8S8I Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_8S8I_002 | 1/1/31:39 | tRNA anticodon loop | homologous HL_5E81_212 NA | |
| HL_8S8I_004 | 1/2/7:17 | No text annotation | homologous HL_8P9A_190 NA | |
| HL_8S8I_009 | 1/2/242:249 | T-loop with 1 bulged base | homologous HL_8P9A_195 NA | |
| HL_8S8I_011 | 1/2/329:337 | GNRA related | homologous HL_8C3A_199 NA | |
| HL_8S8I_012 | 1/2/367:372 | No text annotation | homologous HL_8P9A_198 NA | |
| HL_8S8I_013 | 1/2/392:403 | No text annotation | homologous HL_8C3A_201 NA | |
| HL_8S8I_015 | 1/2/449:455 | No text annotation | homologous HL_8P9A_201 NA | |
| HL_8S8I_017 | 1/2/519:531 | No text annotation | homologous HL_8C3A_205 NA | |
| HL_8S8I_018 | 1/2/568:573 | GNRA variation | homologous HL_8C3A_206 NA | |
| HL_8S8I_020 | 1/2/764:772 | No text annotation | homologous HL_8C3A_208 NA | |
| HL_8S8I_024 | 1/2/936:941 | GNRA | homologous HL_8C3A_212 NA | |
| HL_8S8I_025 | 1/2/994:1008 | No text annotation | ||
| HL_8S8I_041 | 1/2/1083:1088 | GNRA | homologous HL_8P9A_213 NA | |
| HL_8S8I_028 | 1/2/1120:1125 | GNRA | homologous HL_8C3A_216 NA | |
| HL_8S8I_029 | 1/2/1187:1196 | No text annotation | homologous HL_8C3A_217 NA | |
| HL_8S8I_030 | 1/2/1237:1246 | GNRA with extra near cWW | homologous HL_8P9A_216 NA | |
| HL_8S8I_031 | 1/2/1295:1300 | GNRA | homologous HL_8P9A_217 NA | |
| HL_8S8I_032 | 1/2/1308:1315 | T-loop related | homologous HL_8P9A_218 NA | |
| HL_8S8I_034 | 1/2/1394:1400 | No text annotation | homologous HL_8C3A_222 NA | |
| HL_8S8I_037 | 1/2/1592:1600 | No text annotation | homologous HL_8C3A_225 NA | |
| HL_8S8I_038 | 1/2/1688:1709 | No text annotation | ||
| HL_8S8I_039 | 1/2/1776:1781 | GNRA variation | homologous HL_8C3A_227 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_8S8I_001 | No text annotation | ||
| HL_8S8I_003 | T-loop with 2 stacked bulged bases | ||
| HL_8S8I_005 | Externally structured | ||
| HL_8S8I_006 | GNRA related | ||
| HL_8S8I_007 | No text annotation | ||
| HL_8S8I_008 | No text annotation | ||
| HL_8S8I_010 | Mini UNCG | ||
| HL_8S8I_014 | UNCG | ||
| HL_8S8I_016 | Externally structured | ||
| HL_8S8I_019 | No text annotation | ||
| HL_8S8I_021 | No text annotation | ||
| HL_8S8I_022 | Pseudoknot geometry | ||
| HL_8S8I_023 | No text annotation | ||
| HL_8S8I_026 | No text annotation | ||
| HL_8S8I_040 | No text annotation | ||
| HL_8S8I_027 | GNRA with extra near cWW | ||
| HL_8S8I_033 | No text annotation | ||
| HL_8S8I_035 | GNRA | ||
| HL_8S8I_036 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_8S8I_001 | 1/2/24:26, 1/2/599:600 | Single bulged C | homologous IL_8P9A_373 NA | |
| IL_8S8I_003 | 1/2/35:37, 1/2/470:472 | Isolated non-canonical cWW pair | geometric IL_4V88_385 NA | |
| IL_8S8I_004 | 1/2/37:41, 1/2/465:470 | Triple sheared related | homologous IL_8C3A_394 NA | |
| IL_8S8I_005 | 1/2/42:48, 1/2/430:432 | No text annotation | homologous IL_8P9A_376 NA | |
| IL_8S8I_093 | 1/2/50:52, 1/2/427:428 | Minor groove platform | homologous IL_8CRE_394 IL_26092.1 | |
| IL_8S8I_007 | 1/2/58:63, 1/2/87:89 | No text annotation | homologous IL_8P9A_378 NA | |
| IL_8S8I_008 | 1/2/64:69, 1/2/82:86 | No text annotation | homologous IL_8C3A_398 NA | |
| IL_8S8I_009 | 1/2/109:112, 1/2/301:304 | Tandem non-canonical cWW pairs | homologous IL_8C3A_399 NA | |
| IL_8S8I_010 | 1/2/113:117, 1/2/298:300 | Isolated non-canonical cWW pair | geometric IL_4KYY_002 IL_81485.1 | |
| IL_8S8I_011 | 1/2/117:122, 1/2/294:298 | No text annotation | homologous IL_8P9A_382 NA | |
| IL_8S8I_012 | 1/2/142:148, 1/2/164:171 | No text annotation | homologous IL_8C3A_402 NA | |
| IL_8S8I_015 | 1/2/203:205, 1/2/258:262 | Major groove platform with extra cWW | homologous IL_8C3A_405 NA | |
| IL_8S8I_016 | 1/2/205:207, 1/2/256:258 | Isolated non-canonical cWW pair | homologous IL_8P9A_387 NA | |
| IL_8S8I_017 | 1/2/264:266, 1/2/287:288 | Single bulged A | homologous IL_8P9A_388 NA | |
| IL_8S8I_020 | 1/2/310:315, 1/2/347:354 | Kink-turn with non-sequential stacking | homologous IL_8P9A_391 NA | |
| IL_8S8I_021 | 1/2/317:322, 1/2/344:345 | No text annotation | homologous IL_8P9A_392 NA | |
| IL_8S8I_022 | 1/2/362:364, 1/2/375:380 | No text annotation | homologous IL_8P9A_393 NA | |
| IL_8S8I_023 | 1/2/388:390, 1/2/405:407 | Isolated cWH basepair | homologous IL_8P9A_394 NA | |
| IL_8S8I_024 | 1/2/410:412, 1/2/419:421 | Isolated non-canonical cWW pair | homologous IL_8C3A_414 NA | |
| IL_8S8I_025 | 1/2/438:440, 1/2/462:463 | Single bulged U | homologous IL_8P9A_396 NA | |
| IL_8S8I_026 | 1/2/442:446, 1/2/459:460 | C-loop | homologous IL_8P9A_397 NA | |
| IL_8S8I_027 | 1/2/446:447, 1/2/457:459 | Single bulged G | homologous IL_8P9A_398 NA | |
| IL_8S8I_029 | 1/2/513:515, 1/2/535:542 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_8S8I_030 | 1/2/516:517, 1/2/532:534 | Minor groove platform | homologous IL_8C3A_501 NA | |
| IL_8S8I_031 | 1/2/517:519, 1/2/531:532 | Minor groove platform | homologous IL_8P9A_401 NA | |
| IL_8S8I_032 | 1/2/549:556, 1/2/586:587 | SSU/LSU pseudoknot | homologous IL_8C3A_423 NA | |
| IL_8S8I_033 | 1/2/556:558, 1/2/585:586 | Single bulged U | homologous IL_8P9A_403 NA | |
| IL_8S8I_034 | 1/2/561:567, 1/2/574:582 | No text annotation | homologous IL_8P9A_404 NA | |
| IL_8S8I_035 | 1/2/615:621, 1/2/1103:1104 | No text annotation | homologous IL_8P9A_405 NA | |
| IL_8S8I_036 | 1/2/623:625, 1/2/972:974 | Isolated non-canonical cWW pair | homologous IL_8C3A_427 NA | |
| IL_8S8I_037 | 1/2/626:630, 1/2/967:971 | tSH-tWH-tHS | homologous IL_8P9A_407 NA | |
| IL_8S8I_041 | 1/2/745:747, 1/2/801:805 | No text annotation | geometric IL_9NLN_006 IL_24466.1 | |
| IL_8S8I_042 | 1/2/748:750, 1/2/798:800 | Isolated non-canonical cWW pair | homologous IL_8C3A_431 NA | |
| IL_8S8I_043 | 1/2/751:759, 1/2/790:797 | No text annotation | homologous IL_8C3A_503 NA | |
| IL_8S8I_046 | 1/2/867:869, 1/2/956:959 | Isolated cWH basepair | homologous IL_8C3A_510 NA | |
| IL_8S8I_047 | 1/2/870:872, 1/2/953:955 | Isolated non-canonical cWW pair | geometric IL_8C3A_074 NA | |
| IL_8S8I_048 | 1/2/873:877, 1/2/949:952 | Tandem non-canonical cWW pairs | homologous IL_8C3A_438 NA | |
| IL_8S8I_049 | 1/2/885:887, 1/2/923:925 | Isolated non-canonical cWW pair | geometric IL_4V88_472 NA | |
| IL_8S8I_050 | 1/2/892:898, 1/2/909:918 | Kink-turn related | homologous IL_8C3A_440 NA | |
| IL_8S8I_051 | 1/2/982:993, 1/2/1009:1017 | No text annotation | ||
| IL_8S8I_052 | 1/2/1033:1035, 1/2/1094:1100 | No text annotation | homologous IL_8P9A_425 NA | |
| IL_8S8I_053 | 1/2/1040:1044, 1/2/1072:1076 | No text annotation | geometric IL_9JA9_001 IL_71154.6 | |
| IL_8S8I_055 | 1/2/1110:1117, 1/2/1128:1133 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_8P9A_428 NA | |
| IL_8S8I_056 | 1/2/1145:1146, 1/2/1628:1630 | Single bulged A | homologous IL_8C3A_447 NA | |
| IL_8S8I_058 | 1/2/1156:1159, 1/2/1615:1619 | C-loop | homologous IL_8C3A_449 NA | |
| IL_8S8I_059 | 1/2/1172:1175, 1/2/1461:1464 | Tandem non-canonical cWW pairs | geometric IL_4XW1_002 NA | |
| IL_8S8I_060 | 1/2/1177:1178, 1/2/1457:1459 | Minor groove platform | homologous IL_8C3A_451 NA | |
| IL_8S8I_061 | 1/2/1212:1214, 1/2/1446:1448 | Isolated non-canonical cWW pair | homologous IL_8C3A_452 NA | |
| IL_8S8I_065 | 1/2/1233:1235, 1/2/1248:1250 | Other IL | homologous IL_8C3A_454 NA | |
| IL_8S8I_066 | 1/2/1267:1269, 1/2/1438:1439 | Single bulged U | homologous IL_8C3A_455 NA | |
| IL_8S8I_067 | 1/2/1271:1275, 1/2/1434:1436 | No text annotation | geometric IL_8C3A_456 NA | |
| IL_8S8I_068 | 1/2/1271:1277, 1/2/1428:1436 | No text annotation | geometric IL_4V88_510 NA | |
| IL_8S8I_069 | 1/2/1275:1277, 1/2/1428:1434 | No text annotation | homologous IL_8P9A_440 NA | |
| IL_8S8I_071 | 1/2/1289:1291, 1/2/1322:1324 | Isolated non-canonical cWW pair | homologous IL_8C3A_459 NA | |
| IL_8S8I_072 | 1/2/1305:1307, 1/2/1316:1317 | Minor groove platform | homologous IL_8C3A_460 NA | |
| IL_8S8I_074 | 1/2/1344:1347, 1/2/1375:1378 | No text annotation | homologous IL_8C3A_462 NA | |
| IL_8S8I_075 | 1/2/1352:1353, 1/2/1368:1370 | Single bulged U | geometric IL_6UFH_004 IL_97561.9 | |
| IL_8S8I_076 | 1/2/1387:1389, 1/2/1405:1410 | Major groove platform; stack outside cWW | geometric IL_4V88_458 NA | |
| IL_8S8I_097 | 1/2/1478:1485, 1/2/1517:1525 | No text annotation | homologous IL_8P9A_448 NA | |
| IL_8S8I_078 | 1/2/1486:1492, 1/2/1511:1516 | No text annotation | homologous IL_8P9A_449 NA | |
| IL_8S8I_080 | 1/2/1538:1543, 1/2/1564:1569 | No text annotation | homologous IL_8P9A_451 NA | |
| IL_8S8I_081 | 1/2/1634:1636, 1/2/1762:1765 | No text annotation | homologous IL_8P9A_452 NA | |
| IL_8S8I_082 | 1/2/1636:1639, 1/2/1758:1762 | No text annotation | homologous IL_8P9A_453 NA | |
| IL_8S8I_084 | 1/2/1642:1645, 1/2/1751:1755 | Tandem non-canonical cWW pairs | geometric IL_5J7L_033 NA | |
| IL_8S8I_085 | 1/2/1648:1650, 1/2/1746:1748 | Isolated non-canonical cWW pair | homologous IL_8C3A_474 NA | |
| IL_8S8I_086 | 1/2/1651:1654, 1/2/1742:1745 | Double sheared | homologous IL_8C3A_475 NA | |
| IL_8S8I_089 | 1/2/1667:1670, 1/2/1727:1730 | Double sheared | homologous IL_8C3A_478 NA | |
| IL_8S8I_090 | 1/2/1673:1676, 1/2/1721:1724 | Tandem non-canonical cWW pairs | homologous IL_8P9A_462 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_8S8I_002 | Isolated cWH basepair | ||
| IL_8S8I_006 | No text annotation | ||
| IL_8S8I_013 | No text annotation | ||
| IL_8S8I_014 | Double sheared | ||
| IL_8S8I_018 | No text annotation | ||
| IL_8S8I_019 | Single bulged U | ||
| IL_8S8I_028 | No text annotation | ||
| IL_8S8I_038 | No text annotation | ||
| IL_8S8I_039 | No text annotation | ||
| IL_8S8I_094 | No text annotation | ||
| IL_8S8I_040 | No text annotation | ||
| IL_8S8I_044 | Isolated non-canonical cWW pair | ||
| IL_8S8I_045 | No text annotation | ||
| IL_8S8I_054 | Single bulged U | ||
| IL_8S8I_057 | Single bulged G | ||
| IL_8S8I_062 | No text annotation | ||
| IL_8S8I_063 | No text annotation | ||
| IL_8S8I_095 | No text annotation | ||
| IL_8S8I_096 | No text annotation | ||
| IL_8S8I_064 | No text annotation | ||
| IL_8S8I_070 | Single bulged A | ||
| IL_8S8I_073 | Isolated non-canonical cWW pair | ||
| IL_8S8I_077 | No text annotation | ||
| IL_8S8I_079 | Isolated non-canonical cWW pair | ||
| IL_8S8I_083 | Isolated non-canonical cWW pair | ||
| IL_8S8I_087 | Single bulged U | ||
| IL_8S8I_088 | Isolated non-canonical cWW pair | ||
| IL_8S8I_091 | Triple sheared | ||
| IL_8S8I_092 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_8S8I_001 | 1/2/41:42, 1/2/432:438, 1/2/463:465 | No text annotation | homologous J3_8C3A_082 NA | |
| J3_8S8I_002 | 1/2/212:227, 1/2/236:242, 1/2/249:251 | No text annotation | ||
| J3_8S8I_003 | 1/2/632:634, 1/2/860:865, 1/2/961:965 | No text annotation | homologous J3_8C3A_034 NA | |
| J3_8S8I_004 | 1/2/759:763, 1/2/773:775, 1/2/784:790 | No text annotation | ||
| J3_8S8I_005 | 1/2/880:883, 1/2/927:935, 1/2/942:946 | No text annotation | homologous J3_8P9A_074 NA | |
| J3_8S8I_006 | 1/2/1036:1038, 1/2/1078:1082, 1/2/1089:1093 | No text annotation | geometric J3_4V88_034 NA | |
| J3_8S8I_007 | 1/2/1160:1163, 1/2/1579:1585, 1/2/1607:1614 | No text annotation | homologous J3_8P9A_076 NA | |
| J3_8S8I_008 | 1/2/1167:1170, 1/2/1466:1468, 1/2/1572:1575 | No text annotation | homologous J3_8C3A_039 NA | |
| J3_8S8I_009 | 1/2/1179:1186, 1/2/1197:1208, 1/2/1452:1456 | No text annotation | homologous J3_8C3A_040 NA | |
| J3_8S8I_010 | 1/2/1214:1219, 1/2/1262:1266, 1/2/1440:1446 | No text annotation | homologous J3_8C3A_041 NA | |
| J3_8S8I_016 | 1/2/1282:1287, 1/2/1326:1331, 1/2/1417:1422 | No text annotation | homologous J3_8P9A_080 NA | |
| J3_8S8I_017 | 1/2/1291:1293, 1/2/1302:1305, 1/2/1317:1322 | No text annotation | ||
| J3_8S8I_013 | 1/2/1335:1337, 1/2/1384:1387, 1/2/1410:1413 | No text annotation | geometric J3_8C3A_043 NA | |
| J3_8S8I_014 | 1/2/1335:1337, 1/2/1384:1389, 1/2/1405:1413 | No text annotation | homologous J3_8C3A_086 NA | |
| J3_8S8I_015 | 1/2/1468:1472, 1/2/1531:1538, 1/2/1569:1572 | No text annotation | homologous J3_8C3A_044 NA | |
| J4_8S8I_002 | 1/2/99:107, 1/2/306:308, 1/2/356:360, 1/2/382:383 | No text annotation | homologous J4_8P9A_021 NA | |
| J4_8S8I_005 | 1/2/621:623, 1/2/974:979, 1/2/1020:1031, 1/2/1102:1103 | No text annotation | homologous J4_8CRE_022 J4_14595.4 | |
| J5_8S8I_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_8S8I_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_8S8I_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_8P9A_017 NA | |
| J5_8S8I_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_8S8I_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_8S8I_007 | 1/2/635:640, 1/2/693:699, 1/2/739:744, 1/2/806:816, 1/2/853:859 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_8S8I_011 | No text annotation | ||
| J3_8S8I_012 | No text annotation | ||
| J4_8S8I_004 | tRNA junction | ||
| J4_8S8I_001 | No text annotation | ||
| J4_8S8I_003 | No text annotation | ||
| J5_8S8I_006 | No text annotation |
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