9BLN Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9BLN_001 | 1/A/7:17 | No text annotation | homologous HL_8C3A_192 NA | |
| HL_9BLN_003 | 1/A/156:162 | GNRA related | homologous HL_8C3A_194 NA | |
| HL_9BLN_005 | 1/A/288:295 | T-loop with 1 bulged base | homologous HL_4V88_191 NA | |
| HL_9BLN_007 | 1/A/377:387 | No text annotation | geometric HL_1KH6_003 HL_33487.1 | |
| HL_9BLN_008 | 1/A/416:421 | No text annotation | homologous HL_4V88_194 NA | |
| HL_9BLN_009 | 1/A/441:452 | No text annotation | homologous HL_8C3A_201 NA | |
| HL_9BLN_010 | 1/A/462:467 | UNCG | homologous HL_8C3A_202 NA | |
| HL_9BLN_011 | 1/A/498:504 | No text annotation | homologous HL_4V88_197 NA | |
| HL_9BLN_035 | 1/A/533:551 | No text annotation | ||
| HL_9BLN_013 | 1/A/569:581 | No text annotation | homologous HL_8C3A_205 NA | |
| HL_9BLN_014 | 1/A/618:623 | GNRA variation | homologous HL_8C3A_206 NA | |
| HL_9BLN_015 | 1/A/820:828 | No text annotation | homologous HL_4V88_203 NA | |
| HL_9BLN_016 | 1/A/833:841 | No text annotation | ||
| HL_9BLN_018 | 1/A/957:966 | No text annotation | homologous HL_8C3A_211 NA | |
| HL_9BLN_019 | 1/A/994:999 | GNRA | homologous HL_8C3A_212 NA | |
| HL_9BLN_020 | 1/A/1054:1064 | No text annotation | homologous HL_4V88_208 NA | |
| HL_9BLN_022 | 1/A/1141:1146 | GNRA | homologous HL_8C3A_215 NA | |
| HL_9BLN_023 | 1/A/1178:1183 | GNRA | homologous HL_8C3A_216 NA | |
| HL_9BLN_024 | 1/A/1245:1254 | No text annotation | homologous HL_8C3A_217 NA | |
| HL_9BLN_025 | 1/A/1295:1304 | Anticodon loop related | homologous HL_8C3A_218 NA | |
| HL_9BLN_026 | 1/A/1353:1358 | GNRA | homologous HL_8C3A_219 NA | |
| HL_9BLN_027 | 1/A/1366:1373 | T-loop related | homologous HL_8C3A_220 NA | |
| HL_9BLN_028 | 1/A/1416:1424 | No text annotation | homologous HL_8C3A_221 NA | |
| HL_9BLN_029 | 1/A/1460:1466 | No text annotation | homologous HL_8C3A_222 NA | |
| HL_9BLN_030 | 1/A/1565:1570 | GNRA | homologous HL_8C3A_223 NA | |
| HL_9BLN_031 | 1/A/1614:1625 | No text annotation | homologous HL_4V88_219 NA | |
| HL_9BLN_032 | 1/A/1658:1666 | No text annotation | homologous HL_4V88_220 NA | |
| HL_9BLN_034 | 1/A/1847:1852 | GNRA variation | homologous HL_8C3A_227 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9BLN_002 | No text annotation | ||
| HL_9BLN_004 | No text annotation | ||
| HL_9BLN_006 | No text annotation | ||
| HL_9BLN_012 | No text annotation | ||
| HL_9BLN_017 | No text annotation | ||
| HL_9BLN_021 | No text annotation | ||
| HL_9BLN_036 | No text annotation | ||
| HL_9BLN_033 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9BLN_001 | 1/A/23:25, 1/A/649:651 | Isolated non-canonical cWW pair | geometric IL_3MEI_002 IL_01003.3 | |
| IL_9BLN_003 | 1/A/34:36, 1/A/519:521 | Isolated non-canonical cWW pair | homologous IL_8C3A_393 NA | |
| IL_9BLN_004 | 1/A/37:40, 1/A/514:518 | Double sheared | geometric IL_4WF9_016 IL_58355.2 | |
| IL_9BLN_005 | 1/A/41:47, 1/A/479:481 | No text annotation | homologous IL_4V88_387 NA | |
| IL_9BLN_006 | 1/A/49:51, 1/A/476:477 | Minor groove platform | homologous IL_8C3A_396 NA | |
| IL_9BLN_007 | 1/A/57:62, 1/A/86:88 | No text annotation | homologous IL_4V88_389 NA | |
| IL_9BLN_008 | 1/A/63:68, 1/A/81:85 | No text annotation | homologous IL_4V88_390 NA | |
| IL_9BLN_009 | 1/A/69:72, 1/A/74:80 | No text annotation | ||
| IL_9BLN_010 | 1/A/108:110, 1/A/351:353 | Isolated non-canonical cWW pair | geometric IL_1ZX7_006 IL_71625.3 | |
| IL_9BLN_011 | 1/A/110:112, 1/A/349:351 | Isolated non-canonical cWW pair | geometric IL_4WF9_042 IL_01003.3 | |
| IL_9BLN_012 | 1/A/112:115, 1/A/348:349 | Multiple bulged bases | geometric IL_5WLH_001 IL_71421.2 | |
| IL_9BLN_097 | 1/A/116:121, 1/A/343:347 | No text annotation | homologous IL_8C3A_401 NA | |
| IL_9BLN_014 | 1/A/123:124, 1/A/339:341 | Minor groove platform | geometric IL_4V88_388 NA | |
| IL_9BLN_098 | 1/A/145:151, 1/A/167:174 | No text annotation | homologous IL_8C3A_402 NA | |
| IL_9BLN_099 | 1/A/152:154, 1/A/164:166 | No text annotation | homologous IL_8P9A_384 IL_87720.1 | |
| IL_9BLN_019 | 1/A/216:219, 1/A/302:309 | No text annotation | ||
| IL_9BLN_020 | 1/A/223:288, 1/A/295:298 | No text annotation | ||
| IL_9BLN_021 | 1/A/312:314, 1/A/336:337 | Single bulged A | homologous IL_4V88_399 NA | |
| IL_9BLN_022 | 1/A/317:319, 1/A/332:333 | Single stack bend | geometric IL_5TBW_009 NA | |
| IL_9BLN_023 | 1/A/359:364, 1/A/396:403 | Kink-turn with non-sequential stacking | homologous IL_8C3A_410 NA | |
| IL_9BLN_024 | 1/A/366:371, 1/A/393:394 | No text annotation | homologous IL_8C3A_411 NA | |
| IL_9BLN_025 | 1/A/411:413, 1/A/424:429 | No text annotation | homologous IL_8P9A_393 IL_93336.1 | |
| IL_9BLN_026 | 1/A/437:439, 1/A/454:456 | Isolated cWH basepair | homologous IL_8C3A_413 NA | |
| IL_9BLN_027 | 1/A/459:461, 1/A/468:470 | Isolated non-canonical cWW pair | homologous IL_8C3A_414 NA | |
| IL_9BLN_028 | 1/A/487:489, 1/A/511:512 | Single bulged U | homologous IL_8C3A_415 NA | |
| IL_9BLN_100 | 1/A/491:495, 1/A/508:509 | C-loop | homologous IL_8C3A_416 NA | |
| IL_9BLN_030 | 1/A/495:496, 1/A/506:508 | Single bulged G | homologous IL_8C3A_417 NA | |
| IL_9BLN_031 | 1/A/530:531, 1/A/553:555 | No text annotation | ||
| IL_9BLN_032 | 1/A/533:538, 1/A/544:551 | No text annotation | ||
| IL_9BLN_033 | 1/A/563:565, 1/A/585:592 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_9BLN_034 | 1/A/566:569, 1/A/581:584 | tSH-tHW | geometric IL_5UNE_005 IL_76776.1 | |
| IL_9BLN_035 | 1/A/599:606, 1/A/636:637 | SSU/LSU pseudoknot | homologous IL_8C3A_423 NA | |
| IL_9BLN_036 | 1/A/606:608, 1/A/635:636 | Single bulged U | geometric IL_6UFG_004 IL_97561.3 | |
| IL_9BLN_037 | 1/A/611:617, 1/A/624:632 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_9BLN_038 | 1/A/663:665, 1/A/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_01003.3 | |
| IL_9BLN_039 | 1/A/665:671, 1/A/1161:1162 | No text annotation | homologous IL_8C3A_426 NA | |
| IL_9BLN_040 | 1/A/673:675, 1/A/1030:1032 | Isolated non-canonical cWW pair | homologous IL_8C3A_427 NA | |
| IL_9BLN_041 | 1/A/676:680, 1/A/1025:1029 | tSH-tHW-tHS | homologous IL_8C3A_428 NA | |
| IL_9BLN_042 | 1/A/802:803, 1/A/860:863 | Major groove minor groove platform; mini C-loop | homologous IL_4V88_423 NA | |
| IL_9BLN_043 | 1/A/805:807, 1/A/856:858 | Isolated non-canonical cWW pair | homologous IL_8C3A_431 NA | |
| IL_9BLN_106 | 1/A/807:815, 1/A/849:856 | No text annotation | homologous IL_8CRE_430 IL_59049.2 | |
| IL_9BLN_045 | 1/A/874:876, 1/A/910:912 | Isolated non-canonical cWW pair | geometric IL_1YZ9_002 IL_01003.3 | |
| IL_9BLN_046 | 1/A/877:879, 1/A/907:909 | Isolated non-canonical cWW pair | geometric IL_5TBW_042 NA | |
| IL_9BLN_047 | 1/A/922:923, 1/A/1019:1022 | Major groove platform; stack outside cWW | homologous IL_4V88_428 NA | |
| IL_9BLN_048 | 1/A/925:927, 1/A/1014:1017 | Single bulged G, near cWW | geometric IL_6CZR_128 NA | |
| IL_9BLN_049 | 1/A/928:931, 1/A/1010:1013 | Tandem non-canonical cWW pairs | geometric IL_4V88_430 NA | |
| IL_9BLN_050 | 1/A/931:935, 1/A/1007:1010 | Tandem non-canonical cWW pairs | homologous IL_8C3A_438 NA | |
| IL_9BLN_051 | 1/A/942:945, 1/A/981:984 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_9BLN_052 | 1/A/952:956, 1/A/967:974 | Kink-turn | homologous IL_4V88_434 NA | |
| IL_9BLN_053 | 1/A/1042:1047, 1/A/1071:1073 | Other IL | homologous IL_4V88_435 NA | |
| IL_9BLN_054 | 1/A/1047:1051, 1/A/1067:1071 | tSH-tHW-tHS | geometric IL_4V88_436 NA | |
| IL_9BLN_055 | 1/A/1091:1093, 1/A/1152:1158 | No text annotation | homologous IL_8C3A_443 NA | |
| IL_9BLN_056 | 1/A/1098:1101, 1/A/1131:1134 | Tandem non-canonical cWW pairs | geometric IL_4V88_438 NA | |
| IL_9BLN_057 | 1/A/1101:1103, 1/A/1129:1131 | Isolated non-canonical cWW pair | geometric IL_5MWI_007 NA | |
| IL_9BLN_058 | 1/A/1108:1110, 1/A/1123:1124 | Minor groove platform | geometric IL_4V88_412 NA | |
| IL_9BLN_059 | 1/A/1168:1175, 1/A/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_8C3A_446 NA | |
| IL_9BLN_060 | 1/A/1203:1204, 1/A/1694:1696 | Single bulged A | homologous IL_8C3A_447 NA | |
| IL_9BLN_061 | 1/A/1206:1208, 1/A/1691:1692 | Single bulged G | homologous IL_4V88_442 NA | |
| IL_9BLN_062 | 1/A/1214:1217, 1/A/1681:1685 | C-loop | homologous IL_8C3A_449 NA | |
| IL_9BLN_063 | 1/A/1230:1232, 1/A/1526:1528 | Isolated non-canonical cWW pair | homologous IL_4V88_444 NA | |
| IL_9BLN_064 | 1/A/1235:1236, 1/A/1521:1523 | Minor groove platform | homologous IL_8C3A_451 NA | |
| IL_9BLN_065 | 1/A/1270:1272, 1/A/1510:1512 | Isolated non-canonical cWW pair | homologous IL_8C3A_452 NA | |
| IL_9BLN_107 | 1/A/1282:1287, 1/A/1314:1315 | No text annotation | ||
| IL_9BLN_108 | 1/A/1282:1290, 1/A/1309:1315 | No text annotation | ||
| IL_9BLN_067 | 1/A/1287:1290, 1/A/1309:1314 | No text annotation | ||
| IL_9BLN_068 | 1/A/1291:1293, 1/A/1306:1308 | No text annotation | homologous IL_4V88_448 NA | |
| IL_9BLN_069 | 1/A/1325:1327, 1/A/1502:1503 | Single bulged U | homologous IL_8C3A_455 NA | |
| IL_9BLN_071 | 1/A/1329:1333, 1/A/1498:1500 | No text annotation | homologous IL_8C3A_456 NA | |
| IL_9BLN_102 | 1/A/1329:1335, 1/A/1492:1500 | No text annotation | homologous IL_8P9A_439 IL_99893.1 | |
| IL_9BLN_072 | 1/A/1333:1335, 1/A/1492:1498 | Minor groove platform with extra cWW | geometric IL_4V88_451 NA | |
| IL_9BLN_103 | 1/A/1337:1338, 1/A/1488:1490 | Single bulged A | homologous IL_8C3A_458 NA | |
| IL_9BLN_074 | 1/A/1347:1349, 1/A/1380:1382 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_9BLN_104 | 1/A/1363:1365, 1/A/1374:1375 | Minor groove platform | homologous IL_8C3A_460 NA | |
| IL_9BLN_076 | 1/A/1395:1399, 1/A/1447:1450 | No text annotation | homologous IL_8C3A_461 NA | |
| IL_9BLN_077 | 1/A/1402:1405, 1/A/1441:1444 | Minor groove platform | homologous IL_4V88_456 NA | |
| IL_9BLN_080 | 1/A/1537:1539, 1/A/1594:1596 | Isolated non-canonical cWW pair | geometric IL_3SZX_002 IL_01003.3 | |
| IL_9BLN_105 | 1/A/1541:1550, 1/A/1582:1592 | No text annotation | ||
| IL_9BLN_081 | 1/A/1550:1558, 1/A/1577:1582 | 180 degree turn | geometric IL_5J7L_055 NA | |
| IL_9BLN_082 | 1/A/1560:1562, 1/A/1573:1575 | Isolated non-canonical cWW pair | homologous IL_8C3A_468 NA | |
| IL_9BLN_083 | 1/A/1604:1610, 1/A/1629:1635 | No text annotation | homologous IL_8C3A_469 NA | |
| IL_9BLN_084 | 1/A/1700:1702, 1/A/1833:1836 | No text annotation | homologous IL_8C3A_470 NA | |
| IL_9BLN_085 | 1/A/1702:1705, 1/A/1829:1833 | No text annotation | geometric IL_4V88_464 NA | |
| IL_9BLN_086 | 1/A/1706:1708, 1/A/1826:1828 | Isolated non-canonical cWW pair | homologous IL_8C3A_472 NA | |
| IL_9BLN_087 | 1/A/1708:1711, 1/A/1822:1826 | No text annotation | homologous IL_8C3A_473 NA | |
| IL_9BLN_088 | 1/A/1714:1716, 1/A/1817:1819 | Isolated non-canonical cWW pair | homologous IL_4V88_467 NA | |
| IL_9BLN_091 | 1/A/1729:1731, 1/A/1803:1805 | Isolated non-canonical cWW pair | homologous IL_8C3A_477 NA | |
| IL_9BLN_092 | 1/A/1733:1736, 1/A/1798:1801 | Double sheared | homologous IL_4V88_471 NA | |
| IL_9BLN_093 | 1/A/1739:1741, 1/A/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4E48_002 IL_01003.3 | |
| IL_9BLN_094 | 1/A/1742:1746, 1/A/1788:1792 | Triple sheared | homologous IL_8C3A_480 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9BLN_002 | Isolated non-canonical cWW pair | ||
| IL_9BLN_013 | No text annotation | ||
| IL_9BLN_015 | No text annotation | ||
| IL_9BLN_016 | No text annotation | ||
| IL_9BLN_017 | No text annotation | ||
| IL_9BLN_018 | Double sheared with non-canonical cWW | ||
| IL_9BLN_029 | No text annotation | ||
| IL_9BLN_044 | No text annotation | ||
| IL_9BLN_066 | No text annotation | ||
| IL_9BLN_101 | No text annotation | ||
| IL_9BLN_070 | Isolated non-canonical cWW pair | ||
| IL_9BLN_073 | Isolated non-canonical cWW pair | ||
| IL_9BLN_075 | Minor groove platform with extra cWW | ||
| IL_9BLN_078 | No text annotation | ||
| IL_9BLN_079 | Single bulged G | ||
| IL_9BLN_089 | Double sheared | ||
| IL_9BLN_090 | No text annotation | ||
| IL_9BLN_095 | No text annotation | ||
| IL_9BLN_096 | Isolated non-canonical cWW pair |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9BLN_012 | 1/A/40:41, 1/A/481:487, 1/A/512:514 | No text annotation | geometric J3_8C3A_082 NA | |
| J3_9BLN_013 | 1/A/40:47, 1/A/479:487, 1/A/512:514 | No text annotation | homologous J3_8P9A_069 J3_63856.1 | |
| J3_9BLN_014 | 1/A/682:685, 1/A/917:922, 1/A/1022:1023 | No text annotation | ||
| J3_9BLN_015 | 1/A/682:685, 1/A/917:923, 1/A/1019:1023 | No text annotation | ||
| J3_9BLN_002 | 1/A/816:819, 1/A/829:831, 1/A/843:848 | No text annotation | homologous J3_8P9A_073 J3_97642.2 | |
| J3_9BLN_003 | 1/A/938:941, 1/A/985:993, 1/A/1000:1004 | No text annotation | homologous J3_4V88_033 NA | |
| J3_9BLN_004 | 1/A/1094:1096, 1/A/1136:1140, 1/A/1147:1151 | No text annotation | ||
| J3_9BLN_005 | 1/A/1218:1221, 1/A/1645:1651, 1/A/1673:1680 | No text annotation | homologous J3_4V88_035 NA | |
| J3_9BLN_006 | 1/A/1225:1228, 1/A/1530:1532, 1/A/1638:1641 | No text annotation | homologous J3_8C3A_039 NA | |
| J3_9BLN_007 | 1/A/1237:1244, 1/A/1255:1266, 1/A/1516:1520 | No text annotation | homologous J3_8C3A_040 NA | |
| J3_9BLN_008 | 1/A/1272:1277, 1/A/1320:1324, 1/A/1504:1510 | No text annotation | homologous J3_8C3A_041 NA | |
| J3_9BLN_009 | 1/A/1340:1345, 1/A/1384:1389, 1/A/1481:1486 | No text annotation | homologous J3_8P9A_080 J3_17077.1 | |
| J3_9BLN_016 | 1/A/1350:1351, 1/A/1360:1363, 1/A/1375:1379 | No text annotation | homologous J3_8C3A_085 NA | |
| J3_9BLN_010 | 1/A/1391:1395, 1/A/1450:1456, 1/A/1470:1479 | No text annotation | ||
| J3_9BLN_011 | 1/A/1532:1536, 1/A/1597:1604, 1/A/1635:1638 | No text annotation | homologous J3_8C3A_044 NA | |
| J4_9BLN_001 | 1/A/98:106, 1/A/355:357, 1/A/405:409, 1/A/431:432 | No text annotation | homologous J4_8P9A_021 J4_15241.2 | |
| J4_9BLN_002 | 1/A/671:673, 1/A/1032:1037, 1/A/1078:1089, 1/A/1160:1161 | No text annotation | homologous J4_8P9A_022 J4_14595.1 | |
| J5_9BLN_001 | 1/A/30:34, 1/A/521:527, 1/A/558:563, 1/A/592:595, 1/A/641:644 | No text annotation | homologous J5_8C3A_018 NA | |
| J5_9BLN_002 | 1/A/30:34, 1/A/521:527, 1/A/558:565, 1/A/585:595, 1/A/641:644 | No text annotation | ||
| J5_9BLN_003 | 1/A/53:56, 1/A/89:96, 1/A/434:436, 1/A/457:459, 1/A/470:474 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_9BLN_004 | 1/A/123:129, 1/A/183:185, 1/A/214:215, 1/A/310:312, 1/A/337:341 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9BLN_001 | No text annotation | ||
| J3_9BLN_017 | No text annotation |
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