RNA 3D Hub //

3J2C Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3J2C_0011/M/963:972No text annotation
HL_3J2C_0021/M/1012:1017GNRA
homologous
HL_4LFB_022
HL_37824.8
HL_3J2C_0031/M/1028:1033No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_3J2C_0381/M/1076:1081No text annotation
HL_3J2C_0051/M/1089:1096No text annotation
geometric
HL_7Z4O_002
HL_49922.4
HL_3J2C_0061/M/1134:1140No text annotation
homologous
HL_4LFB_026
HL_87954.2
HL_3J2C_0071/M/1165:1171GNRA
homologous
HL_5J7L_026
HL_93535.1
HL_3J2C_0081/M/1265:1270GNRA
homologous
HL_4LFB_028
HL_37824.8
HL_3J2C_0091/M/1314:1323T-loop with 3 stacked bulged bases
homologous
HL_5J7L_028
HL_02887.3
HL_3J2C_0101/M/1356:1366No text annotation
HL_3J2C_0111/N/12:22No text annotation
homologous
HL_5J7L_001
HL_89881.5
HL_3J2C_0121/N/82:87No text annotation
HL_3J2C_0131/N/158:163GNRA
homologous
HL_4LFB_003
HL_37824.8
HL_3J2C_0141/N/186:191GNRA
homologous
HL_5J7L_004
HL_37824.8
HL_3J2C_0151/N/207:212No text annotation
HL_3J2C_0161/N/258:268No text annotation
geometric
HL_6DME_003
HL_60266.1
HL_3J2C_0171/N/296:301GNRA
homologous
HL_5J7L_007
HL_37824.8
HL_3J2C_0181/N/320:333No text annotation
HL_3J2C_0191/N/342:347UNCG
homologous
HL_6CZR_080
NA
HL_3J2C_0201/N/379:384GNRA
homologous
HL_5J7L_010
HL_37824.8
HL_3J2C_0211/N/419:424UNCG
homologous
HL_4LFB_011
HL_34617.5
HL_3J2C_0221/N/460:471No text annotation
HL_3J2C_0231/N/522:527No text annotation
geometric
HL_2Y9H_003
HL_75660.5
HL_3J2C_0241/N/617:623GNRA-like with tWH
homologous
HL_5J7L_014
HL_10453.3
HL_3J2C_0251/N/689:698No text annotation
homologous
HL_4LFB_015
HL_75293.5
HL_3J2C_0261/N/726:731GNRA
homologous
HL_5J7L_016
HL_37824.8
HL_3J2C_0271/N/786:796No text annotation
HL_3J2C_0281/N/840:846No text annotation
HL_3J2C_0291/N/862:867GNRA
homologous
HL_5J7L_019
HL_37824.8
HL_3J2C_0301/N/897:902GNRA
homologous
HL_4LFB_020
HL_37824.8
HL_3J2C_0321/O/1449:1454UNCG
homologous
HL_5J7L_030
HL_34617.5
HL_3J2C_0331/O/1515:1520GNRA
homologous
HL_4LFB_032
HL_37824.8

Problematic loops

#loop idProblemSequence
HL_3J2C_004No text annotation
HL_3J2C_034No text annotation
HL_3J2C_035No text annotation
HL_3J2C_036No text annotation
HL_3J2C_037No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3J2C_0011/M/933:935,
1/M/1380:1384		Minor groove platform
homologous
IL_4LFB_037
IL_47078.3
IL_3J2C_0021/M/953:954,
1/M/1226:1228		Minor groove platform
homologous
IL_4LFB_038
IL_51454.3
IL_3J2C_0041/M/993:997,
1/M/1044:1045		Minor groove platform
homologous
IL_5J7L_043
IL_47078.3
IL_3J2C_0051/M/998:999,
1/M/1041:1043		Single stack bend
homologous
IL_5J7L_044
IL_26793.1
IL_3J2C_0091/M/1048:1050,
1/M/1208:1209		Single bulged U
homologous
IL_5J7L_046
IL_89505.4
IL_3J2C_0101/M/1052:1057,
1/M/1203:1206		No text annotation
IL_3J2C_0921/M/1052:1058,
1/M/1199:1206		No text annotation
geometric
IL_8P9A_439
IL_86012.1
IL_3J2C_0111/M/1057:1058,
1/M/1199:1203		Minor groove platform
geometric
IL_6CZR_155
NA
IL_3J2C_0121/M/1060:1061,
1/M/1195:1197		Single bulged U
homologous
IL_6CZR_156
NA
IL_3J2C_0131/M/1121:1128,
1/M/1144:1152		No text annotation
IL_3J2C_0141/M/1129:1132,
1/M/1142:1143		Minor groove platform
homologous
IL_5J7L_052
IL_15052.4
IL_3J2C_0151/M/1158:1163,
1/M/1173:1181		No text annotation
IL_3J2C_0181/M/1247:1253,
1/M/1284:1290		No text annotation
IL_3J2C_0191/M/1255:1258,
1/M/1277:1282		180 degree turn
homologous
IL_5J7L_055
IL_11344.2
IL_3J2C_0201/M/1259:1263,
1/M/1272:1276		Double sheared with non-canonical cWW
geometric
IL_5J7L_274
IL_17948.2
IL_3J2C_0221/M/1303:1308,
1/M/1329:1334		No text annotation
homologous
IL_4LFB_055
IL_85536.2
IL_3J2C_0251/N/30:32,
1/N/552:553		Single bulged G
homologous
IL_6CZR_113
NA
IL_3J2C_0811/N/44:45,
1/N/396:398		Single bulged A
homologous
IL_5J7L_002
IL_31462.7
IL_3J2C_0271/N/54:56,
1/N/356:357		Minor groove platform
homologous
IL_5J7L_004
IL_51454.3
IL_3J2C_0281/N/61:66,
1/N/103:106		No text annotation
IL_3J2C_0291/N/67:69,
1/N/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
IL_90351.1
IL_3J2C_0301/N/70:73,
1/N/97:98		Minor groove platform
homologous
IL_5J7L_007
IL_15052.4
IL_3J2C_0931/N/75:76,
1/N/93:95		No text annotation
IL_3J2C_0321/N/128:136,
1/N/227:233		No text annotation
IL_3J2C_0341/N/144:146,
1/N/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
IL_10167.6
IL_3J2C_0351/N/147:153,
1/N/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_3J2C_0841/N/202:206,
1/N/213:215		No text annotation
IL_3J2C_0371/N/242:247,
1/N/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
IL_46174.3
IL_3J2C_0381/N/249:252,
1/N/274:275		No text annotation
homologous
IL_5J7L_015
IL_47074.2
IL_3J2C_0391/N/292:293,
1/N/304:308		No text annotation
IL_3J2C_0411/N/367:369,
1/N/392:393		Single bulged U
homologous
IL_4LFB_014
IL_89505.4
IL_3J2C_0951/N/371:375,
1/N/389:390		C-loop
homologous
IL_5J7L_018
IL_03109.3
IL_3J2C_0431/N/375:376,
1/N/387:389		Single bulged G
homologous
IL_4LFB_016
IL_00225.14
IL_3J2C_0851/N/409:416,
1/N/427:433		No text annotation
homologous
IL_4LFB_017
IL_28026.3
IL_3J2C_0461/N/440:442,
1/N/492:497		No text annotation
homologous
IL_5J7L_021
IL_33323.1
IL_3J2C_0471/N/446:450,
1/N/483:488		6x5 Sarcin-Ricin; G-bulge
homologous
IL_4LFB_018
IL_88269.4
IL_3J2C_0481/N/450:455,
1/N/477:483		No text annotation
IL_3J2C_0501/N/458:459,
1/N/472:474		No text annotation
IL_3J2C_0511/N/504:511,
1/N/540:541		SSU/LSU pseudoknot
homologous
IL_5J7L_024
IL_41203.4
IL_3J2C_0521/N/515:521,
1/N/528:536		No text annotation
IL_3J2C_0861/N/569:575,
1/N/880:881		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_3J2C_0531/N/580:584,
1/N/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
IL_17136.7
IL_3J2C_0541/N/594:596,
1/N/644:645		Major groove platform
homologous
IL_5J7L_028
IL_48076.6
IL_3J2C_0551/N/597:598,
1/N/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_029
IL_68140.4
IL_3J2C_0571/N/605:612,
1/N/628:633		No text annotation
IL_3J2C_0581/N/654:655,
1/N/751:754		Major groove platform; stack outside cWW
homologous
IL_5J7L_031
IL_50694.7
IL_3J2C_0591/N/658:659,
1/N/746:748		Single stack bend
homologous
IL_5J7L_032
IL_26793.1
IL_3J2C_0601/N/662:666,
1/N/740:743		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
IL_85033.2
IL_3J2C_0961/N/673:677,
1/N/713:717		Triple non-canonical cWW pairs
geometric
IL_4LFB_065
IL_49751.4
IL_3J2C_0611/N/684:688,
1/N/699:706		Kink-turn
homologous
IL_5J7L_035
IL_01488.3
IL_3J2C_0971/N/773:778,
1/N/804:806		No text annotation
IL_3J2C_0631/N/779:783,
1/N/799:803		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_17136.7
IL_3J2C_0651/N/887:894,
1/N/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
IL_41756.4
IL_3J2C_0661/O/1399:1401,
1/O/1501:1504		No text annotation
homologous
IL_5J7L_058
IL_61438.4
IL_3J2C_0671/O/1401:1404,
1/O/1497:1501		No text annotation
IL_3J2C_0681/O/1405:1409,
1/O/1491:1496		No text annotation
IL_3J2C_0691/O/1412:1414,
1/O/1486:1488		Isolated non-canonical cWW pair
homologous
IL_4LFB_059
IL_87907.2
IL_3J2C_0701/O/1416:1419,
1/O/1481:1484		Double sheared
homologous
IL_5J7L_062
IL_09705.15
IL_3J2C_0981/O/1430:1435,
1/O/1466:1470		Triple sheared related
homologous
IL_5J7L_063
IL_80231.1
IL_3J2C_0991/O/1440:1442,
1/O/1460:1461		Single bulged A
homologous
IL_5J7L_064
IL_31462.7
IL_3J2C_1001/O/1445:1448,
1/O/1455:1457		No text annotation

Problematic loops

#loop idProblemSequence
IL_3J2C_077Tandem non-canonical cWW pairs
IL_3J2C_003Tandem non-canonical cWW pairs
IL_3J2C_078No text annotation
IL_3J2C_006Isolated non-canonical cWW pair
IL_3J2C_007No text annotation
IL_3J2C_008Self complementary
IL_3J2C_079No text annotation
IL_3J2C_080No text annotation
IL_3J2C_016No text annotation
IL_3J2C_017Isolated non-canonical cWW pair
IL_3J2C_021Isolated cWS basepair
IL_3J2C_023Isolated non-canonical cWW pair
IL_3J2C_024Tandem non-canonical cWW pairs
IL_3J2C_026Isolated non-canonical cWW pair
IL_3J2C_082No text annotation
IL_3J2C_031No text annotation
IL_3J2C_033Isolated non-canonical cWW pair
IL_3J2C_083Tandem non-canonical cWW pairs
IL_3J2C_094Isolated non-canonical cWW pair
IL_3J2C_036No text annotation
IL_3J2C_040Isolated non-canonical cWW pair
IL_3J2C_042No text annotation
IL_3J2C_044Isolated non-canonical cWW pair
IL_3J2C_045No text annotation
IL_3J2C_049Isolated non-canonical cWW pair
IL_3J2C_056Isolated cWS basepair
IL_3J2C_087Tandem non-canonical cWW pairs
IL_3J2C_088No text annotation
IL_3J2C_062No text annotation
IL_3J2C_064Tandem non-canonical cWW pairs
IL_3J2C_089No text annotation
IL_3J2C_090No text annotation
IL_3J2C_076No text annotation
IL_3J2C_091No text annotation
IL_3J2C_073No text annotation
IL_3J2C_074No text annotation
IL_3J2C_075Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3J2C_0111/M/936:939,
1/M/1344:1350,
1/M/1372:1379		No text annotation
homologous
J3_4LFB_002
J3_25303.4
J3_3J2C_0191/M/942:946,
1/M/1235:1237,
1/M/1337:1341		No text annotation
homologous
J3_6CZR_019
NA
J3_3J2C_0201/M/954:962,
1/M/973:984,
1/M/1221:1226		No text annotation
J3_3J2C_0031/M/990:993,
1/M/1045:1047,
1/M/1210:1215		No text annotation
homologous
J3_5J7L_007
J3_82572.1
J3_3J2C_0211/M/990:997,
1/M/1044:1047,
1/M/1210:1215		No text annotation
homologous
J3_5J7L_053
J3_76475.2
J3_3J2C_0221/M/1003:1006,
1/M/1023:1027,
1/M/1034:1037		No text annotation
J3_3J2C_0091/M/1073:1074,
1/M/1083:1087,
1/M/1098:1102		No text annotation
J3_3J2C_0051/M/1116:1118,
1/M/1155:1158,
1/M/1181:1184		No text annotation
homologous
J3_5J7L_010
J3_82365.4
J3_3J2C_0061/M/1237:1241,
1/M/1296:1303,
1/M/1334:1337		No text annotation
J3_3J2C_0151/M/1237:1241,
1/M/1296:1308,
1/M/1329:1337		No text annotation
J3_3J2C_0071/N/46:52,
1/N/359:367,
1/N/393:395		No text annotation
homologous
J3_4LFB_014
J3_46317.4
J3_3J2C_0101/N/586:588,
1/N/651:654,
1/N/754:755		No text annotation
homologous
J3_5J7L_002
J3_56052.5
J3_3J2C_0231/N/586:588,
1/N/651:655,
1/N/751:755		No text annotation
homologous
J3_5J7L_051
J3_17385.4
J3_3J2C_0241/N/672:673,
1/N/717:725,
1/N/732:734		No text annotation
J3_3J2C_0081/N/826:829,
1/N/857:861,
1/N/868:874		No text annotation
J4_3J2C_0061/M/1061:1068,
1/M/1107:1118,
1/M/1155:1158,
1/M/1181:1195		No text annotation
J4_3J2C_0071/M/1061:1068,
1/M/1107:1118,
1/M/1155:1163,
1/M/1173:1195		No text annotation
J4_3J2C_0081/N/115:122,
1/N/239:240,
1/N/286:289,
1/N/311:312		No text annotation
J4_3J2C_0091/N/142:144,
1/N/178:184,
1/N/193:198,
1/N/219:221		No text annotation
homologous
J4_5J7L_002
J4_01665.1
J4_3J2C_0051/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_3J2C_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_3J2C_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_3J2C_0031/N/58:61,
1/N/106:113,
1/N/314:316,
1/N/337:339,
1/N/350:354		No text annotation
homologous
J5_4LFB_002
J5_59910.6

Problematic loops

#loop idProblemSequence
J3_3J2C_001No text annotation
J3_3J2C_012No text annotation
J3_3J2C_002No text annotation
J3_3J2C_013No text annotation
J3_3J2C_004No text annotation
J3_3J2C_014No text annotation
J3_3J2C_016No text annotation
J3_3J2C_017No text annotation
J3_3J2C_018No text annotation
J4_3J2C_001No text annotation
J4_3J2C_002No text annotation
J4_3J2C_003No text annotation
J4_3J2C_004No text annotation

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