RNA 3D Hub //

9N77 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9N77_0011/L0/4:9GNRA related
geometric
HL_8G9Z_003
HL_37569.4
HL_9N77_0021/L1/8:16Pseudoknot geometry
geometric
HL_3DIL_002
HL_52651.5
HL_9N77_0031/L1/70:81No text annotation
HL_9N77_0041/L1/154:160No text annotation
homologous
HL_9PN5_079
HL_34789.7
HL_9N77_0071/L1/243:250No text annotation
homologous
HL_9PN5_082
HL_67772.4
HL_9N77_0091/L1/330:338No text annotation
homologous
HL_9PN5_084
HL_87268.5
HL_9N77_0101/L1/368:373No text annotation
homologous
HL_9PN5_085
HL_34789.7
HL_9N77_0111/L1/393:404No text annotation
homologous
HL_9PN5_086
HL_86432.4
HL_9N77_0121/L1/414:419No text annotation
homologous
HL_9H3G_087
HL_61337.7
HL_9N77_0131/L1/450:456No text annotation
homologous
HL_9PN5_088
HL_25795.2
HL_9N77_0141/L1/491:496GNRA
geometric
HL_9DFE_033
HL_34789.7
HL_9N77_0151/L1/520:532No text annotation
homologous
HL_9PN5_090
HL_68749.4
HL_9N77_0161/L1/561:566No text annotation
HL_9N77_0171/L1/764:772No text annotation
homologous
HL_9PN5_092
HL_11974.5
HL_9N77_0191/L1/937:942No text annotation
homologous
HL_9PN5_096
HL_34789.7
HL_9N77_0211/L1/1055:1064Anticodon loop related
geometric
HL_5T83_002
HL_81376.5
HL_9N77_0221/L1/1084:1089No text annotation
homologous
HL_9PN5_099
HL_34789.7
HL_9N77_0251/L1/1594:1602No text annotation
HL_9N77_0261/L1/1629:1636No text annotation
geometric
HL_8K1E_001
HL_97725.1

Problematic loops

#loop idProblemSequence
HL_9N77_005UNCG variation
HL_9N77_006No text annotation
HL_9N77_008No text annotation
HL_9N77_018No text annotation
HL_9N77_020No text annotation
HL_9N77_023No text annotation
HL_9N77_024No text annotation
HL_9N77_027Mini UNCG
HL_9N77_028No text annotation
HL_9N77_029No text annotation
HL_9N77_030No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9N77_0021/L1/37:41,
1/L1/466:471		No text annotation
IL_9N77_0031/L1/50:52,
1/L1/428:429		Minor groove platform
homologous
IL_9PN5_146
IL_26092.1
IL_9N77_0041/L1/58:63,
1/L1/87:89		No text annotation
homologous
IL_9PN5_147
IL_61299.9
IL_9N77_0051/L1/64:69,
1/L1/82:86		No text annotation
homologous
IL_9PN5_148
IL_21667.4
IL_9N77_0061/L1/109:112,
1/L1/302:305		Tandem non-canonical cWW pairs
homologous
IL_9PN5_149
IL_71194.5
IL_9N77_0071/L1/113:116,
1/L1/300:301		No text annotation
homologous
IL_9PN5_150
IL_71421.6
IL_9N77_0081/L1/117:122,
1/L1/295:299		No text annotation
homologous
IL_9PN5_151
IL_31545.4
IL_9N77_0091/L1/142:149,
1/L1/165:172		No text annotation
homologous
IL_9H3G_165
IL_24485.3
IL_9N77_0101/L1/150:152,
1/L1/162:164		Isolated cWH basepair
homologous
IL_9PN5_153
IL_10892.5
IL_9N77_0111/L1/186:189,
1/L1/196:199		No text annotation
homologous
IL_9H3G_167
NA
IL_9N77_0121/L1/204:206,
1/L1/259:263		Isolated non-canonical cWW pair
geometric
IL_5B2P_002
IL_71625.6
IL_9N77_0131/L1/206:208,
1/L1/257:259		Isolated non-canonical cWW pair
homologous
IL_9PN5_155
IL_71625.6
IL_9N77_0141/L1/265:267,
1/L1/288:289		Single bulged A
homologous
IL_9H3G_171
IL_14190.5
IL_9N77_0151/L1/270:273,
1/L1/283:285		No text annotation
homologous
IL_9H3G_172
IL_77718.1
IL_9N77_0161/L1/275:276,
1/L1/279:281		Single bulged U
homologous
IL_9PN5_158
IL_97561.8
IL_9N77_0171/L1/311:316,
1/L1/348:355		Kink-turn with non-sequential stacking
homologous
IL_9H3G_173
IL_46174.7
IL_9N77_0181/L1/318:323,
1/L1/345:346		No text annotation
homologous
IL_9PN5_160
IL_01372.4
IL_9N77_0191/L1/363:365,
1/L1/376:381		No text annotation
homologous
IL_9PN5_161
IL_93336.4
IL_9N77_0201/L1/389:391,
1/L1/406:408		Isolated cWH basepair
geometric
IL_8GLP_213
IL_10892.5
IL_9N77_0211/L1/411:413,
1/L1/420:422		Isolated non-canonical cWW pair
homologous
IL_9PN5_163
IL_19025.1
IL_9N77_0221/L1/439:441,
1/L1/463:464		Single bulged U
homologous
IL_9PN5_164
IL_97561.8
IL_9N77_0231/L1/443:447,
1/L1/460:461		No text annotation
homologous
IL_9PN5_165
IL_26900.4
IL_9N77_0241/L1/447:448,
1/L1/458:460		Single bulged G
homologous
IL_9H3G_180
IL_28408.5
IL_9N77_0251/L1/482:483,
1/L1/504:506		Single bulged A
geometric
IL_8OI5_026
IL_14190.5
IL_9N77_0261/L1/514:516,
1/L1/536:543		No text annotation
homologous
IL_9PN5_168
IL_02511.3
IL_9N77_0271/L1/517:518,
1/L1/533:535		Minor groove platform
homologous
IL_9H3G_183
IL_26092.1
IL_9N77_0281/L1/518:520,
1/L1/532:533		Minor groove platform
homologous
IL_9H3G_184
IL_26092.1
IL_9N77_0291/L1/551:552,
1/L1/584:587		No text annotation
geometric
IL_8B0X_156
IL_44609.5
IL_9N77_0301/L1/552:559,
1/L1/568:584		No text annotation
IL_9N77_0311/L1/616:622,
1/L1/1104:1105		No text annotation
homologous
IL_9PN5_174
IL_20847.4
IL_9N77_0321/L1/624:626,
1/L1/973:975		Isolated non-canonical cWW pair
homologous
IL_9H3G_190
IL_01003.7
IL_9N77_0331/L1/627:631,
1/L1/968:972		No text annotation
homologous
IL_9PN5_176
IL_05821.4
IL_9N77_0351/L1/746:747,
1/L1/802:805		Minor groove platform
geometric
IL_9DFE_073
IL_26092.1
IL_9N77_0361/L1/748:750,
1/L1/799:801		Isolated non-canonical cWW pair
homologous
IL_9PN5_179
IL_71625.6
IL_9N77_0371/L1/751:759,
1/L1/791:798		No text annotation
homologous
IL_9H3G_194
IL_59049.5
IL_9N77_0391/L1/865:866,
1/L1/962:965		Major groove platform; stack outside cWW
geometric
IL_8GLP_235
IL_74641.5
IL_9N77_0401/L1/868:869,
1/L1/958:960		Single bulged U
geometric
IL_9AXU_050
IL_97561.8
IL_9N77_0411/L1/871:874,
1/L1/953:956		Tandem non-canonical cWW pairs
homologous
IL_9PN5_184
IL_15225.5
IL_9N77_0421/L1/874:878,
1/L1/950:953		Tandem non-canonical cWW pairs
homologous
IL_9PN5_185
IL_15225.5
IL_9N77_0471/L1/1034:1036,
1/L1/1095:1101		No text annotation
homologous
IL_9H3G_205
IL_82706.5
IL_9N77_0481/L1/1041:1044,
1/L1/1074:1077		Tandem non-canonical cWW pairs
homologous
IL_9PN5_192
IL_15225.5
IL_9N77_0491/L1/1051:1053,
1/L1/1066:1067		Single bulged U
homologous
IL_9PN5_193
IL_97561.8
IL_9N77_0501/L1/1117:1119,
1/L2/6:7		Single bulged G
geometric
IL_9PN5_036
IL_28408.5
IL_9N77_0511/L1/1122:1123,
1/L2/1:3		Single bulged U
geometric
IL_8GLP_130
IL_97561.8
IL_9N77_0521/L1/1157:1160,
1/L1/1617:1621		No text annotation
homologous
IL_9H3G_212
IL_63596.15
IL_9N77_0531/L1/1173:1175,
1/L1/1464:1466		Isolated non-canonical cWW pair
homologous
IL_9PN5_198
IL_01003.7
IL_9N77_0591/L1/1540:1545,
1/L1/1566:1571		No text annotation
homologous
IL_9PN5_219
IL_28265.2
IL_9N77_0611/L1/1650:1652,
1/L1/1748:1750		Isolated non-canonical cWW pair
homologous
IL_9PN5_224
IL_01003.7
IL_9N77_0651/L2/78:85,
1/L2/325:329		No text annotation
IL_9N77_0661/L2/85:96,
1/L2/320:325		No text annotation
IL_9N77_0681/L2/111:115,
1/L2/252:259		No text annotation
IL_9N77_0691/L2/139:142,
1/L2/169:171		No text annotation
IL_9N77_0701/L2/144:146,
1/L2/166:167		No text annotation

Problematic loops

#loop idProblemSequence
IL_9N77_001Single bulged G
IL_9N77_034Isolated non-canonical cWW pair
IL_9N77_038No text annotation
IL_9N77_043Tandem non-canonical cWW pairs
IL_9N77_044No text annotation
IL_9N77_045No text annotation
IL_9N77_046No text annotation
IL_9N77_054Isolated non-canonical cWW pair
IL_9N77_055No text annotation
IL_9N77_056Single bulged U
IL_9N77_057Single bulged A
IL_9N77_058No text annotation
IL_9N77_060Isolated non-canonical cWW pair
IL_9N77_062Tandem non-canonical cWW pairs
IL_9N77_063No text annotation
IL_9N77_064No text annotation
IL_9N77_067No text annotation
IL_9N77_071No text annotation
IL_9N77_072No text annotation
IL_9N77_073No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9N77_0011/L1/41:48,
1/L1/431:439,
1/L1/464:466		No text annotation
J3_9N77_0021/L1/633:635,
1/L1/861:865,
1/L1/965:966		No text annotation
geometric
J3_9H3G_030
J3_01633.3
J3_9N77_0031/L1/633:635,
1/L1/861:866,
1/L1/962:966		No text annotation
homologous
J3_9PN5_031
J3_17385.8
J3_9N77_0041/L1/760:763,
1/L1/773:775,
1/L1/786:790		No text annotation
J3_9N77_0051/L1/881:884,
1/L1/928:936,
1/L1/943:947		No text annotation
homologous
J3_9PN5_033
NA
J3_9N77_0061/L1/1037:1039,
1/L1/1079:1083,
1/L1/1090:1094		No text annotation
homologous
J3_9H3G_034
NA
J3_9N77_0071/L1/1150:1151,
1/L1/1627:1629,
1/L1/1636:1640		No text annotation
J3_9N77_0081/L1/1161:1164,
1/L1/1581:1587,
1/L1/1609:1616		No text annotation
homologous
J3_9PN5_035
J3_85722.4
J3_9N77_0091/L1/1168:1171,
1/L1/1468:1470,
1/L1/1574:1577		No text annotation
homologous
J3_9PN5_036
J3_44359.4
J3_9N77_0101/L1/1470:1474,
1/L1/1533:1540,
1/L1/1571:1574		No text annotation
homologous
J3_9PN5_043
J3_03192.4
J4_9N77_0011/L1/99:107,
1/L1/307:309,
1/L1/357:361,
1/L1/383:384		No text annotation
homologous
J4_9PN5_010
J4_15241.5
J4_9N77_0021/L1/622:624,
1/L1/975:980,
1/L1/1021:1032,
1/L1/1103:1104		No text annotation
homologous
J4_9PN5_011
J4_14595.4
J5_9N77_0011/L1/31:37,
1/L1/471:479,
1/L1/509:514,
1/L1/543:546,
1/L1/592:595		No text annotation
J5_9N77_0021/L1/31:41,
1/L1/466:479,
1/L1/509:514,
1/L1/543:546,
1/L1/592:595		No text annotation
J5_9N77_0031/L1/31:41,
1/L1/466:479,
1/L1/509:516,
1/L1/536:546,
1/L1/592:595		No text annotation
J5_9N77_0041/L1/54:57,
1/L1/90:97,
1/L1/386:388,
1/L1/409:411,
1/L1/422:426		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 0.0528 s