RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9KMX_0011/2/7:17No text annotation
homologous
HL_9H3G_079
HL_73535.4
HL_9KMX_0021/2/69:80No text annotation
HL_9KMX_0031/2/156:162No text annotation
homologous
HL_9PN5_079
HL_34789.7
HL_9KMX_0051/2/288:295No text annotation
homologous
HL_9PN5_082
HL_67772.4
HL_9KMX_0061/2/377:387No text annotation
geometric
HL_8GLP_091
HL_50525.1
HL_9KMX_0071/2/414:423No text annotation
HL_9KMX_0081/2/441:452No text annotation
homologous
HL_9PN5_086
HL_86432.4
HL_9KMX_0091/2/462:467No text annotation
homologous
HL_9H3G_087
HL_61337.7
HL_9KMX_0101/2/498:504No text annotation
homologous
HL_9H3G_088
HL_25795.2
HL_9KMX_0121/2/569:581No text annotation
HL_9KMX_0131/2/618:623No text annotation
homologous
HL_9PN5_091
HL_34789.7
HL_9KMX_0141/2/820:828No text annotation
homologous
HL_9PN5_092
HL_11974.5
HL_9KMX_0161/2/957:966No text annotation
HL_9KMX_0171/2/994:999No text annotation
homologous
HL_9H3G_094
HL_34789.7
HL_9KMX_0181/2/1054:1064No text annotation
HL_9KMX_0191/2/1113:1120No text annotation
HL_9KMX_0201/2/1141:1146No text annotation
homologous
HL_9H3G_097
HL_34789.7
HL_9KMX_0211/2/1178:1183No text annotation
homologous
HL_9PN5_100
HL_34789.7
HL_9KMX_0221/2/1245:1254No text annotation
homologous
HL_9PN5_101
HL_97521.4
HL_9KMX_0241/2/1353:1358No text annotation
homologous
HL_9H3G_101
HL_34789.7
HL_9KMX_0251/2/1366:1373No text annotation
homologous
HL_9H3G_102
HL_63894.5
HL_9KMX_0261/2/1460:1466No text annotation
geometric
HL_9AXU_017
HL_37569.4
HL_9KMX_0281/2/1613:1626No text annotation
HL_9KMX_0291/2/1658:1666No text annotation
HL_9KMX_0301/2/1847:1852No text annotation
homologous
HL_9PN5_111
HL_34789.7

Problematic loops

#loop idProblemSequence
HL_9KMX_004No text annotation
HL_9KMX_011No text annotation
HL_9KMX_015No text annotation
HL_9KMX_023No text annotation
HL_9KMX_027No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9KMX_0011/2/23:25,
1/2/649:651		Isolated non-canonical cWW pair
geometric
IL_9PN5_105
IL_01003.7
IL_9KMX_0021/2/37:40,
1/2/514:518		No text annotation
IL_9KMX_0031/2/41:47,
1/2/479:481		No text annotation
geometric
IL_8GLP_191
IL_88082.5
IL_9KMX_0041/2/49:51,
1/2/476:477		Minor groove platform
homologous
IL_9PN5_146
IL_26092.1
IL_9KMX_0051/2/57:62,
1/2/86:88		No text annotation
homologous
IL_9PN5_147
IL_61299.9
IL_9KMX_0061/2/63:68,
1/2/81:85		No text annotation
homologous
IL_9PN5_148
IL_21667.4
IL_9KMX_0071/2/108:110,
1/2/351:353		Stack and bulge
geometric
IL_8VFS_003
IL_53541.1
IL_9KMX_0081/2/110:112,
1/2/349:351		Isolated non-canonical cWW pair
geometric
IL_8GLP_197
IL_01003.7
IL_9KMX_0091/2/112:115,
1/2/348:349		No text annotation
homologous
IL_9H3G_163
IL_71421.6
IL_9KMX_0101/2/116:121,
1/2/343:347		No text annotation
IL_9KMX_0111/2/145:151,
1/2/167:174		No text annotation
homologous
IL_9H3G_165
IL_24485.3
IL_9KMX_0121/2/152:154,
1/2/164:166		Isolated cWH basepair
homologous
IL_9PN5_153
IL_10892.5
IL_9KMX_0141/2/359:364,
1/2/396:403		Kink-turn with non-sequential stacking
homologous
IL_9PN5_159
IL_46174.7
IL_9KMX_0151/2/366:371,
1/2/393:394		No text annotation
homologous
IL_9PN5_160
IL_01372.4
IL_9KMX_0161/2/411:413,
1/2/424:429		No text annotation
homologous
IL_9H3G_175
IL_93336.4
IL_9KMX_0171/2/437:439,
1/2/454:456		Isolated cWH basepair
homologous
IL_9PN5_162
IL_10892.5
IL_9KMX_0181/2/459:461,
1/2/468:470		Isolated non-canonical cWW pair
homologous
IL_9PN5_163
IL_19025.1
IL_9KMX_0191/2/491:495,
1/2/508:509		No text annotation
homologous
IL_9PN5_165
IL_26900.4
IL_9KMX_0201/2/495:496,
1/2/506:508		Single bulged G
homologous
IL_9PN5_166
IL_28408.5
IL_9KMX_0211/2/527:534,
1/2/550:558		No text annotation
IL_9KMX_0221/2/534:539,
1/2/544:550		No text annotation
IL_9KMX_0231/2/563:565,
1/2/585:592		No text annotation
homologous
IL_9H3G_182
IL_02511.3
IL_9KMX_0241/2/566:569,
1/2/581:584		No text annotation
geometric
IL_9H3G_166
IL_37443.2
IL_9KMX_0251/2/599:606,
1/2/636:637		No text annotation
homologous
IL_9H3G_185
IL_11411.4
IL_9KMX_0261/2/606:608,
1/2/635:636		Single bulged U
homologous
IL_9PN5_172
IL_97561.8
IL_9KMX_0271/2/611:617,
1/2/624:632		Kink-turn related
homologous
IL_9PN5_173
IL_52042.4
IL_9KMX_0281/2/663:665,
1/2/1162:1164		Isolated non-canonical cWW pair
homologous
IL_9H3G_188
IL_19025.1
IL_9KMX_0291/2/665:671,
1/2/1161:1162		No text annotation
homologous
IL_9H3G_189
IL_20847.4
IL_9KMX_0301/2/673:675,
1/2/1030:1032		Isolated non-canonical cWW pair
homologous
IL_9H3G_190
IL_01003.7
IL_9KMX_0311/2/676:680,
1/2/1025:1029		No text annotation
homologous
IL_9H3G_191
IL_05821.4
IL_9KMX_0321/2/807:815,
1/2/849:856		No text annotation
homologous
IL_9H3G_194
IL_59049.5
IL_9KMX_0351/2/922:923,
1/2/1019:1022		Major groove platform; stack outside cWW
homologous
IL_9PN5_182
IL_74641.5
IL_9KMX_0361/2/925:926,
1/2/1015:1017		Single bulged U
geometric
IL_6UFH_004
IL_97561.8
IL_9KMX_0371/2/928:931,
1/2/1010:1013		Tandem non-canonical cWW pairs
homologous
IL_9PN5_184
IL_15225.5
IL_9KMX_0381/2/931:935,
1/2/1007:1010		Tandem non-canonical cWW pairs
homologous
IL_9PN5_185
IL_15225.5
IL_9KMX_0391/2/942:945,
1/2/981:984		Tandem non-canonical cWW pairs
homologous
IL_9PN5_186
IL_15225.5
IL_9KMX_0401/2/952:957,
1/2/966:974		No text annotation
IL_9KMX_0411/2/1042:1047,
1/2/1071:1073		No text annotation
homologous
IL_9H3G_203
IL_31690.2
IL_9KMX_0421/2/1047:1051,
1/2/1067:1071		No text annotation
homologous
IL_9H3G_204
IL_05821.4
IL_9KMX_0431/2/1091:1093,
1/2/1152:1158		No text annotation
homologous
IL_9H3G_205
IL_82706.5
IL_9KMX_0441/2/1098:1101,
1/2/1131:1134		Tandem non-canonical cWW pairs
homologous
IL_9PN5_192
IL_15225.5
IL_9KMX_0451/2/1101:1103,
1/2/1129:1131		Isolated cWH basepair
geometric
IL_8GLP_245
IL_10892.5
IL_9KMX_0461/2/1108:1110,
1/2/1123:1124		Minor groove platform
geometric
IL_8GLP_246
IL_26092.1
IL_9KMX_0471/2/1168:1175,
1/2/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_9PN5_194
IL_84044.4
IL_9KMX_0481/2/1203:1204,
1/2/1694:1696		Single bulged A
homologous
IL_9PN5_195
IL_14190.5
IL_9KMX_0491/2/1206:1208,
1/2/1691:1692		Single bulged G
homologous
IL_9PN5_196
IL_28408.5
IL_9KMX_0501/2/1214:1217,
1/2/1681:1685		No text annotation
homologous
IL_9H3G_212
IL_63596.15
IL_9KMX_0511/2/1333:1335,
1/2/1492:1498		No text annotation
homologous
IL_9H3G_221
IL_09439.2
IL_9KMX_0521/2/1337:1338,
1/2/1488:1490		Single bulged A
homologous
IL_9H3G_222
IL_14190.5
IL_9KMX_0531/2/1347:1349,
1/2/1380:1382		Isolated cWH basepair
homologous
IL_9H3G_223
IL_10892.5
IL_9KMX_0541/2/1363:1365,
1/2/1374:1375		Minor groove platform
homologous
IL_9PN5_211
IL_37129.1
IL_9KMX_0551/2/1395:1400,
1/2/1446:1450		No text annotation
IL_9KMX_0561/2/1550:1558,
1/2/1577:1582		No text annotation
IL_9KMX_0571/2/1560:1562,
1/2/1573:1575		No text annotation
homologous
IL_9H3G_231
IL_81485.1
IL_9KMX_0581/2/1604:1610,
1/2/1629:1635		No text annotation
IL_9KMX_0591/2/1700:1702,
1/2/1833:1836		No text annotation
homologous
IL_9PN5_220
IL_18228.4
IL_9KMX_0601/2/1702:1731,
1/2/1803:1833		No text annotation
IL_9KMX_0611/2/1732:1736,
1/2/1798:1802		No text annotation
homologous
IL_9PN5_228
IL_87767.5

Problematic loops

#loop idProblemSequence
IL_9KMX_013No text annotation
IL_9KMX_033No text annotation
IL_9KMX_034No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9KMX_0011/2/40:41,
1/2/481:489,
1/2/511:514		No text annotation
J3_9KMX_0021/2/40:47,
1/2/479:489,
1/2/511:514		No text annotation
J3_9KMX_0031/2/938:941,
1/2/985:993,
1/2/1000:1004		No text annotation
homologous
J3_9PN5_033
NA
J3_9KMX_0041/2/1218:1221,
1/2/1646:1651,
1/2/1673:1680		No text annotation
J3_9KMX_0051/2/1233:1245,
1/2/1254:1267,
1/2/1515:1525		No text annotation
J3_9KMX_0061/2/1267:1277,
1/2/1320:1333,
1/2/1498:1515		No text annotation
J3_9KMX_0071/2/1267:1277,
1/2/1320:1335,
1/2/1492:1515		No text annotation
J3_9KMX_0081/2/1338:1345,
1/2/1384:1390,
1/2/1480:1488		No text annotation
J3_9KMX_0091/2/1350:1351,
1/2/1360:1363,
1/2/1375:1379		No text annotation
homologous
J3_9H3G_040
J3_76043.7
J3_9KMX_0101/2/1390:1395,
1/2/1450:1456,
1/2/1470:1480		No text annotation
J4_9KMX_0011/2/98:106,
1/2/355:357,
1/2/405:409,
1/2/431:432		No text annotation
homologous
J4_9PN5_010
J4_15241.5
J4_9KMX_0021/2/671:673,
1/2/1032:1037,
1/2/1078:1089,
1/2/1160:1161		No text annotation
homologous
J4_9H3G_014
J4_14595.4
J5_9KMX_0011/2/30:36,
1/2/519:527,
1/2/558:563,
1/2/592:595,
1/2/641:644		No text annotation
J5_9KMX_0021/2/30:36,
1/2/519:527,
1/2/558:565,
1/2/585:595,
1/2/641:644		No text annotation
J5_9KMX_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_9PN5_009
J5_58574.4

Problematic loops

No problematic loops


Coloring options:
Copyright 2026 BGSU RNA group. Database contents are licensed under Creative Commons Attribution 4.0 International (CC BY 4.0). Page generated in 0.0411 s