8BYV Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8BYV_001 | 1/a/13:23 | No text annotation | homologous HL_4LFB_001 HL_73535.2 | |
| HL_8BYV_003 | 1/a/158:163 | GNRA | homologous HL_4LFB_003 HL_34789.5 | |
| HL_8BYV_004 | 1/a/193:198 | No text annotation | geometric HL_5NFV_001 HL_69752.4 | |
| HL_8BYV_005 | 1/a/217:223 | No text annotation | geometric HL_7KI3_001 HL_75660.9 | |
| HL_8BYV_006 | 1/a/267:275 | GNRA related | homologous HL_5J7L_006 NA | |
| HL_8BYV_007 | 1/a/304:309 | GNRA | homologous HL_5J7L_007 NA | |
| HL_8BYV_008 | 1/a/328:341 | No text annotation | homologous HL_5J7L_008 NA | |
| HL_8BYV_009 | 1/a/350:355 | UNCG | homologous HL_4LFB_009 HL_61337.5 | |
| HL_8BYV_010 | 1/a/387:392 | GNRA | homologous HL_4LFB_010 HL_34789.5 | |
| HL_8BYV_011 | 1/a/427:432 | UNCG | homologous HL_5J7L_011 NA | |
| HL_8BYV_012 | 1/a/454:496 | No text annotation | ||
| HL_8BYV_013 | 1/a/530:535 | No text annotation | geometric HL_4WF9_003 HL_75660.9 | |
| HL_8BYV_014 | 1/a/625:631 | GNRA-like with tWH | homologous HL_5J7L_014 NA | |
| HL_8BYV_015 | 1/a/697:706 | No text annotation | homologous HL_4LFB_015 HL_38491.3 | |
| HL_8BYV_016 | 1/a/734:739 | GNRA | homologous HL_4LFB_016 HL_34789.5 | |
| HL_8BYV_017 | 1/a/794:804 | No text annotation | homologous HL_5J7L_017 NA | |
| HL_8BYV_018 | 1/a/848:856 | No text annotation | ||
| HL_8BYV_019 | 1/a/872:877 | GNRA | homologous HL_4LFB_019 HL_34789.5 | |
| HL_8BYV_020 | 1/a/907:912 | GNRA | homologous HL_4LFB_020 HL_34789.5 | |
| HL_8BYV_024 | 1/a/1088:1093 | GNRA | geometric HL_5J7L_196 NA | |
| HL_8BYV_025 | 1/a/1101:1108 | T-loop related | homologous HL_4LFB_025 HL_63894.3 | |
| HL_8BYV_032 | 1/a/1527:1532 | GNRA | geometric HL_3E5C_002 HL_34789.5 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8BYV_002 | Mini UNCG | ||
| HL_8BYV_021 | No text annotation | ||
| HL_8BYV_022 | GNRA | ||
| HL_8BYV_023 | No text annotation | ||
| HL_8BYV_033 | No text annotation | ||
| HL_8BYV_026 | No text annotation | ||
| HL_8BYV_027 | GNRA | ||
| HL_8BYV_028 | GNRA | ||
| HL_8BYV_029 | T-loop with 3 stacked bulged bases | ||
| HL_8BYV_030 | No text annotation | ||
| HL_8BYV_031 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8BYV_001 | 1/a/31:33, 1/a/560:561 | Single bulged G | homologous IL_5J7L_001 NA | |
| IL_8BYV_002 | 1/a/45:46, 1/a/404:406 | Single bulged A | homologous IL_5J7L_002 NA | |
| IL_8BYV_003 | 1/a/48:53, 1/a/367:369 | No text annotation | homologous IL_5J7L_003 NA | |
| IL_8BYV_004 | 1/a/55:57, 1/a/364:365 | Minor groove platform | homologous IL_4LFB_004 IL_34520.4 | |
| IL_8BYV_005 | 1/a/64:67, 1/a/102:103 | Multiple bulged bases | homologous IL_4LFB_005 IL_71421.4 | |
| IL_8BYV_006 | 1/a/68:70, 1/a/99:101 | Isolated non-canonical cWW pair | homologous IL_6CZR_118 NA | |
| IL_8BYV_007 | 1/a/72:78, 1/a/91:97 | No text annotation | ||
| IL_8BYV_009 | 1/a/128:131, 1/a/239:240 | Multiple bulged bases | homologous IL_4LFB_007 IL_75289.2 | |
| IL_8BYV_010 | 1/a/132:136, 1/a/235:238 | No text annotation | homologous IL_4LFB_008 IL_60988.3 | |
| IL_8BYV_011 | 1/a/147:153, 1/a/168:175 | tWH-tWH-tHW-tHW | homologous IL_5J7L_012 NA | |
| IL_8BYV_012 | 1/a/154:156, 1/a/165:167 | Isolated non-canonical cWW pair | geometric IL_2O3V_001 IL_71625.4 | |
| IL_8BYV_013 | 1/a/184:187, 1/a/204:208 | No text annotation | ||
| IL_8BYV_014 | 1/a/250:255, 1/a/285:292 | Kink-turn with non-sequential stacking | homologous IL_5J7L_014 NA | |
| IL_8BYV_015 | 1/a/257:260, 1/a/282:283 | No text annotation | homologous IL_4LFB_012 IL_22002.1 | |
| IL_8BYV_016 | 1/a/300:301, 1/a/312:316 | C-loop | homologous IL_5J7L_016 NA | |
| IL_8BYV_017 | 1/a/375:377, 1/a/400:401 | Single bulged U | homologous IL_4LFB_014 IL_97561.6 | |
| IL_8BYV_018 | 1/a/379:383, 1/a/397:398 | C-loop | geometric IL_5J7L_018 NA | |
| IL_8BYV_019 | 1/a/383:384, 1/a/395:397 | Single bulged G | homologous IL_5J7L_019 NA | |
| IL_8BYV_020 | 1/a/417:424, 1/a/435:441 | No text annotation | homologous IL_4LFB_017 IL_62329.1 | |
| IL_8BYV_021 | 1/a/512:519, 1/a/548:549 | SSU/LSU pseudoknot | homologous IL_5J7L_024 NA | |
| IL_8BYV_022 | 1/a/523:529, 1/a/536:544 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_8BYV_023 | 1/a/577:583, 1/a/890:891 | No text annotation | homologous IL_5J7L_026 NA | |
| IL_8BYV_024 | 1/a/588:592, 1/a/765:769 | tSH-tWH-tHS | homologous IL_4LFB_023 IL_05821.2 | |
| IL_8BYV_025 | 1/a/602:604, 1/a/652:653 | Major groove platform | homologous IL_5J7L_028 NA | |
| IL_8BYV_026 | 1/a/605:606, 1/a/648:651 | Major groove minor groove platform; mini C-loop | homologous IL_5J7L_029 NA | |
| IL_8BYV_027 | 1/a/612:613, 1/a/640:642 | Single bulged U | geometric IL_5J7L_298 NA | |
| IL_8BYV_028 | 1/a/613:620, 1/a/636:640 | No text annotation | geometric IL_5J7L_030 NA | |
| IL_8BYV_030 | 1/a/662:663, 1/a/759:762 | Major groove platform; stack outside cWW | homologous IL_5J7L_031 NA | |
| IL_8BYV_031 | 1/a/664:667, 1/a/754:758 | Tandem non-canonical cWW pairs | geometric IL_3WBM_002 IL_37443.1 | |
| IL_8BYV_032 | 1/a/670:674, 1/a/748:751 | Tandem non-canonical cWW pairs | homologous IL_5J7L_033 NA | |
| IL_8BYV_070 | 1/a/681:685, 1/a/721:725 | Triple non-canonical cWW pairs | homologous IL_4LFB_065 IL_71154.4 | |
| IL_8BYV_034 | 1/a/692:696, 1/a/707:714 | Kink-turn | homologous IL_5J7L_035 NA | |
| IL_8BYV_035 | 1/a/782:787, 1/a/811:813 | Other IL | geometric IL_4V88_435 NA | |
| IL_8BYV_036 | 1/a/787:791, 1/a/807:811 | tSH-tWH-tHS | geometric IL_4LFB_033 IL_05821.2 | |
| IL_8BYV_037 | 1/a/897:904, 1/a/915:920 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4LFB_034 IL_84044.2 | |
| IL_8BYV_038 | 1/a/932:933, 1/a/1404:1406 | Single bulged A | homologous IL_5J7L_039 NA | |
| IL_8BYV_071 | 1/a/935:937, 1/a/1401:1402 | Single bulged G | homologous IL_6CZR_148 NA | |
| IL_8BYV_072 | 1/a/942:945, 1/a/1391:1396 | No text annotation | ||
| IL_8BYV_051 | 1/a/1073:1075, 1/a/1204:1206 | Isolated non-canonical cWW pair | geometric IL_5J7L_050 NA | |
| IL_8BYV_062 | 1/a/1423:1425, 1/a/1498:1500 | Isolated non-canonical cWW pair | homologous IL_5J7L_061 NA | |
| IL_8BYV_065 | 1/a/1441:1446, 1/a/1478:1482 | Triple sheared related | geometric IL_5J7L_063 NA | |
| IL_8BYV_066 | 1/a/1446:1448, 1/a/1476:1478 | Isolated non-canonical cWW pair | homologous IL_4LFB_063 IL_01003.5 | |
| IL_8BYV_067 | 1/a/1451:1454, 1/a/1471:1473 | No text annotation | geometric IL_8VTW_011 NA | |
| IL_8BYV_068 | 1/a/1456:1459, 1/a/1467:1469 | No text annotation | homologous IL_5J7L_065 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8BYV_069 | Tandem non-canonical cWW pairs | ||
| IL_8BYV_008 | No text annotation | ||
| IL_8BYV_029 | Isolated non-canonical cWW pair | ||
| IL_8BYV_033 | No text annotation | ||
| IL_8BYV_039 | No text annotation | ||
| IL_8BYV_040 | No text annotation | ||
| IL_8BYV_041 | Isolated cWS basepair | ||
| IL_8BYV_042 | Isolated non-canonical cWW pair | ||
| IL_8BYV_043 | Minor groove platform | ||
| IL_8BYV_044 | Minor groove platform | ||
| IL_8BYV_045 | Single stack bend | ||
| IL_8BYV_046 | Minor groove platform | ||
| IL_8BYV_047 | Single bulged U | ||
| IL_8BYV_048 | Isolated cWS basepair | ||
| IL_8BYV_049 | Minor groove platform | ||
| IL_8BYV_050 | Single bulged A | ||
| IL_8BYV_052 | Isolated non-canonical cWW pair | ||
| IL_8BYV_053 | Minor groove platform | ||
| IL_8BYV_054 | Minor groove platform | ||
| IL_8BYV_055 | No text annotation | ||
| IL_8BYV_056 | No text annotation | ||
| IL_8BYV_057 | 180 degree turn | ||
| IL_8BYV_058 | Double sheared with non-canonical cWW | ||
| IL_8BYV_059 | No text annotation | ||
| IL_8BYV_060 | Isolated non-canonical cWW pair | ||
| IL_8BYV_061 | Partly complementary | ||
| IL_8BYV_063 | No text annotation | ||
| IL_8BYV_064 | Tandem non-canonical cWW pairs |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8BYV_010 | 1/a/47:48, 1/a/369:375, 1/a/401:403 | No text annotation | geometric J3_8C3A_082 NA | |
| J3_8BYV_011 | 1/a/47:53, 1/a/367:375, 1/a/401:403 | No text annotation | homologous J3_5J7L_050 NA | |
| J3_8BYV_012 | 1/a/594:596, 1/a/659:662, 1/a/762:763 | No text annotation | geometric J3_5J7L_002 NA | |
| J3_8BYV_013 | 1/a/594:596, 1/a/659:663, 1/a/759:763 | No text annotation | homologous J3_5J7L_051 NA | |
| J3_8BYV_014 | 1/a/680:681, 1/a/725:733, 1/a/740:742 | No text annotation | homologous J3_5J7L_003 NA | |
| J3_8BYV_001 | 1/a/834:837, 1/a/867:871, 1/a/878:884 | No text annotation | homologous J3_4LFB_001 J3_02285.1 | |
| J3_8BYV_006 | 1/a/1075:1080, 1/a/1119:1125, 1/a/1198:1204 | No text annotation | homologous J3_5J7L_008 NA | |
| J3_8BYV_019 | 1/a/1085:1088, 1/a/1093:1098, 1/a/1111:1114 | No text annotation | ||
| J4_8BYV_001 | 1/a/114:122, 1/a/246:248, 1/a/294:297, 1/a/319:320 | No text annotation | ||
| J4_8BYV_004 | 1/a/142:144, 1/a/178:185, 1/a/206:213, 1/a/227:229 | No text annotation | ||
| J4_8BYV_003 | 1/a/583:585, 1/a/772:777, 1/a/818:829, 1/a/889:890 | No text annotation | homologous J4_5J7L_003 NA | |
| J5_8BYV_001 | 1/a/37:40, 1/a/411:414, 1/a/444:449, 1/a/501:508, 1/a/553:556 | No text annotation | ||
| J5_8BYV_002 | 1/a/59:62, 1/a/105:112, 1/a/322:324, 1/a/345:347, 1/a/358:362 | No text annotation | homologous J5_5J7L_003 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8BYV_015 | No text annotation | ||
| J3_8BYV_021 | No text annotation | ||
| J3_8BYV_002 | No text annotation | ||
| J3_8BYV_003 | No text annotation | ||
| J3_8BYV_016 | No text annotation | ||
| J3_8BYV_004 | No text annotation | ||
| J3_8BYV_017 | No text annotation | ||
| J3_8BYV_005 | No text annotation | ||
| J3_8BYV_018 | No text annotation | ||
| J3_8BYV_007 | No text annotation | ||
| J3_8BYV_008 | No text annotation | ||
| J3_8BYV_020 | No text annotation | ||
| J3_8BYV_009 | No text annotation | ||
| J4_8BYV_002 | No text annotation |
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