6YAL Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6YAL_001 | 1/1/14:22 | No text annotation | geometric HL_4V88_198 NA | |
| HL_6YAL_002 | 1/1/31:39 | tRNA anticodon loop | homologous HL_4TUE_034 HL_06059.5 | |
| HL_6YAL_003 | 1/1/53:61 | T-loop with 2 stacked bulged bases | homologous HL_4V9Q_215 HL_28252.6 | |
| HL_6YAL_004 | 1/2/7:17 | No text annotation | homologous HL_4V88_186 NA | |
| HL_6YAL_005 | 1/2/69:80 | No text annotation | geometric HL_2ZZM_002 HL_13963.3 | |
| HL_6YAL_006 | 1/2/156:162 | GNRA related | homologous HL_4V88_188 NA | |
| HL_6YAL_007 | 1/2/194:201 | No text annotation | ||
| HL_6YAL_009 | 1/2/279:286 | T-loop with 1 bulged base | homologous HL_4V88_191 NA | |
| HL_6YAL_010 | 1/2/312:319 | No text annotation | ||
| HL_6YAL_011 | 1/2/367:377 | No text annotation | ||
| HL_6YAL_012 | 1/2/406:411 | No text annotation | homologous HL_4V88_194 NA | |
| HL_6YAL_013 | 1/2/431:442 | No text annotation | homologous HL_4V88_195 NA | |
| HL_6YAL_014 | 1/2/452:457 | UNCG | homologous HL_4V88_196 NA | |
| HL_6YAL_015 | 1/2/488:494 | No text annotation | homologous HL_4V88_197 NA | |
| HL_6YAL_016 | 1/2/529:534 | GNRA | geometric HL_5TBW_017 NA | |
| HL_6YAL_017 | 1/2/559:571 | No text annotation | homologous HL_4V88_199 NA | |
| HL_6YAL_018 | 1/2/608:613 | GNRA variation | homologous HL_4V88_200 NA | |
| HL_6YAL_020 | 1/2/816:824 | No text annotation | homologous HL_4V88_203 NA | |
| HL_6YAL_021 | 1/2/829:837 | No text annotation | geometric HL_8S95_003 HL_53890.2 | |
| HL_6YAL_022 | 1/2/881:897 | No text annotation | homologous HL_8C3A_210 NA | |
| HL_6YAL_023 | 1/2/953:962 | No text annotation | homologous HL_4V88_206 NA | |
| HL_6YAL_024 | 1/2/990:995 | GNRA | homologous HL_4V88_207 NA | |
| HL_6YAL_025 | 1/2/1050:1060 | No text annotation | homologous HL_4V88_208 NA | |
| HL_6YAL_026 | 1/2/1109:1116 | No text annotation | ||
| HL_6YAL_027 | 1/2/1137:1142 | GNRA | homologous HL_4V88_210 NA | |
| HL_6YAL_028 | 1/2/1174:1179 | GNRA | homologous HL_4V88_211 NA | |
| HL_6YAL_029 | 1/2/1241:1250 | No text annotation | homologous HL_8C3A_217 NA | |
| HL_6YAL_030 | 1/2/1291:1300 | Anticodon loop related | homologous HL_4V88_213 NA | |
| HL_6YAL_031 | 1/2/1349:1354 | GNRA | homologous HL_4V88_214 NA | |
| HL_6YAL_032 | 1/2/1362:1369 | No text annotation | homologous HL_4V88_215 NA | |
| HL_6YAL_033 | 1/2/1417:1422 | No text annotation | ||
| HL_6YAL_034 | 1/2/1456:1462 | GNRA | homologous HL_4V88_217 NA | |
| HL_6YAL_035 | 1/2/1560:1565 | GNRA | homologous HL_4V88_218 NA | |
| HL_6YAL_036 | 1/2/1609:1620 | No text annotation | homologous HL_4V88_219 NA | |
| HL_6YAL_037 | 1/2/1653:1661 | No text annotation | homologous HL_4V88_220 NA | |
| HL_6YAL_039 | 1/2/1841:1846 | GNRA variation | homologous HL_4V88_222 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6YAL_008 | No text annotation | ||
| HL_6YAL_019 | No text annotation | ||
| HL_6YAL_038 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6YAL_001 | 1/2/23:25, 1/2/639:641 | Isolated non-canonical cWW pair | geometric IL_3MEI_002 IL_87907.2 | |
| IL_6YAL_107 | 1/2/34:36, 1/2/509:511 | Isolated non-canonical cWW pair | homologous IL_8P9A_374 IL_87907.2 | |
| IL_6YAL_002 | 1/2/37:40, 1/2/504:508 | Double sheared | geometric IL_4WF9_016 IL_09705.15 | |
| IL_6YAL_003 | 1/2/41:47, 1/2/469:471 | No text annotation | geometric IL_4V88_387 NA | |
| IL_6YAL_004 | 1/2/49:51, 1/2/466:467 | Minor groove platform | homologous IL_4V88_388 NA | |
| IL_6YAL_005 | 1/2/57:62, 1/2/86:88 | No text annotation | homologous IL_4V88_389 NA | |
| IL_6YAL_006 | 1/2/63:68, 1/2/81:85 | No text annotation | homologous IL_4V88_390 NA | |
| IL_6YAL_007 | 1/2/108:110, 1/2/341:343 | Isolated non-canonical cWW pair | geometric IL_1T0E_002 IL_28037.2 | |
| IL_6YAL_098 | 1/2/108:112, 1/2/339:343 | Triple non-canonical cWW pairs | geometric IL_8VMB_003 IL_49751.4 | |
| IL_6YAL_008 | 1/2/110:112, 1/2/339:341 | Isolated non-canonical cWW pair | geometric IL_4WF9_042 IL_87907.2 | |
| IL_6YAL_009 | 1/2/112:115, 1/2/338:339 | Multiple bulged bases | homologous IL_4V88_392 NA | |
| IL_6YAL_010 | 1/2/116:121, 1/2/333:337 | No text annotation | homologous IL_4V88_393 NA | |
| IL_6YAL_011 | 1/2/145:151, 1/2/167:174 | tWH-tWH-tHW-tHW | homologous IL_4V88_394 NA | |
| IL_6YAL_012 | 1/2/152:154, 1/2/164:166 | Isolated cWH basepair | geometric IL_3R1C_018 IL_10167.5 | |
| IL_6YAL_013 | 1/2/187:191, 1/2/204:208 | Triple sheared | geometric IL_4V9F_085 IL_17948.2 | |
| IL_6YAL_014 | 1/2/192:194, 1/2/201:203 | Isolated non-canonical cWW pair | geometric IL_5J7L_273 IL_28037.2 | |
| IL_6YAL_015 | 1/2/213:216, 1/2/293:300 | No text annotation | geometric IL_1GID_008 NA | |
| IL_6YAL_016 | 1/2/303:305, 1/2/326:327 | Single bulged A | homologous IL_4V88_399 NA | |
| IL_6YAL_017 | 1/2/308:310, 1/2/321:323 | Isolated non-canonical cWW pair | geometric IL_5ED1_002 IL_87907.2 | |
| IL_6YAL_018 | 1/2/349:354, 1/2/386:393 | Kink-turn with non-sequential stacking | homologous IL_4V88_402 NA | |
| IL_6YAL_019 | 1/2/356:361, 1/2/383:384 | No text annotation | geometric IL_5Y58_001 IL_59877.1 | |
| IL_6YAL_020 | 1/2/401:403, 1/2/414:419 | No text annotation | homologous IL_4V88_404 NA | |
| IL_6YAL_021 | 1/2/427:429, 1/2/444:446 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_6YAL_022 | 1/2/449:451, 1/2/458:460 | Isolated near basepair | homologous IL_4V88_406 NA | |
| IL_6YAL_023 | 1/2/477:479, 1/2/501:502 | Single bulged U | homologous IL_4V88_407 NA | |
| IL_6YAL_024 | 1/2/481:486, 1/2/496:499 | C-loop with extra cWW pair | homologous IL_4V88_408 NA | |
| IL_6YAL_099 | 1/2/519:521, 1/2/543:546 | No text annotation | ||
| IL_6YAL_026 | 1/2/522:524, 1/2/539:542 | No text annotation | geometric IL_4N0T_004 IL_99358.1 | |
| IL_6YAL_027 | 1/2/525:527, 1/2/536:538 | Isolated non-canonical cWW pair | geometric IL_5Y85_006 IL_87907.2 | |
| IL_6YAL_028 | 1/2/553:555, 1/2/575:582 | No text annotation | geometric IL_8VTW_081 NA | |
| IL_6YAL_029 | 1/2/556:559, 1/2/571:574 | Tandem non-canonical cWW pairs | geometric IL_6JDV_001 IL_77658.1 | |
| IL_6YAL_030 | 1/2/589:596, 1/2/626:627 | SSU/LSU pseudoknot | homologous IL_4V88_413 NA | |
| IL_6YAL_031 | 1/2/596:598, 1/2/625:626 | Single bulged U | geometric IL_5TBW_146 NA | |
| IL_6YAL_032 | 1/2/601:607, 1/2/614:622 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_6YAL_033 | 1/2/653:655, 1/2/1158:1160 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_87907.2 | |
| IL_6YAL_034 | 1/2/655:661, 1/2/1157:1158 | No text annotation | geometric IL_4V88_416 NA | |
| IL_6YAL_035 | 1/2/663:665, 1/2/1026:1028 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_6YAL_036 | 1/2/666:670, 1/2/1021:1025 | tSH-tHW-tHS | homologous IL_4V88_418 NA | |
| IL_6YAL_037 | 1/2/741:748, 1/2/788:792 | No text annotation | ||
| IL_6YAL_038 | 1/2/748:751, 1/2/785:788 | Tandem non-canonical cWW pairs | geometric IL_1MFQ_004 IL_85033.2 | |
| IL_6YAL_039 | 1/2/798:799, 1/2/856:859 | Major groove minor groove platform; mini C-loop | homologous IL_4V88_423 NA | |
| IL_6YAL_040 | 1/2/801:803, 1/2/852:854 | Isolated non-canonical cWW pair | homologous IL_4V88_424 NA | |
| IL_6YAL_108 | 1/2/803:811, 1/2/845:852 | No text annotation | homologous IL_8CRE_430 IL_59049.1 | |
| IL_6YAL_042 | 1/2/869:870, 1/2/907:910 | No text annotation | ||
| IL_6YAL_043 | 1/2/870:872, 1/2/906:907 | Single stack bend | geometric IL_7KGA_003 IL_90729.1 | |
| IL_6YAL_044 | 1/2/872:875, 1/2/903:906 | No text annotation | ||
| IL_6YAL_045 | 1/2/918:919, 1/2/1015:1018 | Major groove platform; stack outside cWW | geometric IL_4V88_428 NA | |
| IL_6YAL_100 | 1/2/921:922, 1/2/1011:1013 | Single bulged U | geometric IL_6UFH_004 IL_89505.4 | |
| IL_6YAL_047 | 1/2/924:927, 1/2/1006:1009 | Tandem non-canonical cWW pairs | homologous IL_4V88_430 NA | |
| IL_6YAL_048 | 1/2/927:931, 1/2/1003:1006 | Tandem non-canonical cWW pairs | geometric IL_4V88_431 NA | |
| IL_6YAL_049 | 1/2/938:941, 1/2/977:980 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_6YAL_050 | 1/2/948:952, 1/2/963:970 | Kink-turn | homologous IL_4V88_434 NA | |
| IL_6YAL_051 | 1/2/1038:1043, 1/2/1067:1069 | Other IL | homologous IL_4V88_435 NA | |
| IL_6YAL_052 | 1/2/1043:1047, 1/2/1063:1067 | tSH-tHW-tHS | geometric IL_5J7L_037 IL_17136.7 | |
| IL_6YAL_053 | 1/2/1087:1089, 1/2/1148:1154 | No text annotation | homologous IL_4V88_437 NA | |
| IL_6YAL_054 | 1/2/1094:1097, 1/2/1127:1130 | Tandem non-canonical cWW pairs | homologous IL_4V88_438 NA | |
| IL_6YAL_101 | 1/2/1094:1099, 1/2/1125:1130 | No text annotation | geometric IL_5TBW_476 NA | |
| IL_6YAL_055 | 1/2/1097:1099, 1/2/1125:1127 | Isolated cWH basepair | geometric IL_2H1M_003 IL_10167.5 | |
| IL_6YAL_056 | 1/2/1104:1106, 1/2/1119:1120 | Minor groove platform | geometric IL_5TBW_039 NA | |
| IL_6YAL_057 | 1/2/1164:1171, 1/2/1182:1187 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_6YAL_058 | 1/2/1199:1200, 1/2/1689:1691 | Single bulged A | homologous IL_4V88_441 NA | |
| IL_6YAL_059 | 1/2/1202:1204, 1/2/1686:1687 | Single bulged G | homologous IL_4V88_442 NA | |
| IL_6YAL_060 | 1/2/1210:1213, 1/2/1676:1680 | C-loop | homologous IL_4V88_443 NA | |
| IL_6YAL_061 | 1/2/1226:1228, 1/2/1521:1523 | Isolated non-canonical cWW pair | homologous IL_4V88_444 NA | |
| IL_6YAL_062 | 1/2/1231:1232, 1/2/1516:1518 | Minor groove platform | homologous IL_4V88_445 NA | |
| IL_6YAL_063 | 1/2/1266:1268, 1/2/1506:1507 | Single stack bend | geometric IL_7A0S_022 IL_90729.1 | |
| IL_6YAL_064 | 1/2/1277:1283, 1/2/1310:1312 | No text annotation | ||
| IL_6YAL_102 | 1/2/1277:1286, 1/2/1305:1312 | No text annotation | homologous IL_8P9A_470 IL_28304.1 | |
| IL_6YAL_065 | 1/2/1283:1286, 1/2/1305:1310 | No text annotation | ||
| IL_6YAL_066 | 1/2/1287:1289, 1/2/1302:1304 | No text annotation | homologous IL_4V88_448 NA | |
| IL_6YAL_067 | 1/2/1321:1323, 1/2/1498:1499 | Single bulged U | homologous IL_4V88_449 NA | |
| IL_6YAL_068 | 1/2/1325:1329, 1/2/1494:1496 | Isolated cWS basepair | geometric IL_4LFB_044 IL_76319.5 | |
| IL_6YAL_103 | 1/2/1325:1331, 1/2/1488:1496 | No text annotation | homologous IL_8P9A_439 IL_86012.1 | |
| IL_6YAL_069 | 1/2/1329:1331, 1/2/1488:1494 | Minor groove platform with extra cWW | homologous IL_4V88_451 NA | |
| IL_6YAL_070 | 1/2/1333:1334, 1/2/1484:1486 | Single bulged A | homologous IL_4V88_452 NA | |
| IL_6YAL_071 | 1/2/1343:1345, 1/2/1376:1378 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_6YAL_072 | 1/2/1359:1361, 1/2/1370:1371 | Minor groove platform | geometric IL_5TBW_039 NA | |
| IL_6YAL_073 | 1/2/1391:1395, 1/2/1443:1446 | Tandem non-canonical cWW pairs | geometric IL_6JDV_002 IL_85033.2 | |
| IL_6YAL_074 | 1/2/1398:1401, 1/2/1437:1440 | Minor groove platform | homologous IL_4V88_456 NA | |
| IL_6YAL_075 | 1/2/1404:1407, 1/2/1430:1434 | No text annotation | ||
| IL_6YAL_104 | 1/2/1404:1409, 1/2/1429:1434 | No text annotation | ||
| IL_6YAL_076 | 1/2/1407:1409, 1/2/1429:1430 | No text annotation | ||
| IL_6YAL_077 | 1/2/1411:1413, 1/2/1425:1427 | No text annotation | ||
| IL_6YAL_078 | 1/2/1413:1415, 1/2/1424:1425 | Multiple bulged bases | geometric IL_1R3E_002 IL_84476.1 | |
| IL_6YAL_079 | 1/2/1449:1452, 1/2/1466:1471 | No text annotation | ||
| IL_6YAL_080 | 1/2/1532:1534, 1/2/1589:1591 | Isolated non-canonical cWW pair | geometric IL_3GM7_002 IL_87907.2 | |
| IL_6YAL_106 | 1/2/1536:1545, 1/2/1577:1587 | No text annotation | ||
| IL_6YAL_081 | 1/2/1545:1553, 1/2/1572:1577 | No text annotation | ||
| IL_6YAL_082 | 1/2/1555:1557, 1/2/1568:1570 | Isolated non-canonical cWW pair | geometric IL_5TBW_016 NA | |
| IL_6YAL_083 | 1/2/1599:1605, 1/2/1624:1630 | No text annotation | homologous IL_8C3A_469 NA | |
| IL_6YAL_084 | 1/2/1695:1697, 1/2/1827:1830 | No text annotation | geometric IL_4V88_463 NA | |
| IL_6YAL_085 | 1/2/1697:1700, 1/2/1823:1827 | No text annotation | homologous IL_8C3A_471 NA | |
| IL_6YAL_086 | 1/2/1701:1703, 1/2/1820:1822 | Isolated non-canonical cWW pair | geometric IL_4P3T_006 NA | |
| IL_6YAL_087 | 1/2/1703:1708, 1/2/1814:1820 | No text annotation | ||
| IL_6YAL_088 | 1/2/1709:1711, 1/2/1811:1813 | Isolated non-canonical cWW pair | homologous IL_4V88_467 NA | |
| IL_6YAL_089 | 1/2/1712:1715, 1/2/1807:1810 | Double sheared | geometric IL_4LFB_060 IL_09705.15 | |
| IL_6YAL_090 | 1/2/1715:1717, 1/2/1806:1807 | No text annotation | ||
| IL_6YAL_091 | 1/2/1724:1726, 1/2/1797:1799 | Isolated non-canonical cWW pair | homologous IL_4V88_470 NA | |
| IL_6YAL_092 | 1/2/1728:1731, 1/2/1792:1795 | Double sheared | homologous IL_4V88_471 NA | |
| IL_6YAL_093 | 1/2/1734:1736, 1/2/1787:1789 | Isolated non-canonical cWW pair | geometric IL_3BNN_005 IL_28037.2 | |
| IL_6YAL_094 | 1/2/1737:1741, 1/2/1782:1786 | Triple sheared | homologous IL_4V88_474 NA | |
| IL_6YAL_095 | 1/2/1745:1746, 1/2/1776:1778 | Multiple bulged bases | geometric IL_7Q82_001 NA | |
| IL_6YAL_096 | 1/2/1746:1747, 1/2/1774:1776 | Single stack bend | geometric IL_7KGA_003 IL_90729.1 | |
| IL_6YAL_097 | 1/2/1747:1748, 1/2/1772:1774 | Single stack bend | geometric IL_7A0S_005 IL_90729.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6YAL_025 | No text annotation | ||
| IL_6YAL_041 | No text annotation | ||
| IL_6YAL_046 | Tandem non-canonical cWW pairs | ||
| IL_6YAL_105 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6YAL_001 | 1/2/40:41, 1/2/471:477, 1/2/502:504 | No text annotation | geometric J3_4V88_078 NA | |
| J3_6YAL_014 | 1/2/40:47, 1/2/469:477, 1/2/502:504 | No text annotation | homologous J3_8P9A_069 J3_46317.4 | |
| J3_6YAL_015 | 1/2/220:235, 1/2/274:279, 1/2/286:289 | No text annotation | ||
| J3_6YAL_018 | 1/2/672:674, 1/2/914:918, 1/2/1018:1019 | No text annotation | geometric J3_8P9A_071 J3_56052.5 | |
| J3_6YAL_019 | 1/2/672:674, 1/2/914:919, 1/2/1015:1019 | No text annotation | homologous J3_8P9A_072 J3_17385.4 | |
| J3_6YAL_003 | 1/2/812:815, 1/2/825:827, 1/2/839:844 | No text annotation | homologous J3_4V88_032 NA | |
| J3_6YAL_004 | 1/2/934:937, 1/2/981:989, 1/2/996:1000 | No text annotation | homologous J3_4V88_033 NA | |
| J3_6YAL_005 | 1/2/1090:1092, 1/2/1132:1136, 1/2/1143:1147 | No text annotation | ||
| J3_6YAL_006 | 1/2/1214:1217, 1/2/1640:1646, 1/2/1668:1675 | No text annotation | homologous J3_4V88_035 NA | |
| J3_6YAL_007 | 1/2/1221:1224, 1/2/1525:1527, 1/2/1633:1636 | No text annotation | homologous J3_8C3A_039 NA | |
| J3_6YAL_008 | 1/2/1233:1240, 1/2/1251:1262, 1/2/1511:1515 | No text annotation | homologous J3_8C3A_040 NA | |
| J3_6YAL_009 | 1/2/1268:1273, 1/2/1316:1320, 1/2/1500:1506 | No text annotation | homologous J3_4V88_038 NA | |
| J3_6YAL_010 | 1/2/1336:1341, 1/2/1380:1385, 1/2/1477:1482 | No text annotation | homologous J3_4V88_039 NA | |
| J3_6YAL_011 | 1/2/1346:1347, 1/2/1356:1359, 1/2/1371:1375 | No text annotation | homologous J3_8P9A_081 J3_76043.3 | |
| J3_6YAL_012 | 1/2/1387:1391, 1/2/1446:1449, 1/2/1471:1475 | No text annotation | ||
| J3_6YAL_017 | 1/2/1387:1391, 1/2/1446:1452, 1/2/1466:1475 | No text annotation | ||
| J3_6YAL_013 | 1/2/1527:1531, 1/2/1592:1599, 1/2/1630:1633 | No text annotation | homologous J3_4V88_041 NA | |
| J4_6YAL_001 | 1/1/8:11, 1/1/25:27, 1/1/43:49, 1/1/65:66 | No text annotation | ||
| J4_6YAL_002 | 1/2/98:106, 1/2/345:347, 1/2/395:399, 1/2/421:422 | No text annotation | homologous J4_8P9A_021 J4_15241.1 | |
| J4_6YAL_003 | 1/2/661:663, 1/2/1028:1033, 1/2/1074:1085, 1/2/1156:1157 | No text annotation | homologous J4_8P9A_022 J4_61885.6 | |
| J5_6YAL_005 | 1/2/30:34, 1/2/511:517, 1/2/548:553, 1/2/582:585, 1/2/631:634 | No text annotation | homologous J5_8CRE_018 J5_80702.1 | |
| J5_6YAL_006 | 1/2/30:34, 1/2/511:517, 1/2/548:555, 1/2/575:585, 1/2/631:634 | No text annotation | ||
| J5_6YAL_003 | 1/2/53:56, 1/2/89:96, 1/2/424:426, 1/2/447:449, 1/2/460:464 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_6YAL_004 | 1/2/675:680, 1/2/734:740, 1/2/793:796, 1/2/861:869, 1/2/910:913 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6YAL_002 | No text annotation | ||
| J3_6YAL_016 | No text annotation | ||
| J5_6YAL_001 | No text annotation | ||
| J5_6YAL_002 | No text annotation |
Coloring options: