8A3D Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8A3D_001 | 1/A/37:44 | No text annotation | geometric HL_5TBW_001 NA | |
| HL_8A3D_002 | 1/A/68:73 | No text annotation | homologous HL_5TBW_002 NA | |
| HL_8A3D_003 | 1/A/89:95 | No text annotation | homologous HL_5TBW_003 NA | |
| HL_8A3D_004 | 1/A/129:139 | No text annotation | ||
| HL_8A3D_005 | 1/A/204:211 | T-loop with 2 bulged bases not stacked | geometric HL_1P6V_004 NA | |
| HL_8A3D_006 | 1/A/222:226 | No text annotation | homologous HL_5TBW_006 NA | |
| HL_8A3D_007 | 1/A/230:238 | T-loop with unstacked turn | homologous HL_5TBW_007 NA | |
| HL_8A3D_008 | 1/A/289:298 | No text annotation | homologous HL_8C3A_008 NA | |
| HL_8A3D_009 | 1/A/314:323 | Pseudoknot geometry | geometric HL_4QLM_002 HL_00911.2 | |
| HL_8A3D_010 | 1/A/368:373 | GNRA | homologous HL_5TBW_010 NA | |
| HL_8A3D_082 | 1/A/393:398 | GNRA | homologous HL_8C3A_011 NA | |
| HL_8A3D_015 | 1/A/1178:1183 | Mini UNCG | geometric HL_4OOG_001 HL_12626.2 | |
| HL_8A3D_083 | 1/A/1317:1326 | T-loop with 2 stacked bulged bases | homologous HL_8P9A_126 HL_33597.2 | |
| HL_8A3D_084 | 1/A/1364:1373 | No text annotation | ||
| HL_8A3D_019 | 1/A/1389:1394 | GNRA | homologous HL_8C3A_016 NA | |
| HL_8A3D_022 | 1/A/1480:1484 | Mini UNCG | geometric HL_4V9F_041 HL_90436.2 | |
| HL_8A3D_023 | 1/A/1561:1566 | GNRA | homologous HL_5TBW_019 NA | |
| HL_8A3D_024 | 1/A/1593:1602 | No text annotation | homologous HL_5TBW_020 NA | |
| HL_8A3D_025 | 1/A/1627:1635 | No text annotation | homologous HL_5TBW_021 NA | |
| HL_8A3D_026 | 1/A/1675:1680 | Externally structured | homologous HL_8C3A_022 NA | |
| HL_8A3D_028 | 1/A/1816:1823 | No text annotation | geometric HL_5TBW_024 NA | |
| HL_8A3D_029 | 1/A/1864:1870 | GNRA | homologous HL_5TBW_025 NA | |
| HL_8A3D_030 | 1/A/1886:1893 | No text annotation | homologous HL_5TBW_026 NA | |
| HL_8A3D_033 | 1/A/2317:2322 | GNRA | homologous HL_8C3A_030 NA | |
| HL_8A3D_034 | 1/A/2376:2384 | T-loop with 2 stacked bulged bases | homologous HL_8C3A_031 NA | |
| HL_8A3D_035 | 1/A/2420:2426 | Pseudoknot geometry with 3' bulge | homologous HL_5TBW_032 NA | |
| HL_8A3D_036 | 1/A/2458:2463 | GNRA variation | homologous HL_5TBW_033 NA | |
| HL_8A3D_037 | 1/A/2469:2471 | No text annotation | ||
| HL_8A3D_038 | 1/A/2523:2532 | No text annotation | homologous HL_5TBW_035 NA | |
| HL_8A3D_040 | 1/A/2578:2583 | GNRA | homologous HL_5TBW_036 NA | |
| HL_8A3D_086 | 1/A/2624:2632 | No text annotation | homologous HL_8C3A_037 NA | |
| HL_8A3D_042 | 1/A/2664:2670 | No text annotation | homologous HL_8C3A_038 NA | |
| HL_8A3D_043 | 1/A/2705:2710 | No text annotation | ||
| HL_8A3D_044 | 1/A/2738:2742 | No text annotation | homologous HL_8C3A_040 NA | |
| HL_8A3D_045 | 1/A/2792:2799 | No text annotation | homologous HL_5TBW_041 NA | |
| HL_8A3D_046 | 1/A/2810:2816 | GNRA | homologous HL_5TBW_042 NA | |
| HL_8A3D_047 | 1/A/2872:2877 | UNCG | geometric HL_4V9F_044 HL_61337.2 | |
| HL_8A3D_049 | 1/A/3614:3618 | No text annotation | homologous HL_8C3A_045 NA | |
| HL_8A3D_087 | 1/A/3639:3649 | No text annotation | homologous HL_8P9A_157 HL_87681.1 | |
| HL_8A3D_051 | 1/A/3668:3674 | GNRA | homologous HL_8C3A_047 NA | |
| HL_8A3D_088 | 1/A/3724:3729 | GNRA | homologous HL_8P9A_159 HL_34789.2 | |
| HL_8A3D_054 | 1/A/3796:3804 | No text annotation | homologous HL_5TBW_050 NA | |
| HL_8A3D_055 | 1/A/3873:3882 | No text annotation | homologous HL_8C3A_051 NA | |
| HL_8A3D_058 | 1/A/4193:4201 | No text annotation | homologous HL_8C3A_055 NA | |
| HL_8A3D_059 | 1/A/4210:4222 | No text annotation | homologous HL_8P9A_166 HL_02042.1 | |
| HL_8A3D_060 | 1/A/4250:4258 | No text annotation | homologous HL_5TBW_056 NA | |
| HL_8A3D_061 | 1/A/4270:4277 | Pseudoknot geometry | homologous HL_5TBW_057 NA | |
| HL_8A3D_062 | 1/A/4301:4309 | No text annotation | homologous HL_8C3A_059 NA | |
| HL_8A3D_063 | 1/A/4321:4326 | GNRA | homologous HL_5TBW_059 NA | |
| HL_8A3D_064 | 1/A/4352:4362 | Pseudoknot geometry | homologous HL_5TBW_060 NA | |
| HL_8A3D_065 | 1/A/4417:4425 | No text annotation | homologous HL_8C3A_062 NA | |
| HL_8A3D_066 | 1/A/4474:4481 | No text annotation | homologous HL_5TBW_062 NA | |
| HL_8A3D_067 | 1/A/4497:4503 | No text annotation | homologous HL_5TBW_063 NA | |
| HL_8A3D_068 | 1/A/4540:4545 | GNRA | homologous HL_8C3A_065 NA | |
| HL_8A3D_069 | 1/A/4603:4608 | GNRA | homologous HL_8C3A_066 NA | |
| HL_8A3D_070 | 1/A/4646:4651 | Ribsomal LSU H95 | homologous HL_8C3A_067 NA | |
| HL_8A3D_071 | 1/A/4688:4702 | No text annotation | homologous HL_8C3A_068 NA | |
| HL_8A3D_073 | 1/A/4907:4914 | No text annotation | geometric HL_2Y9H_003 HL_75660.7 | |
| HL_8A3D_074 | 1/A/4975:4983 | No text annotation | homologous HL_8C3A_071 NA | |
| HL_8A3D_089 | 1/B/32:45 | No text annotation | homologous HL_8C3A_228 NA | |
| HL_8A3D_076 | 1/B/36:41 | No text annotation | geometric HL_5TBW_185 NA | |
| HL_8A3D_077 | 1/B/86:91 | GNRA | homologous HL_5TBW_186 NA | |
| HL_8A3D_078 | 1/C/47:56 | Pseudoknot with intercalation | geometric HL_4V9F_001 HL_17803.1 | |
| HL_8A3D_080 | 1/C/107:112 | No text annotation | homologous HL_5TBW_075 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8A3D_011 | No text annotation | ||
| HL_8A3D_012 | UNCG variation | ||
| HL_8A3D_013 | No text annotation | ||
| HL_8A3D_014 | Mini UNCG | ||
| HL_8A3D_016 | Mini UNCG | ||
| HL_8A3D_017 | No text annotation | ||
| HL_8A3D_018 | No text annotation | ||
| HL_8A3D_020 | No text annotation | ||
| HL_8A3D_021 | No text annotation | ||
| HL_8A3D_027 | Mini UNCG | ||
| HL_8A3D_031 | No text annotation | ||
| HL_8A3D_032 | Mini UNCG | ||
| HL_8A3D_039 | GNRA with extra cWW | ||
| HL_8A3D_085 | GNRA | ||
| HL_8A3D_041 | No text annotation | ||
| HL_8A3D_048 | Mini UNCG | ||
| HL_8A3D_050 | No text annotation | ||
| HL_8A3D_052 | GNRA with extra near cWW | ||
| HL_8A3D_053 | No text annotation | ||
| HL_8A3D_056 | No text annotation | ||
| HL_8A3D_057 | No text annotation | ||
| HL_8A3D_072 | Mini UNCG | ||
| HL_8A3D_075 | Externally structured | ||
| HL_8A3D_079 | No text annotation | ||
| HL_8A3D_081 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8A3D_001 | 1/A/6:7, 1/C/149:151 | Single bulged C | homologous IL_8C3A_002 NA | |
| IL_8A3D_002 | 1/A/12:14, 1/C/143:144 | Single bulged U | homologous IL_8C3A_003 NA | |
| IL_8A3D_003 | 1/A/16:18, 1/C/139:141 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_01003.2 | |
| IL_8A3D_004 | 1/A/26:27, 1/A/55:57 | Single stack bend | homologous IL_5TBW_004 NA | |
| IL_8A3D_005 | 1/A/30:37, 1/A/44:52 | 9x8 Sarcin-Ricin; G-bulge | geometric IL_4WF9_008 IL_93502.1 | |
| IL_8A3D_006 | 1/A/81:88, 1/A/96:102 | No text annotation | homologous IL_8C3A_006 NA | |
| IL_8A3D_007 | 1/A/118:121, 1/A/152:153 | Major groove intercalation | geometric IL_1NBS_009 IL_71421.2 | |
| IL_8A3D_167 | 1/A/118:122, 1/A/147:153 | No text annotation | ||
| IL_8A3D_008 | 1/A/121:122, 1/A/147:152 | No text annotation | homologous IL_8C3A_007 NA | |
| IL_8A3D_009 | 1/A/125:126, 1/A/142:144 | Single bulged C | geometric IL_1DQF_001 NA | |
| IL_8A3D_010 | 1/A/195:196, 1/A/244:246 | Single bulged C | geometric IL_1DQF_001 NA | |
| IL_8A3D_011 | 1/A/199:201, 1/A/214:215 | Single bulged U | homologous IL_8C3A_013 NA | |
| IL_8A3D_012 | 1/A/339:342, 1/C/32:33 | Minor groove platform | geometric IL_7RQB_073 NA | |
| IL_8A3D_013 | 1/A/348:350, 1/C/25:26 | Single bulged A | homologous IL_8C3A_014 NA | |
| IL_8A3D_014 | 1/A/387:390, 1/A/401:414 | No text annotation | homologous IL_5TBW_014 NA | |
| IL_8A3D_016 | 1/A/415:421, 1/C/13:19 | Triple sheared with non-canonical cWW | homologous IL_5TBW_015 NA | |
| IL_8A3D_017 | 1/A/443:446, 1/A/1300:1304 | No text annotation | geometric IL_7MLW_007 IL_49140.1 | |
| IL_8A3D_018 | 1/A/448:450, 1/A/1297:1298 | No text annotation | ||
| IL_8A3D_019 | 1/A/459:460, 1/A/695:697 | Single bulged C | geometric IL_5TBW_069 NA | |
| IL_8A3D_020 | 1/A/462:464, 1/A/691:693 | Isolated non-canonical cWW pair | geometric IL_5J7L_061 NA | |
| IL_8A3D_021 | 1/A/466:472, 1/A/682:689 | No text annotation | ||
| IL_8A3D_022 | 1/A/482:485, 1/A/671:672 | Multiple bulged bases | geometric IL_5WTK_001 IL_71421.2 | |
| IL_8A3D_023 | 1/A/487:488, 1/A/665:669 | No text annotation | geometric IL_8C3A_483 NA | |
| IL_8A3D_024 | 1/A/508:510, 1/A/649:650 | Single bulged A | geometric IL_6WPI_001 IL_14190.2 | |
| IL_8A3D_025 | 1/A/709:710, 1/A/1286:1288 | Single bulged G | geometric IL_4LFB_036 IL_28408.2 | |
| IL_8A3D_026 | 1/A/723:724, 1/A/942:945 | Multiple bulged bases | geometric IL_7V9E_001 NA | |
| IL_8A3D_027 | 1/A/727:731, 1/A/938:939 | No text annotation | ||
| IL_8A3D_028 | 1/A/732:735, 1/A/928:937 | No text annotation | ||
| IL_8A3D_029 | 1/A/737:740, 1/A/924:926 | Single stack bend | geometric IL_3MOJ_004 IL_75501.1 | |
| IL_8A3D_169 | 1/A/737:742, 1/A/922:926 | No text annotation | ||
| IL_8A3D_030 | 1/A/740:742, 1/A/922:924 | Isolated cWS basepair | geometric IL_7RQB_030 NA | |
| IL_8A3D_031 | 1/A/745:752, 1/A/911:919 | No text annotation | geometric IL_5TBW_020 NA | |
| IL_8A3D_032 | 1/A/1073:1074, 1/A/1237:1239 | Single bulged A | geometric IL_2VPL_002 IL_14190.2 | |
| IL_8A3D_034 | 1/A/1082:1084, 1/A/1213:1217 | Isolated cWH basepair | geometric IL_4KQ0_005 IL_10892.2 | |
| IL_8A3D_035 | 1/A/1086:1087, 1/A/1209:1211 | Single bulged C | geometric IL_3W3S_001 IL_05642.2 | |
| IL_8A3D_036 | 1/A/1093:1096, 1/A/1199:1203 | Tandem non-canonical cWW pairs | geometric IL_6CZR_168 NA | |
| IL_8A3D_037 | 1/A/1173:1175, 1/A/1186:1188 | Isolated cWH basepair | geometric IL_3W3S_003 IL_10892.2 | |
| IL_8A3D_038 | 1/A/1244:1245, 1/A/1265:1267 | Single bulged G | geometric IL_4V88_442 NA | |
| IL_8A3D_039 | 1/A/1357:1360, 1/A/1379:1382 | No text annotation | ||
| IL_8A3D_170 | 1/A/1357:1361, 1/A/1376:1382 | No text annotation | ||
| IL_8A3D_040 | 1/A/1360:1361, 1/A/1376:1379 | Major groove intercalation | geometric IL_1NBS_009 IL_71421.2 | |
| IL_8A3D_041 | 1/A/1425:1429, 1/A/1455:1460 | Triple sheared related | geometric IL_4V9F_018 IL_67427.1 | |
| IL_8A3D_042 | 1/A/1431:1434, 1/A/1450:1453 | Double sheared | geometric IL_4LFB_060 IL_58355.2 | |
| IL_8A3D_043 | 1/A/1467:1468, 1/A/1496:1498 | Single bulged A | homologous IL_5TBW_024 NA | |
| IL_8A3D_044 | 1/A/1474:1476, 1/A/1489:1490 | No text annotation | ||
| IL_8A3D_045 | 1/A/1479:1480, 1/A/1484:1486 | No text annotation | ||
| IL_8A3D_172 | 1/A/1520:1522, 1/A/1655:1657 | Isolated non-canonical cWW pair | homologous IL_8P9A_255 IL_01003.2 | |
| IL_8A3D_173 | 1/A/1522:1526, 1/A/1648:1655 | No text annotation | homologous IL_8P9A_256 IL_73855.1 | |
| IL_8A3D_047 | 1/A/1545:1546, 1/A/1612:1614 | Single bulged A | geometric IL_4WF9_022 IL_14190.2 | |
| IL_8A3D_048 | 1/A/1550:1551, 1/A/1576:1578 | Single bulged G | geometric IL_4V9F_026 IL_28408.2 | |
| IL_8A3D_049 | 1/A/1551:1555, 1/A/1572:1576 | Triple sheared | homologous IL_5TBW_030 NA | |
| IL_8A3D_050 | 1/A/1586:1589, 1/A/1605:1607 | Major groove platform with extra cWW | homologous IL_8C3A_034 NA | |
| IL_8A3D_051 | 1/A/1590:1592, 1/A/1603:1604 | Single bulged U | homologous IL_8C3A_035 NA | |
| IL_8A3D_052 | 1/A/1624:1626, 1/A/1636:1640 | No text annotation | homologous IL_8C3A_036 NA | |
| IL_8A3D_053 | 1/A/1671:1673, 1/A/1682:1684 | Isolated non-canonical cWW pair | homologous IL_8C3A_037 NA | |
| IL_8A3D_054 | 1/A/1686:1688, 1/A/1848:1851 | No text annotation | ||
| IL_8A3D_056 | 1/A/1723:1725, 1/A/1838:1839 | Single bulged G | homologous IL_8C3A_040 NA | |
| IL_8A3D_174 | 1/A/1732:1737, 1/A/1792:1797 | No text annotation | ||
| IL_8A3D_175 | 1/A/1737:1738, 1/A/1790:1792 | Minor groove platform | homologous IL_8C3A_042 NA | |
| IL_8A3D_176 | 1/A/1739:1744, 1/A/1786:1789 | C-loop with bulged stacked A's | homologous IL_8C3A_043 NA | |
| IL_8A3D_177 | 1/A/1746:1749, 1/A/1781:1784 | Tandem non-canonical cWW pairs | homologous IL_8P9A_269 IL_71194.2 | |
| IL_8A3D_178 | 1/A/1749:1751, 1/A/1779:1781 | Isolated non-canonical cWW pair | homologous IL_8C3A_045 NA | |
| IL_8A3D_060 | 1/A/1814:1816, 1/A/1823:1824 | Single bulged A | homologous IL_5TBW_045 NA | |
| IL_8A3D_179 | 1/A/1858:1860, 1/A/1874:1876 | Isolated non-canonical cWW pair | homologous IL_8P9A_274 IL_01003.2 | |
| IL_8A3D_062 | 1/A/1905:1909, 1/A/2067:2071 | UAA/GAN | homologous IL_5TBW_048 NA | |
| IL_8A3D_063 | 1/A/1911:1918, 1/A/2064:2065 | SSU/LSU pseudoknot | homologous IL_8C3A_052 NA | |
| IL_8A3D_064 | 1/A/1918:1920, 1/A/2063:2064 | No text annotation | ||
| IL_8A3D_065 | 1/A/1920:1922, 1/A/2062:2063 | No text annotation | ||
| IL_8A3D_066 | 1/A/1926:1933, 1/A/2053:2058 | No text annotation | geometric IL_5TBW_051 NA | |
| IL_8A3D_067 | 1/A/1933:1944, 1/A/2038:2053 | No text annotation | geometric IL_5TBW_052 NA | |
| IL_8A3D_068 | 1/A/1946:1948, 1/A/2035:2036 | Single bulged U | homologous IL_5TBW_053 NA | |
| IL_8A3D_069 | 1/A/2083:2085, 1/A/2272:2273 | No text annotation | ||
| IL_8A3D_070 | 1/A/2290:2292, 1/A/2342:2345 | Isolated cWS basepair | homologous IL_5TBW_057 NA | |
| IL_8A3D_071 | 1/A/2299:2301, 1/A/2334:2335 | Single bulged A | homologous IL_8C3A_062 NA | |
| IL_8A3D_072 | 1/A/2302:2309, 1/A/2329:2333 | Kink-turn | homologous IL_5TBW_059 NA | |
| IL_8A3D_073 | 1/A/2312:2314, 1/A/2325:2326 | Single bulged A | homologous IL_5TBW_060 NA | |
| IL_8A3D_181 | 1/A/2358:2364, 1/A/3858:3863 | 7x6 Sarcin-Ricin; G-bulge | homologous IL_8P9A_289 IL_02666.1 | |
| IL_8A3D_074 | 1/A/2406:2409, 1/A/2783:2784 | Major groove platform; stack outside cWW | geometric IL_4V9F_050 IL_74641.2 | |
| IL_8A3D_182 | 1/A/2415:2419, 1/A/2427:2429 | C-loop | homologous IL_8C3A_482 NA | |
| IL_8A3D_076 | 1/A/2446:2450, 1/A/2509:2514 | UAA/GAN | homologous IL_8C3A_067 NA | |
| IL_8A3D_078 | 1/A/2549:2550, 1/A/2768:2770 | Single bulged U | geometric IL_2A64_002 IL_97561.2 | |
| IL_8A3D_079 | 1/A/2589:2593, 1/A/2752:2756 | Triple sheared | geometric IL_7RQB_075 NA | |
| IL_8A3D_080 | 1/A/2613:2614, 1/A/2724:2726 | Single bulged A | geometric IL_7RQB_069 NA | |
| IL_8A3D_081 | 1/A/2614:2615, 1/A/2722:2724 | Single stack bend | homologous IL_8C3A_076 NA | |
| IL_8A3D_082 | 1/A/2646:2648, 1/A/2685:2688 | Isolated tHS basepair with bulges | geometric IL_4V9F_076 IL_87316.1 | |
| IL_8A3D_083 | 1/A/2651:2653, 1/A/2681:2682 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_8A3D_084 | 1/A/2656:2662, 1/A/2672:2678 | Kink-turn | homologous IL_5TBW_073 NA | |
| IL_8A3D_085 | 1/A/2704:2705, 1/A/2710:2712 | No text annotation | ||
| IL_8A3D_183 | 1/A/2832:2838, 1/A/3850:3853 | No text annotation | homologous IL_8C3A_080 NA | |
| IL_8A3D_184 | 1/A/2844:2846, 1/A/3842:3844 | No text annotation | homologous IL_8C3A_081 NA | |
| IL_8A3D_185 | 1/A/2847:2850, 1/A/3840:3841 | Major groove platform; stack outside cWW | geometric IL_5TBW_076 NA | |
| IL_8A3D_186 | 1/A/2847:2855, 1/A/3837:3841 | No text annotation | homologous IL_8P9A_305 IL_80252.1 | |
| IL_8A3D_090 | 1/A/2850:2855, 1/A/3837:3840 | Intercalated tWH | geometric IL_5TBW_077 NA | |
| IL_8A3D_091 | 1/A/2867:2872, 1/A/2877:2883 | No text annotation | homologous IL_8C3A_084 NA | |
| IL_8A3D_092 | 1/A/2889:2891, 1/A/3610:3612 | Isolated non-canonical cWW pair | homologous IL_8C3A_085 NA | |
| IL_8A3D_093 | 1/A/2896:2897, 1/A/3602:3605 | No text annotation | homologous IL_8C3A_086 NA | |
| IL_8A3D_096 | 1/A/3632:3633, 1/A/3827:3829 | Single bulged A | geometric IL_4V9F_064 IL_14190.2 | |
| IL_8A3D_097 | 1/A/3660:3665, 1/A/3677:3684 | Kink-turn related | homologous IL_5TBW_083 NA | |
| IL_8A3D_099 | 1/A/3700:3703, 1/A/3749:3750 | Major groove intercalation | homologous IL_5TBW_084 NA | |
| IL_8A3D_100 | 1/A/3704:3705, 1/A/3745:3748 | Major groove intercalation | homologous IL_5TBW_085 NA | |
| IL_8A3D_102 | 1/A/3708:3714, 1/A/3739:3742 | No text annotation | ||
| IL_8A3D_187 | 1/A/3715:3721, 1/A/3732:3738 | No text annotation | homologous IL_8C3A_093 NA | |
| IL_8A3D_104 | 1/A/3780:3781, 1/A/3811:3814 | Bulged stacked bases | homologous IL_5TBW_089 NA | |
| IL_8A3D_188 | 1/A/3781:3792, 1/A/3808:3811 | No text annotation | homologous IL_8P9A_318 IL_84014.1 | |
| IL_8A3D_107 | 1/A/3895:3898, 1/A/4563:4565 | Major groove platform with extra pair | homologous IL_5TBW_091 NA | |
| IL_8A3D_109 | 1/A/3900:3902, 1/A/4558:4561 | No text annotation | homologous IL_8C3A_097 NA | |
| IL_8A3D_110 | 1/A/3913:3915, 1/A/4388:4389 | Single bulged U | homologous IL_5TBW_093 NA | |
| IL_8A3D_111 | 1/A/3916:3917, 1/A/4384:4387 | Minor groove platform | homologous IL_5TBW_094 NA | |
| IL_8A3D_113 | 1/A/3927:3929, 1/A/4181:4184 | No text annotation | homologous IL_8C3A_100 NA | |
| IL_8A3D_114 | 1/A/4082:4088, 1/A/4161:4164 | No text annotation | homologous IL_8C3A_106 NA | |
| IL_8A3D_116 | 1/A/4191:4192, 1/A/4202:4204 | Single bulged A | homologous IL_8C3A_107 NA | |
| IL_8A3D_117 | 1/A/4243:4245, 1/A/4263:4267 | Isolated tHS basepair with bulges | geometric IL_5TBW_099 NA | |
| IL_8A3D_189 | 1/A/4291:4293, 1/A/4317:4318 | Single bulged A | geometric IL_7A0S_064 IL_14190.2 | |
| IL_8A3D_190 | 1/A/4295:4298, 1/A/4312:4315 | Tandem non-canonical cWW pairs | homologous IL_8C3A_109 NA | |
| IL_8A3D_120 | 1/A/4347:4350, 1/A/4364:4365 | Single stack bend | geometric IL_5J7L_032 NA | |
| IL_8A3D_191 | 1/A/4400:4401, 1/A/4442:4444 | Major groove platform | homologous IL_8P9A_329 IL_48076.8 | |
| IL_8A3D_192 | 1/A/4401:4403, 1/A/4440:4442 | Isolated non-canonical cWW pair | homologous IL_8P9A_330 IL_01003.2 | |
| IL_8A3D_193 | 1/A/4403:4405, 1/A/4439:4440 | No text annotation | homologous IL_8P9A_331 IL_46637.2 | |
| IL_8A3D_122 | 1/A/4405:4407, 1/A/4435:4439 | Major groove minor groove platform with extra cWW | homologous IL_5TBW_105 NA | |
| IL_8A3D_124 | 1/A/4412:4416, 1/A/4426:4430 | Triple sheared | geometric IL_5TBW_106 NA | |
| IL_8A3D_125 | 1/A/4453:4454, 1/A/4526:4528 | Major groove platform | homologous IL_5TBW_107 NA | |
| IL_8A3D_194 | 1/A/4456:4458, 1/A/4520:4524 | No text annotation | homologous IL_8C3A_116 NA | |
| IL_8A3D_127 | 1/A/4458:4459, 1/A/4517:4520 | Multiple bulged bases | geometric IL_5TBW_109 NA | |
| IL_8A3D_128 | 1/A/4466:4468, 1/A/4489:4491 | Isolated non-canonical cWW pair | geometric IL_5TBW_110 NA | |
| IL_8A3D_195 | 1/A/4466:4470, 1/A/4485:4491 | No text annotation | ||
| IL_8A3D_129 | 1/A/4468:4470, 1/A/4485:4489 | No text annotation | geometric IL_3DD2_004 IL_09353.1 | |
| IL_8A3D_131 | 1/A/4495:4497, 1/A/4503:4505 | Isolated non-canonical cWW pair | geometric IL_5TBW_112 NA | |
| IL_8A3D_133 | 1/A/4537:4538, 1/A/4547:4549 | Single bulged A | homologous IL_5TBW_113 NA | |
| IL_8A3D_136 | 1/A/4580:4582, 1/A/4721:4723 | No text annotation | geometric IL_3ICQ_003 NA | |
| IL_8A3D_137 | 1/A/4582:4585, 1/A/4717:4721 | Double sheared | geometric IL_6E7L_002 IL_69065.1 | |
| IL_8A3D_196 | 1/A/4590:4592, 1/A/4618:4620 | Isolated non-canonical cWW pair | homologous IL_8P9A_343 IL_71625.2 | |
| IL_8A3D_138 | 1/A/4596:4603, 1/A/4608:4614 | 8x7 Sarcin-Ricin; G-bulge | geometric IL_5TBW_116 NA | |
| IL_8A3D_197 | 1/A/4624:4629, 1/A/4669:4673 | No text annotation | ||
| IL_8A3D_198 | 1/A/4632:4637, 1/A/4662:4666 | UAA/GAN related | homologous IL_8C3A_127 NA | |
| IL_8A3D_141 | 1/A/4638:4640, 1/A/4659:4661 | Isolated cWH basepair | geometric IL_3R1C_012 IL_10892.2 | |
| IL_8A3D_142 | 1/A/4641:4642, 1/A/4655:4658 | Multiple bulged bases | homologous IL_5TBW_119 NA | |
| IL_8A3D_143 | 1/A/4680:4685, 1/A/4705:4710 | UAA/GAN with extra cWW | geometric IL_5J7L_350 NA | |
| IL_8A3D_144 | 1/A/4739:4742, 1/A/4958:4960 | Isolated non-canonical cWW pair | homologous IL_8C3A_130 NA | |
| IL_8A3D_145 | 1/A/4743:4746, 1/A/4954:4957 | Tandem non-canonical cWW pairs | geometric IL_5J7L_283 NA | |
| IL_8A3D_146 | 1/A/4749:4751, 1/A/4948:4951 | No text annotation | ||
| IL_8A3D_147 | 1/A/4756:4765, 1/A/4869:4877 | No text annotation | ||
| IL_8A3D_148 | 1/A/4769:4771, 1/A/4863:4865 | Isolated non-canonical cWW pair | geometric IL_1YZ9_001 NA | |
| IL_8A3D_149 | 1/A/4885:4889, 1/A/4930:4934 | Triple non-canonical cWW pairs | geometric IL_8S95_002 IL_71154.2 | |
| IL_8A3D_150 | 1/A/4891:4896, 1/A/4924:4928 | No text annotation | ||
| IL_8A3D_199 | 1/A/4972:4975, 1/A/4983:4986 | Tandem non-canonical cWW pairs | geometric IL_3TZR_003 IL_71194.2 | |
| IL_8A3D_152 | 1/A/4992:4994, 1/A/5057:5059 | Isolated non-canonical cWW pair | geometric IL_3IVK_002 IL_01003.2 | |
| IL_8A3D_153 | 1/A/4996:4997, 1/A/5053:5055 | Single bulged C | geometric IL_1KUQ_002 IL_05642.2 | |
| IL_8A3D_154 | 1/A/5000:5002, 1/A/5045:5050 | Isolated non-canonical cWW pair | homologous IL_5TBW_132 NA | |
| IL_8A3D_155 | 1/A/5003:5009, 1/A/5039:5044 | No text annotation | ||
| IL_8A3D_157 | 1/A/5012:5014, 1/A/5035:5036 | Single bulged U | homologous IL_8C3A_140 NA | |
| IL_8A3D_158 | 1/A/5014:5017, 1/A/5032:5035 | Double sheared; A in syn | homologous IL_8C3A_141 NA | |
| IL_8A3D_159 | 1/B/15:16, 1/B/62:64 | Single bulged A | homologous IL_5TBW_372 NA | |
| IL_8A3D_160 | 1/B/21:27, 1/B/52:57 | Minor groove platform related | homologous IL_5TBW_373 NA | |
| IL_8A3D_161 | 1/B/28:29, 1/B/48:51 | Major groove minor groove platform; mini C-loop | homologous IL_7RQB_113 NA | |
| IL_8A3D_162 | 1/B/32:36, 1/B/41:45 | Symmetric double minor groove platform | homologous IL_7RQB_114 NA | |
| IL_8A3D_163 | 1/B/71:78, 1/B/98:104 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_5TBW_377 NA | |
| IL_8A3D_164 | 1/B/79:81, 1/B/95:97 | No text annotation | geometric IL_7RQB_015 NA | |
| IL_8A3D_165 | 1/B/82:85, 1/B/92:94 | Isolated non-canonical cWW pair | homologous IL_5TBW_378 NA | |
| IL_8A3D_166 | 1/C/64:66, 1/C/92:95 | Isolated non-canonical cWW pair | homologous IL_5TBW_145 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8A3D_015 | Isolated non-canonical cWW pair | ||
| IL_8A3D_168 | Isolated cWH basepair | ||
| IL_8A3D_033 | No text annotation | ||
| IL_8A3D_171 | No text annotation | ||
| IL_8A3D_046 | No text annotation | ||
| IL_8A3D_055 | No text annotation | ||
| IL_8A3D_057 | No text annotation | ||
| IL_8A3D_058 | No text annotation | ||
| IL_8A3D_059 | No text annotation | ||
| IL_8A3D_061 | Tandem non-canonical cWW pairs | ||
| IL_8A3D_180 | No text annotation | ||
| IL_8A3D_075 | No text annotation | ||
| IL_8A3D_077 | Self complementary | ||
| IL_8A3D_086 | No text annotation | ||
| IL_8A3D_087 | Stack and bulge | ||
| IL_8A3D_088 | No text annotation | ||
| IL_8A3D_089 | Major groove platform with extra pair | ||
| IL_8A3D_094 | Isolated non-canonical cWW pair | ||
| IL_8A3D_095 | Isolated non-canonical cWW pair | ||
| IL_8A3D_098 | Stack and bulge | ||
| IL_8A3D_101 | No text annotation | ||
| IL_8A3D_103 | No text annotation | ||
| IL_8A3D_105 | No text annotation | ||
| IL_8A3D_106 | Stack and bulge | ||
| IL_8A3D_108 | Isolated non-canonical cWW pair | ||
| IL_8A3D_112 | Isolated non-canonical cWW pair | ||
| IL_8A3D_115 | No text annotation | ||
| IL_8A3D_118 | Decoding loop related | ||
| IL_8A3D_119 | No text annotation | ||
| IL_8A3D_121 | No text annotation | ||
| IL_8A3D_123 | Not an internal loop | ||
| IL_8A3D_126 | No text annotation | ||
| IL_8A3D_130 | Isolated cWH basepair | ||
| IL_8A3D_132 | No text annotation | ||
| IL_8A3D_134 | Isolated non-canonical cWW pair | ||
| IL_8A3D_135 | Stack and bulge | ||
| IL_8A3D_139 | No text annotation | ||
| IL_8A3D_140 | No text annotation | ||
| IL_8A3D_151 | Single bulged C | ||
| IL_8A3D_156 | Stack and bulge |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8A3D_001 | 1/A/112:116, 1/A/155:160, 1/A/275:278 | No text annotation | ||
| J3_8A3D_018 | 1/A/196:199, 1/A/215:228, 1/A/240:244 | No text annotation | ||
| J3_8A3D_019 | 1/A/351:367, 1/A/374:379, 1/C/21:24 | No text annotation | homologous J3_8P9A_045 J3_07616.1 | |
| J3_8A3D_002 | 1/A/380:387, 1/A/414:415, 1/C/19:20 | No text annotation | homologous J3_5TBW_002 NA | |
| J3_8A3D_020 | 1/A/380:390, 1/A/401:415, 1/C/19:20 | No text annotation | homologous J3_8C3A_049 NA | |
| J3_8A3D_021 | 1/A/451:455, 1/A/701:705, 1/A/1292:1296 | No text annotation | ||
| J3_8A3D_004 | 1/A/1531:1537, 1/A/1622:1624, 1/A/1640:1643 | No text annotation | homologous J3_8C3A_003 NA | |
| J3_8A3D_005 | 1/A/1546:1548, 1/A/1580:1584, 1/A/1609:1612 | No text annotation | homologous J3_8C3A_004 NA | |
| J3_8A3D_022 | 1/A/1726:1727, 1/A/1802:1806, 1/A/1832:1837 | No text annotation | homologous J3_8P9A_051 J3_84137.1 | |
| J3_8A3D_006 | 1/A/2393:2399, 1/A/2805:2807, 1/A/2819:2822 | No text annotation | homologous J3_5TBW_008 NA | |
| J3_8A3D_007 | 1/A/2402:2405, 1/A/2785:2791, 1/A/2800:2802 | No text annotation | homologous J3_5TBW_009 NA | |
| J3_8A3D_008 | 1/A/2440:2445, 1/A/2515:2519, 1/A/2536:2537 | No text annotation | homologous J3_5TBW_010 NA | |
| J3_8A3D_010 | 1/A/2551:2555, 1/A/2572:2575, 1/A/2757:2767 | No text annotation | ||
| J3_8A3D_011 | 1/A/2575:2576, 1/A/2585:2589, 1/A/2756:2757 | No text annotation | homologous J3_8C3A_054 NA | |
| J3_8A3D_023 | 1/A/2598:2602, 1/A/2737:2738, 1/A/2742:2747 | No text annotation | homologous J3_8C3A_055 NA | |
| J3_8A3D_012 | 1/A/3937:3939, 1/A/4074:4078, 1/A/4168:4173 | No text annotation | geometric J3_8VTW_006 NA | |
| J3_8A3D_024 | 1/A/4228:4230, 1/A/4331:4342, 1/A/4370:4375 | No text annotation | homologous J3_8C3A_056 NA | |
| J3_8A3D_013 | 1/A/4241:4243, 1/A/4267:4269, 1/A/4278:4283 | No text annotation | homologous J3_5TBW_013 NA | |
| J3_8A3D_025 | 1/A/4463:4466, 1/A/4491:4493, 1/A/4507:4513 | No text annotation | homologous J3_8C3A_011 NA | |
| J3_8A3D_026 | 1/A/4751:4754, 1/A/4879:4883, 1/A/4936:4948 | No text annotation | ||
| J3_8A3D_016 | 1/B/9:14, 1/B/65:66, 1/B/109:110 | No text annotation | homologous J3_5TBW_045 NA | |
| J3_8A3D_017 | 1/C/44:45, 1/C/58:64, 1/C/95:99 | No text annotation | homologous J3_8C3A_060 NA | |
| J4_8A3D_001 | 1/A/111:112, 1/A/278:283, 1/A/304:310, 1/A/327:330 | No text annotation | homologous J4_8P9A_012 J4_94698.1 | |
| J4_8A3D_002 | 1/A/196:199, 1/A/215:222, 1/A/226:228, 1/A/240:244 | No text annotation | ||
| J4_8A3D_003 | 1/A/981:983, 1/A/1070:1072, 1/A/1240:1243, 1/A/1268:1273 | No text annotation | ||
| J4_8A3D_004 | 1/A/2365:2371, 1/A/2389:2391, 1/A/2824:2829, 1/A/3856:3857 | No text annotation | ||
| J4_8A3D_005 | 1/A/2406:2410, 1/A/2434:2439, 1/A/2538:2539, 1/A/2777:2784 | No text annotation | ||
| J4_8A3D_006 | 1/A/2409:2410, 1/A/2434:2439, 1/A/2538:2539, 1/A/2777:2783 | No text annotation | ||
| J4_8A3D_007 | 1/A/2618:2619, 1/A/2637:2642, 1/A/2692:2698, 1/A/2718:2719 | No text annotation | ||
| J4_8A3D_008 | 1/A/3634:3638, 1/A/3650:3654, 1/A/3690:3694, 1/A/3821:3826 | No text annotation | homologous J4_8P9A_017 J4_78485.1 | |
| J4_8A3D_009 | 1/A/3696:3698, 1/A/3752:3753, 1/A/3771:3780, 1/A/3814:3819 | No text annotation | homologous J4_8P9A_018 J4_42306.1 | |
| J4_8A3D_010 | 1/A/4231:4235, 1/A/4289:4291, 1/A/4318:4319, 1/A/4328:4330 | No text annotation | ||
| J4_8A3D_011 | 1/A/4231:4235, 1/A/4289:4293, 1/A/4317:4319, 1/A/4328:4330 | No text annotation | homologous J4_8P9A_019 J4_59590.1 | |
| J4_8A3D_012 | 1/A/4587:4590, 1/A/4620:4621, 1/A/4676:4678, 1/A/4712:4715 | No text annotation | ||
| J5_8A3D_001 | 1/A/19:21, 1/C/35:42, 1/C/101:106, 1/C/113:114, 1/C/136:138 | No text annotation | homologous J5_8P9A_010 J5_27223.1 | |
| J5_8A3D_002 | 1/A/1335:1340, 1/A/1516:1519, 1/A/1658:1661, 1/A/2288:2290, 1/A/2345:2351 | No text annotation | homologous J5_8P9A_011 J5_08384.1 | |
| J5_8A3D_003 | 1/A/2855:2863, 1/A/2887:2888, 1/A/3613:3614, 1/A/3618:3626, 1/A/3835:3837 | No text annotation | homologous J5_8C3A_004 NA | |
| J5_8A3D_004 | 1/A/3903:3910, 1/A/4392:4400, 1/A/4444:4453, 1/A/4528:4534, 1/A/4552:4557 | No text annotation | ||
| J5_8A3D_005 | 1/A/3920:3923, 1/A/4188:4191, 1/A/4204:4205, 1/A/4227:4228, 1/A/4375:4381 | No text annotation | homologous J5_8P9A_015 J5_96125.1 | |
| J6_8A3D_001 | 1/A/21:26, 1/A/57:67, 1/A/74:78, 1/A/105:109, 1/A/332:339, 1/C/33:35 | No text annotation | ||
| J6_8A3D_002 | 1/A/1352:1355, 1/A/1384:1388, 1/A/1395:1399, 1/A/1418:1421, 1/A/1464:1466, 1/A/1499:1504 | No text annotation | ||
| J6_8A3D_003 | 1/A/3920:3923, 1/A/4188:4191, 1/A/4204:4205, 1/A/4227:4230, 1/A/4331:4342, 1/A/4370:4381 | No text annotation | ||
| J7_8A3D_001 | 1/A/1666:1671, 1/A/1684:1685, 1/A/1852:1855, 1/A/1879:1884, 1/A/1895:1899, 1/A/2077:2078, 1/A/2278:2283 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8A3D_003 | No text annotation | ||
| J3_8A3D_009 | No text annotation | ||
| J3_8A3D_014 | No text annotation | ||
| J3_8A3D_015 | No text annotation |
Coloring options: