5WYJ Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5WYJ_004 | 1/5A/120:125 | No text annotation Not in a motif group | geometric HL_2Y8W_001 HL_01057.1 | |
| HL_5WYJ_005 | 1/5A/196:201 | GNRA Not in a motif group | geometric HL_5TBW_017 HL_42097.1 | |
| HL_5WYJ_007 | 1/5A/360:365 | No text annotation Not in a motif group | geometric HL_5J7L_179 HL_42097.1 | |
| HL_5WYJ_009 | 1/5A/515:522 | No text annotation Not in a motif group | geometric HL_4PQV_003 HL_20146.1 | |
| HL_5WYJ_011 | 1/SA/154:160 | No text annotation Not in a motif group | geometric HL_7RQB_011 HL_75407.1 | |
| HL_5WYJ_012 | 1/SA/190:195 | No text annotation Not in a motif group | ||
| HL_5WYJ_014 | 1/SA/276:279 | No text annotation Not in a motif group | homologous HL_4V88_192 HL_53837.1 | |
| HL_5WYJ_015 | 1/SA/330:338 | No text annotation Not in a motif group | homologous HL_4V88_193 HL_69023.2 | |
| HL_5WYJ_016 | 1/SA/368:373 | No text annotation Not in a motif group | ||
| HL_5WYJ_017 | 1/SA/393:404 | No text annotation Not in a motif group | homologous HL_4V88_195 HL_84288.1 | |
| HL_5WYJ_018 | 1/SA/414:419 | UNCG Not in a motif group | homologous HL_4V88_196 HL_03562.2 | |
| HL_5WYJ_019 | 1/SA/450:456 | No text annotation Not in a motif group | homologous HL_4V88_197 HL_09136.1 | |
| HL_5WYJ_020 | 1/SA/491:496 | Other HL Not in a motif group | geometric HL_1P6V_001 HL_03562.2 | |
| HL_5WYJ_021 | 1/SA/520:532 | No text annotation Not in a motif group | homologous HL_4V88_199 HL_06285.2 | |
| HL_5WYJ_022 | 1/SA/569:574 | No text annotation Not in a motif group | ||
| HL_5WYJ_024 | 1/SA/900:909 | No text annotation Not in a motif group | homologous HL_4V88_206 HL_12326.1 | |
| HL_5WYJ_025 | 1/SA/937:942 | Other HL Not in a motif group | homologous HL_4V88_207 HL_87030.2 | |
| HL_5WYJ_026 | 1/SA/1055:1064 | No text annotation Not in a motif group | geometric HL_2ZZM_002 HL_23083.1 | |
| HL_5WYJ_028 | 1/SA/1501:1506 | GNRA Not in a motif group | homologous HL_4V88_218 HL_42097.1 | |
| HL_5WYJ_029 | 1/SA/1594:1602 | No text annotation Not in a motif group | ||
| HL_5WYJ_031 | 1/SA/1802:1807 | No text annotation Not in a motif group | geometric HL_5J7L_179 HL_42097.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5WYJ_001 | No text annotation | ||
| HL_5WYJ_002 | No text annotation | ||
| HL_5WYJ_003 | No text annotation | ||
| HL_5WYJ_006 | No text annotation | ||
| HL_5WYJ_008 | No text annotation | ||
| HL_5WYJ_010 | No text annotation | ||
| HL_5WYJ_013 | No text annotation | ||
| HL_5WYJ_023 | No text annotation | ||
| HL_5WYJ_027 | No text annotation | ||
| HL_5WYJ_030 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5WYJ_001 | 1/3A/1:4, 1/SA/1120:1123 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_1MFQ_004 IL_30621.2 | |
| IL_5WYJ_002 | 1/3A/4:6, 1/SA/1118:1120 | No text annotation Not in a motif group | geometric IL_7A0S_014 IL_95997.1 | |
| IL_5WYJ_003 | 1/3A/48:50, 1/5A/468:470 | No text annotation Not in a motif group | geometric IL_4E48_003 IL_95997.1 | |
| IL_5WYJ_004 | 1/3A/50:52, 1/5A/466:468 | No text annotation Not in a motif group | geometric IL_5C5W_002 IL_95997.1 | |
| IL_5WYJ_005 | 1/3A/78:85, 1/3A/325:329 | No text annotation Not in a motif group | ||
| IL_5WYJ_007 | 1/3A/97:98, 1/3A/317:319 | No text annotation Not in a motif group | ||
| IL_5WYJ_008 | 1/5A/11:15, 1/5A/66:71 | No text annotation Not in a motif group | ||
| IL_5WYJ_009 | 1/5A/17:18, 1/5A/62:64 | Single stack bend Not in a motif group | geometric IL_5J7L_032 IL_76488.2 | |
| IL_5WYJ_010 | 1/5A/93:95, 1/5A/149:157 | No text annotation Not in a motif group | geometric IL_4P3U_012 IL_95997.1 | |
| IL_5WYJ_011 | 1/5A/97:99, 1/5A/145:147 | No text annotation Not in a motif group | geometric IL_6OL3_002 IL_95997.1 | |
| IL_5WYJ_012 | 1/5A/100:104, 1/5A/140:144 | No text annotation Not in a motif group | ||
| IL_5WYJ_013 | 1/5A/107:111, 1/5A/135:137 | No text annotation Not in a motif group | ||
| IL_5WYJ_014 | 1/5A/115:119, 1/5A/126:131 | No text annotation Not in a motif group | ||
| IL_5WYJ_015 | 1/5A/167:172, 1/5A/224:228 | No text annotation Not in a motif group | ||
| IL_5WYJ_016 | 1/5A/175:178, 1/5A/219:221 | No text annotation Not in a motif group | geometric IL_4V84_070 IL_23164.1 | |
| IL_5WYJ_017 | 1/5A/187:189, 1/5A/208:210 | No text annotation Not in a motif group | geometric IL_1L9A_003 IL_51629.2 | |
| IL_5WYJ_018 | 1/5A/246:247, 1/5A/265:267 | Single bulged U Not in a motif group | geometric IL_4LFB_046 IL_83039.13 | |
| IL_5WYJ_019 | 1/5A/336:341, 1/5A/384:387 | No text annotation Not in a motif group | ||
| IL_5WYJ_020 | 1/5A/342:343, 1/5A/381:383 | Single bulged U Not in a motif group | geometric IL_4FRG_002 IL_83039.13 | |
| IL_5WYJ_021 | 1/5A/346:349, 1/5A/375:378 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_6MWN_005 IL_30621.2 | |
| IL_5WYJ_022 | 1/5A/352:357, 1/5A/368:372 | No text annotation Not in a motif group | ||
| IL_5WYJ_023 | 1/5A/395:397, 1/5A/460:462 | No text annotation Not in a motif group | geometric IL_3IVK_002 IL_95997.1 | |
| IL_5WYJ_024 | 1/5A/402:406, 1/5A/450:455 | No text annotation Not in a motif group | ||
| IL_5WYJ_025 | 1/5A/413:414, 1/5A/440:443 | Minor groove platform Not in a motif group | geometric IL_3RW6_003 IL_93353.1 | |
| IL_5WYJ_026 | 1/5A/501:503, 1/5A/533:537 | No text annotation Not in a motif group | ||
| IL_5WYJ_027 | 1/5A/505:507, 1/5A/529:531 | No text annotation Not in a motif group | geometric IL_3DIL_006 IL_95997.1 | |
| IL_5WYJ_028 | 1/5A/513:515, 1/5A/522:523 | Single stack bend Not in a motif group | geometric IL_7KGA_006 IL_76488.2 | |
| IL_5WYJ_029 | 1/5A/550:552, 1/5A/585:587 | No text annotation Not in a motif group | geometric IL_4V88_419 IL_95997.1 | |
| IL_5WYJ_030 | 1/5A/555:558, 1/5A/579:582 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_5J7L_283 IL_30621.2 | |
| IL_5WYJ_031 | 1/5A/559:561, 1/5A/576:578 | No text annotation Not in a motif group | geometric IL_3MEI_002 IL_95997.1 | |
| IL_5WYJ_032 | 1/SA/24:26, 1/SA/600:601 | No text annotation Not in a motif group | ||
| IL_5WYJ_033 | 1/SA/50:52, 1/SA/428:429 | Minor groove platform Not in a motif group | homologous IL_4V88_388 IL_93353.1 | |
| IL_5WYJ_034 | 1/SA/109:112, 1/SA/302:305 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_391 IL_30621.2 | |
| IL_5WYJ_035 | 1/SA/113:116, 1/SA/300:301 | Multiple bulged bases Not in a motif group | homologous IL_4V88_392 IL_44546.1 | |
| IL_5WYJ_036 | 1/SA/117:122, 1/SA/295:299 | No text annotation Not in a motif group | homologous IL_4V88_393 IL_64181.2 | |
| IL_5WYJ_037 | 1/SA/144:149, 1/SA/165:171 | tWH-tWH-tHW-tHW Not in a motif group | geometric IL_4LFB_009 IL_39753.1 | |
| IL_5WYJ_038 | 1/SA/150:152, 1/SA/162:164 | No text annotation Not in a motif group | homologous IL_4V88_395 IL_53251.2 | |
| IL_5WYJ_039 | 1/SA/186:189, 1/SA/196:199 | Double sheared Not in a motif group | homologous IL_4V88_396 IL_09705.9 | |
| IL_5WYJ_040 | 1/SA/204:206, 1/SA/259:263 | Major groove platform with extra cWW Not in a motif group | homologous IL_4V88_397 IL_05564.2 | |
| IL_5WYJ_041 | 1/SA/206:208, 1/SA/257:259 | No text annotation Not in a motif group | geometric IL_4V88_433 IL_95997.1 | |
| IL_5WYJ_042 | 1/SA/265:268, 1/SA/287:289 | No text annotation Not in a motif group | geometric IL_6IA2_001 IL_95997.1 | |
| IL_5WYJ_043 | 1/SA/270:273, 1/SA/283:285 | No text annotation Not in a motif group | ||
| IL_5WYJ_044 | 1/SA/274:276, 1/SA/279:282 | Intercalated cWW Not in a motif group | geometric IL_7RQB_025 IL_52767.2 | |
| IL_5WYJ_045 | 1/SA/311:316, 1/SA/348:355 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_4V88_402 IL_45067.2 | |
| IL_5WYJ_046 | 1/SA/318:323, 1/SA/345:346 | No text annotation Not in a motif group | ||
| IL_5WYJ_047 | 1/SA/363:365, 1/SA/376:381 | No text annotation Not in a motif group | ||
| IL_5WYJ_048 | 1/SA/389:391, 1/SA/406:408 | Isolated cWH basepair Not in a motif group | homologous IL_4V88_405 IL_51629.2 | |
| IL_5WYJ_049 | 1/SA/443:447, 1/SA/460:461 | C-loop Not in a motif group | geometric IL_5J7L_018 IL_75255.1 | |
| IL_5WYJ_050 | 1/SA/447:448, 1/SA/458:460 | Single bulged G Not in a motif group | geometric IL_3NDB_004 IL_00225.2 | |
| IL_5WYJ_051 | 1/SA/480:485, 1/SA/502:508 | No text annotation Not in a motif group | ||
| IL_5WYJ_052 | 1/SA/517:518, 1/SA/533:535 | No text annotation Not in a motif group | ||
| IL_5WYJ_053 | 1/SA/518:520, 1/SA/532:533 | Minor groove platform Not in a motif group | homologous IL_4V88_412 IL_93353.1 | |
| IL_5WYJ_056 | 1/SA/627:631, 1/SA/968:972 | tSH-tHW-tHS Not in a motif group | homologous IL_4V88_418 IL_17136.1 | |
| IL_5WYJ_057 | 1/SA/865:866, 1/SA/962:965 | Major groove platform; stack outside cWW Not in a motif group | geometric IL_6N5P_003 IL_50694.2 | |
| IL_5WYJ_058 | 1/SA/867:869, 1/SA/958:961 | CA cWW with bulged A Not in a motif group | geometric IL_4P3T_005 IL_95997.1 | |
| IL_5WYJ_059 | 1/SA/871:874, 1/SA/953:956 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_430 IL_30621.2 | |
| IL_5WYJ_060 | 1/SA/874:878, 1/SA/950:953 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_5TBW_100 IL_30621.2 | |
| IL_5WYJ_061 | 1/SA/885:888, 1/SA/924:927 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_432 IL_30621.2 | |
| IL_5WYJ_062 | 1/SA/893:895, 1/SA/917:919 | No text annotation Not in a motif group | homologous IL_4V88_433 IL_95997.1 | |
| IL_5WYJ_063 | 1/SA/895:899, 1/SA/910:917 | Kink-turn Not in a motif group | geometric IL_6UFG_001 IL_45067.2 | |
| IL_5WYJ_064 | 1/SA/1041:1044, 1/SA/1074:1077 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_438 IL_30621.2 | |
| IL_5WYJ_065 | 1/SA/1051:1053, 1/SA/1066:1067 | No text annotation Not in a motif group | ||
| IL_5WYJ_066 | 1/SA/1149:1151, 1/SA/1627:1628 | Single bulged G Not in a motif group | homologous IL_4V88_442 IL_00225.2 | |
| IL_5WYJ_067 | 1/SA/1157:1161, 1/SA/1616:1621 | No text annotation Not in a motif group | ||
| IL_5WYJ_068 | 1/SA/1173:1175, 1/SA/1464:1466 | No text annotation Not in a motif group | homologous IL_4V88_444 IL_95997.1 | |
| IL_5WYJ_077 | 1/SA/1470:1474, 1/SA/1533:1574 | No text annotation Not in a motif group | ||
| IL_5WYJ_078 | 1/SA/1495:1498, 1/SA/1509:1512 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_461 IL_30621.2 | |
| IL_5WYJ_079 | 1/SA/1642:1644, 1/SA/1757:1759 | No text annotation Not in a motif group | homologous IL_4V88_465 IL_95997.1 | |
| IL_5WYJ_080 | 1/SA/1644:1647, 1/SA/1753:1757 | No text annotation Not in a motif group | ||
| IL_5WYJ_081 | 1/SA/1650:1652, 1/SA/1748:1750 | AA cWW Not in a motif group | homologous IL_4V88_467 IL_95997.1 | |
| IL_5WYJ_082 | 1/SA/1653:1656, 1/SA/1744:1747 | Double sheared Not in a motif group | homologous IL_4V88_468 IL_09705.9 | |
| IL_5WYJ_083 | 1/SA/1656:1658, 1/SA/1743:1744 | No text annotation Not in a motif group | ||
| IL_5WYJ_084 | 1/SA/1665:1667, 1/SA/1734:1736 | No text annotation Not in a motif group | homologous IL_4V88_470 IL_51629.2 | |
| IL_5WYJ_085 | 1/SA/1669:1672, 1/SA/1729:1732 | Double sheared Not in a motif group | homologous IL_4V88_471 IL_09705.9 | |
| IL_5WYJ_086 | 1/SA/1672:1674, 1/SA/1727:1729 | No text annotation Not in a motif group | geometric IL_5UNE_001 IL_53251.2 | |
| IL_5WYJ_087 | 1/SA/1675:1678, 1/SA/1723:1726 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_4V88_473 IL_30621.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5WYJ_006 | No text annotation | ||
| IL_5WYJ_054 | Isolated near basepair | ||
| IL_5WYJ_055 | No text annotation | ||
| IL_5WYJ_069 | No text annotation | ||
| IL_5WYJ_070 | No text annotation | ||
| IL_5WYJ_071 | No text annotation | ||
| IL_5WYJ_072 | No text annotation | ||
| IL_5WYJ_073 | Single bulged U | ||
| IL_5WYJ_074 | No text annotation | ||
| IL_5WYJ_075 | No text annotation | ||
| IL_5WYJ_076 | Single bulged A |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5WYJ_001 | 1/3A/105:111, 1/3A/259:263, 1/3A/308:310 | No text annotation Not in a motif group | ||
| J3_5WYJ_002 | 1/SA/633:635, 1/SA/861:865, 1/SA/965:966 | No text annotation Not in a motif group | ||
| J3_5WYJ_003 | 1/SA/881:884, 1/SA/928:936, 1/SA/943:947 | No text annotation Not in a motif group | homologous J3_4V88_033 NA | |
| J3_5WYJ_004 | 1/SA/1168:1171, 1/SA/1468:1470, 1/SA/1574:1577 | No text annotation Not in a motif group | homologous J3_4V88_036 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5WYJ_005 | No text annotation |
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