RNA 3D Hub //

8S8J Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8S8J_0041/2/7:17No text annotation
homologous
HL_8C3A_192
NA
HL_8S8J_0061/2/153:159GNRA related
homologous
HL_8C3A_194
NA
HL_8S8J_0091/2/242:249T-loop with 1 bulged base
homologous
HL_8P9A_195
NA
HL_8S8J_0131/2/392:403No text annotation
homologous
HL_8C3A_201
NA
HL_8S8J_0141/2/413:418UNCG
homologous
HL_8C3A_202
NA
HL_8S8J_0151/2/449:455No text annotation
homologous
HL_8C3A_203
NA
HL_8S8J_0171/2/519:531No text annotation
homologous
HL_8C3A_205
NA
HL_8S8J_0211/2/764:772No text annotation
homologous
HL_8C3A_208
NA
HL_8S8J_0251/2/936:941GNRA
homologous
HL_8C3A_212
NA
HL_8S8J_0421/2/996:1006No text annotation
homologous
HL_8CRE_212
HL_38491.5
HL_8S8J_0281/2/1083:1088GNRA
homologous
HL_8P9A_213
NA
HL_8S8J_0291/2/1120:1125GNRA
homologous
HL_8P9A_214
NA
HL_8S8J_0301/2/1187:1196No text annotation
homologous
HL_8P9A_215
NA
HL_8S8J_0321/2/1295:1300GNRA
homologous
HL_8P9A_217
NA
HL_8S8J_0331/2/1308:1315T-loop related
homologous
HL_8P9A_218
NA
HL_8S8J_0351/2/1394:1400No text annotation
homologous
HL_8C3A_222
NA
HL_8S8J_0361/2/1499:1504GNRA
homologous
HL_8C3A_223
NA
HL_8S8J_0391/2/1688:1709No text annotation

Problematic loops

#loop idProblemSequence
HL_8S8J_001Externally structured
HL_8S8J_002No text annotation
HL_8S8J_003T-loop with 2 stacked bulged bases
HL_8S8J_005No text annotation
HL_8S8J_007No text annotation
HL_8S8J_008No text annotation
HL_8S8J_010No text annotation
HL_8S8J_011GNRA related
HL_8S8J_012GNRA variation
HL_8S8J_016No text annotation
HL_8S8J_041No text annotation
HL_8S8J_018GNRA variation
HL_8S8J_019No text annotation
HL_8S8J_020No text annotation
HL_8S8J_022Externally structured
HL_8S8J_023Pseudoknot geometry
HL_8S8J_024No text annotation
HL_8S8J_026No text annotation
HL_8S8J_027No text annotation
HL_8S8J_031GNRA with extra near cWW
HL_8S8J_034No text annotation
HL_8S8J_037No text annotation
HL_8S8J_038No text annotation
HL_8S8J_040GNRA variation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8S8J_0031/2/35:37,
1/2/470:472		Isolated non-canonical cWW pair
homologous
IL_8P9A_374
NA
IL_8S8J_0041/2/42:48,
1/2/430:432		No text annotation
homologous
IL_8P9A_376
NA
IL_8S8J_0081/2/109:112,
1/2/301:304		Tandem non-canonical cWW pairs
homologous
IL_8C3A_399
NA
IL_8S8J_0091/2/113:122,
1/2/294:300		No text annotation
IL_8S8J_0101/2/142:148,
1/2/164:171		No text annotation
homologous
IL_8C3A_402
NA
IL_8S8J_0141/2/205:207,
1/2/255:258		No text annotation
geometric
IL_7KJT_002
IL_32983.4
IL_8S8J_0921/2/310:315,
1/2/347:354		Kink-turn with non-sequential stacking
homologous
IL_8CRE_408
IL_46174.7
IL_8S8J_0201/2/317:322,
1/2/344:345		No text annotation
homologous
IL_8P9A_392
NA
IL_8S8J_0211/2/362:364,
1/2/375:380		No text annotation
homologous
IL_8P9A_393
NA
IL_8S8J_0231/2/410:412,
1/2/419:421		Isolated non-canonical cWW pair
homologous
IL_8C3A_414
NA
IL_8S8J_0241/2/438:440,
1/2/462:463		Single bulged U
homologous
IL_8P9A_396
NA
IL_8S8J_0261/2/446:447,
1/2/457:459		Single bulged G
homologous
IL_8P9A_398
NA
IL_8S8J_0281/2/513:515,
1/2/535:542		No text annotation
homologous
IL_8C3A_420
NA
IL_8S8J_0291/2/516:517,
1/2/532:534		Minor groove platform
homologous
IL_8C3A_501
NA
IL_8S8J_0301/2/517:519,
1/2/531:532		Minor groove platform
homologous
IL_8P9A_401
NA
IL_8S8J_0311/2/549:556,
1/2/586:587		SSU/LSU pseudoknot
homologous
IL_8C3A_423
NA
IL_8S8J_0321/2/556:558,
1/2/585:586		Single bulged U
homologous
IL_8C3A_424
NA
IL_8S8J_0331/2/561:567,
1/2/574:582		No text annotation
homologous
IL_8P9A_404
NA
IL_8S8J_0341/2/615:621,
1/2/1103:1104		No text annotation
homologous
IL_8P9A_405
NA
IL_8S8J_0351/2/623:625,
1/2/972:974		Isolated non-canonical cWW pair
homologous
IL_8C3A_427
NA
IL_8S8J_0361/2/626:631,
1/2/966:971		No text annotation
geometric
IL_8ZA4_001
NA
IL_8S8J_0411/2/748:750,
1/2/798:800		Isolated non-canonical cWW pair
homologous
IL_8C3A_431
NA
IL_8S8J_0421/2/751:759,
1/2/790:797		No text annotation
homologous
IL_8C3A_503
NA
IL_8S8J_0431/2/818:821,
1/2/849:851		Isolated non-canonical cWW pair
geometric
IL_1L9A_009
NA
IL_8S8J_0441/2/866:869,
1/2/956:960		No text annotation
homologous
IL_8C3A_436
NA
IL_8S8J_0461/2/873:877,
1/2/949:952		Tandem non-canonical cWW pairs
homologous
IL_8C3A_438
NA
IL_8S8J_0491/2/982:993,
1/2/1009:1017		No text annotation
IL_8S8J_0501/2/1033:1035,
1/2/1094:1100		No text annotation
homologous
IL_8P9A_425
NA
IL_8S8J_0521/2/1050:1052,
1/2/1065:1066		Single bulged U
geometric
IL_3NDB_005
NA
IL_8S8J_0531/2/1110:1117,
1/2/1128:1133		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_8P9A_428
NA
IL_8S8J_0541/2/1145:1146,
1/2/1628:1630		Single bulged A
homologous
IL_8C3A_447
NA
IL_8S8J_0561/2/1156:1159,
1/2/1615:1619		C-loop
homologous
IL_8P9A_431
NA
IL_8S8J_0641/2/1267:1269,
1/2/1438:1439		Single bulged U
homologous
IL_8C3A_455
NA
IL_8S8J_0691/2/1289:1291,
1/2/1322:1324		Isolated non-canonical cWW pair
homologous
IL_8C3A_459
NA
IL_8S8J_0701/2/1305:1307,
1/2/1316:1317		Minor groove platform
homologous
IL_8C3A_460
NA
IL_8S8J_0721/2/1344:1347,
1/2/1375:1378		No text annotation
homologous
IL_8C3A_462
NA
IL_8S8J_0741/2/1387:1389,
1/2/1405:1410		Major groove platform; stack outside cWW
geometric
IL_4V88_458
NA
IL_8S8J_0751/2/1478:1486,
1/2/1516:1525		No text annotation
IL_8S8J_0761/2/1486:1492,
1/2/1511:1516		No text annotation
homologous
IL_8P9A_449
NA
IL_8S8J_0771/2/1494:1496,
1/2/1507:1509		Isolated non-canonical cWW pair
homologous
IL_8C3A_468
NA
IL_8S8J_0791/2/1634:1636,
1/2/1762:1765		No text annotation
homologous
IL_8C3A_470
NA
IL_8S8J_0801/2/1636:1639,
1/2/1758:1762		No text annotation
homologous
IL_8C3A_471
NA
IL_8S8J_0811/2/1640:1642,
1/2/1755:1757		Isolated non-canonical cWW pair
homologous
IL_8C3A_472
NA
IL_8S8J_0971/2/1642:1645,
1/2/1751:1755		No text annotation
homologous
IL_9PN5_223
IL_37443.2
IL_8S8J_0881/2/1673:1676,
1/2/1721:1724		Tandem non-canonical cWW pairs
homologous
IL_8P9A_462
NA

Problematic loops

#loop idProblemSequence
IL_8S8J_001Single bulged C
IL_8S8J_002Isolated cWH basepair
IL_8S8J_091Minor groove platform
IL_8S8J_005No text annotation
IL_8S8J_006No text annotation
IL_8S8J_007No text annotation
IL_8S8J_011No text annotation
IL_8S8J_012Double sheared
IL_8S8J_013No text annotation
IL_8S8J_015Single stack bend
IL_8S8J_016Single bulged A
IL_8S8J_017No text annotation
IL_8S8J_018Isolated non-canonical cWW pair
IL_8S8J_019No text annotation
IL_8S8J_022Isolated cWH basepair
IL_8S8J_025C-loop
IL_8S8J_027No text annotation
IL_8S8J_037No text annotation
IL_8S8J_038No text annotation
IL_8S8J_093No text annotation
IL_8S8J_039No text annotation
IL_8S8J_040No text annotation
IL_8S8J_045Isolated non-canonical cWW pair
IL_8S8J_047Isolated non-canonical cWW pair
IL_8S8J_048Kink-turn related
IL_8S8J_051No text annotation
IL_8S8J_055Single bulged G
IL_8S8J_057No text annotation
IL_8S8J_058Minor groove platform
IL_8S8J_059Isolated non-canonical cWW pair
IL_8S8J_060No text annotation
IL_8S8J_061No text annotation
IL_8S8J_094No text annotation
IL_8S8J_095No text annotation
IL_8S8J_062No text annotation
IL_8S8J_063Tandem non-canonical cWW pairs
IL_8S8J_096Isolated non-canonical cWW contact
IL_8S8J_065No text annotation
IL_8S8J_066No text annotation
IL_8S8J_067No text annotation
IL_8S8J_068Isolated non-canonical cWW contact
IL_8S8J_071Isolated non-canonical cWW pair
IL_8S8J_073Single bulged U
IL_8S8J_078No text annotation
IL_8S8J_082No text annotation
IL_8S8J_083Isolated non-canonical cWW pair
IL_8S8J_084Double sheared
IL_8S8J_085Single bulged U
IL_8S8J_086Isolated non-canonical cWW pair
IL_8S8J_087Double sheared
IL_8S8J_089Triple sheared
IL_8S8J_090No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8S8J_0011/2/37:42,
1/2/432:438,
1/2/463:470		No text annotation
J3_8S8J_0031/2/632:634,
1/2/860:865,
1/2/961:965		No text annotation
homologous
J3_8P9A_072
NA
J3_8S8J_0041/2/759:763,
1/2/773:775,
1/2/784:790		No text annotation
J3_8S8J_0051/2/880:883,
1/2/927:935,
1/2/942:946		No text annotation
homologous
J3_8P9A_074
NA
J3_8S8J_0061/2/1036:1038,
1/2/1078:1082,
1/2/1089:1093		No text annotation
geometric
J3_4V88_034
NA
J3_8S8J_0071/2/1160:1163,
1/2/1579:1585,
1/2/1607:1614		No text annotation
homologous
J3_8P9A_076
NA
J3_8S8J_0091/2/1179:1186,
1/2/1197:1208,
1/2/1452:1456		No text annotation
homologous
J3_8C3A_040
NA
J3_8S8J_0111/2/1282:1287,
1/2/1326:1331,
1/2/1417:1422		No text annotation
homologous
J3_8P9A_080
NA
J3_8S8J_0121/2/1291:1293,
1/2/1302:1305,
1/2/1317:1322		No text annotation
J3_8S8J_0131/2/1335:1337,
1/2/1384:1387,
1/2/1410:1413		No text annotation
geometric
J3_4V88_040
NA
J3_8S8J_0141/2/1335:1337,
1/2/1384:1389,
1/2/1405:1413		No text annotation
homologous
J3_8C3A_086
NA
J3_8S8J_0151/2/1468:1472,
1/2/1531:1538,
1/2/1569:1572		No text annotation
homologous
J3_8C3A_044
NA
J4_8S8J_0021/2/99:107,
1/2/306:308,
1/2/356:360,
1/2/382:383		No text annotation
homologous
J4_8P9A_021
NA
J4_8S8J_0041/2/621:623,
1/2/974:979,
1/2/1020:1031,
1/2/1102:1103		No text annotation
homologous
J4_8CRE_022
J4_14595.4
J5_8S8J_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_8S8J_0021/2/31:35,
1/2/472:478,
1/2/508:515,
1/2/535:545,
1/2/591:594		No text annotation
J5_8S8J_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_8P9A_017
NA
J5_8S8J_0041/2/124:141,
1/2/172:181,
1/2/202:203,
1/2/262:264,
1/2/288:292		No text annotation
J5_8S8J_0051/2/124:141,
1/2/172:181,
1/2/202:203,
1/2/262:266,
1/2/287:292		No text annotation
J5_8S8J_0071/2/635:641,
1/2/692:699,
1/2/739:744,
1/2/806:816,
1/2/853:859		No text annotation

Problematic loops

#loop idProblemSequence
J3_8S8J_002No text annotation
J3_8S8J_008No text annotation
J3_8S8J_010No text annotation
J4_8S8J_001tRNA junction
J4_8S8J_003No text annotation
J5_8S8J_006No text annotation

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