RNA 3D Hub //

4YHH Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_4YHH_0011/A/12:22No text annotation
geometric
HL_4LFB_001
HL_73535.1
HL_4YHH_0021/A/80:89Pseudoknot geometry
geometric
HL_4GXY_003
HL_97725.1
HL_4YHH_0031/A/158:163GNRA
homologous
HL_6CZR_074
NA
HL_4YHH_0041/A/190B:190GNo text annotation
homologous
HL_4LFB_004
HL_89167.2
HL_4YHH_0051/A/201:216Mini UNCG
homologous
HL_4LFB_005
HL_90436.3
HL_4YHH_0381/A/259:267GNRA related
homologous
HL_6CZR_077
NA
HL_4YHH_0071/A/296:301GNRA
homologous
HL_5J7L_007
NA
HL_4YHH_0081/A/320:333No text annotation
homologous
HL_6CZR_079
NA
HL_4YHH_0091/A/342:347UNCG
homologous
HL_6CZR_080
NA
HL_4YHH_0391/A/378:385tRNA anticodon loop
geometric
HL_3RG5_006
HL_87268.2
HL_4YHH_0101/A/379:384GNRA
homologous
HL_4LFB_010
HL_34789.4
HL_4YHH_0111/A/419:424No text annotation
homologous
HL_6CZR_082
NA
HL_4YHH_0121/A/458:474GNRA
homologous
HL_6CZR_083
NA
HL_4YHH_0131/A/522:527GNRA variation
homologous
HL_4LFB_033
HL_34789.4
HL_4YHH_0141/A/617:623GNRA-like with tWH
homologous
HL_4LFB_014
HL_86621.1
HL_4YHH_0151/A/689:698No text annotation
homologous
HL_4LFB_015
HL_38491.2
HL_4YHH_0161/A/726:731GNRA
homologous
HL_4LFB_016
HL_34789.4
HL_4YHH_0171/A/786:796No text annotation
homologous
HL_5J7L_017
NA
HL_4YHH_0181/A/838:848Mini UNCG
homologous
HL_6CZR_089
NA
HL_4YHH_0191/A/862:867GNRA
homologous
HL_4LFB_019
HL_34789.4
HL_4YHH_0201/A/897:902GNRA
homologous
HL_4LFB_020
HL_34789.4
HL_4YHH_0361/A/963:972No text annotation
homologous
HL_4LFB_021
HL_97521.1
HL_4YHH_0221/A/1012:1017GNRA
homologous
HL_4LFB_022
HL_34789.4
HL_4YHH_0231/A/1030:1031GNRA
geometric
HL_7A0S_057
HL_34789.4
HL_4YHH_0241/A/1076:1081GNRA
homologous
HL_5J7L_023
NA
HL_4YHH_0251/A/1089:1096T-loop related
homologous
HL_4LFB_025
HL_63894.2
HL_4YHH_0261/A/1134:1140No text annotation
homologous
HL_4LFB_026
HL_92935.1
HL_4YHH_0271/A/1165:1171GNRA
homologous
HL_4LFB_027
HL_34789.4
HL_4YHH_0281/A/1265:1270GNRA
homologous
HL_4LFB_028
HL_34789.4
HL_4YHH_0291/A/1314:1323T-loop with 3 stacked bulged bases
homologous
HL_5J7L_028
NA
HL_4YHH_0301/A/1356:1366No text annotation
homologous
HL_4LFB_030
HL_86432.1
HL_4YHH_0311/A/1449:1454UNCG
homologous
HL_4LFB_031
HL_61337.3
HL_4YHH_0321/A/1514:1521No text annotation
geometric
HL_8H9D_001
NA

Problematic loops

#loop idProblemSequence
HL_4YHH_033No text annotation
HL_4YHH_034No text annotation
HL_4YHH_006No text annotation
HL_4YHH_035No text annotation
HL_4YHH_021No text annotation
HL_4YHH_037No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_4YHH_0011/A/30:32,
1/A/552:553		Single bulged G
geometric
IL_4LFB_001
IL_28408.2
IL_4YHH_0041/A/44:45,
1/A/396:398		Single bulged A
homologous
IL_4LFB_002
IL_14190.2
IL_4YHH_0711/A/47:52,
1/A/359:361		No text annotation
geometric
IL_4LFB_003
IL_32983.2
IL_4YHH_0051/A/54:57,
1/A/355:357		No text annotation
geometric
IL_4P3T_002
NA
IL_4YHH_0061/A/63:66,
1/A/103:104		Multiple bulged bases
homologous
IL_5J7L_005
NA
IL_4YHH_0071/A/67:69,
1/A/99:102		Isolated non-canonical cWW pair
homologous
IL_4LFB_006
IL_01003.3
IL_4YHH_0091/A/129:131,
1/A/231:232		Multiple bulged bases
geometric
IL_4LFB_007
IL_75289.1
IL_4YHH_0891/A/129:136,
1/A/227:232		No text annotation
IL_4YHH_0101/A/132:137,
1/A/226:230		No text annotation
geometric
IL_8C3A_401
NA
IL_4YHH_0111/A/147:153,
1/A/168:175		tWH-tWH-tHW-tHW
geometric
IL_4V88_394
NA
IL_4YHH_0131/A/186:188,
1/A/190K:191		Isolated non-canonical cWW pair
geometric
IL_8VTW_016
NA
IL_4YHH_0141/A/242:247,
1/A/277:284		Kink-turn with non-sequential stacking
geometric
IL_5J7L_014
NA
IL_4YHH_0151/A/249:252,
1/A/274:275		No text annotation
homologous
IL_4LFB_012
IL_22002.1
IL_4YHH_0901/A/292:293,
1/A/304:308		C-loop
homologous
IL_6CZR_125
NA
IL_4YHH_0171/A/367:369,
1/A/392:393		Single bulged U
homologous
IL_4LFB_014
IL_97561.3
IL_4YHH_0911/A/371:376,
1/A/387:390		No text annotation
IL_4YHH_0921/A/409:416,
1/A/427:433		No text annotation
homologous
IL_4LFB_017
IL_62329.1
IL_4YHH_0771/A/444:450,
1/A/483:490		No text annotation
IL_4YHH_0211/A/446:450,
1/A/483:488		6x5 Sarcin-Ricin; G-bulge
geometric
IL_4LFB_018
IL_82100.1
IL_4YHH_0221/A/450:455,
1/A/477:483		No text annotation
homologous
IL_4LFB_019
IL_31561.1
IL_4YHH_0231/A/504:511,
1/A/540:541		SSU/LSU pseudoknot
homologous
IL_5J7L_024
NA
IL_4YHH_0931/A/515:521,
1/A/528:536		Kink-turn related
homologous
IL_6CZR_133
NA
IL_4YHH_0251/A/569:575,
1/A/880:881		No text annotation
homologous
IL_4LFB_022
IL_20847.1
IL_4YHH_0261/A/580:584,
1/A/757:761		tSH-tHW-tHS
homologous
IL_4LFB_023
IL_05821.1
IL_4YHH_0271/A/594:596,
1/A/644:645		Major groove platform
homologous
IL_4LFB_024
IL_48076.8
IL_4YHH_0281/A/597:598,
1/A/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_73108.2
IL_4YHH_0291/A/605:612,
1/A/628:633		No text annotation
homologous
IL_6CZR_408
NA
IL_4YHH_0781/A/657:658,
1/A/747:749		Major groove platform
homologous
IL_4LFB_028
IL_48076.8
IL_4YHH_0311/A/662:668,
1/A/738:743		No text annotation
IL_4YHH_0941/A/673:677,
1/A/713:717		Triple non-canonical cWW pairs
homologous
IL_5J7L_361
NA
IL_4YHH_0791/A/683:688,
1/A/699:707		Kink-turn
homologous
IL_4LFB_031
IL_95727.1
IL_4YHH_0351/A/774:778,
1/A/804:805		Left turn
geometric
IL_5J7L_036
NA
IL_4YHH_0361/A/779:783,
1/A/799:803		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_05821.1
IL_4YHH_0371/A/887:894,
1/A/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4LFB_034
IL_84044.1
IL_4YHH_0381/A/922:925,
1/A/1391:1395		No text annotation
IL_4YHH_0391/A/925:927,
1/A/1390:1391		Single bulged G
homologous
IL_5J7L_040
NA
IL_4YHH_0401/A/933:935,
1/A/1380:1384		Minor groove platform
homologous
IL_5J7L_041
NA
IL_4YHH_0421/A/953:954,
1/A/1226:1228		No text annotation
homologous
IL_6CZR_150
NA
IL_4YHH_0431/A/993:997,
1/A/1044:1045		Minor groove platform
geometric
IL_6CZR_151
NA
IL_4YHH_0471/A/1048:1050,
1/A/1208:1209		Single bulged U
geometric
IL_5J7L_046
NA
IL_4YHH_0831/A/1052:1058,
1/A/1199:1206		No text annotation
geometric
IL_4V88_510
NA
IL_4YHH_0841/A/1059:1061,
1/A/1195:1198		Isolated non-canonical cWW pair
geometric
IL_5C5W_002
IL_01003.3
IL_4YHH_0491/A/1060:1061,
1/A/1195:1197		Single bulged U
homologous
IL_4LFB_046
IL_97561.3
IL_4YHH_0501/A/1061:1063,
1/A/1193:1195		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_68118.3
IL_4YHH_0951/A/1122:1127,
1/A/1145:1151		No text annotation
IL_4YHH_0531/A/1129:1132,
1/A/1142:1143		Minor groove platform
homologous
IL_5J7L_052
NA
IL_4YHH_0541/A/1158:1161,
1/A/1175:1181		No text annotation
geometric
IL_5J7L_053
NA
IL_4YHH_0551/A/1247:1253,
1/A/1284:1290		No text annotation
homologous
IL_4LFB_051
IL_12056.1
IL_4YHH_0561/A/1255:1258,
1/A/1277:1282		180 degree turn
homologous
IL_4LFB_052
IL_08849.1
IL_4YHH_0861/A/1259:1262,
1/A/1273:1276		Double sheared
homologous
IL_4LFB_067
IL_58355.2
IL_4YHH_0581/A/1303:1308,
1/A/1329:1334		No text annotation
homologous
IL_4LFB_055
IL_57885.2
IL_4YHH_0591/A/1399:1401,
1/A/1501:1504		No text annotation
homologous
IL_5J7L_058
NA
IL_4YHH_0601/A/1401:1404,
1/A/1497:1501		No text annotation
homologous
IL_4LFB_068
IL_25873.2
IL_4YHH_0611/A/1405:1407,
1/A/1494:1496		Isolated non-canonical cWW pair
homologous
IL_5J7L_363
NA
IL_4YHH_0621/A/1407:1409,
1/A/1491:1494		Decoding loop related
geometric
IL_3C3Z_002
IL_53541.1
IL_4YHH_0641/A/1412:1414,
1/A/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_4YHH_0661/A/1416:1419,
1/A/1481:1484		Double sheared
geometric
IL_6YL5_010
IL_58355.2
IL_4YHH_0961/A/1431:1437,
1/A/1464:1469		No text annotation
IL_4YHH_0691/A/1440:1447,
1/A/1459:1461		No text annotation

Problematic loops

#loop idProblemSequence
IL_4YHH_070Tandem non-canonical cWW pairs
IL_4YHH_002Isolated non-canonical cWW pair
IL_4YHH_003Isolated non-canonical cWW pair
IL_4YHH_008Isolated cWS basepair
IL_4YHH_072No text annotation
IL_4YHH_073No text annotation
IL_4YHH_012Isolated non-canonical cWW pair
IL_4YHH_074Tandem non-canonical cWW pairs
IL_4YHH_075No text annotation
IL_4YHH_016No text annotation
IL_4YHH_018No text annotation
IL_4YHH_076No text annotation
IL_4YHH_019No text annotation
IL_4YHH_020Isolated non-canonical cWW pair
IL_4YHH_024No text annotation
IL_4YHH_030Major groove platform with extra cWW
IL_4YHH_032No text annotation
IL_4YHH_033No text annotation
IL_4YHH_034No text annotation
IL_4YHH_080No text annotation
IL_4YHH_081No text annotation
IL_4YHH_041Isolated non-canonical cWW pair
IL_4YHH_044Isolated non-canonical cWW pair
IL_4YHH_045Isolated non-canonical cWW pair
IL_4YHH_046Isolated non-canonical cWW pair
IL_4YHH_082Isolated non-canonical cWW pair
IL_4YHH_048No text annotation
IL_4YHH_051Isolated non-canonical cWW pair
IL_4YHH_052No text annotation
IL_4YHH_085No text annotation
IL_4YHH_057Double sheared with non-canonical cWW
IL_4YHH_063Isolated non-canonical cWW contact
IL_4YHH_065Isolated non-canonical cWW pair
IL_4YHH_087Double sheared with non-canonical cWW
IL_4YHH_067Isolated non-canonical cWW pair
IL_4YHH_068No text annotation
IL_4YHH_088No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_4YHH_0131/A/46:47,
1/A/361:367,
1/A/393:395		No text annotation
homologous
J3_4LFB_010
J3_58657.1
J3_4YHH_0011/A/46:52,
1/A/359:367,
1/A/393:395		No text annotation
geometric
J3_4LFB_014
J3_63856.1
J3_4YHH_0021/A/586:588,
1/A/651:655,
1/A/751:755		No text annotation
geometric
J3_4LFB_015
J3_17385.5
J3_4YHH_0151/A/672:673,
1/A/717:725,
1/A/732:734		No text annotation
homologous
J3_4LFB_012
J3_74074.1
J3_4YHH_0031/A/826:829,
1/A/857:861,
1/A/868:874		No text annotation
homologous
J3_4LFB_001
J3_02285.1
J3_4YHH_0041/A/936:939,
1/A/1344:1350,
1/A/1372:1379		No text annotation
geometric
J3_5J7L_052
NA
J3_4YHH_0051/A/943:946,
1/A/1235:1237,
1/A/1337:1340		No text annotation
homologous
J3_4LFB_003
J3_44359.1
J3_4YHH_0061/A/955:962,
1/A/973:984,
1/A/1221:1225		No text annotation
homologous
J3_4LFB_004
J3_88451.1
J3_4YHH_0071/A/990:993,
1/A/1045:1047,
1/A/1210:1215		No text annotation
geometric
J3_5J7L_007
NA
J3_4YHH_0171/A/990:997,
1/A/1044:1047,
1/A/1210:1215		No text annotation
homologous
J3_5J7L_053
NA
J3_4YHH_0201/A/1003A:1006,
1/A/1023:1027,
1/A/1034:1037		No text annotation
J3_4YHH_0091/A/1063:1068,
1/A/1107:1113,
1/A/1187:1193		No text annotation
homologous
J3_4LFB_007
J3_01343.1
J3_4YHH_0211/A/1073:1074,
1/A/1083:1086,
1/A/1099:1102		No text annotation
homologous
J3_4LFB_017
J3_11018.1
J3_4YHH_0111/A/1116:1118,
1/A/1155:1158,
1/A/1181:1184		No text annotation
geometric
J3_4LFB_008
J3_82365.5
J3_4YHH_0191/A/1116:1118,
1/A/1155:1161,
1/A/1175:1184		No text annotation
homologous
J3_4LFB_018
J3_40706.1
J3_4YHH_0121/A/1237:1241,
1/A/1296:1303,
1/A/1334:1337		No text annotation
homologous
J3_4LFB_009
J3_03192.1
J4_4YHH_0011/A/115:122,
1/A/239:240,
1/A/286:289,
1/A/311:312		No text annotation
homologous
J4_4LFB_001
J4_90044.1
J4_4YHH_0021/A/142:144,
1/A/178:183,
1/A/194:198,
1/A/219:221		No text annotation
homologous
J4_4LFB_002
J4_88771.1
J4_4YHH_0031/A/575:577,
1/A/764:769,
1/A/810:821,
1/A/879:880		No text annotation
homologous
J4_4LFB_003
J4_14595.1
J4_4YHH_0041/A/943:946,
1/A/1235:1241,
1/A/1296:1308,
1/A/1329:1340		No text annotation
J5_4YHH_0031/A/36:39,
1/A/403:406,
1/A/436:442,
1/A/492:500,
1/A/545:548		No text annotation
homologous
J5_4LFB_001
J5_70703.1
J5_4YHH_0021/A/54:61,
1/A/106:113,
1/A/314:316,
1/A/337:339,
1/A/350:357		No text annotation

Problematic loops

#loop idProblemSequence
J3_4YHH_014No text annotation
J3_4YHH_016No text annotation
J3_4YHH_018No text annotation
J3_4YHH_008No text annotation
J3_4YHH_010No text annotation
J5_4YHH_001No text annotation

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