RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9KMZ_0011/2/7:17No text annotation
homologous
HL_9H3G_079
HL_73535.4
HL_9KMZ_0021/2/69:80No text annotation
HL_9KMZ_0031/2/156:162No text annotation
homologous
HL_9PN5_079
HL_34789.7
HL_9KMZ_0051/2/288:295No text annotation
homologous
HL_9PN5_082
HL_67772.4
HL_9KMZ_0061/2/377:387No text annotation
geometric
HL_8GLP_091
HL_50525.1
HL_9KMZ_0071/2/416:421No text annotation
homologous
HL_9PN5_085
HL_34789.7
HL_9KMZ_0081/2/441:452No text annotation
homologous
HL_9PN5_086
HL_86432.4
HL_9KMZ_0091/2/462:467No text annotation
homologous
HL_9H3G_087
HL_61337.7
HL_9KMZ_0101/2/498:504No text annotation
homologous
HL_9H3G_088
HL_25795.2
HL_9KMZ_0121/2/569:581No text annotation
homologous
HL_9PN5_090
HL_68749.4
HL_9KMZ_0131/2/618:623No text annotation
homologous
HL_9PN5_091
HL_34789.7
HL_9KMZ_0141/2/820:828No text annotation
homologous
HL_9PN5_092
HL_11974.5
HL_9KMZ_0161/2/957:966No text annotation
homologous
HL_9H3G_093
HL_38491.5
HL_9KMZ_0171/2/994:999No text annotation
homologous
HL_9H3G_094
HL_34789.7
HL_9KMZ_0181/2/1054:1064No text annotation
homologous
HL_9H3G_095
HL_38491.5
HL_9KMZ_0191/2/1113:1120No text annotation
HL_9KMZ_0201/2/1141:1146No text annotation
homologous
HL_9H3G_097
HL_34789.7
HL_9KMZ_0211/2/1178:1183No text annotation
homologous
HL_9PN5_100
HL_34789.7
HL_9KMZ_0221/2/1281:1316No text annotation
HL_9KMZ_0231/2/1353:1358No text annotation
homologous
HL_9H3G_101
HL_34789.7
HL_9KMZ_0241/2/1366:1373No text annotation
homologous
HL_9H3G_102
HL_63894.5
HL_9KMZ_0251/2/1460:1466No text annotation
geometric
HL_8CRE_221
HL_76371.5
HL_9KMZ_0261/2/1565:1570No text annotation
HL_9KMZ_0271/2/1613:1626No text annotation
HL_9KMZ_0281/2/1658:1666No text annotation
homologous
HL_9PN5_109
HL_25307.3
HL_9KMZ_0291/2/1847:1852No text annotation
homologous
HL_9PN5_111
HL_34789.7

Problematic loops

#loop idProblemSequence
HL_9KMZ_004No text annotation
HL_9KMZ_011No text annotation
HL_9KMZ_015No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9KMZ_0011/2/23:25,
1/2/649:651		Isolated non-canonical cWW pair
geometric
IL_8GLP_149
IL_01003.7
IL_9KMZ_0021/2/34:36,
1/2/519:521		Isolated non-canonical cWW pair
homologous
IL_9PN5_143
IL_01003.7
IL_9KMZ_0031/2/37:40,
1/2/514:518		Double sheared
geometric
IL_8GLP_190
IL_58355.5
IL_9KMZ_0041/2/41:47,
1/2/479:481		No text annotation
geometric
IL_8GLP_191
IL_88082.5
IL_9KMZ_0051/2/49:51,
1/2/476:477		Minor groove platform
homologous
IL_9H3G_159
IL_26092.1
IL_9KMZ_0061/2/57:62,
1/2/86:88		No text annotation
homologous
IL_9PN5_147
IL_61299.9
IL_9KMZ_0071/2/63:68,
1/2/81:85		No text annotation
homologous
IL_9PN5_148
IL_21667.4
IL_9KMZ_0081/2/108:110,
1/2/351:353		Isolated non-canonical cWW pair
geometric
IL_1T0E_002
IL_71625.6
IL_9KMZ_0091/2/110:112,
1/2/349:351		Isolated non-canonical cWW pair
geometric
IL_8GLP_197
IL_01003.7
IL_9KMZ_0101/2/112:115,
1/2/348:349		No text annotation
homologous
IL_9H3G_163
IL_71421.6
IL_9KMZ_0111/2/116:121,
1/2/343:347		No text annotation
homologous
IL_9PN5_151
IL_31545.4
IL_9KMZ_0121/2/145:151,
1/2/167:174		No text annotation
homologous
IL_9H3G_165
IL_24485.3
IL_9KMZ_0131/2/152:154,
1/2/164:166		Isolated cWH basepair
homologous
IL_9PN5_153
IL_10892.5
IL_9KMZ_0141/2/188:192,
1/2/207:211		No text annotation
geometric
IL_8GLP_204
IL_87767.5
IL_9KMZ_0151/2/216:219,
1/2/302:309		No text annotation
IL_9KMZ_0161/2/312:314,
1/2/336:337		Single bulged A
homologous
IL_9H3G_171
IL_14190.5
IL_9KMZ_0171/2/317:319,
1/2/332:333		Single stack bend
geometric
IL_9H3G_071
IL_15011.6
IL_9KMZ_0181/2/359:364,
1/2/396:403		Kink-turn with non-sequential stacking
homologous
IL_9PN5_159
IL_46174.7
IL_9KMZ_0191/2/366:371,
1/2/393:394		No text annotation
homologous
IL_9H3G_174
IL_01372.4
IL_9KMZ_0201/2/411:413,
1/2/424:429		No text annotation
homologous
IL_9H3G_175
IL_93336.4
IL_9KMZ_0211/2/437:439,
1/2/454:456		Isolated cWH basepair
homologous
IL_9PN5_162
IL_10892.5
IL_9KMZ_0221/2/459:461,
1/2/468:470		Isolated non-canonical cWW pair
homologous
IL_9PN5_163
IL_19025.1
IL_9KMZ_0231/2/487:489,
1/2/511:512		Single bulged U
homologous
IL_9PN5_164
IL_97561.8
IL_9KMZ_0241/2/491:495,
1/2/508:509		No text annotation
homologous
IL_9PN5_165
IL_26900.4
IL_9KMZ_0251/2/495:496,
1/2/506:508		Single bulged G
homologous
IL_9H3G_180
IL_28408.5
IL_9KMZ_0261/2/529:532,
1/2/552:556		No text annotation
IL_9KMZ_0271/2/534:539,
1/2/544:550		No text annotation
IL_9KMZ_0281/2/563:565,
1/2/585:592		No text annotation
homologous
IL_9PN5_168
IL_02511.3
IL_9KMZ_0291/2/566:569,
1/2/581:584		Tandem non-canonical cWW pairs
geometric
IL_4WF9_110
IL_39691.1
IL_9KMZ_0301/2/599:606,
1/2/636:637		No text annotation
homologous
IL_9H3G_185
IL_11411.4
IL_9KMZ_0311/2/606:608,
1/2/635:636		Single bulged U
homologous
IL_9PN5_172
IL_97561.8
IL_9KMZ_0321/2/611:617,
1/2/624:632		Kink-turn related
homologous
IL_9PN5_173
IL_52042.4
IL_9KMZ_0331/2/663:665,
1/2/1162:1164		Isolated non-canonical cWW pair
homologous
IL_9H3G_188
IL_19025.1
IL_9KMZ_0341/2/665:671,
1/2/1161:1162		No text annotation
homologous
IL_9H3G_189
IL_20847.4
IL_9KMZ_0351/2/673:675,
1/2/1030:1032		Isolated non-canonical cWW pair
homologous
IL_9PN5_175
IL_01003.7
IL_9KMZ_0361/2/676:680,
1/2/1025:1029		No text annotation
homologous
IL_9H3G_191
IL_05821.4
IL_9KMZ_0371/2/802:803,
1/2/860:863		No text annotation
homologous
IL_9H3G_192
IL_73108.5
IL_9KMZ_0381/2/805:807,
1/2/856:858		Isolated non-canonical cWW pair
homologous
IL_9PN5_179
IL_71625.6
IL_9KMZ_0391/2/807:815,
1/2/849:856		No text annotation
homologous
IL_9H3G_194
IL_59049.5
IL_9KMZ_0401/2/874:876,
1/2/910:912		No text annotation
geometric
IL_9H3G_152
IL_81485.1
IL_9KMZ_0421/2/925:927,
1/2/1014:1017		Isolated non-canonical cWW pair
homologous
IL_9PN5_183
IL_01003.7
IL_9KMZ_0431/2/928:931,
1/2/1010:1013		Tandem non-canonical cWW pairs
homologous
IL_9H3G_199
IL_15225.5
IL_9KMZ_0441/2/931:935,
1/2/1007:1010		Tandem non-canonical cWW pairs
homologous
IL_9PN5_185
IL_15225.5
IL_9KMZ_0451/2/942:945,
1/2/981:984		Tandem non-canonical cWW pairs
homologous
IL_9PN5_186
IL_15225.5
IL_9KMZ_0461/2/952:956,
1/2/967:974		Kink-turn
geometric
IL_8GLP_240
IL_71972.2
IL_9KMZ_0471/2/1042:1047,
1/2/1071:1073		No text annotation
homologous
IL_9PN5_189
IL_31690.2
IL_9KMZ_0481/2/1047:1051,
1/2/1067:1071		No text annotation
homologous
IL_9H3G_204
IL_05821.4
IL_9KMZ_0491/2/1091:1093,
1/2/1152:1158		No text annotation
homologous
IL_9H3G_205
IL_82706.5
IL_9KMZ_0501/2/1098:1101,
1/2/1131:1134		Tandem non-canonical cWW pairs
homologous
IL_9PN5_192
IL_15225.5
IL_9KMZ_0511/2/1101:1103,
1/2/1129:1131		Isolated cWH basepair
geometric
IL_8GLP_245
IL_10892.5
IL_9KMZ_0521/2/1108:1110,
1/2/1123:1124		Minor groove platform
geometric
IL_8GLP_246
IL_26092.1
IL_9KMZ_0531/2/1168:1175,
1/2/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_9PN5_194
IL_84044.4
IL_9KMZ_0541/2/1203:1204,
1/2/1694:1696		Single bulged A
homologous
IL_9H3G_210
IL_14190.5
IL_9KMZ_0551/2/1206:1208,
1/2/1691:1692		Single bulged G
homologous
IL_9PN5_196
IL_28408.5
IL_9KMZ_0561/2/1214:1217,
1/2/1681:1685		No text annotation
homologous
IL_9H3G_212
IL_63596.15
IL_9KMZ_0581/2/1236:1272,
1/2/1510:1521		No text annotation
IL_9KMZ_0601/2/1329:1332,
1/2/1499:1500		Multiple bulged bases
geometric
IL_9DID_004
IL_71421.6
IL_9KMZ_0611/2/1333:1335,
1/2/1492:1498		No text annotation
homologous
IL_9H3G_221
IL_09439.2
IL_9KMZ_0621/2/1337:1338,
1/2/1488:1490		Single bulged A
homologous
IL_9H3G_222
IL_14190.5
IL_9KMZ_0631/2/1347:1349,
1/2/1380:1382		Isolated cWH basepair
homologous
IL_9H3G_223
IL_10892.5
IL_9KMZ_0641/2/1363:1365,
1/2/1374:1375		Minor groove platform
homologous
IL_9H3G_224
IL_37129.1
IL_9KMZ_0651/2/1395:1399,
1/2/1447:1450		No text annotation
IL_9KMZ_0671/2/1536:1550,
1/2/1582:1597		No text annotation
IL_9KMZ_0681/2/1550:1558,
1/2/1577:1582		No text annotation
IL_9KMZ_0691/2/1560:1562,
1/2/1573:1575		No text annotation
homologous
IL_9H3G_231
IL_81485.1
IL_9KMZ_0711/2/1700:1702,
1/2/1833:1836		No text annotation
homologous
IL_9PN5_220
IL_18228.4
IL_9KMZ_0721/2/1702:1705,
1/2/1829:1833		No text annotation
homologous
IL_9PN5_221
IL_25873.5
IL_9KMZ_0731/2/1706:1708,
1/2/1826:1828		Isolated non-canonical cWW pair
homologous
IL_9PN5_222
IL_01003.7
IL_9KMZ_0741/2/1708:1711,
1/2/1822:1826		No text annotation
homologous
IL_9PN5_223
IL_37443.2
IL_9KMZ_0751/2/1714:1716,
1/2/1817:1819		Isolated non-canonical cWW pair
homologous
IL_9PN5_224
IL_01003.7
IL_9KMZ_0761/2/1717:1723,
1/2/1811:1816		No text annotation
IL_9KMZ_0771/2/1729:1731,
1/2/1803:1805		No text annotation
homologous
IL_9PN5_227
IL_55553.3
IL_9KMZ_0781/2/1733:1736,
1/2/1798:1801		Double sheared
homologous
IL_9H3G_241
IL_58355.5
IL_9KMZ_0791/2/1739:1741,
1/2/1793:1795		Isolated non-canonical cWW pair
geometric
IL_3SZX_002
IL_71625.6
IL_9KMZ_0801/2/1742:1746,
1/2/1788:1792		No text annotation
homologous
IL_9PN5_231
IL_15190.5
IL_9KMZ_0811/2/1750:1751,
1/2/1782:1784		Single bulged C
geometric
IL_6ZDP_001
IL_05642.6

Problematic loops

#loop idProblemSequence
IL_9KMZ_041No text annotation
IL_9KMZ_057No text annotation
IL_9KMZ_059No text annotation
IL_9KMZ_066No text annotation
IL_9KMZ_070No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9KMZ_0011/2/40:41,
1/2/481:487,
1/2/512:514		No text annotation
geometric
J3_8CRE_071
J3_58657.4
J3_9KMZ_0021/2/40:47,
1/2/479:487,
1/2/512:514		No text annotation
homologous
J3_9H3G_029
J3_63856.4
J3_9KMZ_0031/2/816:819,
1/2/829:831,
1/2/843:848		No text annotation
homologous
J3_9H3G_032
J3_97642.5
J3_9KMZ_0041/2/938:941,
1/2/985:993,
1/2/1000:1004		No text annotation
J3_9KMZ_0051/2/1094:1097,
1/2/1135:1140,
1/2/1147:1151		No text annotation
J3_9KMZ_0061/2/1218:1221,
1/2/1645:1654,
1/2/1670:1680		No text annotation
J3_9KMZ_0071/2/1272:1277,
1/2/1320:1327,
1/2/1502:1510		No text annotation
J3_9KMZ_0081/2/1340:1345,
1/2/1384:1389,
1/2/1481:1486		No text annotation
homologous
J3_9PN5_039
NA
J3_9KMZ_0091/2/1350:1351,
1/2/1360:1363,
1/2/1375:1379		No text annotation
homologous
J3_9PN5_040
J3_76043.7
J3_9KMZ_0101/2/1391:1395,
1/2/1450:1456,
1/2/1470:1479		No text annotation
J4_9KMZ_0011/2/98:106,
1/2/355:357,
1/2/405:409,
1/2/431:432		No text annotation
homologous
J4_9H3G_013
J4_15241.5
J4_9KMZ_0021/2/671:673,
1/2/1032:1037,
1/2/1078:1089,
1/2/1160:1161		No text annotation
homologous
J4_9PN5_011
J4_14595.4
J4_9KMZ_0031/2/1225:1230,
1/2/1528:1536,
1/2/1597:1604,
1/2/1635:1641		No text annotation
J5_9KMZ_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_9H3G_007
J5_04786.3
J5_9KMZ_0021/2/30:34,
1/2/521:527,
1/2/558:565,
1/2/585:595,
1/2/641:644		No text annotation
J5_9KMZ_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
J5_9KMZ_0041/2/123:130,
1/2/182:185,
1/2/214:215,
1/2/310:312,
1/2/337:341		No text annotation

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 0.0514 s