RNA 3D Hub //

6FYY Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6FYY_0011/1/13:22No text annotation
homologous
HL_5UD5_001
HL_48417.5
HL_6FYY_0021/1/31:39tRNA anticodon loop
homologous
HL_5E81_212
HL_06059.6
HL_6FYY_0031/1/53:61No text annotation
homologous
HL_1YFG_003
NA
HL_6FYY_0041/2/7:17No text annotation
homologous
HL_4V88_186
NA
HL_6FYY_0051/2/70:81No text annotation
geometric
HL_2ZNI_001
HL_75660.5
HL_6FYY_0061/2/153:159GNRA related
homologous
HL_4V88_188
NA
HL_6FYY_0071/2/189:194No text annotation
homologous
HL_8P9A_193
HL_53890.2
HL_6FYY_0081/2/229:234No text annotation
geometric
HL_3SKI_003
HL_48417.5
HL_6FYY_0091/2/242:249T-loop with 1 bulged base
homologous
HL_4V88_191
NA
HL_6FYY_0101/2/274:280No text annotation
geometric
HL_5J7L_018
HL_37344.1
HL_6FYY_0111/2/329:337GNRA related
homologous
HL_4V88_193
NA
HL_6FYY_0121/2/367:372No text annotation
homologous
HL_4V88_194
NA
HL_6FYY_0131/2/392:403No text annotation
homologous
HL_4V88_195
NA
HL_6FYY_0141/2/413:418UNCG
homologous
HL_4V88_196
NA
HL_6FYY_0151/2/449:455No text annotation
homologous
HL_4V88_197
NA
HL_6FYY_0161/2/490:495No text annotation
homologous
HL_4V88_198
NA
HL_6FYY_0171/2/519:531No text annotation
geometric
HL_4V88_199
NA
HL_6FYY_0181/2/568:573GNRA variation
homologous
HL_4V88_200
NA
HL_6FYY_0191/2/714:724No text annotation
HL_6FYY_0201/2/764:772No text annotation
homologous
HL_4V88_203
NA
HL_6FYY_0211/2/777:782No text annotation
HL_6FYY_0221/2/828:842Pseudoknot geometry
homologous
HL_4V88_205
NA
HL_6FYY_0231/2/899:908No text annotation
homologous
HL_4V88_206
NA
HL_6FYY_0241/2/936:941GNRA
homologous
HL_4V88_207
NA
HL_6FYY_0401/2/996:1006No text annotation
homologous
HL_8C3A_213
NA
HL_6FYY_0261/2/1053:1064No text annotation
HL_6FYY_0271/2/1083:1088GNRA
homologous
HL_4V88_210
NA
HL_6FYY_0281/2/1120:1125GNRA
homologous
HL_4V88_211
NA
HL_6FYY_0291/2/1187:1196No text annotation
homologous
HL_8C3A_217
NA
HL_6FYY_0301/2/1237:1246Anticodon loop related
homologous
HL_4V88_213
NA
HL_6FYY_0311/2/1295:1300GNRA
homologous
HL_4V88_214
NA
HL_6FYY_0321/2/1308:1315No text annotation
homologous
HL_4V88_215
NA
HL_6FYY_0331/2/1358:1363No text annotation
geometric
HL_2Y9H_003
HL_75660.5
HL_6FYY_0341/2/1394:1400GNRA
homologous
HL_4V88_217
NA
HL_6FYY_0351/2/1499:1504GNRA
homologous
HL_4V88_218
NA
HL_6FYY_0361/2/1548:1559No text annotation
homologous
HL_4V88_219
NA
HL_6FYY_0371/2/1592:1600No text annotation
homologous
HL_4V88_220
NA
HL_6FYY_0391/2/1776:1781GNRA variation
homologous
HL_4V88_222
NA

Problematic loops

#loop idProblemSequence
HL_6FYY_025tRNA D-loop
HL_6FYY_038No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6FYY_0011/2/24:26,
1/2/599:600		Single bulged C
homologous
IL_4V88_384
NA
IL_6FYY_0021/2/35:37,
1/2/470:472		Isolated non-canonical cWW pair
homologous
IL_4V88_385
NA
IL_6FYY_0901/2/37:41,
1/2/465:470		No text annotation
homologous
IL_8P9A_375
IL_12697.1
IL_6FYY_0031/2/42:48,
1/2/430:432		No text annotation
homologous
IL_4V88_387
NA
IL_6FYY_0041/2/50:52,
1/2/427:428		Minor groove platform
homologous
IL_4V88_388
NA
IL_6FYY_0051/2/58:63,
1/2/87:89		No text annotation
homologous
IL_4V88_389
NA
IL_6FYY_0061/2/64:69,
1/2/82:86		No text annotation
homologous
IL_4V88_390
NA
IL_6FYY_0071/2/109:112,
1/2/301:304		Tandem non-canonical cWW pairs
homologous
IL_4V88_391
NA
IL_6FYY_0081/2/112:113,
1/2/299:301		Single stack bend
geometric
IL_4LFB_041
IL_90729.1
IL_6FYY_0091/2/113:117,
1/2/298:299		Not an internal loop
geometric
IL_4UYK_002
NA
IL_6FYY_0911/2/117:122,
1/2/294:298		No text annotation
homologous
IL_8P9A_382
IL_29223.1
IL_6FYY_0111/2/123:124,
1/2/291:293		Single stack bend
geometric
IL_4LFB_041
IL_90729.1
IL_6FYY_0121/2/142:148,
1/2/164:171		tWH-tWH-tHW-tHW
homologous
IL_4V88_394
NA
IL_6FYY_0131/2/149:151,
1/2/161:163		Isolated cWH basepair
geometric
IL_6RA4_002
IL_10167.6
IL_6FYY_0141/2/185:188,
1/2/195:198		Double sheared
homologous
IL_4V88_396
NA
IL_6FYY_0151/2/203:205,
1/2/258:262		Major groove platform with extra cWW
geometric
IL_4V88_397
NA
IL_6FYY_0161/2/205:207,
1/2/255:258		No text annotation
geometric
IL_4N0T_004
IL_99358.1
IL_6FYY_0171/2/207:209,
1/2/254:255		Single stack bend
geometric
IL_4LFB_041
IL_90729.1
IL_6FYY_0181/2/264:266,
1/2/287:288		Single bulged A
homologous
IL_4V88_399
NA
IL_6FYY_0191/2/269:272,
1/2/282:284		No text annotation
homologous
IL_4V88_400
NA
IL_6FYY_0201/2/310:315,
1/2/347:354		Kink-turn with non-sequential stacking
homologous
IL_4V88_402
NA
IL_6FYY_0211/2/317:322,
1/2/344:345		No text annotation
geometric
IL_5Y58_001
IL_59877.1
IL_6FYY_0221/2/362:364,
1/2/375:380		No text annotation
homologous
IL_4V88_404
NA
IL_6FYY_0231/2/388:390,
1/2/405:407		Isolated cWH basepair
homologous
IL_4V88_405
NA
IL_6FYY_0241/2/410:412,
1/2/419:421		Isolated near basepair
homologous
IL_4V88_406
NA
IL_6FYY_0251/2/438:440,
1/2/462:463		Single bulged U
homologous
IL_4V88_407
NA
IL_6FYY_0261/2/442:446,
1/2/459:460		C-loop
geometric
IL_5J7L_018
IL_03109.3
IL_6FYY_0271/2/446:447,
1/2/457:459		Single bulged G
geometric
IL_5J7L_019
IL_00225.13
IL_6FYY_0991/2/479:481,
1/2/504:507		Isolated cWH basepair
geometric
IL_4WF9_121
IL_10167.6
IL_6FYY_0291/2/513:515,
1/2/535:542		No text annotation
homologous
IL_8C3A_420
NA
IL_6FYY_1001/2/516:517,
1/2/532:534		No text annotation
homologous
IL_8CRE_419
IL_51454.3
IL_6FYY_1011/2/517:519,
1/2/531:532		Minor groove platform
homologous
IL_8P9A_401
IL_51454.3
IL_6FYY_0311/2/549:556,
1/2/586:587		SSU/LSU pseudoknot
homologous
IL_4V88_413
NA
IL_6FYY_0321/2/556:558,
1/2/585:586		Single bulged U
geometric
IL_4V88_407
NA
IL_6FYY_0331/2/561:567,
1/2/574:582		Kink-turn related
homologous
IL_4V88_415
NA
IL_6FYY_0341/2/615:621,
1/2/1103:1104		No text annotation
homologous
IL_4V88_416
NA
IL_6FYY_0351/2/623:625,
1/2/972:974		Isolated non-canonical cWW pair
homologous
IL_4V88_417
NA
IL_6FYY_0361/2/626:630,
1/2/967:971		tSH-tHW-tHS
homologous
IL_4V88_418
NA
IL_6FYY_1021/2/650:656,
1/2/677:683		No text annotation
IL_6FYY_0381/2/703:713,
1/2/725:735		No text annotation
IL_6FYY_0391/2/745:747,
1/2/801:805		Major groove minor groove platform with extra cWW
geometric
IL_4WF9_012
IL_49061.1
IL_6FYY_0401/2/748:750,
1/2/798:800		Isolated non-canonical cWW pair
homologous
IL_4V88_424
NA
IL_6FYY_1031/2/751:759,
1/2/790:797		No text annotation
homologous
IL_8CRE_430
IL_59049.1
IL_6FYY_0411/2/818:821,
1/2/849:851		Isolated cWH basepair
homologous
IL_4V88_427
NA
IL_6FYY_0931/2/867:869,
1/2/956:959		Isolated non-canonical cWW pair
homologous
IL_8P9A_418
IL_57744.1
IL_6FYY_0431/2/870:873,
1/2/952:955		Tandem non-canonical cWW pairs
geometric
IL_4V88_430
NA
IL_6FYY_0441/2/873:877,
1/2/949:952		Tandem non-canonical cWW pairs
homologous
IL_4V88_431
NA
IL_6FYY_0451/2/884:887,
1/2/922:926		No text annotation
geometric
IL_1HYS_004
IL_64231.5
IL_6FYY_0461/2/887:889,
1/2/921:922		Single stack bend
geometric
IL_4V83_236
IL_90729.1
IL_6FYY_0471/2/892:898,
1/2/909:918		Kink-turn related
homologous
IL_8C3A_440
NA
IL_6FYY_0481/2/982:993,
1/2/1009:1017		No text annotation
IL_6FYY_0491/2/1033:1035,
1/2/1094:1100		No text annotation
homologous
IL_4V88_437
NA
IL_6FYY_0501/2/1040:1044,
1/2/1072:1076		No text annotation
geometric
IL_5TBW_121
NA
IL_6FYY_0511/2/1050:1052,
1/2/1065:1066		Single bulged U
homologous
IL_4V88_439
NA
IL_6FYY_0521/2/1110:1117,
1/2/1128:1133		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_4V88_440
NA
IL_6FYY_0531/2/1143:1145,
1/2/1630:1631		No text annotation
IL_6FYY_0541/2/1145:1146,
1/2/1628:1630		Single bulged A
geometric
IL_4LFB_035
IL_31462.6
IL_6FYY_0551/2/1148:1150,
1/2/1625:1626		Single bulged G
homologous
IL_4V88_442
NA
IL_6FYY_0561/2/1156:1159,
1/2/1615:1619		C-loop
homologous
IL_4V88_443
NA
IL_6FYY_0571/2/1172:1175,
1/2/1461:1464		Tandem non-canonical cWW pairs
geometric
IL_5EW4_002
IL_85033.2
IL_6FYY_0581/2/1177:1178,
1/2/1457:1459		Minor groove platform
homologous
IL_4V88_445
NA
IL_6FYY_0591/2/1212:1214,
1/2/1446:1448		Isolated non-canonical cWW pair
homologous
IL_4V88_446
NA
IL_6FYY_1041/2/1223:1229,
1/2/1256:1258		No text annotation
IL_6FYY_1051/2/1223:1232,
1/2/1251:1258		No text annotation
homologous
IL_8P9A_470
IL_28304.1
IL_6FYY_0611/2/1229:1232,
1/2/1251:1256		No text annotation
IL_6FYY_0621/2/1233:1235,
1/2/1248:1250		No text annotation
homologous
IL_4V88_448
NA
IL_6FYY_0631/2/1267:1269,
1/2/1438:1439		Single bulged U
homologous
IL_4V88_449
NA
IL_6FYY_0641/2/1271:1275,
1/2/1434:1436		Isolated cWS basepair
geometric
IL_4V88_450
NA
IL_6FYY_0951/2/1271:1277,
1/2/1428:1436		No text annotation
homologous
IL_8P9A_439
IL_86012.1
IL_6FYY_0651/2/1275:1277,
1/2/1428:1434		Minor groove platform with extra cWW
homologous
IL_4V88_451
NA
IL_6FYY_0961/2/1279:1280,
1/2/1424:1426		Single bulged A
homologous
IL_8C3A_458
NA
IL_6FYY_0971/2/1289:1291,
1/2/1322:1324		Isolated non-canonical cWW pair
homologous
IL_8C3A_459
NA
IL_6FYY_0681/2/1305:1307,
1/2/1316:1317		Minor groove platform
geometric
IL_4V88_388
NA
IL_6FYY_0691/2/1338:1341,
1/2/1381:1383		Isolated non-canonical cWW pair
homologous
IL_4V88_455
NA
IL_6FYY_0701/2/1344:1347,
1/2/1375:1378		Minor groove platform
homologous
IL_4V88_456
NA
IL_6FYY_0711/2/1352:1353,
1/2/1368:1370		Single bulged U
geometric
IL_6UFH_004
IL_89505.4
IL_6FYY_0721/2/1387:1389,
1/2/1405:1410		Major groove platform; stack outside cWW
homologous
IL_4V88_458
NA
IL_6FYY_0731/2/1478:1485,
1/2/1517:1525		No text annotation
homologous
IL_4V88_459
NA
IL_6FYY_0741/2/1486:1492,
1/2/1511:1516		180 degree turn
homologous
IL_4V88_460
NA
IL_6FYY_0751/2/1494:1496,
1/2/1507:1509		Isolated non-canonical cWW pair
geometric
IL_4WF9_018
IL_07785.1
IL_6FYY_0761/2/1538:1543,
1/2/1564:1569		No text annotation
homologous
IL_4V88_462
NA
IL_6FYY_0771/2/1634:1636,
1/2/1762:1765		No text annotation
homologous
IL_4V88_463
NA
IL_6FYY_0781/2/1636:1639,
1/2/1758:1762		No text annotation
geometric
IL_4V88_464
NA
IL_6FYY_0791/2/1640:1642,
1/2/1755:1757		Isolated non-canonical cWW pair
geometric
IL_3GM7_003
IL_87907.2
IL_6FYY_0801/2/1642:1645,
1/2/1751:1755		Tandem non-canonical cWW pairs
geometric
IL_5J7L_033
IL_85033.2
IL_6FYY_0811/2/1648:1650,
1/2/1746:1748		Isolated non-canonical cWW pair
homologous
IL_4V88_467
NA
IL_6FYY_0821/2/1651:1654,
1/2/1742:1745		Double sheared
geometric
IL_4KZD_002
IL_09705.15
IL_6FYY_0831/2/1654:1656,
1/2/1741:1742		Single bulged U
homologous
IL_4V88_469
NA
IL_6FYY_0841/2/1663:1665,
1/2/1732:1734		Isolated non-canonical cWW pair
homologous
IL_4V88_470
NA
IL_6FYY_0851/2/1667:1670,
1/2/1727:1730		Double sheared
homologous
IL_4V88_471
NA
IL_6FYY_0861/2/1673:1676,
1/2/1721:1724		Tandem non-canonical cWW pairs
geometric
IL_4V88_473
NA
IL_6FYY_0981/2/1673:1680,
1/2/1717:1724		No text annotation
IL_6FYY_0871/2/1676:1680,
1/2/1717:1721		Triple sheared
homologous
IL_4V88_474
NA
IL_6FYY_1061/2/1685:1688,
1/2/1709:1712		No text annotation
IL_6FYY_0891/2/1768:1770,
1/2/1787:1788		Single stack bend
geometric
IL_4LFB_041
IL_90729.1

Problematic loops

#loop idProblemSequence
IL_6FYY_010No text annotation
IL_6FYY_028Triple non-canonical cWW pairs
IL_6FYY_030Double sheared
IL_6FYY_037No text annotation
IL_6FYY_092Tandem non-canonical cWW pairs
IL_6FYY_042Tandem non-canonical cWW pairs
IL_6FYY_060No text annotation
IL_6FYY_094No text annotation
IL_6FYY_066Isolated non-canonical cWW pair
IL_6FYY_067Tandem non-canonical cWW pairs
IL_6FYY_088No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6FYY_0121/2/41:42,
1/2/432:438,
1/2/463:465		No text annotation
geometric
J3_4V88_078
NA
J3_6FYY_0131/2/41:48,
1/2/430:438,
1/2/463:465		No text annotation
homologous
J3_8P9A_069
J3_46317.4
J3_6FYY_0141/2/212:227,
1/2/236:242,
1/2/249:251		No text annotation
J3_6FYY_0011/2/632:634,
1/2/860:865,
1/2/961:965		No text annotation
homologous
J3_8C3A_034
NA
J3_6FYY_0171/2/759:763,
1/2/773:775,
1/2/784:790		No text annotation
J3_6FYY_0021/2/880:883,
1/2/927:935,
1/2/942:946		No text annotation
homologous
J3_4V88_033
NA
J3_6FYY_0031/2/1036:1038,
1/2/1078:1082,
1/2/1089:1093		No text annotation
homologous
J3_4V88_034
NA
J3_6FYY_0041/2/1160:1163,
1/2/1579:1585,
1/2/1607:1614		No text annotation
homologous
J3_4V88_035
NA
J3_6FYY_0051/2/1167:1170,
1/2/1466:1468,
1/2/1572:1575		No text annotation
homologous
J3_4V88_036
NA
J3_6FYY_0061/2/1179:1186,
1/2/1197:1208,
1/2/1452:1456		No text annotation
homologous
J3_8C3A_040
NA
J3_6FYY_0071/2/1214:1219,
1/2/1262:1266,
1/2/1440:1446		No text annotation
homologous
J3_4V88_038
NA
J3_6FYY_0081/2/1282:1287,
1/2/1326:1331,
1/2/1417:1422		No text annotation
homologous
J3_4V88_039
NA
J3_6FYY_0091/2/1291:1293,
1/2/1302:1305,
1/2/1317:1322		No text annotation
J3_6FYY_0101/2/1335:1337,
1/2/1384:1387,
1/2/1410:1413		No text annotation
homologous
J3_4V88_040
NA
J3_6FYY_0161/2/1335:1337,
1/2/1384:1389,
1/2/1405:1413		No text annotation
homologous
J3_8C3A_086
NA
J3_6FYY_0111/2/1468:1472,
1/2/1531:1538,
1/2/1569:1572		No text annotation
homologous
J3_8C3A_044
NA
J4_6FYY_0011/1/7:10,
1/1/25:27,
1/1/43:49,
1/1/65:66		No text annotation
homologous
J4_6UGG_002
J4_70449.28
J4_6FYY_0021/2/99:107,
1/2/306:308,
1/2/356:360,
1/2/382:383		No text annotation
homologous
J4_8P9A_021
J4_15241.1
J4_6FYY_0031/2/621:623,
1/2/974:979,
1/2/1020:1031,
1/2/1102:1103		No text annotation
homologous
J4_8C3A_022
NA
J5_6FYY_0011/2/31:35,
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_6FYY_0021/2/31:35,
1/2/472:478,
1/2/508:515,
1/2/535:545,
1/2/591:594		No text annotation
J5_6FYY_0031/2/54:57,
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_6FYY_0041/2/124:141,
1/2/172:181,
1/2/202:203,
1/2/262:264,
1/2/288:291		No text annotation
J5_6FYY_0051/2/124:141,
1/2/172:181,
1/2/202:203,
1/2/262:266,
1/2/287:291		No text annotation
J5_6FYY_0061/2/635:640,
1/2/693:700,
1/2/738:744,
1/2/806:816,
1/2/853:859		No text annotation

Problematic loops

#loop idProblemSequence
J3_6FYY_015No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.0546 s