7SYP Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_7SYP_001 | 1/2/7:17 | No text annotation | geometric HL_4V88_186 NA | |
| HL_7SYP_002 | 1/2/69:80 | No text annotation | geometric HL_361D_002 HL_13963.3 | |
| HL_7SYP_003 | 1/2/156:162 | No text annotation | geometric HL_7A0S_011 HL_75660.5 | |
| HL_7SYP_004 | 1/2/197:202 | UNCG variation | geometric HL_1P6V_001 HL_53890.2 | |
| HL_7SYP_005 | 1/2/288:295 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_7SYP_007 | 1/2/377:387 | tRNA D-loop | geometric HL_5AXM_001 HL_20811.4 | |
| HL_7SYP_008 | 1/2/416:421 | No text annotation | geometric HL_4V88_194 NA | |
| HL_7SYP_009 | 1/2/441:452 | No text annotation | geometric HL_4V88_195 NA | |
| HL_7SYP_010 | 1/2/462:467 | UNCG | geometric HL_4LFB_009 HL_34617.5 | |
| HL_7SYP_011 | 1/2/498:504 | No text annotation | geometric HL_5NFV_001 HL_69752.2 | |
| HL_7SYP_012 | 1/2/539:544 | No text annotation | geometric HL_4V9F_003 HL_75660.5 | |
| HL_7SYP_013 | 1/2/569:581 | No text annotation | geometric HL_4V88_199 NA | |
| HL_7SYP_014 | 1/2/618:623 | GNRA variation | geometric HL_4V88_200 NA | |
| HL_7SYP_015 | 1/2/820:828 | No text annotation | geometric HL_4V88_203 NA | |
| HL_7SYP_017 | 1/2/884:902 | No text annotation | ||
| HL_7SYP_018 | 1/2/957:966 | No text annotation | geometric HL_4LFB_015 HL_75293.5 | |
| HL_7SYP_019 | 1/2/994:999 | GNRA | geometric HL_4V88_207 NA | |
| HL_7SYP_020 | 1/2/1054:1064 | No text annotation | homologous HL_8C3A_213 NA | |
| HL_7SYP_021 | 1/2/1113:1120 | Purine riboswitch | geometric HL_4LX6_002 HL_31585.4 | |
| HL_7SYP_022 | 1/2/1141:1146 | GNRA | geometric HL_4V88_210 NA | |
| HL_7SYP_023 | 1/2/1178:1183 | GNRA | geometric HL_5M0J_001 HL_37824.8 | |
| HL_7SYP_024 | 1/2/1245:1254 | No text annotation | geometric HL_5J7L_143 HL_75660.5 | |
| HL_7SYP_025 | 1/2/1294:1305 | No text annotation | ||
| HL_7SYP_026 | 1/2/1353:1358 | GNRA | geometric HL_4LFB_028 HL_37824.8 | |
| HL_7SYP_027 | 1/2/1366:1373 | No text annotation | geometric HL_4V88_215 NA | |
| HL_7SYP_029 | 1/2/1460:1466 | GNRA | geometric HL_5J7L_026 HL_93535.1 | |
| HL_7SYP_030 | 1/2/1565:1570 | GNRA | geometric HL_4WF9_015 HL_37824.8 | |
| HL_7SYP_031 | 1/2/1614:1625 | No text annotation | geometric HL_4V88_219 NA | |
| HL_7SYP_032 | 1/2/1658:1666 | No text annotation | geometric HL_4V88_220 NA | |
| HL_7SYP_034 | 1/2/1847:1852 | GNRA variation | geometric HL_4V88_222 NA | |
| HL_7SYP_035 | 1/z/79:87 | No text annotation | ||
| HL_7SYP_036 | 1/z/161:166 | No text annotation | ||
| HL_7SYP_038 | 1/z/232:235 | No text annotation | ||
| HL_7SYP_045 | 1/z/263:270 | No text annotation | ||
| HL_7SYP_040 | 1/z/280:283 | No text annotation | ||
| HL_7SYP_041 | 1/z/294:299 | No text annotation | ||
| HL_7SYP_042 | 1/z/304:313 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_7SYP_043 | No text annotation | ||
| HL_7SYP_006 | No text annotation | ||
| HL_7SYP_016 | No text annotation | ||
| HL_7SYP_028 | No text annotation | ||
| HL_7SYP_033 | Externally structured | ||
| HL_7SYP_044 | No text annotation | ||
| HL_7SYP_037 | No text annotation | ||
| HL_7SYP_039 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_7SYP_001 | 1/2/23:25, 1/2/649:651 | Isolated non-canonical cWW pair | geometric IL_4WF9_020 IL_87907.2 | |
| IL_7SYP_002 | 1/2/34:36, 1/2/519:521 | Isolated cWH basepair | geometric IL_3R1C_031 NA | |
| IL_7SYP_003 | 1/2/37:40, 1/2/514:518 | Double sheared | geometric IL_4WF9_016 IL_09705.15 | |
| IL_7SYP_004 | 1/2/41:47, 1/2/479:481 | No text annotation | geometric IL_4V88_387 NA | |
| IL_7SYP_005 | 1/2/49:51, 1/2/476:477 | Minor groove platform | geometric IL_4V88_412 NA | |
| IL_7SYP_006 | 1/2/56:62, 1/2/86:89 | Other IL | geometric IL_5TBW_043 NA | |
| IL_7SYP_007 | 1/2/63:68, 1/2/81:85 | No text annotation | geometric IL_4V88_390 NA | |
| IL_7SYP_008 | 1/2/108:110, 1/2/351:353 | Isolated non-canonical cWW pair | geometric IL_1KFO_003 NA | |
| IL_7SYP_009 | 1/2/110:112, 1/2/349:351 | Isolated non-canonical cWW contact | geometric IL_5UNE_001 IL_44465.1 | |
| IL_7SYP_010 | 1/2/112:115, 1/2/348:349 | Multiple bulged bases | geometric IL_5WLH_001 IL_82107.5 | |
| IL_7SYP_011 | 1/2/116:121, 1/2/343:347 | No text annotation | geometric IL_4V88_393 NA | |
| IL_7SYP_013 | 1/2/145:151, 1/2/167:174 | tWH-tWH-tHW-tHW | geometric IL_4V88_394 NA | |
| IL_7SYP_014 | 1/2/152:155, 1/2/163:166 | Tandem non-canonical cWW pairs | geometric IL_1D4R_001 IL_85033.2 | |
| IL_7SYP_015 | 1/2/188:192, 1/2/207:211 | Double sheared with non-canonical cWW | geometric IL_5J7L_274 IL_17948.2 | |
| IL_7SYP_016 | 1/2/216:219, 1/2/302:309 | No text annotation | ||
| IL_7SYP_018 | 1/2/312:314, 1/2/336:337 | Single bulged A | geometric IL_4V88_399 NA | |
| IL_7SYP_019 | 1/2/317:319, 1/2/332:333 | Single stack bend | geometric IL_5TBW_009 NA | |
| IL_7SYP_020 | 1/2/320:322, 1/2/330:331 | Single stack bend | geometric IL_4V9F_005 IL_90729.1 | |
| IL_7SYP_021 | 1/2/359:364, 1/2/396:403 | Kink-turn with non-sequential stacking | geometric IL_5J7L_014 IL_46174.3 | |
| IL_7SYP_022 | 1/2/366:371, 1/2/393:394 | No text annotation | geometric IL_5Y58_001 IL_59877.1 | |
| IL_7SYP_100 | 1/2/366:372, 1/2/392:394 | No text annotation | ||
| IL_7SYP_023 | 1/2/411:413, 1/2/424:429 | No text annotation | geometric IL_4V88_404 NA | |
| IL_7SYP_024 | 1/2/437:439, 1/2/454:456 | Isolated non-canonical cWW pair | geometric IL_7A0S_014 IL_87907.2 | |
| IL_7SYP_025 | 1/2/459:461, 1/2/468:470 | Isolated near basepair | geometric IL_3NJ7_003 IL_42997.3 | |
| IL_7SYP_026 | 1/2/487:489, 1/2/511:512 | Single bulged U | geometric IL_4LFB_014 IL_89505.4 | |
| IL_7SYP_027 | 1/2/491:495, 1/2/508:509 | C-loop | geometric IL_5J7L_018 IL_03109.3 | |
| IL_7SYP_028 | 1/2/495:496, 1/2/506:508 | Single bulged G | geometric IL_5J7L_019 IL_00225.14 | |
| IL_7SYP_029 | 1/2/529:532, 1/2/552:556 | No text annotation | ||
| IL_7SYP_030 | 1/2/534:537, 1/2/546:550 | No text annotation | ||
| IL_7SYP_031 | 1/2/563:565, 1/2/585:592 | No text annotation | homologous IL_8C3A_420 NA | |
| IL_7SYP_032 | 1/2/566:569, 1/2/581:584 | Tandem non-canonical cWW pairs | geometric IL_5C5W_003 NA | |
| IL_7SYP_033 | 1/2/599:608, 1/2/635:637 | Isolated non-canonical cWW pair | geometric IL_4V88_470 NA | |
| IL_7SYP_034 | 1/2/611:617, 1/2/624:632 | Kink-turn related | geometric IL_4V88_415 NA | |
| IL_7SYP_035 | 1/2/663:665, 1/2/1162:1164 | Isolated non-canonical cWW pair | geometric IL_1Y27_001 IL_87907.2 | |
| IL_7SYP_036 | 1/2/665:671, 1/2/1161:1162 | Multiple bulged bases | geometric IL_1R3E_001 IL_84476.1 | |
| IL_7SYP_037 | 1/2/673:675, 1/2/1030:1032 | Isolated non-canonical cWW pair | geometric IL_4YHW_001 IL_87907.2 | |
| IL_7SYP_038 | 1/2/676:682, 1/2/1023:1029 | No text annotation | ||
| IL_7SYP_112 | 1/2/752:754, 1/2/790:791 | No text annotation | ||
| IL_7SYP_041 | 1/2/802:803, 1/2/860:863 | Major groove minor groove platform; mini C-loop | geometric IL_5J7L_029 IL_68140.4 | |
| IL_7SYP_042 | 1/2/805:807, 1/2/856:858 | Isolated non-canonical cWW pair | geometric IL_4JGN_004 NA | |
| IL_7SYP_043 | 1/2/807:815, 1/2/849:856 | No text annotation | geometric IL_4V88_425 NA | |
| IL_7SYP_044 | 1/2/874:876, 1/2/910:912 | Isolated non-canonical cWW pair | geometric IL_5MWI_002 IL_87907.2 | |
| IL_7SYP_045 | 1/2/877:879, 1/2/907:909 | Isolated non-canonical cWW pair | geometric IL_5TBW_042 NA | |
| IL_7SYP_047 | 1/2/922:923, 1/2/1019:1022 | Major groove platform; stack outside cWW | geometric IL_4V88_428 NA | |
| IL_7SYP_113 | 1/2/925:926, 1/2/1015:1017 | Single bulged U | geometric IL_7KVT_002 IL_89505.4 | |
| IL_7SYP_049 | 1/2/927:931, 1/2/1010:1014 | No text annotation | geometric IL_5TBW_121 NA | |
| IL_7SYP_050 | 1/2/931:935, 1/2/1007:1010 | Tandem non-canonical cWW pairs | geometric IL_4V88_431 NA | |
| IL_7SYP_051 | 1/2/942:945, 1/2/981:984 | Tandem non-canonical cWW pairs | geometric IL_4V88_430 NA | |
| IL_7SYP_052 | 1/2/952:956, 1/2/967:974 | Kink-turn | geometric IL_4V88_434 NA | |
| IL_7SYP_114 | 1/2/1041:1047, 1/2/1071:1074 | No text annotation | ||
| IL_7SYP_054 | 1/2/1047:1051, 1/2/1067:1071 | tSH-tHW-tHS | geometric IL_6CZR_145 NA | |
| IL_7SYP_055 | 1/2/1091:1093, 1/2/1152:1158 | No text annotation | geometric IL_4V88_437 NA | |
| IL_7SYP_056 | 1/2/1098:1101, 1/2/1131:1134 | Tandem non-canonical cWW pairs | geometric IL_4V88_438 NA | |
| IL_7SYP_104 | 1/2/1098:1103, 1/2/1129:1134 | No text annotation | geometric IL_6O5F_001 NA | |
| IL_7SYP_057 | 1/2/1101:1103, 1/2/1129:1131 | Isolated non-canonical cWW pair | geometric IL_4KNQ_002 IL_87907.2 | |
| IL_7SYP_105 | 1/2/1108:1110, 1/2/1123:1124 | Minor groove platform | geometric IL_4V88_388 NA | |
| IL_7SYP_059 | 1/2/1168:1175, 1/2/1186:1191 | 8x6 Sarcin-Ricin with inserted Y; G-bulge | geometric IL_4V88_440 NA | |
| IL_7SYP_060 | 1/2/1214:1217, 1/2/1681:1685 | C-loop | geometric IL_4V88_443 NA | |
| IL_7SYP_061 | 1/2/1230:1232, 1/2/1526:1528 | Isolated non-canonical cWW pair | geometric IL_4V88_444 NA | |
| IL_7SYP_062 | 1/2/1235:1236, 1/2/1521:1523 | Minor groove platform | geometric IL_4V88_445 NA | |
| IL_7SYP_063 | 1/2/1270:1273, 1/2/1510:1512 | No text annotation | geometric IL_4N0T_004 IL_99358.1 | |
| IL_7SYP_064 | 1/2/1282:1287, 1/2/1314:1315 | No text annotation | ||
| IL_7SYP_106 | 1/2/1282:1294, 1/2/1305:1315 | No text annotation | ||
| IL_7SYP_065 | 1/2/1287:1294, 1/2/1305:1314 | No text annotation | ||
| IL_7SYP_066 | 1/2/1325:1327, 1/2/1502:1503 | Single bulged U | geometric IL_3MEI_001 IL_89505.4 | |
| IL_7SYP_067 | 1/2/1329:1333, 1/2/1498:1500 | Isolated cWS basepair | geometric IL_4LFB_044 IL_76319.5 | |
| IL_7SYP_107 | 1/2/1329:1335, 1/2/1492:1500 | No text annotation | homologous IL_8P9A_439 IL_86012.1 | |
| IL_7SYP_068 | 1/2/1333:1335, 1/2/1492:1498 | Minor groove platform with extra cWW | geometric IL_4V88_451 NA | |
| IL_7SYP_069 | 1/2/1337:1338, 1/2/1488:1490 | Single bulged A | geometric IL_4WF9_006 IL_31462.7 | |
| IL_7SYP_070 | 1/2/1347:1349, 1/2/1380:1382 | Isolated cWH basepair | geometric IL_4WF9_045 IL_10167.6 | |
| IL_7SYP_071 | 1/2/1363:1365, 1/2/1374:1375 | Minor groove platform | geometric IL_6DLR_003 IL_51454.3 | |
| IL_7SYP_072 | 1/2/1395:1399, 1/2/1447:1450 | No text annotation | geometric IL_4PHY_003 IL_99358.1 | |
| IL_7SYP_115 | 1/2/1402:1405, 1/2/1441:1444 | No text annotation | homologous IL_8P9A_445 IL_78800.1 | |
| IL_7SYP_074 | 1/2/1412:1413, 1/2/1427:1429 | Single bulged G | geometric IL_5J7L_019 IL_00225.14 | |
| IL_7SYP_075 | 1/2/1537:1539, 1/2/1594:1596 | Isolated non-canonical cWW pair | geometric IL_4E48_005 IL_87907.2 | |
| IL_7SYP_108 | 1/2/1541:1550, 1/2/1582:1592 | No text annotation | ||
| IL_7SYP_076 | 1/2/1550:1558, 1/2/1577:1582 | 180 degree turn | geometric IL_5J7L_055 IL_11344.2 | |
| IL_7SYP_077 | 1/2/1560:1562, 1/2/1573:1575 | Isolated non-canonical cWW pair | geometric IL_4P3U_007 IL_28037.2 | |
| IL_7SYP_078 | 1/2/1604:1610, 1/2/1629:1635 | No text annotation | homologous IL_8C3A_469 NA | |
| IL_7SYP_079 | 1/2/1702:1706, 1/2/1828:1833 | No text annotation | ||
| IL_7SYP_109 | 1/2/1702:1708, 1/2/1826:1833 | No text annotation | ||
| IL_7SYP_080 | 1/2/1706:1708, 1/2/1826:1828 | Isolated non-canonical cWW pair | geometric IL_4E59_001 IL_87907.2 | |
| IL_7SYP_081 | 1/2/1708:1711, 1/2/1822:1826 | No text annotation | ||
| IL_7SYP_116 | 1/2/1714:1720, 1/2/1813:1819 | No text annotation | ||
| IL_7SYP_117 | 1/2/1720:1722, 1/2/1812:1813 | Single bulged U | homologous IL_8P9A_458 IL_89505.4 | |
| IL_7SYP_084 | 1/2/1729:1731, 1/2/1803:1805 | Isolated non-canonical cWW pair | geometric IL_6E7L_003 NA | |
| IL_7SYP_085 | 1/2/1733:1736, 1/2/1798:1801 | Double sheared | geometric IL_4V88_471 NA | |
| IL_7SYP_086 | 1/2/1739:1741, 1/2/1793:1795 | Isolated non-canonical cWW pair | geometric IL_4E48_003 IL_87907.2 | |
| IL_7SYP_087 | 1/2/1742:1746, 1/2/1788:1792 | Triple sheared | geometric IL_7RQB_075 NA | |
| IL_7SYP_088 | 1/2/1750:1751, 1/2/1782:1784 | No text annotation | ||
| IL_7SYP_089 | 1/2/1751:1753, 1/2/1780:1782 | No text annotation | ||
| IL_7SYP_090 | 1/2/1753:1754, 1/2/1778:1780 | No text annotation | ||
| IL_7SYP_091 | 1/z/47:49, 1/z/114:115 | No text annotation | ||
| IL_7SYP_092 | 1/z/52:58, 1/z/110:111 | No text annotation | ||
| IL_7SYP_093 | 1/z/60:62, 1/z/105:108 | No text annotation | ||
| IL_7SYP_094 | 1/z/62:65, 1/z/102:105 | No text annotation | ||
| IL_7SYP_095 | 1/z/67:69, 1/z/98:100 | No text annotation | ||
| IL_7SYP_096 | 1/z/70:75, 1/z/91:97 | No text annotation | ||
| IL_7SYP_118 | 1/z/135:137, 1/z/287:289 | No text annotation | ||
| IL_7SYP_098 | 1/z/149:150, 1/z/242:244 | No text annotation | ||
| IL_7SYP_099 | 1/z/255:261, 1/z/272:277 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_7SYP_012 | No text annotation | ||
| IL_7SYP_017 | No text annotation | ||
| IL_7SYP_101 | Triple non-canonical cWW pairs | ||
| IL_7SYP_039 | No text annotation | ||
| IL_7SYP_040 | Tandem non-canonical cWW pairs | ||
| IL_7SYP_102 | No text annotation | ||
| IL_7SYP_046 | No text annotation | ||
| IL_7SYP_103 | Isolated non-canonical cWW pair | ||
| IL_7SYP_048 | Tandem non-canonical cWW pairs | ||
| IL_7SYP_053 | No text annotation | ||
| IL_7SYP_058 | No text annotation | ||
| IL_7SYP_073 | No text annotation | ||
| IL_7SYP_082 | No text annotation | ||
| IL_7SYP_083 | Isolated non-canonical cWW pair | ||
| IL_7SYP_110 | No text annotation | ||
| IL_7SYP_111 | No text annotation | ||
| IL_7SYP_097 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_7SYP_012 | 1/2/37:41, 1/2/481:487, 1/2/512:518 | No text annotation | ||
| J3_7SYP_001 | 1/2/40:41, 1/2/481:487, 1/2/512:514 | No text annotation | ||
| J3_7SYP_002 | 1/2/816:819, 1/2/829:831, 1/2/843:848 | No text annotation | homologous J3_8C3A_035 NA | |
| J3_7SYP_003 | 1/2/938:941, 1/2/985:993, 1/2/1000:1004 | No text annotation | homologous J3_8P9A_074 J3_76375.1 | |
| J3_7SYP_004 | 1/2/1094:1096, 1/2/1136:1140, 1/2/1147:1151 | No text annotation | ||
| J3_7SYP_005 | 1/2/1218:1221, 1/2/1645:1651, 1/2/1673:1680 | No text annotation | homologous J3_8C3A_038 NA | |
| J3_7SYP_006 | 1/2/1225:1228, 1/2/1530:1532, 1/2/1638:1641 | No text annotation | homologous J3_8C3A_039 NA | |
| J3_7SYP_016 | 1/2/1237:1244, 1/2/1255:1266, 1/2/1516:1520 | No text annotation | homologous J3_8CRE_080 J3_83516.4 | |
| J3_7SYP_008 | 1/2/1273:1277, 1/2/1320:1324, 1/2/1504:1510 | No text annotation | homologous J3_8C3A_041 NA | |
| J3_7SYP_009 | 1/2/1340:1345, 1/2/1384:1389, 1/2/1481:1486 | No text annotation | homologous J3_8P9A_080 J3_99563.1 | |
| J3_7SYP_010 | 1/2/1350:1351, 1/2/1360:1363, 1/2/1375:1379 | No text annotation | geometric J3_4V88_082 NA | |
| J3_7SYP_015 | 1/2/1391:1395, 1/2/1450:1456, 1/2/1470:1479 | No text annotation | ||
| J3_7SYP_011 | 1/2/1532:1536, 1/2/1597:1604, 1/2/1635:1638 | No text annotation | homologous J3_8C3A_044 NA | |
| J4_7SYP_001 | 1/2/98:106, 1/2/355:357, 1/2/405:409, 1/2/431:432 | No text annotation | homologous J4_8C3A_021 NA | |
| J4_7SYP_002 | 1/2/671:673, 1/2/1032:1037, 1/2/1078:1089, 1/2/1160:1161 | No text annotation | homologous J4_8C3A_022 NA | |
| J4_7SYP_003 | 1/z/133:134, 1/z/290:291, 1/z/302:303, 1/z/314:315 | No text annotation | ||
| J4_7SYP_004 | 1/z/140:141, 1/z/252:253, 1/z/279:280, 1/z/283:284 | No text annotation | ||
| J4_7SYP_005 | 1/z/153:156, 1/z/171:172, 1/z/227:229, 1/z/238:239 | No text annotation | ||
| J5_7SYP_001 | 1/2/30:34, 1/2/521:528, 1/2/557:563, 1/2/592:596, 1/2/640:644 | No text annotation | ||
| J5_7SYP_002 | 1/2/30:34, 1/2/521:528, 1/2/557:565, 1/2/585:596, 1/2/640:644 | No text annotation | ||
| J5_7SYP_005 | 1/2/53:62, 1/2/86:96, 1/2/434:436, 1/2/457:459, 1/2/470:474 | No text annotation | ||
| J5_7SYP_004 | 1/2/123:129, 1/2/183:185, 1/2/214:219, 1/2/302:312, 1/2/337:341 | No text annotation |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_7SYP_013 | No text annotation | ||
| J3_7SYP_007 | No text annotation | ||
| J3_7SYP_014 | No text annotation | ||
| J5_7SYP_003 | No text annotation |
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