RNA 3D Hub //

1N34 Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_1N34_0011/A/12:22No text annotation
homologous
HL_4LFB_001
HL_89881.5
HL_1N34_0021/A/79:90tRNA anticodon loop
geometric
HL_3WFS_002
HL_06059.7
HL_1N34_0031/A/158:163GNRA
homologous
HL_4LFB_003
HL_37824.8
HL_1N34_0041/A/190B:190GNo text annotation
homologous
HL_4LFB_004
HL_48417.6
HL_1N34_0051/A/199:218No text annotation
geometric
HL_5XUZ_001
HL_69752.2
HL_1N34_0061/A/259:267GNRA related
homologous
HL_4LFB_006
HL_84299.4
HL_1N34_0071/A/296:301GNRA
homologous
HL_4LFB_007
HL_37824.8
HL_1N34_0081/A/320:333No text annotation
homologous
HL_4LFB_008
HL_81205.3
HL_1N34_0331/A/339:350No text annotation
HL_1N34_0091/A/342:347UNCG
homologous
HL_4LFB_009
HL_34617.5
HL_1N34_0101/A/377:386No text annotation
geometric
HL_8KAL_008
NA
HL_1N34_0111/A/419:424No text annotation
homologous
HL_6CZR_082
NA
HL_1N34_0121/A/457:475No text annotation
geometric
HL_8C3A_221
NA
HL_1N34_0141/A/617:623GNRA-like with tWH
homologous
HL_4LFB_014
HL_10453.3
HL_1N34_0151/A/689:698No text annotation
homologous
HL_5J7L_015
HL_75293.5
HL_1N34_0171/A/786:796No text annotation
homologous
HL_4LFB_017
HL_75293.5
HL_1N34_0181/A/838:848Mini UNCG
homologous
HL_6CZR_089
NA
HL_1N34_0211/A/963:972No text annotation
homologous
HL_4LFB_021
HL_50779.4
HL_1N34_0241/A/1076:1081GNRA
homologous
HL_4LFB_024
HL_37824.8
HL_1N34_0251/A/1089:1096T-loop related
homologous
HL_5J7L_024
HL_77436.5
HL_1N34_0381/A/1122:1151No text annotation
HL_1N34_0271/A/1164:1172GNRA with extra near cWW
geometric
HL_2IL9_007
NA
HL_1N34_0311/A/1449:1454UNCG
homologous
HL_4LFB_031
HL_34617.5

Problematic loops

#loop idProblemSequence
HL_1N34_013No text annotation
HL_1N34_016GNRA
HL_1N34_034GNRA with extra near cWW
HL_1N34_019GNRA
HL_1N34_020GNRA
HL_1N34_022No text annotation
HL_1N34_023No text annotation
HL_1N34_035No text annotation
HL_1N34_026No text annotation
HL_1N34_036No text annotation
HL_1N34_037No text annotation
HL_1N34_039No text annotation
HL_1N34_028No text annotation
HL_1N34_029T-loop with 3 stacked bulged bases
HL_1N34_030No text annotation
HL_1N34_032GNRA

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_1N34_0011/A/30:32,
1/A/552:553		Single bulged G
homologous
IL_4LFB_001
IL_00225.14
IL_1N34_0681/A/43:45,
1/A/396:399		Decoding loop related
geometric
IL_2O3X_003
IL_31737.3
IL_1N34_0021/A/44:45,
1/A/396:398		Single bulged A
homologous
IL_4LFB_002
IL_31462.7
IL_1N34_0031/A/47:52,
1/A/359:361		No text annotation
homologous
IL_4LFB_003
IL_14177.2
IL_1N34_0821/A/54:56,
1/A/356:357		Minor groove platform
homologous
IL_6CZR_116
NA
IL_1N34_0051/A/63:66,
1/A/103:104		Multiple bulged bases
homologous
IL_5J7L_005
IL_82107.5
IL_1N34_0061/A/67:69,
1/A/99:102		Isolated non-canonical cWW pair
geometric
IL_4LFB_006
IL_87907.2
IL_1N34_0701/A/67:76,
1/A/93:102		No text annotation
IL_1N34_0081/A/128:131,
1/A/231:233		Isolated non-canonical cWW pair
homologous
IL_5J7L_009
IL_57744.1
IL_1N34_0091/A/132:136,
1/A/227:230		No text annotation
homologous
IL_4LFB_008
IL_64231.5
IL_1N34_0111/A/186:188,
1/A/190K:191		Isolated non-canonical cWW pair
homologous
IL_4LFB_010
IL_87907.2
IL_1N34_0121/A/242:247,
1/A/277:284		Kink-turn with non-sequential stacking
homologous
IL_4LFB_011
IL_46174.3
IL_1N34_0831/A/249:252,
1/A/274:275		No text annotation
homologous
IL_4LFB_012
IL_47074.2
IL_1N34_0141/A/292:293,
1/A/304:308		C-loop
homologous
IL_4LFB_013
IL_03109.3
IL_1N34_0731/A/292:294,
1/A/303:308		No text annotation
IL_1N34_0841/A/371:375,
1/A/389:390		C-loop
homologous
IL_4LFB_015
IL_03109.3
IL_1N34_0171/A/375:377,
1/A/386:389		Single bulged G, near cWW
geometric
IL_6CZR_128
NA
IL_1N34_0191/A/409:417,
1/A/426:433		No text annotation
homologous
IL_6CZR_129
NA
IL_1N34_0201/A/446:450,
1/A/483:488		6x5 Sarcin-Ricin; G-bulge
geometric
IL_4LFB_018
IL_88269.4
IL_1N34_0211/A/450:456,
1/A/476:483		No text annotation
homologous
IL_6CZR_131
NA
IL_1N34_0221/A/504:511,
1/A/540:541		SSU/LSU pseudoknot
geometric
IL_4LFB_020
IL_41203.4
IL_1N34_0751/A/504:521,
1/A/528:541		No text annotation
IL_1N34_0241/A/515:521,
1/A/528:536		Kink-turn related
geometric
IL_4V88_415
NA
IL_1N34_0291/A/605:612,
1/A/628:633		No text annotation
homologous
IL_4LFB_026
IL_78349.3
IL_1N34_0321/A/662:666,
1/A/740:743		Tandem non-canonical cWW pairs
homologous
IL_4LFB_029
IL_85033.2
IL_1N34_0851/A/673:677,
1/A/713:717		Triple non-canonical cWW pairs
homologous
IL_5J7L_361
IL_49751.4
IL_1N34_0341/A/683:688,
1/A/699:707		Kink-turn
homologous
IL_4LFB_031
IL_95727.1
IL_1N34_0381/A/922:923,
1/A/1393:1395		Single bulged A
homologous
IL_5J7L_039
IL_31462.7
IL_1N34_0391/A/925:927,
1/A/1390:1391		Single bulged G
homologous
IL_5J7L_040
IL_00225.14
IL_1N34_0401/A/933:935,
1/A/1380:1384		Minor groove platform
homologous
IL_4LFB_037
IL_47078.3
IL_1N34_0421/A/953:954,
1/A/1226:1228		Minor groove platform
homologous
IL_5J7L_042
IL_51454.3
IL_1N34_0441/A/1047:1051,
1/A/1207:1210		No text annotation
IL_1N34_0451/A/1051:1056,
1/A/1204:1207		No text annotation
homologous
IL_5J7L_362
IL_49612.1
IL_1N34_0461/A/1056:1059,
1/A/1198:1204		Minor groove platform related
geometric
IL_3BNR_008
IL_64231.5
IL_1N34_0861/A/1060:1061,
1/A/1195:1197		Single bulged U
homologous
IL_4LFB_046
IL_89505.4
IL_1N34_0481/A/1061:1063,
1/A/1193:1195		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_28037.2
IL_1N34_0491/A/1121:1128,
1/A/1143:1152		No text annotation
IL_1N34_0511/A/1247:1253,
1/A/1284:1290		No text annotation
homologous
IL_6CZR_160
NA
IL_1N34_0521/A/1253:1258,
1/A/1277:1284		No text annotation
IL_1N34_0801/A/1253:1262,
1/A/1273:1284		No text annotation
IL_1N34_0551/A/1303:1308,
1/A/1329:1334		No text annotation
geometric
IL_4LFB_055
IL_85536.2
IL_1N34_0571/A/1401:1404,
1/A/1497:1501		No text annotation
geometric
IL_8CRE_467
IL_65718.4
IL_1N34_0581/A/1404:1407,
1/A/1494:1497		Tandem non-canonical cWW pairs
geometric
IL_5EW4_002
IL_85033.2
IL_1N34_0871/A/1405:1412,
1/A/1488:1496		No text annotation
IL_1N34_0591/A/1407:1409,
1/A/1491:1494		No text annotation
geometric
IL_8UO6_002
IL_31737.3
IL_1N34_0611/A/1412:1414,
1/A/1486:1488		Isolated non-canonical cWW pair
homologous
IL_4LFB_059
IL_87907.2
IL_1N34_0881/A/1435:1437,
1/A/1464:1466		Isolated non-canonical cWW pair
homologous
IL_4LFB_063
IL_87907.2
IL_1N34_0671/A/1440:1447,
1/A/1459:1461		No text annotation
homologous
IL_4LFB_064
IL_49061.1

Problematic loops

#loop idProblemSequence
IL_1N34_069No text annotation
IL_1N34_004Minor groove platform with extra cWW
IL_1N34_007No text annotation
IL_1N34_071No text annotation
IL_1N34_010tWH-tWH-tHW-tHW
IL_1N34_072Tandem non-canonical cWW pairs
IL_1N34_013No text annotation
IL_1N34_015Tandem non-canonical cWW pairs
IL_1N34_016No text annotation
IL_1N34_018Isolated non-canonical cWW contact
IL_1N34_074No text annotation
IL_1N34_023No text annotation
IL_1N34_025No text annotation
IL_1N34_026tSH-tHW-tHS
IL_1N34_027Major groove platform
IL_1N34_028Major groove minor groove platform; mini C-loop
IL_1N34_030Major groove platform; stack outside cWW
IL_1N34_076Major groove platform with extra cWW
IL_1N34_031Major groove platform
IL_1N34_077No text annotation
IL_1N34_033No text annotation
IL_1N34_035Left turn
IL_1N34_036tSH-tHW-tHS-cWW
IL_1N34_0378x6 Sarcin-Ricin with inserted Y; G-bulge
IL_1N34_041Isolated non-canonical cWW pair
IL_1N34_078No text annotation
IL_1N34_043Isolated non-canonical cWW pair
IL_1N34_047Isolated non-canonical cWW pair
IL_1N34_050Tandem non-canonical cWW pairs
IL_1N34_079No text annotation
IL_1N34_053Double sheared with non-canonical cWW
IL_1N34_054Isolated non-canonical cWW contact
IL_1N34_056Isolated non-canonical cWW pair
IL_1N34_081No text annotation
IL_1N34_060Tandem non-canonical cWW pairs
IL_1N34_062Isolated non-canonical cWW pair
IL_1N34_063Double sheared
IL_1N34_064No text annotation
IL_1N34_065UAA/GAN variation
IL_1N34_066Tandem non-canonical cWW pairs

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_1N34_0211/A/46:47,
1/A/361:369,
1/A/392:395		No text annotation
J3_1N34_0221/A/46:52,
1/A/359:369,
1/A/392:395		No text annotation
J3_1N34_0121/A/586:588,
1/A/651:654,
1/A/754:755		No text annotation
geometric
J3_4LFB_011
J3_56052.5
J3_1N34_0131/A/586:588,
1/A/651:655,
1/A/751:755		No text annotation
homologous
J3_4LFB_015
J3_17385.4
J3_1N34_0141/A/672:673,
1/A/717:725,
1/A/732:734		No text annotation
homologous
J3_4LFB_012
J3_11934.4
J3_1N34_0011/A/826:829,
1/A/857:861,
1/A/868:874		No text annotation
homologous
J3_4LFB_001
J3_85054.4
J3_1N34_0021/A/936:939,
1/A/1344:1350,
1/A/1372:1379		No text annotation
homologous
J3_4LFB_002
J3_25303.4
J3_1N34_0031/A/941:946,
1/A/1235:1237,
1/A/1337:1342		No text annotation
J3_1N34_0231/A/955:962,
1/A/973:984,
1/A/1221:1225		No text annotation
homologous
J3_5J7L_006
J3_83516.4
J3_1N34_0241/A/988:998,
1/A/1043:1056,
1/A/1204:1217		No text annotation
J3_1N34_0251/A/988:998,
1/A/1043:1059,
1/A/1198:1217		No text annotation
J3_1N34_0191/A/1061:1068,
1/A/1107:1113,
1/A/1187:1195		No text annotation
J3_1N34_0071/A/1063:1068,
1/A/1107:1113,
1/A/1187:1193		No text annotation
geometric
J3_4LFB_007
J3_08394.3
J3_1N34_0261/A/1073:1074,
1/A/1083:1086,
1/A/1099:1102		No text annotation
homologous
J3_4LFB_017
J3_79369.1
J3_1N34_0081/A/1116:1118,
1/A/1155:1161,
1/A/1175:1184		No text annotation
homologous
J3_4LFB_018
J3_17791.2
J3_1N34_0091/A/1237:1241,
1/A/1296:1303,
1/A/1334:1337		No text annotation
homologous
J3_4LFB_009
J3_37047.6
J4_1N34_0041/A/115:122,
1/A/239:240,
1/A/286:289,
1/A/311:312		No text annotation
homologous
J4_4LFB_001
J4_35578.3
J4_1N34_0021/A/142:144,
1/A/178:183,
1/A/194:198,
1/A/219:221		No text annotation
homologous
J4_4LFB_002
J4_88771.1
J4_1N34_0031/A/569:577,
1/A/764:769,
1/A/810:821,
1/A/879:881		No text annotation
J5_1N34_0031/A/36:39,
1/A/403:416,
1/A/427:442,
1/A/492:500,
1/A/545:548		No text annotation
J5_1N34_0021/A/58:61,
1/A/106:113,
1/A/314:316,
1/A/337:339,
1/A/350:354		No text annotation
homologous
J5_4LFB_002
J5_59910.6

Problematic loops

#loop idProblemSequence
J3_1N34_010No text annotation
J3_1N34_011No text annotation
J3_1N34_015No text annotation
J3_1N34_004No text annotation
J3_1N34_016No text annotation
J3_1N34_017No text annotation
J3_1N34_018No text annotation
J3_1N34_005No text annotation
J3_1N34_006No text annotation
J3_1N34_020No text annotation
J4_1N34_001No text annotation
J5_1N34_001No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0565 s