8CDU Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8CDU_001 | 1/A/14:24 | No text annotation | homologous HL_5J7L_001 NA | |
| HL_8CDU_003 | 1/A/157:162 | GNRA | homologous HL_4LFB_003 HL_34789.4 | |
| HL_8CDU_004 | 1/A/192:197 | No text annotation | ||
| HL_8CDU_005 | 1/A/217:222 | UNCG | homologous HL_5J7L_005 NA | |
| HL_8CDU_006 | 1/A/267:275 | GNRA related | homologous HL_4LFB_006 HL_87268.2 | |
| HL_8CDU_007 | 1/A/304:309 | GNRA | homologous HL_4LFB_007 HL_34789.4 | |
| HL_8CDU_008 | 1/A/328:341 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_8CDU_009 | 1/A/350:355 | UNCG | homologous HL_4LFB_009 HL_61337.4 | |
| HL_8CDU_010 | 1/A/387:392 | GNRA | homologous HL_4LFB_010 HL_34789.4 | |
| HL_8CDU_011 | 1/A/427:432 | UNCG | homologous HL_5J7L_011 NA | |
| HL_8CDU_012 | 1/A/472:478 | No text annotation | geometric HL_2ZNI_001 HL_75660.8 | |
| HL_8CDU_013 | 1/A/531:536 | No text annotation | geometric HL_2Y8W_001 HL_40612.1 | |
| HL_8CDU_014 | 1/A/626:632 | GNRA-like with tWH | homologous HL_4LFB_014 HL_86621.1 | |
| HL_8CDU_030 | 1/A/692:716 | No text annotation | ||
| HL_8CDU_016 | 1/A/735:740 | GNRA | homologous HL_4LFB_016 HL_34789.4 | |
| HL_8CDU_017 | 1/A/850:855 | GNRA | geometric HL_4LFB_012 HL_34789.4 | |
| HL_8CDU_018 | 1/A/872:877 | GNRA | homologous HL_4LFB_019 HL_34789.4 | |
| HL_8CDU_019 | 1/A/907:912 | GNRA | homologous HL_6CZR_091 NA | |
| HL_8CDU_021 | 1/A/1021:1028 | No text annotation | homologous HL_6CZR_093 NA | |
| HL_8CDU_023 | 1/A/1086:1091 | GNRA | homologous HL_4LFB_024 HL_34789.4 | |
| HL_8CDU_024 | 1/A/1099:1106 | T-loop related | homologous HL_4LFB_025 HL_63894.2 | |
| HL_8CDU_025 | 1/A/1134:1158 | No text annotation | ||
| HL_8CDU_026 | 1/A/1173:1181 | No text annotation | geometric HL_4WF9_041 NA | |
| HL_8CDU_027 | 1/A/1274:1279 | GNRA | homologous HL_4LFB_028 HL_34789.4 | |
| HL_8CDU_028 | 1/A/1323:1332 | T-loop with 3 stacked bulged bases | homologous HL_4LFB_029 HL_93658.1 | |
| HL_8CDU_029 | 1/A/1365:1375 | No text annotation | homologous HL_5J7L_029 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8CDU_002 | UNCG variation | ||
| HL_8CDU_015 | No text annotation | ||
| HL_8CDU_020 | No text annotation | ||
| HL_8CDU_022 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8CDU_001 | 1/A/32:34, 1/A/561:562 | Single bulged G | homologous IL_4LFB_001 IL_28408.2 | |
| IL_8CDU_002 | 1/A/46:47, 1/A/404:406 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_8CDU_003 | 1/A/49:54, 1/A/367:369 | No text annotation | homologous IL_5J7L_003 NA | |
| IL_8CDU_004 | 1/A/56:58, 1/A/364:365 | Minor groove platform | homologous IL_4LFB_004 IL_34520.3 | |
| IL_8CDU_005 | 1/A/65:68, 1/A/101:102 | Multiple bulged bases | homologous IL_4LFB_005 IL_71421.3 | |
| IL_8CDU_006 | 1/A/69:71, 1/A/98:100 | Isolated non-canonical cWW pair | geometric IL_7A0S_107 IL_71625.3 | |
| IL_8CDU_007 | 1/A/127:130, 1/A/239:240 | Multiple bulged bases | homologous IL_4LFB_007 IL_75289.2 | |
| IL_8CDU_008 | 1/A/131:135, 1/A/235:238 | No text annotation | homologous IL_4LFB_008 IL_60988.2 | |
| IL_8CDU_009 | 1/A/146:152, 1/A/167:174 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 NA | |
| IL_8CDU_010 | 1/A/250:255, 1/A/285:292 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_8CDU_054 | 1/A/257:260, 1/A/282:283 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_8CDU_012 | 1/A/300:301, 1/A/312:316 | C-loop | homologous IL_4LFB_013 IL_06671.1 | |
| IL_8CDU_013 | 1/A/375:377, 1/A/400:401 | Single bulged U | homologous IL_4LFB_014 IL_97561.5 | |
| IL_8CDU_014 | 1/A/379:383, 1/A/397:398 | C-loop | homologous IL_4LFB_015 IL_26900.1 | |
| IL_8CDU_015 | 1/A/383:384, 1/A/395:397 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_8CDU_016 | 1/A/417:424, 1/A/435:441 | No text annotation | homologous IL_5J7L_020 NA | |
| IL_8CDU_017 | 1/A/454:458, 1/A/492:497 | 6x5 Sarcin-Ricin; G-bulge | homologous IL_4LFB_018 IL_82100.1 | |
| IL_8CDU_018 | 1/A/458:464, 1/A/486:492 | No text annotation | ||
| IL_8CDU_019 | 1/A/513:520, 1/A/549:550 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_8CDU_020 | 1/A/524:530, 1/A/537:545 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_8CDU_021 | 1/A/578:584, 1/A/890:891 | No text annotation | homologous IL_5J7L_026 NA | |
| IL_8CDU_022 | 1/A/589:593, 1/A/766:770 | tSH-tHW-tHS | homologous IL_5J7L_027 NA | |
| IL_8CDU_023 | 1/A/603:605, 1/A/653:654 | Major groove platform | homologous IL_5J7L_028 NA | |
| IL_8CDU_024 | 1/A/606:607, 1/A/649:652 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 NA | |
| IL_8CDU_025 | 1/A/613:614, 1/A/641:643 | Single bulged U | geometric IL_5J7L_298 NA | |
| IL_8CDU_026 | 1/A/614:621, 1/A/637:641 | No text annotation | geometric IL_5J7L_030 NA | |
| IL_8CDU_027 | 1/A/666:667, 1/A/756:758 | Major groove platform | homologous IL_4LFB_028 IL_48076.8 | |
| IL_8CDU_028 | 1/A/671:675, 1/A/749:752 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_8CDU_029 | 1/A/682:686, 1/A/722:726 | Triple non-canonical cWW pairs | geometric IL_4LFB_065 IL_71154.3 | |
| IL_8CDU_052 | 1/A/682:689, 1/A/719:726 | No text annotation | ||
| IL_8CDU_031 | 1/A/692:698, 1/A/707:716 | No text annotation | ||
| IL_8CDU_033 | 1/A/897:904, 1/A/915:920 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_84044.1 | |
| IL_8CDU_035 | 1/A/943:945, 1/A/1389:1393 | Minor groove platform | geometric IL_5J7L_041 NA | |
| IL_8CDU_036 | 1/A/963:964, 1/A/1235:1237 | Minor groove platform | homologous IL_5J7L_042 NA | |
| IL_8CDU_038 | 1/A/1003:1007, 1/A/1054:1055 | Minor groove platform | geometric IL_5J7L_043 NA | |
| IL_8CDU_040 | 1/A/1058:1060, 1/A/1217:1218 | No text annotation | homologous IL_6CZR_152 NA | |
| IL_8CDU_053 | 1/A/1062:1066, 1/A/1213:1215 | Isolated cWS basepair | homologous IL_4LFB_044 IL_82453.1 | |
| IL_8CDU_042 | 1/A/1067:1068, 1/A/1208:1212 | Minor groove platform | geometric IL_5J7L_048 NA | |
| IL_8CDU_043 | 1/A/1070:1071, 1/A/1204:1206 | Single bulged A | homologous IL_5J7L_049 NA | |
| IL_8CDU_046 | 1/A/1256:1262, 1/A/1293:1299 | No text annotation | homologous IL_5J7L_054 NA | |
| IL_8CDU_047 | 1/A/1264:1267, 1/A/1286:1291 | 180 degree turn | homologous IL_6CZR_161 NA | |
| IL_8CDU_048 | 1/A/1268:1271, 1/A/1282:1285 | Double sheared | geometric IL_5J7L_256 NA | |
| IL_8CDU_050 | 1/A/1312:1317, 1/A/1338:1343 | No text annotation | homologous IL_5J7L_057 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8CDU_011 | No text annotation | ||
| IL_8CDU_030 | No text annotation | ||
| IL_8CDU_032 | Isolated cWH basepair | ||
| IL_8CDU_055 | Single stack bend | ||
| IL_8CDU_034 | No text annotation | ||
| IL_8CDU_037 | Isolated non-canonical cWW pair | ||
| IL_8CDU_039 | No text annotation | ||
| IL_8CDU_041 | No text annotation | ||
| IL_8CDU_044 | Isolated non-canonical cWW pair | ||
| IL_8CDU_056 | Isolated non-canonical cWW pair | ||
| IL_8CDU_045 | Tandem non-canonical cWW pairs | ||
| IL_8CDU_049 | Isolated non-canonical cWW pair | ||
| IL_8CDU_051 | Isolated non-canonical cWW pair |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8CDU_008 | 1/A/48:49, 1/A/369:375, 1/A/401:403 | No text annotation | geometric J3_8C3A_082 NA | |
| J3_8CDU_009 | 1/A/48:54, 1/A/367:375, 1/A/401:403 | No text annotation | homologous J3_4LFB_014 J3_63856.1 | |
| J3_8CDU_001 | 1/A/595:597, 1/A/660:664, 1/A/760:764 | No text annotation | homologous J3_5J7L_051 NA | |
| J3_8CDU_010 | 1/A/681:682, 1/A/726:734, 1/A/741:743 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_8CDU_002 | 1/A/835:838, 1/A/867:871, 1/A/878:884 | No text annotation | homologous J3_5J7L_004 NA | |
| J3_8CDU_011 | 1/A/943:949, 1/A/1353:1359, 1/A/1381:1393 | No text annotation | ||
| J3_8CDU_003 | 1/A/953:956, 1/A/1244:1246, 1/A/1346:1349 | No text annotation | homologous J3_5J7L_005 NA | |
| J3_8CDU_004 | 1/A/965:972, 1/A/981:994, 1/A/1230:1234 | No text annotation | homologous J3_4LFB_004 J3_88451.1 | |
| J3_8CDU_005 | 1/A/1000:1003, 1/A/1055:1057, 1/A/1219:1224 | No text annotation | homologous J3_5J7L_007 NA | |
| J3_8CDU_012 | 1/A/1000:1007, 1/A/1054:1057, 1/A/1219:1224 | No text annotation | homologous J3_5J7L_053 NA | |
| J3_8CDU_017 | 1/A/1011:1020, 1/A/1029:1036, 1/A/1045:1049 | No text annotation | ||
| J3_8CDU_014 | 1/A/1071:1078, 1/A/1117:1123, 1/A/1196:1204 | No text annotation | ||
| J3_8CDU_015 | 1/A/1083:1084, 1/A/1093:1097, 1/A/1108:1112 | No text annotation | homologous J3_5J7L_009 NA | |
| J3_8CDU_006 | 1/A/1126:1128, 1/A/1164:1170, 1/A/1184:1193 | No text annotation | homologous J3_4LFB_018 J3_40706.1 | |
| J3_8CDU_007 | 1/A/1246:1250, 1/A/1305:1312, 1/A/1343:1346 | No text annotation | homologous J3_4LFB_009 J3_03192.1 | |
| J3_8CDU_016 | 1/A/1246:1250, 1/A/1305:1317, 1/A/1338:1346 | No text annotation | ||
| J4_8CDU_001 | 1/A/113:121, 1/A/246:248, 1/A/294:297, 1/A/319:320 | No text annotation | ||
| J4_8CDU_002 | 1/A/141:143, 1/A/177:183, 1/A/206:212, 1/A/227:229 | No text annotation | ||
| J4_8CDU_004 | 1/A/584:586, 1/A/773:778, 1/A/819:830, 1/A/889:890 | No text annotation | homologous J4_4LFB_003 J4_14595.1 | |
| J5_8CDU_001 | 1/A/38:41, 1/A/411:414, 1/A/444:449, 1/A/502:509, 1/A/554:557 | No text annotation | ||
| J5_8CDU_002 | 1/A/60:63, 1/A/104:111, 1/A/322:324, 1/A/345:347, 1/A/358:362 | No text annotation | homologous J5_5J7L_003 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8CDU_013 | No text annotation | ||
| J4_8CDU_003 | No text annotation |
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