annotation
IL_7A09_099tSH-tHW-tHS-cWW
IL_7A09_040No text annotation
IL_7A09_102No text annotation
IL_7A09_048Tandem non-canonical cWW pairs
IL_7A09_103Isolated cWH basepair
IL_7A09_104Triple non-canonical cWW pairs
IL_7A09_055No text annotation
IL_7A09_105No text annotation
IL_7A09_059Isolated non-canonical cWW with bulges
IL_7A09_107No text annotation
IL_7A09_108No text annotation
IL_7A09_109No text annotation
IL_7A09_071Tandem non-canonical cWW pairs
IL_7A09_110No text annotation
IL_7A09_074No text annotation
IL_7A09_075Isolated non-canonical cWW pair
IL_7A09_113Tandem non-canonical cWW pairs
IL_7A09_114No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7A09_0011/2/40:41,
1/2/481:487,
1/2/512:514		No text annotation
geometric
J3_4V88_078
NA
J3_7A09_0121/2/40:47,
1/2/479:487,
1/2/512:514		No text annotation
homologous
J3_8P9A_069
J3_46317.4
J3_7A09_0021/2/816:819,
1/2/829:831,
1/2/843:848		No text annotation
homologous
J3_4V88_032
NA
J3_7A09_0031/2/937:941,
1/2/985:993,
1/2/1000:1005		No text annotation
J3_7A09_0041/2/1094:1096,
1/2/1136:1140,
1/2/1147:1151		No text annotation
J3_7A09_0051/2/1218:1221,
1/2/1645:1651,
1/2/1673:1680		No text annotation
homologous
J3_4V88_035
NA
J3_7A09_0171/2/1225:1228,
1/2/1530:1532,
1/2/1638:1641		No text annotation
homologous
J3_8CRE_079
J3_52655.4
J3_7A09_0181/2/1237:1244,
1/2/1255:1266,
1/2/1516:1520		No text annotation
homologous
J3_8CRE_080
J3_83516.4
J3_7A09_0081/2/1272:1277,
1/2/1320:1324,
1/2/1504:1510		No text annotation
homologous
J3_4V88_038
NA
J3_7A09_0191/2/1340:1345,
1/2/1384:1389,
1/2/1481:1486		No text annotation
homologous
J3_8P9A_080
J3_99563.1
J3_7A09_0101/2/1350:1351,
1/2/1360:1363,
1/2/1375:1379		No text annotation
geometric
J3_4V88_082
NA
J3_7A09_0161/2/1391:1395,
1/2/1450:1456,
1/2/1470:1479		No text annotation
J3_7A09_0111/2/1532:1536,
1/2/1597:1604,
1/2/1635:1638		No text annotation
homologous
J3_8C3A_044
NA
J4_7A09_0011/2/98:106,
1/2/355:357,
1/2/405:409,
1/2/431:432		No text annotation
homologous
J4_8P9A_021
J4_15241.1
J4_7A09_0021/2/671:673,
1/2/1032:1037,
1/2/1078:1089,
1/2/1160:1161		No text annotation
homologous
J4_8P9A_022
J4_61885.6
J4_7A09_0041/f/7:10,
1/f/25:27,
1/f/43:49,
1/f/65:66		tRNA junction
homologous
J4_8VU0_001
J4_70449.29
J5_7A09_0011/2/30:34,
1/2/521:527,
1/2/558:563,
1/2/592:595,
1/2/641:644		No text annotation
homologous
J5_8C3A_018
NA
J5_7A09_0021/2/30:34,
1/2/521:527,
1/2/558:565,
1/2/585:595,
1/2/641:644		No text annotation
J5_7A09_0031/2/53:56,
1/2/89:96,
1/2/434:436,
1/2/457:459,
1/2/470:474		No text annotation
homologous
J5_8C3A_020
NA
J5_7A09_0071/2/125:129,
1/2/183:185,
1/2/214:215,
1/2/310:314,
1/2/336:338		No text annotation
J5_7A09_0081/2/682:691,
1/2/739:800,
1/2/865:874,
1/2/912:922,
1/2/1022:1023		No text annotation
J5_7A09_0091/2/682:691,
1/2/739:800,
1/2/865:874,
1/2/912:923,
1/2/1019:1023		No text annotation

Problematic loops

#loop idProblemSequence
J3_7A09_013No text annotation
J3_7A09_006No text annotation
J3_7A09_007No text annotation
J3_7A09_014No text annotation
J3_7A09_009No text annotation
J3_7A09_015No text annotation
J4_7A09_003No text annotation
J5_7A09_004No text annotation
J5_7A09_005No text annotation
J5_7A09_006No text annotation

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