5OA3 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_5OA3_004 | 1/2/7:17 | No text annotation | homologous HL_4V88_186 NA | |
| HL_5OA3_005 | 1/2/69:80 | No text annotation | ||
| HL_5OA3_006 | 1/2/156:162 | GNRA related | homologous HL_4V88_188 NA | |
| HL_5OA3_008 | 1/2/288:295 | T-loop with 1 bulged base | homologous HL_4V88_191 NA | |
| HL_5OA3_009 | 1/2/377:387 | No text annotation | ||
| HL_5OA3_010 | 1/2/416:421 | No text annotation | homologous HL_4V88_194 NA | |
| HL_5OA3_011 | 1/2/441:452 | No text annotation | homologous HL_4V88_195 NA | |
| HL_5OA3_012 | 1/2/462:467 | UNCG | homologous HL_4V88_196 NA | |
| HL_5OA3_013 | 1/2/498:504 | No text annotation | homologous HL_4V88_197 NA | |
| HL_5OA3_015 | 1/2/569:581 | No text annotation | homologous HL_4V88_199 NA | |
| HL_5OA3_016 | 1/2/618:623 | GNRA variation | homologous HL_4V88_200 NA | |
| HL_5OA3_017 | 1/2/820:828 | No text annotation | homologous HL_4V88_203 NA | |
| HL_5OA3_020 | 1/2/957:966 | No text annotation | homologous HL_4V88_206 NA | |
| HL_5OA3_021 | 1/2/994:999 | GNRA | homologous HL_4V88_207 NA | |
| HL_5OA3_022 | 1/2/1054:1064 | No text annotation | homologous HL_4V88_208 NA | |
| HL_5OA3_023 | 1/2/1113:1120 | No text annotation | ||
| HL_5OA3_024 | 1/2/1141:1146 | GNRA | homologous HL_4V88_210 NA | |
| HL_5OA3_025 | 1/2/1178:1183 | GNRA | homologous HL_4V88_211 NA | |
| HL_5OA3_029 | 1/2/1366:1373 | No text annotation | homologous HL_4V88_215 NA | |
| HL_5OA3_034 | 1/2/1847:1852 | GNRA variation | homologous HL_4V88_222 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_5OA3_001 | No text annotation | ||
| HL_5OA3_002 | tRNA anticodon loop | ||
| HL_5OA3_003 | T-loop with 2 stacked bulged bases | ||
| HL_5OA3_007 | GNRA | ||
| HL_5OA3_014 | GNRA | ||
| HL_5OA3_018 | No text annotation | ||
| HL_5OA3_019 | No text annotation | ||
| HL_5OA3_026 | No text annotation | ||
| HL_5OA3_027 | Anticodon loop related | ||
| HL_5OA3_028 | GNRA | ||
| HL_5OA3_030 | GNRA | ||
| HL_5OA3_031 | GNRA | ||
| HL_5OA3_032 | No text annotation | ||
| HL_5OA3_042 | No text annotation | ||
| HL_5OA3_033 | No text annotation | ||
| HL_5OA3_035 | No text annotation | ||
| HL_5OA3_036 | No text annotation | ||
| HL_5OA3_037 | No text annotation | ||
| HL_5OA3_038 | No text annotation | ||
| HL_5OA3_039 | No text annotation | ||
| HL_5OA3_040 | No text annotation | ||
| HL_5OA3_041 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_5OA3_001 | 1/2/23:25, 1/2/649:651 | Isolated non-canonical cWW pair | geometric IL_3MEI_002 IL_01003.4 | |
| IL_5OA3_002 | 1/2/34:36, 1/2/519:521 | Isolated non-canonical cWW pair | homologous IL_4V88_385 NA | |
| IL_5OA3_003 | 1/2/37:40, 1/2/514:518 | Double sheared | geometric IL_4WF9_016 IL_58355.2 | |
| IL_5OA3_004 | 1/2/41:47, 1/2/479:481 | No text annotation | geometric IL_4V88_387 NA | |
| IL_5OA3_005 | 1/2/49:51, 1/2/476:477 | Minor groove platform | homologous IL_4V88_388 NA | |
| IL_5OA3_006 | 1/2/57:62, 1/2/86:88 | No text annotation | homologous IL_4V88_389 NA | |
| IL_5OA3_007 | 1/2/63:68, 1/2/81:85 | No text annotation | homologous IL_4V88_390 NA | |
| IL_5OA3_008 | 1/2/108:110, 1/2/351:353 | Isolated non-canonical cWW pair | geometric IL_1ZX7_004 NA | |
| IL_5OA3_009 | 1/2/110:112, 1/2/349:351 | Isolated non-canonical cWW contact | geometric IL_5UNE_001 IL_87720.1 | |
| IL_5OA3_010 | 1/2/112:115, 1/2/348:349 | Multiple bulged bases | geometric IL_5WLH_001 IL_71421.3 | |
| IL_5OA3_011 | 1/2/116:121, 1/2/343:347 | No text annotation | homologous IL_4V88_393 NA | |
| IL_5OA3_012 | 1/2/123:124, 1/2/339:341 | Minor groove platform | geometric IL_4UYK_001 IL_34520.3 | |
| IL_5OA3_014 | 1/2/145:151, 1/2/167:174 | tWH-tWH-tHW-tHW | homologous IL_4V88_394 NA | |
| IL_5OA3_015 | 1/2/152:154, 1/2/164:166 | Isolated cWH basepair | geometric IL_3CZW_002 NA | |
| IL_5OA3_016 | 1/2/188:192, 1/2/207:211 | Double sheared with non-canonical cWW | geometric IL_4WFL_001 IL_87767.2 | |
| IL_5OA3_017 | 1/2/216:219, 1/2/302:309 | Tandem non-canonical cWW pairs | geometric IL_1GID_008 NA | |
| IL_5OA3_103 | 1/2/312:314, 1/2/336:337 | Single bulged A | homologous IL_8P9A_388 IL_14190.2 | |
| IL_5OA3_020 | 1/2/317:319, 1/2/332:333 | Single stack bend | geometric IL_5TBW_009 NA | |
| IL_5OA3_021 | 1/2/359:364, 1/2/396:403 | Kink-turn with non-sequential stacking | homologous IL_4V88_402 NA | |
| IL_5OA3_022 | 1/2/366:371, 1/2/393:394 | No text annotation | geometric IL_5Y58_001 IL_37738.1 | |
| IL_5OA3_023 | 1/2/411:413, 1/2/424:429 | No text annotation | homologous IL_4V88_404 NA | |
| IL_5OA3_024 | 1/2/437:439, 1/2/454:456 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_5OA3_025 | 1/2/459:461, 1/2/468:470 | Isolated near basepair | homologous IL_4V88_406 NA | |
| IL_5OA3_026 | 1/2/487:489, 1/2/511:512 | Single bulged U | geometric IL_4LFB_014 IL_97561.5 | |
| IL_5OA3_104 | 1/2/491:495, 1/2/508:509 | C-loop | homologous IL_8P9A_397 IL_26900.1 | |
| IL_5OA3_105 | 1/2/495:496, 1/2/506:508 | Single bulged G | homologous IL_8P9A_398 IL_28408.2 | |
| IL_5OA3_030 | 1/2/563:565, 1/2/585:592 | Isolated tHS basepair with bulges | geometric IL_7RQB_082 NA | |
| IL_5OA3_031 | 1/2/566:569, 1/2/581:584 | Tandem non-canonical cWW pairs | geometric IL_6JDV_001 IL_71194.2 | |
| IL_5OA3_032 | 1/2/599:606, 1/2/636:637 | SSU/LSU pseudoknot | homologous IL_4V88_413 NA | |
| IL_5OA3_033 | 1/2/606:608, 1/2/635:636 | Single bulged U | geometric IL_3D2V_001 IL_97561.5 | |
| IL_5OA3_034 | 1/2/611:617, 1/2/624:632 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_5OA3_035 | 1/2/663:665, 1/2/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_01003.4 | |
| IL_5OA3_036 | 1/2/665:671, 1/2/1161:1162 | No text annotation | homologous IL_4V88_416 NA | |
| IL_5OA3_037 | 1/2/673:675, 1/2/1030:1032 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_5OA3_038 | 1/2/676:680, 1/2/1025:1029 | tSH-tHW-tHS | homologous IL_4V88_418 NA | |
| IL_5OA3_040 | 1/2/802:803, 1/2/860:863 | Major groove minor groove platform; mini C-loop | homologous IL_4V88_423 NA | |
| IL_5OA3_041 | 1/2/805:807, 1/2/856:858 | Isolated non-canonical cWW pair | homologous IL_4V88_424 NA | |
| IL_5OA3_042 | 1/2/807:815, 1/2/849:856 | No text annotation | homologous IL_4V88_425 NA | |
| IL_5OA3_045 | 1/2/922:923, 1/2/1019:1022 | Major groove platform; stack outside cWW | homologous IL_4V88_428 NA | |
| IL_5OA3_098 | 1/2/925:926, 1/2/1015:1017 | Single bulged U | geometric IL_3NDB_005 NA | |
| IL_5OA3_047 | 1/2/928:931, 1/2/1010:1013 | Tandem non-canonical cWW pairs | geometric IL_4V88_430 NA | |
| IL_5OA3_048 | 1/2/931:935, 1/2/1007:1010 | Tandem non-canonical cWW pairs | homologous IL_4V88_431 NA | |
| IL_5OA3_049 | 1/2/942:945, 1/2/981:984 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_5OA3_050 | 1/2/952:956, 1/2/967:974 | Kink-turn | homologous IL_4V88_434 NA | |
| IL_5OA3_051 | 1/2/1042:1047, 1/2/1071:1073 | Other IL | homologous IL_4V88_435 NA | |
| IL_5OA3_052 | 1/2/1047:1051, 1/2/1067:1071 | tSH-tHW-tHS | geometric IL_5J7L_037 NA | |
| IL_5OA3_053 | 1/2/1091:1093, 1/2/1152:1158 | No text annotation | homologous IL_4V88_437 NA | |
| IL_5OA3_054 | 1/2/1098:1101, 1/2/1131:1134 | Tandem non-canonical cWW pairs | homologous IL_4V88_438 NA | |
| IL_5OA3_055 | 1/2/1101:1103, 1/2/1129:1131 | Isolated non-canonical cWW pair | geometric IL_4V9F_105 IL_01003.4 | |
| IL_5OA3_056 | 1/2/1108:1110, 1/2/1123:1124 | Minor groove platform | geometric IL_4V88_412 NA | |
| IL_5OA3_057 | 1/2/1168:1175, 1/2/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_5OA3_058 | 1/2/1203:1204, 1/2/1694:1696 | Single bulged A | homologous IL_4V88_441 NA | |
| IL_5OA3_059 | 1/2/1206:1208, 1/2/1691:1692 | Single bulged G | homologous IL_4V88_442 NA | |
| IL_5OA3_060 | 1/2/1214:1217, 1/2/1681:1685 | C-loop | homologous IL_4V88_443 NA | |
| IL_5OA3_069 | 1/2/1337:1338, 1/2/1488:1490 | Single bulged A | homologous IL_4V88_452 NA | |
| IL_5OA3_070 | 1/2/1347:1349, 1/2/1380:1382 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_5OA3_071 | 1/2/1363:1365, 1/2/1374:1375 | Minor groove platform | homologous IL_4V88_454 NA | |
| IL_5OA3_080 | 1/2/1700:1702, 1/2/1833:1836 | No text annotation | geometric IL_5J7L_058 NA | |
| IL_5OA3_081 | 1/2/1702:1705, 1/2/1829:1833 | No text annotation | homologous IL_4V88_464 NA | |
| IL_5OA3_082 | 1/2/1706:1708, 1/2/1826:1828 | Isolated non-canonical cWW pair | geometric IL_4JGN_002 IL_01003.4 | |
| IL_5OA3_087 | 1/2/1733:1736, 1/2/1798:1801 | Double sheared | homologous IL_4V88_471 NA | |
| IL_5OA3_088 | 1/2/1739:1741, 1/2/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4E48_004 IL_01003.4 | |
| IL_5OA3_089 | 1/2/1742:1746, 1/2/1788:1792 | Triple sheared | homologous IL_4V88_474 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_5OA3_013 | No text annotation | ||
| IL_5OA3_018 | No text annotation | ||
| IL_5OA3_019 | Isolated non-canonical cWW pair | ||
| IL_5OA3_027 | C-loop with extra cWW pair | ||
| IL_5OA3_028 | Single bulged A | ||
| IL_5OA3_097 | Isolated non-canonical cWW pair | ||
| IL_5OA3_029 | Tandem non-canonical cWW pairs | ||
| IL_5OA3_039 | Single stack bend | ||
| IL_5OA3_043 | Isolated non-canonical cWW pair | ||
| IL_5OA3_044 | Isolated non-canonical cWW pair | ||
| IL_5OA3_046 | Tandem non-canonical cWW pairs | ||
| IL_5OA3_061 | Isolated non-canonical cWW pair | ||
| IL_5OA3_062 | Minor groove platform | ||
| IL_5OA3_063 | Isolated non-canonical cWW pair | ||
| IL_5OA3_099 | No text annotation | ||
| IL_5OA3_064 | No text annotation | ||
| IL_5OA3_100 | No text annotation | ||
| IL_5OA3_106 | No text annotation | ||
| IL_5OA3_107 | No text annotation | ||
| IL_5OA3_065 | No text annotation | ||
| IL_5OA3_101 | No text annotation | ||
| IL_5OA3_066 | No text annotation | ||
| IL_5OA3_067 | Single bulged U | ||
| IL_5OA3_068 | No text annotation | ||
| IL_5OA3_072 | Tandem non-canonical cWW pairs | ||
| IL_5OA3_073 | Minor groove platform | ||
| IL_5OA3_074 | Isolated non-canonical cWW pair | ||
| IL_5OA3_075 | Single bulged G | ||
| IL_5OA3_076 | Isolated non-canonical cWW pair | ||
| IL_5OA3_102 | No text annotation | ||
| IL_5OA3_077 | No text annotation | ||
| IL_5OA3_108 | Isolated non-canonical cWW pair | ||
| IL_5OA3_078 | Tandem non-canonical cWW pairs | ||
| IL_5OA3_079 | No text annotation | ||
| IL_5OA3_083 | Tandem non-canonical cWW pairs | ||
| IL_5OA3_084 | Isolated non-canonical cWW pair | ||
| IL_5OA3_085 | UAA/GAN related | ||
| IL_5OA3_086 | Isolated non-canonical cWW pair | ||
| IL_5OA3_090 | No text annotation | ||
| IL_5OA3_091 | Single stack bend | ||
| IL_5OA3_092 | No text annotation | ||
| IL_5OA3_093 | No text annotation | ||
| IL_5OA3_094 | No text annotation | ||
| IL_5OA3_095 | No text annotation | ||
| IL_5OA3_096 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_5OA3_001 | 1/2/40:41, 1/2/481:487, 1/2/512:514 | No text annotation | homologous J3_8P9A_068 J3_58657.1 | |
| J3_5OA3_002 | 1/2/816:819, 1/2/829:831, 1/2/843:848 | No text annotation | homologous J3_4V88_032 NA | |
| J3_5OA3_003 | 1/2/938:941, 1/2/985:993, 1/2/1000:1004 | No text annotation | homologous J3_4V88_033 NA | |
| J3_5OA3_004 | 1/2/1094:1096, 1/2/1136:1140, 1/2/1147:1151 | No text annotation | ||
| J3_5OA3_005 | 1/2/1218:1221, 1/2/1645:1651, 1/2/1673:1680 | No text annotation | homologous J3_4V88_035 NA | |
| J3_5OA3_009 | 1/2/1340:1345, 1/2/1384:1389, 1/2/1481:1486 | No text annotation | homologous J3_4V88_039 NA | |
| J3_5OA3_010 | 1/2/1350:1351, 1/2/1360:1363, 1/2/1375:1379 | No text annotation | homologous J3_8C3A_085 NA | |
| J3_5OA3_011 | 1/2/1391:1395, 1/2/1450:1456, 1/2/1470:1479 | No text annotation | ||
| J4_5OA3_002 | 1/2/98:106, 1/2/355:357, 1/2/405:409, 1/2/431:432 | No text annotation | homologous J4_8C3A_021 NA | |
| J4_5OA3_003 | 1/2/671:673, 1/2/1032:1037, 1/2/1078:1089, 1/2/1160:1161 | No text annotation | homologous J4_8P9A_022 J4_14595.1 | |
| J5_5OA3_001 | 1/2/30:34, 1/2/521:527, 1/2/558:563, 1/2/592:595, 1/2/641:644 | No text annotation | homologous J5_8C3A_018 NA | |
| J5_5OA3_002 | 1/2/53:56, 1/2/89:96, 1/2/434:436, 1/2/457:459, 1/2/470:474 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_5OA3_003 | 1/2/123:130, 1/2/182:185, 1/2/214:215, 1/2/310:312, 1/2/337:341 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_5OA3_006 | No text annotation | ||
| J3_5OA3_007 | No text annotation | ||
| J3_5OA3_008 | No text annotation | ||
| J3_5OA3_012 | No text annotation | ||
| J4_5OA3_001 | tRNA junction | ||
| J4_5OA3_007 | No text annotation | ||
| J4_5OA3_004 | No text annotation | ||
| J4_5OA3_005 | No text annotation | ||
| J4_5OA3_008 | No text annotation | ||
| J4_5OA3_006 | No text annotation |
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