9C8K Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9C8K_001 | 1/1/7:17 | No text annotation | homologous HL_8C3A_192 NA | |
| HL_9C8K_006 | 1/1/377:387 | No text annotation | ||
| HL_9C8K_007 | 1/1/416:421 | No text annotation | homologous HL_8P9A_198 HL_93535.2 | |
| HL_9C8K_008 | 1/1/441:452 | No text annotation | homologous HL_8C3A_201 NA | |
| HL_9C8K_010 | 1/1/498:504 | No text annotation | homologous HL_8C3A_203 NA | |
| HL_9C8K_012 | 1/1/569:581 | No text annotation | homologous HL_8P9A_203 HL_68749.1 | |
| HL_9C8K_013 | 1/1/618:623 | GNRA variation | homologous HL_8C3A_206 NA | |
| HL_9C8K_016 | 1/1/956:967 | No text annotation | ||
| HL_9C8K_017 | 1/1/994:999 | GNRA | homologous HL_8C3A_212 NA | |
| HL_9C8K_019 | 1/1/1112:1121 | No text annotation | ||
| HL_9C8K_020 | 1/1/1141:1146 | GNRA | homologous HL_8C3A_215 NA | |
| HL_9C8K_021 | 1/1/1178:1183 | GNRA | homologous HL_8C3A_216 NA | |
| HL_9C8K_029 | 1/1/1847:1852 | GNRA variation | homologous HL_8C3A_227 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9C8K_002 | No text annotation | ||
| HL_9C8K_003 | No text annotation | ||
| HL_9C8K_004 | GNRA | ||
| HL_9C8K_005 | No text annotation | ||
| HL_9C8K_009 | UNCG | ||
| HL_9C8K_011 | No text annotation | ||
| HL_9C8K_014 | No text annotation | ||
| HL_9C8K_015 | No text annotation | ||
| HL_9C8K_018 | No text annotation | ||
| HL_9C8K_022 | GNRA wlth extra near cWW | ||
| HL_9C8K_023 | No text annotation | ||
| HL_9C8K_024 | No text annotation | ||
| HL_9C8K_025 | No text annotation | ||
| HL_9C8K_026 | GNRA | ||
| HL_9C8K_027 | No text annotation | ||
| HL_9C8K_028 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9C8K_001 | 1/1/23:25, 1/1/649:651 | Isolated non-canonical cWW pair | geometric IL_7A0S_026 IL_01003.1 | |
| IL_9C8K_002 | 1/1/34:36, 1/1/519:521 | Isolated non-canonical cWW pair | homologous IL_8C3A_393 NA | |
| IL_9C8K_003 | 1/1/37:40, 1/1/514:518 | Double sheared | geometric IL_5AOX_003 IL_58355.1 | |
| IL_9C8K_004 | 1/1/41:47, 1/1/479:481 | No text annotation | homologous IL_8P9A_376 IL_88082.2 | |
| IL_9C8K_005 | 1/1/49:51, 1/1/476:477 | Minor groove platform | homologous IL_8P9A_377 IL_34520.1 | |
| IL_9C8K_006 | 1/1/62:68, 1/1/81:86 | No text annotation | ||
| IL_9C8K_007 | 1/1/108:121, 1/1/343:353 | No text annotation | ||
| IL_9C8K_011 | 1/1/223:238, 1/1/283:298 | No text annotation | ||
| IL_9C8K_014 | 1/1/359:364, 1/1/396:403 | Kink-turn with non-sequential stacking | homologous IL_8C3A_410 NA | |
| IL_9C8K_015 | 1/1/366:371, 1/1/393:394 | No text annotation | homologous IL_8P9A_392 IL_01372.1 | |
| IL_9C8K_016 | 1/1/411:413, 1/1/424:429 | No text annotation | homologous IL_8P9A_393 IL_93336.1 | |
| IL_9C8K_017 | 1/1/437:439, 1/1/454:456 | Isolated cWH basepair | homologous IL_8C3A_413 NA | |
| IL_9C8K_018 | 1/1/491:497, 1/1/505:509 | No text annotation | ||
| IL_9C8K_021 | 1/1/566:569, 1/1/581:584 | Tandem non-canonical cWW pairs | geometric IL_402D_001 NA | |
| IL_9C8K_022 | 1/1/599:606, 1/1/636:637 | SSU/LSU pseudoknot | homologous IL_8C3A_423 NA | |
| IL_9C8K_023 | 1/1/606:608, 1/1/635:636 | Single bulged U | homologous IL_8C3A_424 NA | |
| IL_9C8K_024 | 1/1/611:617, 1/1/624:632 | No text annotation | homologous IL_8P9A_404 IL_52042.1 | |
| IL_9C8K_025 | 1/1/663:665, 1/1/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 NA | |
| IL_9C8K_026 | 1/1/665:671, 1/1/1161:1162 | No text annotation | homologous IL_8C3A_426 NA | |
| IL_9C8K_027 | 1/1/673:675, 1/1/1030:1032 | Isolated non-canonical cWW pair | homologous IL_8C3A_427 NA | |
| IL_9C8K_028 | 1/1/676:680, 1/1/1025:1029 | tSH-tHW-tHS | homologous IL_8C3A_428 NA | |
| IL_9C8K_031 | 1/1/802:803, 1/1/860:863 | Major groove minor groove platform; mini C-loop | homologous IL_8C3A_430 NA | |
| IL_9C8K_032 | 1/1/805:807, 1/1/856:858 | Isolated non-canonical cWW pair | homologous IL_8P9A_413 IL_71625.1 | |
| IL_9C8K_033 | 1/1/807:815, 1/1/849:856 | No text annotation | homologous IL_8C3A_503 NA | |
| IL_9C8K_034 | 1/1/816:831, 1/1/843:848 | No text annotation | ||
| IL_9C8K_036 | 1/1/927:935, 1/1/1007:1014 | No text annotation | ||
| IL_9C8K_037 | 1/1/942:945, 1/1/981:984 | Tandem non-canonical cWW pairs | homologous IL_8C3A_439 NA | |
| IL_9C8K_038 | 1/1/952:956, 1/1/967:974 | Kink-turn | geometric IL_4V88_434 NA | |
| IL_9C8K_039 | 1/1/1042:1051, 1/1/1067:1073 | No text annotation | ||
| IL_9C8K_040 | 1/1/1091:1093, 1/1/1152:1158 | No text annotation | homologous IL_8P9A_425 IL_82706.2 | |
| IL_9C8K_041 | 1/1/1098:1101, 1/1/1131:1134 | Tandem non-canonical cWW pairs | homologous IL_8C3A_444 NA | |
| IL_9C8K_042 | 1/1/1101:1103, 1/1/1129:1131 | Isolated cWH basepair | geometric IL_8C3A_413 NA | |
| IL_9C8K_043 | 1/1/1108:1110, 1/1/1123:1124 | Single stack bend | geometric IL_5TBW_101 NA | |
| IL_9C8K_044 | 1/1/1168:1175, 1/1/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_8P9A_428 IL_84044.1 | |
| IL_9C8K_045 | 1/1/1206:1208, 1/1/1691:1692 | Single bulged G | homologous IL_8C3A_448 NA | |
| IL_9C8K_056 | 1/1/1340:1342, 1/1/1483:1486 | No text annotation | ||
| IL_9C8K_057 | 1/1/1347:1349, 1/1/1380:1382 | Isolated non-canonical cWW pair | homologous IL_8C3A_459 NA | |
| IL_9C8K_066 | 1/1/1700:1702, 1/1/1833:1836 | No text annotation | homologous IL_8P9A_452 IL_18228.1 | |
| IL_9C8K_067 | 1/1/1702:1705, 1/1/1829:1833 | No text annotation | homologous IL_8C3A_471 NA | |
| IL_9C8K_068 | 1/1/1706:1711, 1/1/1822:1828 | No text annotation | ||
| IL_9C8K_069 | 1/1/1714:1716, 1/1/1817:1819 | Isolated non-canonical cWW pair | homologous IL_8P9A_456 IL_01003.1 | |
| IL_9C8K_073 | 1/1/1731:1737, 1/1/1798:1803 | No text annotation | ||
| IL_9C8K_078 | 1/2/4:12, 1/2/49:50 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9C8K_008 | No text annotation | ||
| IL_9C8K_009 | Double sheared with non-canonical cWW | ||
| IL_9C8K_010 | No text annotation | ||
| IL_9C8K_012 | Single bulged A | ||
| IL_9C8K_013 | No text annotation | ||
| IL_9C8K_019 | Single bulged A | ||
| IL_9C8K_020 | No text annotation | ||
| IL_9C8K_029 | Isolated non-canonical cWW pair | ||
| IL_9C8K_030 | No text annotation | ||
| IL_9C8K_035 | No text annotation | ||
| IL_9C8K_046 | Minor groove platform | ||
| IL_9C8K_047 | No text annotation | ||
| IL_9C8K_048 | Isolated non-canonical cWW pair | ||
| IL_9C8K_049 | No text annotation | ||
| IL_9C8K_050 | Other IL | ||
| IL_9C8K_051 | Single bulged U | ||
| IL_9C8K_052 | No text annotation | ||
| IL_9C8K_053 | No text annotation | ||
| IL_9C8K_054 | No text annotation | ||
| IL_9C8K_055 | Single bulged A | ||
| IL_9C8K_058 | No text annotation | ||
| IL_9C8K_059 | No text annotation | ||
| IL_9C8K_060 | No text annotation | ||
| IL_9C8K_061 | Isolated non-canonical cWW pair | ||
| IL_9C8K_062 | No text annotation | ||
| IL_9C8K_063 | No text annotation | ||
| IL_9C8K_064 | Isolated non-canonical cWW pair | ||
| IL_9C8K_065 | No text annotation | ||
| IL_9C8K_070 | Double sheared | ||
| IL_9C8K_071 | Single bulged U | ||
| IL_9C8K_072 | Isolated non-canonical cWW pair | ||
| IL_9C8K_074 | Single stack bend | ||
| IL_9C8K_075 | Isolated non-canonical cWW pair | ||
| IL_9C8K_076 | Triple sheared | ||
| IL_9C8K_077 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9C8K_001 | 1/1/40:41, 1/1/481:489, 1/1/511:514 | No text annotation | ||
| J3_9C8K_002 | 1/1/682:685, 1/1/917:927, 1/1/1014:1023 | No text annotation | ||
| J3_9C8K_003 | 1/1/938:941, 1/1/985:993, 1/1/1000:1004 | No text annotation | homologous J3_8P9A_074 J3_23895.1 | |
| J3_9C8K_004 | 1/1/1094:1096, 1/1/1136:1140, 1/1/1147:1151 | No text annotation | ||
| J3_9C8K_007 | 1/1/1272:1277, 1/1/1320:1324, 1/1/1504:1510 | No text annotation | homologous J3_8C3A_041 NA | |
| J3_9C8K_008 | 1/1/1342:1345, 1/1/1384:1390, 1/1/1480:1483 | No text annotation | ||
| J4_9C8K_001 | 1/1/98:106, 1/1/355:357, 1/1/405:409, 1/1/431:432 | No text annotation | homologous J4_8C3A_021 NA | |
| J4_9C8K_002 | 1/1/671:673, 1/1/1032:1037, 1/1/1078:1089, 1/1/1160:1161 | No text annotation | homologous J4_8P9A_022 J4_14595.1 | |
| J5_9C8K_001 | 1/1/30:34, 1/1/521:527, 1/1/558:565, 1/1/585:595, 1/1/641:644 | No text annotation | ||
| J5_9C8K_002 | 1/1/53:62, 1/1/86:97, 1/1/433:436, 1/1/457:461, 1/1/468:474 | No text annotation | ||
| J5_9C8K_003 | 1/1/685:691, 1/1/739:745, 1/1/796:800, 1/1/865:877, 1/1/910:917 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9C8K_005 | No text annotation | ||
| J3_9C8K_006 | No text annotation | ||
| J3_9C8K_009 | No text annotation | ||
| J3_9C8K_010 | No text annotation |
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