RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6VYS_0071/D/12:22No text annotation
homologous
HL_4LFB_001
HL_73535.1
HL_6VYS_0231/D/786:796No text annotation
homologous
HL_5J7L_017
NA
HL_6VYS_0251/D/862:867GNRA
homologous
HL_5J7L_019
NA
HL_6VYS_0261/D/897:902GNRA
homologous
HL_4LFB_020
HL_34789.2
HL_6VYS_0291/D/1076:1081GNRA
homologous
HL_5J7L_023
NA
HL_6VYS_0301/D/1089:1096T-loop related
homologous
HL_4LFB_025
HL_63894.2
HL_6VYS_0451/a/246:252No text annotation
homologous
HL_5J7L_141
NA
HL_6VYS_0541/a/566:575T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_6VYS_0601/a/779:785No text annotation
homologous
HL_5J7L_156
NA
HL_6VYS_0641/a/978:985No text annotation
homologous
HL_5J7L_160
NA
HL_6VYS_0701/a/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_6VYS_0821/a/1777:1787No text annotation
homologous
HL_5J7L_178
NA
HL_6VYS_0861/a/1949:1957No text annotation
homologous
HL_5J7L_182
NA
HL_6VYS_0911/a/2264:2276No text annotation
homologous
HL_5J7L_187
NA
HL_6VYS_1001/a/2594:2599GNRA
homologous
HL_5J7L_196
NA
HL_6VYS_1081/d/86:90Mini UNCG
homologous
HL_5J7L_204
NA

Problematic loops

#loop idProblemSequence
HL_6VYS_001No text annotation
HL_6VYS_002tRNA anticodon loop
HL_6VYS_003T-loop with 2 stacked bulged bases
HL_6VYS_004No text annotation
HL_6VYS_005No text annotation
HL_6VYS_006T-loop with 2 stacked bulged bases
HL_6VYS_008No text annotation
HL_6VYS_009GNRA
HL_6VYS_010GNRA
HL_6VYS_109No text annotation
HL_6VYS_011UNCG
HL_6VYS_012GNRA related
HL_6VYS_013GNRA
HL_6VYS_014No text annotation
HL_6VYS_015UNCG
HL_6VYS_016GNRA
HL_6VYS_017UNCG
HL_6VYS_018GNRA wlth extra near cWW
HL_6VYS_019No text annotation
HL_6VYS_020GNRA-like with tWH
HL_6VYS_021No text annotation
HL_6VYS_022GNRA
HL_6VYS_024No text annotation
HL_6VYS_027No text annotation
HL_6VYS_028GNRA
HL_6VYS_110No text annotation
HL_6VYS_031No text annotation
HL_6VYS_032GNRA
HL_6VYS_033GNRA
HL_6VYS_034T-loop with 3 stacked bulged bases
HL_6VYS_035No text annotation
HL_6VYS_036UNCG
HL_6VYS_037GNRA
HL_6VYS_038No text annotation
HL_6VYS_039No text annotation
HL_6VYS_040No text annotation
HL_6VYS_041UNCG
HL_6VYS_042No text annotation
HL_6VYS_043No text annotation
HL_6VYS_044No text annotation
HL_6VYS_046T-loop with 2 stacked bulged bases
HL_6VYS_047No text annotation
HL_6VYS_048T-loop with unstacked turn
HL_6VYS_049No text annotation
HL_6VYS_050Pseudoknot geometry
HL_6VYS_051GNRA
HL_6VYS_052GNRA
HL_6VYS_053No text annotation
HL_6VYS_055No text annotation
HL_6VYS_056GNRA
HL_6VYS_057No text annotation
HL_6VYS_058GNRA wlth tandem sheared
HL_6VYS_059No text annotation
HL_6VYS_061No text annotation
HL_6VYS_111No text annotation
HL_6VYS_062No text annotation
HL_6VYS_063No text annotation
HL_6VYS_065No text annotation
HL_6VYS_066GNRA wlth tandem sheared
HL_6VYS_067No text annotation
HL_6VYS_068GNRA
HL_6VYS_069T-loop with 2 stacked bulged bases
HL_6VYS_071GNRA
HL_6VYS_072No text annotation
HL_6VYS_073Mini UNCG with extended bulge
HL_6VYS_074Pseudoknot geometry with 3' bulge
HL_6VYS_075UNCG
HL_6VYS_076Mini UNCG
HL_6VYS_077No text annotation
HL_6VYS_078GNRA
HL_6VYS_079UNCG
HL_6VYS_112No text annotation
HL_6VYS_080No text annotation
HL_6VYS_081No text annotation
HL_6VYS_083GNRA related
HL_6VYS_084GNRA variation
HL_6VYS_085No text annotation
HL_6VYS_087No text annotation
HL_6VYS_088No text annotation
HL_6VYS_089No text annotation
HL_6VYS_090No text annotation
HL_6VYS_092No text annotation
HL_6VYS_114No text annotation
HL_6VYS_093Pseudoknot geometry
HL_6VYS_094GNRA
HL_6VYS_095GNRA
HL_6VYS_096No text annotation
HL_6VYS_097No text annotation
HL_6VYS_098GNRA variation
HL_6VYS_099No text annotation
HL_6VYS_101GNRA
HL_6VYS_102Ribsomal LSU H95
HL_6VYS_103No text annotation
HL_6VYS_104No text annotation
HL_6VYS_115UNCG variation
HL_6VYS_105No text annotation
HL_6VYS_106GNRA
HL_6VYS_113No text annotation
HL_6VYS_107No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6VYS_0011/D/30:32,
1/D/552:553		Single bulged G
homologous
IL_4LFB_001
IL_28408.2
IL_6VYS_0141/D/242:247,
1/D/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
NA
IL_6VYS_0241/D/504:511,
1/D/540:541		SSU/LSU pseudoknot
homologous
IL_5J7L_024
NA
IL_6VYS_0261/D/569:575,
1/D/880:881		No text annotation
homologous
IL_5J7L_026
NA
IL_6VYS_0371/D/779:783,
1/D/799:803		tSH-tHW-tHS
homologous
IL_5J7L_037
NA
IL_6VYS_0381/D/887:894,
1/D/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_6VYS_0391/D/922:923,
1/D/1393:1395		Single bulged A
homologous
IL_5J7L_039
NA
IL_6VYS_0401/D/925:927,
1/D/1390:1391		Single bulged G
homologous
IL_5J7L_040
NA
IL_6VYS_0411/D/933:935,
1/D/1380:1384		Minor groove platform
homologous
IL_5J7L_041
NA
IL_6VYS_0481/D/1052:1056,
1/D/1204:1206		Isolated cWS basepair
geometric
IL_4LFB_044
IL_82453.1
IL_6VYS_0501/D/1060:1061,
1/D/1195:1197		Single bulged U
homologous
IL_4LFB_046
IL_97561.2
IL_6VYS_0511/D/1061:1063,
1/D/1193:1195		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_68118.2
IL_6VYS_0591/D/1399:1401,
1/D/1501:1504		No text annotation
homologous
IL_5J7L_058
NA
IL_6VYS_0621/D/1412:1414,
1/D/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_6VYS_0631/D/1416:1419,
1/D/1481:1484		Double sheared
homologous
IL_5J7L_062
NA
IL_6VYS_0671/a/24:30,
1/a/510:516		Triple sheared with non-canonical cWW
geometric
IL_5J7L_245
NA
IL_6VYS_0771/a/481:484,
1/a/496:509		No text annotation
geometric
IL_5J7L_255
NA
IL_6VYS_0791/a/564:566,
1/a/575:577		Isolated non-canonical cWW pair
geometric
IL_5J7L_257
NA
IL_6VYS_0811/a/672:674,
1/a/806:808		No text annotation
geometric
IL_7RQB_017
NA
IL_6VYS_0821/a/674:678,
1/a/799:806		tHW-tHW cross-strand stack
homologous
IL_7RQB_018
NA
IL_6VYS_0881/a/742:744,
1/a/753:754		Single stack bend
geometric
IL_4V83_236
IL_15011.2
IL_6VYS_0891/a/775:777,
1/a/787:791		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_6VYS_1011/a/1004:1011,
1/a/1150:1151		SSU/LSU pseudoknot
homologous
IL_5J7L_278
NA
IL_6VYS_1031/a/1018:1024,
1/a/1140:1144		Kink-turn related
geometric
IL_5J7L_280
NA
IL_6VYS_1041/a/1024:1030,
1/a/1124:1140		No text annotation
geometric
IL_5J7L_281
NA
IL_6VYS_1051/a/1031:1034,
1/a/1121:1123		Isolated non-canonical cWW pair
homologous
IL_7RQB_041
NA
IL_6VYS_1131/a/1262:1269,
1/a/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_6VYS_1301/a/1651:1656,
1/a/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_6VYS_1311/a/1663:1665,
1/a/1995:1997		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_6VYS_1321/a/1666:1669,
1/a/1993:1994		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_6VYS_1971/a/1666:1674,
1/a/1990:1994		No text annotation
homologous
IL_5J7L_386
NA
IL_6VYS_1331/a/1669:1674,
1/a/1990:1993		Intercalated tWH
homologous
IL_5J7L_307
NA
IL_6VYS_1461/a/2050:2052,
1/a/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_6VYS_1471/a/2054:2056,
1/a/2612:2615		No text annotation
homologous
IL_5J7L_321
NA
IL_6VYS_1501/a/2070:2071,
1/a/2438:2441		Minor groove platform
homologous
IL_5J7L_324
NA
IL_6VYS_1631/a/2459:2461,
1/a/2489:2493		Major groove minor groove platform with extra cWW
geometric
IL_5J7L_337
NA
IL_6VYS_1661/a/2510:2512,
1/a/2574:2578		Isolated non-canonical cWW with bulges
homologous
IL_5J7L_340
NA
IL_6VYS_1671/a/2512:2513,
1/a/2571:2574		No text annotation
geometric
IL_5J7L_341
NA
IL_6VYS_1701/a/2591:2592,
1/a/2601:2603		Single bulged A
homologous
IL_7RQB_101
NA
IL_6VYS_1741/a/2687:2691,
1/a/2718:2722		UAA/GAN related, with intercalation
homologous
IL_5J7L_348
NA

Problematic loops

#loop idProblemSequence
IL_6VYS_186No text annotation
IL_6VYS_187No text annotation
IL_6VYS_188No text annotation
IL_6VYS_002Single bulged A
IL_6VYS_003No text annotation
IL_6VYS_004Minor groove platform
IL_6VYS_005Multiple bulged bases
IL_6VYS_006Minor groove platform with extra cWW
IL_6VYS_007Minor groove platform
IL_6VYS_189Single bulged G
IL_6VYS_008Single bulged G, near cWW
IL_6VYS_009Isolated non-canonical cWW pair
IL_6VYS_010Minor groove platform related
IL_6VYS_011Isolated cWH basepair
IL_6VYS_190No text annotation
IL_6VYS_012tWH-tWH-tHW-tHW
IL_6VYS_013No text annotation
IL_6VYS_015No text annotation
IL_6VYS_016C-loop
IL_6VYS_017Single bulged U
IL_6VYS_018C-loop
IL_6VYS_019Single bulged G
IL_6VYS_020No text annotation
IL_6VYS_021No text annotation
IL_6VYS_022tSH-tHW-tWW
IL_6VYS_023No text annotation
IL_6VYS_025Kink-turn related
IL_6VYS_027tSH-tHW-tHS
IL_6VYS_028Major groove platform
IL_6VYS_029Major groove minor groove platform; mini C-loop
IL_6VYS_030No text annotation
IL_6VYS_031Major groove platform; stack outside cWW
IL_6VYS_032Single stack bend
IL_6VYS_033Tandem non-canonical cWW pairs
IL_6VYS_034No text annotation
IL_6VYS_035Kink-turn
IL_6VYS_036Left turn
IL_6VYS_042No text annotation
IL_6VYS_043Minor groove platform
IL_6VYS_201Single stack bend
IL_6VYS_044No text annotation
IL_6VYS_045No text annotation
IL_6VYS_046Single bulged U
IL_6VYS_047No text annotation
IL_6VYS_049Minor groove platform
IL_6VYS_052No text annotation
IL_6VYS_053Minor groove platform
IL_6VYS_054No text annotation
IL_6VYS_055No text annotation
IL_6VYS_056180 degree turn
IL_6VYS_191No text annotation
IL_6VYS_057Double sheared with non-canonical cWW
IL_6VYS_058No text annotation
IL_6VYS_060No text annotation
IL_6VYS_061Partly complementary
IL_6VYS_064Triple sheared related
IL_6VYS_065Single bulged A
IL_6VYS_066No text annotation
IL_6VYS_068Single bulged A
IL_6VYS_069Minor groove platform
IL_6VYS_070No text annotation
IL_6VYS_071Single stack bend
IL_6VYS_0728x7 Sarcin-Ricin; G-bulge
IL_6VYS_0737x6 Sarcin-Ricin; G-bulge
IL_6VYS_074No text annotation
IL_6VYS_075No text annotation
IL_6VYS_076No text annotation
IL_6VYS_078Double sheared
IL_6VYS_080AAA cross-strand stack
IL_6VYS_083Single bulged A
IL_6VYS_084Single bulged G
IL_6VYS_085Triple sheared
IL_6VYS_086Major groove platform
IL_6VYS_087Single stack bend
IL_6VYS_09090 degree turn
IL_6VYS_192No text annotation
IL_6VYS_091Stack outside cWW
IL_6VYS_092Single stack bend
IL_6VYS_193No text annotation
IL_6VYS_0937x7 Sarcin-Ricin with intercalated A; G-bulge
IL_6VYS_094Single bulged G
IL_6VYS_095C-loop with bulged stacked A's
IL_6VYS_096Isolated non-canonical cWW pair
IL_6VYS_097Double sheared with non-canonical cWW
IL_6VYS_194No text annotation
IL_6VYS_098No text annotation
IL_6VYS_099Single bulged C
IL_6VYS_100UAA/GAN
IL_6VYS_102Single bulged U
IL_6VYS_106Tandem non-canonical cWW pairs
IL_6VYS_107Kink-turn
IL_6VYS_195No text annotation
IL_6VYS_108No text annotation
IL_6VYS_109No text annotation
IL_6VYS_110Isolated cWS basepair
IL_6VYS_111No text annotation
IL_6VYS_112Kink-turn
IL_6VYS_114Major groove platform; stack outside cWW
IL_6VYS_115C-loop
IL_6VYS_116UAA/GAN
IL_6VYS_117tSH-tHW-tHS
IL_6VYS_118Single stack bend
IL_6VYS_119Single stack bend
IL_6VYS_196No text annotation
IL_6VYS_120No text annotation
IL_6VYS_121UAA/GAN
IL_6VYS_122Tandem non-canonical cWW pairs
IL_6VYS_123tSH-tHW
IL_6VYS_124Single bulged U
IL_6VYS_125No text annotation
IL_6VYS_126tSH-tHW-tHS
IL_6VYS_127No text annotation
IL_6VYS_200180 degree turn
IL_6VYS_128Single bulged A
IL_6VYS_129UAA/GAN variation
IL_6VYS_134tSH-tSH-tHH-tHS
IL_6VYS_1356x5 Sarcin-Ricin; G-bulge
IL_6VYS_136Triple sheared
IL_6VYS_137Single bulged C
IL_6VYS_138Single bulged A
IL_6VYS_139Kink-turn related
IL_6VYS_140Minor groove platform, major groove intercalation
IL_6VYS_141Major groove intercalation
IL_6VYS_142Major groove minor groove platform; mini C-loop
IL_6VYS_198No text annotation
IL_6VYS_143UAA/GAN related
IL_6VYS_144Bulged stacked bases
IL_6VYS_145No text annotation
IL_6VYS_148No text annotation
IL_6VYS_149Not an internal loop
IL_6VYS_151Isolated tHS basepair with bulges
IL_6VYS_152Isolated non-canonical cWW pair
IL_6VYS_153Isolated non-canonical cWW pair
IL_6VYS_154Isolated non-canonical cWW pair
IL_6VYS_155Isolated non-canonical cWW pair
IL_6VYS_156No text annotation
IL_6VYS_199No text annotation
IL_6VYS_157Kink-turn
IL_6VYS_158Single bulged U
IL_6VYS_159Double sheared
IL_6VYS_160No text annotation
IL_6VYS_161No text annotation
IL_6VYS_162No text annotation
IL_6VYS_164Double sheared with non-canonical cWW
IL_6VYS_165No text annotation
IL_6VYS_168Major groove platform with intercalation
IL_6VYS_169No text annotation
IL_6VYS_171tSH-tHS-tHW
IL_6VYS_172Sarcin-Ricin target in LSU H95; G-bulge
IL_6VYS_173C-loop
IL_6VYS_175Multiple bulged bases
IL_6VYS_176UAA/GAN with extra cWW
IL_6VYS_177No text annotation
IL_6VYS_178Major groove intercalation
IL_6VYS_179Multiple bulged bases with non-canonical cWW
IL_6VYS_180tHS double platform
IL_6VYS_181Major groove intercalation
IL_6VYS_182No text annotation
IL_6VYS_183Major groove minor groove platform; mini C-loop
IL_6VYS_184Symmetric double minor groove platform
IL_6VYS_185Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6VYS_0091/D/1063:1068,
1/D/1107:1113,
1/D/1187:1193		No text annotation
homologous
J3_5J7L_008
NA
J3_6VYS_0101/D/1073:1074,
1/D/1083:1087,
1/D/1098:1102		No text annotation
homologous
J3_5J7L_009
NA
J3_6VYS_0131/a/30:31,
1/a/474:481,
1/a/509:510		No text annotation
homologous
J3_7RQB_001
NA
J3_6VYS_0321/a/30:31,
1/a/474:484,
1/a/496:510		No text annotation
homologous
J3_9DFE_002
J3_17917.1
J3_6VYS_0331/a/32:35,
1/a/445:461,
1/a/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_6VYS_0151/a/683:689,
1/a/773:775,
1/a/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_6VYS_0231/a/2517:2520,
1/a/2545:2547,
1/a/2561:2567		No text annotation
homologous
J3_5J7L_046
NA
J4_6VYS_0031/D/115:122,
1/D/239:240,
1/D/286:289,
1/D/311:312		No text annotation
homologous
J4_5J7L_001
NA
J4_6VYS_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_6VYS_0091/a/1270:1276,
1/a/1294:1295,
1/a/1645:1648,
1/a/2009:2010		No text annotation
homologous
J4_5J7L_021
NA
J5_6VYS_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_6VYS_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_6VYS_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_6VYS_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_6VYS_001No text annotation
J3_6VYS_027No text annotation
J3_6VYS_002No text annotation
J3_6VYS_028No text annotation
J3_6VYS_003No text annotation
J3_6VYS_004No text annotation
J3_6VYS_005No text annotation
J3_6VYS_006No text annotation
J3_6VYS_029No text annotation
J3_6VYS_007No text annotation
J3_6VYS_008No text annotation
J3_6VYS_030No text annotation
J3_6VYS_011No text annotation
J3_6VYS_031No text annotation
J3_6VYS_012No text annotation
J3_6VYS_014No text annotation
J3_6VYS_034No text annotation
J3_6VYS_016No text annotation
J3_6VYS_017No text annotation
J3_6VYS_018No text annotation
J3_6VYS_019No text annotation
J3_6VYS_020No text annotation
J3_6VYS_035No text annotation
J3_6VYS_021Kink-turn 3-way junction
J3_6VYS_036No text annotation
J3_6VYS_022No text annotation
J3_6VYS_024No text annotation
J3_6VYS_025No text annotation
J3_6VYS_026No text annotation
J4_6VYS_001tRNA junction
J4_6VYS_002tRNA junction
J4_6VYS_004No text annotation
J4_6VYS_006No text annotation
J4_6VYS_007No text annotation
J4_6VYS_008No text annotation
J4_6VYS_010No text annotation
J4_6VYS_011No text annotation
J4_6VYS_012No text annotation
J4_6VYS_013No text annotation
J4_6VYS_014No text annotation
J4_6VYS_015No text annotation
J5_6VYS_001No text annotation
J5_6VYS_002No text annotation
J5_6VYS_003No text annotation
J5_6VYS_004No text annotation
J5_6VYS_007No text annotation
J6_6VYS_001No text annotation

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