RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8QRM_0011/A/654:664No text annotation
homologous
HL_4LFB_001
HL_73535.1
HL_8QRM_0021/A/701:708No text annotation
HL_8QRM_0041/A/768:773GNRA
geometric
HL_5TBW_019
NA
HL_8QRM_0051/A/792:796No text annotation
geometric
HL_6U8D_003
HL_32346.6
HL_8QRM_0061/A/804:809No text annotation
HL_8QRM_0071/A/842:847GNRA
homologous
HL_4LFB_010
HL_34789.4
HL_8QRM_0081/A/894:899GNRA
geometric
HL_4V9F_040
HL_34789.4
HL_8QRM_0101/A/1023:1028GNRA
geometric
HL_6SVS_001
HL_34789.4
HL_8QRM_0111/A/1074:1084No text annotation
homologous
HL_5J7L_017
NA
HL_8QRM_0121/A/1115:1126Externally structured
geometric
HL_5TBW_022
NA
HL_8QRM_0131/A/1150:1155No text annotation
geometric
HL_4V9F_003
HL_75660.8
HL_8QRM_0151/A/1281:1287No text annotation
geometric
HL_5U3G_001
HL_75660.8
HL_8QRM_0211/A/1580:1585GNRA
homologous
HL_4LFB_032
HL_34789.4

Problematic loops

#loop idProblemSequence
HL_8QRM_003Pseudoknot geometry
HL_8QRM_009No text annotation
HL_8QRM_014No text annotation
HL_8QRM_016Externally structured
HL_8QRM_017No text annotation
HL_8QRM_018T-loop with 2 bulged bases not stacked
HL_8QRM_019No text annotation
HL_8QRM_020No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8QRM_0011/A/649:651,
1/A/667:668		No text annotation
IL_8QRM_0021/A/674:676,
1/A/921:923		Isolated tHS basepair with bulges
geometric
IL_1L9A_004
NA
IL_8QRM_0031/A/685:686,
1/A/859:861		Single bulged A
homologous
IL_5J7L_002
NA
IL_8QRM_0041/A/690:692,
1/A/822:823		Single bulged A
geometric
IL_4R4V_004
IL_14190.2
IL_8QRM_0051/A/694:696,
1/A/819:820		Minor groove platform
homologous
IL_4LFB_004
IL_34520.3
IL_8QRM_0081/A/756:761,
1/A/779:786		Kink-turn with non-sequential stacking
geometric
IL_4LFB_011
IL_46174.4
IL_8QRM_0091/A/762:765,
1/A/777:778		Major groove platform; stack outside cWW
geometric
IL_3DIL_004
IL_74641.2
IL_8QRM_0471/A/762:766,
1/A/775:778		No text annotation
IL_8QRM_0101/A/765:766,
1/A/775:777		No text annotation
IL_8QRM_0111/A/830:832,
1/A/855:856		Single bulged U
geometric
IL_5J7L_017
NA
IL_8QRM_0121/A/834:838,
1/A/852:853		C-loop
homologous
IL_5J7L_018
NA
IL_8QRM_0131/A/838:839,
1/A/850:852		Single bulged A
geometric
IL_2QUX_002
IL_14190.2
IL_8QRM_0141/A/876:885,
1/A/910:913		No text annotation
IL_8QRM_0151/A/887:893,
1/A/900:908		Kink-turn related
geometric
IL_4V88_415
NA
IL_8QRM_0161/A/935:941,
1/A/1133:1134		No text annotation
homologous
IL_5J7L_026
NA
IL_8QRM_0171/A/946:950,
1/A/1044:1049		UAA/GAN
geometric
IL_5TBW_063
NA
IL_8QRM_0481/A/952:968,
1/A/1036:1042		No text annotation
IL_8QRM_0181/A/974:980,
1/A/1008:1014		No text annotation
IL_8QRM_0201/A/986:988,
1/A/999:1002		No text annotation
IL_8QRM_0211/A/1020:1022,
1/A/1029:1030		Other IL
geometric
IL_3WBM_004
IL_18188.1
IL_8QRM_0221/A/1062:1066,
1/A/1092:1093		Left turn
homologous
IL_5J7L_036
NA
IL_8QRM_0231/A/1067:1071,
1/A/1087:1091		tSH-tHW-tHS
homologous
IL_4LFB_033
IL_05821.1
IL_8QRM_0241/A/1109:1111,
1/A/1130:1132		Isolated non-canonical cWW pair
geometric
IL_1Z7F_002
NA
IL_8QRM_0251/A/1139:1147,
1/A/1158:1164		No text annotation
IL_8QRM_0261/A/1175:1176,
1/A/1477:1479		Single bulged A
homologous
IL_6CZR_147
NA
IL_8QRM_0271/A/1178:1180,
1/A/1474:1475		Single bulged G
homologous
IL_6CZR_148
NA
IL_8QRM_0281/A/1186:1190,
1/A/1464:1468		C-loop
geometric
IL_4V9F_093
IL_63596.12
IL_8QRM_0341/A/1265:1266,
1/A/1325:1327		Single bulged A
homologous
IL_5J7L_049
NA
IL_8QRM_0361/A/1274:1277,
1/A/1298:1301		Double sheared
geometric
IL_1SA9_002
IL_58355.2
IL_8QRM_0371/A/1278:1279,
1/A/1289:1297		No text annotation
geometric
IL_8S95_001
IL_25652.1
IL_8QRM_0391/A/1483:1485,
1/A/1566:1569		No text annotation
homologous
IL_5J7L_058
NA
IL_8QRM_0501/A/1485:1488,
1/A/1562:1566		No text annotation
homologous
IL_5J7L_059
NA
IL_8QRM_0411/A/1489:1491,
1/A/1559:1561		Isolated non-canonical cWW pair
geometric
IL_3MEI_002
IL_01003.4
IL_8QRM_0421/A/1491:1495,
1/A/1554:1559		No text annotation

Problematic loops

#loop idProblemSequence
IL_8QRM_006Minor groove platform with extra cWW
IL_8QRM_007Minor groove platform with extra cWW
IL_8QRM_019Isolated non-canonical cWW pair
IL_8QRM_049No text annotation
IL_8QRM_029Minor groove platform
IL_8QRM_030No text annotation
IL_8QRM_031Single bulged U
IL_8QRM_032Isolated cWS basepair
IL_8QRM_033Minor groove platform
IL_8QRM_035Isolated non-canonical cWW pair
IL_8QRM_038No text annotation
IL_8QRM_040No text annotation
IL_8QRM_043No text annotation
IL_8QRM_044Tandem non-canonical cWW pairs
IL_8QRM_045No text annotation
IL_8QRM_046No text annotation
IL_8QRM_052No text annotation
IL_8QRM_051No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8QRM_0011/A/677:680,
1/A/866:872,
1/A/917:920		No text annotation
J3_8QRM_0021/A/687:690,
1/A/823:830,
1/A/856:858		No text annotation
J3_8QRM_0081/A/973:974,
1/A/1014:1020,
1/A/1030:1031		No text annotation
J3_8QRM_0061/A/1268:1273,
1/A/1302:1308,
1/A/1317:1323		No text annotation
J4_8QRM_0011/A/698:701,
1/A/708:715,
1/A/800:802,
1/A/811:817		No text annotation
J4_8QRM_0021/A/717:724,
1/A/750:753,
1/A/789:791,
1/A/797:798		No text annotation
J4_8QRM_0031/A/941:943,
1/A/1052:1057,
1/A/1098:1109,
1/A/1132:1133		No text annotation
homologous
J4_5J7L_003
NA

Problematic loops

#loop idProblemSequence
J3_8QRM_003No text annotation
J3_8QRM_004No text annotation
J3_8QRM_005No text annotation
J3_8QRM_009No text annotation
J3_8QRM_007No text annotation

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