RNA 3D Hub //

5NO4 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_5NO4_0011/A/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_5NO4_0021/A/77:92No text annotation
HL_5NO4_0031/A/158:163GNRA
homologous
HL_5J7L_003
HL_37824.7
HL_5NO4_0041/A/186:191GNRA
homologous
HL_5J7L_004
HL_37824.7
HL_5NO4_0051/A/207:212UNCG
homologous
HL_5J7L_005
HL_34617.5
HL_5NO4_0061/A/259:267GNRA related
homologous
HL_5J7L_006
HL_84299.4
HL_5NO4_0071/A/296:301GNRA
homologous
HL_4LFB_007
HL_37824.7
HL_5NO4_0081/A/320:333No text annotation
homologous
HL_5J7L_008
HL_81205.3
HL_5NO4_0091/A/342:347UNCG
homologous
HL_4LFB_009
HL_34617.5
HL_5NO4_0101/A/379:384GNRA
homologous
HL_6CZR_081
NA
HL_5NO4_0111/A/419:424UNCG
homologous
HL_5J7L_011
HL_34617.5
HL_5NO4_0121/A/462:470GNRA related
homologous
HL_5J7L_012
HL_81538.2
HL_5NO4_0341/A/522:527GNRA variation
homologous
HL_5J7L_205
HL_37824.7
HL_5NO4_0141/A/617:623No text annotation
homologous
HL_4LFB_014
HL_10453.3
HL_5NO4_0151/A/689:698No text annotation
homologous
HL_4LFB_015
HL_75293.5
HL_5NO4_0161/A/726:731GNRA
homologous
HL_4LFB_016
HL_37824.7
HL_5NO4_0171/A/786:796No text annotation
homologous
HL_4LFB_017
HL_75293.5
HL_5NO4_0181/A/840:846No text annotation
HL_5NO4_0191/A/862:867GNRA
homologous
HL_5J7L_019
HL_37824.7
HL_5NO4_0201/A/897:902GNRA
homologous
HL_4LFB_020
HL_37824.7
HL_5NO4_0211/A/963:972No text annotation
homologous
HL_5J7L_021
HL_50779.4
HL_5NO4_0361/A/1012:1017GNRA
homologous
HL_4LFB_022
HL_37824.7
HL_5NO4_0231/A/1027:1033No text annotation
HL_5NO4_0241/A/1076:1081GNRA
homologous
HL_5J7L_023
HL_37824.7
HL_5NO4_0251/A/1089:1096T-loop related
homologous
HL_5J7L_024
HL_77436.5
HL_5NO4_0261/A/1133:1141No text annotation
geometric
HL_6CF2_001
HL_87553.1
HL_5NO4_0271/A/1165:1171GNRA
homologous
HL_5J7L_026
HL_93535.1
HL_5NO4_0281/A/1265:1270GNRA
homologous
HL_5J7L_027
HL_37824.7
HL_5NO4_0291/A/1314:1323T-loop with 3 stacked bulged bases
homologous
HL_5J7L_028
HL_02887.3
HL_5NO4_0301/A/1356:1366No text annotation
homologous
HL_5J7L_029
HL_06226.4
HL_5NO4_0311/A/1449:1454UNCG
homologous
HL_5J7L_030
HL_34617.5
HL_5NO4_0321/A/1515:1520GNRA
homologous
HL_6CZR_103
NA

Problematic loops

#loop idProblemSequence
HL_5NO4_033No text annotation
HL_5NO4_013No text annotation
HL_5NO4_035No text annotation
HL_5NO4_022No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_5NO4_0011/A/30:32,
1/A/552:553		Single bulged G
homologous
IL_6CZR_113
NA
IL_5NO4_0021/A/44:45,
1/A/396:398		Single bulged A
homologous
IL_5J7L_002
IL_31462.5
IL_5NO4_0031/A/47:52,
1/A/359:361		No text annotation
geometric
IL_5J7L_003
IL_14177.2
IL_5NO4_0041/A/54:56,
1/A/356:357		Minor groove platform
homologous
IL_4LFB_004
IL_51454.2
IL_5NO4_0051/A/63:66,
1/A/103:104		Multiple bulged bases
homologous
IL_4LFB_005
IL_82107.4
IL_5NO4_0061/A/67:69,
1/A/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
IL_90351.1
IL_5NO4_0071/A/70:73,
1/A/97:98		Minor groove platform
homologous
IL_5J7L_007
IL_15052.4
IL_5NO4_0661/A/75:76,
1/A/93:95		Single bulged G
homologous
IL_5J7L_395
IL_00225.13
IL_5NO4_0091/A/128:131,
1/A/231:233		Isolated non-canonical cWW pair
homologous
IL_5J7L_009
IL_57744.1
IL_5NO4_0101/A/132:136,
1/A/227:230		No text annotation
homologous
IL_4LFB_008
IL_64231.5
IL_5NO4_0111/A/144:146,
1/A/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
IL_10167.5
IL_5NO4_0121/A/147:153,
1/A/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
IL_80604.6
IL_5NO4_0131/A/203:206,
1/A/213:214		Minor groove platform
geometric
IL_5J7L_007
IL_15052.4
IL_5NO4_0141/A/242:247,
1/A/277:284		Kink-turn with non-sequential stacking
homologous
IL_4LFB_011
IL_46174.3
IL_5NO4_0151/A/249:252,
1/A/274:275		No text annotation
homologous
IL_5J7L_015
IL_47074.2
IL_5NO4_0161/A/292:293,
1/A/304:308		C-loop
homologous
IL_4LFB_013
IL_03109.3
IL_5NO4_0171/A/367:369,
1/A/392:393		Single bulged U
geometric
IL_5J7L_017
IL_89505.4
IL_5NO4_0181/A/371:375,
1/A/389:390		C-loop
homologous
IL_5J7L_018
IL_03109.3
IL_5NO4_0191/A/375:376,
1/A/387:389		Single bulged G
geometric
IL_5J7L_019
IL_00225.13
IL_5NO4_0201/A/409:416,
1/A/427:433		No text annotation
homologous
IL_4LFB_017
IL_28026.3
IL_5NO4_0211/A/440:442,
1/A/492:497		No text annotation
homologous
IL_5J7L_021
IL_33323.1
IL_5NO4_0221/A/446:450,
1/A/483:488		tSH-tHW-tWW
geometric
IL_5J7L_022
IL_88269.4
IL_5NO4_0231/A/450:455,
1/A/477:483		No text annotation
homologous
IL_5J7L_023
IL_70801.1
IL_5NO4_0241/A/504:511,
1/A/540:541		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_41203.4
IL_5NO4_0251/A/515:521,
1/A/528:536		Kink-turn related
homologous
IL_5J7L_025
IL_54177.4
IL_5NO4_0261/A/569:575,
1/A/880:881		No text annotation
homologous
IL_4LFB_022
IL_38186.6
IL_5NO4_0671/A/580:584,
1/A/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
IL_17136.7
IL_5NO4_0281/A/594:596,
1/A/644:645		Major groove platform
homologous
IL_5J7L_028
IL_48076.6
IL_5NO4_0291/A/597:598,
1/A/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_5J7L_029
IL_68140.4
IL_5NO4_0301/A/605:612,
1/A/628:633		No text annotation
homologous
IL_5J7L_030
IL_78349.3
IL_5NO4_0311/A/654:655,
1/A/751:754		Major groove platform; stack outside cWW
geometric
IL_4LFB_027
IL_50694.7
IL_5NO4_0321/A/658:659,
1/A/746:748		Single stack bend
homologous
IL_5J7L_032
IL_26793.1
IL_5NO4_0331/A/662:666,
1/A/740:743		Tandem non-canonical cWW pairs
homologous
IL_5J7L_033
IL_85033.2
IL_5NO4_0691/A/673:677,
1/A/713:717		Triple non-canonical cWW pairs
homologous
IL_4LFB_065
IL_49751.4
IL_5NO4_0351/A/684:688,
1/A/699:706		Kink-turn
homologous
IL_5J7L_035
IL_01488.3
IL_5NO4_0361/A/774:778,
1/A/804:805		Left turn
homologous
IL_5J7L_036
IL_29346.2
IL_5NO4_0371/A/779:783,
1/A/799:803		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_17136.7
IL_5NO4_0381/A/887:894,
1/A/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
IL_41756.4
IL_5NO4_0391/A/922:923,
1/A/1393:1395		Single bulged A
homologous
IL_5J7L_039
IL_31462.5
IL_5NO4_0401/A/925:927,
1/A/1390:1391		Single bulged G
homologous
IL_4LFB_036
IL_00225.13
IL_5NO4_0411/A/933:935,
1/A/1380:1384		Minor groove platform
homologous
IL_4LFB_037
IL_47078.3
IL_5NO4_0421/A/953:954,
1/A/1226:1228		Minor groove platform
homologous
IL_4LFB_038
IL_51454.2
IL_5NO4_0431/A/993:997,
1/A/1044:1045		Minor groove platform
homologous
IL_5J7L_043
IL_47078.3
IL_5NO4_0441/A/998:999,
1/A/1041:1043		Single stack bend
homologous
IL_5J7L_044
IL_26793.1
IL_5NO4_0451/A/1048:1050,
1/A/1208:1209		Single bulged U
geometric
IL_5J7L_046
IL_89505.4
IL_5NO4_0721/A/1052:1056,
1/A/1204:1206		Isolated cWS basepair
homologous
IL_4LFB_044
IL_76319.5
IL_5NO4_0471/A/1057:1058,
1/A/1199:1203		Minor groove platform
homologous
IL_4LFB_045
IL_95583.2
IL_5NO4_0481/A/1060:1061,
1/A/1195:1197		Single bulged A
geometric
IL_5J7L_049
IL_31462.5
IL_5NO4_0491/A/1061:1063,
1/A/1193:1195		Isolated non-canonical cWW pair
homologous
IL_5J7L_050
IL_28037.2
IL_5NO4_0501/A/1124:1128,
1/A/1144:1149		No text annotation
homologous
IL_5J7L_051
IL_06691.1
IL_5NO4_0511/A/1129:1132,
1/A/1142:1143		Minor groove platform
homologous
IL_5J7L_052
IL_15052.4
IL_5NO4_0521/A/1158:1161,
1/A/1175:1181		No text annotation
homologous
IL_5J7L_053
IL_42032.1
IL_5NO4_0531/A/1247:1253,
1/A/1284:1290		No text annotation
homologous
IL_5J7L_054
IL_09129.2
IL_5NO4_0541/A/1255:1258,
1/A/1277:1282		180 degree turn
homologous
IL_5J7L_055
IL_11344.2
IL_5NO4_0551/A/1259:1263,
1/A/1272:1276		Triple sheared
homologous
IL_5J7L_056
IL_17948.2
IL_5NO4_0561/A/1303:1308,
1/A/1329:1334		No text annotation
homologous
IL_5J7L_057
IL_85536.2
IL_5NO4_0571/A/1399:1401,
1/A/1501:1504		No text annotation
geometric
IL_5J7L_058
IL_61438.4
IL_5NO4_0581/A/1401:1404,
1/A/1497:1501		No text annotation
homologous
IL_5J7L_059
IL_65718.4
IL_5NO4_0731/A/1405:1407,
1/A/1494:1496		Isolated non-canonical cWW pair
homologous
IL_5J7L_363
IL_87907.2
IL_5NO4_0741/A/1407:1409,
1/A/1491:1494		No text annotation
homologous
IL_4LFB_070
IL_31531.3
IL_5NO4_0601/A/1412:1414,
1/A/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
IL_87907.2
IL_5NO4_0611/A/1416:1419,
1/A/1481:1484		Double sheared
homologous
IL_4LFB_060
IL_09705.15
IL_5NO4_0621/A/1430:1435,
1/A/1466:1470		Triple sheared related
homologous
IL_5J7L_063
IL_80231.1
IL_5NO4_0631/A/1440:1442,
1/A/1460:1461		Single bulged A
homologous
IL_5J7L_064
IL_31462.5
IL_5NO4_0641/A/1445:1448,
1/A/1455:1457		No text annotation
homologous
IL_5J7L_065
IL_31531.3

Problematic loops

#loop idProblemSequence
IL_5NO4_065Isolated non-canonical cWW pair
IL_5NO4_008Single bulged G, near cWW
IL_5NO4_027No text annotation
IL_5NO4_068No text annotation
IL_5NO4_034No text annotation
IL_5NO4_070Kink-turn
IL_5NO4_071No text annotation
IL_5NO4_046No text annotation
IL_5NO4_059No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_5NO4_0011/A/46:47,
1/A/361:367,
1/A/393:395		No text annotation
homologous
J3_5J7L_001
J3_67856.4
J3_5NO4_0131/A/46:52,
1/A/359:367,
1/A/393:395		No text annotation
homologous
J3_5J7L_050
J3_46317.4
J3_5NO4_0021/A/586:588,
1/A/651:654,
1/A/754:755		No text annotation
homologous
J3_5J7L_002
J3_56052.5
J3_5NO4_0141/A/586:588,
1/A/651:655,
1/A/751:755		No text annotation
homologous
J3_4LFB_015
J3_17385.4
J3_5NO4_0031/A/672:673,
1/A/717:725,
1/A/732:734		No text annotation
homologous
J3_5J7L_003
J3_11934.4
J3_5NO4_0041/A/826:829,
1/A/857:861,
1/A/868:874		No text annotation
homologous
J3_5J7L_004
J3_85054.4
J3_5NO4_0151/A/936:939,
1/A/1344:1350,
1/A/1372:1379		No text annotation
homologous
J3_5J7L_052
J3_25303.4
J3_5NO4_0051/A/943:946,
1/A/1235:1237,
1/A/1337:1340		No text annotation
homologous
J3_4LFB_003
J3_52655.4
J3_5NO4_0061/A/955:962,
1/A/973:984,
1/A/1221:1225		No text annotation
homologous
J3_5J7L_006
J3_83516.4
J3_5NO4_0071/A/990:993,
1/A/1045:1047,
1/A/1210:1215		No text annotation
homologous
J3_5J7L_007
J3_82572.1
J3_5NO4_0161/A/990:997,
1/A/1044:1047,
1/A/1210:1215		No text annotation
homologous
J3_5J7L_053
J3_76475.2
J3_5NO4_0171/A/1003:1008,
1/A/1021:1027,
1/A/1033:1037		No text annotation
J3_5NO4_0091/A/1063:1068,
1/A/1107:1113,
1/A/1187:1193		No text annotation
homologous
J3_4LFB_007
J3_08394.3
J3_5NO4_0101/A/1073:1074,
1/A/1083:1087,
1/A/1098:1102		No text annotation
homologous
J3_5J7L_009
J3_76043.3
J3_5NO4_0111/A/1116:1118,
1/A/1155:1158,
1/A/1181:1184		No text annotation
homologous
J3_5J7L_010
J3_82365.4
J3_5NO4_0181/A/1116:1118,
1/A/1155:1161,
1/A/1175:1184		No text annotation
homologous
J3_5J7L_054
J3_17791.2
J3_5NO4_0121/A/1237:1241,
1/A/1296:1303,
1/A/1334:1337		No text annotation
homologous
J3_5J7L_011
J3_37047.6
J4_5NO4_0011/A/115:122,
1/A/239:240,
1/A/286:289,
1/A/311:312		No text annotation
homologous
J4_5J7L_001
J4_35578.3
J4_5NO4_0021/A/142:144,
1/A/178:184,
1/A/193:198,
1/A/219:221		No text annotation
homologous
J4_5J7L_002
J4_01665.1
J4_5NO4_0041/A/575:577,
1/A/764:769,
1/A/810:821,
1/A/879:880		No text annotation
homologous
J4_5J7L_003
J4_61885.6
J5_5NO4_0011/A/36:39,
1/A/403:406,
1/A/436:440,
1/A/497:500,
1/A/545:548		No text annotation
homologous
J5_5J7L_001
J5_92941.1
J5_5NO4_0021/A/36:39,
1/A/403:406,
1/A/436:442,
1/A/492:500,
1/A/545:548		No text annotation
homologous
J5_5J7L_002
J5_67416.1
J5_5NO4_0031/A/58:61,
1/A/106:113,
1/A/314:316,
1/A/337:339,
1/A/350:354		No text annotation
homologous
J5_5J7L_003
J5_59910.6

Problematic loops

#loop idProblemSequence
J3_5NO4_008No text annotation
J4_5NO4_003No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0624 s