RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8OIT_0011/AG/13:19tRNA D-loop
geometric
HL_3AL0_001
NA
HL_8OIT_0021/AG/28:36tRNA anticodon loop
geometric
HL_4TUE_034
NA
HL_8OIT_0041/B8/52:59No text annotation
geometric
HL_4WF9_006
HL_48677.1
HL_8OIT_0051/B8/76:82No text annotation
geometric
HL_7A0S_008
HL_76371.1
HL_8OIT_0061/B8/116:121GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_8OIT_0071/B8/161:169No text annotation
homologous
HL_7RQB_017
NA
HL_8OIT_0081/B8/177:186T-loop with 2 stacked bulged bases
geometric
HL_5J7L_150
NA
HL_8OIT_0091/B8/214:219No text annotation
geometric
HL_5J7L_143
NA
HL_8OIT_0101/B8/264:270GNRA related
geometric
HL_5J7L_179
NA
HL_8OIT_0111/B8/284:293No text annotation
homologous
HL_7RQB_023
NA
HL_8OIT_0121/B8/318:326No text annotation
geometric
HL_5TBW_021
NA
HL_8OIT_0131/B8/365:370No text annotation
homologous
HL_4WF9_025
HL_27530.1
HL_8OIT_0141/B8/394:405No text annotation
HL_8OIT_0151/B8/437:444GNRA
homologous
HL_4WF9_027
HL_34789.1
HL_8OIT_0161/B8/459:466No text annotation
homologous
HL_5J7L_160
NA
HL_8OIT_0171/B8/505:515No text annotation
homologous
HL_6PRV_001
HL_20174.1
HL_8OIT_0181/B8/532:539GNRA wlth tandem sheared
homologous
HL_6PRV_002
HL_98423.1
HL_8OIT_0191/B8/609:616No text annotation
geometric
HL_1KH6_003
HL_05426.1
HL_8OIT_0201/B8/649:654UNCG variation
geometric
HL_6DME_002
HL_61337.1
HL_8OIT_0221/B8/730:733Mini UNCG
geometric
HL_7A0S_039
HL_90436.1
HL_8OIT_0231/B8/758:765No text annotation
homologous
HL_7RQB_040
NA
HL_8OIT_0241/B8/827:837No text annotation
homologous
HL_7RQB_045
NA
HL_8OIT_0251/B8/848:862No text annotation
HL_8OIT_0261/B8/885:890No text annotation
geometric
HL_5TBW_006
NA
HL_8OIT_0271/B8/904:913No text annotation
homologous
HL_9DFE_046
HL_82185.1
HL_8OIT_0281/B8/942:950No text annotation
homologous
HL_7A0S_048
HL_61418.1
HL_8OIT_0291/B8/1020:1029No text annotation
homologous
HL_4WF9_047
HL_78372.1
HL_8OIT_0311/B8/1142:1150No text annotation
homologous
HL_7RQB_053
NA
HL_8OIT_0321/B8/1158:1170No text annotation
HL_8OIT_0331/B8/1192:1200No text annotation
geometric
HL_2ZZM_002
NA
HL_8OIT_0341/B8/1232:1237GNRA
geometric
HL_5TBW_019
NA
HL_8OIT_0351/B8/1288:1296No text annotation
homologous
HL_4WF9_056
HL_52011.1
HL_8OIT_0361/B8/1345:1352GNRA variation
homologous
HL_4WF9_057
HL_46665.1
HL_8OIT_0371/B8/1368:1374No text annotation
homologous
HL_5J7L_195
NA
HL_8OIT_0381/B8/1411:1416GNRA
homologous
HL_7RQB_063
NA
HL_8OIT_0391/B8/1456:1461GNRA
geometric
HL_5B2T_003
HL_34789.1
HL_8OIT_0401/B8/1484:1489No text annotation
geometric
HL_5FMZ_001
HL_19413.1
HL_8OIT_0411/B8/1506:1523No text annotation
geometric
HL_7A0S_074
NA
HL_8OIT_0421/B8/1546:1554No text annotation
geometric
HL_7RQB_068
NA
HL_8OIT_0431/B9/12:21tRNA D-loop
geometric
HL_5B63_003
HL_65478.1
HL_8OIT_0461/B9/29:37tRNA anticodon loop
geometric
HL_1FIR_005
NA

Problematic loops

#loop idProblemSequence
HL_8OIT_003No text annotation
HL_8OIT_021No text annotation
HL_8OIT_030UNCG variation
HL_8OIT_044No text annotation
HL_8OIT_045No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8OIT_0011/AG/4:6,
1/AG/62:64		Isolated non-canonical cWW pair
geometric
IL_4J50_002
IL_01003.1
IL_8OIT_0031/B8/2:8,
1/B8/127:146		No text annotation
IL_8OIT_0041/B8/12:13,
1/B8/98:100		Single bulged A
homologous
IL_7RQB_002
NA
IL_8OIT_0051/B8/69:75,
1/B8/83:88		7x6 Sarcin-Ricin; G-bulge
geometric
IL_4V9F_106
IL_02666.1
IL_8OIT_0061/B8/175:177,
1/B8/186:188		Isolated non-canonical cWW pair
homologous
IL_5J7L_257
NA
IL_8OIT_0071/B8/207:209,
1/B8/225:227		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_01003.1
IL_8OIT_0081/B8/210:213,
1/B8/220:224		No text annotation
IL_8OIT_0091/B8/234:236,
1/B8/346:348		Isolated non-canonical cWW pair
homologous
IL_4WF9_020
IL_01003.1
IL_8OIT_0101/B8/236:240,
1/B8/339:346		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_8OIT_0111/B8/243:245,
1/B8/334:336		Isolated non-canonical cWW pair
geometric
IL_5TBW_079
NA
IL_8OIT_0121/B8/255:257,
1/B8/307:309		Isolated non-canonical cWW contact
geometric
IL_5UNE_001
NA
IL_8OIT_0131/B8/259:260,
1/B8/303:305		Single bulged A
homologous
IL_5J7L_261
NA
IL_8OIT_0141/B8/278:281,
1/B8/296:298		Major groove platform with extra cWW
homologous
IL_7RQB_022
NA
IL_8OIT_0151/B8/315:317,
1/B8/327:331		Multiple bulged bases
homologous
IL_7A0S_021
IL_89509.1
IL_8OIT_0161/B8/376:378,
1/B8/421:424		No text annotation
geometric
IL_4N0T_004
IL_32983.1
IL_8OIT_0171/B8/387:393,
1/B8/406:412		No text annotation
geometric
IL_5XWG_002
NA
IL_8OIT_0181/B8/475:477,
1/B8/584:585		Single bulged C
homologous
IL_5J7L_276
NA
IL_8OIT_0191/B8/479:483,
1/B8/578:582		UAA/GAN
homologous
IL_7RQB_036
NA
IL_8OIT_0201/B8/498:500,
1/B8/520:522		Isolated near basepair
geometric
IL_2ZI0_001
IL_42997.4
IL_8OIT_0211/B8/500:503,
1/B8/517:520		No text annotation
homologous
IL_6PRV_001
IL_28482.1
IL_8OIT_0221/B8/527:530,
1/B8/541:542		No text annotation
homologous
IL_6PRV_002
NA
IL_8OIT_0231/B8/636:643,
1/B8/1004:1010		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_8OIT_0241/B8/659:663,
1/B8/771:778		No text annotation
IL_8OIT_0251/B8/679:681,
1/B8/692:694		No text annotation
IL_8OIT_0621/B8/707:711,
1/B8/741:749		No text annotation
IL_8OIT_0631/B8/714:730,
1/B8/733:738		No text annotation
IL_8OIT_0681/B8/786:791,
1/B8/996:998		No text annotation
IL_8OIT_0271/B8/797:799,
1/B8/988:990		Isolated tWW turn
homologous
IL_4WF9_063
IL_10432.1
IL_8OIT_0281/B8/800:803,
1/B8/986:987		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_8OIT_0641/B8/800:808,
1/B8/983:987		No text annotation
homologous
IL_4WF9_117
IL_80252.1
IL_8OIT_0291/B8/803:808,
1/B8/983:986		Intercalated tWH
geometric
IL_5J7L_307
NA
IL_8OIT_0301/B8/808:817,
1/B8/978:983		No text annotation
IL_8OIT_0311/B8/820:821,
1/B8/973:975		Single bulged A
homologous
IL_7RQB_069
NA
IL_8OIT_0321/B8/878:881,
1/B8/896:897		Minor groove platform, major groove intercalation
homologous
IL_5J7L_314
NA
IL_8OIT_0331/B8/882:883,
1/B8/892:895		Major groove intercalation
homologous
IL_5J7L_315
NA
IL_8OIT_0341/B8/926:927,
1/B8/957:960		Multiple bulged bases
geometric
IL_7V9E_001
NA
IL_8OIT_0351/B8/927:938,
1/B8/954:957		No text annotation
homologous
IL_4WF9_077
IL_84014.1
IL_8OIT_0361/B8/1042:1045,
1/B8/1434:1436		Major groove platform with extra pair
geometric
IL_5TBW_091
NA
IL_8OIT_0371/B8/1047:1049,
1/B8/1429:1432		No text annotation
homologous
IL_5J7L_321
NA
IL_8OIT_0381/B8/1060:1062,
1/B8/1259:1260		Single bulged U
homologous
IL_7RQB_080
NA
IL_8OIT_0391/B8/1063:1064,
1/B8/1255:1258		Minor groove platform
homologous
IL_4WF9_081
IL_34520.1
IL_8OIT_0651/B8/1074:1076,
1/B8/1132:1133		Minor groove platform
geometric
IL_8VTW_003
NA
IL_8OIT_0411/B8/1083:1088,
1/B8/1118:1125		No text annotation
IL_8OIT_0421/B8/1179:1185,
1/B8/1207:1219		No text annotation
IL_8OIT_0431/B8/1186:1190,
1/B8/1202:1206		Double sheared with non-canonical cWW
geometric
IL_5J7L_274
NA
IL_8OIT_0441/B8/1270:1271,
1/B8/1315:1317		Single stack bend
geometric
IL_4WF9_089
IL_15011.1
IL_8OIT_0451/B8/1271:1272,
1/B8/1313:1315		Major groove platform
homologous
IL_7RQB_092
NA
IL_8OIT_0461/B8/1273:1276,
1/B8/1310:1312		Major groove platform with extra pair
geometric
IL_7RQB_093
NA
IL_8OIT_0471/B8/1276:1278,
1/B8/1306:1310		Major groove minor groove platform with extra cWW
homologous
IL_7RQB_094
NA
IL_8OIT_0481/B8/1283:1285,
1/B8/1298:1301		No text annotation
geometric
IL_4P3T_002
NA
IL_8OIT_0491/B8/1285:1287,
1/B8/1297:1298		Minor groove platform
geometric
IL_4V88_454
NA
IL_8OIT_0671/B8/1324:1325,
1/B8/1397:1399		Major groove platform
homologous
IL_5J7L_394
NA
IL_8OIT_0511/B8/1327:1329,
1/B8/1391:1395		Isolated non-canonical cWW with bulges
homologous
IL_7RQB_097
NA
IL_8OIT_0521/B8/1329:1330,
1/B8/1388:1391		No text annotation
geometric
IL_5J7L_341
NA
IL_8OIT_0531/B8/1338:1340,
1/B8/1357:1361		No text annotation
IL_8OIT_0551/B8/1408:1409,
1/B8/1418:1420		Single bulged A
homologous
IL_7RQB_101
NA
IL_8OIT_0561/B8/1445:1447,
1/B8/1469:1471		No text annotation
geometric
IL_2ZNI_001
NA
IL_8OIT_0571/B8/1449:1456,
1/B8/1461:1467		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_8OIT_0581/B8/1478:1482,
1/B8/1491:1493		C-loop
geometric
IL_7RQB_051
NA
IL_8OIT_0591/B8/1542:1543,
1/B8/1557:1560		Major groove intercalation
geometric
IL_1U9S_003
NA
IL_8OIT_0611/B9/26:28,
1/B9/38:40		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_01003.1

Problematic loops

#loop idProblemSequence
IL_8OIT_002Tandem non-canonical cWW pairs
IL_8OIT_026No text annotation
IL_8OIT_040No text annotation
IL_8OIT_066No text annotation
IL_8OIT_050No text annotation
IL_8OIT_054Isolated non-canonical cWW pair
IL_8OIT_060Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8OIT_0011/B8/8:11,
1/B8/101:115,
1/B8/122:127		No text annotation
J3_8OIT_0071/B8/14:52,
1/B8/59:69,
1/B8/88:97		No text annotation
J3_8OIT_0021/B8/245:251,
1/B8/313:315,
1/B8/331:334		No text annotation
homologous
J3_4WF9_002
J3_46658.1
J3_8OIT_0031/B8/260:262,
1/B8/272:276,
1/B8/300:303		No text annotation
homologous
J3_7RQB_005
NA
J3_8OIT_0081/B8/483:498,
1/B8/522:527,
1/B8/542:578		No text annotation
J3_8OIT_0041/B8/666:673,
1/B8/753:757,
1/B8/766:768		No text annotation
J3_8OIT_0051/B8/673:675,
1/B8/698:705,
1/B8/751:753		No text annotation
J3_8OIT_0091/B8/1176:1178,
1/B8/1220:1230,
1/B8/1239:1245		No text annotation
J3_8OIT_0061/B8/1334:1337,
1/B8/1362:1364,
1/B8/1378:1384		No text annotation
homologous
J3_7RQB_012
NA
J4_8OIT_0011/AG/7:10,
1/AG/22:24,
1/AG/40:45,
1/AG/60:61		No text annotation
J4_8OIT_0021/B8/644:647,
1/B8/656:657,
1/B8/780:783,
1/B8/1001:1003		No text annotation
J4_8OIT_0031/B8/666:675,
1/B8/698:705,
1/B8/751:757,
1/B8/766:768		No text annotation
J4_8OIT_0041/B8/822:826,
1/B8/838:843,
1/B8/867:872,
1/B8/967:972		No text annotation
J4_8OIT_0051/B8/874:876,
1/B8/899:900,
1/B8/917:926,
1/B8/960:965		No text annotation
homologous
J4_5J7L_026
NA
J4_8OIT_0061/B8/1441:1443,
1/B8/1473:1474,
1/B8/1497:1504,
1/B8/1525:1532		No text annotation
J4_8OIT_0071/B9/7:10,
1/B9/23:25,
1/B9/41:47,
1/B9/60:62		No text annotation
J5_8OIT_0011/B8/157:159,
1/B8/171:175,
1/B8/188:190,
1/B8/635:636,
1/B8/1010:1011		No text annotation
homologous
J5_9DFE_003
J5_43153.6
J5_8OIT_0051/B8/195:205,
1/B8/229:233,
1/B8/349:352,
1/B8/601:605,
1/B8/620:630		No text annotation
J5_8OIT_0031/B8/1050:1057,
1/B8/1263:1270,
1/B8/1317:1324,
1/B8/1399:1405,
1/B8/1423:1428		No text annotation
J5_8OIT_0041/B8/1067:1070,
1/B8/1137:1140,
1/B8/1152:1153,
1/B8/1175:1176,
1/B8/1245:1252		No text annotation
homologous
J5_7A0S_007
J5_39529.2
J6_8OIT_0011/B8/357:362,
1/B8/373:375,
1/B8/425:428,
1/B8/453:457,
1/B8/468:473,
1/B8/587:596		No text annotation
J6_8OIT_0021/B8/1067:1070,
1/B8/1137:1140,
1/B8/1152:1153,
1/B8/1175:1178,
1/B8/1220:1230,
1/B8/1239:1252		No text annotation

Problematic loops

#loop idProblemSequence
J5_8OIT_002No text annotation

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