RNA 3D Hub //

9SS1 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9SS1_0011/D1/12:22No text annotation
homologous
HL_6CZR_072
NA
HL_9SS1_0031/D1/158:163GNRA
homologous
HL_6CZR_074
NA
HL_9SS1_0041/D1/186:191GNRA
geometric
HL_8X5V_001
HL_34789.5
HL_9SS1_0051/D1/207:212No text annotation
HL_9SS1_0061/D1/259:267GNRA related
homologous
HL_6CZR_077
NA
HL_9SS1_0071/D1/296:301GNRA
homologous
HL_6CZR_078
NA
HL_9SS1_0081/D1/320:333No text annotation
homologous
HL_6CZR_079
NA
HL_9SS1_0091/D1/342:347UNCG
homologous
HL_6CZR_080
NA
HL_9SS1_0101/D1/379:384GNRA
homologous
HL_6CZR_081
NA
HL_9SS1_0111/D1/419:424No text annotation
homologous
HL_6CZR_082
NA
HL_9SS1_0121/D1/462:470No text annotation
geometric
HL_8B0X_011
HL_98423.4
HL_9SS1_0131/D1/522:527GNRA variation
homologous
HL_6CZR_216
NA
HL_9SS1_0141/D1/617:623No text annotation
homologous
HL_6CZR_085
NA
HL_9SS1_0151/D1/689:698No text annotation
homologous
HL_6CZR_086
NA
HL_9SS1_0161/D1/726:731GNRA
homologous
HL_6CZR_087
NA
HL_9SS1_0171/D1/786:796No text annotation
homologous
HL_6CZR_088
NA
HL_9SS1_0181/D1/840:846No text annotation
HL_9SS1_0191/D1/862:867GNRA
homologous
HL_6CZR_090
NA
HL_9SS1_0201/D1/897:902GNRA
homologous
HL_6CZR_091
NA
HL_9SS1_0231/D1/1076:1081GNRA
homologous
HL_6CZR_095
NA
HL_9SS1_0241/D1/1089:1096T-loop related
homologous
HL_6CZR_096
NA
HL_9SS1_0291/D1/1356:1366No text annotation
homologous
HL_6CZR_101
NA
HL_9SS1_0301/D1/1449:1454No text annotation
geometric
HL_5HR7_005
HL_50006.5
HL_9SS1_0311/D1/1515:1520GNRA
homologous
HL_6CZR_103
NA

Problematic loops

#loop idProblemSequence
HL_9SS1_002No text annotation
HL_9SS1_021No text annotation
HL_9SS1_022No text annotation
HL_9SS1_025No text annotation
HL_9SS1_026GNRA
HL_9SS1_027No text annotation
HL_9SS1_028T-loop with 3 stacked bulged bases

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9SS1_0011/D1/30:32,
1/D1/552:553		Single bulged G
homologous
IL_6CZR_113
NA
IL_9SS1_0021/D1/44:45,
1/D1/396:398		Single bulged A
homologous
IL_6CZR_114
NA
IL_9SS1_0031/D1/47:52,
1/D1/359:361		No text annotation
geometric
IL_8B0X_003
IL_32983.2
IL_9SS1_0041/D1/54:56,
1/D1/356:357		Minor groove platform
homologous
IL_6CZR_116
NA
IL_9SS1_0051/D1/63:66,
1/D1/103:104		Multiple bulged bases
homologous
IL_6CZR_117
NA
IL_9SS1_0061/D1/67:69,
1/D1/99:102		No text annotation
geometric
IL_8B0X_006
IL_82096.1
IL_9SS1_0071/D1/70:73,
1/D1/97:98		No text annotation
geometric
IL_8B0X_007
IL_87975.1
IL_9SS1_0081/D1/75:76,
1/D1/93:95		No text annotation
geometric
IL_8B0X_008
IL_28408.3
IL_9SS1_0091/D1/128:131,
1/D1/231:233		No text annotation
IL_9SS1_0101/D1/132:136,
1/D1/227:230		Minor groove platform related
homologous
IL_6CZR_120
NA
IL_9SS1_0111/D1/144:146,
1/D1/176:178		No text annotation
geometric
IL_8B0X_011
IL_10892.3
IL_9SS1_0121/D1/147:153,
1/D1/168:175		tWH-tWH-tHW-tHW
homologous
IL_6CZR_121
NA
IL_9SS1_0131/D1/203:206,
1/D1/213:214		No text annotation
geometric
IL_9E6Q_071
IL_87975.1
IL_9SS1_0141/D1/242:247,
1/D1/277:284		Kink-turn with non-sequential stacking
homologous
IL_6CZR_123
NA
IL_9SS1_0151/D1/249:252,
1/D1/274:275		No text annotation
homologous
IL_6CZR_405
NA
IL_9SS1_0161/D1/292:293,
1/D1/304:308		C-loop
homologous
IL_6CZR_125
NA
IL_9SS1_0171/D1/367:369,
1/D1/392:393		Single bulged U
homologous
IL_6CZR_126
NA
IL_9SS1_0181/D1/371:375,
1/D1/389:390		C-loop
homologous
IL_6CZR_127
NA
IL_9SS1_0191/D1/375:376,
1/D1/387:389		Single bulged G
homologous
IL_6CZR_358
NA
IL_9SS1_0201/D1/409:416,
1/D1/427:433		No text annotation
geometric
IL_8B0X_019
IL_62329.1
IL_9SS1_0211/D1/440:442,
1/D1/492:497		No text annotation
geometric
IL_8B0X_020
IL_02111.1
IL_9SS1_0221/D1/446:450,
1/D1/483:488		tWW-tWH-tHS
geometric
IL_8B0X_021
IL_82100.1
IL_9SS1_0231/D1/450:455,
1/D1/477:483		No text annotation
homologous
IL_6CZR_406
NA
IL_9SS1_0241/D1/504:511,
1/D1/540:541		SSU/LSU pseudoknot
homologous
IL_6CZR_132
NA
IL_9SS1_0251/D1/515:521,
1/D1/528:536		Kink-turn related
homologous
IL_6CZR_133
NA
IL_9SS1_0261/D1/569:575,
1/D1/880:881		No text annotation
homologous
IL_6CZR_134
NA
IL_9SS1_0271/D1/580:584,
1/D1/757:761		tSH-tWH-tHS
homologous
IL_6CZR_135
NA
IL_9SS1_0281/D1/594:596,
1/D1/644:645		Major groove platform
homologous
IL_6CZR_407
NA
IL_9SS1_0291/D1/597:598,
1/D1/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_6CZR_137
NA
IL_9SS1_0301/D1/605:612,
1/D1/628:633		No text annotation
homologous
IL_6CZR_408
NA
IL_9SS1_0311/D1/654:655,
1/D1/751:754		Major groove platform; stack outside cWW
geometric
IL_4LFB_027
IL_74641.3
IL_9SS1_0321/D1/659:660,
1/D1/745:747		Single stack bend
geometric
IL_7A0S_054
IL_15011.4
IL_9SS1_0331/D1/662:666,
1/D1/740:743		Tandem non-canonical cWW pairs
homologous
IL_6CZR_141
NA
IL_9SS1_0341/D1/673:678,
1/D1/712:717		No text annotation
IL_9SS1_0351/D1/684:688,
1/D1/699:706		Kink-turn
geometric
IL_8B0X_034
IL_71972.2
IL_9SS1_0361/D1/774:778,
1/D1/804:805		Left turn
homologous
IL_6CZR_144
NA
IL_9SS1_0371/D1/779:783,
1/D1/799:803		tSH-tWH-tHS
homologous
IL_6CZR_145
NA
IL_9SS1_0381/D1/887:894,
1/D1/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_6CZR_364
NA
IL_9SS1_0391/D1/922:923,
1/D1/1393:1395		Single bulged A
homologous
IL_6CZR_147
NA
IL_9SS1_0401/D1/925:927,
1/D1/1390:1391		Single bulged G
homologous
IL_6CZR_148
NA
IL_9SS1_0411/D1/933:935,
1/D1/1380:1384		No text annotation
homologous
IL_6CZR_410
NA
IL_9SS1_0481/D1/1247:1253,
1/D1/1284:1290		No text annotation
homologous
IL_6CZR_160
NA
IL_9SS1_0521/D1/1399:1401,
1/D1/1501:1504		No text annotation
homologous
IL_6CZR_165
NA
IL_9SS1_0531/D1/1401:1404,
1/D1/1497:1501		No text annotation
geometric
IL_8CRE_467
IL_25873.3
IL_9SS1_0541/D1/1405:1407,
1/D1/1494:1496		Isolated non-canonical cWW pair
geometric
IL_1U9S_007
IL_01003.5
IL_9SS1_0551/D1/1407:1409,
1/D1/1491:1494		Single bulged A
geometric
IL_8UO6_002
IL_53541.1
IL_9SS1_0561/D1/1412:1414,
1/D1/1486:1488		Isolated non-canonical cWW pair
homologous
IL_6CZR_411
NA
IL_9SS1_0571/D1/1416:1419,
1/D1/1481:1484		Double sheared
homologous
IL_6CZR_169
NA
IL_9SS1_0581/D1/1430:1435,
1/D1/1466:1470		No text annotation
geometric
IL_8B0X_062
IL_47352.3
IL_9SS1_0591/D1/1440:1442,
1/D1/1460:1461		No text annotation
geometric
IL_9E6Q_055
IL_34520.4
IL_9SS1_0601/D1/1445:1448,
1/D1/1455:1457		No text annotation
geometric
IL_4WF9_107
IL_05502.1

Problematic loops

#loop idProblemSequence
IL_9SS1_042No text annotation
IL_9SS1_043No text annotation
IL_9SS1_044Single stack bend
IL_9SS1_045Single stack bend
IL_9SS1_046No text annotation
IL_9SS1_047No text annotation
IL_9SS1_049No text annotation
IL_9SS1_050No text annotation
IL_9SS1_051No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9SS1_0011/D1/46:47,
1/D1/361:367,
1/D1/393:395		No text annotation
geometric
J3_8B0X_001
J3_58657.2
J3_9SS1_0021/D1/46:52,
1/D1/359:367,
1/D1/393:395		No text annotation
homologous
J3_6CZR_058
NA
J3_9SS1_0031/D1/586:588,
1/D1/651:654,
1/D1/754:755		No text annotation
geometric
J3_8B0X_002
J3_01633.2
J3_9SS1_0041/D1/586:588,
1/D1/651:655,
1/D1/751:755		No text annotation
homologous
J3_6CZR_077
NA
J3_9SS1_0051/D1/672:673,
1/D1/717:725,
1/D1/732:734		No text annotation
homologous
J3_6CZR_017
NA
J3_9SS1_0061/D1/826:829,
1/D1/857:861,
1/D1/868:874		No text annotation
homologous
J3_6CZR_018
NA
J3_9SS1_0071/D1/936:939,
1/D1/1344:1350,
1/D1/1372:1379		No text annotation
homologous
J3_6CZR_061
NA
J3_9SS1_0121/D1/1073:1074,
1/D1/1083:1086,
1/D1/1099:1102		No text annotation
homologous
J3_6CZR_079
NA
J3_9SS1_0131/D1/1116:1118,
1/D1/1155:1158,
1/D1/1181:1184		No text annotation
geometric
J3_8B0X_012
J3_82365.6
J3_9SS1_0141/D1/1116:1118,
1/D1/1155:1161,
1/D1/1175:1184		No text annotation
homologous
J3_6CZR_025
NA
J4_9SS1_0011/D1/115:122,
1/D1/239:240,
1/D1/286:289,
1/D1/311:312		No text annotation
homologous
J4_6CZR_027
NA
J4_9SS1_0021/D1/142:144,
1/D1/178:184,
1/D1/193:198,
1/D1/219:221		No text annotation
J4_9SS1_0031/D1/575:577,
1/D1/764:769,
1/D1/810:821,
1/D1/879:880		No text annotation
homologous
J4_6CZR_013
NA
J5_9SS1_0011/D1/36:39,
1/D1/403:406,
1/D1/436:440,
1/D1/497:500,
1/D1/545:548		No text annotation
J5_9SS1_0021/D1/36:39,
1/D1/403:406,
1/D1/436:442,
1/D1/492:500,
1/D1/545:548		No text annotation
J5_9SS1_0031/D1/58:61,
1/D1/106:113,
1/D1/314:316,
1/D1/337:339,
1/D1/350:354		No text annotation
homologous
J5_6CZR_021
NA

Problematic loops

#loop idProblemSequence
J3_9SS1_008No text annotation
J3_9SS1_009No text annotation
J3_9SS1_010No text annotation
J3_9SS1_011No text annotation
J3_9SS1_015No text annotation

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