RNA 3D Hub //

3J2D Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3J2D_0011/N/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_3J2D_0021/N/82:87No text annotation
HL_3J2D_0031/N/158:163GNRA
homologous
HL_4LFB_003
HL_37824.8
HL_3J2D_0041/N/186:191GNRA
homologous
HL_5J7L_004
HL_37824.8
HL_3J2D_0051/N/207:212No text annotation
HL_3J2D_0371/N/259:267GNRA related
homologous
HL_4LFB_006
HL_84299.4
HL_3J2D_0071/N/296:301GNRA
homologous
HL_4LFB_007
HL_37824.8
HL_3J2D_0081/N/320:333No text annotation
homologous
HL_5J7L_008
HL_81205.3
HL_3J2D_0091/N/342:347UNCG
homologous
HL_6CZR_080
NA
HL_3J2D_0101/N/379:384GNRA
homologous
HL_5J7L_010
HL_37824.8
HL_3J2D_0111/N/419:424UNCG
homologous
HL_5J7L_011
HL_34617.5
HL_3J2D_0121/N/459:472No text annotation
HL_3J2D_0381/N/459:473No text annotation
HL_3J2D_0131/N/522:527Mini UNCG
geometric
HL_4YAZ_004
HL_48778.2
HL_3J2D_0141/N/617:623GNRA-like with tWH
homologous
HL_5J7L_014
HL_10453.3
HL_3J2D_0151/N/689:698No text annotation
homologous
HL_4LFB_015
HL_75293.5
HL_3J2D_0161/N/726:731GNRA
homologous
HL_5J7L_016
HL_37824.8
HL_3J2D_0341/N/785:797No text annotation
HL_3J2D_0171/N/786:796No text annotation
HL_3J2D_0181/N/840:846No text annotation
geometric
HL_8VM9_005
HL_32346.4
HL_3J2D_0191/N/862:867GNRA
homologous
HL_4LFB_019
HL_37824.8
HL_3J2D_0201/N/897:902GNRA
homologous
HL_4LFB_020
HL_37824.8
HL_3J2D_0211/N/963:972No text annotation
HL_3J2D_0221/N/1012:1017GNRA
homologous
HL_4LFB_022
HL_37824.8
HL_3J2D_0231/N/1028:1033No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_3J2D_0241/N/1076:1081UNCG variation
geometric
HL_1P6V_001
HL_53890.2
HL_3J2D_0251/N/1089:1096No text annotation
HL_3J2D_0261/N/1134:1140No text annotation
homologous
HL_5J7L_025
HL_87954.2
HL_3J2D_0271/N/1165:1171GNRA
homologous
HL_5J7L_026
HL_93535.1
HL_3J2D_0281/N/1265:1270GNRA
homologous
HL_4LFB_028
HL_37824.8
HL_3J2D_0291/N/1314:1323T-loop with 3 stacked bulged bases
homologous
HL_5J7L_028
HL_02887.3
HL_3J2D_0301/N/1356:1366No text annotation
HL_3J2D_0311/N/1444:1458No text annotation
HL_3J2D_0321/N/1515:1520GNRA
homologous
HL_4LFB_032
HL_37824.8

Problematic loops

#loop idProblemSequence
HL_3J2D_006No text annotation
HL_3J2D_033No text annotation
HL_3J2D_035No text annotation
HL_3J2D_036No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3J2D_0011/N/30:32,
1/N/552:553		Single bulged G
homologous
IL_6CZR_113
NA
IL_3J2D_0021/N/44:45,
1/N/396:398		Single bulged A
homologous
IL_5J7L_002
IL_31462.7
IL_3J2D_0031/N/54:56,
1/N/356:357		Minor groove platform
homologous
IL_5J7L_004
IL_51454.3
IL_3J2D_0051/N/63:66,
1/N/103:104		Multiple bulged bases
geometric
IL_1FUF_002
IL_82107.5
IL_3J2D_0061/N/67:69,
1/N/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
IL_90351.1
IL_3J2D_0071/N/70:73,
1/N/97:98		Minor groove platform
homologous
IL_5J7L_007
IL_15052.4
IL_3J2D_0881/N/75:81,
1/N/88:95		No text annotation
IL_3J2D_0091/N/128:136,
1/N/227:233		No text annotation
IL_3J2D_0111/N/144:146,
1/N/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
IL_10167.6
IL_3J2D_0121/N/147:153,
1/N/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_3J2D_0891/N/202:206,
1/N/213:215		No text annotation
IL_3J2D_0161/N/242:247,
1/N/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
IL_46174.3
IL_3J2D_0781/N/249:252,
1/N/274:275		No text annotation
homologous
IL_5J7L_015
IL_47074.2
IL_3J2D_0181/N/292:293,
1/N/304:308		No text annotation
IL_3J2D_0191/N/367:369,
1/N/392:393		Single bulged U
geometric
IL_5TBW_130
NA
IL_3J2D_0901/N/371:375,
1/N/389:390		C-loop
homologous
IL_5J7L_018
IL_03109.3
IL_3J2D_0211/N/375:376,
1/N/387:389		Single bulged G
homologous
IL_5J7L_019
IL_00225.14
IL_3J2D_0791/N/409:416,
1/N/427:433		No text annotation
homologous
IL_6CZR_359
NA
IL_3J2D_0241/N/440:442,
1/N/492:497		No text annotation
homologous
IL_5J7L_021
IL_33323.1
IL_3J2D_0251/N/446:450,
1/N/483:488		tSH-tHW-tWW
homologous
IL_5J7L_022
IL_88269.4
IL_3J2D_0261/N/450:455,
1/N/477:483		No text annotation
IL_3J2D_0281/N/457:459,
1/N/472:475		No text annotation
IL_3J2D_0291/N/504:511,
1/N/540:541		SSU/LSU pseudoknot
homologous
IL_5J7L_024
IL_41203.4
IL_3J2D_0301/N/515:521,
1/N/528:536		No text annotation
IL_3J2D_0311/N/569:575,
1/N/880:881		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_3J2D_0321/N/580:584,
1/N/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
IL_17136.7
IL_3J2D_0341/N/594:596,
1/N/644:645		Major groove platform
homologous
IL_5J7L_028
IL_48076.6
IL_3J2D_0351/N/597:598,
1/N/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_029
IL_68140.4
IL_3J2D_0911/N/605:610,
1/N/629:633		No text annotation
IL_3J2D_0921/N/610:612,
1/N/628:629		Minor groove platform
geometric
IL_5J7L_247
IL_51454.3
IL_3J2D_0381/N/654:655,
1/N/751:754		Major groove platform; stack outside cWW
geometric
IL_5J7L_031
IL_50694.7
IL_3J2D_0401/N/658:659,
1/N/746:748		Single stack bend
homologous
IL_5J7L_032
IL_26793.1
IL_3J2D_0421/N/662:666,
1/N/740:743		Tandem non-canonical cWW pairs
homologous
IL_4LFB_029
IL_85033.2
IL_3J2D_0811/N/684:688,
1/N/699:706		Kink-turn
homologous
IL_5J7L_035
IL_01488.3
IL_3J2D_0441/N/773:779,
1/N/803:806		No text annotation
IL_3J2D_0451/N/779:783,
1/N/799:803		tSH-tHW-tHS
geometric
IL_4LFB_033
IL_17136.7
IL_3J2D_0471/N/887:894,
1/N/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4LFB_034
IL_41756.4
IL_3J2D_0481/N/922:924,
1/N/1392:1395		Isolated non-canonical cWW pair
geometric
IL_4P3U_007
IL_28037.2
IL_3J2D_0491/N/924:927,
1/N/1390:1392		No text annotation
IL_3J2D_0501/N/933:935,
1/N/1380:1384		Minor groove platform
homologous
IL_4LFB_037
IL_47078.3
IL_3J2D_0521/N/993:997,
1/N/1044:1045		Minor groove platform
homologous
IL_5J7L_043
IL_47078.3
IL_3J2D_0531/N/998:999,
1/N/1041:1043		Single stack bend
homologous
IL_5J7L_044
IL_26793.1
IL_3J2D_0541/N/1048:1050,
1/N/1208:1209		Single bulged U
homologous
IL_4LFB_042
IL_89505.4
IL_3J2D_0551/N/1052:1056,
1/N/1204:1206		Isolated cWS basepair
homologous
IL_4LFB_044
IL_76319.5
IL_3J2D_0831/N/1057:1058,
1/N/1199:1203		Minor groove platform
homologous
IL_5J7L_048
IL_95583.2
IL_3J2D_0841/N/1124:1128,
1/N/1144:1149		No text annotation
homologous
IL_5J7L_051
IL_06691.1
IL_3J2D_0591/N/1129:1132,
1/N/1142:1143		Minor groove platform
homologous
IL_5J7L_052
IL_15052.4
IL_3J2D_0601/N/1158:1161,
1/N/1175:1181		No text annotation
geometric
IL_5J7L_053
IL_42032.1
IL_3J2D_0611/N/1247:1253,
1/N/1284:1290		No text annotation
IL_3J2D_0931/N/1247:1254,
1/N/1283:1290		No text annotation
IL_3J2D_0631/N/1255:1258,
1/N/1277:1282		180 degree turn
geometric
IL_5J7L_055
IL_11344.2
IL_3J2D_0641/N/1259:1263,
1/N/1272:1276		Double sheared with non-canonical cWW
homologous
IL_5J7L_056
IL_17948.2
IL_3J2D_0651/N/1303:1308,
1/N/1329:1334		No text annotation
geometric
IL_5J7L_057
IL_85536.2
IL_3J2D_0671/N/1401:1404,
1/N/1497:1501		No text annotation
homologous
IL_4LFB_068
IL_65718.4
IL_3J2D_0681/N/1405:1407,
1/N/1494:1496		Isolated non-canonical cWW pair
geometric
IL_4ZC7_001
IL_87907.2
IL_3J2D_0691/N/1407:1409,
1/N/1491:1494		Isolated non-canonical cWW pair
homologous
IL_5J7L_363
IL_87907.2
IL_3J2D_0711/N/1412:1414,
1/N/1486:1488		Isolated near basepair
geometric
IL_3NJ7_004
IL_42997.3
IL_3J2D_0871/N/1412:1416,
1/N/1484:1488		No text annotation
IL_3J2D_0731/N/1416:1419,
1/N/1481:1484		Double sheared
homologous
IL_4LFB_060
IL_09705.15
IL_3J2D_0741/N/1430:1435,
1/N/1466:1470		Triple sheared related
homologous
IL_5J7L_063
IL_80231.1
IL_3J2D_0941/N/1440:1443,
1/N/1459:1461		No text annotation

Problematic loops

#loop idProblemSequence
IL_3J2D_077Isolated non-canonical cWW pair
IL_3J2D_004Isolated non-canonical cWW pair
IL_3J2D_008No text annotation
IL_3J2D_010Isolated non-canonical cWW pair
IL_3J2D_013Isolated non-canonical cWW pair
IL_3J2D_014Isolated non-canonical cWW pair
IL_3J2D_015No text annotation
IL_3J2D_017No text annotation
IL_3J2D_020No text annotation
IL_3J2D_022Isolated cWH basepair
IL_3J2D_023No text annotation
IL_3J2D_027Isolated non-canonical cWW pair
IL_3J2D_080Tandem non-canonical cWW pairs
IL_3J2D_033Isolated non-canonical cWW pair
IL_3J2D_036Stack and bulge
IL_3J2D_037No text annotation
IL_3J2D_039No text annotation
IL_3J2D_041No text annotation
IL_3J2D_043Kink-turn
IL_3J2D_046No text annotation
IL_3J2D_051Isolated non-canonical cWW pair
IL_3J2D_082No text annotation
IL_3J2D_056Tandem non-canonical cWW pairs
IL_3J2D_057Isolated cWS basepair
IL_3J2D_058No text annotation
IL_3J2D_085No text annotation
IL_3J2D_086No text annotation
IL_3J2D_062No text annotation
IL_3J2D_066Isolated non-canonical cWW pair
IL_3J2D_070No text annotation
IL_3J2D_072No text annotation
IL_3J2D_075Isolated non-canonical cWW pair
IL_3J2D_076No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3J2D_0011/N/46:52,
1/N/359:367,
1/N/393:395		No text annotation
homologous
J3_6CZR_058
NA
J3_3J2D_0111/N/586:588,
1/N/651:654,
1/N/754:755		No text annotation
geometric
J3_4LFB_011
J3_56052.5
J3_3J2D_0131/N/586:588,
1/N/651:655,
1/N/751:755		No text annotation
homologous
J3_5J7L_051
J3_17385.4
J3_3J2D_0211/N/672:677,
1/N/713:725,
1/N/732:734		No text annotation
J3_3J2D_0021/N/826:829,
1/N/857:861,
1/N/868:874		No text annotation
homologous
J3_5J7L_004
J3_85054.4
J3_3J2D_0031/N/936:939,
1/N/1344:1350,
1/N/1372:1379		No text annotation
homologous
J3_4LFB_002
J3_25303.4
J3_3J2D_0221/N/941:946,
1/N/1235:1237,
1/N/1337:1342		No text annotation
J3_3J2D_0231/N/951:962,
1/N/973:984,
1/N/1221:1230		No text annotation
J3_3J2D_0051/N/953:962,
1/N/973:984,
1/N/1221:1228		No text annotation
J3_3J2D_0061/N/990:993,
1/N/1045:1047,
1/N/1210:1215		No text annotation
homologous
J3_5J7L_007
J3_82572.1
J3_3J2D_0241/N/990:997,
1/N/1044:1047,
1/N/1210:1215		No text annotation
homologous
J3_5J7L_053
J3_76475.2
J3_3J2D_0251/N/1003:1006,
1/N/1023:1027,
1/N/1034:1037		No text annotation
J3_3J2D_0191/N/1060:1068,
1/N/1107:1113,
1/N/1187:1197		No text annotation
J3_3J2D_0121/N/1073:1074,
1/N/1083:1087,
1/N/1098:1102		No text annotation
J3_3J2D_0091/N/1116:1118,
1/N/1155:1158,
1/N/1181:1184		No text annotation
homologous
J3_5J7L_010
J3_82365.4
J3_3J2D_0261/N/1116:1118,
1/N/1155:1161,
1/N/1175:1184		No text annotation
homologous
J3_5J7L_054
J3_17791.2
J3_3J2D_0101/N/1237:1241,
1/N/1296:1303,
1/N/1334:1337		No text annotation
homologous
J3_5J7L_011
J3_37047.6
J4_3J2D_0011/N/115:123,
1/N/238:240,
1/N/286:289,
1/N/311:312		No text annotation
J4_3J2D_0021/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_3J2D_0031/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_3J2D_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_3J2D_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_3J2D_0031/N/58:63,
1/N/104:113,
1/N/314:316,
1/N/337:339,
1/N/350:354		No text annotation
homologous
J5_6CZR_008
NA

Problematic loops

#loop idProblemSequence
J3_3J2D_014No text annotation
J3_3J2D_015No text annotation
J3_3J2D_004No text annotation
J3_3J2D_016No text annotation
J3_3J2D_017No text annotation
J3_3J2D_007No text annotation
J3_3J2D_018No text annotation
J3_3J2D_008No text annotation
J3_3J2D_020No text annotation

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