RNA 3D Hub //

7SYN Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_7SYN_0011/2/7:17No text annotation
geometric
HL_4V88_186
NA
HL_7SYN_0021/2/69:80No text annotation
geometric
HL_361D_002
HL_13963.3
HL_7SYN_0031/2/155:163No text annotation
HL_7SYN_0041/2/196:203No text annotation
HL_7SYN_0051/2/288:295No text annotation
geometric
HL_5NFV_001
HL_69752.2
HL_7SYN_0071/2/377:387No text annotation
HL_7SYN_0081/2/416:421No text annotation
geometric
HL_4V88_194
NA
HL_7SYN_0091/2/441:452No text annotation
geometric
HL_4V88_195
NA
HL_7SYN_0101/2/462:467UNCG
geometric
HL_4LFB_009
HL_34617.5
HL_7SYN_0111/2/498:504No text annotation
geometric
HL_5NFV_001
HL_69752.2
HL_7SYN_0121/2/539:544UNCG variation
geometric
HL_1P6V_001
HL_53890.2
HL_7SYN_0131/2/569:581No text annotation
geometric
HL_4V88_199
NA
HL_7SYN_0141/2/618:623GNRA variation
geometric
HL_4V88_200
NA
HL_7SYN_0161/2/820:828No text annotation
geometric
HL_4V88_203
NA
HL_7SYN_0181/2/884:902No text annotation
HL_7SYN_0191/2/957:966No text annotation
geometric
HL_4V88_206
NA
HL_7SYN_0201/2/994:999GNRA
geometric
HL_4V88_207
NA
HL_7SYN_0211/2/1054:1064No text annotation
geometric
HL_4V88_208
NA
HL_7SYN_0221/2/1113:1120Purine riboswitch
geometric
HL_4LX6_002
HL_31585.4
HL_7SYN_0231/2/1141:1146GNRA
geometric
HL_4V88_210
NA
HL_7SYN_0241/2/1178:1183GNRA
geometric
HL_5U3G_002
HL_37824.8
HL_7SYN_0251/2/1245:1254No text annotation
geometric
HL_4V88_212
NA
HL_7SYN_0261/2/1295:1304GNRA wlth extra near cWW
homologous
HL_8P9A_216
HL_81538.2
HL_7SYN_0271/2/1366:1373No text annotation
geometric
HL_5TBW_024
NA
HL_7SYN_0291/2/1460:1466UNCG variation
geometric
HL_2CZJ_007
NA
HL_7SYN_0301/2/1565:1570GNRA
geometric
HL_5FQ5_001
HL_37824.8
HL_7SYN_0311/2/1614:1625No text annotation
geometric
HL_4V88_219
NA
HL_7SYN_0321/2/1658:1666No text annotation
geometric
HL_4V88_220
NA
HL_7SYN_0341/2/1846:1853No text annotation
geometric
HL_5NFV_001
HL_69752.2
HL_7SYN_0351/z/161:166No text annotation
HL_7SYN_0371/z/232:235No text annotation
HL_7SYN_0431/z/262:271No text annotation
HL_7SYN_0391/z/280:283No text annotation
HL_7SYN_0401/z/294:299No text annotation
HL_7SYN_0411/z/304:313No text annotation

Problematic loops

#loop idProblemSequence
HL_7SYN_006No text annotation
HL_7SYN_015No text annotation
HL_7SYN_017No text annotation
HL_7SYN_042GNRA with extra near cWW
HL_7SYN_028No text annotation
HL_7SYN_033No text annotation
HL_7SYN_036No text annotation
HL_7SYN_038No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_7SYN_0011/2/23:25,
1/2/649:651		Isolated non-canonical cWW pair
geometric
IL_4M4O_001
IL_87907.2
IL_7SYN_0021/2/34:36,
1/2/519:521		Isolated non-canonical cWW pair
geometric
IL_5ED2_004
NA
IL_7SYN_0031/2/37:40,
1/2/514:518		Double sheared
geometric
IL_4WF9_016
IL_09705.15
IL_7SYN_0041/2/41:47,
1/2/479:481		No text annotation
geometric
IL_4V88_387
NA
IL_7SYN_0051/2/49:51,
1/2/476:477		Minor groove platform
geometric
IL_4V88_388
NA
IL_7SYN_0061/2/57:62,
1/2/86:88		No text annotation
geometric
IL_4V88_389
NA
IL_7SYN_0071/2/63:68,
1/2/81:85		No text annotation
geometric
IL_4V88_390
NA
IL_7SYN_0081/2/108:110,
1/2/351:353		Isolated non-canonical cWW pair
geometric
IL_1ZX7_006
IL_28037.2
IL_7SYN_0951/2/108:112,
1/2/349:353		Triple non-canonical cWW pairs
geometric
IL_8VMB_003
IL_49751.4
IL_7SYN_0091/2/110:112,
1/2/349:351		Isolated non-canonical cWW pair
geometric
IL_4WF9_042
IL_87907.2
IL_7SYN_0101/2/112:115,
1/2/348:349		Multiple bulged bases
geometric
IL_5WLH_001
IL_82107.5
IL_7SYN_0111/2/116:121,
1/2/343:347		No text annotation
geometric
IL_4V88_393
NA
IL_7SYN_0121/2/123:124,
1/2/339:341		Minor groove platform
geometric
IL_4V88_412
NA
IL_7SYN_0141/2/145:151,
1/2/167:174		tWH-tWH-tHW-tHW
geometric
IL_4V88_394
NA
IL_7SYN_0151/2/152:155,
1/2/163:166		Tandem non-canonical cWW pairs
geometric
IL_6CZR_168
NA
IL_7SYN_0161/2/188:192,
1/2/207:211		Double sheared with non-canonical cWW
geometric
IL_5J7L_274
IL_17948.2
IL_7SYN_0171/2/216:219,
1/2/302:309		No text annotation
IL_7SYN_0191/2/312:314,
1/2/336:337		Single bulged A
geometric
IL_4V88_399
NA
IL_7SYN_0201/2/316:319,
1/2/332:334		No text annotation
IL_7SYN_0211/2/359:364,
1/2/396:403		Kink-turn with non-sequential stacking
geometric
IL_5J7L_014
IL_46174.3
IL_7SYN_0221/2/366:371,
1/2/393:394		No text annotation
geometric
IL_5Y58_001
IL_59877.1
IL_7SYN_0231/2/411:413,
1/2/424:429		No text annotation
geometric
IL_4V88_404
NA
IL_7SYN_0971/2/437:439,
1/2/454:457		No text annotation
IL_7SYN_0251/2/459:461,
1/2/468:470		Isolated near basepair
geometric
IL_3NJ7_004
IL_42997.3
IL_7SYN_0261/2/487:489,
1/2/511:512		Single bulged U
geometric
IL_3D2V_001
IL_89505.4
IL_7SYN_0271/2/491:495,
1/2/508:509		C-loop
geometric
IL_5J7L_018
IL_03109.3
IL_7SYN_0281/2/495:496,
1/2/506:508		Single bulged G
geometric
IL_5J7L_019
IL_00225.14
IL_7SYN_0291/2/529:532,
1/2/552:556		No text annotation
IL_7SYN_0981/2/535:537,
1/2/546:549		No text annotation
IL_7SYN_0311/2/563:565,
1/2/585:592		No text annotation
homologous
IL_8C3A_420
NA
IL_7SYN_0321/2/566:569,
1/2/581:584		Tandem non-canonical cWW pairs
geometric
IL_402D_001
IL_77658.1
IL_7SYN_0331/2/599:608,
1/2/635:637		No text annotation
IL_7SYN_0341/2/611:617,
1/2/624:632		Kink-turn related
geometric
IL_4V88_415
NA
IL_7SYN_0351/2/663:665,
1/2/1162:1164		Isolated non-canonical cWW pair
geometric
IL_1Y27_001
IL_87907.2
IL_7SYN_0361/2/665:671,
1/2/1161:1162		No text annotation
geometric
IL_4LFB_022
IL_38186.6
IL_7SYN_0371/2/673:675,
1/2/1030:1032		Isolated non-canonical cWW pair
geometric
IL_4YHW_001
IL_87907.2
IL_7SYN_0381/2/676:680,
1/2/1025:1029		tSH-tHW-tHS
geometric
IL_4V88_418
NA
IL_7SYN_0391/2/692:695,
1/2/731:734		Tandem non-canonical cWW pairs
geometric
IL_4EYA_008
IL_51479.1
IL_7SYN_0411/2/750:754,
1/2/790:793		Tandem non-canonical cWW pairs
geometric
IL_7VYX_002
IL_85033.2
IL_7SYN_0421/2/802:805,
1/2/858:863		No text annotation
IL_7SYN_0431/2/805:807,
1/2/856:858		Isolated non-canonical cWW pair
geometric
IL_4KNQ_003
IL_87907.2
IL_7SYN_0441/2/807:815,
1/2/849:856		No text annotation
geometric
IL_4V88_425
NA
IL_7SYN_0451/2/874:876,
1/2/910:912		Isolated non-canonical cWW pair
geometric
IL_5MWI_007
NA
IL_7SYN_1011/2/877:879,
1/2/907:909		Isolated non-canonical cWW pair
geometric
IL_5J7L_061
IL_87907.2
IL_7SYN_0471/2/922:923,
1/2/1019:1022		Major groove platform; stack outside cWW
geometric
IL_6N5P_003
IL_50694.7
IL_7SYN_1101/2/925:926,
1/2/1015:1017		Single bulged U
geometric
IL_8P9A_281
IL_89505.4
IL_7SYN_0491/2/927:931,
1/2/1010:1014		No text annotation
geometric
IL_5TBW_121
NA
IL_7SYN_0501/2/931:935,
1/2/1007:1010		Tandem non-canonical cWW pairs
geometric
IL_4V88_431
NA
IL_7SYN_0511/2/942:945,
1/2/981:984		Tandem non-canonical cWW pairs
geometric
IL_4V88_432
NA
IL_7SYN_0521/2/952:956,
1/2/967:974		Kink-turn
geometric
IL_4V88_434
NA
IL_7SYN_0531/2/1042:1047,
1/2/1071:1073		Other IL
geometric
IL_4V88_435
NA
IL_7SYN_1031/2/1042:1051,
1/2/1067:1073		No text annotation
IL_7SYN_0541/2/1047:1051,
1/2/1067:1071		tSH-tHW-tHS
geometric
IL_6CZR_145
NA
IL_7SYN_0551/2/1091:1093,
1/2/1152:1158		No text annotation
geometric
IL_4V88_437
NA
IL_7SYN_0561/2/1098:1103,
1/2/1129:1134		No text annotation
geometric
IL_6O5F_001
NA
IL_7SYN_0571/2/1108:1110,
1/2/1123:1124		Minor groove platform
geometric
IL_4V88_412
NA
IL_7SYN_0581/2/1168:1175,
1/2/1186:1191		8x6 Sarcin-Ricin with inserted Y; G-bulge
geometric
IL_4LFB_034
IL_41756.4
IL_7SYN_0591/2/1214:1217,
1/2/1681:1685		C-loop
geometric
IL_4V88_443
NA
IL_7SYN_0601/2/1230:1233,
1/2/1525:1528		Tandem non-canonical cWW pairs
geometric
IL_5EW4_002
IL_85033.2
IL_7SYN_0611/2/1235:1236,
1/2/1521:1523		Minor groove platform
geometric
IL_7A0S_028
IL_51454.3
IL_7SYN_1111/2/1269:1273,
1/2/1510:1513		No text annotation
IL_7SYN_0631/2/1281:1287,
1/2/1314:1316		No text annotation
IL_7SYN_1051/2/1281:1290,
1/2/1309:1316		No text annotation
homologous
IL_8P9A_470
IL_28304.1
IL_7SYN_0641/2/1287:1290,
1/2/1309:1314		No text annotation
IL_7SYN_0651/2/1291:1294,
1/2/1305:1308		No text annotation
IL_7SYN_0661/2/1325:1327,
1/2/1502:1503		Single bulged U
geometric
IL_3MEI_001
IL_89505.4
IL_7SYN_1061/2/1329:1335,
1/2/1492:1500		No text annotation
homologous
IL_8P9A_439
IL_86012.1
IL_7SYN_0681/2/1337:1338,
1/2/1488:1490		Single bulged A
geometric
IL_4V88_452
NA
IL_7SYN_0691/2/1347:1349,
1/2/1380:1382		Isolated cWH basepair
geometric
IL_4WF9_045
IL_10167.6
IL_7SYN_1121/2/1350:1363,
1/2/1375:1379		No text annotation
IL_7SYN_0711/2/1363:1365,
1/2/1374:1375		Minor groove platform
geometric
IL_5ML7_009
IL_51454.3
IL_7SYN_0721/2/1395:1399,
1/2/1447:1450		Tandem non-canonical cWW pairs
geometric
IL_1L9A_005
IL_85033.2
IL_7SYN_0731/2/1402:1405,
1/2/1441:1444		Minor groove platform
geometric
IL_4V88_456
NA
IL_7SYN_0741/2/1412:1413,
1/2/1427:1429		Single bulged G
geometric
IL_5J7L_019
IL_00225.14
IL_7SYN_0751/2/1537:1539,
1/2/1594:1596		Isolated non-canonical cWW pair
geometric
IL_4E48_005
IL_87907.2
IL_7SYN_1081/2/1541:1550,
1/2/1582:1592		No text annotation
IL_7SYN_0761/2/1550:1558,
1/2/1577:1582		180 degree turn
geometric
IL_4LFB_052
IL_11344.2
IL_7SYN_1131/2/1560:1563,
1/2/1572:1575		No text annotation
IL_7SYN_0781/2/1604:1610,
1/2/1629:1635		No text annotation
homologous
IL_8C3A_469
NA
IL_7SYN_0791/2/1702:1705,
1/2/1829:1833		No text annotation
homologous
IL_8C3A_471
NA
IL_7SYN_0801/2/1706:1708,
1/2/1826:1828		Isolated non-canonical cWW pair
geometric
IL_4V83_235
IL_07785.1
IL_7SYN_0811/2/1708:1711,
1/2/1822:1826		No text annotation
homologous
IL_8CRE_469
IL_11399.2
IL_7SYN_1141/2/1714:1716,
1/2/1817:1819		Isolated non-canonical cWW pair
homologous
IL_8P9A_456
IL_87907.2
IL_7SYN_0831/2/1717:1720,
1/2/1813:1816		Double sheared
geometric
IL_7A0S_081
IL_09705.15
IL_7SYN_1151/2/1720:1722,
1/2/1812:1813		Single bulged U
homologous
IL_8P9A_458
IL_89505.4
IL_7SYN_0851/2/1727:1731,
1/2/1803:1807		Triple non-canonical cWW pairs
geometric
IL_5BTM_001
IL_49751.4
IL_7SYN_0861/2/1733:1736,
1/2/1798:1801		Double sheared
geometric
IL_4V88_471
NA
IL_7SYN_0871/2/1739:1741,
1/2/1793:1795		Isolated non-canonical cWW pair
geometric
IL_4E48_002
IL_87907.2
IL_7SYN_0881/2/1742:1746,
1/2/1788:1792		Triple sheared
geometric
IL_7RQB_075
NA
IL_7SYN_0891/2/1750:1751,
1/2/1782:1784		No text annotation
IL_7SYN_0901/2/1751:1753,
1/2/1780:1782		Single stack bend
geometric
IL_4WF9_089
IL_26793.1
IL_7SYN_0911/2/1753:1754,
1/2/1778:1780		No text annotation
IL_7SYN_1161/z/135:137,
1/z/287:289		No text annotation
IL_7SYN_0931/z/149:150,
1/z/242:244		No text annotation
IL_7SYN_0941/z/255:261,
1/z/272:277		No text annotation

Problematic loops

#loop idProblemSequence
IL_7SYN_013No text annotation
IL_7SYN_018No text annotation
IL_7SYN_096No text annotation
IL_7SYN_024Tandem non-canonical cWW pairs
IL_7SYN_030No text annotation
IL_7SYN_099No text annotation
IL_7SYN_100No text annotation
IL_7SYN_040No text annotation
IL_7SYN_046Tandem non-canonical cWW pairs
IL_7SYN_102Isolated non-canonical cWW pair
IL_7SYN_048Tandem non-canonical cWW pairs
IL_7SYN_104No text annotation
IL_7SYN_062No text annotation
IL_7SYN_067No text annotation
IL_7SYN_070No text annotation
IL_7SYN_107No text annotation
IL_7SYN_077No text annotation
IL_7SYN_082Tandem non-canonical cWW pairs
IL_7SYN_084No text annotation
IL_7SYN_109No text annotation
IL_7SYN_092No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_7SYN_0011/2/40:41,
1/2/481:487,
1/2/512:514		No text annotation
geometric
J3_4V88_078
NA
J3_7SYN_0111/2/40:47,
1/2/479:487,
1/2/512:514		No text annotation
homologous
J3_8P9A_069
J3_46317.4
J3_7SYN_0021/2/682:685,
1/2/917:922,
1/2/1022:1023		No text annotation
J3_7SYN_0121/2/682:685,
1/2/917:923,
1/2/1019:1023		No text annotation
J3_7SYN_0031/2/816:819,
1/2/829:831,
1/2/843:848		No text annotation
homologous
J3_8C3A_035
NA
J3_7SYN_0041/2/938:941,
1/2/985:993,
1/2/1000:1004		No text annotation
homologous
J3_8P9A_074
J3_76375.1
J3_7SYN_0051/2/1094:1096,
1/2/1136:1140,
1/2/1147:1151		No text annotation
J3_7SYN_0061/2/1218:1221,
1/2/1645:1651,
1/2/1673:1680		No text annotation
homologous
J3_8P9A_076
J3_25303.4
J3_7SYN_0071/2/1225:1228,
1/2/1530:1532,
1/2/1638:1641		No text annotation
homologous
J3_8C3A_039
NA
J3_7SYN_0081/2/1237:1244,
1/2/1255:1266,
1/2/1516:1520		No text annotation
geometric
J3_8C3A_040
NA
J3_7SYN_0091/2/1273:1277,
1/2/1320:1324,
1/2/1504:1510		No text annotation
homologous
J3_8P9A_079
J3_87797.1
J3_7SYN_0141/2/1338:1347,
1/2/1382:1389,
1/2/1481:1488		No text annotation
J3_7SYN_0151/2/1391:1395,
1/2/1450:1456,
1/2/1470:1479		No text annotation
J3_7SYN_0101/2/1532:1536,
1/2/1597:1604,
1/2/1635:1638		No text annotation
homologous
J3_8C3A_044
NA
J4_7SYN_0011/2/98:106,
1/2/355:357,
1/2/405:409,
1/2/431:432		No text annotation
homologous
J4_8C3A_021
NA
J4_7SYN_0061/2/671:673,
1/2/1032:1037,
1/2/1078:1089,
1/2/1160:1161		No text annotation
homologous
J4_8P9A_022
J4_61885.6
J4_7SYN_0071/z/133:134,
1/z/290:291,
1/z/302:303,
1/z/314:315		No text annotation
J4_7SYN_0031/z/133:135,
1/z/289:291,
1/z/302:303,
1/z/314:315		No text annotation
J4_7SYN_0041/z/140:141,
1/z/252:253,
1/z/279:280,
1/z/283:284		No text annotation
J4_7SYN_0051/z/153:156,
1/z/171:172,
1/z/227:229,
1/z/238:239		No text annotation
J5_7SYN_0051/2/30:34,
1/2/521:527,
1/2/558:563,
1/2/592:596,
1/2/640:644		No text annotation
homologous
J5_8CRE_018
J5_80702.1
J5_7SYN_0061/2/30:34,
1/2/521:527,
1/2/558:565,
1/2/585:596,
1/2/640:644		No text annotation
J5_7SYN_0031/2/53:62,
1/2/86:96,
1/2/434:437,
1/2/457:461,
1/2/468:474		No text annotation
J5_7SYN_0071/2/123:129,
1/2/183:185,
1/2/214:219,
1/2/302:312,
1/2/337:341		No text annotation

Problematic loops

#loop idProblemSequence
J3_7SYN_013No text annotation
J4_7SYN_002No text annotation
J5_7SYN_001No text annotation
J5_7SYN_002No text annotation
J5_7SYN_004No text annotation

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