RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8FKX_0011/L1/47:56No text annotation
HL_8FKX_0021/L1/68:90No text annotation
homologous
HL_8C3A_075
NA
HL_8FKX_0031/L1/107:112No text annotation
geometric
HL_3DIL_004
HL_78347.5
HL_8FKX_0071/L3/68:73No text annotation
homologous
HL_8C3A_002
NA
HL_8FKX_0081/L3/89:95No text annotation
geometric
HL_5J7L_151
NA
HL_8FKX_0101/L3/204:211T-loop with 2 stacked bulged bases
homologous
HL_8C3A_005
NA
HL_8FKX_0111/L3/222:226No text annotation
homologous
HL_5TBW_006
NA
HL_8FKX_0121/L3/230:238T-loop with unstacked turn
homologous
HL_8C3A_007
NA
HL_8FKX_0131/L3/289:298No text annotation
homologous
HL_5TBW_008
NA
HL_8FKX_0151/L3/368:373GNRA
homologous
HL_8C3A_010
NA
HL_8FKX_0161/L3/393:398GNRA
homologous
HL_8C3A_011
NA
HL_8FKX_0181/L3/1317:1326No text annotation
geometric
HL_5J7L_015
NA
HL_8FKX_0191/L3/1363:1374No text annotation
geometric
HL_2ZZM_002
HL_33487.1
HL_8FKX_0211/L3/1628:1633GNRA
geometric
HL_5J7L_197
NA
HL_8FKX_0241/L3/1864:1870Other HL
geometric
HL_4V9F_039
HL_67772.1
HL_8FKX_0251/L3/1886:1893No text annotation
homologous
HL_5TBW_026
NA
HL_8FKX_0261/L3/1978:1988No text annotation
homologous
HL_8C3A_027
NA
HL_8FKX_0271/L3/2006:2013GNRA wlth tandem sheared
homologous
HL_8C3A_028
NA
HL_8FKX_0291/L3/2317:2322GNRA
homologous
HL_8C3A_030
NA
HL_8FKX_0301/L3/2376:2384GNRA with extra cWW
geometric
HL_7A0S_056
HL_87268.2
HL_8FKX_0341/L3/3873:3882No text annotation
geometric
HL_1WZ2_007
HL_75660.7
HL_8FKX_0361/L3/4352:4362No text annotation
HL_8FKX_0371/L3/4474:4481No text annotation
homologous
HL_5TBW_062
NA
HL_8FKX_0381/L3/4495:4505No text annotation
geometric
HL_4UYK_001
HL_14063.2
HL_8FKX_0391/L3/4540:4545No text annotation
geometric
HL_5TBW_006
NA
HL_8FKX_0401/L3/4603:4608GNRA
homologous
HL_5TBW_065
NA
HL_8FKX_0421/L3/4688:4702No text annotation
homologous
HL_8C3A_068
NA
HL_8FKX_0431/L3/4907:4914No text annotation
geometric
HL_2Y9H_003
HL_75660.7
HL_8FKX_0441/L3/4975:4983No text annotation
geometric
HL_5TBW_070
NA

Problematic loops

#loop idProblemSequence
HL_8FKX_004Externally structured
HL_8FKX_005No text annotation
HL_8FKX_006No text annotation
HL_8FKX_009No text annotation
HL_8FKX_014No text annotation
HL_8FKX_017Externally structured
HL_8FKX_020Mini UNCG
HL_8FKX_022No text annotation
HL_8FKX_023No text annotation
HL_8FKX_028Mini UNCG
HL_8FKX_031No text annotation
HL_8FKX_032No text annotation
HL_8FKX_033No text annotation
HL_8FKX_035No text annotation
HL_8FKX_046tRNA anticodon loop
HL_8FKX_041Ribsomal LSU H95
HL_8FKX_045Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8FKX_0011/L1/13:19,
1/L3/415:421		Triple sheared with non-canonical cWW
homologous
IL_5TBW_015
NA
IL_8FKX_0021/L1/25:26,
1/L3/348:350		Single bulged A
homologous
IL_5TBW_013
NA
IL_8FKX_0031/L1/32:33,
1/L3/339:342		Minor groove platform
geometric
IL_7RQB_073
NA
IL_8FKX_0041/L1/64:66,
1/L1/92:95		Isolated non-canonical cWW pair
homologous
IL_5TBW_145
NA
IL_8FKX_0051/L1/139:141,
1/L3/16:18		Isolated non-canonical cWW pair
geometric
IL_1Y27_001
IL_01003.3
IL_8FKX_0061/L1/143:144,
1/L3/12:14		Single bulged U
homologous
IL_5TBW_003
NA
IL_8FKX_0071/L1/149:151,
1/L3/6:7		Single bulged C
geometric
IL_7A0S_032
IL_05642.2
IL_8FKX_0081/L2/13:14,
1/L2/42:44		Single stack bend
geometric
IL_4C7O_002
IL_15011.2
IL_8FKX_0091/L2/51:52,
1/L2/93:96		Multiple bulged bases
geometric
IL_1R3E_002
IL_05670.1
IL_8FKX_0111/L2/64:66,
1/L2/84:86		Isolated cWH basepair
geometric
IL_3W3S_003
IL_10892.2
IL_8FKX_0121/L3/26:27,
1/L3/55:57		No text annotation
homologous
IL_8C3A_004
NA
IL_8FKX_0131/L3/81:88,
1/L3/96:102		No text annotation
homologous
IL_8C3A_006
NA
IL_8FKX_0141/L3/118:122,
1/L3/147:153		No text annotation
IL_8FKX_0151/L3/125:126,
1/L3/142:144		Single bulged C
geometric
IL_1DQF_001
NA
IL_8FKX_0161/L3/169:173,
1/L3/263:266		No text annotation
IL_8FKX_0171/L3/180:182,
1/L3/255:256		Single bulged C
geometric
IL_3HHN_003
IL_05642.2
IL_8FKX_0181/L3/183:189,
1/L3/252:254		Decoding loop related
geometric
IL_5Z1I_002
NA
IL_8FKX_0191/L3/195:196,
1/L3/244:246		Single bulged C
geometric
IL_1DQF_001
NA
IL_8FKX_0201/L3/199:201,
1/L3/214:215		Single bulged U
homologous
IL_8C3A_013
NA
IL_8FKX_0211/L3/387:390,
1/L3/401:414		No text annotation
homologous
IL_8C3A_015
NA
IL_8FKX_0221/L3/443:446,
1/L3/1300:1304		No text annotation
geometric
IL_7MLW_007
IL_49140.1
IL_8FKX_0231/L3/448:450,
1/L3/1297:1298		No text annotation
IL_8FKX_0241/L3/459:460,
1/L3/695:697		Single bulged C
geometric
IL_1S03_006
IL_05642.2
IL_8FKX_0251/L3/462:464,
1/L3/691:693		Isolated non-canonical cWW pair
geometric
IL_5TBW_042
NA
IL_8FKX_0261/L3/466:472,
1/L3/682:689		No text annotation
IL_8FKX_0271/L3/709:710,
1/L3/1286:1288		Single bulged G
geometric
IL_4LFB_036
IL_28408.2
IL_8FKX_0281/L3/723:724,
1/L3/942:945		Multiple bulged bases
geometric
IL_7V9E_001
NA
IL_8FKX_0291/L3/727:731,
1/L3/938:939		No text annotation
IL_8FKX_0301/L3/732:735,
1/L3/928:937		No text annotation
IL_8FKX_0311/L3/737:739,
1/L3/924:926		No text annotation
geometric
IL_5J7L_341
NA
IL_8FKX_0321/L3/740:742,
1/L3/922:923		No text annotation
IL_8FKX_0331/L3/745:752,
1/L3/911:919		No text annotation
geometric
IL_5TBW_020
NA
IL_8FKX_0341/L3/1073:1074,
1/L3/1237:1239		Single bulged A
geometric
IL_2VPL_002
IL_14190.2
IL_8FKX_0351/L3/1357:1360,
1/L3/1379:1382		No text annotation
IL_8FKX_1121/L3/1357:1361,
1/L3/1376:1382		No text annotation
IL_8FKX_0361/L3/1360:1361,
1/L3/1376:1379		Major groove intercalation
geometric
IL_1NBS_009
IL_71421.2
IL_8FKX_0371/L3/1425:1429,
1/L3/1455:1460		Triple sheared related
geometric
IL_4V9F_018
IL_67427.1
IL_8FKX_0381/L3/1431:1434,
1/L3/1450:1453		Double sheared
geometric
IL_4LFB_060
IL_58355.2
IL_8FKX_0391/L3/1467:1468,
1/L3/1496:1498		Single bulged A
homologous
IL_8C3A_026
NA
IL_8FKX_0411/L3/1520:1522,
1/L3/1655:1657		Isolated non-canonical cWW pair
homologous
IL_8C3A_029
NA
IL_8FKX_0421/L3/1522:1526,
1/L3/1648:1655		No text annotation
IL_8FKX_0431/L3/1626:1628,
1/L3/1633:1635		Isolated non-canonical cWW pair
geometric
IL_3D0U_006
IL_01003.3
IL_8FKX_0441/L3/1671:1673,
1/L3/1682:1684		Isolated non-canonical cWW pair
homologous
IL_5TBW_034
NA
IL_8FKX_0451/L3/1686:1688,
1/L3/1848:1851		No text annotation
IL_8FKX_0471/L3/1723:1725,
1/L3/1838:1839		Single bulged G
homologous
IL_8C3A_040
NA
IL_8FKX_0481/L3/1858:1860,
1/L3/1874:1876		Isolated non-canonical cWW pair
homologous
IL_8C3A_049
NA
IL_8FKX_0491/L3/1905:1909,
1/L3/2067:2071		UAA/GAN
homologous
IL_8C3A_051
NA
IL_8FKX_0501/L3/1911:1918,
1/L3/2064:2065		SSU/LSU pseudoknot
geometric
IL_7RQB_037
NA
IL_8FKX_0511/L3/1918:1920,
1/L3/2063:2064		Single bulged G
geometric
IL_7D7V_002
IL_28408.2
IL_8FKX_0521/L3/1920:1922,
1/L3/2062:2063		No text annotation
IL_8FKX_0531/L3/1926:1933,
1/L3/2053:2058		No text annotation
homologous
IL_8C3A_054
NA
IL_8FKX_0541/L3/1933:1944,
1/L3/2038:2053		No text annotation
IL_8FKX_0551/L3/1946:1948,
1/L3/2035:2036		Single bulged U
homologous
IL_5TBW_053
NA
IL_8FKX_0561/L3/1957:1965,
1/L3/2022:2026		Kink-turn
homologous
IL_5TBW_054
NA
IL_8FKX_0571/L3/1973:1977,
1/L3/1989:1993		No text annotation
homologous
IL_8C3A_058
NA
IL_8FKX_0581/L3/2001:2005,
1/L3/2014:2016		Major groove platform with extra cWW
geometric
IL_5D8H_003
IL_36931.2
IL_8FKX_0591/L3/2083:2085,
1/L3/2272:2273		Single bulged C
geometric
IL_3DIL_001
IL_05642.2
IL_8FKX_0601/L3/2290:2292,
1/L3/2342:2345		No text annotation
homologous
IL_8C3A_061
NA
IL_8FKX_0611/L3/2299:2301,
1/L3/2334:2335		Single bulged A
homologous
IL_8C3A_062
NA
IL_8FKX_0621/L3/2302:2309,
1/L3/2329:2333		Kink-turn
homologous
IL_8C3A_063
NA
IL_8FKX_0631/L3/2312:2314,
1/L3/2325:2326		Single bulged A
homologous
IL_5TBW_060
NA
IL_8FKX_0641/L3/2358:2364,
1/L3/3858:3863		No text annotation
homologous
IL_8C3A_065
NA
IL_8FKX_0671/L3/2849:2850,
1/L3/3838:3840		Single bulged G
geometric
IL_5TBW_037
NA
IL_8FKX_0691/L3/3895:3897,
1/L3/4563:4565		Isolated non-canonical cWW pair
geometric
IL_6IA2_002
IL_01003.3
IL_8FKX_0701/L3/3904:3909,
1/L3/4393:4398		No text annotation
IL_8FKX_0711/L3/3914:3916,
1/L3/4386:4388		Isolated non-canonical cWW pair
geometric
IL_4E59_001
IL_01003.3
IL_8FKX_0721/L3/3916:3917,
1/L3/4384:4386		Single bulged A
geometric
IL_2VPL_002
IL_14190.2
IL_8FKX_0731/L3/3927:3929,
1/L3/4181:4184		No text annotation
homologous
IL_8C3A_100
NA
IL_8FKX_0751/L3/3948:3949,
1/L3/4063:4065		Single bulged C
geometric
IL_1S03_002
IL_05642.2
IL_8FKX_0761/L3/3950:3952,
1/L3/4060:4062		Isolated cWH basepair
geometric
IL_4KQ0_002
IL_10892.2
IL_8FKX_0771/L3/3955:3966,
1/L3/4055:4057		No text annotation
IL_8FKX_0781/L3/3970:3973,
1/L3/4038:4051		No text annotation
geometric
IL_3U4M_003
IL_75283.2
IL_8FKX_0791/L3/4347:4350,
1/L3/4364:4365		Multiple bulged bases
geometric
IL_5XWP_001
IL_71421.2
IL_8FKX_0801/L3/4412:4416,
1/L3/4426:4430		No text annotation
homologous
IL_8C3A_114
NA
IL_8FKX_0811/L3/4458:4459,
1/L3/4517:4522		Multiple bulged bases
homologous
IL_5TBW_109
NA
IL_8FKX_0821/L3/4466:4468,
1/L3/4489:4491		Isolated non-canonical cWW pair
geometric
IL_5TBW_110
NA
IL_8FKX_1131/L3/4466:4470,
1/L3/4485:4491		No text annotation
IL_8FKX_0831/L3/4468:4470,
1/L3/4485:4489		No text annotation
geometric
IL_5DO4_004
IL_15698.5
IL_8FKX_0841/L3/4537:4538,
1/L3/4547:4549		No text annotation
IL_8FKX_0851/L3/4580:4582,
1/L3/4721:4723		No text annotation
geometric
IL_3ICQ_003
NA
IL_8FKX_0861/L3/4582:4585,
1/L3/4717:4721		Other IL
geometric
IL_4WF9_054
IL_74317.1
IL_8FKX_0871/L3/4590:4592,
1/L3/4618:4620		Isolated non-canonical cWW pair
homologous
IL_5TBW_115
NA
IL_8FKX_0881/L3/4596:4603,
1/L3/4608:4614		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5TBW_116
NA
IL_8FKX_0891/L3/4624:4629,
1/L3/4669:4673		No text annotation
IL_8FKX_0911/L3/4638:4640,
1/L3/4659:4661		Isolated cWH basepair
geometric
IL_3R1C_018
IL_10892.2
IL_8FKX_0921/L3/4641:4642,
1/L3/4655:4658		Multiple bulged bases
homologous
IL_5TBW_119
NA
IL_8FKX_0931/L3/4681:4685,
1/L3/4705:4709		UAA/GAN
homologous
IL_8C3A_129
NA
IL_8FKX_0941/L3/4740:4742,
1/L3/4958:4959		No text annotation
IL_8FKX_0951/L3/4743:4746,
1/L3/4954:4957		Tandem non-canonical cWW pairs
geometric
IL_5TBW_100
NA
IL_8FKX_0961/L3/4749:4751,
1/L3/4948:4951		No text annotation
IL_8FKX_0971/L3/4756:4765,
1/L3/4869:4877		No text annotation
IL_8FKX_0981/L3/4769:4771,
1/L3/4863:4865		Isolated non-canonical cWW pair
geometric
IL_3GM7_006
IL_01003.3
IL_8FKX_0991/L3/4885:4889,
1/L3/4930:4934		Triple non-canonical cWW pairs
geometric
IL_8S95_002
IL_71154.3
IL_8FKX_1001/L3/4891:4896,
1/L3/4924:4928		No text annotation
IL_8FKX_1011/L3/4899:4901,
1/L3/4920:4921		Single bulged C
geometric
IL_3HHN_003
IL_05642.2
IL_8FKX_1021/L3/4972:4975,
1/L3/4983:4986		Tandem non-canonical cWW pairs
geometric
IL_3TZR_003
IL_71194.2
IL_8FKX_1031/L3/4992:4994,
1/L3/5057:5059		Isolated non-canonical cWW pair
geometric
IL_3D0U_006
IL_01003.3
IL_8FKX_1041/L3/4996:4997,
1/L3/5053:5055		No text annotation
IL_8FKX_1051/L3/5000:5002,
1/L3/5045:5050		Isolated non-canonical cWW pair
homologous
IL_5TBW_132
NA
IL_8FKX_1061/L3/5003:5009,
1/L3/5039:5044		No text annotation
IL_8FKX_1071/L3/5012:5014,
1/L3/5035:5036		No text annotation
IL_8FKX_1081/L3/5014:5017,
1/L3/5032:5035		Double sheared
geometric
IL_4V9F_100
IL_58355.2

Problematic loops

#loop idProblemSequence
IL_8FKX_010Isolated non-canonical cWW pair
IL_8FKX_110Isolated non-canonical cWW pair
IL_8FKX_111Isolated non-canonical cWW pair
IL_8FKX_040Single stack bend
IL_8FKX_046No text annotation
IL_8FKX_065Single bulged U
IL_8FKX_066No text annotation
IL_8FKX_068No text annotation
IL_8FKX_074No text annotation
IL_8FKX_090No text annotation
IL_8FKX_109No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8FKX_0061/L1/19:20,
1/L3/380:387,
1/L3/414:415		No text annotation
geometric
J3_4V9F_011
J3_68715.1
J3_8FKX_0071/L1/19:20,
1/L3/380:390,
1/L3/401:415		No text annotation
geometric
J3_4WF9_011
J3_17917.1
J3_8FKX_0081/L1/21:24,
1/L3/351:367,
1/L3/374:379		No text annotation
geometric
J3_5TBW_061
NA
J3_8FKX_0091/L1/44:45,
1/L1/58:64,
1/L1/95:99		No text annotation
homologous
J3_8C3A_060
NA
J3_8FKX_0011/L3/112:116,
1/L3/155:160,
1/L3/275:278		No text annotation
J3_8FKX_0101/L3/196:199,
1/L3/215:228,
1/L3/240:244		No text annotation
J3_8FKX_0111/L3/451:455,
1/L3/701:705,
1/L3/1292:1296		No text annotation
J3_8FKX_0121/L3/1726:1727,
1/L3/1802:1806,
1/L3/1832:1837		No text annotation
homologous
J3_8P9A_051
J3_84137.1
J3_8FKX_0021/L3/1969:1971,
1/L3/1995:2001,
1/L3/2016:2018		No text annotation
homologous
J3_5TBW_007
NA
J3_8FKX_0041/L3/4463:4466,
1/L3/4491:4493,
1/L3/4507:4513		No text annotation
homologous
J3_8C3A_011
NA
J3_8FKX_0131/L3/4751:4754,
1/L3/4879:4883,
1/L3/4936:4948		No text annotation
J3_8FKX_0051/L3/4970:4972,
1/L3/4986:4991,
1/L3/5060:5063		No text annotation
J4_8FKX_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_8FKX_0021/L3/196:199,
1/L3/215:222,
1/L3/226:228,
1/L3/240:244		No text annotation
J4_8FKX_0031/L3/4587:4590,
1/L3/4620:4621,
1/L3/4676:4678,
1/L3/4712:4715		No text annotation
J5_8FKX_0011/L1/35:42,
1/L1/101:106,
1/L1/113:114,
1/L1/136:138,
1/L3/19:21		No text annotation
J5_8FKX_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_8FKX_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_8FKX_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_8FKX_003No text annotation

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