RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8FKS_0011/L1/47:56Pseudoknot with intercalation
geometric
HL_7A0S_001
HL_17803.1
HL_8FKS_0021/L1/68:90No text annotation
homologous
HL_8C3A_075
NA
HL_8FKS_0031/L1/107:112No text annotation
homologous
HL_5TBW_075
NA
HL_8FKS_0071/L3/68:73No text annotation
homologous
HL_8C3A_002
NA
HL_8FKS_0081/L3/89:95No text annotation
geometric
HL_5J7L_151
NA
HL_8FKS_0101/L3/204:211T-loop with 2 stacked bulged bases
homologous
HL_5TBW_005
NA
HL_8FKS_0111/L3/222:226No text annotation
homologous
HL_5TBW_006
NA
HL_8FKS_0121/L3/230:238T-loop with unstacked turn
homologous
HL_5TBW_007
NA
HL_8FKS_0131/L3/289:298No text annotation
homologous
HL_5TBW_008
NA
HL_8FKS_0151/L3/368:373GNRA
homologous
HL_5TBW_010
NA
HL_8FKS_0161/L3/393:398GNRA
homologous
HL_8C3A_011
NA
HL_8FKS_0381/L3/1364:1373No text annotation
HL_8FKS_0231/L3/1864:1870Other HL
geometric
HL_4V9F_039
HL_67772.1
HL_8FKS_0241/L3/1886:1893GNRA
geometric
HL_5LM7_001
HL_34789.2
HL_8FKS_0251/L3/1978:1988No text annotation
homologous
HL_8C3A_027
NA
HL_8FKS_0261/L3/2006:2013GNRA wlth tandem sheared
homologous
HL_8C3A_028
NA
HL_8FKS_0281/L3/2317:2322GNRA
homologous
HL_8C3A_030
NA
HL_8FKS_0311/L3/4474:4481No text annotation
homologous
HL_5TBW_062
NA
HL_8FKS_0321/L3/4603:4608GNRA
geometric
HL_5J7L_003
NA
HL_8FKS_0331/L3/4646:4651Mini UNCG
geometric
HL_4TUW_002
HL_12626.2
HL_8FKS_0341/L3/4688:4702No text annotation
homologous
HL_8C3A_068
NA
HL_8FKS_0351/L3/4907:4914No text annotation
geometric
HL_4V9F_003
HL_75660.7
HL_8FKS_0361/L3/4975:4983No text annotation
homologous
HL_8C3A_071
NA

Problematic loops

#loop idProblemSequence
HL_8FKS_004Externally structured
HL_8FKS_005No text annotation
HL_8FKS_006No text annotation
HL_8FKS_009No text annotation
HL_8FKS_014No text annotation
HL_8FKS_017Externally structured
HL_8FKS_018No text annotation
HL_8FKS_019No text annotation
HL_8FKS_020No text annotation
HL_8FKS_021Externally structured
HL_8FKS_022No text annotation
HL_8FKS_027Mini UNCG
HL_8FKS_029Externally structured
HL_8FKS_030No text annotation
HL_8FKS_037No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8FKS_0011/L1/13:19,
1/L3/415:421		Triple sheared with non-canonical cWW
homologous
IL_5TBW_015
NA
IL_8FKS_0021/L1/25:26,
1/L3/348:350		Single bulged A
homologous
IL_5TBW_013
NA
IL_8FKS_0031/L1/32:33,
1/L3/339:342		Minor groove platform
geometric
IL_7RQB_073
NA
IL_8FKS_0041/L1/64:66,
1/L1/92:95		Isolated non-canonical cWW pair
homologous
IL_5TBW_145
NA
IL_8FKS_0051/L1/139:141,
1/L3/16:18		No text annotation
geometric
IL_3ICQ_003
NA
IL_8FKS_0061/L1/143:144,
1/L3/12:14		Single bulged U
homologous
IL_5TBW_003
NA
IL_8FKS_0071/L1/149:151,
1/L3/6:7		Single bulged C
geometric
IL_7A0S_032
IL_05642.2
IL_8FKS_0081/L2/13:14,
1/L2/42:44		Single stack bend
geometric
IL_4C7O_002
IL_15011.2
IL_8FKS_0091/L2/51:52,
1/L2/93:96		Multiple bulged bases
geometric
IL_1R3E_002
IL_05670.1
IL_8FKS_0111/L2/64:66,
1/L2/84:86		Isolated cWH basepair
geometric
IL_3W3S_003
IL_10892.2
IL_8FKS_0121/L3/26:27,
1/L3/55:57		No text annotation
homologous
IL_8C3A_004
NA
IL_8FKS_0131/L3/81:88,
1/L3/96:102		No text annotation
homologous
IL_8C3A_006
NA
IL_8FKS_0141/L3/118:122,
1/L3/147:153		No text annotation
IL_8FKS_0151/L3/125:126,
1/L3/142:144		Single bulged C
geometric
IL_1DQF_001
NA
IL_8FKS_0161/L3/169:173,
1/L3/263:266		No text annotation
IL_8FKS_0171/L3/180:182,
1/L3/255:256		Single bulged C
geometric
IL_5J7L_276
NA
IL_8FKS_0181/L3/183:189,
1/L3/252:254		Decoding loop related
geometric
IL_5Z1I_003
NA
IL_8FKS_0191/L3/195:196,
1/L3/244:246		Single bulged C
geometric
IL_1DQF_001
NA
IL_8FKS_0201/L3/199:201,
1/L3/214:215		Single bulged U
homologous
IL_8C3A_013
NA
IL_8FKS_0211/L3/387:390,
1/L3/401:414		No text annotation
homologous
IL_8C3A_015
NA
IL_8FKS_0221/L3/443:446,
1/L3/1300:1304		No text annotation
geometric
IL_4PHY_003
IL_49140.1
IL_8FKS_0231/L3/448:450,
1/L3/1297:1298		No text annotation
IL_8FKS_0251/L3/462:464,
1/L3/691:693		Isolated non-canonical cWW pair
geometric
IL_5TBW_042
NA
IL_8FKS_0261/L3/466:472,
1/L3/682:689		No text annotation
IL_8FKS_0271/L3/709:710,
1/L3/1286:1288		Single bulged G
geometric
IL_4LFB_036
IL_28408.2
IL_8FKS_0281/L3/723:724,
1/L3/942:945		Multiple bulged bases
geometric
IL_7V9E_001
NA
IL_8FKS_0291/L3/727:731,
1/L3/938:939		No text annotation
IL_8FKS_0301/L3/732:735,
1/L3/928:937		No text annotation
IL_8FKS_0311/L3/737:739,
1/L3/924:926		No text annotation
geometric
IL_5J7L_341
NA
IL_8FKS_0321/L3/740:742,
1/L3/922:923		No text annotation
IL_8FKS_0331/L3/745:752,
1/L3/911:919		No text annotation
geometric
IL_5TBW_020
NA
IL_8FKS_0341/L3/1073:1074,
1/L3/1237:1239		Single bulged A
geometric
IL_2VPL_002
IL_14190.2
IL_8FKS_0351/L3/1357:1360,
1/L3/1379:1382		No text annotation
IL_8FKS_0961/L3/1357:1361,
1/L3/1376:1382		No text annotation
IL_8FKS_0361/L3/1360:1361,
1/L3/1376:1379		Major groove intercalation
geometric
IL_1U9S_003
IL_71421.2
IL_8FKS_0371/L3/1425:1429,
1/L3/1455:1460		Triple sheared related
geometric
IL_4V9F_018
IL_67427.1
IL_8FKS_0381/L3/1431:1434,
1/L3/1450:1453		Double sheared
geometric
IL_5J7L_333
NA
IL_8FKS_0391/L3/1467:1468,
1/L3/1496:1498		Single bulged A
homologous
IL_8C3A_026
NA
IL_8FKS_0411/L3/1520:1522,
1/L3/1655:1657		Isolated non-canonical cWW pair
geometric
IL_4WF9_020
IL_01003.2
IL_8FKS_0421/L3/1522:1526,
1/L3/1648:1655		No text annotation
IL_8FKS_0431/L3/1671:1673,
1/L3/1682:1684		Isolated non-canonical cWW pair
homologous
IL_5TBW_034
NA
IL_8FKS_0441/L3/1686:1688,
1/L3/1848:1851		No text annotation
IL_8FKS_0461/L3/1723:1725,
1/L3/1838:1839		Single bulged G
homologous
IL_8C3A_040
NA
IL_8FKS_0481/L3/1905:1909,
1/L3/2067:2071		UAA/GAN
homologous
IL_8C3A_051
NA
IL_8FKS_0491/L3/1911:1918,
1/L3/2064:2065		SSU/LSU pseudoknot
homologous
IL_8C3A_052
NA
IL_8FKS_0501/L3/1918:1920,
1/L3/2063:2064		No text annotation
IL_8FKS_0511/L3/1920:1922,
1/L3/2062:2063		No text annotation
IL_8FKS_0531/L3/1939:1944,
1/L3/2038:2044		No text annotation
IL_8FKS_0541/L3/1946:1948,
1/L3/2035:2036		Single bulged U
homologous
IL_5TBW_053
NA
IL_8FKS_0551/L3/1957:1965,
1/L3/2022:2026		Kink-turn
homologous
IL_8C3A_057
NA
IL_8FKS_0561/L3/1973:1977,
1/L3/1989:1993		No text annotation
homologous
IL_8C3A_058
NA
IL_8FKS_0571/L3/2001:2005,
1/L3/2014:2016		Major groove platform with extra cWW
homologous
IL_8C3A_059
NA
IL_8FKS_0581/L3/2083:2085,
1/L3/2272:2273		Single bulged C
geometric
IL_3W3S_001
IL_05642.2
IL_8FKS_0591/L3/2290:2292,
1/L3/2342:2345		No text annotation
homologous
IL_8C3A_061
NA
IL_8FKS_0601/L3/2299:2301,
1/L3/2334:2335		Single bulged A
homologous
IL_8C3A_062
NA
IL_8FKS_0611/L3/2302:2309,
1/L3/2329:2333		Kink-turn
homologous
IL_8C3A_063
NA
IL_8FKS_0621/L3/2312:2314,
1/L3/2325:2326		Single bulged A
geometric
IL_7RQB_033
NA
IL_8FKS_0631/L3/2358:2364,
1/L3/3858:3863		No text annotation
homologous
IL_8C3A_065
NA
IL_8FKS_0651/L3/2832:2838,
1/L3/3850:3853		No text annotation
IL_8FKS_0671/L3/3895:3897,
1/L3/4563:4565		Isolated non-canonical cWW pair
geometric
IL_6IA2_002
IL_01003.2
IL_8FKS_0681/L3/4412:4416,
1/L3/4426:4430		No text annotation
homologous
IL_8C3A_114
NA
IL_8FKS_0691/L3/4580:4582,
1/L3/4721:4723		No text annotation
geometric
IL_3ICQ_003
NA
IL_8FKS_0701/L3/4582:4585,
1/L3/4717:4721		Other IL
geometric
IL_4WF9_054
IL_74317.1
IL_8FKS_0711/L3/4590:4592,
1/L3/4618:4620		Isolated non-canonical cWW pair
homologous
IL_8C3A_124
NA
IL_8FKS_0731/L3/4596:4603,
1/L3/4608:4614		8x7 Sarcin-Ricin; G-bulge
homologous
IL_8C3A_125
NA
IL_8FKS_0741/L3/4624:4629,
1/L3/4669:4673		No text annotation
IL_8FKS_0751/L3/4632:4637,
1/L3/4662:4666		No text annotation
IL_8FKS_0761/L3/4638:4640,
1/L3/4658:4661		No text annotation
geometric
IL_6DME_003
IL_75527.2
IL_8FKS_0771/L3/4640:4641,
1/L3/4656:4658		Multiple bulged bases
geometric
IL_6IV9_001
IL_71421.2
IL_8FKS_0781/L3/4681:4685,
1/L3/4705:4709		tSH-tHW-tHS
geometric
IL_6CZR_145
NA
IL_8FKS_0801/L3/4743:4746,
1/L3/4954:4957		Tandem non-canonical cWW pairs
geometric
IL_5TBW_100
NA
IL_8FKS_0811/L3/4749:4751,
1/L3/4948:4951		No text annotation
IL_8FKS_0821/L3/4756:4765,
1/L3/4869:4877		No text annotation
IL_8FKS_0831/L3/4769:4771,
1/L3/4863:4865		Isolated non-canonical cWW pair
geometric
IL_3GM7_006
IL_01003.2
IL_8FKS_0841/L3/4885:4889,
1/L3/4930:4934		Triple non-canonical cWW pairs
geometric
IL_8S95_002
IL_71154.2
IL_8FKS_0851/L3/4891:4896,
1/L3/4924:4928		No text annotation
IL_8FKS_0871/L3/4972:4975,
1/L3/4983:4986		Tandem non-canonical cWW pairs
geometric
IL_3TZR_003
IL_71194.2
IL_8FKS_0881/L3/4992:4994,
1/L3/5057:5059		Isolated non-canonical cWW contact
geometric
IL_5UNE_001
IL_87720.1
IL_8FKS_0891/L3/4996:4997,
1/L3/5053:5055		Single bulged U
homologous
IL_8C3A_137
NA
IL_8FKS_0911/L3/5003:5009,
1/L3/5039:5044		No text annotation
IL_8FKS_0921/L3/5012:5014,
1/L3/5035:5036		No text annotation
IL_8FKS_0931/L3/5014:5017,
1/L3/5032:5035		Double sheared
geometric
IL_4V9F_100
IL_58355.2

Problematic loops

#loop idProblemSequence
IL_8FKS_010Isolated non-canonical cWW pair
IL_8FKS_024Single bulged C
IL_8FKS_094Isolated non-canonical cWW pair
IL_8FKS_095Isolated non-canonical cWW pair
IL_8FKS_040Single stack bend
IL_8FKS_045No text annotation
IL_8FKS_047Isolated non-canonical cWW pair
IL_8FKS_052No text annotation
IL_8FKS_064Multiple bulged bases
IL_8FKS_066Isolated non-canonical cWW pair
IL_8FKS_072Isolated non-canonical cWW pair
IL_8FKS_097Isolated non-canonical cWW pair
IL_8FKS_079No text annotation
IL_8FKS_086Single bulged C
IL_8FKS_090No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8FKS_0041/L1/19:20,
1/L3/380:387,
1/L3/414:415		No text annotation
geometric
J3_4V9F_011
J3_68715.1
J3_8FKS_0051/L1/19:20,
1/L3/380:390,
1/L3/401:415		No text annotation
geometric
J3_4WF9_011
J3_17917.1
J3_8FKS_0061/L1/21:24,
1/L3/351:367,
1/L3/374:379		No text annotation
geometric
J3_5TBW_061
NA
J3_8FKS_0071/L1/44:45,
1/L1/58:64,
1/L1/95:99		No text annotation
homologous
J3_8C3A_060
NA
J3_8FKS_0011/L3/112:116,
1/L3/155:160,
1/L3/275:278		No text annotation
J3_8FKS_0081/L3/196:199,
1/L3/215:228,
1/L3/240:244		No text annotation
J3_8FKS_0091/L3/451:455,
1/L3/701:705,
1/L3/1292:1296		No text annotation
J3_8FKS_0101/L3/1726:1727,
1/L3/1802:1806,
1/L3/1832:1837		No text annotation
homologous
J3_8P9A_051
J3_84137.1
J3_8FKS_0031/L3/1969:1971,
1/L3/1995:2001,
1/L3/2016:2018		No text annotation
homologous
J3_5TBW_007
NA
J3_8FKS_0111/L3/4751:4754,
1/L3/4879:4883,
1/L3/4936:4948		No text annotation
J4_8FKS_0011/L3/111:112,
1/L3/278:283,
1/L3/304:310,
1/L3/327:330		No text annotation
homologous
J4_8P9A_012
J4_94698.1
J4_8FKS_0021/L3/196:199,
1/L3/215:222,
1/L3/226:228,
1/L3/240:244		No text annotation
J4_8FKS_0031/L3/4587:4590,
1/L3/4620:4621,
1/L3/4676:4678,
1/L3/4712:4715		No text annotation
J5_8FKS_0031/L1/35:42,
1/L1/101:106,
1/L1/113:114,
1/L1/136:137,
1/L3/20:21		No text annotation
J5_8FKS_0021/L3/1335:1340,
1/L3/1516:1519,
1/L3/1658:1661,
1/L3/2288:2290,
1/L3/2345:2351		No text annotation
homologous
J5_8P9A_011
J5_08384.1
J6_8FKS_0011/L1/33:35,
1/L3/21:26,
1/L3/57:67,
1/L3/74:78,
1/L3/105:109,
1/L3/332:339		No text annotation
J7_8FKS_0011/L3/1666:1671,
1/L3/1684:1685,
1/L3/1852:1855,
1/L3/1879:1884,
1/L3/1895:1899,
1/L3/2077:2078,
1/L3/2278:2283		No text annotation

Problematic loops

#loop idProblemSequence
J3_8FKS_002No text annotation
J5_8FKS_001No text annotation

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