RNA 3D Hub //

8K4E Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8K4E_0011/A/12:22No text annotation
homologous
HL_4LFB_001
HL_73535.1
HL_8K4E_0031/A/157:164No text annotation
HL_8K4E_0041/A/186:191GNRA
homologous
HL_5J7L_004
NA
HL_8K4E_0061/A/259:267GNRA related
homologous
HL_5J7L_006
NA
HL_8K4E_0071/A/296:301GNRA
homologous
HL_5J7L_007
NA
HL_8K4E_0081/A/320:333No text annotation
homologous
HL_4LFB_008
HL_39665.1
HL_8K4E_0091/A/342:347UNCG
homologous
HL_4LFB_009
HL_61337.2
HL_8K4E_0101/A/379:384GNRA
homologous
HL_5J7L_010
NA
HL_8K4E_0111/A/419:424UNCG
homologous
HL_5J7L_011
NA
HL_8K4E_0121/A/462:470GNRA wlth extra near cWW
homologous
HL_5J7L_012
NA
HL_8K4E_0131/A/522:527No text annotation
geometric
HL_2ZNI_001
HL_75660.7
HL_8K4E_0141/A/617:623GNRA-like with tWH
homologous
HL_5J7L_014
NA
HL_8K4E_0151/A/689:698No text annotation
homologous
HL_6CZR_086
NA
HL_8K4E_0161/A/726:731GNRA
homologous
HL_5J7L_016
NA
HL_8K4E_0171/A/786:796No text annotation
geometric
HL_5U3G_001
HL_75660.7
HL_8K4E_0191/A/862:867GNRA
homologous
HL_4LFB_019
HL_34789.2
HL_8K4E_0201/A/897:902GNRA
homologous
HL_4LFB_020
HL_34789.2
HL_8K4E_0211/A/963:972No text annotation
homologous
HL_4LFB_021
HL_97521.1
HL_8K4E_0241/A/1076:1081GNRA
homologous
HL_5J7L_023
NA
HL_8K4E_0251/A/1089:1096T-loop related
homologous
HL_4LFB_025
HL_63894.2
HL_8K4E_0311/A/1515:1520GNRA
homologous
HL_5J7L_031
NA

Problematic loops

#loop idProblemSequence
HL_8K4E_002No text annotation
HL_8K4E_005No text annotation
HL_8K4E_018Externally structured
HL_8K4E_022No text annotation
HL_8K4E_023UNCG
HL_8K4E_026No text annotation
HL_8K4E_027GNRA
HL_8K4E_028GNRA
HL_8K4E_029T-loop with 3 stacked bulged bases
HL_8K4E_030No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8K4E_0011/A/30:32,
1/A/552:553		Single bulged G
homologous
IL_6CZR_113
NA
IL_8K4E_0021/A/44:45,
1/A/396:398		Single bulged A
geometric
IL_5J7L_002
NA
IL_8K4E_0031/A/63:66,
1/A/103:104		Multiple bulged bases
homologous
IL_5J7L_005
NA
IL_8K4E_0041/A/67:69,
1/A/99:102		Minor groove platform with extra cWW
homologous
IL_5J7L_006
NA
IL_8K4E_0051/A/70:73,
1/A/97:98		Minor groove platform
homologous
IL_5J7L_007
NA
IL_8K4E_0061/A/75:77,
1/A/92:95		Single bulged G, near cWW
homologous
IL_5J7L_008
NA
IL_8K4E_0081/A/128:131,
1/A/231:233		Isolated non-canonical cWW pair
homologous
IL_5J7L_009
NA
IL_8K4E_0091/A/132:136,
1/A/227:230		No text annotation
homologous
IL_4LFB_008
IL_60988.2
IL_8K4E_0101/A/144:146,
1/A/176:178		Isolated cWH basepair
homologous
IL_5J7L_011
NA
IL_8K4E_0111/A/147:153,
1/A/168:175		tWH-tWH-tHW-tHW
homologous
IL_5J7L_012
NA
IL_8K4E_0141/A/242:247,
1/A/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
NA
IL_8K4E_0151/A/249:252,
1/A/274:275		No text annotation
homologous
IL_4LFB_012
IL_22002.1
IL_8K4E_0171/A/292:293,
1/A/304:308		C-loop
homologous
IL_4LFB_013
IL_06671.1
IL_8K4E_0181/A/371:375,
1/A/389:390		C-loop
homologous
IL_5J7L_018
NA
IL_8K4E_0191/A/375:378,
1/A/385:389		No text annotation
IL_8K4E_0201/A/409:416,
1/A/427:433		No text annotation
homologous
IL_5J7L_020
NA
IL_8K4E_0211/A/440:442,
1/A/492:497		No text annotation
homologous
IL_5J7L_021
NA
IL_8K4E_0221/A/446:450,
1/A/483:488		tSH-tHW-tWW
geometric
IL_5J7L_022
NA
IL_8K4E_0231/A/450:455,
1/A/477:483		No text annotation
homologous
IL_5J7L_023
NA
IL_8K4E_0241/A/504:511,
1/A/540:541		SSU/LSU pseudoknot
homologous
IL_4LFB_020
IL_11411.1
IL_8K4E_0251/A/515:521,
1/A/528:536		Kink-turn related
geometric
IL_4V88_415
NA
IL_8K4E_0261/A/569:575,
1/A/880:881		No text annotation
homologous
IL_5J7L_026
NA
IL_8K4E_0271/A/580:584,
1/A/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
NA
IL_8K4E_0281/A/594:596,
1/A/644:645		Major groove platform
homologous
IL_4LFB_024
IL_48076.8
IL_8K4E_0291/A/597:598,
1/A/640:643		Major groove minor groove platform; mini C-loop
homologous
IL_4LFB_025
IL_73108.2
IL_8K4E_0301/A/605:612,
1/A/628:633		No text annotation
homologous
IL_5J7L_030
NA
IL_8K4E_0311/A/654:655,
1/A/751:754		Major groove platform; stack outside cWW
homologous
IL_5J7L_031
NA
IL_8K4E_0331/A/659:660,
1/A/745:747		Single stack bend
geometric
IL_7A0S_054
IL_15011.2
IL_8K4E_0341/A/662:667,
1/A/739:743		No text annotation
IL_8K4E_0351/A/673:678,
1/A/712:717		No text annotation
homologous
IL_4LFB_030
NA
IL_8K4E_0371/A/774:778,
1/A/804:805		Left turn
homologous
IL_4LFB_032
IL_29346.3
IL_8K4E_0381/A/779:783,
1/A/799:803		tSH-tHW-tHS
homologous
IL_5J7L_037
NA
IL_8K4E_0391/A/887:894,
1/A/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_8K4E_0641/A/1052:1056,
1/A/1204:1206		No text annotation
homologous
IL_6CZR_154
NA
IL_8K4E_0481/A/1060:1061,
1/A/1195:1197		Single bulged A
geometric
IL_5J7L_049
NA
IL_8K4E_0491/A/1061:1063,
1/A/1193:1195		Isolated non-canonical cWW pair
geometric
IL_5J7L_050
NA
IL_8K4E_0541/A/1247:1253,
1/A/1284:1290		No text annotation
homologous
IL_5J7L_054
NA

Problematic loops

#loop idProblemSequence
IL_8K4E_060Isolated non-canonical cWW pair
IL_8K4E_007No text annotation
IL_8K4E_061Tandem non-canonical cWW pairs
IL_8K4E_012Isolated non-canonical cWW pair
IL_8K4E_013Minor groove platform
IL_8K4E_016Isolated non-canonical cWW pair
IL_8K4E_062No text annotation
IL_8K4E_032Isolated non-canonical cWW pair
IL_8K4E_036Kink-turn
IL_8K4E_06310x8 Sarcin-Ricin; G-bulge
IL_8K4E_040Minor groove platform
IL_8K4E_041No text annotation
IL_8K4E_042Minor groove platform
IL_8K4E_043Single stack bend
IL_8K4E_044Isolated cWH basepair
IL_8K4E_045Single bulged U
IL_8K4E_046Tandem non-canonical cWW pairs
IL_8K4E_047Minor groove platform
IL_8K4E_050Isolated non-canonical cWW pair
IL_8K4E_051No text annotation
IL_8K4E_052No text annotation
IL_8K4E_065No text annotation
IL_8K4E_053No text annotation
IL_8K4E_055180 degree turn
IL_8K4E_056Double sheared with non-canonical cWW
IL_8K4E_057No text annotation
IL_8K4E_058Isolated cWH basepair
IL_8K4E_059Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8K4E_0011/A/45:47,
1/A/361:369,
1/A/392:396		No text annotation
J3_8K4E_0101/A/586:588,
1/A/651:654,
1/A/754:755		No text annotation
geometric
J3_5J7L_002
NA
J3_8K4E_0111/A/586:588,
1/A/651:655,
1/A/751:755		No text annotation
homologous
J3_5J7L_051
NA
J3_8K4E_0121/A/672:677,
1/A/713:725,
1/A/732:734		No text annotation
J3_8K4E_0021/A/826:829,
1/A/857:861,
1/A/868:874		No text annotation
homologous
J3_5J7L_004
NA
J3_8K4E_0051/A/990:993,
1/A/1045:1047,
1/A/1210:1215		No text annotation
homologous
J3_5J7L_007
NA
J3_8K4E_0151/A/990:997,
1/A/1044:1047,
1/A/1210:1215		No text annotation
homologous
J3_4LFB_016
J3_28881.1
J3_8K4E_0071/A/1063:1068,
1/A/1107:1113,
1/A/1187:1193		No text annotation
homologous
J3_4LFB_007
J3_01343.1
J3_8K4E_0161/A/1073:1074,
1/A/1083:1087,
1/A/1098:1102		No text annotation
homologous
J3_5J7L_009
NA
J3_8K4E_0081/A/1116:1118,
1/A/1155:1158,
1/A/1181:1184		No text annotation
homologous
J3_5J7L_010
NA
J3_8K4E_0171/A/1116:1118,
1/A/1155:1161,
1/A/1175:1184		No text annotation
homologous
J3_5J7L_054
NA
J4_8K4E_0011/A/115:122,
1/A/239:240,
1/A/286:289,
1/A/311:312		No text annotation
homologous
J4_5J7L_001
NA
J4_8K4E_0021/A/142:144,
1/A/178:184,
1/A/193:198,
1/A/219:221		No text annotation
homologous
J4_5J7L_002
NA
J4_8K4E_0031/A/575:577,
1/A/764:769,
1/A/810:821,
1/A/879:880		No text annotation
homologous
J4_5J7L_003
NA
J5_8K4E_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
NA
J5_8K4E_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
NA
J5_8K4E_0031/A/47:61,
1/A/106:113,
1/A/314:316,
1/A/337:339,
1/A/350:361		No text annotation
J6_8K4E_0011/A/45:61,
1/A/106:113,
1/A/314:316,
1/A/337:339,
1/A/350:369,
1/A/392:396		No text annotation

Problematic loops

#loop idProblemSequence
J3_8K4E_013No text annotation
J3_8K4E_003No text annotation
J3_8K4E_018No text annotation
J3_8K4E_014No text annotation
J3_8K4E_004No text annotation
J3_8K4E_006No text annotation
J3_8K4E_009No text annotation

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