RNA 3D Hub //

3J2F Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3J2F_0011/N/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_3J2F_0021/N/82:87No text annotation
HL_3J2F_0031/N/158:163GNRA
homologous
HL_4LFB_003
HL_37824.8
HL_3J2F_0041/N/186:191UNCG variation
geometric
HL_2CZJ_007
NA
HL_3J2F_0051/N/207:212No text annotation
HL_3J2F_0371/N/259:267GNRA related
homologous
HL_5J7L_006
HL_84299.4
HL_3J2F_0071/N/296:301GNRA
homologous
HL_4LFB_007
HL_37824.8
HL_3J2F_0081/N/320:333No text annotation
homologous
HL_4LFB_008
HL_81205.3
HL_3J2F_0091/N/342:347UNCG
homologous
HL_6CZR_080
NA
HL_3J2F_0101/N/379:384GNRA
homologous
HL_5J7L_010
HL_37824.8
HL_3J2F_0111/N/419:424No text annotation
homologous
HL_6CZR_082
NA
HL_3J2F_0331/N/462:470No text annotation
HL_3J2F_0131/N/522:527Mini UNCG
geometric
HL_4YAZ_004
HL_48778.2
HL_3J2F_0141/N/617:623No text annotation
homologous
HL_5J7L_014
HL_10453.3
HL_3J2F_0151/N/689:698No text annotation
homologous
HL_4LFB_015
HL_75293.5
HL_3J2F_0161/N/726:731GNRA
homologous
HL_5J7L_016
HL_37824.8
HL_3J2F_0341/N/785:797No text annotation
HL_3J2F_0171/N/786:796No text annotation
HL_3J2F_0181/N/840:846No text annotation
geometric
HL_8VM9_005
HL_32346.4
HL_3J2F_0191/N/862:867GNRA
homologous
HL_5J7L_019
HL_37824.8
HL_3J2F_0201/N/897:902GNRA
homologous
HL_4LFB_020
HL_37824.8
HL_3J2F_0381/N/963:972No text annotation
HL_3J2F_0221/N/1012:1017GNRA
homologous
HL_4LFB_022
HL_37824.8
HL_3J2F_0231/N/1028:1033No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_3J2F_0241/N/1076:1081GNRA
homologous
HL_4LFB_024
HL_37824.8
HL_3J2F_0251/N/1089:1096T-loop related
homologous
HL_5J7L_024
HL_77436.5
HL_3J2F_0351/N/1134:1140No text annotation
homologous
HL_4LFB_026
HL_87954.2
HL_3J2F_0271/N/1165:1171GNRA
homologous
HL_5J7L_026
HL_93535.1
HL_3J2F_0281/N/1265:1270GNRA
homologous
HL_4LFB_028
HL_37824.8
HL_3J2F_0291/N/1314:1323T-loop with 1 bulged base
geometric
HL_8VTW_009
NA
HL_3J2F_0301/N/1356:1366No text annotation
homologous
HL_5J7L_029
HL_06226.4
HL_3J2F_0311/N/1449:1454UNCG
homologous
HL_4LFB_031
HL_34617.5
HL_3J2F_0321/N/1515:1520GNRA
homologous
HL_4LFB_032
HL_37824.8

Problematic loops

#loop idProblemSequence
HL_3J2F_006No text annotation
HL_3J2F_012No text annotation
HL_3J2F_021No text annotation
HL_3J2F_026No text annotation
HL_3J2F_036No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3J2F_0781/N/30:32,
1/N/552:553		Single bulged G
homologous
IL_5J7L_001
IL_00225.14
IL_3J2F_0791/N/44:45,
1/N/396:398		Single bulged A
homologous
IL_5J7L_002
IL_31462.7
IL_3J2F_0041/N/54:56,
1/N/356:357		Minor groove platform
homologous
IL_5J7L_004
IL_51454.3
IL_3J2F_0061/N/63:66,
1/N/103:104		Multiple bulged bases
geometric
IL_6IV9_001
IL_82107.5
IL_3J2F_0071/N/67:69,
1/N/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
IL_90351.1
IL_3J2F_0081/N/70:73,
1/N/97:98		Minor groove platform
homologous
IL_5J7L_007
IL_15052.4
IL_3J2F_0921/N/75:79,
1/N/90:95		No text annotation
IL_3J2F_0101/N/128:136,
1/N/227:233		No text annotation
IL_3J2F_0111/N/144:146,
1/N/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
IL_10167.6
IL_3J2F_0121/N/147:153,
1/N/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_3J2F_0801/N/202:206,
1/N/213:215		No text annotation
IL_3J2F_0151/N/242:247,
1/N/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
IL_46174.3
IL_3J2F_0811/N/249:252,
1/N/274:275		No text annotation
homologous
IL_5J7L_015
IL_47074.2
IL_3J2F_0171/N/292:293,
1/N/304:308		C-loop
homologous
IL_4LFB_013
IL_03109.3
IL_3J2F_0181/N/367:369,
1/N/392:393		Single bulged U
homologous
IL_4LFB_014
IL_89505.4
IL_3J2F_0191/N/371:375,
1/N/389:390		C-loop
geometric
IL_5J7L_018
IL_03109.3
IL_3J2F_0201/N/375:376,
1/N/387:389		Single bulged G
homologous
IL_4LFB_016
IL_00225.14
IL_3J2F_0831/N/409:416,
1/N/427:433		No text annotation
homologous
IL_6CZR_359
NA
IL_3J2F_0231/N/440:442,
1/N/492:497		No text annotation
homologous
IL_5J7L_021
IL_33323.1
IL_3J2F_0241/N/446:450,
1/N/483:488		tSH-tHW-tWW
homologous
IL_5J7L_022
IL_88269.4
IL_3J2F_0251/N/450:455,
1/N/477:483		No text annotation
IL_3J2F_0271/N/458:459,
1/N/472:474		No text annotation
IL_3J2F_0841/N/460:462,
1/N/470:471		No text annotation
IL_3J2F_0281/N/504:511,
1/N/540:541		SSU/LSU pseudoknot
homologous
IL_5J7L_024
IL_41203.4
IL_3J2F_0291/N/515:521,
1/N/528:536		No text annotation
IL_3J2F_0301/N/569:575,
1/N/880:881		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_3J2F_0311/N/580:584,
1/N/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
IL_17136.7
IL_3J2F_0321/N/594:596,
1/N/644:645		Major groove platform
homologous
IL_5J7L_028
IL_48076.6
IL_3J2F_0331/N/597:598,
1/N/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_029
IL_68140.4
IL_3J2F_0351/N/605:612,
1/N/628:633		No text annotation
IL_3J2F_0361/N/654:655,
1/N/751:754		Major groove platform; stack outside cWW
homologous
IL_5J7L_031
IL_50694.7
IL_3J2F_0371/N/658:659,
1/N/746:748		Single stack bend
homologous
IL_5J7L_032
IL_26793.1
IL_3J2F_0391/N/662:666,
1/N/740:743		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
IL_85033.2
IL_3J2F_0401/N/673:677,
1/N/713:717		Triple non-canonical cWW pairs
homologous
IL_5J7L_361
IL_49751.4
IL_3J2F_0411/N/684:688,
1/N/699:706		Kink-turn
homologous
IL_5J7L_035
IL_01488.3
IL_3J2F_0421/N/773:779,
1/N/803:806		No text annotation
IL_3J2F_0431/N/779:783,
1/N/799:803		tSH-tHW-tHS
geometric
IL_4LFB_033
IL_17136.7
IL_3J2F_0451/N/887:894,
1/N/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4LFB_034
IL_41756.4
IL_3J2F_0931/N/922:923,
1/N/1393:1395		Single bulged A
geometric
IL_8VFS_004
IL_31462.7
IL_3J2F_0471/N/924:928,
1/N/1389:1392		No text annotation
IL_3J2F_0481/N/933:935,
1/N/1380:1384		Minor groove platform
homologous
IL_4LFB_037
IL_47078.3
IL_3J2F_0871/N/951:954,
1/N/1226:1230		Tandem non-canonical cWW pairs
geometric
IL_5EW4_002
IL_85033.2
IL_3J2F_0491/N/953:954,
1/N/1226:1228		Minor groove platform
homologous
IL_4LFB_038
IL_51454.3
IL_3J2F_0501/N/993:997,
1/N/1044:1045		Minor groove platform
homologous
IL_5J7L_043
IL_47078.3
IL_3J2F_0511/N/998:999,
1/N/1041:1043		Single stack bend
homologous
IL_5J7L_044
IL_26793.1
IL_3J2F_0531/N/1048:1050,
1/N/1208:1209		Single bulged U
homologous
IL_4LFB_042
IL_89505.4
IL_3J2F_0541/N/1052:1056,
1/N/1204:1206		Isolated cWS basepair
homologous
IL_4LFB_044
IL_76319.5
IL_3J2F_0891/N/1057:1058,
1/N/1199:1203		Minor groove platform
homologous
IL_5J7L_048
IL_95583.2
IL_3J2F_0561/N/1060:1061,
1/N/1195:1197		No text annotation
IL_3J2F_0581/N/1121:1128,
1/N/1144:1152		No text annotation
IL_3J2F_0591/N/1129:1132,
1/N/1142:1143		Minor groove platform
homologous
IL_5J7L_052
IL_15052.4
IL_3J2F_0601/N/1158:1161,
1/N/1175:1181		No text annotation
homologous
IL_5J7L_053
IL_42032.1
IL_3J2F_0611/N/1247:1253,
1/N/1284:1290		No text annotation
geometric
IL_5J7L_054
IL_09129.2
IL_3J2F_0631/N/1255:1258,
1/N/1277:1282		180 degree turn
geometric
IL_5J7L_055
IL_11344.2
IL_3J2F_0641/N/1259:1263,
1/N/1272:1276		Triple sheared
homologous
IL_5J7L_056
IL_17948.2
IL_3J2F_0651/N/1303:1308,
1/N/1329:1334		No text annotation
homologous
IL_5J7L_057
IL_85536.2
IL_3J2F_0671/N/1399:1401,
1/N/1501:1504		No text annotation
homologous
IL_5J7L_058
IL_61438.4
IL_3J2F_0681/N/1401:1404,
1/N/1497:1501		No text annotation
homologous
IL_4LFB_068
IL_65718.4
IL_3J2F_0691/N/1405:1407,
1/N/1494:1496		Isolated non-canonical cWW pair
geometric
IL_4E48_004
IL_87907.2
IL_3J2F_0911/N/1405:1409,
1/N/1491:1496		Partly complementary
homologous
IL_6CZR_167
NA
IL_3J2F_0701/N/1407:1410,
1/N/1490:1494		No text annotation
IL_3J2F_0711/N/1412:1414,
1/N/1486:1488		Isolated non-canonical cWW pair
homologous
IL_4LFB_059
IL_87907.2
IL_3J2F_0721/N/1416:1419,
1/N/1481:1484		Double sheared
homologous
IL_5J7L_062
IL_09705.15
IL_3J2F_0741/N/1430:1435,
1/N/1466:1470		Triple sheared related
homologous
IL_5J7L_063
IL_80231.1
IL_3J2F_0761/N/1440:1442,
1/N/1460:1461		Single bulged A
homologous
IL_5J7L_064
IL_31462.7
IL_3J2F_0941/N/1445:1448,
1/N/1455:1457		No text annotation

Problematic loops

#loop idProblemSequence
IL_3J2F_001Isolated non-canonical cWW pair
IL_3J2F_002Isolated non-canonical cWW pair
IL_3J2F_003Isolated non-canonical cWW pair
IL_3J2F_005Isolated non-canonical cWW pair
IL_3J2F_009No text annotation
IL_3J2F_013No text annotation
IL_3J2F_014No text annotation
IL_3J2F_016No text annotation
IL_3J2F_082No text annotation
IL_3J2F_021Isolated cWH basepair
IL_3J2F_022No text annotation
IL_3J2F_026Isolated non-canonical cWW pair
IL_3J2F_034Isolated non-canonical cWW pair
IL_3J2F_085No text annotation
IL_3J2F_038Not an internal loop
IL_3J2F_044No text annotation
IL_3J2F_086Isolated non-canonical cWW pair
IL_3J2F_046Isolated non-canonical cWW pair
IL_3J2F_052Isolated near basepair
IL_3J2F_088No text annotation
IL_3J2F_055No text annotation
IL_3J2F_057Isolated cWS basepair
IL_3J2F_090No text annotation
IL_3J2F_062Isolated non-canonical cWW pair
IL_3J2F_066Isolated cWH basepair
IL_3J2F_073Isolated cWH basepair
IL_3J2F_075Isolated non-canonical cWW pair
IL_3J2F_077No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3J2F_0011/N/46:52,
1/N/359:367,
1/N/393:395		No text annotation
J3_3J2F_0111/N/586:588,
1/N/651:654,
1/N/754:755		No text annotation
geometric
J3_1G1X_001
J3_56052.5
J3_3J2F_0141/N/586:588,
1/N/651:655,
1/N/751:755		No text annotation
homologous
J3_4LFB_015
J3_17385.4
J3_3J2F_0121/N/672:673,
1/N/717:725,
1/N/732:734		No text annotation
J3_3J2F_0021/N/826:829,
1/N/857:861,
1/N/868:874		No text annotation
J3_3J2F_0031/N/936:939,
1/N/1344:1350,
1/N/1372:1379		No text annotation
homologous
J3_4LFB_002
J3_25303.4
J3_3J2F_0191/N/943:946,
1/N/1235:1237,
1/N/1337:1340		No text annotation
homologous
J3_6CZR_019
NA
J3_3J2F_0151/N/955:962,
1/N/973:984,
1/N/1221:1225		No text annotation
homologous
J3_5J7L_006
J3_83516.4
J3_3J2F_0061/N/990:993,
1/N/1045:1047,
1/N/1210:1215		No text annotation
homologous
J3_5J7L_007
J3_82572.1
J3_3J2F_0161/N/990:997,
1/N/1044:1047,
1/N/1210:1215		No text annotation
homologous
J3_5J7L_053
J3_76475.2
J3_3J2F_0071/N/1002:1006,
1/N/1023:1027,
1/N/1034:1038		No text annotation
J3_3J2F_0081/N/1061:1068,
1/N/1107:1114,
1/N/1186:1195		No text annotation
J3_3J2F_0131/N/1073:1074,
1/N/1083:1087,
1/N/1098:1102		No text annotation
J3_3J2F_0091/N/1116:1118,
1/N/1155:1158,
1/N/1181:1184		No text annotation
homologous
J3_5J7L_010
J3_82365.4
J3_3J2F_0201/N/1116:1118,
1/N/1155:1161,
1/N/1175:1184		No text annotation
homologous
J3_5J7L_054
J3_17791.2
J3_3J2F_0101/N/1237:1241,
1/N/1296:1303,
1/N/1334:1337		No text annotation
geometric
J3_5J7L_011
J3_37047.6
J3_3J2F_0181/N/1237:1241,
1/N/1296:1308,
1/N/1329:1337		No text annotation
J4_3J2F_0011/N/115:122,
1/N/239:240,
1/N/286:289,
1/N/311:312		No text annotation
J4_3J2F_0021/N/141:144,
1/N/178:184,
1/N/193:198,
1/N/219:222		No text annotation
J4_3J2F_0041/N/575:577,
1/N/764:769,
1/N/810:821,
1/N/879:880		No text annotation
homologous
J4_5J7L_003
J4_61885.6
J5_3J2F_0011/N/36:39,
1/N/403:406,
1/N/436:440,
1/N/497:500,
1/N/545:548		No text annotation
homologous
J5_5J7L_001
J5_92941.1
J5_3J2F_0021/N/36:39,
1/N/403:406,
1/N/436:442,
1/N/492:500,
1/N/545:548		No text annotation
homologous
J5_5J7L_002
J5_67416.1
J5_3J2F_0031/N/58:66,
1/N/103:113,
1/N/314:316,
1/N/337:339,
1/N/350:354		No text annotation

Problematic loops

#loop idProblemSequence
J3_3J2F_004No text annotation
J3_3J2F_005No text annotation
J3_3J2F_017No text annotation
J4_3J2F_003No text annotation

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