8C01 Internal, Hairpin and 3-way Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8C01_001 | 1/2/7:17 | No text annotation Not in a motif group | homologous HL_4V88_186 HL_89881.2 | |
| HL_8C01_003 | 1/2/154:160 | Other HL Not in a motif group | homologous HL_4V88_188 HL_76539.2 | |
| HL_8C01_005 | 1/2/243:250 | T-loop with 1 bulged base Not in a motif group | homologous HL_4V88_191 HL_27930.1 | |
| HL_8C01_007 | 1/2/330:338 | No text annotation Not in a motif group | homologous HL_4V88_193 HL_69023.2 | |
| HL_8C01_008 | 1/2/368:373 | No text annotation Not in a motif group | homologous HL_4V88_194 HL_50142.2 | |
| HL_8C01_009 | 1/2/393:404 | No text annotation Not in a motif group | homologous HL_4V88_195 HL_84288.1 | |
| HL_8C01_010 | 1/2/414:419 | UNCG Not in a motif group | homologous HL_4V88_196 HL_03562.2 | |
| HL_8C01_011 | 1/2/450:456 | No text annotation Not in a motif group | homologous HL_4V88_197 HL_09136.1 | |
| HL_8C01_013 | 1/2/520:532 | No text annotation Not in a motif group | homologous HL_4V88_199 HL_06285.2 | |
| HL_8C01_014 | 1/2/569:574 | Other HL Not in a motif group | homologous HL_4V88_200 HL_53845.1 | |
| HL_8C01_015 | 1/2/764:772 | No text annotation Not in a motif group | homologous HL_4V88_203 HL_46766.2 | |
| HL_8C01_018 | 1/2/900:909 | No text annotation Not in a motif group | homologous HL_4V88_206 HL_12326.1 | |
| HL_8C01_019 | 1/2/937:942 | Other HL Not in a motif group | homologous HL_4V88_207 HL_87030.2 | |
| HL_8C01_020 | 1/2/997:1007 | No text annotation Not in a motif group | geometric HL_5NFV_001 HL_76539.2 | |
| HL_8C01_022 | 1/2/1084:1089 | Other HL Not in a motif group | homologous HL_4V88_210 HL_42097.1 | |
| HL_8C01_023 | 1/2/1121:1126 | GNRA Not in a motif group | homologous HL_4V88_211 HL_42097.1 | |
| HL_8C01_024 | 1/2/1238:1247 | No text annotation Not in a motif group | geometric HL_5NFV_001 HL_76539.2 | |
| HL_8C01_025 | 1/2/1296:1301 | GNRA Not in a motif group | homologous HL_4V88_214 HL_42097.1 | |
| HL_8C01_026 | 1/2/1309:1316 | No text annotation Not in a motif group | homologous HL_4V88_215 HL_71554.2 | |
| HL_8C01_027 | 1/2/1359:1364 | No text annotation Not in a motif group | geometric HL_1WZ2_007 HL_10278.1 | |
| HL_8C01_029 | 1/2/1501:1506 | GNRA Not in a motif group | homologous HL_4V88_218 HL_42097.1 | |
| HL_8C01_030 | 1/2/1550:1561 | No text annotation Not in a motif group | homologous HL_4V88_219 HL_22554.1 | |
| HL_8C01_031 | 1/2/1594:1602 | No text annotation Not in a motif group | homologous HL_4V88_220 HL_60812.1 | |
| HL_8C01_033 | 1/2/1777:1784 | T-loop with 1 bulged base Not in a motif group | geometric HL_4V88_191 HL_27930.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8C01_002 | No text annotation | ||
| HL_8C01_004 | No text annotation | ||
| HL_8C01_006 | No text annotation | ||
| HL_8C01_012 | No text annotation | ||
| HL_8C01_016 | No text annotation | ||
| HL_8C01_017 | No text annotation | ||
| HL_8C01_021 | No text annotation | ||
| HL_8C01_028 | No text annotation | ||
| HL_8C01_032 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8C01_001 | 1/2/24:26, 1/2/600:601 | Single bulged C Not in a motif group | homologous IL_4V88_384 IL_61258.12 | |
| IL_8C01_002 | 1/2/35:37, 1/2/471:473 | UC cWW Not in a motif group | geometric IL_4V88_385 IL_51629.2 | |
| IL_8C01_003 | 1/2/37:41, 1/2/466:471 | No text annotation Not in a motif group | homologous IL_4V88_386 IL_41507.1 | |
| IL_8C01_004 | 1/2/42:48, 1/2/431:433 | No text annotation Not in a motif group | homologous IL_4V88_387 IL_33912.1 | |
| IL_8C01_005 | 1/2/50:52, 1/2/428:429 | Minor groove platform Not in a motif group | homologous IL_4V88_388 IL_93353.1 | |
| IL_8C01_006 | 1/2/58:63, 1/2/87:89 | No text annotation Not in a motif group | homologous IL_4V88_389 IL_95004.1 | |
| IL_8C01_007 | 1/2/64:69, 1/2/82:86 | No text annotation Not in a motif group | homologous IL_4V88_390 IL_77691.1 | |
| IL_8C01_008 | 1/2/109:112, 1/2/302:305 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_391 IL_30621.2 | |
| IL_8C01_009 | 1/2/113:116, 1/2/300:301 | Multiple bulged bases Not in a motif group | homologous IL_4V88_392 IL_44546.1 | |
| IL_8C01_010 | 1/2/117:122, 1/2/295:299 | No text annotation Not in a motif group | homologous IL_4V88_393 IL_64181.2 | |
| IL_8C01_011 | 1/2/142:149, 1/2/165:172 | tWH-tWH-tHW-tHW Not in a motif group | homologous IL_4V88_394 IL_80604.2 | |
| IL_8C01_012 | 1/2/150:152, 1/2/162:164 | Isolated cWH basepair Not in a motif group | geometric IL_6RA4_002 IL_51629.2 | |
| IL_8C01_013 | 1/2/204:206, 1/2/259:263 | Major groove platform with extra cWW Not in a motif group | homologous IL_4V88_397 IL_05564.2 | |
| IL_8C01_014 | 1/2/206:208, 1/2/257:259 | No text annotation Not in a motif group | geometric IL_3U4M_001 IL_95997.1 | |
| IL_8C01_016 | 1/2/265:267, 1/2/288:289 | Single bulged A Not in a motif group | homologous IL_4V88_399 IL_37497.2 | |
| IL_8C01_017 | 1/2/270:273, 1/2/283:285 | No text annotation Not in a motif group | homologous IL_4V88_400 IL_47298.1 | |
| IL_8C01_018 | 1/2/311:316, 1/2/348:355 | Kink-turn with non-sequential stacking Not in a motif group | homologous IL_4V88_402 IL_45067.2 | |
| IL_8C01_019 | 1/2/318:323, 1/2/345:346 | No text annotation Not in a motif group | geometric IL_5Y58_001 IL_48100.2 | |
| IL_8C01_020 | 1/2/363:365, 1/2/376:381 | No text annotation Not in a motif group | homologous IL_4V88_404 IL_11347.1 | |
| IL_8C01_021 | 1/2/389:391, 1/2/406:408 | Isolated cWH basepair Not in a motif group | homologous IL_4V88_405 IL_51629.2 | |
| IL_8C01_022 | 1/2/411:413, 1/2/420:422 | Isolated near basepair Not in a motif group | homologous IL_4V88_406 IL_52767.2 | |
| IL_8C01_023 | 1/2/439:441, 1/2/463:464 | Single bulged U Not in a motif group | geometric IL_4V88_407 IL_83039.13 | |
| IL_8C01_024 | 1/2/443:447, 1/2/460:461 | C-loop Not in a motif group | geometric IL_5J7L_018 IL_75255.1 | |
| IL_8C01_025 | 1/2/447:448, 1/2/458:460 | Single bulged G Not in a motif group | geometric IL_5J7L_019 IL_00225.2 | |
| IL_8C01_026 | 1/2/514:516, 1/2/536:543 | No text annotation Not in a motif group | homologous IL_8C3A_420 IL_55023.1 | |
| IL_8C01_027 | 1/2/517:518, 1/2/533:535 | Minor groove platform Not in a motif group | geometric IL_4V88_388 IL_93353.1 | |
| IL_8C01_028 | 1/2/518:520, 1/2/532:533 | Minor groove platform Not in a motif group | geometric IL_4V88_412 IL_93353.1 | |
| IL_8C01_029 | 1/2/550:557, 1/2/587:588 | SSU/LSU pseudoknot Not in a motif group | homologous IL_4V88_413 IL_15861.7 | |
| IL_8C01_030 | 1/2/557:559, 1/2/586:587 | Single bulged U Not in a motif group | geometric IL_2PJP_001 IL_83039.13 | |
| IL_8C01_031 | 1/2/562:568, 1/2/575:583 | No text annotation Not in a motif group | homologous IL_4V88_415 IL_55871.1 | |
| IL_8C01_032 | 1/2/616:622, 1/2/1104:1105 | No text annotation Not in a motif group | homologous IL_4V88_416 IL_69996.1 | |
| IL_8C01_033 | 1/2/624:626, 1/2/973:975 | No text annotation Not in a motif group | homologous IL_4V88_417 IL_95997.1 | |
| IL_8C01_034 | 1/2/627:631, 1/2/968:972 | tSH-tHW-tHS Not in a motif group | homologous IL_4V88_418 IL_17136.1 | |
| IL_8C01_035 | 1/2/646:648, 1/2/686:688 | No text annotation Not in a motif group | homologous IL_4V88_419 IL_95997.1 | |
| IL_8C01_036 | 1/2/746:747, 1/2/802:805 | Major groove minor groove platform; mini C-loop Not in a motif group | homologous IL_4V88_423 IL_09061.6 | |
| IL_8C01_037 | 1/2/748:750, 1/2/799:801 | No text annotation Not in a motif group | homologous IL_4V88_424 IL_95997.1 | |
| IL_8C01_038 | 1/2/751:759, 1/2/791:798 | No text annotation Not in a motif group | homologous IL_4V88_425 IL_69091.1 | |
| IL_8C01_039 | 1/2/817:822, 1/2/850:854 | No text annotation Not in a motif group | geometric IL_4V88_422 IL_05145.2 | |
| IL_8C01_040 | 1/2/822:824, 1/2/848:850 | Isolated cWH basepair Not in a motif group | homologous IL_4V88_427 IL_51629.2 | |
| IL_8C01_041 | 1/2/865:866, 1/2/962:965 | Major groove platform; stack outside cWW Not in a motif group | homologous IL_4V88_428 IL_50694.2 | |
| IL_8C01_042 | 1/2/867:870, 1/2/957:961 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_429 IL_30621.2 | |
| IL_8C01_043 | 1/2/871:874, 1/2/953:956 | Tandem non-canonical cWW pairs Not in a motif group | geometric IL_4V88_430 IL_30621.2 | |
| IL_8C01_044 | 1/2/874:878, 1/2/950:953 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_431 IL_30621.2 | |
| IL_8C01_045 | 1/2/885:888, 1/2/924:927 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_432 IL_30621.2 | |
| IL_8C01_046 | 1/2/893:899, 1/2/910:919 | No text annotation Not in a motif group | homologous IL_8C3A_440 IL_22252.1 | |
| IL_8C01_047 | 1/2/985:990, 1/2/1014:1016 | Other IL Not in a motif group | homologous IL_4V88_435 IL_22046.1 | |
| IL_8C01_048 | 1/2/990:994, 1/2/1010:1014 | tSH-tHW-tHS Not in a motif group | geometric IL_4V88_436 IL_17136.1 | |
| IL_8C01_049 | 1/2/1034:1036, 1/2/1095:1101 | No text annotation Not in a motif group | homologous IL_4V88_437 IL_19557.3 | |
| IL_8C01_050 | 1/2/1041:1044, 1/2/1074:1077 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_438 IL_30621.2 | |
| IL_8C01_051 | 1/2/1051:1053, 1/2/1066:1067 | Single bulged U Not in a motif group | geometric IL_2A64_003 IL_83039.13 | |
| IL_8C01_052 | 1/2/1111:1118, 1/2/1129:1134 | 8x6 Sarcin-Ricin with inserted Y; G-bulge Not in a motif group | homologous IL_4V88_440 IL_24606.2 | |
| IL_8C01_053 | 1/2/1157:1160, 1/2/1617:1621 | C-loop Not in a motif group | homologous IL_4V88_443 IL_63596.6 | |
| IL_8C01_054 | 1/2/1173:1175, 1/2/1464:1466 | No text annotation Not in a motif group | homologous IL_4V88_444 IL_95997.1 | |
| IL_8C01_055 | 1/2/1178:1179, 1/2/1459:1461 | Minor groove platform Not in a motif group | homologous IL_4V88_445 IL_42622.2 | |
| IL_8C01_057 | 1/2/1213:1215, 1/2/1448:1450 | No text annotation Not in a motif group | homologous IL_4V88_446 IL_95997.1 | |
| IL_8C01_059 | 1/2/1230:1233, 1/2/1252:1257 | No text annotation Not in a motif group | ||
| IL_8C01_060 | 1/2/1234:1236, 1/2/1249:1251 | No text annotation Not in a motif group | homologous IL_4V88_448 IL_10023.1 | |
| IL_8C01_061 | 1/2/1290:1292, 1/2/1323:1325 | Isolated cWH basepair Not in a motif group | homologous IL_4V88_453 IL_51629.2 | |
| IL_8C01_062 | 1/2/1306:1308, 1/2/1317:1318 | Minor groove platform Not in a motif group | geometric IL_4LFB_054 IL_93353.1 | |
| IL_8C01_065 | 1/2/1352:1354, 1/2/1369:1373 | No text annotation Not in a motif group | homologous IL_4V88_457 IL_95997.1 | |
| IL_8C01_066 | 1/2/1480:1487, 1/2/1519:1527 | No text annotation Not in a motif group | homologous IL_4V88_459 IL_10447.1 | |
| IL_8C01_067 | 1/2/1488:1494, 1/2/1513:1518 | No text annotation Not in a motif group | homologous IL_4V88_460 IL_75461.4 | |
| IL_8C01_068 | 1/2/1495:1498, 1/2/1509:1512 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_461 IL_30621.2 | |
| IL_8C01_069 | 1/2/1540:1545, 1/2/1566:1571 | No text annotation Not in a motif group | homologous IL_4V88_462 IL_19954.2 | |
| IL_8C01_070 | 1/2/1650:1652, 1/2/1748:1750 | AA cWW Not in a motif group | homologous IL_4V88_467 IL_95997.1 | |
| IL_8C01_071 | 1/2/1653:1656, 1/2/1744:1747 | No text annotation Not in a motif group | ||
| IL_8C01_072 | 1/2/1656:1658, 1/2/1743:1744 | No text annotation Not in a motif group | ||
| IL_8C01_073 | 1/2/1665:1667, 1/2/1734:1736 | No text annotation Not in a motif group | homologous IL_4V88_470 IL_51629.2 | |
| IL_8C01_074 | 1/2/1669:1672, 1/2/1729:1732 | Double sheared Not in a motif group | homologous IL_4V88_471 IL_09705.9 | |
| IL_8C01_075 | 1/2/1672:1674, 1/2/1727:1729 | No text annotation Not in a motif group | geometric IL_5TBW_068 IL_95997.1 | |
| IL_8C01_076 | 1/2/1675:1678, 1/2/1723:1726 | Tandem non-canonical cWW pairs Not in a motif group | homologous IL_4V88_473 IL_30621.2 | |
| IL_8C01_077 | 1/2/1678:1682, 1/2/1719:1723 | Triple sheared Not in a motif group | geometric IL_4V88_474 IL_56467.8 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8C01_015 | Isolated tHS basepair with bulges | ||
| IL_8C01_056 | No text annotation | ||
| IL_8C01_058 | No text annotation | ||
| IL_8C01_063 | No text annotation | ||
| IL_8C01_064 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8C01_001 | 1/2/41:42, 1/2/433:439, 1/2/464:466 | No text annotation Not in a motif group | ||
| J3_8C01_002 | 1/2/633:635, 1/2/861:865, 1/2/965:966 | No text annotation Not in a motif group | ||
| J3_8C01_003 | 1/2/760:763, 1/2/773:775, 1/2/785:790 | No text annotation Not in a motif group | homologous J3_4V88_032 NA | |
| J3_8C01_004 | 1/2/881:884, 1/2/928:936, 1/2/943:947 | No text annotation Not in a motif group | homologous J3_4V88_033 NA | |
| J3_8C01_005 | 1/2/1037:1039, 1/2/1079:1083, 1/2/1090:1094 | No text annotation Not in a motif group | homologous J3_4V88_034 NA | |
| J3_8C01_006 | 1/2/1161:1164, 1/2/1581:1587, 1/2/1609:1616 | No text annotation Not in a motif group | homologous J3_4V88_035 NA | |
| J3_8C01_007 | 1/2/1168:1171, 1/2/1468:1470, 1/2/1574:1577 | No text annotation Not in a motif group | homologous J3_4V88_036 NA | |
| J3_8C01_009 | 1/2/1293:1294, 1/2/1303:1306, 1/2/1318:1322 | No text annotation Not in a motif group | ||
| J3_8C01_010 | 1/2/1335:1338, 1/2/1386:1389, 1/2/1412:1416 | No text annotation Not in a motif group | ||
| J3_8C01_011 | 1/2/1470:1474, 1/2/1533:1540, 1/2/1571:1574 | No text annotation Not in a motif group | homologous J3_8C3A_044 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8C01_008 | No text annotation |
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