RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6VYR_0071/D/12:22No text annotation
homologous
HL_4LFB_001
HL_31940.1
HL_6VYR_0221/D/726:731GNRA
homologous
HL_5J7L_016
NA
HL_6VYR_0231/D/786:796No text annotation
homologous
HL_5J7L_017
NA
HL_6VYR_0251/D/862:867GNRA
homologous
HL_5J7L_019
NA
HL_6VYR_0261/D/897:902GNRA
homologous
HL_4LFB_020
HL_34789.1
HL_6VYR_0291/D/1076:1081GNRA
homologous
HL_5J7L_023
NA
HL_6VYR_0301/D/1089:1096T-loop related
homologous
HL_4LFB_025
HL_63894.1
HL_6VYR_0511/a/462:467GNRA
homologous
HL_5J7L_147
NA
HL_6VYR_0541/a/566:575T-loop with 2 stacked bulged bases
geometric
HL_5J7L_150
NA
HL_6VYR_0601/a/779:785No text annotation
homologous
HL_5J7L_156
NA
HL_6VYR_0641/a/978:985No text annotation
homologous
HL_5J7L_160
NA
HL_6VYR_0831/a/1806:1811GNRA related
homologous
HL_5J7L_179
NA
HL_6VYR_0861/a/1949:1957No text annotation
homologous
HL_5J7L_182
NA
HL_6VYR_0911/a/2264:2276No text annotation
homologous
HL_5J7L_187
NA

Problematic loops

#loop idProblemSequence
HL_6VYR_001No text annotation
HL_6VYR_002tRNA anticodon loop
HL_6VYR_003T-loop with 2 stacked bulged bases
HL_6VYR_004No text annotation
HL_6VYR_005No text annotation
HL_6VYR_006T-loop with 2 stacked bulged bases
HL_6VYR_008No text annotation
HL_6VYR_009GNRA
HL_6VYR_010GNRA
HL_6VYR_109No text annotation
HL_6VYR_011No text annotation
HL_6VYR_012GNRA related
HL_6VYR_013GNRA
HL_6VYR_014No text annotation
HL_6VYR_015UNCG
HL_6VYR_016GNRA
HL_6VYR_017UNCG
HL_6VYR_018GNRA wlth extra near cWW
HL_6VYR_019No text annotation
HL_6VYR_020GNRA-like with tWH
HL_6VYR_021No text annotation
HL_6VYR_024No text annotation
HL_6VYR_027No text annotation
HL_6VYR_028GNRA
HL_6VYR_110No text annotation
HL_6VYR_031No text annotation
HL_6VYR_032GNRA
HL_6VYR_033GNRA
HL_6VYR_034T-loop with 3 stacked bulged bases
HL_6VYR_035No text annotation
HL_6VYR_036UNCG
HL_6VYR_037GNRA
HL_6VYR_038No text annotation
HL_6VYR_039No text annotation
HL_6VYR_040No text annotation
HL_6VYR_041UNCG
HL_6VYR_042No text annotation
HL_6VYR_043No text annotation
HL_6VYR_044No text annotation
HL_6VYR_045No text annotation
HL_6VYR_046T-loop with 2 stacked bulged bases
HL_6VYR_047No text annotation
HL_6VYR_048T-loop with unstacked turn
HL_6VYR_049No text annotation
HL_6VYR_050Pseudoknot geometry
HL_6VYR_052GNRA
HL_6VYR_053No text annotation
HL_6VYR_055No text annotation
HL_6VYR_056GNRA
HL_6VYR_057No text annotation
HL_6VYR_058GNRA wlth tandem sheared
HL_6VYR_059No text annotation
HL_6VYR_061No text annotation
HL_6VYR_111No text annotation
HL_6VYR_062No text annotation
HL_6VYR_063No text annotation
HL_6VYR_065No text annotation
HL_6VYR_066GNRA wlth tandem sheared
HL_6VYR_067No text annotation
HL_6VYR_068GNRA
HL_6VYR_069T-loop with 2 stacked bulged bases
HL_6VYR_070Pseudoknot geometry with 3' bulge
HL_6VYR_071GNRA
HL_6VYR_072No text annotation
HL_6VYR_073Mini UNCG with extended bulge
HL_6VYR_074Pseudoknot geometry with 3' bulge
HL_6VYR_075UNCG
HL_6VYR_076Mini UNCG
HL_6VYR_077No text annotation
HL_6VYR_078GNRA
HL_6VYR_079UNCG
HL_6VYR_112No text annotation
HL_6VYR_080No text annotation
HL_6VYR_081No text annotation
HL_6VYR_082No text annotation
HL_6VYR_084GNRA variation
HL_6VYR_085No text annotation
HL_6VYR_087No text annotation
HL_6VYR_088No text annotation
HL_6VYR_089No text annotation
HL_6VYR_090No text annotation
HL_6VYR_092No text annotation
HL_6VYR_114No text annotation
HL_6VYR_093Pseudoknot geometry
HL_6VYR_094GNRA
HL_6VYR_095GNRA
HL_6VYR_096No text annotation
HL_6VYR_097No text annotation
HL_6VYR_098GNRA variation
HL_6VYR_099No text annotation
HL_6VYR_100GNRA
HL_6VYR_101GNRA
HL_6VYR_102Ribsomal LSU H95
HL_6VYR_103No text annotation
HL_6VYR_104No text annotation
HL_6VYR_115UNCG variation
HL_6VYR_105No text annotation
HL_6VYR_106GNRA
HL_6VYR_113No text annotation
HL_6VYR_107No text annotation
HL_6VYR_108Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6VYR_0141/D/242:247,
1/D/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
NA
IL_6VYR_0161/D/292:293,
1/D/304:308		C-loop
homologous
IL_4LFB_013
IL_06671.1
IL_6VYR_0261/D/569:575,
1/D/880:881		No text annotation
homologous
IL_5J7L_026
NA
IL_6VYR_0361/D/774:778,
1/D/804:805		Left turn
homologous
IL_4LFB_032
IL_29346.3
IL_6VYR_0371/D/779:783,
1/D/799:803		tSH-tHW-tHS
homologous
IL_5J7L_037
NA
IL_6VYR_0381/D/887:894,
1/D/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_6VYR_0391/D/922:923,
1/D/1393:1395		Single bulged A
homologous
IL_5J7L_039
NA
IL_6VYR_0401/D/925:927,
1/D/1390:1391		Single bulged G
homologous
IL_5J7L_040
NA
IL_6VYR_0591/D/1399:1401,
1/D/1501:1504		No text annotation
geometric
IL_5J7L_058
NA
IL_6VYR_0621/D/1412:1414,
1/D/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_6VYR_0631/D/1416:1419,
1/D/1481:1484		Double sheared
homologous
IL_5J7L_062
NA
IL_6VYR_0671/a/24:30,
1/a/510:516		Triple sheared with non-canonical cWW
homologous
IL_5J7L_245
NA
IL_6VYR_0791/a/564:566,
1/a/575:577		Isolated non-canonical cWW pair
homologous
IL_5J7L_257
NA
IL_6VYR_0811/a/672:674,
1/a/806:808		No text annotation
homologous
IL_7RQB_017
NA
IL_6VYR_0821/a/674:678,
1/a/799:806		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_6VYR_0891/a/775:777,
1/a/787:791		Multiple bulged bases
homologous
IL_5J7L_265
NA
IL_6VYR_1011/a/1004:1011,
1/a/1150:1151		SSU/LSU pseudoknot
geometric
IL_5J7L_278
NA
IL_6VYR_1041/a/1024:1030,
1/a/1124:1140		No text annotation
geometric
IL_5J7L_281
NA
IL_6VYR_1101/a/1196:1198,
1/a/1247:1250		Isolated cWS basepair
homologous
IL_5J7L_286
NA
IL_6VYR_1131/a/1262:1269,
1/a/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_6VYR_1301/a/1651:1656,
1/a/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_6VYR_1311/a/1663:1665,
1/a/1995:1997		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_6VYR_1321/a/1666:1669,
1/a/1993:1994		Major groove platform; stack outside cWW
homologous
IL_7RQB_066
NA
IL_6VYR_1971/a/1666:1674,
1/a/1990:1994		No text annotation
homologous
IL_5J7L_386
NA
IL_6VYR_1331/a/1669:1674,
1/a/1990:1993		Intercalated tWH
geometric
IL_5J7L_307
NA
IL_6VYR_1461/a/2050:2052,
1/a/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_6VYR_1471/a/2054:2056,
1/a/2612:2615		No text annotation
homologous
IL_5J7L_321
NA
IL_6VYR_1501/a/2070:2071,
1/a/2438:2441		Minor groove platform
homologous
IL_5J7L_324
NA
IL_6VYR_1631/a/2459:2461,
1/a/2489:2493		Major groove minor groove platform with extra cWW
homologous
IL_5J7L_337
NA
IL_6VYR_1661/a/2510:2512,
1/a/2574:2578		Isolated non-canonical cWW with bulges
geometric
IL_5J7L_340
NA
IL_6VYR_1701/a/2591:2592,
1/a/2601:2603		Single bulged A
homologous
IL_7RQB_101
NA
IL_6VYR_1731/a/2680:2684,
1/a/2725:2727		C-loop
homologous
IL_5J7L_347
NA

Problematic loops

#loop idProblemSequence
IL_6VYR_186No text annotation
IL_6VYR_187No text annotation
IL_6VYR_188No text annotation
IL_6VYR_001Single bulged G
IL_6VYR_002Single bulged A
IL_6VYR_003No text annotation
IL_6VYR_004Minor groove platform
IL_6VYR_005Multiple bulged bases
IL_6VYR_006Minor groove platform with extra cWW
IL_6VYR_007Minor groove platform
IL_6VYR_189Single bulged G
IL_6VYR_008Single bulged G, near cWW
IL_6VYR_009Isolated non-canonical cWW pair
IL_6VYR_010Minor groove platform related
IL_6VYR_011Isolated cWH basepair
IL_6VYR_190No text annotation
IL_6VYR_012tWH-tWH-tHW-tHW
IL_6VYR_013No text annotation
IL_6VYR_015No text annotation
IL_6VYR_017Single bulged U
IL_6VYR_018C-loop
IL_6VYR_019Single bulged G
IL_6VYR_020No text annotation
IL_6VYR_021No text annotation
IL_6VYR_022tSH-tHW-tWW
IL_6VYR_023No text annotation
IL_6VYR_024SSU/LSU pseudoknot
IL_6VYR_025Kink-turn related
IL_6VYR_027tSH-tHW-tHS
IL_6VYR_028Major groove platform
IL_6VYR_029Major groove minor groove platform; mini C-loop
IL_6VYR_030No text annotation
IL_6VYR_031Major groove platform; stack outside cWW
IL_6VYR_032Single stack bend
IL_6VYR_033Tandem non-canonical cWW pairs
IL_6VYR_034No text annotation
IL_6VYR_035Kink-turn
IL_6VYR_041Minor groove platform
IL_6VYR_042No text annotation
IL_6VYR_043Minor groove platform
IL_6VYR_200Single stack bend
IL_6VYR_044No text annotation
IL_6VYR_045No text annotation
IL_6VYR_046Single bulged U
IL_6VYR_047Not an internal loop
IL_6VYR_048Isolated cWS basepair
IL_6VYR_049Minor groove platform
IL_6VYR_050Single bulged A
IL_6VYR_051Isolated non-canonical cWW pair
IL_6VYR_052No text annotation
IL_6VYR_053Minor groove platform
IL_6VYR_054No text annotation
IL_6VYR_055No text annotation
IL_6VYR_056180 degree turn
IL_6VYR_191No text annotation
IL_6VYR_057Double sheared with non-canonical cWW
IL_6VYR_058No text annotation
IL_6VYR_060No text annotation
IL_6VYR_061No text annotation
IL_6VYR_064Triple sheared related
IL_6VYR_065Single bulged A
IL_6VYR_066No text annotation
IL_6VYR_068Single bulged A
IL_6VYR_069Minor groove platform
IL_6VYR_070No text annotation
IL_6VYR_071Single stack bend
IL_6VYR_0728x7 Sarcin-Ricin; G-bulge
IL_6VYR_0737x6 Sarcin-Ricin; G-bulge
IL_6VYR_074No text annotation
IL_6VYR_075No text annotation
IL_6VYR_076No text annotation
IL_6VYR_077No text annotation
IL_6VYR_078Double sheared
IL_6VYR_080AAA cross-strand stack
IL_6VYR_083Single bulged A
IL_6VYR_084Single bulged G
IL_6VYR_085Triple sheared
IL_6VYR_086Major groove platform
IL_6VYR_087Single stack bend
IL_6VYR_088Single stack bend
IL_6VYR_09090 degree turn
IL_6VYR_192No text annotation
IL_6VYR_091Stack outside cWW
IL_6VYR_092Single stack bend
IL_6VYR_193No text annotation
IL_6VYR_0937x7 Sarcin-Ricin with intercalated A; G-bulge
IL_6VYR_094Single bulged G
IL_6VYR_095C-loop with bulged stacked A's
IL_6VYR_096Isolated non-canonical cWW pair
IL_6VYR_097Double sheared with non-canonical cWW
IL_6VYR_194No text annotation
IL_6VYR_098No text annotation
IL_6VYR_099Single bulged C
IL_6VYR_100UAA/GAN
IL_6VYR_102Single bulged U
IL_6VYR_103Kink-turn related
IL_6VYR_105Isolated non-canonical cWW pair
IL_6VYR_106Tandem non-canonical cWW pairs
IL_6VYR_107Kink-turn
IL_6VYR_195No text annotation
IL_6VYR_108No text annotation
IL_6VYR_109Major groove platform
IL_6VYR_111No text annotation
IL_6VYR_112Kink-turn
IL_6VYR_114Major groove platform; stack outside cWW
IL_6VYR_115C-loop
IL_6VYR_116UAA/GAN
IL_6VYR_117tSH-tHW-tHS
IL_6VYR_118Single stack bend
IL_6VYR_119Single stack bend
IL_6VYR_196No text annotation
IL_6VYR_120No text annotation
IL_6VYR_121UAA/GAN
IL_6VYR_122Tandem non-canonical cWW pairs
IL_6VYR_123tSH-tHW
IL_6VYR_124Single bulged U
IL_6VYR_125No text annotation
IL_6VYR_126tSH-tHW-tHS
IL_6VYR_127No text annotation
IL_6VYR_201180 degree turn
IL_6VYR_128Single bulged A
IL_6VYR_129UAA/GAN variation
IL_6VYR_134tSH-tSH-tHH-tHS
IL_6VYR_1356x5 Sarcin-Ricin; G-bulge
IL_6VYR_136Triple sheared
IL_6VYR_137Single bulged C
IL_6VYR_138Single bulged A
IL_6VYR_139Kink-turn related
IL_6VYR_140Minor groove platform, major groove intercalation
IL_6VYR_141Major groove intercalation
IL_6VYR_142Major groove minor groove platform; mini C-loop
IL_6VYR_198No text annotation
IL_6VYR_143UAA/GAN related
IL_6VYR_144Bulged stacked bases
IL_6VYR_145No text annotation
IL_6VYR_148No text annotation
IL_6VYR_149Not an internal loop
IL_6VYR_151Isolated tHS basepair with bulges
IL_6VYR_152Isolated non-canonical cWW pair
IL_6VYR_153Isolated non-canonical cWW pair
IL_6VYR_154Isolated non-canonical cWW pair
IL_6VYR_155Isolated non-canonical cWW pair
IL_6VYR_156No text annotation
IL_6VYR_199No text annotation
IL_6VYR_157Kink-turn
IL_6VYR_158Single bulged U
IL_6VYR_159Double sheared
IL_6VYR_160No text annotation
IL_6VYR_161No text annotation
IL_6VYR_162No text annotation
IL_6VYR_164Double sheared with non-canonical cWW
IL_6VYR_165No text annotation
IL_6VYR_167No text annotation
IL_6VYR_168Major groove platform with intercalation
IL_6VYR_169No text annotation
IL_6VYR_171tSH-tHS-tHW
IL_6VYR_172Sarcin-Ricin target in LSU H95; G-bulge
IL_6VYR_174UAA/GAN related, with intercalation
IL_6VYR_175Multiple bulged bases
IL_6VYR_176UAA/GAN with extra cWW
IL_6VYR_177No text annotation
IL_6VYR_178Major groove intercalation
IL_6VYR_179Multiple bulged bases with non-canonical cWW
IL_6VYR_180tHS double platform
IL_6VYR_181Major groove intercalation
IL_6VYR_182No text annotation
IL_6VYR_183Major groove minor groove platform; mini C-loop
IL_6VYR_184Symmetric double minor groove platform
IL_6VYR_185Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6VYR_0041/D/826:829,
1/D/857:861,
1/D/868:874		No text annotation
homologous
J3_5J7L_004
NA
J3_6VYR_0091/D/1063:1068,
1/D/1107:1113,
1/D/1187:1193		No text annotation
homologous
J3_5J7L_008
NA
J3_6VYR_0131/a/30:31,
1/a/474:481,
1/a/509:510		No text annotation
homologous
J3_7RQB_001
NA
J3_6VYR_0321/a/30:31,
1/a/474:484,
1/a/496:510		No text annotation
homologous
J3_9DFE_002
J3_17917.1
J3_6VYR_0331/a/32:35,
1/a/445:461,
1/a/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_6VYR_0151/a/683:689,
1/a/773:775,
1/a/791:794		No text annotation
homologous
J3_5J7L_038
NA
J4_6VYR_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_6VYR_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_6VYR_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_6VYR_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_6VYR_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
J5_6VYR_0071/a/1674:1682,
1/a/1706:1707,
1/a/1751:1752,
1/a/1756:1764,
1/a/1988:1990		No text annotation
homologous
J5_5J7L_016
NA
J7_6VYR_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_6VYR_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_6VYR_001No text annotation
J3_6VYR_027No text annotation
J3_6VYR_002No text annotation
J3_6VYR_028No text annotation
J3_6VYR_003No text annotation
J3_6VYR_005No text annotation
J3_6VYR_006No text annotation
J3_6VYR_029No text annotation
J3_6VYR_007No text annotation
J3_6VYR_008No text annotation
J3_6VYR_030No text annotation
J3_6VYR_010No text annotation
J3_6VYR_011No text annotation
J3_6VYR_031No text annotation
J3_6VYR_012No text annotation
J3_6VYR_014No text annotation
J3_6VYR_034No text annotation
J3_6VYR_016No text annotation
J3_6VYR_017No text annotation
J3_6VYR_018No text annotation
J3_6VYR_019No text annotation
J3_6VYR_020No text annotation
J3_6VYR_035No text annotation
J3_6VYR_021Kink-turn 3-way junction
J3_6VYR_036No text annotation
J3_6VYR_022No text annotation
J3_6VYR_023No text annotation
J3_6VYR_024No text annotation
J3_6VYR_025No text annotation
J3_6VYR_026No text annotation
J4_6VYR_001tRNA junction
J4_6VYR_002tRNA junction
J4_6VYR_004No text annotation
J4_6VYR_006No text annotation
J4_6VYR_007No text annotation
J4_6VYR_008No text annotation
J4_6VYR_010No text annotation
J4_6VYR_011No text annotation
J4_6VYR_012No text annotation
J4_6VYR_013No text annotation
J4_6VYR_014No text annotation
J4_6VYR_015No text annotation
J5_6VYR_001No text annotation
J5_6VYR_002No text annotation
J5_6VYR_003No text annotation
J5_6VYR_004No text annotation
J6_6VYR_001No text annotation

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