6LQQ Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/SA/70:81 | NA | NA | ||
| 1/SA/154:160 | Other HL homologous HL_4V88_188 | NA HL_43074.18* | ||
| 1/SA/186:199 | NA | NA | ||
| 1/SA/230:235 | geometric HL_4WF9_009 | NA HL_68478.1* | ||
| 1/SA/275:281 | NA | NA | ||
| 1/SA/330:338 | homologous HL_4V88_193 | NA HL_93727.5* | ||
| 1/SA/364:381 | NA | NA | ||
| 1/SA/393:404 | homologous HL_4V88_195 | NA HL_22443.1* | ||
| 1/SA/450:456 | geometric HL_4WF9_003 | NA HL_62869.3* | ||
| 1/SA/491:496 | GNRA geometric HL_4V9F_040 | NA HL_43074.18* | ||
| 1/SA/520:532 | geometric HL_4V88_199 | NA HL_17086.2* | ||
| 1/SA/561:566 | geometric HL_5NFV_001 | NA HL_58912.1* | ||
| 1/SA/1129:1139 | NA | NA | ||
| 1/SA/1594:1602 | geometric HL_4OOG_001 | NA HL_68529.2* | ||
| 1/SA/1629:1636 | NA | NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6LQQ_001 | NA | ||
| HL_6LQQ_002 | NA | ||
| HL_6LQQ_003 | NA | ||
| HL_6LQQ_004 | NA | ||
| HL_6LQQ_005 | NA | ||
| HL_6LQQ_006 | NA | ||
| HL_6LQQ_007 | NA | ||
| HL_6LQQ_008 | NA | ||
| HL_6LQQ_009 | NA | ||
| HL_6LQQ_022 | NA | ||
| HL_6LQQ_023 | NA | ||
| HL_6LQQ_024 | homologous HL_4V88_206 | ||
| HL_6LQQ_025 | Other HL homologous HL_4V88_207 | ||
| HL_6LQQ_026 | NA | ||
| HL_6LQQ_028 | NA | ||
| HL_6LQQ_029 | geometric HL_4WF9_003 | ||
| HL_6LQQ_030 | GNRA homologous HL_4V88_218 | ||
| HL_6LQQ_033 | NA | ||
| HL_6LQQ_034 | geometric HL_2Y8W_001 |
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/3A/6:7, 1/SA/1117:1119 | Single bulged G geometric IL_3IGI_004 | NA IL_59137.10* | ||
| 1/3A/48:50, 1/5A/466:470 | NA | NA | ||
| 1/3A/78:85, 1/3A/325:329 | NA | NA | ||
| 1/3A/97:98, 1/3A/317:319 | NA | NA | ||
| 1/5A/17:18, 1/5A/62:64 | NA | NA | ||
| 1/5A/497:499, 1/5A/539:542 | NA | NA | ||
| 1/5A/501:503, 1/5A/533:537 | NA | NA | ||
| 1/5A/550:552, 1/5A/585:587 | NA | NA | ||
| 1/SA/24:26, 1/SA/600:601 | Single bulged C geometric IL_7KGA_001 | NA IL_61258.10* | ||
| 1/SA/50:53, 1/SA/427:429 | geometric IL_4N0T_004 | NA IL_87332.1* | ||
| 1/SA/58:63, 1/SA/87:89 | homologous IL_4V88_389 | NA IL_96451.1* | ||
| 1/SA/64:70, 1/SA/81:86 | Triple sheared related geometric IL_4V9F_018 | NA IL_64879.1* | ||
| 1/SA/109:112, 1/SA/302:305 | Tandem non-canonical cWW pairs homologous IL_4V88_391 | NA IL_85877.10* | ||
| 1/SA/113:116, 1/SA/300:301 | Multiple bulged bases homologous IL_4V88_392 | NA IL_13730.12* | ||
| 1/SA/117:122, 1/SA/295:299 | homologous IL_4V88_393 | NA IL_76386.1* | ||
| 1/SA/143:149, 1/SA/165:172 | tWH-tWH-tHW-tHW homologous IL_4V88_394 | NA IL_92440.5* | ||
| 1/SA/150:152, 1/SA/162:164 | Isolated cWH basepair geometric IL_4KQ0_004 | NA IL_42589.6* | ||
| 1/SA/204:206, 1/SA/259:263 | Major groove platform with extra cWW homologous IL_4V88_397 | NA IL_95485.6* | ||
| 1/SA/206:208, 1/SA/257:259 | geometric IL_5ZTM_002 | NA IL_01312.13* | ||
| 1/SA/226:228, 1/SA/237:241 | NA | NA | ||
| 1/SA/265:267, 1/SA/288:289 | Single bulged A homologous IL_4V88_399 | NA IL_80007.16* | ||
| 1/SA/270:274, 1/SA/282:285 | NA | NA | ||
| 1/SA/311:316, 1/SA/348:355 | Kink-turn with non-sequential stacking homologous IL_4V88_402 | NA IL_29549.9* | ||
| 1/SA/318:323, 1/SA/345:346 | geometric IL_5Y58_001 | NA IL_98882.3* | ||
| 1/SA/389:391, 1/SA/406:408 | Isolated cWH basepair homologous IL_4V88_405 | NA IL_42589.6* | ||
| 1/SA/443:447, 1/SA/460:461 | C-loop geometric IL_5J7L_018 | NA IL_08376.2* | ||
| 1/SA/447:448, 1/SA/458:460 | Single bulged G geometric IL_5J7L_019 | NA IL_59137.10* | ||
| 1/SA/482:483, 1/SA/504:506 | Single bulged A homologous IL_4V88_409 | NA IL_80007.16* | ||
| 1/SA/514:516, 1/SA/536:543 | NA | NA | ||
| 1/SA/517:520, 1/SA/532:535 | Tandem non-canonical cWW pairs geometric IL_6JDV_001 | NA IL_85877.10* | ||
| 1/SA/551:552, 1/SA/584:587 | geometric IL_5J7L_341 | NA IL_44093.1* | ||
| 1/SA/552:559, 1/SA/568:584 | NA | NA | ||
| 1/SA/1157:1160, 1/SA/1617:1621 | C-loop homologous IL_4V88_443 | NA IL_63596.4* | ||
| 1/SA/1173:1174, 1/SA/1464:1466 | Single stack bend geometric IL_7RQB_058 | NA IL_31836.1* | ||
| 1/SA/1174:1176, 1/SA/1463:1464 | Minor groove platform geometric IL_5TBW_039 | NA IL_06437.11* | ||
| 1/SA/1212:1216, 1/SA/1448:1451 | NA | NA | ||
| 1/SA/1268:1270, 1/SA/1440:1441 | NA | NA | ||
| 1/SA/1470:1474, 1/SA/1533:1574 | NA | NA | ||
| 1/SA/1650:1652, 1/SA/1748:1750 | AA cWW homologous IL_4V88_467 | NA IL_01312.13* | ||
| 1/SA/1653:1660, 1/SA/1741:1747 | NA | NA | ||
| 1/SA/1664:1667, 1/SA/1734:1737 | Tandem non-canonical cWW pairs geometric IL_5TBW_041 | NA IL_85877.10* | ||
| 1/SA/1669:1672, 1/SA/1729:1732 | Double sheared homologous IL_4V88_471 | NA IL_09705.7* | ||
| 1/SA/1672:1674, 1/SA/1727:1729 | geometric IL_3RW6_004 | NA IL_01312.13* |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6LQQ_005 | NA | ||
| IL_6LQQ_006 | NA | ||
| IL_6LQQ_008 | NA | ||
| IL_6LQQ_009 | NA | ||
| IL_6LQQ_010 | NA | ||
| IL_6LQQ_011 | NA | ||
| IL_6LQQ_012 | NA | ||
| IL_6LQQ_013 | NA | ||
| IL_6LQQ_014 | NA | ||
| IL_6LQQ_015 | NA | ||
| IL_6LQQ_016 | NA | ||
| IL_6LQQ_017 | NA | ||
| IL_6LQQ_018 | NA | ||
| IL_6LQQ_019 | NA | ||
| IL_6LQQ_022 | NA | ||
| IL_6LQQ_023 | NA | ||
| IL_6LQQ_049 | homologous IL_4V88_417 | ||
| IL_6LQQ_050 | NA | ||
| IL_6LQQ_051 | Single stack bend geometric IL_7A0S_054 | ||
| IL_6LQQ_052 | homologous IL_4V88_419 | ||
| IL_6LQQ_053 | NA | ||
| IL_6LQQ_054 | Major groove platform; stack outside cWW geometric IL_4V88_428 | ||
| IL_6LQQ_055 | Tandem non-canonical cWW pairs homologous IL_4V88_429 | ||
| IL_6LQQ_056 | Tandem non-canonical cWW pairs homologous IL_4V88_430 | ||
| IL_6LQQ_057 | Tandem non-canonical cWW pairs geometric IL_4V88_431 | ||
| IL_6LQQ_058 | Tandem non-canonical cWW pairs homologous IL_4V88_432 | ||
| IL_6LQQ_059 | NA | ||
| IL_6LQQ_060 | Single bulged A geometric IL_5CNR_002 | ||
| IL_6LQQ_061 | Tandem non-canonical cWW pairs geometric IL_5TBW_041 | ||
| IL_6LQQ_062 | Tandem non-canonical cWW pairs homologous IL_4V88_438 | ||
| IL_6LQQ_063 | Single stack bend geometric IL_4C7O_002 | ||
| IL_6LQQ_070 | Tandem non-canonical cWW pairs homologous IL_4V88_461 | ||
| IL_6LQQ_076 | NA | ||
| IL_6LQQ_077 | Isolated near basepair geometric IL_3NJ7_004 | ||
| IL_6LQQ_078 | NA |
Valid loops
| # | loop id | location | annotation (mapped to, source) | motif group (similar to) |
|---|---|---|---|---|
| 1/SA/1150:1151, 1/SA/1627:1629, 1/SA/1636:1640 | NA | NA | ||
| 1/SA/1168:1171, 1/SA/1468:1470, 1/SA/1574:1577 | NA | NA | ||
| 1/SA/1216:1220, 1/SA/1263:1268, 1/SA/1441:1448 | NA | NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6LQQ_001 | NA | ||
| J3_6LQQ_002 | NA | ||
| J3_6LQQ_003 | homologous J3_4V88_033 |
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