1N34 Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_1N34_001 | 1/A/12:22 | No text annotation Not in a motif group | homologous HL_4LFB_001 HL_89881.2 | |
| HL_1N34_003 | 1/A/158:163 | GNRA Not in a motif group | homologous HL_4LFB_003 HL_42097.1 | |
| HL_1N34_004 | 1/A/190B:190G | No text annotation Not in a motif group | homologous HL_4LFB_004 HL_10278.1 | |
| HL_1N34_005 | 1/A/199:218 | No text annotation Not in a motif group | ||
| HL_1N34_006 | 1/A/259:267 | No text annotation Not in a motif group | homologous HL_4LFB_006 HL_69023.2 | |
| HL_1N34_007 | 1/A/296:301 | GNRA Not in a motif group | homologous HL_4LFB_007 HL_42097.1 | |
| HL_1N34_008 | 1/A/320:333 | No text annotation Not in a motif group | homologous HL_4LFB_008 HL_81205.2 | |
| HL_1N34_010 | 1/A/377:386 | No text annotation Not in a motif group | ||
| HL_1N34_011 | 1/A/419:424 | No text annotation Not in a motif group | homologous HL_6CZR_082 HL_03562.2 | |
| HL_1N34_012 | 1/A/457:475 | No text annotation Not in a motif group | ||
| HL_1N34_013 | 1/A/522:527 | No text annotation Not in a motif group | geometric HL_5J7L_143 HL_75407.1 | |
| HL_1N34_014 | 1/A/617:623 | No text annotation Not in a motif group | homologous HL_4LFB_014 HL_26881.1 | |
| HL_1N34_015 | 1/A/689:698 | No text annotation Not in a motif group | homologous HL_5J7L_015 HL_12326.1 | |
| HL_1N34_017 | 1/A/786:796 | No text annotation Not in a motif group | homologous HL_4LFB_017 HL_12326.1 | |
| HL_1N34_018 | 1/A/838:848 | No text annotation Not in a motif group | homologous HL_6CZR_089 HL_53837.1 | |
| HL_1N34_021 | 1/A/963:972 | No text annotation Not in a motif group | homologous HL_4LFB_021 NA | |
| HL_1N34_024 | 1/A/1076:1081 | GNRA Not in a motif group | homologous HL_4LFB_024 HL_42097.1 | |
| HL_1N34_025 | 1/A/1089:1096 | No text annotation Not in a motif group | homologous HL_5J7L_024 HL_71554.2 | |
| HL_1N34_027 | 1/A/1164:1172 | No text annotation Not in a motif group | ||
| HL_1N34_031 | 1/A/1449:1454 | UNCG Not in a motif group | homologous HL_4LFB_031 HL_03562.2 | |
| HL_1N34_032 | 1/A/1515:1520 | GNRA Not in a motif group | geometric HL_4V9F_020 HL_42097.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_1N34_002 | tRNA anticodon loop | ||
| HL_1N34_009 | UNCG | ||
| HL_1N34_016 | Other HL | ||
| HL_1N34_019 | GNRA | ||
| HL_1N34_020 | GNRA | ||
| HL_1N34_022 | No text annotation | ||
| HL_1N34_023 | No text annotation | ||
| HL_1N34_026 | No text annotation | ||
| HL_1N34_028 | No text annotation | ||
| HL_1N34_029 | No text annotation | ||
| HL_1N34_030 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_1N34_001 | 1/A/30:32, 1/A/552:553 | Single bulged G Not in a motif group | homologous IL_4LFB_001 IL_00225.2 | |
| IL_1N34_002 | 1/A/44:45, 1/A/396:398 | Single bulged A Not in a motif group | homologous IL_4LFB_002 IL_37497.2 | |
| IL_1N34_003 | 1/A/47:52, 1/A/359:361 | No text annotation Not in a motif group | homologous IL_4LFB_003 IL_11178.1 | |
| IL_1N34_004 | 1/A/54:57, 1/A/355:357 | Minor groove platform with extra cWW Not in a motif group | geometric IL_7RQB_031 IL_46796.1 | |
| IL_1N34_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_1N34_006 | 1/A/67:69, 1/A/99:102 | No text annotation Not in a motif group | geometric IL_4LFB_006 IL_95997.1 | |
| IL_1N34_008 | 1/A/128:131, 1/A/231:233 | Isolated non-canonical cWW with bulges Not in a motif group | homologous IL_5J7L_009 IL_82068.2 | |
| IL_1N34_009 | 1/A/132:136, 1/A/227:230 | No text annotation Not in a motif group | homologous IL_4LFB_008 IL_58764.3 | |
| IL_1N34_011 | 1/A/186:188, 1/A/190K:191 | No text annotation Not in a motif group | homologous IL_4LFB_010 IL_95997.1 | |
| IL_1N34_012 | 1/A/242:247, 1/A/277:284 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_4LFB_011 IL_45067.2 | |
| IL_1N34_013 | 1/A/248:252, 1/A/274:276 | No text annotation Not in a motif group | ||
| IL_1N34_014 | 1/A/292:293, 1/A/304:308 | C-loop Not in a motif group | homologous IL_4LFB_013 IL_37712.2 | |
| IL_1N34_016 | 1/A/370:375, 1/A/389:391 | No text annotation Not in a motif group | ||
| IL_1N34_017 | 1/A/375:377, 1/A/386:389 | Single bulged G, near cWW Not in a motif group | geometric IL_6CZR_128 IL_52767.2 | |
| IL_1N34_019 | 1/A/409:417, 1/A/426:433 | No text annotation Not in a motif group | homologous IL_6CZR_129 IL_58819.1 | |
| IL_1N34_020 | 1/A/446:450, 1/A/483:488 | 6x5 Sarcin-Ricin; G-bulge Not in a motif group | geometric IL_4LFB_018 IL_88269.3 | |
| IL_1N34_021 | 1/A/450:456, 1/A/476:483 | No text annotation Not in a motif group | homologous IL_6CZR_131 IL_30149.1 | |
| IL_1N34_022 | 1/A/504:511, 1/A/540:541 | SSU/LSU pseudoknot Not in a motif group | geometric IL_4LFB_020 IL_15861.7 | |
| IL_1N34_024 | 1/A/515:521, 1/A/528:536 | No text annotation Not in a motif group | geometric IL_4V88_415 IL_55871.1 | |
| IL_1N34_029 | 1/A/605:612, 1/A/628:633 | No text annotation Not in a motif group | homologous IL_4LFB_026 IL_78349.1 | |
| IL_1N34_032 | 1/A/662:666, 1/A/740:743 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4LFB_029 IL_71110.1 | |
| IL_1N34_033 | 1/A/673:679, 1/A/711:717 | No text annotation Not in a motif group | ||
| IL_1N34_034 | 1/A/683:688, 1/A/699:707 | Kink-turn Not in a motif group | homologous IL_4LFB_031 IL_37722.1 | |
| IL_1N34_038 | 1/A/922:923, 1/A/1393:1395 | Single bulged A Not in a motif group | homologous IL_5J7L_039 IL_37497.2 | |
| IL_1N34_039 | 1/A/925:927, 1/A/1390:1391 | Single bulged G Not in a motif group | homologous IL_5J7L_040 IL_00225.2 | |
| IL_1N34_040 | 1/A/933:935, 1/A/1380:1384 | Minor groove platform Not in a motif group | homologous IL_4LFB_037 IL_47078.1 | |
| IL_1N34_042 | 1/A/953:954, 1/A/1226:1228 | Minor groove platform Not in a motif group | homologous IL_5J7L_042 IL_42622.2 | |
| IL_1N34_044 | 1/A/1047:1051, 1/A/1207:1210 | No text annotation Not in a motif group | ||
| IL_1N34_045 | 1/A/1051:1056, 1/A/1204:1207 | No text annotation Not in a motif group | ||
| IL_1N34_046 | 1/A/1056:1059, 1/A/1198:1204 | Minor groove platform related Not in a motif group | geometric IL_3BNR_008 IL_58764.3 | |
| IL_1N34_047 | 1/A/1059:1061, 1/A/1195:1198 | No text annotation Not in a motif group | geometric IL_7A0S_031 IL_95997.1 | |
| IL_1N34_048 | 1/A/1061:1063, 1/A/1193:1195 | No text annotation Not in a motif group | geometric IL_4LFB_047 IL_95997.1 | |
| IL_1N34_049 | 1/A/1121:1128, 1/A/1143:1152 | No text annotation Not in a motif group | ||
| IL_1N34_051 | 1/A/1247:1253, 1/A/1284:1290 | No text annotation Not in a motif group | homologous IL_6CZR_160 IL_09129.1 | |
| IL_1N34_052 | 1/A/1253:1258, 1/A/1277:1284 | No text annotation Not in a motif group | ||
| IL_1N34_055 | 1/A/1303:1308, 1/A/1329:1334 | No text annotation Not in a motif group | geometric IL_4LFB_055 IL_19954.2 | |
| IL_1N34_057 | 1/A/1401:1404, 1/A/1497:1501 | No text annotation Not in a motif group | ||
| IL_1N34_058 | 1/A/1404:1407, 1/A/1494:1497 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_5EW4_002 IL_30621.2 | |
| IL_1N34_059 | 1/A/1407:1409, 1/A/1491:1494 | No text annotation Not in a motif group | ||
| IL_1N34_061 | 1/A/1412:1414, 1/A/1486:1488 | No text annotation Not in a motif group | homologous IL_4LFB_059 IL_95997.1 | |
| IL_1N34_062 | 1/A/1414:1416, 1/A/1484:1486 | No text annotation Not in a motif group | geometric IL_4V88_424 IL_95997.1 | |
| IL_1N34_066 | 1/A/1435:1438, 1/A/1463:1466 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_4K27_001 IL_30621.2 | |
| IL_1N34_067 | 1/A/1440:1447, 1/A/1459:1461 | No text annotation Not in a motif group | homologous IL_4LFB_064 IL_92788.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_1N34_007 | No text annotation | ||
| IL_1N34_010 | tWH-tWH-tHW-tHW | ||
| IL_1N34_015 | Tandem non-canonical cWW pairs | ||
| IL_1N34_018 | No text annotation | ||
| IL_1N34_023 | No text annotation | ||
| IL_1N34_025 | No text annotation | ||
| IL_1N34_026 | tSH-tHW-tHS | ||
| IL_1N34_027 | Major groove platform | ||
| IL_1N34_028 | Major groove minor groove platform; mini C-loop | ||
| IL_1N34_030 | Major groove platform; stack outside cWW | ||
| IL_1N34_031 | Major groove platform | ||
| IL_1N34_035 | Left turn | ||
| IL_1N34_036 | tSH-tHW-tHS-cWW | ||
| IL_1N34_037 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_1N34_041 | No text annotation | ||
| IL_1N34_043 | No text annotation | ||
| IL_1N34_050 | Tandem non-canonical cWW pairs | ||
| IL_1N34_053 | Triple sheared | ||
| IL_1N34_054 | No text annotation | ||
| IL_1N34_056 | No text annotation | ||
| IL_1N34_060 | Tandem non-canonical cWW pairs | ||
| IL_1N34_063 | Double sheared | ||
| IL_1N34_064 | No text annotation | ||
| IL_1N34_065 | UAA/GAN variation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_1N34_001 | 1/A/826:829, 1/A/857:861, 1/A/868:874 | No text annotation Not in a motif group | homologous J3_4LFB_001 NA | |
| J3_1N34_002 | 1/A/936:939, 1/A/1344:1350, 1/A/1372:1379 | No text annotation Not in a motif group | homologous J3_4LFB_002 NA | |
| J3_1N34_003 | 1/A/941:946, 1/A/1235:1237, 1/A/1337:1342 | No text annotation Not in a motif group | ||
| J3_1N34_004 | 1/A/955:962, 1/A/973:985, 1/A/1220:1225 | No text annotation Not in a motif group | ||
| J3_1N34_007 | 1/A/1063:1068, 1/A/1107:1113, 1/A/1187:1193 | No text annotation Not in a motif group | ||
| J3_1N34_008 | 1/A/1116:1118, 1/A/1155:1161, 1/A/1175:1184 | No text annotation Not in a motif group | ||
| J3_1N34_009 | 1/A/1237:1241, 1/A/1296:1303, 1/A/1334:1337 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_1N34_005 | No text annotation | ||
| J3_1N34_006 | No text annotation |
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