RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6FTI_0051/u/68:73No text annotation
homologous
HL_5TBW_002
NA
HL_6FTI_0131/u/368:373GNRA
homologous
HL_8C3A_010
NA
HL_6FTI_0141/u/393:398GNRA
homologous
HL_8C3A_011
NA
HL_6FTI_0171/u/1317:1326T-loop with 2 stacked bulged bases
homologous
HL_5TBW_014
NA
HL_6FTI_0241/u/1593:1602No text annotation
homologous
HL_5TBW_020
NA
HL_6FTI_0251/u/1627:1635No text annotation
homologous
HL_5TBW_021
NA
HL_6FTI_0291/u/1864:1870GNRA
homologous
HL_5TBW_025
NA
HL_6FTI_0351/u/2376:2384T-loop with 2 stacked bulged bases
homologous
HL_5TBW_031
NA
HL_6FTI_0391/u/2523:2532No text annotation
homologous
HL_5TBW_035
NA
HL_6FTI_0841/u/2622:2634No text annotation
HL_6FTI_0421/u/2623:2632No text annotation
geometric
HL_5NFV_001
HL_69752.4
HL_6FTI_0451/u/2738:2742No text annotation
homologous
HL_8C3A_040
NA
HL_6FTI_0461/u/2792:2799No text annotation
homologous
HL_5TBW_041
NA
HL_6FTI_0501/u/3639:3649No text annotation
homologous
HL_5TBW_046
NA
HL_6FTI_0541/u/3796:3804No text annotation
homologous
HL_8C3A_050
NA
HL_6FTI_0611/u/4250:4258No text annotation
homologous
HL_8C3A_057
NA
HL_6FTI_0681/u/4497:4503No text annotation
homologous
HL_8C3A_064
NA
HL_6FTI_0691/u/4540:4545GNRA
homologous
HL_8C3A_065
NA
HL_6FTI_0741/u/4975:4983No text annotation
geometric
HL_5J7L_201
NA
HL_6FTI_0781/w/47:56Pseudoknot with intercalation
geometric
HL_4V9F_001
HL_17803.1

Problematic loops

#loop idProblemSequence
HL_6FTI_001No text annotation
HL_6FTI_002tRNA anticodon loop
HL_6FTI_003T-loop with 2 stacked bulged bases
HL_6FTI_004No text annotation
HL_6FTI_006No text annotation
HL_6FTI_007No text annotation
HL_6FTI_008T-loop with 2 stacked bulged bases
HL_6FTI_009No text annotation
HL_6FTI_010T-loop with unstacked turn
HL_6FTI_011No text annotation
HL_6FTI_012Pseudoknot geometry
HL_6FTI_082No text annotation
HL_6FTI_015GNRA
HL_6FTI_016GNRA
HL_6FTI_018No text annotation
HL_6FTI_019GNRA
HL_6FTI_020No text annotation
HL_6FTI_021No text annotation
HL_6FTI_022No text annotation
HL_6FTI_023GNRA
HL_6FTI_026Externally structured
HL_6FTI_027GNRA
HL_6FTI_028No text annotation
HL_6FTI_030No text annotation
HL_6FTI_083No text annotation
HL_6FTI_031No text annotation
HL_6FTI_032GNRA wlth tandem sheared
HL_6FTI_033No text annotation
HL_6FTI_034GNRA
HL_6FTI_036Pseudoknot geometry with 3' bulge
HL_6FTI_037GNRA variation
HL_6FTI_038No text annotation
HL_6FTI_040GNRA
HL_6FTI_041GNRA
HL_6FTI_043No text annotation
HL_6FTI_044No text annotation
HL_6FTI_047GNRA
HL_6FTI_048No text annotation
HL_6FTI_085No text annotation
HL_6FTI_049No text annotation
HL_6FTI_051GNRA
HL_6FTI_052No text annotation
HL_6FTI_053No text annotation
HL_6FTI_055No text annotation
HL_6FTI_056No text annotation
HL_6FTI_057UNCG
HL_6FTI_058No text annotation
HL_6FTI_059No text annotation
HL_6FTI_060No text annotation
HL_6FTI_062Pseudoknot geometry
HL_6FTI_063No text annotation
HL_6FTI_064GNRA
HL_6FTI_065No text annotation
HL_6FTI_066No text annotation
HL_6FTI_067GNRA with extra cWW
HL_6FTI_070GNRA
HL_6FTI_071Ribsomal LSU H95
HL_6FTI_072No text annotation
HL_6FTI_073No text annotation
HL_6FTI_075UNCG variation
HL_6FTI_086No text annotation
HL_6FTI_076No text annotation
HL_6FTI_077GNRA
HL_6FTI_079No text annotation
HL_6FTI_080No text annotation
HL_6FTI_081No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6FTI_0041/u/16:18,
1/w/139:141		Isolated non-canonical cWW pair
geometric
IL_6IA2_005
IL_01003.3
IL_6FTI_0551/u/1522:1526,
1/u/1648:1655		tHW-tHW cross-strand stack
homologous
IL_5TBW_028
NA
IL_6FTI_0561/u/1550:1551,
1/u/1576:1578		Single bulged G
geometric
IL_4V9F_026
IL_28408.2
IL_6FTI_0581/u/1586:1589,
1/u/1605:1607		Major groove platform with extra cWW
homologous
IL_5TBW_031
NA
IL_6FTI_0591/u/1590:1592,
1/u/1603:1604		Single bulged U
homologous
IL_8C3A_035
NA
IL_6FTI_0601/u/1624:1626,
1/u/1636:1640		Multiple bulged bases
geometric
IL_5TBW_033
NA
IL_6FTI_0891/u/2358:2364,
1/u/3858:3863		7x6 Sarcin-Ricin; G-bulge
homologous
IL_5TBW_061
NA
IL_6FTI_0901/u/2415:2419,
1/u/2427:2429		C-loop
geometric
IL_7A0S_047
IL_06671.1
IL_6FTI_1851/u/2847:2855,
1/u/3837:3841		No text annotation
homologous
IL_8C3A_484
NA
IL_6FTI_1051/u/2850:2855,
1/u/3837:3840		No text annotation
homologous
IL_8C3A_083
NA
IL_6FTI_1101/u/3632:3633,
1/u/3827:3829		Single bulged A
homologous
IL_5TBW_082
NA
IL_6FTI_1131/u/3704:3705,
1/u/3745:3748		Multiple bulged bases
homologous
IL_8C3A_090
NA
IL_6FTI_1181/u/3780:3781,
1/u/3811:3814		Bulged stacked bases
homologous
IL_5TBW_089
NA
IL_6FTI_1191/u/3781:3792,
1/u/3808:3811		No text annotation
geometric
IL_5TBW_090
NA
IL_6FTI_1201/u/3895:3898,
1/u/4563:4565		Major groove platform with extra pair
homologous
IL_5TBW_091
NA
IL_6FTI_1211/u/3900:3902,
1/u/4558:4561		No text annotation
homologous
IL_8C3A_097
NA
IL_6FTI_1221/u/3913:3915,
1/u/4388:4389		Single bulged U
homologous
IL_5TBW_093
NA
IL_6FTI_1231/u/3916:3917,
1/u/4384:4387		Minor groove platform
homologous
IL_5TBW_094
NA
IL_6FTI_1371/u/4453:4454,
1/u/4526:4528		Major groove platform
homologous
IL_8C3A_115
NA
IL_6FTI_1381/u/4456:4458,
1/u/4520:4524		Isolated non-canonical cWW with bulges
homologous
IL_5TBW_108
NA
IL_6FTI_1391/u/4458:4459,
1/u/4517:4520		Multiple bulged bases
geometric
IL_5TBW_109
NA
IL_6FTI_1431/u/4495:4497,
1/u/4503:4505		Isolated non-canonical cWW pair
geometric
IL_5TBW_112
NA
IL_6FTI_1441/u/4537:4538,
1/u/4547:4549		Single bulged A
geometric
IL_7RQB_101
NA
IL_6FTI_1521/u/4641:4642,
1/u/4655:4658		Multiple bulged bases
homologous
IL_5TBW_119
NA

Problematic loops

#loop idProblemSequence
IL_6FTI_001No text annotation
IL_6FTI_002Single bulged C
IL_6FTI_003Single bulged U
IL_6FTI_005Single stack bend
IL_6FTI_0069x8 Sarcin-Ricin; G-bulge
IL_6FTI_007No text annotation
IL_6FTI_008Multiple bulged bases
IL_6FTI_177No text annotation
IL_6FTI_009No text annotation
IL_6FTI_010No text annotation
IL_6FTI_011No text annotation
IL_6FTI_012Single stack bend
IL_6FTI_013Major groove intercalation
IL_6FTI_014Single bulged C
IL_6FTI_015Single bulged U
IL_6FTI_016Not an internal loop
IL_6FTI_017Single stack bend
IL_6FTI_018Minor groove platform, major groove intercalation
IL_6FTI_019Single bulged A
IL_6FTI_020No text annotation
IL_6FTI_021Triple sheared with non-canonical cWW
IL_6FTI_022No text annotation
IL_6FTI_023No text annotation
IL_6FTI_024Isolated non-canonical cWW pair
IL_6FTI_178No text annotation
IL_6FTI_025No text annotation
IL_6FTI_026Decoding loop related
IL_6FTI_027No text annotation
IL_6FTI_028Single stack bend
IL_6FTI_029No text annotation
IL_6FTI_179Single stack bend
IL_6FTI_030No text annotation
IL_6FTI_031Single bulged A
IL_6FTI_032Isolated non-canonical cWW pair
IL_6FTI_033Single bulged G
IL_6FTI_034No text annotation
IL_6FTI_180No text annotation
IL_6FTI_035No text annotation
IL_6FTI_036No text annotation
IL_6FTI_037Single stack bend
IL_6FTI_038Isolated non-canonical cWW pair
IL_6FTI_181No text annotation
IL_6FTI_039No text annotation
IL_6FTI_040No text annotation
IL_6FTI_041Tandem non-canonical cWW pairs
IL_6FTI_182No text annotation
IL_6FTI_042No text annotation
IL_6FTI_043Minor groove platform
IL_6FTI_044No text annotation
IL_6FTI_045Single bulged C
IL_6FTI_046Single stack bend
IL_6FTI_047Isolated near basepair
IL_6FTI_048No text annotation
IL_6FTI_049No text annotation
IL_6FTI_050Triple sheared related
IL_6FTI_051Double sheared
IL_6FTI_052Single bulged A
IL_6FTI_053Single base bend
IL_6FTI_054Isolated non-canonical cWW pair
IL_6FTI_057Triple sheared
IL_6FTI_190Isolated non-canonical cWW pair
IL_6FTI_061Tandem non-canonical cWW pairs
IL_6FTI_062No text annotation
IL_6FTI_063No text annotation
IL_6FTI_0645x5 Sarcin-Ricin with intercalated A; G-bulge
IL_6FTI_065Minor groove platform
IL_6FTI_066C-loop
IL_6FTI_067Tandem non-canonical cWW pairs
IL_6FTI_068Isolated non-canonical cWW pair
IL_6FTI_069Intercalated cWW
IL_6FTI_070Single stack bend
IL_6FTI_183Tandem non-canonical cWW pairs
IL_6FTI_071Isolated non-canonical cWW pair
IL_6FTI_072Isolated non-canonical cWW pair
IL_6FTI_073Isolated cWS basepair
IL_6FTI_074UAA/GAN
IL_6FTI_075SSU/LSU pseudoknot
IL_6FTI_076No text annotation
IL_6FTI_077No text annotation
IL_6FTI_078No text annotation
IL_6FTI_079No text annotation
IL_6FTI_080Single bulged U
IL_6FTI_081Kink-turn
IL_6FTI_082No text annotation
IL_6FTI_083Major groove platform with extra cWW
IL_6FTI_084Single bulged C
IL_6FTI_184No text annotation
IL_6FTI_085Isolated cWS basepair
IL_6FTI_086Single bulged A
IL_6FTI_087Kink-turn
IL_6FTI_088Single bulged A
IL_6FTI_091UAA/GAN
IL_6FTI_092Not an internal loop
IL_6FTI_093Isolated non-canonical cWW pair
IL_6FTI_094Triple sheared
IL_6FTI_095Single bulged C
IL_6FTI_096Single stack bend
IL_6FTI_097Single stack bend
IL_6FTI_098Isolated tHS basepair with bulges
IL_6FTI_099Single bulged G
IL_6FTI_100Kink-turn
IL_6FTI_101No text annotation
IL_6FTI_102No text annotation
IL_6FTI_103Isolated tWW turn
IL_6FTI_104Major groove platform; stack outside cWW
IL_6FTI_106No text annotation
IL_6FTI_107Isolated non-canonical cWW pair
IL_6FTI_108No text annotation
IL_6FTI_109No text annotation
IL_6FTI_111Kink-turn related
IL_6FTI_112No text annotation
IL_6FTI_114Single stack bend
IL_6FTI_115No text annotation
IL_6FTI_116No text annotation
IL_6FTI_117Single stack bend
IL_6FTI_124No text annotation
IL_6FTI_125No text annotation
IL_6FTI_126Minor groove platform
IL_6FTI_127Single bulged A
IL_6FTI_128Isolated tHS basepair with bulges
IL_6FTI_129Single bulged A
IL_6FTI_130Tandem non-canonical cWW pairs
IL_6FTI_131Single stack bend
IL_6FTI_132Major groove platform
IL_6FTI_133Isolated non-canonical cWW pair
IL_6FTI_134Major groove platform
IL_6FTI_135Major groove minor groove platform with extra cWW
IL_6FTI_136No text annotation
IL_6FTI_140Isolated non-canonical cWW pair
IL_6FTI_186No text annotation
IL_6FTI_141No text annotation
IL_6FTI_142Single stack bend
IL_6FTI_187No text annotation
IL_6FTI_145Tandem non-canonical cWW pairs
IL_6FTI_146Double sheared
IL_6FTI_147Isolated non-canonical cWW pair
IL_6FTI_1488x7 Sarcin-Ricin; G-bulge
IL_6FTI_149No text annotation
IL_6FTI_150UAA/GAN related
IL_6FTI_151Isolated cWH basepair
IL_6FTI_153UAA/GAN
IL_6FTI_154No text annotation
IL_6FTI_188No text annotation
IL_6FTI_155Tandem non-canonical cWW pairs
IL_6FTI_156No text annotation
IL_6FTI_157Tandem non-canonical cWW pairs
IL_6FTI_189No text annotation
IL_6FTI_158Tandem non-canonical cWW pairs
IL_6FTI_159No text annotation
IL_6FTI_160No text annotation
IL_6FTI_161Single stack bend
IL_6FTI_162Tandem non-canonical cWW pairs
IL_6FTI_163Isolated non-canonical cWW pair
IL_6FTI_164Single bulged C
IL_6FTI_165Isolated non-canonical cWW pair
IL_6FTI_166No text annotation
IL_6FTI_167Single bulged C
IL_6FTI_168Double sheared; A in syn
IL_6FTI_169Single bulged A
IL_6FTI_170Minor groove platform related
IL_6FTI_171Major groove minor groove platform; mini C-loop
IL_6FTI_172Symmetric double minor groove platform
IL_6FTI_1738x7 Sarcin-Ricin; G-bulge
IL_6FTI_174No text annotation
IL_6FTI_175Isolated non-canonical cWW pair
IL_6FTI_176Isolated non-canonical cWW pair

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6FTI_0191/u/351:367,
1/u/374:379,
1/w/21:24		No text annotation
homologous
J3_8P9A_045
J3_07616.1
J3_6FTI_0021/u/380:387,
1/u/414:415,
1/w/19:20		No text annotation
homologous
J3_5TBW_002
NA
J3_6FTI_0201/u/380:390,
1/u/401:415,
1/w/19:20		No text annotation
homologous
J3_8C3A_049
NA
J3_6FTI_0051/u/1531:1537,
1/u/1622:1624,
1/u/1640:1643		No text annotation
homologous
J3_5TBW_004
NA
J3_6FTI_0061/u/1545:1548,
1/u/1580:1584,
1/u/1609:1614		No text annotation
homologous
J3_5TBW_005
NA
J3_6FTI_0071/u/2393:2399,
1/u/2805:2807,
1/u/2819:2822		No text annotation
homologous
J3_5TBW_008
NA
J3_6FTI_0081/u/2402:2405,
1/u/2785:2791,
1/u/2800:2802		No text annotation
homologous
J3_5TBW_009
NA
J3_6FTI_0111/u/3937:3939,
1/u/4074:4078,
1/u/4168:4173		No text annotation
geometric
J3_8VTW_006
NA
J3_6FTI_0171/w/44:45,
1/w/58:64,
1/w/95:99		No text annotation
homologous
J3_8C3A_060
NA
J4_6FTI_0051/u/2365:2371,
1/u/2389:2391,
1/u/2824:2829,
1/u/3856:3857		No text annotation
J4_6FTI_0061/u/2406:2410,
1/u/2434:2439,
1/u/2538:2539,
1/u/2777:2784		No text annotation
homologous
J4_8C3A_004
NA
J4_6FTI_0081/u/3634:3638,
1/u/3650:3654,
1/u/3690:3694,
1/u/3821:3826		No text annotation
homologous
J4_8C3A_006
NA
J4_6FTI_0091/u/3696:3698,
1/u/3752:3754,
1/u/3770:3780,
1/u/3814:3819		No text annotation
J5_6FTI_0021/u/1335:1340,
1/u/1516:1519,
1/u/1658:1661,
1/u/2288:2290,
1/u/2345:2351		No text annotation
homologous
J5_8P9A_011
J5_08384.1
J5_6FTI_0031/u/2855:2863,
1/u/2887:2888,
1/u/3613:3614,
1/u/3618:3626,
1/u/3835:3837		No text annotation
homologous
J5_8C3A_004
NA
J5_6FTI_0041/u/3903:3910,
1/u/4392:4400,
1/u/4444:4453,
1/u/4528:4534,
1/u/4552:4557		No text annotation
J5_6FTI_0051/u/3920:3923,
1/u/4188:4191,
1/u/4204:4205,
1/u/4227:4228,
1/u/4375:4381		No text annotation
homologous
J5_8C3A_006
NA
J6_6FTI_0011/u/21:26,
1/u/57:67,
1/u/74:78,
1/u/105:109,
1/u/332:339,
1/w/33:35		No text annotation
J6_6FTI_0021/u/1352:1355,
1/u/1384:1388,
1/u/1395:1399,
1/u/1418:1421,
1/u/1464:1466,
1/u/1499:1504		No text annotation
J6_6FTI_0031/u/3920:3923,
1/u/4188:4191,
1/u/4204:4205,
1/u/4227:4230,
1/u/4331:4342,
1/u/4370:4381		No text annotation

Problematic loops

#loop idProblemSequence
J3_6FTI_001No text annotation
J3_6FTI_018No text annotation
J3_6FTI_003No text annotation
J3_6FTI_004No text annotation
J3_6FTI_021No text annotation
J3_6FTI_022No text annotation
J3_6FTI_009No text annotation
J3_6FTI_023No text annotation
J3_6FTI_024No text annotation
J3_6FTI_010No text annotation
J3_6FTI_025No text annotation
J3_6FTI_012No text annotation
J3_6FTI_026No text annotation
J3_6FTI_013No text annotation
J3_6FTI_014No text annotation
J3_6FTI_027No text annotation
J3_6FTI_015No text annotation
J3_6FTI_016No text annotation
J4_6FTI_001tRNA junction
J4_6FTI_002No text annotation
J4_6FTI_003No text annotation
J4_6FTI_004No text annotation
J4_6FTI_007No text annotation
J4_6FTI_010No text annotation
J4_6FTI_011No text annotation
J4_6FTI_012No text annotation
J5_6FTI_001No text annotation
J7_6FTI_001No text annotation

Coloring options:
Copyright 2025 BGSU RNA group. Page generated in 0.1829 s