6LQQ Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6LQQ_010 | 1/SA/70:81 | No text annotation Not in a motif group | ||
| HL_6LQQ_011 | 1/SA/154:160 | Other HL Not in a motif group | homologous HL_4V88_188 HL_76539.2 | |
| HL_6LQQ_012 | 1/SA/186:199 | No text annotation Not in a motif group | ||
| HL_6LQQ_013 | 1/SA/230:235 | No text annotation Not in a motif group | geometric HL_4WF9_009 HL_09829.1 | |
| HL_6LQQ_014 | 1/SA/275:281 | No text annotation Not in a motif group | ||
| HL_6LQQ_015 | 1/SA/330:338 | No text annotation Not in a motif group | homologous HL_4V88_193 HL_69023.2 | |
| HL_6LQQ_016 | 1/SA/364:381 | No text annotation Not in a motif group | ||
| HL_6LQQ_017 | 1/SA/393:404 | No text annotation Not in a motif group | homologous HL_4V88_195 HL_84288.1 | |
| HL_6LQQ_018 | 1/SA/450:456 | No text annotation Not in a motif group | geometric HL_4WF9_003 HL_75407.1 | |
| HL_6LQQ_019 | 1/SA/491:496 | GNRA Not in a motif group | geometric HL_4V9F_040 HL_42097.1 | |
| HL_6LQQ_020 | 1/SA/520:532 | No text annotation Not in a motif group | geometric HL_4V88_199 HL_06285.2 | |
| HL_6LQQ_021 | 1/SA/561:566 | No text annotation Not in a motif group | geometric HL_5NFV_001 HL_76539.2 | |
| HL_6LQQ_027 | 1/SA/1129:1139 | No text annotation Not in a motif group | ||
| HL_6LQQ_031 | 1/SA/1594:1602 | No text annotation Not in a motif group | geometric HL_4OOG_001 HL_65572.2 | |
| HL_6LQQ_032 | 1/SA/1629:1636 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6LQQ_001 | No text annotation | ||
| HL_6LQQ_002 | No text annotation | ||
| HL_6LQQ_003 | No text annotation | ||
| HL_6LQQ_004 | No text annotation | ||
| HL_6LQQ_005 | No text annotation | ||
| HL_6LQQ_006 | No text annotation | ||
| HL_6LQQ_007 | No text annotation | ||
| HL_6LQQ_008 | No text annotation | ||
| HL_6LQQ_009 | No text annotation | ||
| HL_6LQQ_022 | No text annotation | ||
| HL_6LQQ_023 | No text annotation | ||
| HL_6LQQ_024 | No text annotation | ||
| HL_6LQQ_025 | Other HL | ||
| HL_6LQQ_026 | No text annotation | ||
| HL_6LQQ_028 | No text annotation | ||
| HL_6LQQ_029 | No text annotation | ||
| HL_6LQQ_030 | GNRA | ||
| HL_6LQQ_033 | No text annotation | ||
| HL_6LQQ_034 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6LQQ_001 | 1/3A/6:7, 1/SA/1117:1119 | Single bulged G Not in a motif group | geometric IL_3IGI_004 IL_00225.2 | |
| IL_6LQQ_002 | 1/3A/48:50, 1/5A/466:470 | No text annotation Not in a motif group | geometric IL_4V9F_053 IL_46796.1 | |
| IL_6LQQ_003 | 1/3A/78:85, 1/3A/325:329 | No text annotation Not in a motif group | ||
| IL_6LQQ_004 | 1/3A/97:98, 1/3A/317:319 | No text annotation Not in a motif group | ||
| IL_6LQQ_007 | 1/5A/17:18, 1/5A/62:64 | Single bulged G Not in a motif group | geometric IL_3NDB_004 IL_00225.2 | |
| IL_6LQQ_020 | 1/5A/497:499, 1/5A/539:542 | Isolated non-canonical cWW with bulges Not in a motif group | geometric IL_3TD0_005 IL_82068.2 | |
| IL_6LQQ_021 | 1/5A/501:503, 1/5A/533:537 | No text annotation Not in a motif group | ||
| IL_6LQQ_024 | 1/5A/550:552, 1/5A/585:587 | No text annotation Not in a motif group | geometric IL_5UNE_001 IL_53251.2 | |
| IL_6LQQ_025 | 1/SA/24:26, 1/SA/600:601 | Single bulged C Not in a motif group | geometric IL_7KGA_001 IL_61258.12 | |
| IL_6LQQ_026 | 1/SA/50:53, 1/SA/427:429 | No text annotation Not in a motif group | geometric IL_4N0T_004 IL_46796.1 | |
| IL_6LQQ_027 | 1/SA/58:63, 1/SA/87:89 | No text annotation Not in a motif group | homologous IL_4V88_389 IL_95004.1 | |
| IL_6LQQ_028 | 1/SA/64:70, 1/SA/81:86 | Triple sheared related Not in a motif group | geometric IL_4V9F_018 IL_64879.2 | |
| IL_6LQQ_029 | 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_6LQQ_030 | 1/SA/113:116, 1/SA/300:301 | Multiple bulged bases Not in a motif group | homologous IL_4V88_392 IL_44546.1 | |
| IL_6LQQ_031 | 1/SA/117:122, 1/SA/295:299 | No text annotation Not in a motif group | homologous IL_4V88_393 IL_64181.2 | |
| IL_6LQQ_032 | 1/SA/143:149, 1/SA/165:172 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_4V88_394 IL_80604.2 | |
| IL_6LQQ_033 | 1/SA/150:152, 1/SA/162:164 | Isolated cWH basepair Not in a motif group | geometric IL_4KQ0_004 IL_51629.2 | |
| IL_6LQQ_034 | 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_6LQQ_035 | 1/SA/206:208, 1/SA/257:259 | No text annotation Not in a motif group | geometric IL_5ZTM_002 IL_95997.1 | |
| IL_6LQQ_036 | 1/SA/226:228, 1/SA/237:241 | No text annotation Not in a motif group | ||
| IL_6LQQ_037 | 1/SA/265:267, 1/SA/288:289 | Single bulged A Not in a motif group | homologous IL_4V88_399 IL_37497.2 | |
| IL_6LQQ_038 | 1/SA/270:274, 1/SA/282:285 | No text annotation Not in a motif group | ||
| IL_6LQQ_039 | 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_6LQQ_040 | 1/SA/318:323, 1/SA/345:346 | No text annotation Not in a motif group | geometric IL_5Y58_001 IL_48100.2 | |
| IL_6LQQ_041 | 1/SA/389:391, 1/SA/406:408 | Isolated cWH basepair Not in a motif group | homologous IL_4V88_405 IL_51629.2 | |
| IL_6LQQ_042 | 1/SA/443:447, 1/SA/460:461 | C-loop Not in a motif group | geometric IL_5J7L_018 IL_75255.1 | |
| IL_6LQQ_043 | 1/SA/447:448, 1/SA/458:460 | Single bulged G Not in a motif group | geometric IL_5J7L_019 IL_00225.2 | |
| IL_6LQQ_044 | 1/SA/482:483, 1/SA/504:506 | Single bulged A Not in a motif group | homologous IL_4V88_409 IL_37497.2 | |
| IL_6LQQ_045 | 1/SA/514:516, 1/SA/536:543 | No text annotation Not in a motif group | homologous IL_8C3A_420 IL_55023.1 | |
| IL_6LQQ_046 | 1/SA/517:520, 1/SA/532:535 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_6JDV_001 IL_30621.2 | |
| IL_6LQQ_047 | 1/SA/551:552, 1/SA/584:587 | No text annotation Not in a motif group | geometric IL_5J7L_341 IL_71530.2 | |
| IL_6LQQ_048 | 1/SA/552:559, 1/SA/568:584 | No text annotation Not in a motif group | ||
| IL_6LQQ_064 | 1/SA/1157:1160, 1/SA/1617:1621 | C-loop Not in a motif group | homologous IL_4V88_443 IL_63596.6 | |
| IL_6LQQ_065 | 1/SA/1173:1174, 1/SA/1464:1466 | Single stack bend Not in a motif group | geometric IL_7RQB_058 IL_76488.2 | |
| IL_6LQQ_066 | 1/SA/1174:1176, 1/SA/1463:1464 | Minor groove platform Not in a motif group | geometric IL_5TBW_039 IL_42622.2 | |
| IL_6LQQ_067 | 1/SA/1212:1216, 1/SA/1448:1451 | No text annotation Not in a motif group | ||
| IL_6LQQ_068 | 1/SA/1268:1270, 1/SA/1440:1441 | No text annotation Not in a motif group | ||
| IL_6LQQ_069 | 1/SA/1470:1474, 1/SA/1533:1574 | No text annotation Not in a motif group | ||
| IL_6LQQ_071 | 1/SA/1650:1652, 1/SA/1748:1750 | AA cWW Not in a motif group | homologous IL_4V88_467 IL_95997.1 | |
| IL_6LQQ_072 | 1/SA/1653:1660, 1/SA/1741:1747 | No text annotation Not in a motif group | ||
| IL_6LQQ_073 | 1/SA/1664:1667, 1/SA/1734:1737 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_5TBW_041 IL_30621.2 | |
| IL_6LQQ_074 | 1/SA/1669:1672, 1/SA/1729:1732 | Double sheared Not in a motif group | homologous IL_4V88_471 IL_09705.9 | |
| IL_6LQQ_075 | 1/SA/1672:1674, 1/SA/1727:1729 | No text annotation Not in a motif group | geometric IL_3RW6_004 IL_95997.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6LQQ_005 | No text annotation | ||
| IL_6LQQ_006 | No text annotation | ||
| IL_6LQQ_008 | No text annotation | ||
| IL_6LQQ_009 | Isolated cWH basepair | ||
| IL_6LQQ_010 | Single bulged U | ||
| IL_6LQQ_011 | Single bulged U | ||
| IL_6LQQ_012 | Major groove minor groove platform; mini C-loop | ||
| IL_6LQQ_013 | Single bulged A | ||
| IL_6LQQ_014 | Single bulged U | ||
| IL_6LQQ_015 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_016 | No text annotation | ||
| IL_6LQQ_017 | Stack outside cWW | ||
| IL_6LQQ_018 | Single stack bend | ||
| IL_6LQQ_019 | Single bulged U | ||
| IL_6LQQ_022 | No text annotation | ||
| IL_6LQQ_023 | Single bulged U | ||
| IL_6LQQ_049 | No text annotation | ||
| IL_6LQQ_050 | No text annotation | ||
| IL_6LQQ_051 | Single stack bend | ||
| IL_6LQQ_052 | No text annotation | ||
| IL_6LQQ_053 | No text annotation | ||
| IL_6LQQ_054 | Major groove platform; stack outside cWW | ||
| IL_6LQQ_055 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_056 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_057 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_058 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_059 | No text annotation | ||
| IL_6LQQ_060 | Single bulged A | ||
| IL_6LQQ_061 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_062 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_063 | Single stack bend | ||
| IL_6LQQ_070 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_076 | No text annotation | ||
| IL_6LQQ_077 | Isolated near basepair | ||
| IL_6LQQ_078 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6LQQ_004 | 1/SA/1150:1151, 1/SA/1627:1629, 1/SA/1636:1640 | No text annotation Not in a motif group | ||
| J3_6LQQ_005 | 1/SA/1168:1171, 1/SA/1468:1470, 1/SA/1574:1577 | No text annotation Not in a motif group | ||
| J3_6LQQ_006 | 1/SA/1216:1220, 1/SA/1263:1268, 1/SA/1441:1448 | No text annotation Not in a motif group |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6LQQ_001 | No text annotation | ||
| J3_6LQQ_002 | No text annotation | ||
| J3_6LQQ_003 | No text annotation |
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