RNA 3D Hub //

8OIQ Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8OIQ_0011/AG/13:19tRNA D-loop
geometric
HL_2AZX_004
NA
HL_8OIQ_0021/AG/28:36tRNA anticodon loop
geometric
HL_4TUE_034
NA
HL_8OIQ_0531/B8/54:61No text annotation
geometric
HL_7A0S_006
HL_48677.1
HL_8OIQ_0041/B8/80:86No text annotation
geometric
HL_7A0S_008
HL_76371.2
HL_8OIQ_0051/B8/121:126GNRA
homologous
HL_4WF9_015
HL_34789.2
HL_8OIQ_0061/B8/167:175No text annotation
geometric
HL_8C3A_039
NA
HL_8OIQ_0071/B8/183:192T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_8OIQ_0081/B8/220:225No text annotation
geometric
HL_4WF9_011
HL_75660.7
HL_8OIQ_0471/B8/270:277No text annotation
geometric
HL_3FOZ_005
HL_37569.2
HL_8OIQ_0101/B8/291:300No text annotation
homologous
HL_7RQB_023
NA
HL_8OIQ_0111/B8/326:332No text annotation
homologous
HL_7RQB_024
NA
HL_8OIQ_0121/B8/372:377No text annotation
homologous
HL_4WF9_025
HL_27530.1
HL_8OIQ_0131/B8/401:410No text annotation
HL_8OIQ_0141/B8/442:449GNRA
homologous
HL_7A0S_026
HL_34789.2
HL_8OIQ_0151/B8/462:469No text annotation
homologous
HL_5J7L_160
NA
HL_8OIQ_0161/B8/509:519No text annotation
homologous
HL_5J7L_161
NA
HL_8OIQ_0171/B8/536:543GNRA wlth tandem sheared
homologous
HL_6PRV_002
HL_98423.2
HL_8OIQ_0181/B8/613:620No text annotation
geometric
HL_5E6M_002
HL_10874.1
HL_8OIQ_0191/B8/653:658No text annotation
HL_8OIQ_0481/B8/682:697No text annotation
HL_8OIQ_0201/B8/688:693No text annotation
geometric
HL_5TBW_044
NA
HL_8OIQ_0211/B8/719:737No text annotation
HL_8OIQ_0221/B8/760:767No text annotation
homologous
HL_7RQB_040
NA
HL_8OIQ_0231/B8/829:839No text annotation
homologous
HL_7RQB_045
NA
HL_8OIQ_0241/B8/850:864No text annotation
HL_8OIQ_0251/B8/887:892No text annotation
geometric
HL_5U3G_001
HL_75660.7
HL_8OIQ_0261/B8/906:915No text annotation
homologous
HL_9DFE_046
HL_82185.1
HL_8OIQ_0271/B8/944:952No text annotation
homologous
HL_7A0S_048
HL_61418.2
HL_8OIQ_0281/B8/1022:1031No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_8OIQ_0301/B8/1148:1156No text annotation
homologous
HL_7RQB_053
NA
HL_8OIQ_0311/B8/1164:1176No text annotation
HL_8OIQ_0321/B8/1187:1190Mini UNCG
geometric
HL_4V88_192
NA
HL_8OIQ_0331/B8/1198:1205GNRA with extra cWW
geometric
HL_4WF9_053
HL_87268.1
HL_8OIQ_0341/B8/1238:1243No text annotation
geometric
HL_4V9F_003
HL_75660.7
HL_8OIQ_0351/B8/1294:1302No text annotation
homologous
HL_4WF9_056
HL_52011.1
HL_8OIQ_0361/B8/1351:1358GNRA variation
homologous
HL_7A0S_060
HL_46665.2
HL_8OIQ_0371/B8/1374:1380No text annotation
homologous
HL_4WF9_058
HL_48677.1
HL_8OIQ_0381/B8/1417:1422GNRA
homologous
HL_7RQB_063
NA
HL_8OIQ_0391/B8/1461:1466GNRA
geometric
HL_3P22_001
HL_34789.2
HL_8OIQ_0401/B8/1489:1495No text annotation
HL_8OIQ_0511/B8/1513:1533No text annotation
HL_8OIQ_0421/B8/1557:1565No text annotation
geometric
HL_7RQB_068
NA
HL_8OIQ_0431/B9/12:24No text annotation
homologous
HL_4YYE_001
NA
HL_8OIQ_0441/B9/32:40tRNA anticodon loop
homologous
HL_6UGG_005
HL_11974.2

Problematic loops

#loop idProblemSequence
HL_8OIQ_003No text annotation
HL_8OIQ_046No text annotation
HL_8OIQ_009GNRA wlth tandem sheared
HL_8OIQ_049No text annotation
HL_8OIQ_029No text annotation
HL_8OIQ_050tRNA anticodon loop
HL_8OIQ_041No text annotation
HL_8OIQ_052No text annotation
HL_8OIQ_045No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8OIQ_0041/B8/2:4,
1/B8/147:152		No text annotation
IL_8OIQ_0691/B8/2:8,
1/B8/132:152		No text annotation
IL_8OIQ_0051/B8/4:8,
1/B8/132:147		No text annotation
IL_8OIQ_0061/B8/12:13,
1/B8/103:105		Single bulged A
homologous
IL_7A0S_002
IL_14190.2
IL_8OIQ_0071/B8/14:70,
1/B8/95:102		No text annotation
IL_8OIQ_0081/B8/70:73,
1/B8/92:95		Tandem non-canonical cWW pairs
geometric
IL_3R2D_002
IL_71194.2
IL_8OIQ_0091/B8/73:79,
1/B8/87:92		7x6 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_251
NA
IL_8OIQ_0111/B8/181:183,
1/B8/192:194		Isolated non-canonical cWW pair
geometric
IL_5J7L_257
NA
IL_8OIQ_0121/B8/214:216,
1/B8/230:232		Isolated non-canonical cWW pair
geometric
IL_1U9S_007
IL_01003.2
IL_8OIQ_0131/B8/216:219,
1/B8/226:230		No text annotation
IL_8OIQ_0141/B8/240:242,
1/B8/353:355		Isolated non-canonical cWW pair
geometric
IL_4WF9_020
IL_01003.2
IL_8OIQ_0151/B8/242:246,
1/B8/346:353		tHW-tHW cross-strand stack
homologous
IL_7RQB_018
NA
IL_8OIQ_0161/B8/249:251,
1/B8/341:343		No text annotation
geometric
IL_3LA5_001
NA
IL_8OIQ_0171/B8/259:261,
1/B8/316:318		Isolated non-canonical cWW pair
geometric
IL_4LFB_061
NA
IL_8OIQ_0181/B8/265:266,
1/B8/310:312		Single bulged A
geometric
IL_5J7L_261
NA
IL_8OIQ_0191/B8/285:288,
1/B8/303:305		Major groove platform with extra cWW
homologous
IL_7RQB_022
NA
IL_8OIQ_0201/B8/322:324,
1/B8/334:338		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_8OIQ_0221/B8/394:400,
1/B8/411:417		No text annotation
geometric
IL_5XWG_002
IL_74768.1
IL_8OIQ_0231/B8/478:480,
1/B8/588:589		Single bulged C
homologous
IL_5J7L_276
NA
IL_8OIQ_0781/B8/502:504,
1/B8/524:526		No text annotation
IL_8OIQ_0241/B8/504:507,
1/B8/521:524		No text annotation
homologous
IL_5J7L_285
NA
IL_8OIQ_0251/B8/531:534,
1/B8/545:546		No text annotation
homologous
IL_6PRV_002
NA
IL_8OIQ_0261/B8/640:647,
1/B8/1006:1012		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_8OIQ_0271/B8/663:666,
1/B8/773:779		No text annotation
IL_8OIQ_0281/B8/682:687,
1/B8/694:697		C-loop
homologous
IL_7RQB_051
NA
IL_8OIQ_0291/B8/710:713,
1/B8/743:751		No text annotation
IL_8OIQ_0791/B8/787:792,
1/B8/998:1000		No text annotation
IL_8OIQ_0311/B8/798:800,
1/B8/990:992		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_8OIQ_0321/B8/801:804,
1/B8/988:989		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_8OIQ_0721/B8/801:809,
1/B8/985:989		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_8OIQ_0331/B8/804:809,
1/B8/985:988		Intercalated tWH
homologous
IL_4WF9_065
IL_28217.1
IL_8OIQ_0341/B8/809:817,
1/B8/982:985		No text annotation
IL_8OIQ_0351/B8/822:823,
1/B8/975:977		Single bulged A
homologous
IL_7RQB_069
NA
IL_8OIQ_0361/B8/880:883,
1/B8/898:899		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_8OIQ_0371/B8/884:885,
1/B8/894:897		Major groove intercalation
homologous
IL_5J7L_315
NA
IL_8OIQ_0391/B8/928:929,
1/B8/959:962		Multiple bulged bases
geometric
IL_7V9E_001
NA
IL_8OIQ_0401/B8/929:940,
1/B8/956:959		No text annotation
IL_8OIQ_0421/B8/1045:1047,
1/B8/1440:1441		Major groove platform
homologous
IL_5J7L_320
NA
IL_8OIQ_0431/B8/1049:1051,
1/B8/1435:1438		No text annotation
homologous
IL_4WF9_079
IL_80025.1
IL_8OIQ_0451/B8/1062:1064,
1/B8/1265:1266		Single bulged U
geometric
IL_7RQB_080
NA
IL_8OIQ_0461/B8/1065:1066,
1/B8/1261:1264		Minor groove platform
homologous
IL_7RQB_081
NA
IL_8OIQ_0801/B8/1075:1078,
1/B8/1138:1140		No text annotation
geometric
IL_4V9F_053
IL_49140.1
IL_8OIQ_0481/B8/1080:1082,
1/B8/1134:1136		Isolated non-canonical cWW pair
homologous
IL_4WF9_083
IL_01003.2
IL_8OIQ_0491/B8/1085:1087,
1/B8/1126:1131		No text annotation
IL_8OIQ_0751/B8/1186:1191,
1/B8/1212:1222		No text annotation
IL_8OIQ_0511/B8/1192:1196,
1/B8/1207:1211		Double sheared with non-canonical cWW
geometric
IL_5J7L_274
NA
IL_8OIQ_0521/B8/1276:1277,
1/B8/1321:1323		Single stack bend
geometric
IL_4WF9_089
IL_15011.2
IL_8OIQ_0531/B8/1277:1278,
1/B8/1319:1321		Major groove platform
homologous
IL_4WF9_090
IL_48076.8
IL_8OIQ_0541/B8/1279:1282,
1/B8/1316:1318		No text annotation
geometric
IL_6DME_003
IL_75527.2
IL_8OIQ_0551/B8/1282:1284,
1/B8/1312:1316		Major groove minor groove platform with extra cWW
homologous
IL_4WF9_092
IL_36931.2
IL_8OIQ_0571/B8/1289:1293,
1/B8/1303:1307		Double sheared with non-canonical cWW
homologous
IL_7A0S_087
IL_87767.2
IL_8OIQ_0581/B8/1330:1332,
1/B8/1402:1405		No text annotation
homologous
IL_5J7L_339
NA
IL_8OIQ_0591/B8/1333:1335,
1/B8/1397:1401		Isolated non-canonical cWW with bulges
homologous
IL_4WF9_095
IL_68118.2
IL_8OIQ_0601/B8/1335:1336,
1/B8/1394:1397		No text annotation
geometric
IL_4WF9_096
IL_44609.2
IL_8OIQ_0611/B8/1344:1346,
1/B8/1363:1367		No text annotation
IL_8OIQ_0631/B8/1414:1415,
1/B8/1424:1426		Single bulged A
homologous
IL_7RQB_101
NA
IL_8OIQ_0641/B8/1454:1461,
1/B8/1466:1472		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_8OIQ_0651/B8/1483:1487,
1/B8/1497:1499		C-loop
geometric
IL_7RQB_051
NA
IL_8OIQ_0661/B8/1487:1489,
1/B8/1495:1497		Isolated non-canonical cWW pair
geometric
IL_6IA2_005
IL_01003.2
IL_8OIQ_0671/B8/1507:1512,
1/B8/1534:1539		No text annotation
geometric
IL_4QLM_002
IL_74322.2

Problematic loops

#loop idProblemSequence
IL_8OIQ_001Isolated non-canonical cWW pair
IL_8OIQ_002Isolated non-canonical cWW pair
IL_8OIQ_003Tandem non-canonical cWW pairs
IL_8OIQ_010No text annotation
IL_8OIQ_021Intercalated cWW
IL_8OIQ_070No text annotation
IL_8OIQ_030No text annotation
IL_8OIQ_071No text annotation
IL_8OIQ_073Isolated non-canonical cWW pair
IL_8OIQ_038Isolated cWH basepair
IL_8OIQ_041Isolated non-canonical cWW pair
IL_8OIQ_044Isolated non-canonical cWW pair
IL_8OIQ_074No text annotation
IL_8OIQ_047No text annotation
IL_8OIQ_050Isolated non-canonical cWW pair
IL_8OIQ_056Isolated non-canonical cWW pair
IL_8OIQ_076Isolated non-canonical cWW contact
IL_8OIQ_077No text annotation
IL_8OIQ_062Isolated non-canonical cWW pair
IL_8OIQ_068No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8OIQ_0061/B8/8:11,
1/B8/106:120,
1/B8/127:132		No text annotation
J3_8OIQ_0091/B8/14:54,
1/B8/61:70,
1/B8/95:102		No text annotation
J3_8OIQ_0011/B8/251:257,
1/B8/320:322,
1/B8/338:341		No text annotation
homologous
J3_5J7L_038
NA
J3_8OIQ_0021/B8/266:268,
1/B8/279:283,
1/B8/307:310		No text annotation
homologous
J3_7RQB_005
NA
J3_8OIQ_0101/B8/482:502,
1/B8/526:531,
1/B8/546:586		No text annotation
J3_8OIQ_0031/B8/669:676,
1/B8/755:759,
1/B8/768:770		No text annotation
J3_8OIQ_0041/B8/676:678,
1/B8/701:708,
1/B8/753:755		No text annotation
J3_8OIQ_0081/B8/1182:1183,
1/B8/1225:1236,
1/B8/1245:1251		No text annotation
J3_8OIQ_0051/B8/1340:1343,
1/B8/1368:1370,
1/B8/1384:1390		No text annotation
homologous
J3_4WF9_009
J3_32601.6
J4_8OIQ_0081/AG/7:10,
1/AG/22:24,
1/AG/40:45,
1/AG/60:61		No text annotation
J4_8OIQ_0021/B8/648:651,
1/B8/660:661,
1/B8/781:784,
1/B8/1003:1005		No text annotation
J4_8OIQ_0031/B8/669:678,
1/B8/701:708,
1/B8/753:759,
1/B8/768:770		No text annotation
J4_8OIQ_0041/B8/824:828,
1/B8/840:845,
1/B8/869:874,
1/B8/969:974		No text annotation
J4_8OIQ_0051/B8/876:878,
1/B8/901:902,
1/B8/919:928,
1/B8/962:967		No text annotation
homologous
J4_9DFE_008
J4_42306.1
J4_8OIQ_0061/B8/1446:1448,
1/B8/1478:1479,
1/B8/1503:1505,
1/B8/1541:1543		No text annotation
J4_8OIQ_0071/B9/7:10,
1/B9/26:28,
1/B9/44:49,
1/B9/62:63		tRNA junction
homologous
J4_5HR7_002
J4_95067.1
J5_8OIQ_0041/B8/201:210,
1/B8/236:239,
1/B8/356:359,
1/B8/605:609,
1/B8/624:634		No text annotation
J5_8OIQ_0021/B8/1052:1059,
1/B8/1269:1276,
1/B8/1323:1331,
1/B8/1403:1411,
1/B8/1429:1434		No text annotation
J5_8OIQ_0051/B8/1069:1072,
1/B8/1143:1146,
1/B8/1158:1159,
1/B8/1181:1182,
1/B8/1251:1258		No text annotation
homologous
J5_7A0S_007
J5_39529.2
J6_8OIQ_0011/B8/363:369,
1/B8/380:384,
1/B8/427:434,
1/B8/457:461,
1/B8/470:475,
1/B8/592:601		No text annotation
J6_8OIQ_0031/B8/1069:1072,
1/B8/1143:1146,
1/B8/1158:1159,
1/B8/1181:1183,
1/B8/1225:1236,
1/B8/1245:1258		No text annotation
J6_8OIQ_0021/B8/1069:1072,
1/B8/1143:1146,
1/B8/1158:1160,
1/B8/1180:1183,
1/B8/1225:1236,
1/B8/1245:1258		No text annotation

Problematic loops

#loop idProblemSequence
J3_8OIQ_007No text annotation
J4_8OIQ_001No text annotation
J5_8OIQ_001No text annotation
J5_8OIQ_003No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0677 s