6ZU9 Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6ZU9_001 | 1/1/13:22 | No text annotation Not in a motif group | homologous HL_5UD5_001 HL_09136.1 | |
| HL_6ZU9_002 | 1/1/31:39 | No text annotation Not in a motif group | homologous HL_5E81_212 NA | |
| HL_6ZU9_003 | 1/1/53:61 | No text annotation Not in a motif group | homologous HL_1YFG_003 NA | |
| HL_6ZU9_005 | 1/2/70:81 | No text annotation Not in a motif group | ||
| HL_6ZU9_006 | 1/2/154:160 | Other HL Not in a motif group | homologous HL_4V88_188 HL_76539.2 | |
| HL_6ZU9_007 | 1/2/190:195 | No text annotation Not in a motif group | geometric HL_4V88_198 HL_56691.2 | |
| HL_6ZU9_009 | 1/2/243:250 | T-loop with 1 bulged base Not in a motif group | homologous HL_4V88_191 HL_27930.1 | |
| HL_6ZU9_010 | 1/2/276:279 | No text annotation Not in a motif group | homologous HL_4V88_192 HL_53837.1 | |
| HL_6ZU9_011 | 1/2/330:338 | No text annotation Not in a motif group | homologous HL_4V88_193 HL_69023.2 | |
| HL_6ZU9_012 | 1/2/368:373 | GNRA Not in a motif group | geometric HL_4QLM_001 HL_30784.2 | |
| HL_6ZU9_013 | 1/2/393:404 | No text annotation Not in a motif group | homologous HL_4V88_195 HL_84288.1 | |
| HL_6ZU9_014 | 1/2/414:419 | UNCG Not in a motif group | homologous HL_4V88_196 HL_03562.2 | |
| HL_6ZU9_015 | 1/2/450:456 | No text annotation Not in a motif group | homologous HL_4V88_197 HL_09136.1 | |
| HL_6ZU9_017 | 1/2/520:532 | No text annotation Not in a motif group | homologous HL_4V88_199 HL_06285.2 | |
| HL_6ZU9_025 | 1/2/937:942 | Other HL Not in a motif group | homologous HL_4V88_207 HL_87030.2 | |
| HL_6ZU9_028 | 1/2/1084:1089 | Other HL Not in a motif group | homologous HL_4V88_210 HL_42097.1 | |
| HL_6ZU9_038 | 1/2/1594:1602 | No text annotation Not in a motif group | homologous HL_4V88_220 HL_60812.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6ZU9_004 | No text annotation | ||
| HL_6ZU9_008 | No text annotation | ||
| HL_6ZU9_016 | No text annotation | ||
| HL_6ZU9_018 | Other HL | ||
| HL_6ZU9_019 | No text annotation | ||
| HL_6ZU9_020 | No text annotation | ||
| HL_6ZU9_021 | No text annotation | ||
| HL_6ZU9_022 | No text annotation | ||
| HL_6ZU9_023 | No text annotation | ||
| HL_6ZU9_024 | No text annotation | ||
| HL_6ZU9_026 | No text annotation | ||
| HL_6ZU9_027 | No text annotation | ||
| HL_6ZU9_029 | GNRA | ||
| HL_6ZU9_030 | No text annotation | ||
| HL_6ZU9_031 | No text annotation | ||
| HL_6ZU9_032 | GNRA | ||
| HL_6ZU9_033 | No text annotation | ||
| HL_6ZU9_034 | No text annotation | ||
| HL_6ZU9_035 | No text annotation | ||
| HL_6ZU9_036 | GNRA | ||
| HL_6ZU9_037 | No text annotation | ||
| HL_6ZU9_039 | No text annotation | ||
| HL_6ZU9_040 | Other HL |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6ZU9_001 | 1/2/24:26, 1/2/600:601 | Single bulged C Not in a motif group | homologous IL_4V88_384 IL_61258.12 | |
| IL_6ZU9_002 | 1/2/35:37, 1/2/471:473 | UC cWW Not in a motif group | geometric IL_4V88_385 IL_51629.2 | |
| IL_6ZU9_003 | 1/2/37:41, 1/2/466:471 | No text annotation Not in a motif group | geometric IL_4V88_386 IL_41507.1 | |
| IL_6ZU9_004 | 1/2/42:48, 1/2/431:433 | No text annotation Not in a motif group | geometric IL_4V88_387 IL_33912.1 | |
| IL_6ZU9_005 | 1/2/50:52, 1/2/428:429 | Minor groove platform Not in a motif group | homologous IL_4V88_388 IL_93353.1 | |
| IL_6ZU9_006 | 1/2/58:63, 1/2/87:89 | No text annotation Not in a motif group | homologous IL_4V88_389 IL_95004.1 | |
| IL_6ZU9_007 | 1/2/64:69, 1/2/82:86 | No text annotation Not in a motif group | homologous IL_4V88_390 IL_77691.1 | |
| IL_6ZU9_008 | 1/2/109:112, 1/2/302:305 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_391 IL_30621.2 | |
| IL_6ZU9_009 | 1/2/113:116, 1/2/300:301 | Multiple bulged bases Not in a motif group | homologous IL_4V88_392 IL_44546.1 | |
| IL_6ZU9_010 | 1/2/117:122, 1/2/295:299 | No text annotation Not in a motif group | homologous IL_4V88_393 IL_64181.2 | |
| IL_6ZU9_011 | 1/2/144:149, 1/2/165:171 | tWH-tWH-tHW-tHW Not in a motif group | geometric IL_4LFB_009 IL_39753.1 | |
| IL_6ZU9_012 | 1/2/150:152, 1/2/162:164 | No text annotation Not in a motif group | geometric IL_1YZ9_002 IL_95997.1 | |
| IL_6ZU9_013 | 1/2/186:189, 1/2/196:199 | Double sheared Not in a motif group | homologous IL_4V88_396 IL_09705.9 | |
| IL_6ZU9_014 | 1/2/204:206, 1/2/259:263 | Major groove platform with extra cWW Not in a motif group | homologous IL_4V88_397 IL_05564.2 | |
| IL_6ZU9_015 | 1/2/206:208, 1/2/257:259 | No text annotation Not in a motif group | geometric IL_4V88_398 IL_95997.1 | |
| IL_6ZU9_016 | 1/2/265:267, 1/2/288:289 | Single bulged A Not in a motif group | homologous IL_4V88_399 IL_37497.2 | |
| IL_6ZU9_017 | 1/2/270:273, 1/2/283:285 | No text annotation Not in a motif group | homologous IL_4V88_400 IL_47298.1 | |
| IL_6ZU9_018 | 1/2/275:276, 1/2/279:281 | No text annotation Not in a motif group | homologous IL_8C3A_409 IL_83039.13 | |
| IL_6ZU9_019 | 1/2/311:316, 1/2/348:355 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_4V88_402 IL_45067.2 | |
| IL_6ZU9_020 | 1/2/318:323, 1/2/345:346 | No text annotation Not in a motif group | homologous IL_4V88_403 IL_48100.2 | |
| IL_6ZU9_022 | 1/2/389:391, 1/2/406:408 | Isolated cWH basepair Not in a motif group | homologous IL_4V88_405 IL_51629.2 | |
| IL_6ZU9_023 | 1/2/411:413, 1/2/420:422 | Isolated near basepair Not in a motif group | homologous IL_4V88_406 IL_52767.2 | |
| IL_6ZU9_024 | 1/2/439:441, 1/2/463:464 | Single bulged U Not in a motif group | geometric IL_4V88_407 IL_83039.13 | |
| IL_6ZU9_025 | 1/2/443:447, 1/2/460:461 | C-loop Not in a motif group | geometric IL_5J7L_018 IL_75255.1 | |
| IL_6ZU9_026 | 1/2/447:448, 1/2/458:460 | Single bulged G Not in a motif group | geometric IL_5J7L_019 IL_00225.2 | |
| IL_6ZU9_027 | 1/2/481:482, 1/2/505:507 | Single bulged A Not in a motif group | homologous IL_4V88_409 IL_37497.2 | |
| IL_6ZU9_028 | 1/2/514:516, 1/2/536:543 | No text annotation Not in a motif group | ||
| IL_6ZU9_029 | 1/2/517:518, 1/2/533:535 | Minor groove platform Not in a motif group | geometric IL_4LFB_004 IL_93353.1 | |
| IL_6ZU9_030 | 1/2/518:520, 1/2/532:533 | Minor groove platform Not in a motif group | geometric IL_4V88_412 IL_93353.1 | |
| IL_6ZU9_034 | 1/2/616:622, 1/2/1104:1105 | No text annotation Not in a motif group | homologous IL_4V88_416 IL_69996.1 | |
| IL_6ZU9_035 | 1/2/624:626, 1/2/973:975 | No text annotation Not in a motif group | homologous IL_4V88_417 IL_95997.1 | |
| IL_6ZU9_036 | 1/2/627:631, 1/2/968:972 | tSH-tHW-tHS Not in a motif group | homologous IL_4V88_418 IL_17136.1 | |
| IL_6ZU9_043 | 1/2/865:866, 1/2/962:965 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_4V88_428 IL_50694.2 | |
| IL_6ZU9_044 | 1/2/867:870, 1/2/957:961 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_429 IL_30621.2 | |
| IL_6ZU9_045 | 1/2/871:874, 1/2/953:956 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_430 IL_30621.2 | |
| IL_6ZU9_046 | 1/2/874:878, 1/2/950:953 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_4V88_431 IL_30621.2 | |
| IL_6ZU9_047 | 1/2/885:888, 1/2/924:927 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_432 IL_30621.2 | |
| IL_6ZU9_052 | 1/2/1034:1036, 1/2/1095:1101 | No text annotation Not in a motif group | homologous IL_4V88_437 IL_19557.3 | |
| IL_6ZU9_053 | 1/2/1041:1044, 1/2/1074:1077 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_438 IL_30621.2 | |
| IL_6ZU9_054 | 1/2/1051:1053, 1/2/1066:1067 | Single bulged U Not in a motif group | homologous IL_4V88_439 IL_83039.13 | |
| IL_6ZU9_058 | 1/2/1157:1160, 1/2/1617:1621 | C-loop Not in a motif group | homologous IL_4V88_443 IL_63596.6 | |
| IL_6ZU9_059 | 1/2/1173:1175, 1/2/1464:1466 | No text annotation Not in a motif group | homologous IL_4V88_444 IL_95997.1 | |
| IL_6ZU9_060 | 1/2/1178:1179, 1/2/1459:1461 | Minor groove platform Not in a motif group | homologous IL_4V88_445 IL_42622.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6ZU9_021 | No text annotation | ||
| IL_6ZU9_031 | SSU/LSU pseudoknot | ||
| IL_6ZU9_032 | Single bulged U | ||
| IL_6ZU9_033 | No text annotation | ||
| IL_6ZU9_037 | No text annotation | ||
| IL_6ZU9_038 | Major groove minor groove platform; mini C-loop | ||
| IL_6ZU9_039 | No text annotation | ||
| IL_6ZU9_040 | No text annotation | ||
| IL_6ZU9_041 | No text annotation | ||
| IL_6ZU9_042 | No text annotation | ||
| IL_6ZU9_048 | No text annotation | ||
| IL_6ZU9_049 | Kink-turn | ||
| IL_6ZU9_050 | Other IL | ||
| IL_6ZU9_051 | tSH-tHW-tHS | ||
| IL_6ZU9_055 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | ||
| IL_6ZU9_056 | Single bulged A | ||
| IL_6ZU9_057 | Single bulged G | ||
| IL_6ZU9_061 | No text annotation | ||
| IL_6ZU9_062 | No text annotation | ||
| IL_6ZU9_063 | No text annotation | ||
| IL_6ZU9_064 | No text annotation | ||
| IL_6ZU9_065 | Single bulged U | ||
| IL_6ZU9_066 | Tandem non-canonical cWW pairs | ||
| IL_6ZU9_067 | Minor groove platform with extra cWW | ||
| IL_6ZU9_068 | Single bulged A | ||
| IL_6ZU9_069 | Isolated cWH basepair | ||
| IL_6ZU9_070 | Minor groove platform | ||
| IL_6ZU9_071 | No text annotation | ||
| IL_6ZU9_072 | Minor groove platform | ||
| IL_6ZU9_073 | No text annotation | ||
| IL_6ZU9_074 | Major groove platform; stack outside cWW | ||
| IL_6ZU9_075 | No text annotation | ||
| IL_6ZU9_076 | No text annotation | ||
| IL_6ZU9_077 | Tandem non-canonical cWW pairs | ||
| IL_6ZU9_078 | No text annotation | ||
| IL_6ZU9_079 | No text annotation | ||
| IL_6ZU9_080 | No text annotation | ||
| IL_6ZU9_081 | No text annotation | ||
| IL_6ZU9_082 | Tandem non-canonical cWW pairs | ||
| IL_6ZU9_083 | AA cWW | ||
| IL_6ZU9_084 | Double sheared | ||
| IL_6ZU9_085 | Isolated cWS basepair | ||
| IL_6ZU9_086 | No text annotation | ||
| IL_6ZU9_087 | Double sheared | ||
| IL_6ZU9_088 | No text annotation | ||
| IL_6ZU9_089 | Tandem non-canonical cWW pairs | ||
| IL_6ZU9_090 | Triple sheared | ||
| IL_6ZU9_091 | Other IL | ||
| IL_6ZU9_092 | UU cWW water inserted |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6ZU9_001 | 1/2/41:42, 1/2/433:439, 1/2/464:466 | No text annotation Not in a motif group | ||
| J3_6ZU9_002 | 1/2/633:635, 1/2/861:865, 1/2/965:966 | No text annotation Not in a motif group | ||
| J3_6ZU9_004 | 1/2/881:884, 1/2/928:936, 1/2/943:947 | No text annotation Not in a motif group | homologous J3_4V88_033 NA | |
| J3_6ZU9_005 | 1/2/1037:1039, 1/2/1079:1083, 1/2/1090:1094 | No text annotation Not in a motif group | homologous J3_4V88_034 NA | |
| J3_6ZU9_006 | 1/2/1161:1164, 1/2/1581:1587, 1/2/1609:1616 | No text annotation Not in a motif group | homologous J3_4V88_035 NA | |
| J3_6ZU9_007 | 1/2/1168:1171, 1/2/1468:1470, 1/2/1574:1577 | No text annotation Not in a motif group | homologous J3_4V88_036 NA | |
| J3_6ZU9_013 | 1/2/1470:1474, 1/2/1533:1540, 1/2/1571:1574 | No text annotation Not in a motif group | homologous J3_8C3A_044 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6ZU9_003 | No text annotation | ||
| J3_6ZU9_008 | No text annotation | ||
| J3_6ZU9_009 | No text annotation | ||
| J3_6ZU9_010 | No text annotation | ||
| J3_6ZU9_011 | No text annotation | ||
| J3_6ZU9_012 | No text annotation |
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