6ZMW Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6ZMW_001 | 1/A/7:17 | No text annotation | homologous HL_4V88_186 NA | |
| HL_6ZMW_002 | 1/A/69:80 | No text annotation | geometric HL_2ZZM_002 NA | |
| HL_6ZMW_003 | 1/A/156:162 | GNRA related | homologous HL_4V88_188 NA | |
| HL_6ZMW_005 | 1/A/288:295 | T-loop with 1 bulged base | homologous HL_4V88_191 NA | |
| HL_6ZMW_007 | 1/A/377:387 | No text annotation | ||
| HL_6ZMW_008 | 1/A/416:421 | No text annotation | homologous HL_4V88_194 NA | |
| HL_6ZMW_009 | 1/A/441:452 | No text annotation | homologous HL_4V88_195 NA | |
| HL_6ZMW_010 | 1/A/462:467 | UNCG | homologous HL_4V88_196 NA | |
| HL_6ZMW_011 | 1/A/498:504 | No text annotation | homologous HL_4V88_197 NA | |
| HL_6ZMW_013 | 1/A/569:581 | No text annotation | geometric HL_4V88_199 NA | |
| HL_6ZMW_014 | 1/A/618:623 | GNRA variation | homologous HL_4V88_200 NA | |
| HL_6ZMW_017 | 1/A/820:828 | No text annotation | homologous HL_4V88_203 NA | |
| HL_6ZMW_018 | 1/A/833:841 | No text annotation | ||
| HL_6ZMW_020 | 1/A/957:966 | No text annotation | homologous HL_4V88_206 NA | |
| HL_6ZMW_021 | 1/A/994:999 | GNRA | homologous HL_4V88_207 NA | |
| HL_6ZMW_022 | 1/A/1054:1064 | No text annotation | homologous HL_4V88_208 NA | |
| HL_6ZMW_023 | 1/A/1112:1121 | No text annotation | ||
| HL_6ZMW_024 | 1/A/1141:1146 | GNRA | homologous HL_4V88_210 NA | |
| HL_6ZMW_025 | 1/A/1178:1183 | GNRA | homologous HL_4V88_211 NA | |
| HL_6ZMW_026 | 1/A/1245:1254 | No text annotation | homologous HL_4V88_212 NA | |
| HL_6ZMW_028 | 1/A/1353:1358 | GNRA | homologous HL_4V88_214 NA | |
| HL_6ZMW_029 | 1/A/1366:1373 | No text annotation | geometric HL_4V88_215 NA | |
| HL_6ZMW_031 | 1/A/1460:1466 | GNRA | homologous HL_4V88_217 NA | |
| HL_6ZMW_036 | 1/A/1847:1852 | GNRA variation | homologous HL_4V88_222 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6ZMW_004 | No text annotation | ||
| HL_6ZMW_006 | No text annotation | ||
| HL_6ZMW_012 | No text annotation | ||
| HL_6ZMW_015 | Mini UNCG | ||
| HL_6ZMW_016 | No text annotation | ||
| HL_6ZMW_019 | No text annotation | ||
| HL_6ZMW_027 | Anticodon loop related | ||
| HL_6ZMW_030 | No text annotation | ||
| HL_6ZMW_032 | GNRA | ||
| HL_6ZMW_033 | No text annotation | ||
| HL_6ZMW_034 | No text annotation | ||
| HL_6ZMW_035 | No text annotation | ||
| HL_6ZMW_037 | No text annotation | ||
| HL_6ZMW_038 | tRNA anticodon loop | ||
| HL_6ZMW_039 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6ZMW_001 | 1/A/23:25, 1/A/649:651 | Isolated non-canonical cWW pair | geometric IL_3MEI_002 NA | |
| IL_6ZMW_003 | 1/A/34:36, 1/A/519:521 | Isolated non-canonical cWW pair | homologous IL_4V88_385 NA | |
| IL_6ZMW_004 | 1/A/37:40, 1/A/514:518 | Double sheared | geometric IL_4WF9_016 IL_58355.1 | |
| IL_6ZMW_005 | 1/A/41:47, 1/A/479:481 | No text annotation | geometric IL_4V88_387 NA | |
| IL_6ZMW_006 | 1/A/49:51, 1/A/476:477 | Minor groove platform | homologous IL_4V88_388 NA | |
| IL_6ZMW_007 | 1/A/57:62, 1/A/86:88 | No text annotation | homologous IL_4V88_389 NA | |
| IL_6ZMW_008 | 1/A/63:68, 1/A/81:85 | No text annotation | homologous IL_4V88_390 NA | |
| IL_6ZMW_009 | 1/A/108:110, 1/A/351:353 | Isolated non-canonical cWW pair | geometric IL_4TS2_004 IL_71625.1 | |
| IL_6ZMW_010 | 1/A/110:112, 1/A/349:351 | Isolated non-canonical cWW pair | geometric IL_4WF9_042 IL_01003.1 | |
| IL_6ZMW_093 | 1/A/110:115, 1/A/348:351 | Tandem non-canonical cWW pairs | homologous IL_8P9A_380 IL_71194.1 | |
| IL_6ZMW_011 | 1/A/112:115, 1/A/348:349 | Multiple bulged bases | geometric IL_4V88_392 NA | |
| IL_6ZMW_094 | 1/A/116:121, 1/A/343:347 | No text annotation | homologous IL_8P9A_382 IL_31545.1 | |
| IL_6ZMW_095 | 1/A/145:151, 1/A/167:174 | No text annotation | homologous IL_8C3A_402 NA | |
| IL_6ZMW_096 | 1/A/152:154, 1/A/164:166 | No text annotation | homologous IL_8P9A_384 IL_23751.1 | |
| IL_6ZMW_016 | 1/A/188:192, 1/A/207:211 | Double sheared with non-canonical cWW | geometric IL_4WFL_001 IL_87767.1 | |
| IL_6ZMW_017 | 1/A/216:219, 1/A/302:309 | Tandem non-canonical cWW pairs | geometric IL_1GID_008 NA | |
| IL_6ZMW_019 | 1/A/312:314, 1/A/336:337 | Single bulged A | homologous IL_4V88_399 NA | |
| IL_6ZMW_021 | 1/A/359:364, 1/A/396:403 | Kink-turn with non-sequential stacking | homologous IL_4V88_402 NA | |
| IL_6ZMW_022 | 1/A/366:371, 1/A/393:394 | No text annotation | geometric IL_5Y58_001 IL_45649.1 | |
| IL_6ZMW_023 | 1/A/411:413, 1/A/424:429 | No text annotation | homologous IL_4V88_404 NA | |
| IL_6ZMW_024 | 1/A/437:439, 1/A/454:456 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_6ZMW_025 | 1/A/459:461, 1/A/468:470 | Isolated near basepair | homologous IL_4V88_406 NA | |
| IL_6ZMW_026 | 1/A/487:489, 1/A/511:512 | Single bulged U | geometric IL_4V88_407 NA | |
| IL_6ZMW_097 | 1/A/491:495, 1/A/508:509 | C-loop | homologous IL_8P9A_397 IL_26900.1 | |
| IL_6ZMW_028 | 1/A/495:496, 1/A/506:508 | Single bulged G | geometric IL_5J7L_019 NA | |
| IL_6ZMW_029 | 1/A/527:534, 1/A/549:558 | No text annotation | ||
| IL_6ZMW_031 | 1/A/563:565, 1/A/585:592 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_6ZMW_032 | 1/A/566:569, 1/A/581:584 | Tandem non-canonical cWW pairs | geometric IL_6JDV_001 IL_71194.1 | |
| IL_6ZMW_033 | 1/A/599:606, 1/A/636:637 | SSU/LSU pseudoknot | geometric IL_4V88_413 NA | |
| IL_6ZMW_034 | 1/A/606:608, 1/A/635:636 | Single bulged U | homologous IL_4V88_414 NA | |
| IL_6ZMW_035 | 1/A/611:617, 1/A/624:632 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_6ZMW_036 | 1/A/663:665, 1/A/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 NA | |
| IL_6ZMW_037 | 1/A/665:671, 1/A/1161:1162 | No text annotation | geometric IL_4LFB_022 IL_20847.1 | |
| IL_6ZMW_038 | 1/A/673:675, 1/A/1030:1032 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_6ZMW_039 | 1/A/676:680, 1/A/1025:1029 | tSH-tHW-tHS | homologous IL_4V88_418 NA | |
| IL_6ZMW_041 | 1/A/802:803, 1/A/860:863 | Major groove minor groove platform; mini C-loop | homologous IL_4V88_423 NA | |
| IL_6ZMW_042 | 1/A/805:807, 1/A/856:858 | Isolated non-canonical cWW pair | homologous IL_4V88_424 NA | |
| IL_6ZMW_043 | 1/A/807:815, 1/A/849:856 | No text annotation | homologous IL_4V88_425 NA | |
| IL_6ZMW_044 | 1/A/874:876, 1/A/910:912 | Isolated non-canonical cWW pair | geometric IL_5Y85_006 IL_01003.1 | |
| IL_6ZMW_045 | 1/A/877:879, 1/A/907:909 | Isolated non-canonical cWW pair | geometric IL_4LFB_006 IL_01003.1 | |
| IL_6ZMW_046 | 1/A/922:923, 1/A/1019:1022 | Major groove platform; stack outside cWW | geometric IL_6N5P_003 IL_74641.1 | |
| IL_6ZMW_098 | 1/A/925:926, 1/A/1015:1017 | Single bulged U | geometric IL_6UFH_004 NA | |
| IL_6ZMW_099 | 1/A/928:931, 1/A/1010:1013 | Tandem non-canonical cWW pairs | homologous IL_8P9A_419 IL_15225.1 | |
| IL_6ZMW_049 | 1/A/931:935, 1/A/1007:1010 | Tandem non-canonical cWW pairs | homologous IL_4V88_431 NA | |
| IL_6ZMW_050 | 1/A/942:945, 1/A/981:984 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_6ZMW_051 | 1/A/952:956, 1/A/967:974 | Kink-turn | homologous IL_4V88_434 NA | |
| IL_6ZMW_052 | 1/A/1042:1047, 1/A/1071:1073 | Other IL | homologous IL_4V88_435 NA | |
| IL_6ZMW_053 | 1/A/1047:1051, 1/A/1067:1071 | tSH-tHW-tHS | geometric IL_5J7L_037 NA | |
| IL_6ZMW_054 | 1/A/1091:1093, 1/A/1152:1158 | No text annotation | homologous IL_4V88_437 NA | |
| IL_6ZMW_055 | 1/A/1098:1101, 1/A/1131:1134 | Tandem non-canonical cWW pairs | homologous IL_4V88_438 NA | |
| IL_6ZMW_056 | 1/A/1101:1103, 1/A/1129:1131 | Isolated non-canonical cWW pair | geometric IL_4V9F_105 IL_01003.1 | |
| IL_6ZMW_057 | 1/A/1108:1110, 1/A/1123:1124 | Minor groove platform | geometric IL_4V88_412 NA | |
| IL_6ZMW_058 | 1/A/1168:1175, 1/A/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_6ZMW_059 | 1/A/1203:1204, 1/A/1694:1696 | Single bulged A | homologous IL_4V88_441 NA | |
| IL_6ZMW_060 | 1/A/1206:1208, 1/A/1691:1692 | Single bulged G | homologous IL_4V88_442 NA | |
| IL_6ZMW_061 | 1/A/1214:1217, 1/A/1681:1685 | C-loop | homologous IL_4V88_443 NA | |
| IL_6ZMW_069 | 1/A/1329:1333, 1/A/1498:1500 | Isolated cWS basepair | geometric IL_4LFB_044 IL_82453.1 | |
| IL_6ZMW_102 | 1/A/1329:1335, 1/A/1492:1500 | No text annotation | homologous IL_8P9A_439 IL_99893.1 | |
| IL_6ZMW_072 | 1/A/1347:1349, 1/A/1380:1382 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_6ZMW_103 | 1/A/1363:1365, 1/A/1374:1375 | Minor groove platform | homologous IL_8C3A_460 NA | |
| IL_6ZMW_074 | 1/A/1395:1399, 1/A/1447:1450 | Tandem non-canonical cWW pairs | geometric IL_5EW4_002 IL_71194.1 | |
| IL_6ZMW_075 | 1/A/1402:1405, 1/A/1441:1444 | Minor groove platform | homologous IL_4V88_456 NA | |
| IL_6ZMW_104 | 1/A/1541:1550, 1/A/1582:1592 | No text annotation | ||
| IL_6ZMW_082 | 1/A/1700:1702, 1/A/1833:1836 | No text annotation | homologous IL_4V88_463 NA | |
| IL_6ZMW_083 | 1/A/1702:1705, 1/A/1829:1833 | No text annotation | homologous IL_8P9A_453 IL_25873.1 | |
| IL_6ZMW_084 | 1/A/1706:1708, 1/A/1826:1828 | Isolated non-canonical cWW pair | geometric IL_4E48_004 IL_01003.1 | |
| IL_6ZMW_085 | 1/A/1708:1711, 1/A/1822:1826 | Tandem non-canonical cWW pairs | geometric IL_5EW4_002 IL_71194.1 | |
| IL_6ZMW_086 | 1/A/1714:1716, 1/A/1817:1819 | Isolated non-canonical cWW pair | homologous IL_4V88_467 NA | |
| IL_6ZMW_089 | 1/A/1729:1731, 1/A/1803:1805 | Isolated non-canonical cWW pair | homologous IL_4V88_470 NA | |
| IL_6ZMW_090 | 1/A/1733:1736, 1/A/1798:1801 | Double sheared | homologous IL_4V88_471 NA | |
| IL_6ZMW_091 | 1/A/1739:1741, 1/A/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4E48_002 IL_01003.1 | |
| IL_6ZMW_092 | 1/A/1742:1746, 1/A/1788:1792 | Triple sheared | homologous IL_4V88_474 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6ZMW_002 | Isolated non-canonical cWW pair | ||
| IL_6ZMW_012 | No text annotation | ||
| IL_6ZMW_013 | No text annotation | ||
| IL_6ZMW_014 | No text annotation | ||
| IL_6ZMW_015 | Tandem non-canonical cWW pairs | ||
| IL_6ZMW_018 | No text annotation | ||
| IL_6ZMW_020 | No text annotation | ||
| IL_6ZMW_027 | No text annotation | ||
| IL_6ZMW_030 | No text annotation | ||
| IL_6ZMW_040 | No text annotation | ||
| IL_6ZMW_047 | Tandem non-canonical cWW pairs | ||
| IL_6ZMW_048 | No text annotation | ||
| IL_6ZMW_062 | Isolated non-canonical cWW pair | ||
| IL_6ZMW_063 | No text annotation | ||
| IL_6ZMW_100 | Minor groove platform | ||
| IL_6ZMW_064 | No text annotation | ||
| IL_6ZMW_065 | No text annotation | ||
| IL_6ZMW_101 | No text annotation | ||
| IL_6ZMW_105 | No text annotation | ||
| IL_6ZMW_106 | No text annotation | ||
| IL_6ZMW_066 | No text annotation | ||
| IL_6ZMW_067 | No text annotation | ||
| IL_6ZMW_068 | Single bulged U | ||
| IL_6ZMW_070 | Minor groove platform with extra cWW | ||
| IL_6ZMW_071 | Single bulged A | ||
| IL_6ZMW_073 | Minor groove platform with extra cWW | ||
| IL_6ZMW_076 | Multiple bulged bases | ||
| IL_6ZMW_077 | Single bulged G | ||
| IL_6ZMW_078 | Isolated non-canonical cWW pair | ||
| IL_6ZMW_079 | 180 degree turn | ||
| IL_6ZMW_080 | Isolated non-canonical cWW pair | ||
| IL_6ZMW_081 | No text annotation | ||
| IL_6ZMW_087 | Double sheared | ||
| IL_6ZMW_088 | Single bulged U |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6ZMW_001 | 1/A/40:41, 1/A/481:487, 1/A/512:514 | No text annotation | homologous J3_8P9A_068 J3_58657.1 | |
| J3_6ZMW_002 | 1/A/682:685, 1/A/917:922, 1/A/1022:1023 | No text annotation | ||
| J3_6ZMW_014 | 1/A/682:685, 1/A/917:923, 1/A/1019:1023 | No text annotation | ||
| J3_6ZMW_003 | 1/A/816:819, 1/A/829:831, 1/A/843:848 | No text annotation | homologous J3_4V88_032 NA | |
| J3_6ZMW_004 | 1/A/938:941, 1/A/985:993, 1/A/1000:1004 | No text annotation | homologous J3_4V88_033 NA | |
| J3_6ZMW_005 | 1/A/1094:1096, 1/A/1136:1140, 1/A/1147:1151 | No text annotation | ||
| J3_6ZMW_006 | 1/A/1218:1221, 1/A/1645:1651, 1/A/1673:1680 | No text annotation | homologous J3_8P9A_076 J3_85722.1 | |
| J3_6ZMW_010 | 1/A/1340:1345, 1/A/1384:1389, 1/A/1481:1486 | No text annotation | homologous J3_4V88_039 NA | |
| J3_6ZMW_011 | 1/A/1350:1351, 1/A/1360:1363, 1/A/1375:1379 | No text annotation | homologous J3_8C3A_085 NA | |
| J3_6ZMW_012 | 1/A/1391:1395, 1/A/1450:1456, 1/A/1470:1479 | No text annotation | ||
| J3_6ZMW_013 | 1/A/1532:1536, 1/A/1597:1604, 1/A/1635:1638 | No text annotation | homologous J3_4V88_041 NA | |
| J4_6ZMW_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_6ZMW_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_6ZMW_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_6ZMW_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_6ZMW_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_6ZMW_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_6ZMW_007 | No text annotation | ||
| J3_6ZMW_008 | No text annotation | ||
| J3_6ZMW_009 | No text annotation | ||
| J4_6ZMW_003 | No text annotation |
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