RNA 3D Hub //

3J28 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_3J28_0011/N/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_3J28_0021/N/82:87No text annotation
HL_3J28_0031/N/158:163GNRA
homologous
HL_4LFB_003
HL_37824.7
HL_3J28_0041/N/186:191GNRA
homologous
HL_5J7L_004
HL_37824.7
HL_3J28_0051/N/207:212No text annotation
HL_3J28_0061/N/259:267GNRA related
homologous
HL_4LFB_006
HL_84299.4
HL_3J28_0071/N/296:301GNRA
homologous
HL_4LFB_007
HL_37824.7
HL_3J28_0081/N/320:333No text annotation
HL_3J28_0091/N/342:347UNCG
homologous
HL_6CZR_080
NA
HL_3J28_0101/N/379:384GNRA
homologous
HL_5J7L_010
HL_37824.7
HL_3J28_0111/N/419:424UNCG
homologous
HL_4LFB_011
HL_34617.5
HL_3J28_0391/N/459:473No text annotation
HL_3J28_0121/N/460:471No text annotation
HL_3J28_0131/N/522:527No text annotation
geometric
HL_4WF9_003
HL_75660.5
HL_3J28_0141/N/617:623No text annotation
homologous
HL_5J7L_014
HL_10453.3
HL_3J28_0151/N/689:698No text annotation
homologous
HL_4LFB_015
HL_75293.5
HL_3J28_0161/N/726:731GNRA
homologous
HL_5J7L_016
HL_37824.7
HL_3J28_0171/N/786:796No text annotation
HL_3J28_0181/N/840:846No text annotation
geometric
HL_8VM9_005
HL_32346.4
HL_3J28_0191/N/862:867GNRA
homologous
HL_5J7L_019
HL_37824.7
HL_3J28_0201/N/897:902GNRA
homologous
HL_4LFB_020
HL_37824.7
HL_3J28_0211/N/963:972No text annotation
HL_3J28_0221/N/1012:1017GNRA
homologous
HL_4LFB_022
HL_37824.7
HL_3J28_0231/N/1028:1033No text annotation
geometric
HL_5U3G_001
HL_75660.5
HL_3J28_0241/N/1076:1081GNRA
homologous
HL_5J7L_023
HL_37824.7
HL_3J28_0251/N/1089:1096T-loop related
homologous
HL_4LFB_025
HL_77436.5
HL_3J28_0261/N/1134:1140No text annotation
homologous
HL_5J7L_025
HL_87954.2
HL_3J28_0271/N/1165:1171GNRA
homologous
HL_5J7L_026
HL_93535.1
HL_3J28_0281/N/1265:1270GNRA
homologous
HL_4LFB_028
HL_37824.7
HL_3J28_0291/N/1314:1323T-loop with 2 stacked bulged bases
geometric
HL_5DH6_002
HL_01609.3
HL_3J28_0301/N/1356:1366No text annotation
HL_3J28_0311/N/1449:1454UNCG
homologous
HL_4LFB_031
HL_34617.5
HL_3J28_0321/N/1515:1520GNRA variation
geometric
HL_1JID_001
HL_37824.7

Problematic loops

#loop idProblemSequence
HL_3J28_033No text annotation
HL_3J28_034tRNA D-loop
HL_3J28_035No text annotation
HL_3J28_036No text annotation
HL_3J28_037No text annotation
HL_3J28_038No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_3J28_0011/N/30:32,
1/N/552:553		Single bulged G
homologous
IL_6CZR_113
NA
IL_3J28_0811/N/44:45,
1/N/396:398		Single bulged A
homologous
IL_5J7L_002
IL_31462.6
IL_3J28_0031/N/54:56,
1/N/356:357		Minor groove platform
homologous
IL_5J7L_004
IL_51454.3
IL_3J28_0051/N/63:66,
1/N/103:104		Multiple bulged bases
geometric
IL_5J7L_005
IL_82107.4
IL_3J28_0061/N/67:69,
1/N/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
IL_90351.1
IL_3J28_0071/N/70:73,
1/N/97:98		Minor groove platform
homologous
IL_5J7L_007
IL_15052.4
IL_3J28_0081/N/75:76,
1/N/93:95		No text annotation
IL_3J28_0111/N/128:136,
1/N/227:233		No text annotation
IL_3J28_0131/N/144:146,
1/N/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
IL_10167.6
IL_3J28_0141/N/147:153,
1/N/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_3J28_0821/N/202:206,
1/N/213:215		No text annotation
IL_3J28_1011/N/243:247,
1/N/277:283		No text annotation
IL_3J28_0831/N/249:252,
1/N/274:275		No text annotation
homologous
IL_5J7L_015
IL_47074.2
IL_3J28_0191/N/292:293,
1/N/304:308		No text annotation
IL_3J28_0211/N/371:375,
1/N/389:390		C-loop
homologous
IL_5J7L_018
IL_03109.3
IL_3J28_0221/N/375:376,
1/N/387:389		Single bulged G
homologous
IL_4LFB_016
IL_00225.13
IL_3J28_0851/N/409:416,
1/N/427:433		No text annotation
homologous
IL_4LFB_017
IL_28026.3
IL_3J28_0251/N/440:442,
1/N/492:497		No text annotation
homologous
IL_5J7L_021
IL_33323.1
IL_3J28_0261/N/446:450,
1/N/483:488		tSH-tHW-tWW
homologous
IL_5J7L_022
IL_88269.4
IL_3J28_0271/N/450:455,
1/N/477:483		No text annotation
IL_3J28_0291/N/459:460,
1/N/471:473		Single stack bend
geometric
IL_8C3A_076
NA
IL_3J28_0301/N/504:511,
1/N/540:541		SSU/LSU pseudoknot
homologous
IL_5J7L_024
IL_41203.4
IL_3J28_0311/N/515:521,
1/N/528:536		No text annotation
IL_3J28_0321/N/569:575,
1/N/880:881		Major groove intercalation
geometric
IL_1NBS_009
IL_82107.4
IL_3J28_0331/N/580:584,
1/N/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
IL_17136.7
IL_3J28_0341/N/594:596,
1/N/644:645		Major groove platform
homologous
IL_5J7L_028
IL_48076.6
IL_3J28_0351/N/597:598,
1/N/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_029
IL_68140.4
IL_3J28_0371/N/605:612,
1/N/628:633		No text annotation
IL_3J28_0381/N/654:655,
1/N/751:754		Major groove platform; stack outside cWW
geometric
IL_4V9F_061
IL_50694.7
IL_3J28_0401/N/658:659,
1/N/746:748		Single stack bend
homologous
IL_5J7L_032
IL_26793.1
IL_3J28_0421/N/662:666,
1/N/740:743		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
IL_85033.2
IL_3J28_0871/N/673:677,
1/N/713:717		Triple non-canonical cWW pairs
homologous
IL_5J7L_361
IL_49751.4
IL_3J28_0441/N/684:688,
1/N/699:706		Kink-turn
homologous
IL_5J7L_035
IL_01488.3
IL_3J28_0451/N/773:783,
1/N/799:806		No text annotation
IL_3J28_0471/N/887:894,
1/N/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4LFB_034
IL_41756.4
IL_3J28_0881/N/922:923,
1/N/1393:1395		Single bulged A
homologous
IL_4LFB_035
IL_31462.6
IL_3J28_0491/N/924:929,
1/N/1388:1392		No text annotation
IL_3J28_0501/N/933:935,
1/N/1380:1384		Minor groove platform
homologous
IL_4LFB_037
IL_47078.3
IL_3J28_0961/N/953:954,
1/N/1226:1228		Minor groove platform
homologous
IL_4LFB_038
IL_51454.3
IL_3J28_0971/N/993:997,
1/N/1044:1045		Minor groove platform
geometric
IL_5J7L_043
IL_47078.3
IL_3J28_0521/N/998:999,
1/N/1041:1043		Single stack bend
homologous
IL_5J7L_044
IL_26793.1
IL_3J28_0541/N/1048:1050,
1/N/1208:1209		Single bulged U
homologous
IL_4LFB_042
IL_89505.4
IL_3J28_0551/N/1052:1056,
1/N/1204:1206		Isolated cWS basepair
homologous
IL_4LFB_044
IL_76319.5
IL_3J28_0921/N/1057:1058,
1/N/1199:1203		Minor groove platform
homologous
IL_5J7L_048
IL_95583.2
IL_3J28_0571/N/1060:1061,
1/N/1195:1197		No text annotation
IL_3J28_0931/N/1124:1128,
1/N/1144:1149		No text annotation
homologous
IL_5J7L_051
IL_06691.1
IL_3J28_0621/N/1129:1132,
1/N/1142:1143		Minor groove platform
homologous
IL_5J7L_052
IL_15052.4
IL_3J28_0941/N/1158:1162,
1/N/1174:1181		No text annotation
IL_3J28_0641/N/1247:1253,
1/N/1284:1290		No text annotation
IL_3J28_0981/N/1247:1254,
1/N/1283:1290		No text annotation
IL_3J28_0661/N/1255:1258,
1/N/1277:1282		180 degree turn
geometric
IL_5J7L_055
IL_11344.2
IL_3J28_0671/N/1259:1263,
1/N/1272:1276		Triple sheared
geometric
IL_5J7L_274
IL_17948.2
IL_3J28_0691/N/1303:1308,
1/N/1329:1334		No text annotation
geometric
IL_5J7L_057
IL_85536.2
IL_3J28_0711/N/1401:1404,
1/N/1497:1501		No text annotation
homologous
IL_4LFB_068
IL_65718.4
IL_3J28_0791/N/1405:1409,
1/N/1491:1496		Other IL
geometric
IL_4WF9_084
NA
IL_3J28_0731/N/1412:1414,
1/N/1486:1488		Isolated non-canonical cWW pair
homologous
IL_4LFB_059
IL_87907.2
IL_3J28_0741/N/1416:1419,
1/N/1481:1484		Double sheared
homologous
IL_6CZR_169
NA
IL_3J28_0751/N/1430:1435,
1/N/1466:1470		Triple sheared related
homologous
IL_5J7L_063
IL_80231.1
IL_3J28_0991/N/1440:1442,
1/N/1460:1461		Single bulged A
homologous
IL_5J7L_064
IL_31462.6
IL_3J28_1001/N/1445:1448,
1/N/1455:1457		No text annotation

Problematic loops

#loop idProblemSequence
IL_3J28_080Isolated non-canonical cWW pair
IL_3J28_002Isolated non-canonical cWW pair
IL_3J28_004Isolated non-canonical cWW pair
IL_3J28_009No text annotation
IL_3J28_010Isolated non-canonical cWW pair
IL_3J28_012Isolated non-canonical cWW pair
IL_3J28_015Isolated non-canonical cWW pair
IL_3J28_016No text annotation
IL_3J28_017Kink-turn with non-sequential stacking
IL_3J28_018No text annotation
IL_3J28_020Isolated non-canonical cWW pair
IL_3J28_084No text annotation
IL_3J28_023Isolated non-canonical cWW pair
IL_3J28_024No text annotation
IL_3J28_028Isolated non-canonical cWW pair
IL_3J28_086No text annotation
IL_3J28_036Stack and bulge
IL_3J28_039No text annotation
IL_3J28_041Not an internal loop
IL_3J28_043No text annotation
IL_3J28_046No text annotation
IL_3J28_048Isolated non-canonical cWW pair
IL_3J28_089Tandem non-canonical cWW pairs
IL_3J28_051Isolated non-canonical cWW pair
IL_3J28_090No text annotation
IL_3J28_053Isolated near basepair
IL_3J28_091No text annotation
IL_3J28_056Tandem non-canonical cWW pairs
IL_3J28_058Isolated non-canonical cWW pair
IL_3J28_059Isolated non-canonical cWW pair
IL_3J28_060Isolated non-canonical cWW pair
IL_3J28_061No text annotation
IL_3J28_063No text annotation
IL_3J28_095No text annotation
IL_3J28_065No text annotation
IL_3J28_068Isolated non-canonical cWW pair
IL_3J28_070Isolated non-canonical cWW pair
IL_3J28_076Isolated non-canonical cWW pair
IL_3J28_077Minor groove platform with extra cWW
IL_3J28_078No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_3J28_0011/N/46:52,
1/N/359:369,
1/N/392:395		No text annotation
J3_3J28_0111/N/586:588,
1/N/651:654,
1/N/754:755		No text annotation
homologous
J3_5J7L_002
J3_56052.5
J3_3J28_0141/N/586:588,
1/N/651:655,
1/N/751:755		No text annotation
homologous
J3_5J7L_051
J3_17385.4
J3_3J28_0121/N/672:673,
1/N/717:725,
1/N/732:734		No text annotation
J3_3J28_0021/N/826:829,
1/N/857:861,
1/N/868:874		No text annotation
J3_3J28_0031/N/936:939,
1/N/1344:1350,
1/N/1372:1379		No text annotation
homologous
J3_4LFB_002
J3_25303.4
J3_3J28_0041/N/941:946,
1/N/1235:1237,
1/N/1337:1342		No text annotation
J3_3J28_0211/N/955:962,
1/N/973:984,
1/N/1221:1225		No text annotation
homologous
J3_5J7L_006
J3_83516.4
J3_3J28_0171/N/990:993,
1/N/1045:1047,
1/N/1210:1215		No text annotation
homologous
J3_5J7L_007
J3_82572.1
J3_3J28_0221/N/990:997,
1/N/1044:1047,
1/N/1210:1215		No text annotation
homologous
J3_5J7L_053
J3_76475.2
J3_3J28_0071/N/1003:1006,
1/N/1023:1027,
1/N/1034:1037		No text annotation
J3_3J28_0231/N/1061:1068,
1/N/1107:1113,
1/N/1187:1195		No text annotation
J3_3J28_0131/N/1073:1074,
1/N/1083:1087,
1/N/1098:1102		No text annotation
J3_3J28_0091/N/1116:1118,
1/N/1155:1158,
1/N/1181:1184		No text annotation
J3_3J28_0191/N/1116:1118,
1/N/1155:1162,
1/N/1174:1184		No text annotation
J3_3J28_0101/N/1237:1241,
1/N/1296:1303,
1/N/1334:1337		No text annotation
homologous
J3_4LFB_009
J3_37047.6
J3_3J28_0201/N/1237:1241,
1/N/1296:1308,
1/N/1329:1337		No text annotation
J4_3J28_0011/N/115:122,
1/N/239:240,
1/N/286:289,
1/N/311:312		No text annotation
J4_3J28_0041/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_3J28_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_3J28_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_3J28_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_3J28_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_3J28_015No text annotation
J3_3J28_005No text annotation
J3_3J28_016No text annotation
J3_3J28_006No text annotation
J3_3J28_018No text annotation
J3_3J28_008No text annotation
J4_3J28_002No text annotation

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