RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6VYQ_0071/D/12:22No text annotation
homologous
HL_4LFB_001
HL_73535.1
HL_6VYQ_0231/D/786:796No text annotation
homologous
HL_5J7L_017
NA
HL_6VYQ_0261/D/897:902GNRA
homologous
HL_4LFB_020
HL_34789.4
HL_6VYQ_0521/a/487:493GNRA
homologous
HL_5J7L_148
NA
HL_6VYQ_0541/a/566:575T-loop with 2 stacked bulged bases
geometric
HL_5J7L_150
NA
HL_6VYQ_0611/a/826:831No text annotation
homologous
HL_5J7L_157
NA
HL_6VYQ_0641/a/978:985No text annotation
homologous
HL_5J7L_160
NA
HL_6VYQ_0681/a/1222:1227GNRA
homologous
HL_5J7L_164
NA
HL_6VYQ_0701/a/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_6VYQ_1051/a/2819:2827No text annotation
homologous
HL_5J7L_201
NA
HL_6VYQ_1081/d/86:90Mini UNCG
homologous
HL_5J7L_204
NA

Problematic loops

#loop idProblemSequence
HL_6VYQ_001No text annotation
HL_6VYQ_002tRNA anticodon loop
HL_6VYQ_003T-loop with 2 stacked bulged bases
HL_6VYQ_004No text annotation
HL_6VYQ_005No text annotation
HL_6VYQ_006T-loop with 2 stacked bulged bases
HL_6VYQ_008No text annotation
HL_6VYQ_009GNRA
HL_6VYQ_010GNRA
HL_6VYQ_109No text annotation
HL_6VYQ_011No text annotation
HL_6VYQ_012GNRA related
HL_6VYQ_013GNRA
HL_6VYQ_014No text annotation
HL_6VYQ_015UNCG
HL_6VYQ_016GNRA
HL_6VYQ_017UNCG
HL_6VYQ_018GNRA wlth extra near cWW
HL_6VYQ_019No text annotation
HL_6VYQ_020GNRA-like with tWH
HL_6VYQ_021No text annotation
HL_6VYQ_022GNRA
HL_6VYQ_024No text annotation
HL_6VYQ_025GNRA
HL_6VYQ_027No text annotation
HL_6VYQ_028GNRA
HL_6VYQ_029GNRA
HL_6VYQ_030T-loop related
HL_6VYQ_110No text annotation
HL_6VYQ_031No text annotation
HL_6VYQ_032GNRA
HL_6VYQ_033GNRA
HL_6VYQ_034T-loop with 3 stacked bulged bases
HL_6VYQ_035No text annotation
HL_6VYQ_036UNCG
HL_6VYQ_037GNRA
HL_6VYQ_038No text annotation
HL_6VYQ_039No text annotation
HL_6VYQ_040No text annotation
HL_6VYQ_041UNCG
HL_6VYQ_042No text annotation
HL_6VYQ_043No text annotation
HL_6VYQ_044No text annotation
HL_6VYQ_045No text annotation
HL_6VYQ_046T-loop with 2 stacked bulged bases
HL_6VYQ_047No text annotation
HL_6VYQ_048T-loop with unstacked turn
HL_6VYQ_049No text annotation
HL_6VYQ_050Pseudoknot geometry
HL_6VYQ_051GNRA
HL_6VYQ_053No text annotation
HL_6VYQ_055No text annotation
HL_6VYQ_056GNRA
HL_6VYQ_057No text annotation
HL_6VYQ_058GNRA wlth tandem sheared
HL_6VYQ_059No text annotation
HL_6VYQ_060No text annotation
HL_6VYQ_111No text annotation
HL_6VYQ_062No text annotation
HL_6VYQ_063No text annotation
HL_6VYQ_065No text annotation
HL_6VYQ_066GNRA wlth tandem sheared
HL_6VYQ_067No text annotation
HL_6VYQ_069T-loop with 2 stacked bulged bases
HL_6VYQ_071GNRA
HL_6VYQ_072No text annotation
HL_6VYQ_073Mini UNCG with extended bulge
HL_6VYQ_074Pseudoknot geometry with 3' bulge
HL_6VYQ_075UNCG
HL_6VYQ_076Mini UNCG
HL_6VYQ_077No text annotation
HL_6VYQ_078GNRA
HL_6VYQ_079UNCG
HL_6VYQ_112No text annotation
HL_6VYQ_080No text annotation
HL_6VYQ_081No text annotation
HL_6VYQ_082No text annotation
HL_6VYQ_083GNRA related
HL_6VYQ_084GNRA variation
HL_6VYQ_085No text annotation
HL_6VYQ_086No text annotation
HL_6VYQ_087No text annotation
HL_6VYQ_088No text annotation
HL_6VYQ_089No text annotation
HL_6VYQ_090No text annotation
HL_6VYQ_091No text annotation
HL_6VYQ_092No text annotation
HL_6VYQ_114No text annotation
HL_6VYQ_093Pseudoknot geometry
HL_6VYQ_094GNRA
HL_6VYQ_095GNRA
HL_6VYQ_096No text annotation
HL_6VYQ_097No text annotation
HL_6VYQ_098GNRA variation
HL_6VYQ_099No text annotation
HL_6VYQ_100GNRA
HL_6VYQ_101GNRA
HL_6VYQ_102Ribsomal LSU H95
HL_6VYQ_103No text annotation
HL_6VYQ_104No text annotation
HL_6VYQ_115UNCG variation
HL_6VYQ_106GNRA
HL_6VYQ_113No text annotation
HL_6VYQ_107No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6VYQ_0011/D/30:32,
1/D/552:553		Single bulged G
homologous
IL_4LFB_001
IL_28408.2
IL_6VYQ_0031/D/47:52,
1/D/359:361		No text annotation
homologous
IL_5J7L_003
NA
IL_6VYQ_0141/D/242:247,
1/D/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
NA
IL_6VYQ_0261/D/569:575,
1/D/880:881		No text annotation
homologous
IL_5J7L_026
NA
IL_6VYQ_0361/D/774:778,
1/D/804:805		Left turn
homologous
IL_4LFB_032
IL_29346.3
IL_6VYQ_0371/D/779:783,
1/D/799:803		tSH-tHW-tHS
homologous
IL_5J7L_037
NA
IL_6VYQ_0381/D/887:894,
1/D/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_6VYQ_0391/D/922:923,
1/D/1393:1395		Single bulged A
homologous
IL_5J7L_039
NA
IL_6VYQ_0591/D/1399:1401,
1/D/1501:1504		No text annotation
homologous
IL_5J7L_058
NA
IL_6VYQ_0621/D/1412:1414,
1/D/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_6VYQ_0631/D/1416:1419,
1/D/1481:1484		Double sheared
homologous
IL_5J7L_062
NA
IL_6VYQ_0671/a/24:30,
1/a/510:516		Triple sheared with non-canonical cWW
geometric
IL_5J7L_245
NA
IL_6VYQ_0771/a/481:484,
1/a/496:509		No text annotation
geometric
IL_5J7L_255
NA
IL_6VYQ_0781/a/536:539,
1/a/554:557		Double sheared
homologous
IL_5J7L_256
NA
IL_6VYQ_0791/a/564:566,
1/a/575:577		Isolated non-canonical cWW pair
homologous
IL_5J7L_257
NA
IL_6VYQ_0811/a/672:674,
1/a/806:808		No text annotation
homologous
IL_7RQB_017
NA
IL_6VYQ_0991/a/994:996,
1/a/1159:1160		Single bulged C
homologous
IL_5J7L_276
NA
IL_6VYQ_1001/a/998:1002,
1/a/1153:1157		UAA/GAN
homologous
IL_5J7L_277
NA
IL_6VYQ_1011/a/1004:1011,
1/a/1150:1151		SSU/LSU pseudoknot
homologous
IL_5J7L_278
NA
IL_6VYQ_1031/a/1018:1024,
1/a/1140:1144		Kink-turn related
geometric
IL_5J7L_280
NA
IL_6VYQ_1041/a/1024:1030,
1/a/1124:1140		No text annotation
geometric
IL_5J7L_281
NA
IL_6VYQ_1101/a/1196:1198,
1/a/1247:1250		Isolated cWS basepair
homologous
IL_5J7L_286
NA
IL_6VYQ_1111/a/1202:1206,
1/a/1240:1243		No text annotation
homologous
IL_5J7L_287
NA
IL_6VYQ_1121/a/1208:1215,
1/a/1234:1238		Kink-turn
homologous
IL_5J7L_288
NA
IL_6VYQ_1131/a/1262:1269,
1/a/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_6VYQ_1151/a/1319:1323,
1/a/1331:1333		C-loop
homologous
IL_5J7L_291
NA
IL_6VYQ_1301/a/1651:1656,
1/a/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_6VYQ_1311/a/1663:1665,
1/a/1995:1997		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_6VYQ_1461/a/2050:2052,
1/a/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_6VYQ_1471/a/2054:2056,
1/a/2612:2615		No text annotation
homologous
IL_5J7L_321
NA
IL_6VYQ_1501/a/2070:2071,
1/a/2438:2441		Minor groove platform
homologous
IL_5J7L_324
NA
IL_6VYQ_1631/a/2459:2461,
1/a/2489:2493		Major groove minor groove platform with extra cWW
geometric
IL_5J7L_337
NA
IL_6VYQ_1661/a/2510:2512,
1/a/2574:2578		Isolated non-canonical cWW with bulges
geometric
IL_5J7L_340
NA
IL_6VYQ_1671/a/2512:2513,
1/a/2571:2574		No text annotation
homologous
IL_5J7L_341
NA
IL_6VYQ_1711/a/2636:2640,
1/a/2774:2782		tSH-tHS-tHW
homologous
IL_5J7L_345
NA
IL_6VYQ_1761/a/2737:2742,
1/a/2762:2767		UAA/GAN with extra cWW
homologous
IL_5J7L_350
NA

Problematic loops

#loop idProblemSequence
IL_6VYQ_186No text annotation
IL_6VYQ_187No text annotation
IL_6VYQ_188No text annotation
IL_6VYQ_002Single bulged A
IL_6VYQ_004Minor groove platform
IL_6VYQ_005Multiple bulged bases
IL_6VYQ_006Minor groove platform with extra cWW
IL_6VYQ_007Minor groove platform
IL_6VYQ_189Single bulged G
IL_6VYQ_008Single bulged G, near cWW
IL_6VYQ_009Isolated non-canonical cWW pair
IL_6VYQ_010Minor groove platform related
IL_6VYQ_011Isolated cWH basepair
IL_6VYQ_190No text annotation
IL_6VYQ_012tWH-tWH-tHW-tHW
IL_6VYQ_013No text annotation
IL_6VYQ_015No text annotation
IL_6VYQ_016C-loop
IL_6VYQ_017Single bulged U
IL_6VYQ_018C-loop
IL_6VYQ_019Single bulged G
IL_6VYQ_020No text annotation
IL_6VYQ_021No text annotation
IL_6VYQ_022tSH-tHW-tWW
IL_6VYQ_023No text annotation
IL_6VYQ_024SSU/LSU pseudoknot
IL_6VYQ_025Kink-turn related
IL_6VYQ_027tSH-tHW-tHS
IL_6VYQ_028Major groove platform
IL_6VYQ_029Major groove minor groove platform; mini C-loop
IL_6VYQ_030No text annotation
IL_6VYQ_031Major groove platform; stack outside cWW
IL_6VYQ_032Single stack bend
IL_6VYQ_033Tandem non-canonical cWW pairs
IL_6VYQ_034No text annotation
IL_6VYQ_035Kink-turn
IL_6VYQ_040Single bulged G
IL_6VYQ_041Minor groove platform
IL_6VYQ_042No text annotation
IL_6VYQ_043Minor groove platform
IL_6VYQ_201Single stack bend
IL_6VYQ_044No text annotation
IL_6VYQ_045No text annotation
IL_6VYQ_046Single bulged U
IL_6VYQ_047No text annotation
IL_6VYQ_048Isolated cWS basepair
IL_6VYQ_049Minor groove platform
IL_6VYQ_050Single bulged U
IL_6VYQ_051Isolated non-canonical cWW pair
IL_6VYQ_052No text annotation
IL_6VYQ_053Minor groove platform
IL_6VYQ_054No text annotation
IL_6VYQ_055No text annotation
IL_6VYQ_056180 degree turn
IL_6VYQ_191No text annotation
IL_6VYQ_057Double sheared with non-canonical cWW
IL_6VYQ_058No text annotation
IL_6VYQ_060No text annotation
IL_6VYQ_061Partly complementary
IL_6VYQ_064Triple sheared related
IL_6VYQ_065Single bulged A
IL_6VYQ_066No text annotation
IL_6VYQ_068Single bulged A
IL_6VYQ_069Minor groove platform
IL_6VYQ_070No text annotation
IL_6VYQ_071Single stack bend
IL_6VYQ_0728x7 Sarcin-Ricin; G-bulge
IL_6VYQ_0737x6 Sarcin-Ricin; G-bulge
IL_6VYQ_074No text annotation
IL_6VYQ_075No text annotation
IL_6VYQ_076No text annotation
IL_6VYQ_080AAA cross-strand stack
IL_6VYQ_082tHW-tHW cross-strand stack
IL_6VYQ_083Single bulged A
IL_6VYQ_084Single bulged G
IL_6VYQ_085Triple sheared
IL_6VYQ_086Major groove platform
IL_6VYQ_087Single stack bend
IL_6VYQ_088Single stack bend
IL_6VYQ_089Multiple bulged bases
IL_6VYQ_09090 degree turn
IL_6VYQ_192No text annotation
IL_6VYQ_091Stack outside cWW
IL_6VYQ_092Single stack bend
IL_6VYQ_193No text annotation
IL_6VYQ_0937x7 Sarcin-Ricin with intercalated A; G-bulge
IL_6VYQ_094Single bulged G
IL_6VYQ_095C-loop with bulged stacked A's
IL_6VYQ_096Isolated non-canonical cWW pair
IL_6VYQ_097Double sheared with non-canonical cWW
IL_6VYQ_194No text annotation
IL_6VYQ_098No text annotation
IL_6VYQ_102Single bulged U
IL_6VYQ_105Isolated non-canonical cWW pair
IL_6VYQ_106Tandem non-canonical cWW pairs
IL_6VYQ_107Kink-turn
IL_6VYQ_195No text annotation
IL_6VYQ_108No text annotation
IL_6VYQ_109Major groove platform
IL_6VYQ_114Major groove platform; stack outside cWW
IL_6VYQ_116UAA/GAN
IL_6VYQ_117tSH-tHW-tHS
IL_6VYQ_118Single stack bend
IL_6VYQ_119Single stack bend
IL_6VYQ_196No text annotation
IL_6VYQ_120No text annotation
IL_6VYQ_121UAA/GAN
IL_6VYQ_122Tandem non-canonical cWW pairs
IL_6VYQ_123tSH-tHW
IL_6VYQ_124Single bulged U
IL_6VYQ_125No text annotation
IL_6VYQ_126tSH-tHW-tHS
IL_6VYQ_127No text annotation
IL_6VYQ_200180 degree turn
IL_6VYQ_128Single bulged A
IL_6VYQ_129UAA/GAN variation
IL_6VYQ_132Major groove platform; stack outside cWW
IL_6VYQ_197No text annotation
IL_6VYQ_133Intercalated tWH
IL_6VYQ_134tSH-tSH-tHH-tHS
IL_6VYQ_1356x5 Sarcin-Ricin; G-bulge
IL_6VYQ_136Triple sheared
IL_6VYQ_137Single bulged C
IL_6VYQ_138Single bulged A
IL_6VYQ_139Kink-turn related
IL_6VYQ_140Minor groove platform, major groove intercalation
IL_6VYQ_141Major groove intercalation
IL_6VYQ_142Major groove minor groove platform; mini C-loop
IL_6VYQ_198No text annotation
IL_6VYQ_143UAA/GAN related
IL_6VYQ_144Bulged stacked bases
IL_6VYQ_145No text annotation
IL_6VYQ_148No text annotation
IL_6VYQ_149Not an internal loop
IL_6VYQ_151Isolated tHS basepair with bulges
IL_6VYQ_152Isolated non-canonical cWW pair
IL_6VYQ_153Isolated non-canonical cWW pair
IL_6VYQ_154Isolated non-canonical cWW pair
IL_6VYQ_155Isolated non-canonical cWW pair
IL_6VYQ_156No text annotation
IL_6VYQ_199No text annotation
IL_6VYQ_157Kink-turn
IL_6VYQ_158Single bulged U
IL_6VYQ_159Double sheared
IL_6VYQ_160No text annotation
IL_6VYQ_161No text annotation
IL_6VYQ_162No text annotation
IL_6VYQ_164Double sheared with non-canonical cWW
IL_6VYQ_165No text annotation
IL_6VYQ_168Major groove platform with intercalation
IL_6VYQ_169No text annotation
IL_6VYQ_170Single bulged A
IL_6VYQ_172Sarcin-Ricin target in LSU H95; G-bulge
IL_6VYQ_173C-loop
IL_6VYQ_174UAA/GAN related, with intercalation
IL_6VYQ_175Multiple bulged bases
IL_6VYQ_177No text annotation
IL_6VYQ_178Major groove intercalation
IL_6VYQ_179Multiple bulged bases with non-canonical cWW
IL_6VYQ_180tHS double platform
IL_6VYQ_181Major groove intercalation
IL_6VYQ_182No text annotation
IL_6VYQ_183Major groove minor groove platform; mini C-loop
IL_6VYQ_184Symmetric double minor groove platform
IL_6VYQ_185Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6VYQ_0011/D/46:47,
1/D/361:367,
1/D/393:395		No text annotation
homologous
J3_5J7L_001
NA
J3_6VYQ_0271/D/46:52,
1/D/359:367,
1/D/393:395		No text annotation
homologous
J3_5J7L_050
NA
J3_6VYQ_0131/a/30:31,
1/a/474:481,
1/a/509:510		No text annotation
homologous
J3_7RQB_001
NA
J3_6VYQ_0321/a/30:31,
1/a/474:484,
1/a/496:510		No text annotation
homologous
J3_9DFE_002
J3_17917.1
J3_6VYQ_0331/a/32:35,
1/a/445:461,
1/a/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_6VYQ_0151/a/683:689,
1/a/773:775,
1/a/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_6VYQ_0251/a/2812:2815,
1/a/2831:2836,
1/a/2882:2888		No text annotation
homologous
J3_5J7L_048
NA
J4_6VYQ_0051/D/575:577,
1/D/764:769,
1/D/810:821,
1/D/879:880		No text annotation
homologous
J4_5J7L_003
NA
J4_6VYQ_0091/a/1270:1276,
1/a/1294:1295,
1/a/1645:1648,
1/a/2009:2010		No text annotation
homologous
J4_5J7L_021
NA
J4_6VYQ_0151/a/2643:2646,
1/a/2674:2676,
1/a/2731:2735,
1/a/2769:2771		No text annotation
homologous
J4_5J7L_028
NA
J5_6VYQ_0051/a/531:533,
1/a/560:564,
1/a/577:579,
1/a/1261:1262,
1/a/2017:2018		No text annotation
homologous
J5_5J7L_014
NA
J5_6VYQ_0061/a/584:589,
1/a/668:671,
1/a/809:812,
1/a/1195:1196,
1/a/1250:1256		No text annotation
homologous
J5_5J7L_015
NA
J7_6VYQ_0011/a/8:15,
1/a/525:531,
1/a/2018:2023,
1/a/2040:2043,
1/a/2625:2630,
1/a/2788:2789,
1/a/2894:2895		No text annotation
J7_6VYQ_0021/a/817:822,
1/a/835:838,
1/a/940:946,
1/a/971:976,
1/a/987:991,
1/a/1163:1164,
1/a/1185:1190		No text annotation

Problematic loops

#loop idProblemSequence
J3_6VYQ_002No text annotation
J3_6VYQ_028No text annotation
J3_6VYQ_003No text annotation
J3_6VYQ_004No text annotation
J3_6VYQ_005No text annotation
J3_6VYQ_006No text annotation
J3_6VYQ_029No text annotation
J3_6VYQ_007No text annotation
J3_6VYQ_008No text annotation
J3_6VYQ_030No text annotation
J3_6VYQ_009No text annotation
J3_6VYQ_010No text annotation
J3_6VYQ_011No text annotation
J3_6VYQ_031No text annotation
J3_6VYQ_012No text annotation
J3_6VYQ_014No text annotation
J3_6VYQ_034No text annotation
J3_6VYQ_016No text annotation
J3_6VYQ_017No text annotation
J3_6VYQ_018No text annotation
J3_6VYQ_019No text annotation
J3_6VYQ_020No text annotation
J3_6VYQ_035No text annotation
J3_6VYQ_021Kink-turn 3-way junction
J3_6VYQ_036No text annotation
J3_6VYQ_022No text annotation
J3_6VYQ_023No text annotation
J3_6VYQ_024No text annotation
J3_6VYQ_026No text annotation
J4_6VYQ_001tRNA junction
J4_6VYQ_002tRNA junction
J4_6VYQ_003No text annotation
J4_6VYQ_004No text annotation
J4_6VYQ_006No text annotation
J4_6VYQ_007No text annotation
J4_6VYQ_008No text annotation
J4_6VYQ_010No text annotation
J4_6VYQ_011No text annotation
J4_6VYQ_012No text annotation
J4_6VYQ_013No text annotation
J4_6VYQ_014No text annotation
J5_6VYQ_001No text annotation
J5_6VYQ_002No text annotation
J5_6VYQ_003No text annotation
J5_6VYQ_004No text annotation
J5_6VYQ_007No text annotation
J6_6VYQ_001No text annotation

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