8RW1 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8RW1_002 | 1/1/31:39 | tRNA anticodon loop | homologous HL_5E81_212 NA | |
| HL_8RW1_004 | 1/2/7:17 | No text annotation | homologous HL_8C3A_192 NA | |
| HL_8RW1_005 | 1/2/70:81 | No text annotation | geometric HL_2Y8W_001 NA | |
| HL_8RW1_006 | 1/2/153:159 | GNRA related | homologous HL_8C3A_194 NA | |
| HL_8RW1_009 | 1/2/242:249 | T-loop with 1 bulged base | homologous HL_8C3A_197 NA | |
| HL_8RW1_011 | 1/2/329:337 | GNRA related | homologous HL_8C3A_199 NA | |
| HL_8RW1_012 | 1/2/367:372 | No text annotation | homologous HL_8P9A_198 HL_93535.2 | |
| HL_8RW1_013 | 1/2/392:403 | No text annotation | homologous HL_8P9A_199 HL_86432.1 | |
| HL_8RW1_014 | 1/2/413:418 | UNCG | homologous HL_8P9A_200 HL_61337.1 | |
| HL_8RW1_015 | 1/2/449:455 | No text annotation | homologous HL_8P9A_201 HL_89167.1 | |
| HL_8RW1_017 | 1/2/519:531 | No text annotation | homologous HL_8C3A_205 NA | |
| HL_8RW1_018 | 1/2/568:573 | GNRA variation | homologous HL_8C3A_206 NA | |
| HL_8RW1_021 | 1/2/764:772 | No text annotation | homologous HL_8C3A_208 NA | |
| HL_8RW1_022 | 1/2/777:782 | No text annotation | homologous HL_8P9A_207 HL_89167.1 | |
| HL_8RW1_024 | 1/2/899:908 | No text annotation | homologous HL_8P9A_209 HL_38491.1 | |
| HL_8RW1_025 | 1/2/936:941 | GNRA | homologous HL_8P9A_210 HL_34789.1 | |
| HL_8RW1_026 | 1/2/996:1006 | No text annotation | homologous HL_8C3A_213 NA | |
| HL_8RW1_027 | 1/2/1053:1064 | No text annotation | ||
| HL_8RW1_028 | 1/2/1083:1088 | GNRA | homologous HL_8C3A_215 NA | |
| HL_8RW1_029 | 1/2/1120:1125 | GNRA | homologous HL_8P9A_214 HL_34789.1 | |
| HL_8RW1_030 | 1/2/1187:1196 | No text annotation | homologous HL_8C3A_217 NA | |
| HL_8RW1_031 | 1/2/1237:1246 | GNRA wlth extra near cWW | homologous HL_8P9A_216 HL_45359.1 | |
| HL_8RW1_032 | 1/2/1295:1300 | GNRA | homologous HL_8P9A_217 HL_34789.1 | |
| HL_8RW1_033 | 1/2/1308:1315 | T-loop related | homologous HL_8P9A_218 HL_63894.1 | |
| HL_8RW1_034 | 1/2/1358:1363 | No text annotation | homologous HL_8P9A_219 HL_84585.1 | |
| HL_8RW1_035 | 1/2/1394:1400 | No text annotation | homologous HL_8C3A_222 NA | |
| HL_8RW1_036 | 1/2/1499:1504 | GNRA | homologous HL_8C3A_223 NA | |
| HL_8RW1_037 | 1/2/1548:1559 | No text annotation | homologous HL_8P9A_222 HL_50951.1 | |
| HL_8RW1_038 | 1/2/1592:1600 | No text annotation | homologous HL_8P9A_223 NA | |
| HL_8RW1_040 | 1/2/1776:1781 | GNRA variation | homologous HL_8C3A_227 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8RW1_001 | No text annotation | ||
| HL_8RW1_003 | T-loop with 2 stacked bulged bases | ||
| HL_8RW1_007 | No text annotation | ||
| HL_8RW1_008 | No text annotation | ||
| HL_8RW1_010 | Mini UNCG | ||
| HL_8RW1_016 | No text annotation | ||
| HL_8RW1_019 | No text annotation | ||
| HL_8RW1_020 | No text annotation | ||
| HL_8RW1_023 | Pseudoknot geometry | ||
| HL_8RW1_039 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8RW1_001 | 1/2/24:26, 1/2/599:600 | Single bulged C | homologous IL_8P9A_373 IL_05642.1 | |
| IL_8RW1_002 | 1/2/27:29, 1/2/596:598 | Isolated cWH basepair | geometric IL_4KQ0_002 NA | |
| IL_8RW1_003 | 1/2/35:37, 1/2/470:472 | Isolated non-canonical cWW pair | geometric IL_8C3A_393 NA | |
| IL_8RW1_004 | 1/2/37:41, 1/2/465:470 | Triple sheared related | homologous IL_8C3A_394 NA | |
| IL_8RW1_005 | 1/2/42:48, 1/2/430:432 | No text annotation | homologous IL_8C3A_395 NA | |
| IL_8RW1_006 | 1/2/50:52, 1/2/427:428 | Minor groove platform | homologous IL_8C3A_396 NA | |
| IL_8RW1_007 | 1/2/58:63, 1/2/87:89 | No text annotation | homologous IL_8P9A_378 IL_61299.5 | |
| IL_8RW1_008 | 1/2/64:69, 1/2/82:86 | No text annotation | homologous IL_8C3A_398 NA | |
| IL_8RW1_009 | 1/2/109:112, 1/2/301:304 | Tandem non-canonical cWW pairs | homologous IL_8P9A_380 IL_71194.1 | |
| IL_8RW1_010 | 1/2/113:116, 1/2/299:300 | Multiple bulged bases | homologous IL_8C3A_400 NA | |
| IL_8RW1_011 | 1/2/117:122, 1/2/294:298 | No text annotation | homologous IL_8P9A_382 IL_31545.1 | |
| IL_8RW1_012 | 1/2/142:148, 1/2/164:171 | No text annotation | homologous IL_8C3A_402 NA | |
| IL_8RW1_013 | 1/2/149:151, 1/2/161:163 | No text annotation | homologous IL_8P9A_384 IL_23751.1 | |
| IL_8RW1_015 | 1/2/203:205, 1/2/258:262 | No text annotation | homologous IL_8P9A_386 IL_36931.1 | |
| IL_8RW1_016 | 1/2/205:207, 1/2/256:258 | Isolated non-canonical cWW pair | homologous IL_8C3A_406 NA | |
| IL_8RW1_017 | 1/2/264:266, 1/2/287:288 | Single bulged A | homologous IL_8P9A_388 IL_14190.1 | |
| IL_8RW1_018 | 1/2/269:272, 1/2/282:284 | No text annotation | homologous IL_8C3A_408 NA | |
| IL_8RW1_020 | 1/2/310:315, 1/2/347:354 | Kink-turn with non-sequential stacking | homologous IL_8C3A_410 NA | |
| IL_8RW1_021 | 1/2/317:322, 1/2/344:345 | No text annotation | homologous IL_8P9A_392 IL_01372.1 | |
| IL_8RW1_022 | 1/2/362:364, 1/2/375:380 | No text annotation | homologous IL_8C3A_412 NA | |
| IL_8RW1_023 | 1/2/388:390, 1/2/405:407 | Isolated cWH basepair | homologous IL_8C3A_413 NA | |
| IL_8RW1_024 | 1/2/410:412, 1/2/419:421 | Isolated non-canonical cWW pair | homologous IL_8C3A_414 NA | |
| IL_8RW1_025 | 1/2/438:440, 1/2/462:463 | Single bulged U | homologous IL_8P9A_396 IL_97561.1 | |
| IL_8RW1_026 | 1/2/442:446, 1/2/459:460 | C-loop | homologous IL_8P9A_397 IL_26900.1 | |
| IL_8RW1_027 | 1/2/446:447, 1/2/457:459 | Single bulged G | homologous IL_8C3A_417 NA | |
| IL_8RW1_029 | 1/2/513:515, 1/2/535:542 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_8RW1_030 | 1/2/516:517, 1/2/532:534 | Minor groove platform | homologous IL_8C3A_501 NA | |
| IL_8RW1_031 | 1/2/517:519, 1/2/531:532 | Minor groove platform | homologous IL_8P9A_401 IL_34520.1 | |
| IL_8RW1_032 | 1/2/549:556, 1/2/586:587 | SSU/LSU pseudoknot | homologous IL_8C3A_423 NA | |
| IL_8RW1_033 | 1/2/556:558, 1/2/585:586 | Single bulged U | homologous IL_8C3A_424 NA | |
| IL_8RW1_034 | 1/2/561:567, 1/2/574:582 | No text annotation | homologous IL_8P9A_404 IL_52042.1 | |
| IL_8RW1_035 | 1/2/615:621, 1/2/1103:1104 | No text annotation | homologous IL_8C3A_426 NA | |
| IL_8RW1_036 | 1/2/623:625, 1/2/972:974 | Isolated non-canonical cWW pair | homologous IL_8C3A_427 NA | |
| IL_8RW1_037 | 1/2/626:630, 1/2/967:971 | tSH-tHW-tHS | homologous IL_8C3A_428 NA | |
| IL_8RW1_041 | 1/2/745:747, 1/2/801:805 | No text annotation | ||
| IL_8RW1_042 | 1/2/748:750, 1/2/798:800 | Isolated non-canonical cWW pair | homologous IL_8C3A_431 NA | |
| IL_8RW1_043 | 1/2/751:759, 1/2/790:797 | No text annotation | homologous IL_8C3A_503 NA | |
| IL_8RW1_046 | 1/2/867:869, 1/2/956:959 | Isolated cWH basepair | homologous IL_8C3A_510 NA | |
| IL_8RW1_047 | 1/2/870:873, 1/2/952:955 | Tandem non-canonical cWW pairs | homologous IL_8C3A_437 NA | |
| IL_8RW1_048 | 1/2/873:877, 1/2/949:952 | Tandem non-canonical cWW pairs | homologous IL_8C3A_438 NA | |
| IL_8RW1_049 | 1/2/884:887, 1/2/923:926 | Tandem non-canonical cWW pairs | homologous IL_8C3A_439 NA | |
| IL_8RW1_050 | 1/2/892:898, 1/2/909:918 | Kink-turn related | homologous IL_8C3A_440 NA | |
| IL_8RW1_051 | 1/2/982:993, 1/2/1009:1017 | No text annotation | ||
| IL_8RW1_052 | 1/2/1033:1035, 1/2/1094:1100 | No text annotation | homologous IL_8P9A_425 IL_82706.2 | |
| IL_8RW1_053 | 1/2/1040:1044, 1/2/1072:1076 | No text annotation | ||
| IL_8RW1_054 | 1/2/1050:1052, 1/2/1065:1066 | Single bulged U | geometric IL_8C3A_140 NA | |
| IL_8RW1_055 | 1/2/1110:1117, 1/2/1128:1133 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_8C3A_446 NA | |
| IL_8RW1_056 | 1/2/1145:1146, 1/2/1628:1630 | Single bulged A | homologous IL_8C3A_447 NA | |
| IL_8RW1_057 | 1/2/1148:1150, 1/2/1625:1626 | Single bulged G | homologous IL_8C3A_448 NA | |
| IL_8RW1_058 | 1/2/1156:1159, 1/2/1615:1619 | C-loop | homologous IL_8C3A_449 NA | |
| IL_8RW1_059 | 1/2/1172:1175, 1/2/1461:1464 | Tandem non-canonical cWW pairs | geometric IL_5EW4_002 IL_71194.1 | |
| IL_8RW1_060 | 1/2/1177:1178, 1/2/1457:1459 | Minor groove platform | homologous IL_8C3A_451 NA | |
| IL_8RW1_061 | 1/2/1212:1214, 1/2/1446:1448 | Isolated non-canonical cWW pair | homologous IL_8C3A_452 NA | |
| IL_8RW1_093 | 1/2/1223:1229, 1/2/1256:1258 | No text annotation | ||
| IL_8RW1_094 | 1/2/1223:1232, 1/2/1251:1258 | No text annotation | homologous IL_8P9A_470 IL_28304.1 | |
| IL_8RW1_064 | 1/2/1229:1232, 1/2/1251:1256 | No text annotation | ||
| IL_8RW1_066 | 1/2/1267:1269, 1/2/1438:1439 | Single bulged U | homologous IL_8C3A_455 NA | |
| IL_8RW1_067 | 1/2/1271:1275, 1/2/1434:1436 | No text annotation | geometric IL_8C3A_456 NA | |
| IL_8RW1_068 | 1/2/1271:1277, 1/2/1428:1436 | No text annotation | geometric IL_4V88_510 NA | |
| IL_8RW1_069 | 1/2/1275:1277, 1/2/1428:1434 | No text annotation | homologous IL_8P9A_440 IL_93811.1 | |
| IL_8RW1_070 | 1/2/1278:1280, 1/2/1424:1427 | Isolated non-canonical cWW pair | geometric IL_4X4N_005 NA | |
| IL_8RW1_071 | 1/2/1289:1291, 1/2/1322:1324 | Isolated non-canonical cWW pair | homologous IL_8C3A_459 NA | |
| IL_8RW1_072 | 1/2/1305:1307, 1/2/1316:1317 | Minor groove platform | homologous IL_8C3A_460 NA | |
| IL_8RW1_073 | 1/2/1338:1341, 1/2/1381:1383 | Isolated non-canonical cWW pair | homologous IL_8P9A_444 IL_01003.1 | |
| IL_8RW1_074 | 1/2/1344:1347, 1/2/1375:1378 | No text annotation | homologous IL_8C3A_462 NA | |
| IL_8RW1_076 | 1/2/1387:1389, 1/2/1405:1410 | Major groove platform; stack outside cWW | geometric IL_4V88_458 NA | |
| IL_8RW1_077 | 1/2/1478:1485, 1/2/1517:1525 | No text annotation | homologous IL_8P9A_448 IL_91698.1 | |
| IL_8RW1_078 | 1/2/1486:1492, 1/2/1511:1516 | No text annotation | homologous IL_8P9A_449 IL_22564.1 | |
| IL_8RW1_079 | 1/2/1494:1496, 1/2/1507:1509 | Isolated non-canonical cWW pair | homologous IL_8C3A_468 NA | |
| IL_8RW1_080 | 1/2/1538:1543, 1/2/1564:1569 | No text annotation | homologous IL_8P9A_451 IL_57885.1 | |
| IL_8RW1_081 | 1/2/1634:1636, 1/2/1762:1765 | No text annotation | homologous IL_8C3A_470 NA | |
| IL_8RW1_082 | 1/2/1636:1639, 1/2/1758:1762 | No text annotation | homologous IL_8P9A_453 IL_25873.1 | |
| IL_8RW1_083 | 1/2/1640:1642, 1/2/1755:1757 | Isolated non-canonical cWW pair | homologous IL_8C3A_472 NA | |
| IL_8RW1_084 | 1/2/1642:1645, 1/2/1751:1755 | No text annotation | ||
| IL_8RW1_085 | 1/2/1648:1650, 1/2/1746:1748 | Isolated non-canonical cWW pair | homologous IL_8C3A_474 NA | |
| IL_8RW1_086 | 1/2/1651:1654, 1/2/1742:1745 | Double sheared | homologous IL_8P9A_457 IL_58355.1 | |
| IL_8RW1_088 | 1/2/1663:1665, 1/2/1732:1734 | Isolated non-canonical cWW pair | homologous IL_8C3A_477 NA | |
| IL_8RW1_089 | 1/2/1667:1670, 1/2/1727:1730 | Double sheared | homologous IL_8P9A_460 IL_58355.1 | |
| IL_8RW1_090 | 1/2/1673:1676, 1/2/1721:1724 | Tandem non-canonical cWW pairs | homologous IL_8P9A_462 IL_71194.1 | |
| IL_8RW1_091 | 1/2/1676:1680, 1/2/1717:1721 | Triple sheared | homologous IL_8C3A_480 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8RW1_014 | Double sheared | ||
| IL_8RW1_019 | Single bulged U | ||
| IL_8RW1_028 | Isolated cWH basepair | ||
| IL_8RW1_038 | No text annotation | ||
| IL_8RW1_039 | No text annotation | ||
| IL_8RW1_040 | No text annotation | ||
| IL_8RW1_044 | Isolated non-canonical cWW pair | ||
| IL_8RW1_045 | No text annotation | ||
| IL_8RW1_062 | No text annotation | ||
| IL_8RW1_063 | No text annotation | ||
| IL_8RW1_065 | No text annotation | ||
| IL_8RW1_095 | Single bulged U | ||
| IL_8RW1_075 | No text annotation | ||
| IL_8RW1_087 | Single bulged U | ||
| IL_8RW1_092 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8RW1_001 | 1/2/41:42, 1/2/432:438, 1/2/463:465 | No text annotation | homologous J3_8C3A_082 NA | |
| J3_8RW1_002 | 1/2/212:227, 1/2/236:242, 1/2/249:251 | No text annotation | ||
| J3_8RW1_003 | 1/2/632:634, 1/2/860:865, 1/2/961:965 | No text annotation | homologous J3_8P9A_072 J3_17385.5 | |
| J3_8RW1_004 | 1/2/759:763, 1/2/773:775, 1/2/784:790 | No text annotation | ||
| J3_8RW1_005 | 1/2/880:883, 1/2/927:935, 1/2/942:946 | No text annotation | homologous J3_8P9A_074 J3_23895.1 | |
| J3_8RW1_006 | 1/2/1036:1038, 1/2/1078:1082, 1/2/1089:1093 | No text annotation | ||
| J3_8RW1_007 | 1/2/1160:1163, 1/2/1579:1585, 1/2/1607:1614 | No text annotation | homologous J3_8C3A_038 NA | |
| J3_8RW1_008 | 1/2/1167:1170, 1/2/1466:1468, 1/2/1572:1575 | No text annotation | homologous J3_8C3A_039 NA | |
| J3_8RW1_009 | 1/2/1179:1186, 1/2/1197:1208, 1/2/1452:1456 | No text annotation | homologous J3_8C3A_040 NA | |
| J3_8RW1_010 | 1/2/1214:1219, 1/2/1262:1266, 1/2/1440:1446 | No text annotation | homologous J3_8C3A_041 NA | |
| J3_8RW1_011 | 1/2/1282:1287, 1/2/1326:1331, 1/2/1417:1422 | No text annotation | homologous J3_8P9A_080 J3_17077.1 | |
| J3_8RW1_012 | 1/2/1291:1293, 1/2/1302:1305, 1/2/1317:1322 | No text annotation | ||
| J3_8RW1_013 | 1/2/1335:1337, 1/2/1384:1387, 1/2/1410:1413 | No text annotation | geometric J3_8C3A_043 NA | |
| J3_8RW1_014 | 1/2/1335:1337, 1/2/1384:1389, 1/2/1405:1413 | No text annotation | homologous J3_8C3A_086 NA | |
| J3_8RW1_015 | 1/2/1468:1472, 1/2/1531:1538, 1/2/1569:1572 | No text annotation | homologous J3_8C3A_044 NA | |
| J4_8RW1_004 | 1/1/7:10, 1/1/25:27, 1/1/43:49, 1/1/65:66 | tRNA junction | homologous J4_5AXM_001 J4_58311.1 | |
| J4_8RW1_002 | 1/2/99:107, 1/2/306:308, 1/2/356:360, 1/2/382:383 | No text annotation | homologous J4_8P9A_021 J4_15241.2 | |
| J4_8RW1_003 | 1/2/621:623, 1/2/974:979, 1/2/1020:1031, 1/2/1102:1103 | No text annotation | homologous J4_8C3A_022 NA | |
| J5_8RW1_001 | 1/2/31:35, 1/2/472:478, 1/2/508:513, 1/2/542:545, 1/2/591:594 | No text annotation | homologous J5_8C3A_018 NA | |
| J5_8RW1_002 | 1/2/31:35, 1/2/472:478, 1/2/508:515, 1/2/535:545, 1/2/591:594 | No text annotation | ||
| J5_8RW1_003 | 1/2/54:57, 1/2/90:97, 1/2/385:387, 1/2/408:410, 1/2/421:425 | No text annotation | homologous J5_8C3A_020 NA | |
| J5_8RW1_004 | 1/2/124:141, 1/2/172:181, 1/2/202:203, 1/2/262:264, 1/2/288:292 | No text annotation | ||
| J5_8RW1_005 | 1/2/124:141, 1/2/172:181, 1/2/202:203, 1/2/262:266, 1/2/287:292 | No text annotation | ||
| J5_8RW1_007 | 1/2/635:640, 1/2/693:700, 1/2/738:744, 1/2/806:816, 1/2/853:859 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J4_8RW1_001 | No text annotation | ||
| J5_8RW1_006 | No text annotation |
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