6W6K Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6W6K_001 | 1/A/12:22 | No text annotation Not in a motif group | homologous HL_5J7L_001 HL_89881.2 | |
| HL_6W6K_003 | 1/A/158:163 | GNRA Not in a motif group | homologous HL_4LFB_003 HL_42097.1 | |
| HL_6W6K_004 | 1/A/186:191 | GNRA Not in a motif group | homologous HL_5J7L_004 HL_42097.1 | |
| HL_6W6K_006 | 1/A/259:267 | No text annotation Not in a motif group | homologous HL_5J7L_006 HL_69023.2 | |
| HL_6W6K_007 | 1/A/296:301 | GNRA Not in a motif group | homologous HL_5J7L_007 HL_42097.1 | |
| HL_6W6K_008 | 1/A/320:333 | No text annotation Not in a motif group | homologous HL_4LFB_008 HL_81205.2 | |
| HL_6W6K_009 | 1/A/342:347 | UNCG Not in a motif group | homologous HL_4LFB_009 HL_03562.2 | |
| HL_6W6K_010 | 1/A/379:384 | GNRA Not in a motif group | homologous HL_5J7L_010 HL_42097.1 | |
| HL_6W6K_011 | 1/A/419:424 | UNCG Not in a motif group | homologous HL_5J7L_011 HL_03562.2 | |
| HL_6W6K_013 | 1/A/522:527 | No text annotation Not in a motif group | geometric HL_4WF9_003 HL_75407.1 | |
| HL_6W6K_014 | 1/A/617:623 | No text annotation Not in a motif group | homologous HL_4LFB_014 HL_26881.1 | |
| HL_6W6K_016 | 1/A/726:731 | Other HL Not in a motif group | homologous HL_4LFB_016 HL_87030.2 | |
| HL_6W6K_019 | 1/A/862:867 | GNRA Not in a motif group | homologous HL_5J7L_019 HL_42097.1 | |
| HL_6W6K_020 | 1/A/897:902 | GNRA Not in a motif group | homologous HL_4LFB_020 HL_42097.1 | |
| HL_6W6K_021 | 1/A/963:972 | No text annotation Not in a motif group | homologous HL_4LFB_021 NA | |
| HL_6W6K_022 | 1/A/1012:1017 | GNRA Not in a motif group | homologous HL_4LFB_022 HL_42097.1 | |
| HL_6W6K_023 | 1/A/1028:1033 | No text annotation Not in a motif group | geometric HL_4V88_198 HL_56691.2 | |
| HL_6W6K_024 | 1/A/1076:1081 | GNRA Not in a motif group | homologous HL_4LFB_024 HL_42097.1 | |
| HL_6W6K_025 | 1/A/1089:1096 | No text annotation Not in a motif group | homologous HL_4LFB_025 HL_71554.2 | |
| HL_6W6K_026 | 1/A/1134:1140 | No text annotation Not in a motif group | homologous HL_4LFB_026 HL_03562.2 | |
| HL_6W6K_028 | 1/A/1265:1270 | GNRA Not in a motif group | homologous HL_5J7L_027 HL_42097.1 | |
| HL_6W6K_029 | 1/A/1314:1323 | No text annotation Not in a motif group | homologous HL_4LFB_029 HL_89380.2 | |
| HL_6W6K_030 | 1/A/1356:1366 | No text annotation Not in a motif group | homologous HL_4LFB_030 HL_96366.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6W6K_002 | No text annotation | ||
| HL_6W6K_005 | UNCG | ||
| HL_6W6K_012 | No text annotation | ||
| HL_6W6K_015 | No text annotation | ||
| HL_6W6K_017 | No text annotation | ||
| HL_6W6K_018 | No text annotation | ||
| HL_6W6K_027 | No text annotation | ||
| HL_6W6K_031 | UNCG | ||
| HL_6W6K_032 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6W6K_001 | 1/A/30:32, 1/A/552:553 | Single bulged G Not in a motif group | homologous IL_5J7L_001 IL_00225.2 | |
| IL_6W6K_002 | 1/A/43:45, 1/A/396:399 | CA cWW with bulged A Not in a motif group | geometric IL_4P3T_005 IL_95997.1 | |
| IL_6W6K_003 | 1/A/47:52, 1/A/359:361 | No text annotation Not in a motif group | homologous IL_5J7L_003 IL_11178.1 | |
| IL_6W6K_004 | 1/A/54:56, 1/A/356:357 | Minor groove platform Not in a motif group | homologous IL_4LFB_004 IL_93353.1 | |
| IL_6W6K_005 | 1/A/63:66, 1/A/103:104 | Multiple bulged bases Not in a motif group | homologous IL_5J7L_005 IL_76389.1 | |
| IL_6W6K_006 | 1/A/67:69, 1/A/99:102 | Minor groove platform with extra cWW Not in a motif group | homologous IL_5J7L_006 IL_65006.1 | |
| IL_6W6K_008 | 1/A/75:76, 1/A/93:95 | No text annotation Not in a motif group | ||
| IL_6W6K_009 | 1/A/128:132, 1/A/230:233 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_4V88_431 IL_30621.2 | |
| IL_6W6K_010 | 1/A/132:136, 1/A/227:230 | No text annotation Not in a motif group | geometric IL_4LFB_008 IL_58764.3 | |
| IL_6W6K_011 | 1/A/144:146, 1/A/176:178 | Isolated cWH basepair Not in a motif group | homologous IL_5J7L_011 IL_51629.2 | |
| IL_6W6K_012 | 1/A/146:148, 1/A/175:176 | Single stack bend Not in a motif group | geometric IL_7KGA_003 IL_76488.2 | |
| IL_6W6K_013 | 1/A/148:153, 1/A/168:175 | No text annotation Not in a motif group | ||
| IL_6W6K_015 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_6CZR_123 IL_45067.2 | |
| IL_6W6K_016 | 1/A/249:252, 1/A/274:275 | No text annotation Not in a motif group | homologous IL_5J7L_015 IL_48100.2 | |
| IL_6W6K_017 | 1/A/292:293, 1/A/304:308 | C-loop Not in a motif group | homologous IL_4LFB_013 IL_37712.2 | |
| IL_6W6K_018 | 1/A/339:341, 1/A/348:351 | No text annotation Not in a motif group | geometric IL_4WSM_372 IL_33061.1 | |
| IL_6W6K_019 | 1/A/367:369, 1/A/392:393 | Single bulged U Not in a motif group | geometric IL_4V9F_074 IL_83039.13 | |
| IL_6W6K_020 | 1/A/371:375, 1/A/389:390 | C-loop Not in a motif group | geometric IL_4LFB_015 IL_75255.1 | |
| IL_6W6K_021 | 1/A/375:376, 1/A/387:389 | Single bulged G Not in a motif group | homologous IL_5J7L_019 IL_00225.2 | |
| IL_6W6K_022 | 1/A/408:416, 1/A/427:434 | No text annotation Not in a motif group | ||
| IL_6W6K_024 | 1/A/446:450, 1/A/483:488 | tSH-tHW-tWW Not in a motif group | geometric IL_5J7L_022 IL_88269.3 | |
| IL_6W6K_025 | 1/A/450:455, 1/A/477:483 | No text annotation Not in a motif group | homologous IL_5J7L_023 IL_70801.1 | |
| IL_6W6K_026 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot Not in a motif group | homologous IL_5J7L_024 IL_15861.7 | |
| IL_6W6K_027 | 1/A/515:521, 1/A/528:536 | No text annotation Not in a motif group | geometric IL_4V88_415 IL_55871.1 | |
| IL_6W6K_028 | 1/A/569:575, 1/A/880:881 | No text annotation Not in a motif group | homologous IL_6CZR_134 IL_69996.1 | |
| IL_6W6K_029 | 1/A/578:584, 1/A/757:763 | No text annotation Not in a motif group | ||
| IL_6W6K_030 | 1/A/594:597, 1/A/643:645 | No text annotation Not in a motif group | homologous IL_6CZR_136 IL_05564.2 | |
| IL_6W6K_031 | 1/A/597:598, 1/A/640:643 | Major groove minor groove platform; mini C-loop Not in a motif group | geometric IL_6CZR_137 IL_09061.6 | |
| IL_6W6K_032 | 1/A/604:612, 1/A/628:634 | No text annotation Not in a motif group | homologous IL_4LFB_026 IL_78349.1 | |
| IL_6W6K_033 | 1/A/654:655, 1/A/751:754 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_4LFB_027 IL_50694.2 | |
| IL_6W6K_034 | 1/A/655:660, 1/A/745:751 | No text annotation Not in a motif group | ||
| IL_6W6K_035 | 1/A/662:667, 1/A/739:743 | No text annotation Not in a motif group | ||
| IL_6W6K_036 | 1/A/668:670, 1/A/737:738 | Single stack bend Not in a motif group | geometric IL_5TBW_375 IL_76488.2 | |
| IL_6W6K_039 | 1/A/887:894, 1/A/905:910 | 8x6 Sarcin-Ricin with inserted Y; G-bulge Not in a motif group | homologous IL_4LFB_034 IL_24606.2 | |
| IL_6W6K_040 | 1/A/922:923, 1/A/1393:1395 | Single bulged A Not in a motif group | homologous IL_5J7L_039 IL_37497.2 | |
| IL_6W6K_041 | 1/A/925:927, 1/A/1390:1391 | Single bulged G Not in a motif group | homologous IL_5J7L_040 IL_00225.2 | |
| IL_6W6K_042 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform Not in a motif group | homologous IL_4LFB_037 IL_47078.1 | |
| IL_6W6K_043 | 1/A/953:954, 1/A/1226:1228 | No text annotation Not in a motif group | homologous IL_6CZR_150 NA | |
| IL_6W6K_044 | 1/A/993:997, 1/A/1044:1045 | Minor groove platform Not in a motif group | geometric IL_4LFB_039 IL_47078.1 | |
| IL_6W6K_045 | 1/A/998:999, 1/A/1041:1043 | Single stack bend Not in a motif group | homologous IL_5J7L_044 IL_76488.2 | |
| IL_6W6K_046 | 1/A/1048:1050, 1/A/1208:1209 | Single bulged U Not in a motif group | homologous IL_5J7L_046 IL_83039.13 | |
| IL_6W6K_047 | 1/A/1052:1056, 1/A/1204:1206 | Isolated cWS basepair Not in a motif group | homologous IL_4LFB_044 IL_76319.2 | |
| IL_6W6K_048 | 1/A/1057:1058, 1/A/1199:1203 | Minor groove platform Not in a motif group | homologous IL_4LFB_045 IL_93353.1 | |
| IL_6W6K_049 | 1/A/1060:1061, 1/A/1195:1197 | Single bulged U Not in a motif group | homologous IL_4LFB_046 IL_83039.13 | |
| IL_6W6K_050 | 1/A/1061:1063, 1/A/1193:1195 | No text annotation Not in a motif group | geometric IL_1U9S_007 IL_95997.1 | |
| IL_6W6K_051 | 1/A/1124:1129, 1/A/1143:1149 | No text annotation Not in a motif group | ||
| IL_6W6K_052 | 1/A/1129:1132, 1/A/1142:1143 | Minor groove platform Not in a motif group | geometric IL_3RW6_001 IL_15052.1 | |
| IL_6W6K_053 | 1/A/1158:1161, 1/A/1175:1181 | No text annotation Not in a motif group | geometric IL_5J7L_053 IL_42032.1 | |
| IL_6W6K_054 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation Not in a motif group | homologous IL_5J7L_054 IL_09129.1 | |
| IL_6W6K_055 | 1/A/1255:1258, 1/A/1277:1282 | No text annotation Not in a motif group | ||
| IL_6W6K_056 | 1/A/1259:1263, 1/A/1272:1276 | Triple sheared Not in a motif group | homologous IL_5J7L_056 IL_56467.8 | |
| IL_6W6K_057 | 1/A/1303:1308, 1/A/1329:1334 | No text annotation Not in a motif group | geometric IL_4LFB_055 IL_19954.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6W6K_007 | Minor groove platform | ||
| IL_6W6K_014 | No text annotation | ||
| IL_6W6K_023 | No text annotation | ||
| IL_6W6K_037 | Kink-turn | ||
| IL_6W6K_038 | No text annotation | ||
| IL_6W6K_058 | No text annotation | ||
| IL_6W6K_059 | No text annotation | ||
| IL_6W6K_060 | No text annotation | ||
| IL_6W6K_061 | No text annotation | ||
| IL_6W6K_062 | No text annotation | ||
| IL_6W6K_063 | Double sheared | ||
| IL_6W6K_064 | Triple sheared related | ||
| IL_6W6K_065 | Minor groove platform | ||
| IL_6W6K_066 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6W6K_001 | 1/A/46:47, 1/A/361:367, 1/A/393:395 | No text annotation Not in a motif group | ||
| J3_6W6K_002 | 1/A/586:588, 1/A/651:654, 1/A/754:755 | No text annotation Not in a motif group | ||
| J3_6W6K_003 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation Not in a motif group | homologous J3_5J7L_004 NA | |
| J3_6W6K_004 | 1/A/943:946, 1/A/1235:1237, 1/A/1337:1340 | No text annotation Not in a motif group | homologous J3_4LFB_003 NA | |
| J3_6W6K_005 | 1/A/955:962, 1/A/973:984, 1/A/1221:1225 | No text annotation Not in a motif group | ||
| J3_6W6K_006 | 1/A/990:993, 1/A/1045:1047, 1/A/1210:1215 | No text annotation Not in a motif group | homologous J3_4LFB_005 NA | |
| J3_6W6K_007 | 1/A/1003:1006, 1/A/1023:1027, 1/A/1034:1037 | No text annotation Not in a motif group | ||
| J3_6W6K_008 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation Not in a motif group | ||
| J3_6W6K_009 | 1/A/1073:1074, 1/A/1083:1087, 1/A/1098:1102 | No text annotation Not in a motif group | homologous J3_6CZR_024 NA | |
| J3_6W6K_010 | 1/A/1116:1118, 1/A/1155:1158, 1/A/1181:1184 | No text annotation Not in a motif group | homologous J3_5J7L_010 NA | |
| J3_6W6K_011 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation Not in a motif group |
Problematic loops
No problematic loops
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