8XXM Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8XXM_001 | 1/S2/7:17 | No text annotation | homologous HL_8C3A_192 NA | |
| HL_8XXM_002 | 1/S2/69:80 | No text annotation | geometric HL_361D_002 HL_13963.3 | |
| HL_8XXM_003 | 1/S2/156:162 | GNRA related | homologous HL_8C3A_194 NA | |
| HL_8XXM_004 | 1/S2/195:204 | No text annotation | ||
| HL_8XXM_005 | 1/S2/288:295 | T-loop with 1 bulged base | homologous HL_4V88_191 NA | |
| HL_8XXM_006 | 1/S2/322:329 | No text annotation | ||
| HL_8XXM_007 | 1/S2/377:387 | No text annotation | ||
| HL_8XXM_008 | 1/S2/416:421 | No text annotation | homologous HL_4V88_194 NA | |
| HL_8XXM_009 | 1/S2/441:452 | No text annotation | homologous HL_8C3A_201 NA | |
| HL_8XXM_010 | 1/S2/462:467 | UNCG | homologous HL_8C3A_202 NA | |
| HL_8XXM_011 | 1/S2/498:504 | No text annotation | homologous HL_8C3A_203 NA | |
| HL_8XXM_012 | 1/S2/539:544 | No text annotation | ||
| HL_8XXM_013 | 1/S2/569:581 | No text annotation | homologous HL_8C3A_205 NA | |
| HL_8XXM_014 | 1/S2/618:623 | GNRA variation | homologous HL_8C3A_206 NA | |
| HL_8XXM_016 | 1/S2/820:828 | No text annotation | homologous HL_4V88_203 NA | |
| HL_8XXM_017 | 1/S2/833:841 | No text annotation | ||
| HL_8XXM_018 | 1/S2/885:901 | tRNA D-loop | geometric HL_7EQJ_004 HL_20811.4 | |
| HL_8XXM_019 | 1/S2/957:966 | No text annotation | homologous HL_8C3A_211 NA | |
| HL_8XXM_020 | 1/S2/994:999 | GNRA | homologous HL_4V88_207 NA | |
| HL_8XXM_021 | 1/S2/1054:1064 | No text annotation | homologous HL_4V88_208 NA | |
| HL_8XXM_022 | 1/S2/1113:1120 | No text annotation | ||
| HL_8XXM_023 | 1/S2/1141:1146 | GNRA | homologous HL_8C3A_215 NA | |
| HL_8XXM_024 | 1/S2/1178:1183 | GNRA | homologous HL_8C3A_216 NA | |
| HL_8XXM_025 | 1/S2/1245:1254 | No text annotation | homologous HL_4V88_212 NA | |
| HL_8XXM_026 | 1/S2/1295:1304 | Anticodon loop related | homologous HL_8C3A_218 NA | |
| HL_8XXM_027 | 1/S2/1353:1358 | GNRA | homologous HL_8C3A_219 NA | |
| HL_8XXM_028 | 1/S2/1366:1373 | T-loop related | homologous HL_8C3A_220 NA | |
| HL_8XXM_029 | 1/S2/1416:1424 | No text annotation | ||
| HL_8XXM_030 | 1/S2/1460:1466 | No text annotation | homologous HL_8C3A_222 NA | |
| HL_8XXM_031 | 1/S2/1565:1570 | GNRA | homologous HL_8C3A_223 NA | |
| HL_8XXM_032 | 1/S2/1614:1625 | No text annotation | homologous HL_4V88_219 NA | |
| HL_8XXM_033 | 1/S2/1658:1666 | No text annotation | homologous HL_8C3A_225 NA | |
| HL_8XXM_037 | 1/S2/1750:1784 | No text annotation | ||
| HL_8XXM_035 | 1/S2/1847:1852 | GNRA variation | homologous HL_8C3A_227 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8XXM_015 | No text annotation | ||
| HL_8XXM_036 | No text annotation | ||
| HL_8XXM_034 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8XXM_001 | 1/S2/23:25, 1/S2/649:651 | Isolated non-canonical cWW pair | geometric IL_7A0S_020 IL_87907.2 | |
| IL_8XXM_002 | 1/S2/34:36, 1/S2/519:521 | Isolated non-canonical cWW pair | homologous IL_8C3A_393 NA | |
| IL_8XXM_003 | 1/S2/37:40, 1/S2/514:518 | Double sheared | geometric IL_4WF9_016 IL_09705.15 | |
| IL_8XXM_004 | 1/S2/41:47, 1/S2/479:481 | No text annotation | homologous IL_8C3A_395 NA | |
| IL_8XXM_005 | 1/S2/49:51, 1/S2/476:477 | Minor groove platform | homologous IL_8C3A_396 NA | |
| IL_8XXM_006 | 1/S2/57:62, 1/S2/86:88 | No text annotation | homologous IL_4V88_389 NA | |
| IL_8XXM_007 | 1/S2/63:68, 1/S2/81:85 | No text annotation | homologous IL_4V88_390 NA | |
| IL_8XXM_008 | 1/S2/108:110, 1/S2/351:353 | Isolated non-canonical cWW pair | geometric IL_1ZX7_004 NA | |
| IL_8XXM_009 | 1/S2/110:112, 1/S2/349:351 | Isolated non-canonical cWW pair | geometric IL_4WF9_042 IL_87907.2 | |
| IL_8XXM_010 | 1/S2/112:115, 1/S2/348:349 | Multiple bulged bases | homologous IL_8C3A_400 NA | |
| IL_8XXM_011 | 1/S2/116:121, 1/S2/343:347 | No text annotation | homologous IL_8C3A_401 NA | |
| IL_8XXM_012 | 1/S2/123:124, 1/S2/339:341 | Minor groove platform | geometric IL_4V88_388 NA | |
| IL_8XXM_014 | 1/S2/145:151, 1/S2/167:174 | No text annotation | homologous IL_8C3A_402 NA | |
| IL_8XXM_015 | 1/S2/152:154, 1/S2/164:166 | Isolated cWH basepair | geometric IL_3R1C_032 NA | |
| IL_8XXM_016 | 1/S2/188:192, 1/S2/207:211 | Double sheared with non-canonical cWW | geometric IL_4WFL_001 IL_17948.2 | |
| IL_8XXM_017 | 1/S2/216:219, 1/S2/302:309 | No text annotation | ||
| IL_8XXM_019 | 1/S2/312:314, 1/S2/336:337 | Single bulged A | homologous IL_4V88_399 NA | |
| IL_8XXM_020 | 1/S2/317:319, 1/S2/332:333 | Single stack bend | geometric IL_5TBW_009 NA | |
| IL_8XXM_021 | 1/S2/359:364, 1/S2/396:403 | Kink-turn with non-sequential stacking | homologous IL_8C3A_410 NA | |
| IL_8XXM_022 | 1/S2/366:371, 1/S2/393:394 | No text annotation | homologous IL_8C3A_411 NA | |
| IL_8XXM_023 | 1/S2/411:413, 1/S2/424:429 | No text annotation | homologous IL_8C3A_412 NA | |
| IL_8XXM_024 | 1/S2/437:439, 1/S2/454:456 | Isolated cWH basepair | homologous IL_8C3A_413 NA | |
| IL_8XXM_025 | 1/S2/459:461, 1/S2/468:470 | Isolated non-canonical cWW pair | homologous IL_8C3A_414 NA | |
| IL_8XXM_026 | 1/S2/487:489, 1/S2/511:512 | Single bulged U | homologous IL_4V88_407 NA | |
| IL_8XXM_027 | 1/S2/491:495, 1/S2/508:509 | C-loop | homologous IL_8C3A_416 NA | |
| IL_8XXM_028 | 1/S2/495:496, 1/S2/506:508 | Single bulged G | geometric IL_5J7L_019 IL_00225.14 | |
| IL_8XXM_029 | 1/S2/527:530, 1/S2/554:558 | No text annotation | ||
| IL_8XXM_030 | 1/S2/532:534, 1/S2/549:552 | No text annotation | geometric IL_4N0T_004 IL_99358.1 | |
| IL_8XXM_031 | 1/S2/535:537, 1/S2/546:548 | Multiple bulged bases | geometric IL_4V88_392 NA | |
| IL_8XXM_033 | 1/S2/566:569, 1/S2/581:584 | Tandem non-canonical cWW pairs | geometric IL_5C5W_003 NA | |
| IL_8XXM_034 | 1/S2/599:606, 1/S2/636:637 | SSU/LSU pseudoknot | geometric IL_4V88_413 NA | |
| IL_8XXM_035 | 1/S2/606:608, 1/S2/635:636 | Single bulged U | homologous IL_8C3A_424 NA | |
| IL_8XXM_036 | 1/S2/611:617, 1/S2/624:632 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_8XXM_037 | 1/S2/663:665, 1/S2/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_87907.2 | |
| IL_8XXM_038 | 1/S2/665:671, 1/S2/1161:1162 | No text annotation | geometric IL_4LFB_022 IL_38186.6 | |
| IL_8XXM_039 | 1/S2/673:675, 1/S2/1030:1032 | Isolated non-canonical cWW pair | homologous IL_8C3A_427 NA | |
| IL_8XXM_040 | 1/S2/676:680, 1/S2/1025:1029 | tSH-tHW-tHS | homologous IL_8C3A_428 NA | |
| IL_8XXM_041 | 1/S2/747:749, 1/S2/794:795 | Single stack bend | geometric IL_5J7L_249 IL_90729.1 | |
| IL_8XXM_042 | 1/S2/802:803, 1/S2/860:863 | Major groove minor groove platform; mini C-loop | homologous IL_4V88_423 NA | |
| IL_8XXM_043 | 1/S2/805:807, 1/S2/856:858 | Isolated non-canonical cWW pair | homologous IL_8C3A_431 NA | |
| IL_8XXM_044 | 1/S2/807:815, 1/S2/849:856 | No text annotation | homologous IL_4V88_425 NA | |
| IL_8XXM_045 | 1/S2/874:876, 1/S2/910:912 | Isolated non-canonical cWW pair | geometric IL_4E48_003 IL_87907.2 | |
| IL_8XXM_046 | 1/S2/877:879, 1/S2/907:909 | Isolated non-canonical cWW pair | geometric IL_5J7L_061 IL_87907.2 | |
| IL_8XXM_049 | 1/S2/922:923, 1/S2/1019:1022 | Major groove platform; stack outside cWW | homologous IL_4V88_428 NA | |
| IL_8XXM_050 | 1/S2/925:926, 1/S2/1015:1017 | Single bulged U | geometric IL_3NDB_005 IL_89505.4 | |
| IL_8XXM_051 | 1/S2/928:931, 1/S2/1010:1013 | Tandem non-canonical cWW pairs | homologous IL_8C3A_437 NA | |
| IL_8XXM_052 | 1/S2/931:935, 1/S2/1007:1010 | Tandem non-canonical cWW pairs | geometric IL_4V88_431 NA | |
| IL_8XXM_100 | 1/S2/943:945, 1/S2/981:983 | Isolated non-canonical cWW pair | geometric IL_4V88_472 NA | |
| IL_8XXM_054 | 1/S2/952:956, 1/S2/967:974 | Kink-turn | homologous IL_4V88_434 NA | |
| IL_8XXM_055 | 1/S2/1042:1047, 1/S2/1071:1073 | No text annotation | homologous IL_8C3A_441 NA | |
| IL_8XXM_056 | 1/S2/1047:1051, 1/S2/1067:1071 | tSH-tHW-tHS | geometric IL_4V88_436 NA | |
| IL_8XXM_057 | 1/S2/1091:1093, 1/S2/1152:1158 | No text annotation | homologous IL_8C3A_443 NA | |
| IL_8XXM_058 | 1/S2/1098:1101, 1/S2/1131:1134 | Tandem non-canonical cWW pairs | geometric IL_4V88_438 NA | |
| IL_8XXM_059 | 1/S2/1101:1103, 1/S2/1129:1131 | Isolated non-canonical cWW pair | geometric IL_4V9F_105 IL_87907.2 | |
| IL_8XXM_060 | 1/S2/1108:1110, 1/S2/1123:1124 | Minor groove platform | geometric IL_4V88_412 NA | |
| IL_8XXM_061 | 1/S2/1168:1175, 1/S2/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_8XXM_062 | 1/S2/1203:1204, 1/S2/1694:1696 | Single bulged A | homologous IL_8C3A_447 NA | |
| IL_8XXM_063 | 1/S2/1206:1208, 1/S2/1691:1692 | Single bulged G | homologous IL_4V88_442 NA | |
| IL_8XXM_064 | 1/S2/1214:1217, 1/S2/1681:1685 | C-loop | homologous IL_4V88_443 NA | |
| IL_8XXM_065 | 1/S2/1230:1232, 1/S2/1526:1528 | Isolated non-canonical cWW pair | homologous IL_4V88_444 NA | |
| IL_8XXM_066 | 1/S2/1235:1236, 1/S2/1521:1523 | Minor groove platform | homologous IL_4V88_445 NA | |
| IL_8XXM_067 | 1/S2/1270:1272, 1/S2/1510:1512 | Isolated non-canonical cWW pair | homologous IL_8C3A_452 NA | |
| IL_8XXM_107 | 1/S2/1282:1287, 1/S2/1314:1315 | No text annotation | geometric IL_8P9A_236 IL_92634.2 | |
| IL_8XXM_108 | 1/S2/1282:1290, 1/S2/1309:1315 | No text annotation | ||
| IL_8XXM_069 | 1/S2/1287:1290, 1/S2/1309:1314 | No text annotation | ||
| IL_8XXM_070 | 1/S2/1291:1293, 1/S2/1306:1308 | No text annotation | homologous IL_4V88_448 NA | |
| IL_8XXM_071 | 1/S2/1325:1327, 1/S2/1502:1503 | Single bulged U | homologous IL_8C3A_455 NA | |
| IL_8XXM_102 | 1/S2/1329:1333, 1/S2/1498:1500 | No text annotation | geometric IL_8C3A_456 NA | |
| IL_8XXM_103 | 1/S2/1329:1335, 1/S2/1492:1500 | No text annotation | homologous IL_8P9A_439 IL_86012.1 | |
| IL_8XXM_073 | 1/S2/1333:1335, 1/S2/1492:1498 | Minor groove platform with extra cWW | geometric IL_4V88_451 NA | |
| IL_8XXM_074 | 1/S2/1337:1338, 1/S2/1488:1490 | Single bulged A | homologous IL_8C3A_458 NA | |
| IL_8XXM_075 | 1/S2/1347:1349, 1/S2/1380:1382 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_8XXM_076 | 1/S2/1363:1365, 1/S2/1374:1375 | Minor groove platform | homologous IL_8C3A_460 NA | |
| IL_8XXM_077 | 1/S2/1395:1399, 1/S2/1447:1450 | No text annotation | homologous IL_8C3A_461 NA | |
| IL_8XXM_078 | 1/S2/1402:1405, 1/S2/1441:1444 | Minor groove platform | homologous IL_4V88_456 NA | |
| IL_8XXM_079 | 1/S2/1408:1409, 1/S2/1432:1438 | Multiple bulged bases | geometric IL_8C3A_400 NA | |
| IL_8XXM_080 | 1/S2/1412:1413, 1/S2/1427:1429 | Single bulged G | geometric IL_5J7L_019 IL_00225.14 | |
| IL_8XXM_081 | 1/S2/1537:1539, 1/S2/1594:1596 | Isolated non-canonical cWW pair | geometric IL_2O3Y_001 IL_28037.2 | |
| IL_8XXM_104 | 1/S2/1541:1550, 1/S2/1582:1592 | No text annotation | ||
| IL_8XXM_082 | 1/S2/1550:1558, 1/S2/1577:1582 | 180 degree turn | geometric IL_5J7L_055 IL_11344.2 | |
| IL_8XXM_083 | 1/S2/1560:1562, 1/S2/1573:1575 | Isolated non-canonical cWW pair | homologous IL_8C3A_468 NA | |
| IL_8XXM_084 | 1/S2/1604:1610, 1/S2/1629:1635 | No text annotation | homologous IL_8C3A_469 NA | |
| IL_8XXM_085 | 1/S2/1700:1702, 1/S2/1833:1836 | No text annotation | geometric IL_5J7L_058 IL_61438.4 | |
| IL_8XXM_086 | 1/S2/1702:1705, 1/S2/1829:1833 | No text annotation | homologous IL_8C3A_471 NA | |
| IL_8XXM_087 | 1/S2/1706:1708, 1/S2/1826:1828 | Isolated non-canonical cWW pair | geometric IL_4E48_002 IL_87907.2 | |
| IL_8XXM_088 | 1/S2/1708:1711, 1/S2/1822:1826 | Tandem non-canonical cWW pairs | geometric IL_1MFQ_004 IL_85033.2 | |
| IL_8XXM_089 | 1/S2/1714:1716, 1/S2/1817:1819 | Isolated non-canonical cWW pair | homologous IL_4V88_467 NA | |
| IL_8XXM_090 | 1/S2/1717:1720, 1/S2/1813:1816 | Double sheared | geometric IL_4XWF_001 IL_09705.15 | |
| IL_8XXM_091 | 1/S2/1720:1723, 1/S2/1810:1813 | Isolated non-canonical cWW pair | geometric IL_6TFF_003 IL_57744.1 | |
| IL_8XXM_105 | 1/S2/1720:1726, 1/S2/1808:1813 | No text annotation | ||
| IL_8XXM_092 | 1/S2/1723:1726, 1/S2/1808:1810 | Other IL | geometric IL_5TBW_064 NA | |
| IL_8XXM_106 | 1/S2/1727:1731, 1/S2/1803:1807 | Triple non-canonical cWW pairs | geometric IL_5BTM_001 IL_49751.4 | |
| IL_8XXM_093 | 1/S2/1729:1731, 1/S2/1803:1805 | Isolated non-canonical cWW pair | homologous IL_8C3A_477 NA | |
| IL_8XXM_094 | 1/S2/1733:1736, 1/S2/1798:1801 | Double sheared | homologous IL_8C3A_478 NA | |
| IL_8XXM_095 | 1/S2/1739:1741, 1/S2/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4E48_004 IL_87907.2 | |
| IL_8XXM_096 | 1/S2/1742:1746, 1/S2/1788:1792 | Triple sheared | homologous IL_8C3A_480 NA | |
| IL_8XXM_098 | 1/S2/1750:1755, 1/S2/1777:1784 | No text annotation | ||
| IL_8XXM_099 | 1/S2/1755:1759, 1/S2/1772:1777 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8XXM_013 | No text annotation | ||
| IL_8XXM_018 | No text annotation | ||
| IL_8XXM_032 | Isolated cWH basepair | ||
| IL_8XXM_047 | Isolated non-canonical cWW pair | ||
| IL_8XXM_048 | No text annotation | ||
| IL_8XXM_053 | Tandem non-canonical cWW pairs | ||
| IL_8XXM_068 | No text annotation | ||
| IL_8XXM_101 | No text annotation | ||
| IL_8XXM_072 | Tandem non-canonical cWW pairs | ||
| IL_8XXM_097 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8XXM_011 | 1/S2/40:41, 1/S2/481:487, 1/S2/512:514 | No text annotation | geometric J3_8C3A_082 NA | |
| J3_8XXM_012 | 1/S2/40:47, 1/S2/479:487, 1/S2/512:514 | No text annotation | homologous J3_8P9A_069 J3_46317.4 | |
| J3_8XXM_016 | 1/S2/682:684, 1/S2/918:922, 1/S2/1022:1023 | No text annotation | geometric J3_8P9A_071 J3_56052.5 | |
| J3_8XXM_017 | 1/S2/682:684, 1/S2/918:923, 1/S2/1019:1023 | No text annotation | homologous J3_8P9A_072 J3_17385.4 | |
| J3_8XXM_001 | 1/S2/816:819, 1/S2/829:831, 1/S2/843:848 | No text annotation | homologous J3_4V88_032 NA | |
| J3_8XXM_002 | 1/S2/938:941, 1/S2/985:993, 1/S2/1000:1004 | No text annotation | homologous J3_4V88_033 NA | |
| J3_8XXM_003 | 1/S2/1094:1096, 1/S2/1136:1140, 1/S2/1147:1151 | No text annotation | ||
| J3_8XXM_004 | 1/S2/1218:1221, 1/S2/1645:1651, 1/S2/1673:1680 | No text annotation | homologous J3_4V88_035 NA | |
| J3_8XXM_005 | 1/S2/1225:1228, 1/S2/1530:1532, 1/S2/1638:1641 | No text annotation | homologous J3_8C3A_039 NA | |
| J3_8XXM_006 | 1/S2/1237:1244, 1/S2/1255:1266, 1/S2/1516:1520 | No text annotation | homologous J3_8C3A_040 NA | |
| J3_8XXM_007 | 1/S2/1272:1277, 1/S2/1320:1324, 1/S2/1504:1510 | No text annotation | homologous J3_8C3A_041 NA | |
| J3_8XXM_008 | 1/S2/1340:1345, 1/S2/1384:1389, 1/S2/1481:1486 | No text annotation | homologous J3_8P9A_080 J3_99563.1 | |
| J3_8XXM_015 | 1/S2/1350:1351, 1/S2/1360:1363, 1/S2/1375:1379 | No text annotation | homologous J3_8C3A_085 NA | |
| J3_8XXM_009 | 1/S2/1391:1395, 1/S2/1450:1456, 1/S2/1470:1479 | No text annotation | ||
| J3_8XXM_010 | 1/S2/1532:1536, 1/S2/1597:1604, 1/S2/1635:1638 | No text annotation | homologous J3_8C3A_044 NA | |
| J4_8XXM_001 | 1/S2/98:106, 1/S2/355:357, 1/S2/405:409, 1/S2/431:432 | No text annotation | homologous J4_8P9A_021 J4_15241.1 | |
| J4_8XXM_002 | 1/S2/671:673, 1/S2/1032:1037, 1/S2/1078:1089, 1/S2/1160:1161 | No text annotation | homologous J4_8C3A_022 NA | |
| J5_8XXM_001 | 1/S2/30:34, 1/S2/521:527, 1/S2/558:565, 1/S2/585:595, 1/S2/641:644 | No text annotation | ||
| J5_8XXM_002 | 1/S2/53:56, 1/S2/89:96, 1/S2/434:436, 1/S2/457:459, 1/S2/470:474 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_8XXM_003 | 1/S2/124:129, 1/S2/183:185, 1/S2/214:215, 1/S2/310:312, 1/S2/337:339 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8XXM_013 | No text annotation | ||
| J3_8XXM_014 | No text annotation |
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