6GSN Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_6GSN_001 | 1/1/13:22 | No text annotation | homologous HL_5UD5_001 HL_48417.6 | |
| HL_6GSN_002 | 1/1/31:39 | tRNA anticodon loop | homologous HL_4TUE_034 HL_06059.7 | |
| HL_6GSN_003 | 1/1/53:61 | T-loop with 2 stacked bulged bases | homologous HL_3TUP_003 HL_28252.9 | |
| HL_6GSN_004 | 1/2/7:17 | No text annotation | homologous HL_4V88_186 NA | |
| HL_6GSN_005 | 1/2/70:81 | No text annotation | geometric HL_5J7L_143 HL_75660.5 | |
| HL_6GSN_006 | 1/2/152:160 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_6GSN_007 | 1/2/189:194 | No text annotation | homologous HL_4V88_189 NA | |
| HL_6GSN_008 | 1/2/229:234 | No text annotation | geometric HL_3SKI_003 HL_14333.1 | |
| HL_6GSN_009 | 1/2/242:249 | T-loop with 1 bulged base | homologous HL_4V88_191 NA | |
| HL_6GSN_010 | 1/2/274:280 | No text annotation | geometric HL_5TBW_006 NA | |
| HL_6GSN_011 | 1/2/329:337 | GNRA related | homologous HL_4V88_193 NA | |
| HL_6GSN_012 | 1/2/367:372 | No text annotation | homologous HL_4V88_194 NA | |
| HL_6GSN_013 | 1/2/392:403 | No text annotation | homologous HL_4V88_195 NA | |
| HL_6GSN_014 | 1/2/413:418 | UNCG | homologous HL_4V88_196 NA | |
| HL_6GSN_015 | 1/2/449:455 | No text annotation | homologous HL_4V88_197 NA | |
| HL_6GSN_016 | 1/2/490:495 | No text annotation | ||
| HL_6GSN_017 | 1/2/519:531 | No text annotation | homologous HL_4V88_199 NA | |
| HL_6GSN_018 | 1/2/568:573 | GNRA variation | homologous HL_4V88_200 NA | |
| HL_6GSN_042 | 1/2/660:668 | No text annotation | ||
| HL_6GSN_043 | 1/2/715:723 | No text annotation | ||
| HL_6GSN_021 | 1/2/764:772 | No text annotation | homologous HL_4V88_203 NA | |
| HL_6GSN_022 | 1/2/777:782 | No text annotation | ||
| HL_6GSN_023 | 1/2/828:842 | Pseudoknot geometry | homologous HL_4V88_205 NA | |
| HL_6GSN_044 | 1/2/899:908 | No text annotation | homologous HL_8P9A_209 HL_75293.5 | |
| HL_6GSN_025 | 1/2/936:941 | GNRA | homologous HL_4V88_207 NA | |
| HL_6GSN_026 | 1/2/996:1006 | No text annotation | homologous HL_4V88_208 NA | |
| HL_6GSN_041 | 1/2/1053:1064 | No text annotation | ||
| HL_6GSN_027 | 1/2/1055:1063 | No text annotation | ||
| HL_6GSN_028 | 1/2/1083:1088 | GNRA | homologous HL_4V88_210 NA | |
| HL_6GSN_029 | 1/2/1120:1125 | GNRA | homologous HL_4V88_211 NA | |
| HL_6GSN_030 | 1/2/1187:1196 | No text annotation | homologous HL_4V88_212 NA | |
| HL_6GSN_031 | 1/2/1236:1247 | No text annotation | ||
| HL_6GSN_032 | 1/2/1295:1300 | GNRA | homologous HL_4V88_214 NA | |
| HL_6GSN_033 | 1/2/1308:1315 | No text annotation | homologous HL_4V88_215 NA | |
| HL_6GSN_034 | 1/2/1358:1363 | No text annotation | geometric HL_2Y9H_003 HL_75660.5 | |
| HL_6GSN_035 | 1/2/1394:1400 | GNRA | homologous HL_4V88_217 NA | |
| HL_6GSN_036 | 1/2/1499:1504 | GNRA | homologous HL_4V88_218 NA | |
| HL_6GSN_045 | 1/2/1548:1559 | No text annotation | homologous HL_8CRE_223 HL_67079.1 | |
| HL_6GSN_038 | 1/2/1592:1600 | No text annotation | homologous HL_4V88_220 NA | |
| HL_6GSN_040 | 1/2/1776:1781 | GNRA variation | homologous HL_4V88_222 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_6GSN_019 | No text annotation | ||
| HL_6GSN_020 | No text annotation | ||
| HL_6GSN_024 | No text annotation | ||
| HL_6GSN_037 | No text annotation | ||
| HL_6GSN_039 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_6GSN_001 | 1/2/24:27, 1/2/598:600 | Decoding loop related | geometric IL_2O3X_003 IL_31737.3 | |
| IL_6GSN_002 | 1/2/35:37, 1/2/470:472 | Isolated non-canonical cWW pair | geometric IL_4ZC7_004 IL_87907.2 | |
| IL_6GSN_093 | 1/2/35:41, 1/2/465:472 | No text annotation | ||
| IL_6GSN_003 | 1/2/37:41, 1/2/465:470 | Triple sheared related | geometric IL_8C3A_394 NA | |
| IL_6GSN_004 | 1/2/42:48, 1/2/430:432 | No text annotation | geometric IL_4V88_387 NA | |
| IL_6GSN_005 | 1/2/50:52, 1/2/427:428 | Minor groove platform | homologous IL_4V88_388 NA | |
| IL_6GSN_006 | 1/2/58:63, 1/2/87:89 | No text annotation | geometric IL_4V88_389 NA | |
| IL_6GSN_007 | 1/2/63:64, 1/2/85:87 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_6GSN_095 | 1/2/64:69, 1/2/82:85 | Double sheared | geometric IL_5J7L_256 IL_09705.15 | |
| IL_6GSN_009 | 1/2/109:112, 1/2/301:304 | Tandem non-canonical cWW pairs | homologous IL_4V88_391 NA | |
| IL_6GSN_010 | 1/2/112:113, 1/2/299:301 | Single stack bend | geometric IL_5J7L_032 IL_26793.1 | |
| IL_6GSN_011 | 1/2/113:117, 1/2/298:299 | Multiple bulged bases | geometric IL_4YAZ_007 IL_82107.5 | |
| IL_6GSN_106 | 1/2/113:121, 1/2/294:300 | No text annotation | ||
| IL_6GSN_012 | 1/2/117:121, 1/2/294:298 | No text annotation | ||
| IL_6GSN_013 | 1/2/121:123, 1/2/293:294 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_6GSN_014 | 1/2/123:124, 1/2/291:293 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_6GSN_015 | 1/2/142:148, 1/2/164:171 | tWH-tWH-tHW-tHW | homologous IL_4V88_394 NA | |
| IL_6GSN_016 | 1/2/149:151, 1/2/161:163 | Isolated non-canonical cWW contact | homologous IL_4V88_395 NA | |
| IL_6GSN_017 | 1/2/185:188, 1/2/195:198 | Double sheared | homologous IL_4V88_396 NA | |
| IL_6GSN_018 | 1/2/203:205, 1/2/258:262 | Major groove platform with extra cWW | homologous IL_4V88_397 NA | |
| IL_6GSN_019 | 1/2/205:206, 1/2/256:258 | Single stack bend | geometric IL_7KGA_003 IL_90729.1 | |
| IL_6GSN_020 | 1/2/207:209, 1/2/254:255 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_6GSN_107 | 1/2/264:266, 1/2/287:288 | Single bulged A | homologous IL_8P9A_388 IL_31462.7 | |
| IL_6GSN_022 | 1/2/269:272, 1/2/282:284 | No text annotation | homologous IL_4V88_400 NA | |
| IL_6GSN_023 | 1/2/310:315, 1/2/347:354 | Kink-turn with non-sequential stacking | homologous IL_4V88_402 NA | |
| IL_6GSN_024 | 1/2/317:322, 1/2/344:345 | No text annotation | geometric IL_4ERD_001 IL_84476.1 | |
| IL_6GSN_025 | 1/2/362:364, 1/2/375:380 | No text annotation | homologous IL_4V88_404 NA | |
| IL_6GSN_026 | 1/2/388:390, 1/2/405:407 | Isolated cWH basepair | homologous IL_4V88_405 NA | |
| IL_6GSN_027 | 1/2/438:440, 1/2/462:463 | Single bulged U | geometric IL_4LFB_014 IL_89505.4 | |
| IL_6GSN_028 | 1/2/442:446, 1/2/459:460 | C-loop | geometric IL_5J7L_018 IL_03109.3 | |
| IL_6GSN_029 | 1/2/446:447, 1/2/457:459 | Single bulged G | geometric IL_5J7L_019 IL_00225.14 | |
| IL_6GSN_108 | 1/2/479:482, 1/2/503:507 | Tandem non-canonical cWW pairs | geometric IL_5EW4_002 IL_85033.2 | |
| IL_6GSN_031 | 1/2/486:489, 1/2/496:499 | No text annotation | ||
| IL_6GSN_032 | 1/2/547:556, 1/2/586:589 | No text annotation | ||
| IL_6GSN_033 | 1/2/556:558, 1/2/585:586 | Single bulged U | geometric IL_5J7L_279 IL_89505.4 | |
| IL_6GSN_034 | 1/2/561:567, 1/2/574:582 | Kink-turn related | homologous IL_4V88_415 NA | |
| IL_6GSN_035 | 1/2/615:621, 1/2/1103:1104 | No text annotation | homologous IL_4V88_416 NA | |
| IL_6GSN_036 | 1/2/623:625, 1/2/972:974 | Isolated non-canonical cWW pair | homologous IL_4V88_417 NA | |
| IL_6GSN_037 | 1/2/626:630, 1/2/967:971 | tSH-tHW-tHS | homologous IL_4V88_418 NA | |
| IL_6GSN_038 | 1/2/650:652, 1/2/678:683 | No text annotation | ||
| IL_6GSN_039 | 1/2/656:658, 1/2/670:674 | No text annotation | ||
| IL_6GSN_040 | 1/2/703:713, 1/2/725:735 | No text annotation | ||
| IL_6GSN_097 | 1/2/745:747, 1/2/801:805 | No text annotation | ||
| IL_6GSN_042 | 1/2/748:750, 1/2/798:800 | Isolated non-canonical cWW pair | homologous IL_4V88_424 NA | |
| IL_6GSN_109 | 1/2/748:776, 1/2/783:800 | No text annotation | ||
| IL_6GSN_110 | 1/2/817:821, 1/2/849:852 | No text annotation | homologous IL_8P9A_468 NA | |
| IL_6GSN_100 | 1/2/867:869, 1/2/956:959 | Isolated cWH basepair | homologous IL_8C3A_510 NA | |
| IL_6GSN_045 | 1/2/870:873, 1/2/952:955 | Tandem non-canonical cWW pairs | homologous IL_4V88_430 NA | |
| IL_6GSN_046 | 1/2/873:877, 1/2/949:952 | Tandem non-canonical cWW pairs | geometric IL_5TBW_100 NA | |
| IL_6GSN_047 | 1/2/884:887, 1/2/923:926 | Tandem non-canonical cWW pairs | homologous IL_4V88_432 NA | |
| IL_6GSN_048 | 1/2/892:898, 1/2/909:918 | No text annotation | homologous IL_8P9A_422 IL_57741.1 | |
| IL_6GSN_101 | 1/2/982:996, 1/2/1006:1017 | No text annotation | ||
| IL_6GSN_049 | 1/2/1033:1035, 1/2/1094:1100 | No text annotation | homologous IL_4V88_437 NA | |
| IL_6GSN_050 | 1/2/1040:1044, 1/2/1072:1076 | No text annotation | ||
| IL_6GSN_051 | 1/2/1050:1052, 1/2/1065:1066 | Single bulged U | homologous IL_4V88_439 NA | |
| IL_6GSN_052 | 1/2/1053:1055, 1/2/1063:1064 | Single stack bend | geometric IL_4LFB_041 IL_90729.1 | |
| IL_6GSN_053 | 1/2/1110:1117, 1/2/1128:1133 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | homologous IL_4V88_440 NA | |
| IL_6GSN_055 | 1/2/1143:1145, 1/2/1630:1631 | Single stack bend | geometric IL_4V84_420 IL_10569.1 | |
| IL_6GSN_102 | 1/2/1145:1146, 1/2/1628:1630 | Single bulged A | homologous IL_8C3A_447 NA | |
| IL_6GSN_057 | 1/2/1148:1150, 1/2/1625:1626 | Single bulged G | homologous IL_4V88_442 NA | |
| IL_6GSN_058 | 1/2/1156:1159, 1/2/1615:1619 | C-loop | homologous IL_4V88_443 NA | |
| IL_6GSN_059 | 1/2/1172:1175, 1/2/1461:1464 | Tandem non-canonical cWW pairs | geometric IL_3WBM_003 IL_85033.2 | |
| IL_6GSN_060 | 1/2/1177:1178, 1/2/1457:1459 | Minor groove platform | homologous IL_4V88_445 NA | |
| IL_6GSN_061 | 1/2/1206:1208, 1/2/1452:1453 | Multiple bulged bases | geometric IL_5W1H_001 IL_82107.5 | |
| IL_6GSN_062 | 1/2/1212:1214, 1/2/1446:1448 | Isolated non-canonical cWW pair | homologous IL_4V88_446 NA | |
| IL_6GSN_111 | 1/2/1223:1232, 1/2/1251:1258 | No text annotation | homologous IL_8P9A_470 IL_28304.1 | |
| IL_6GSN_064 | 1/2/1232:1235, 1/2/1248:1251 | No text annotation | ||
| IL_6GSN_065 | 1/2/1267:1269, 1/2/1438:1439 | Single bulged U | homologous IL_4V88_449 NA | |
| IL_6GSN_103 | 1/2/1271:1275, 1/2/1434:1436 | Isolated cWS basepair | geometric IL_4LFB_044 IL_76319.5 | |
| IL_6GSN_104 | 1/2/1271:1277, 1/2/1428:1436 | No text annotation | homologous IL_8P9A_439 IL_86012.1 | |
| IL_6GSN_067 | 1/2/1275:1277, 1/2/1428:1434 | Minor groove platform with extra cWW | homologous IL_4V88_451 NA | |
| IL_6GSN_068 | 1/2/1279:1280, 1/2/1424:1426 | Single bulged A | homologous IL_4V88_452 NA | |
| IL_6GSN_069 | 1/2/1289:1291, 1/2/1322:1324 | Isolated cWH basepair | homologous IL_4V88_453 NA | |
| IL_6GSN_070 | 1/2/1305:1307, 1/2/1316:1317 | Minor groove platform | homologous IL_4V88_454 NA | |
| IL_6GSN_071 | 1/2/1338:1341, 1/2/1381:1383 | Isolated non-canonical cWW pair | homologous IL_4V88_455 NA | |
| IL_6GSN_072 | 1/2/1344:1347, 1/2/1375:1378 | Minor groove platform | homologous IL_4V88_456 NA | |
| IL_6GSN_105 | 1/2/1352:1353, 1/2/1368:1370 | Single bulged U | geometric IL_7PMQ_002 IL_89505.4 | |
| IL_6GSN_074 | 1/2/1387:1389, 1/2/1405:1410 | No text annotation | homologous IL_8C3A_465 NA | |
| IL_6GSN_075 | 1/2/1478:1485, 1/2/1517:1525 | No text annotation | homologous IL_4V88_459 NA | |
| IL_6GSN_076 | 1/2/1486:1492, 1/2/1511:1516 | 180 degree turn | homologous IL_4V88_460 NA | |
| IL_6GSN_112 | 1/2/1494:1496, 1/2/1507:1509 | No text annotation | homologous IL_8CRE_464 IL_07785.1 | |
| IL_6GSN_078 | 1/2/1538:1543, 1/2/1564:1569 | No text annotation | homologous IL_4V88_462 NA | |
| IL_6GSN_079 | 1/2/1634:1636, 1/2/1762:1765 | No text annotation | homologous IL_4V88_463 NA | |
| IL_6GSN_080 | 1/2/1636:1639, 1/2/1758:1762 | No text annotation | geometric IL_4V88_464 NA | |
| IL_6GSN_081 | 1/2/1640:1642, 1/2/1755:1757 | Isolated non-canonical cWW pair | homologous IL_4V88_465 NA | |
| IL_6GSN_082 | 1/2/1642:1645, 1/2/1751:1755 | Tandem non-canonical cWW pairs | geometric IL_6CZR_141 NA | |
| IL_6GSN_083 | 1/2/1648:1650, 1/2/1746:1748 | Isolated non-canonical cWW pair | homologous IL_4V88_467 NA | |
| IL_6GSN_084 | 1/2/1651:1654, 1/2/1742:1745 | Double sheared | geometric IL_5J7L_333 IL_09705.15 | |
| IL_6GSN_085 | 1/2/1654:1656, 1/2/1741:1742 | Single bulged U | homologous IL_4V88_469 NA | |
| IL_6GSN_086 | 1/2/1663:1665, 1/2/1732:1734 | Isolated non-canonical cWW pair | homologous IL_4V88_470 NA | |
| IL_6GSN_087 | 1/2/1667:1670, 1/2/1727:1730 | Double sheared | homologous IL_4V88_471 NA | |
| IL_6GSN_088 | 1/2/1673:1676, 1/2/1721:1724 | Tandem non-canonical cWW pairs | geometric IL_4V88_473 NA | |
| IL_6GSN_089 | 1/2/1676:1680, 1/2/1717:1721 | Triple sheared | homologous IL_4V88_474 NA | |
| IL_6GSN_113 | 1/2/1685:1688, 1/2/1709:1712 | No text annotation | ||
| IL_6GSN_091 | 1/2/1768:1770, 1/2/1787:1788 | Single stack bend | geometric IL_4V83_236 IL_90729.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_6GSN_092 | No text annotation | ||
| IL_6GSN_094 | No text annotation | ||
| IL_6GSN_008 | Triple sheared | ||
| IL_6GSN_096 | No text annotation | ||
| IL_6GSN_021 | Isolated non-canonical cWW pair | ||
| IL_6GSN_030 | No text annotation | ||
| IL_6GSN_041 | No text annotation | ||
| IL_6GSN_098 | No text annotation | ||
| IL_6GSN_043 | No text annotation | ||
| IL_6GSN_099 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_044 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_054 | Isolated non-canonical cWW pair | ||
| IL_6GSN_056 | Isolated non-canonical cWW with bulges | ||
| IL_6GSN_063 | No text annotation | ||
| IL_6GSN_066 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_073 | Isolated non-canonical cWW with bulges | ||
| IL_6GSN_077 | Tandem non-canonical cWW pairs | ||
| IL_6GSN_090 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_6GSN_001 | 1/2/41:42, 1/2/432:438, 1/2/463:465 | No text annotation | homologous J3_8C3A_082 NA | |
| J3_6GSN_013 | 1/2/212:227, 1/2/236:242, 1/2/249:251 | No text annotation | ||
| J3_6GSN_002 | 1/2/632:634, 1/2/860:865, 1/2/961:965 | No text annotation | homologous J3_8C3A_034 NA | |
| J3_6GSN_016 | 1/2/880:883, 1/2/927:935, 1/2/942:946 | No text annotation | homologous J3_8P9A_074 J3_76375.1 | |
| J3_6GSN_004 | 1/2/1036:1038, 1/2/1078:1082, 1/2/1089:1093 | No text annotation | geometric J3_4V88_034 NA | |
| J3_6GSN_005 | 1/2/1160:1162, 1/2/1580:1585, 1/2/1607:1614 | No text annotation | ||
| J3_6GSN_006 | 1/2/1167:1170, 1/2/1466:1468, 1/2/1572:1575 | No text annotation | homologous J3_4V88_036 NA | |
| J3_6GSN_007 | 1/2/1179:1186, 1/2/1197:1206, 1/2/1453:1456 | No text annotation | ||
| J3_6GSN_014 | 1/2/1179:1186, 1/2/1197:1208, 1/2/1452:1456 | No text annotation | homologous J3_8C3A_040 NA | |
| J3_6GSN_008 | 1/2/1214:1219, 1/2/1262:1266, 1/2/1440:1446 | No text annotation | homologous J3_4V88_038 NA | |
| J3_6GSN_009 | 1/2/1282:1287, 1/2/1326:1331, 1/2/1417:1422 | No text annotation | homologous J3_4V88_039 NA | |
| J3_6GSN_010 | 1/2/1291:1293, 1/2/1302:1305, 1/2/1317:1322 | No text annotation | ||
| J3_6GSN_011 | 1/2/1335:1337, 1/2/1384:1387, 1/2/1410:1413 | No text annotation | homologous J3_8C3A_043 NA | |
| J3_6GSN_015 | 1/2/1335:1337, 1/2/1384:1389, 1/2/1405:1413 | No text annotation | homologous J3_8C3A_086 NA | |
| J3_6GSN_012 | 1/2/1468:1472, 1/2/1531:1538, 1/2/1569:1572 | No text annotation | homologous J3_4V88_041 NA | |
| J4_6GSN_001 | 1/1/7:10, 1/1/25:27, 1/1/43:49, 1/1/65:66 | No text annotation | ||
| J4_6GSN_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_15241.1 | |
| J4_6GSN_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_6GSN_001 | 1/2/31:35, 1/2/472:479, 1/2/507:519, 1/2/531:545, 1/2/591:594 | No text annotation | ||
| J5_6GSN_002 | 1/2/54:57, 1/2/90:97, 1/2/385:387, 1/2/408:412, 1/2/419:425 | No text annotation | ||
| J5_6GSN_003 | 1/2/124:141, 1/2/172:181, 1/2/202:203, 1/2/262:264, 1/2/288:292 | No text annotation | ||
| J5_6GSN_006 | 1/2/124:141, 1/2/172:181, 1/2/202:203, 1/2/262:266, 1/2/287:292 | No text annotation | ||
| J5_6GSN_007 | 1/2/635:640, 1/2/693:698, 1/2/740:744, 1/2/806:816, 1/2/853:859 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_6GSN_003 | No text annotation | ||
| J5_6GSN_004 | No text annotation | ||
| J5_6GSN_005 | No text annotation |
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