6LQQ Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6LQQ_003 | 1/5A/4:9 | No text annotation | geometric HL_5U3G_001 HL_75660.5 | |
| HL_6LQQ_007 | 1/5A/301:305 | Mini UNCG | geometric HL_4V9F_021 HL_48778.2 | |
| HL_6LQQ_008 | 1/5A/360:365 | GNRA related | geometric HL_5J7L_179 HL_04783.2 | |
| HL_6LQQ_009 | 1/5A/514:521 | No text annotation | geometric HL_7RQB_022 NA | |
| HL_6LQQ_010 | 1/SA/70:81 | No text annotation | ||
| HL_6LQQ_011 | 1/SA/154:160 | GNRA related | homologous HL_4V88_188 NA | |
| HL_6LQQ_012 | 1/SA/186:199 | No text annotation | ||
| HL_6LQQ_013 | 1/SA/230:235 | No text annotation | geometric HL_4WF9_009 HL_81100.2 | |
| HL_6LQQ_014 | 1/SA/275:281 | No text annotation | ||
| HL_6LQQ_015 | 1/SA/330:338 | GNRA related | homologous HL_4V88_193 NA | |
| HL_6LQQ_016 | 1/SA/364:381 | No text annotation | ||
| HL_6LQQ_017 | 1/SA/393:404 | No text annotation | homologous HL_4V88_195 NA | |
| HL_6LQQ_018 | 1/SA/450:456 | No text annotation | geometric HL_4WF9_003 HL_75660.5 | |
| HL_6LQQ_019 | 1/SA/491:496 | GNRA | geometric HL_4V9F_040 HL_37824.7 | |
| HL_6LQQ_020 | 1/SA/520:532 | No text annotation | geometric HL_4V88_199 NA | |
| HL_6LQQ_021 | 1/SA/561:566 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_6LQQ_024 | 1/SA/900:909 | No text annotation | homologous HL_4V88_206 NA | |
| HL_6LQQ_025 | 1/SA/937:942 | GNRA | homologous HL_4V88_207 NA | |
| HL_6LQQ_026 | 1/SA/1055:1064 | Mini UNCG | geometric HL_4YAZ_004 HL_48778.2 | |
| HL_6LQQ_027 | 1/SA/1129:1139 | No text annotation | ||
| HL_6LQQ_030 | 1/SA/1501:1506 | GNRA | homologous HL_4V88_218 NA | |
| HL_6LQQ_031 | 1/SA/1594:1602 | Mini UNCG | geometric HL_4OOG_001 HL_56334.1 | |
| HL_6LQQ_032 | 1/SA/1629:1636 | No text annotation | geometric HL_4LX6_002 HL_31585.4 | |
| HL_6LQQ_036 | 1/SA/1698:1703 | GNRA | geometric HL_7A0S_047 HL_37824.7 | |
| HL_6LQQ_033 | 1/SA/1699:1703 | No text annotation | ||
| HL_6LQQ_034 | 1/SA/1778:1783 | No text annotation | geometric HL_2Y8W_001 HL_81100.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6LQQ_001 | No text annotation | ||
| HL_6LQQ_002 | No text annotation | ||
| HL_6LQQ_004 | No text annotation | ||
| HL_6LQQ_005 | No text annotation | ||
| HL_6LQQ_006 | No text annotation | ||
| HL_6LQQ_022 | Mini UNCG | ||
| HL_6LQQ_023 | No text annotation | ||
| HL_6LQQ_028 | No text annotation | ||
| HL_6LQQ_029 | No text annotation | ||
| HL_6LQQ_035 | tRNA anticodon loop |
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 | geometric IL_3IGI_004 IL_00225.13 | |
| IL_6LQQ_002 | 1/3A/48:50, 1/5A/466:470 | No text annotation | geometric IL_4V9F_053 IL_09990.4 | |
| IL_6LQQ_003 | 1/3A/78:85, 1/3A/325:329 | No text annotation | ||
| IL_6LQQ_079 | 1/3A/85:96, 1/3A/320:325 | No text annotation | ||
| IL_6LQQ_004 | 1/3A/97:98, 1/3A/317:319 | No text annotation | ||
| IL_6LQQ_005 | 1/3A/111:115, 1/3A/252:259 | No text annotation | ||
| IL_6LQQ_007 | 1/5A/17:18, 1/5A/62:64 | Single bulged G | geometric IL_3NDB_004 IL_00225.13 | |
| IL_6LQQ_090 | 1/5A/94:95, 1/5A/149:156 | No text annotation | ||
| IL_6LQQ_009 | 1/5A/97:99, 1/5A/145:147 | Isolated cWH basepair | geometric IL_3R1C_012 IL_10167.6 | |
| IL_6LQQ_010 | 1/5A/238:240, 1/5A/273:274 | Single bulged U | geometric IL_6JDV_003 IL_89505.4 | |
| IL_6LQQ_011 | 1/5A/245:246, 1/5A/266:268 | Single bulged U | geometric IL_7KVT_002 IL_89505.4 | |
| IL_6LQQ_012 | 1/5A/337:340, 1/5A/386:387 | Major groove minor groove platform; mini C-loop | geometric IL_4V9F_068 IL_68140.4 | |
| IL_6LQQ_013 | 1/5A/340:341, 1/5A/384:386 | Single bulged A | geometric IL_1JZV_002 IL_31462.6 | |
| IL_6LQQ_014 | 1/5A/342:343, 1/5A/381:383 | Single bulged U | geometric IL_4FRG_002 IL_89505.4 | |
| IL_6LQQ_015 | 1/5A/346:349, 1/5A/375:378 | Tandem non-canonical cWW pairs | geometric IL_280D_001 IL_77658.1 | |
| IL_6LQQ_080 | 1/5A/352:355, 1/5A/371:372 | No text annotation | ||
| IL_6LQQ_081 | 1/5A/352:356, 1/5A/369:372 | No text annotation | ||
| IL_6LQQ_017 | 1/5A/355:356, 1/5A/369:371 | Stack outside cWW | geometric IL_1NTA_001 IL_66635.5 | |
| IL_6LQQ_018 | 1/5A/413:414, 1/5A/441:443 | Single stack bend | geometric IL_4C7O_002 IL_90729.1 | |
| IL_6LQQ_019 | 1/5A/414:415, 1/5A/439:441 | Single bulged U | geometric IL_7KVT_002 IL_89505.4 | |
| IL_6LQQ_020 | 1/5A/497:499, 1/5A/539:542 | Isolated non-canonical cWW pair | geometric IL_3TD0_005 IL_57744.1 | |
| IL_6LQQ_021 | 1/5A/501:503, 1/5A/533:537 | No text annotation | ||
| IL_6LQQ_022 | 1/5A/505:507, 1/5A/529:531 | Isolated non-canonical cWW pair | geometric IL_5MSF_001 IL_87907.2 | |
| IL_6LQQ_023 | 1/5A/510:511, 1/5A/524:526 | Single bulged U | geometric IL_6UFH_004 IL_89505.4 | |
| IL_6LQQ_024 | 1/5A/550:552, 1/5A/585:587 | Isolated non-canonical cWW contact | geometric IL_5UNE_001 IL_44465.1 | |
| IL_6LQQ_025 | 1/SA/24:26, 1/SA/600:601 | Single bulged C | geometric IL_7KGA_001 IL_61258.15 | |
| IL_6LQQ_026 | 1/SA/50:53, 1/SA/427:429 | No text annotation | geometric IL_4N0T_004 IL_99358.1 | |
| IL_6LQQ_027 | 1/SA/58:63, 1/SA/87:89 | No text annotation | homologous IL_4V88_389 NA | |
| IL_6LQQ_091 | 1/SA/64:69, 1/SA/82:86 | No text annotation | homologous IL_8CRE_396 IL_21667.1 | |
| IL_6LQQ_029 | 1/SA/109:112, 1/SA/302:305 | Tandem non-canonical cWW pairs | homologous IL_4V88_391 NA | |
| IL_6LQQ_030 | 1/SA/113:116, 1/SA/300:301 | Multiple bulged bases | homologous IL_4V88_392 NA | |
| IL_6LQQ_082 | 1/SA/113:117, 1/SA/299:301 | Decoding loop related | geometric IL_2O3X_003 IL_31737.3 | |
| IL_6LQQ_031 | 1/SA/117:122, 1/SA/295:299 | No text annotation | homologous IL_4V88_393 NA | |
| IL_6LQQ_032 | 1/SA/143:149, 1/SA/165:172 | tWH-tWH-tHW-tHW | homologous IL_4V88_394 NA | |
| IL_6LQQ_033 | 1/SA/150:152, 1/SA/162:164 | Isolated cWH basepair | geometric IL_4KQ0_004 IL_10167.6 | |
| IL_6LQQ_034 | 1/SA/204:206, 1/SA/259:263 | Major groove platform with extra cWW | homologous IL_4V88_397 NA | |
| IL_6LQQ_035 | 1/SA/206:208, 1/SA/257:259 | Isolated non-canonical cWW pair | geometric IL_5ZTM_002 IL_28037.2 | |
| IL_6LQQ_036 | 1/SA/226:228, 1/SA/237:241 | No text annotation | ||
| IL_6LQQ_037 | 1/SA/265:267, 1/SA/288:289 | Single bulged A | homologous IL_4V88_399 NA | |
| IL_6LQQ_038 | 1/SA/270:274, 1/SA/282:285 | No text annotation | ||
| IL_6LQQ_083 | 1/SA/310:311, 1/SA/355:357 | No text annotation | ||
| IL_6LQQ_039 | 1/SA/311:316, 1/SA/348:355 | Kink-turn with non-sequential stacking | homologous IL_4V88_402 NA | |
| IL_6LQQ_040 | 1/SA/318:323, 1/SA/345:346 | No text annotation | geometric IL_5Y58_001 IL_59877.1 | |
| IL_6LQQ_041 | 1/SA/389:391, 1/SA/406:408 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_6LQQ_042 | 1/SA/443:447, 1/SA/460:461 | C-loop | geometric IL_5J7L_018 IL_03109.3 | |
| IL_6LQQ_043 | 1/SA/447:448, 1/SA/458:460 | Single bulged G | geometric IL_5J7L_019 IL_00225.13 | |
| IL_6LQQ_044 | 1/SA/482:483, 1/SA/504:506 | Single bulged A | homologous IL_4V88_409 NA | |
| IL_6LQQ_045 | 1/SA/514:516, 1/SA/536:543 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_6LQQ_046 | 1/SA/517:520, 1/SA/532:535 | Tandem non-canonical cWW pairs | geometric IL_6JDV_001 IL_77658.1 | |
| IL_6LQQ_047 | 1/SA/551:552, 1/SA/584:587 | No text annotation | geometric IL_5J7L_341 IL_42626.2 | |
| IL_6LQQ_048 | 1/SA/552:559, 1/SA/568:584 | No text annotation | ||
| IL_6LQQ_049 | 1/SA/624:626, 1/SA/973:975 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_6LQQ_050 | 1/SA/627:631, 1/SA/969:972 | No text annotation | ||
| IL_6LQQ_051 | 1/SA/631:632, 1/SA/967:969 | Single stack bend | geometric IL_7A0S_054 IL_26793.1 | |
| IL_6LQQ_052 | 1/SA/646:648, 1/SA/686:688 | Isolated non-canonical cWW pair | homologous IL_4V88_419 NA | |
| IL_6LQQ_053 | 1/SA/652:659, 1/SA/677:682 | No text annotation | ||
| IL_6LQQ_054 | 1/SA/865:866, 1/SA/962:965 | Major groove platform; stack outside cWW | geometric IL_4V88_428 NA | |
| IL_6LQQ_084 | 1/SA/868:869, 1/SA/958:960 | Single bulged U | geometric IL_6UFH_004 IL_89505.4 | |
| IL_6LQQ_085 | 1/SA/871:873, 1/SA/954:956 | Isolated non-canonical cWW pair | geometric IL_5TBW_068 NA | |
| IL_6LQQ_057 | 1/SA/874:878, 1/SA/950:953 | Tandem non-canonical cWW pairs | homologous IL_4V88_431 NA | |
| IL_6LQQ_058 | 1/SA/885:888, 1/SA/924:927 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_6LQQ_059 | 1/SA/893:899, 1/SA/910:919 | Kink-turn related | homologous IL_8C3A_440 NA | |
| IL_6LQQ_060 | 1/SA/1033:1034, 1/SA/1083:1085 | Single bulged A | geometric IL_5CNR_002 IL_31462.6 | |
| IL_6LQQ_061 | 1/SA/1035:1039, 1/SA/1079:1082 | Tandem non-canonical cWW pairs | geometric IL_5TBW_041 NA | |
| IL_6LQQ_062 | 1/SA/1041:1044, 1/SA/1074:1077 | Tandem non-canonical cWW pairs | homologous IL_4V88_438 NA | |
| IL_6LQQ_063 | 1/SA/1051:1053, 1/SA/1066:1067 | Single stack bend | geometric IL_4C7O_002 IL_90729.1 | |
| IL_6LQQ_064 | 1/SA/1157:1160, 1/SA/1617:1621 | C-loop | homologous IL_4V88_443 NA | |
| IL_6LQQ_065 | 1/SA/1173:1174, 1/SA/1464:1466 | Single stack bend | geometric IL_7RQB_058 NA | |
| IL_6LQQ_066 | 1/SA/1174:1176, 1/SA/1463:1464 | Minor groove platform | geometric IL_5TBW_039 NA | |
| IL_6LQQ_067 | 1/SA/1212:1216, 1/SA/1448:1451 | No text annotation | ||
| IL_6LQQ_068 | 1/SA/1268:1270, 1/SA/1440:1441 | No text annotation | ||
| IL_6LQQ_086 | 1/SA/1480:1493, 1/SA/1514:1527 | No text annotation | ||
| IL_6LQQ_070 | 1/SA/1495:1498, 1/SA/1509:1512 | Tandem non-canonical cWW pairs | homologous IL_4V88_461 NA | |
| IL_6LQQ_071 | 1/SA/1650:1652, 1/SA/1748:1750 | Isolated non-canonical cWW pair | homologous IL_4V88_467 NA | |
| IL_6LQQ_092 | 1/SA/1653:1659, 1/SA/1742:1747 | No text annotation | ||
| IL_6LQQ_088 | 1/SA/1665:1667, 1/SA/1734:1736 | Isolated non-canonical cWW pair | homologous IL_8C3A_477 NA | |
| IL_6LQQ_074 | 1/SA/1669:1672, 1/SA/1729:1732 | Double sheared | homologous IL_4V88_471 NA | |
| IL_6LQQ_075 | 1/SA/1672:1674, 1/SA/1727:1729 | Isolated non-canonical cWW pair | geometric IL_3RW6_004 IL_87907.2 | |
| IL_6LQQ_089 | 1/SA/1675:1685, 1/SA/1716:1726 | No text annotation | ||
| IL_6LQQ_076 | 1/SA/1688:1690, 1/SA/1711:1713 | No text annotation | ||
| IL_6LQQ_077 | 1/SA/1693:1695, 1/SA/1706:1708 | Isolated near basepair | geometric IL_3NJ7_004 IL_42997.3 | |
| IL_6LQQ_078 | 1/SA/1696:1699, 1/SA/1703:1705 | No text annotation | geometric IL_4V87_185 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6LQQ_006 | No text annotation | ||
| IL_6LQQ_008 | Isolated non-canonical cWW pair | ||
| IL_6LQQ_016 | No text annotation | ||
| IL_6LQQ_028 | Triple sheared related | ||
| IL_6LQQ_055 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_056 | Tandem non-canonical cWW pairs | ||
| IL_6LQQ_069 | No text annotation | ||
| IL_6LQQ_072 | No text annotation | ||
| IL_6LQQ_087 | No text annotation | ||
| IL_6LQQ_073 | Tandem non-canonical cWW pairs |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6LQQ_002 | 1/SA/633:635, 1/SA/861:865, 1/SA/965:966 | No text annotation | geometric J3_4V88_080 NA | |
| J3_6LQQ_007 | 1/SA/633:635, 1/SA/861:866, 1/SA/962:966 | No text annotation | homologous J3_8P9A_072 J3_17385.4 | |
| J3_6LQQ_003 | 1/SA/881:884, 1/SA/928:936, 1/SA/943:947 | No text annotation | homologous J3_4V88_033 NA | |
| J3_6LQQ_004 | 1/SA/1150:1151, 1/SA/1627:1629, 1/SA/1636:1640 | No text annotation | ||
| J3_6LQQ_008 | 1/SA/1161:1164, 1/SA/1581:1587, 1/SA/1609:1616 | No text annotation | homologous J3_8C3A_038 NA | |
| J3_6LQQ_005 | 1/SA/1168:1171, 1/SA/1468:1470, 1/SA/1574:1577 | No text annotation | homologous J3_8C3A_039 NA | |
| J4_6LQQ_001 | 1/SA/99:107, 1/SA/307:310, 1/SA/357:364, 1/SA/381:384 | No text annotation | ||
| J5_6LQQ_001 | 1/SA/31:37, 1/SA/471:479, 1/SA/509:514, 1/SA/543:546, 1/SA/592:595 | No text annotation | ||
| J5_6LQQ_002 | 1/SA/31:37, 1/SA/471:479, 1/SA/509:516, 1/SA/536:546, 1/SA/592:595 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6LQQ_001 | No text annotation | ||
| J3_6LQQ_006 | No text annotation |
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