RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6VZJ_0071/D/12:22No text annotation
homologous
HL_4LFB_001
HL_31940.1
HL_6VZJ_0131/D/296:301GNRA
homologous
HL_4LFB_007
HL_34789.1
HL_6VZJ_0221/D/726:731GNRA
homologous
HL_5J7L_016
NA
HL_6VZJ_0231/D/786:796No text annotation
homologous
HL_5J7L_017
NA
HL_6VZJ_0251/D/862:867GNRA
homologous
HL_5J7L_019
NA
HL_6VZJ_0261/D/897:902GNRA
homologous
HL_4LFB_020
HL_34789.1
HL_6VZJ_0291/D/1076:1081GNRA
homologous
HL_5J7L_023
NA
HL_6VZJ_0511/a/462:467GNRA
homologous
HL_5J7L_147
NA
HL_6VZJ_0541/a/566:575T-loop with 2 stacked bulged bases
homologous
HL_5J7L_150
NA
HL_6VZJ_0601/a/779:785No text annotation
homologous
HL_5J7L_156
NA
HL_6VZJ_0611/a/826:831No text annotation
homologous
HL_5J7L_157
NA
HL_6VZJ_0641/a/978:985No text annotation
homologous
HL_5J7L_160
NA
HL_6VZJ_0701/a/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_6VZJ_0821/a/1777:1787No text annotation
homologous
HL_5J7L_178
NA
HL_6VZJ_0861/a/1949:1957No text annotation
homologous
HL_5J7L_182
NA

Problematic loops

#loop idProblemSequence
HL_6VZJ_001No text annotation
HL_6VZJ_002tRNA anticodon loop
HL_6VZJ_003T-loop with 2 stacked bulged bases
HL_6VZJ_004No text annotation
HL_6VZJ_005No text annotation
HL_6VZJ_006T-loop with 2 stacked bulged bases
HL_6VZJ_008No text annotation
HL_6VZJ_009GNRA
HL_6VZJ_010GNRA
HL_6VZJ_109No text annotation
HL_6VZJ_011No text annotation
HL_6VZJ_012GNRA related
HL_6VZJ_014No text annotation
HL_6VZJ_015UNCG
HL_6VZJ_016GNRA
HL_6VZJ_017UNCG
HL_6VZJ_018GNRA wlth extra near cWW
HL_6VZJ_019No text annotation
HL_6VZJ_020GNRA-like with tWH
HL_6VZJ_021No text annotation
HL_6VZJ_024No text annotation
HL_6VZJ_027No text annotation
HL_6VZJ_028GNRA
HL_6VZJ_030T-loop related
HL_6VZJ_110No text annotation
HL_6VZJ_031No text annotation
HL_6VZJ_032GNRA
HL_6VZJ_033GNRA
HL_6VZJ_034T-loop with 3 stacked bulged bases
HL_6VZJ_035No text annotation
HL_6VZJ_036UNCG
HL_6VZJ_037GNRA
HL_6VZJ_038No text annotation
HL_6VZJ_039No text annotation
HL_6VZJ_040No text annotation
HL_6VZJ_041UNCG
HL_6VZJ_042No text annotation
HL_6VZJ_043No text annotation
HL_6VZJ_044No text annotation
HL_6VZJ_045No text annotation
HL_6VZJ_046T-loop with 2 stacked bulged bases
HL_6VZJ_047No text annotation
HL_6VZJ_048T-loop with unstacked turn
HL_6VZJ_049No text annotation
HL_6VZJ_050Pseudoknot geometry
HL_6VZJ_052GNRA
HL_6VZJ_053No text annotation
HL_6VZJ_055No text annotation
HL_6VZJ_056GNRA
HL_6VZJ_057No text annotation
HL_6VZJ_058GNRA wlth tandem sheared
HL_6VZJ_059No text annotation
HL_6VZJ_111No text annotation
HL_6VZJ_062No text annotation
HL_6VZJ_063No text annotation
HL_6VZJ_065No text annotation
HL_6VZJ_066GNRA wlth tandem sheared
HL_6VZJ_067No text annotation
HL_6VZJ_068GNRA
HL_6VZJ_069T-loop with 2 stacked bulged bases
HL_6VZJ_071GNRA
HL_6VZJ_072No text annotation
HL_6VZJ_073Mini UNCG with extended bulge
HL_6VZJ_074Pseudoknot geometry with 3' bulge
HL_6VZJ_075UNCG
HL_6VZJ_076Mini UNCG
HL_6VZJ_077No text annotation
HL_6VZJ_078GNRA
HL_6VZJ_079UNCG
HL_6VZJ_112No text annotation
HL_6VZJ_080No text annotation
HL_6VZJ_081No text annotation
HL_6VZJ_083GNRA related
HL_6VZJ_084GNRA variation
HL_6VZJ_085No text annotation
HL_6VZJ_087No text annotation
HL_6VZJ_088No text annotation
HL_6VZJ_089No text annotation
HL_6VZJ_090No text annotation
HL_6VZJ_091No text annotation
HL_6VZJ_092No text annotation
HL_6VZJ_114No text annotation
HL_6VZJ_093Pseudoknot geometry
HL_6VZJ_094GNRA
HL_6VZJ_095GNRA
HL_6VZJ_096No text annotation
HL_6VZJ_097No text annotation
HL_6VZJ_098GNRA variation
HL_6VZJ_099No text annotation
HL_6VZJ_100GNRA
HL_6VZJ_101GNRA
HL_6VZJ_102Ribsomal LSU H95
HL_6VZJ_103No text annotation
HL_6VZJ_104No text annotation
HL_6VZJ_115UNCG variation
HL_6VZJ_105No text annotation
HL_6VZJ_106GNRA
HL_6VZJ_113No text annotation
HL_6VZJ_107No text annotation
HL_6VZJ_108Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6VZJ_0011/D/30:32,
1/D/552:553		Single bulged G
homologous
IL_4LFB_001
IL_28408.1
IL_6VZJ_0141/D/242:247,
1/D/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
NA
IL_6VZJ_0261/D/569:575,
1/D/880:881		No text annotation
homologous
IL_5J7L_026
NA
IL_6VZJ_0271/D/580:584,
1/D/757:761		tSH-tHW-tHS
homologous
IL_5J7L_027
NA
IL_6VZJ_0361/D/774:778,
1/D/804:805		Left turn
homologous
IL_4LFB_032
IL_29346.3
IL_6VZJ_0371/D/779:783,
1/D/799:803		tSH-tHW-tHS
homologous
IL_5J7L_037
NA
IL_6VZJ_0381/D/887:894,
1/D/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_6VZJ_0391/D/922:923,
1/D/1393:1395		Single bulged A
homologous
IL_5J7L_039
NA
IL_6VZJ_0481/D/1052:1056,
1/D/1204:1206		Isolated cWS basepair
geometric
IL_4LFB_044
IL_82453.1
IL_6VZJ_0511/D/1061:1063,
1/D/1193:1195		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_68118.1
IL_6VZJ_0591/D/1399:1401,
1/D/1501:1504		No text annotation
homologous
IL_5J7L_058
NA
IL_6VZJ_0621/D/1412:1414,
1/D/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_6VZJ_0631/D/1416:1419,
1/D/1481:1484		Double sheared
homologous
IL_5J7L_062
NA
IL_6VZJ_0671/a/24:30,
1/a/510:516		Triple sheared with non-canonical cWW
geometric
IL_5J7L_245
NA
IL_6VZJ_0771/a/481:484,
1/a/496:509		No text annotation
geometric
IL_5J7L_255
NA
IL_6VZJ_0791/a/564:566,
1/a/575:577		Isolated non-canonical cWW pair
geometric
IL_5J7L_257
NA
IL_6VZJ_0811/a/672:674,
1/a/806:808		No text annotation
geometric
IL_7RQB_017
NA
IL_6VZJ_0821/a/674:678,
1/a/799:806		tHW-tHW cross-strand stack
homologous
IL_7RQB_018
NA
IL_6VZJ_0861/a/738:740,
1/a/757:758		Major groove platform
homologous
IL_5J7L_264
NA
IL_6VZJ_0871/a/741:742,
1/a/754:756		Single stack bend
geometric
IL_4LFB_041
IL_15011.1
IL_6VZJ_0881/a/742:744,
1/a/753:754		Single stack bend
geometric
IL_4V83_236
IL_15011.1
IL_6VZJ_0891/a/775:777,
1/a/787:791		Multiple bulged bases
homologous
IL_5J7L_265
NA
IL_6VZJ_1011/a/1004:1011,
1/a/1150:1151		SSU/LSU pseudoknot
geometric
IL_5J7L_278
NA
IL_6VZJ_1041/a/1024:1030,
1/a/1124:1140		No text annotation
geometric
IL_5J7L_281
NA
IL_6VZJ_1131/a/1262:1269,
1/a/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_6VZJ_1301/a/1651:1656,
1/a/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_6VZJ_1311/a/1663:1665,
1/a/1995:1997		Isolated tWW turn
homologous
IL_5J7L_305
NA
IL_6VZJ_1321/a/1666:1669,
1/a/1993:1994		Major groove platform; stack outside cWW
geometric
IL_7RQB_066
NA
IL_6VZJ_1971/a/1666:1674,
1/a/1990:1994		No text annotation
homologous
IL_5J7L_386
NA
IL_6VZJ_1331/a/1669:1674,
1/a/1990:1993		Intercalated tWH
homologous
IL_5J7L_307
NA
IL_6VZJ_1341/a/1686:1691,
1/a/1696:1702		tSH-tSH-tHH-tHS
homologous
IL_5J7L_308
NA
IL_6VZJ_1441/a/1933:1934,
1/a/1964:1967		Bulged stacked bases
homologous
IL_7RQB_076
NA
IL_6VZJ_1461/a/2050:2052,
1/a/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_6VZJ_1471/a/2054:2056,
1/a/2612:2615		No text annotation
homologous
IL_5J7L_321
NA
IL_6VZJ_1501/a/2070:2071,
1/a/2438:2441		Minor groove platform
geometric
IL_5J7L_324
NA
IL_6VZJ_1661/a/2510:2512,
1/a/2574:2578		Isolated non-canonical cWW with bulges
homologous
IL_5J7L_340
NA
IL_6VZJ_1671/a/2512:2513,
1/a/2571:2574		No text annotation
geometric
IL_5J7L_341
NA
IL_6VZJ_1701/a/2591:2592,
1/a/2601:2603		Single bulged A
homologous
IL_7RQB_101
NA

Problematic loops

#loop idProblemSequence
IL_6VZJ_186No text annotation
IL_6VZJ_187No text annotation
IL_6VZJ_188No text annotation
IL_6VZJ_002Single bulged A
IL_6VZJ_003No text annotation
IL_6VZJ_004Minor groove platform
IL_6VZJ_005Multiple bulged bases
IL_6VZJ_006Minor groove platform with extra cWW
IL_6VZJ_007Minor groove platform
IL_6VZJ_189Single bulged G
IL_6VZJ_008Single bulged G, near cWW
IL_6VZJ_009Isolated non-canonical cWW pair
IL_6VZJ_010Minor groove platform related
IL_6VZJ_011Isolated cWH basepair
IL_6VZJ_190No text annotation
IL_6VZJ_012tWH-tWH-tHW-tHW
IL_6VZJ_013No text annotation
IL_6VZJ_015No text annotation
IL_6VZJ_016C-loop
IL_6VZJ_017Single bulged U
IL_6VZJ_018C-loop
IL_6VZJ_019Single bulged G
IL_6VZJ_020No text annotation
IL_6VZJ_021No text annotation
IL_6VZJ_022tSH-tHW-tWW
IL_6VZJ_023No text annotation
IL_6VZJ_024SSU/LSU pseudoknot
IL_6VZJ_025Kink-turn related
IL_6VZJ_028Major groove platform
IL_6VZJ_029Major groove minor groove platform; mini C-loop
IL_6VZJ_030No text annotation
IL_6VZJ_031Major groove platform; stack outside cWW
IL_6VZJ_032Single stack bend
IL_6VZJ_033Tandem non-canonical cWW pairs
IL_6VZJ_034No text annotation
IL_6VZJ_035Kink-turn
IL_6VZJ_040Single bulged G
IL_6VZJ_041Minor groove platform
IL_6VZJ_042No text annotation
IL_6VZJ_043Minor groove platform
IL_6VZJ_201Single stack bend
IL_6VZJ_044No text annotation
IL_6VZJ_045No text annotation
IL_6VZJ_046Single bulged U
IL_6VZJ_047No text annotation
IL_6VZJ_049Minor groove platform
IL_6VZJ_050Single bulged U
IL_6VZJ_052No text annotation
IL_6VZJ_053Minor groove platform
IL_6VZJ_054No text annotation
IL_6VZJ_055No text annotation
IL_6VZJ_056180 degree turn
IL_6VZJ_191No text annotation
IL_6VZJ_057Double sheared with non-canonical cWW
IL_6VZJ_058No text annotation
IL_6VZJ_060No text annotation
IL_6VZJ_061Partly complementary
IL_6VZJ_064Triple sheared related
IL_6VZJ_065Single bulged A
IL_6VZJ_066No text annotation
IL_6VZJ_068Single bulged A
IL_6VZJ_069Minor groove platform
IL_6VZJ_070No text annotation
IL_6VZJ_071Single stack bend
IL_6VZJ_0728x7 Sarcin-Ricin; G-bulge
IL_6VZJ_0737x6 Sarcin-Ricin; G-bulge
IL_6VZJ_074No text annotation
IL_6VZJ_075No text annotation
IL_6VZJ_076No text annotation
IL_6VZJ_078Double sheared
IL_6VZJ_080AAA cross-strand stack
IL_6VZJ_083Single bulged A
IL_6VZJ_084Single bulged G
IL_6VZJ_085Triple sheared
IL_6VZJ_09090 degree turn
IL_6VZJ_192No text annotation
IL_6VZJ_091Stack outside cWW
IL_6VZJ_092Single stack bend
IL_6VZJ_193No text annotation
IL_6VZJ_0937x7 Sarcin-Ricin with intercalated A; G-bulge
IL_6VZJ_094Single bulged G
IL_6VZJ_095C-loop with bulged stacked A's
IL_6VZJ_096Isolated non-canonical cWW pair
IL_6VZJ_097Double sheared with non-canonical cWW
IL_6VZJ_194No text annotation
IL_6VZJ_098No text annotation
IL_6VZJ_099Single bulged C
IL_6VZJ_100UAA/GAN
IL_6VZJ_102Single bulged U
IL_6VZJ_103Kink-turn related
IL_6VZJ_105Isolated non-canonical cWW pair
IL_6VZJ_106Tandem non-canonical cWW pairs
IL_6VZJ_107Kink-turn
IL_6VZJ_195No text annotation
IL_6VZJ_108No text annotation
IL_6VZJ_109No text annotation
IL_6VZJ_110Isolated cWS basepair
IL_6VZJ_111No text annotation
IL_6VZJ_112Kink-turn
IL_6VZJ_114Major groove platform; stack outside cWW
IL_6VZJ_115C-loop
IL_6VZJ_116UAA/GAN
IL_6VZJ_117tSH-tHW-tHS
IL_6VZJ_118Single stack bend
IL_6VZJ_119Single stack bend
IL_6VZJ_196No text annotation
IL_6VZJ_120No text annotation
IL_6VZJ_121UAA/GAN
IL_6VZJ_122Tandem non-canonical cWW pairs
IL_6VZJ_123tSH-tHW
IL_6VZJ_124Single bulged U
IL_6VZJ_125No text annotation
IL_6VZJ_126tSH-tHW-tHS
IL_6VZJ_127No text annotation
IL_6VZJ_200180 degree turn
IL_6VZJ_128Single bulged A
IL_6VZJ_129UAA/GAN variation
IL_6VZJ_1356x5 Sarcin-Ricin; G-bulge
IL_6VZJ_136Triple sheared
IL_6VZJ_137Single bulged C
IL_6VZJ_138Single bulged A
IL_6VZJ_139Kink-turn related
IL_6VZJ_140Minor groove platform, major groove intercalation
IL_6VZJ_141Major groove intercalation
IL_6VZJ_142Major groove minor groove platform; mini C-loop
IL_6VZJ_198No text annotation
IL_6VZJ_143UAA/GAN related
IL_6VZJ_145No text annotation
IL_6VZJ_148No text annotation
IL_6VZJ_149No text annotation
IL_6VZJ_151Isolated tHS basepair with bulges
IL_6VZJ_152Isolated non-canonical cWW pair
IL_6VZJ_153Isolated non-canonical cWW pair
IL_6VZJ_154Isolated non-canonical cWW pair
IL_6VZJ_155Isolated non-canonical cWW pair
IL_6VZJ_156No text annotation
IL_6VZJ_199No text annotation
IL_6VZJ_157Kink-turn
IL_6VZJ_158Single bulged U
IL_6VZJ_159Double sheared
IL_6VZJ_160No text annotation
IL_6VZJ_161No text annotation
IL_6VZJ_162No text annotation
IL_6VZJ_163Major groove minor groove platform with extra cWW
IL_6VZJ_164Double sheared with non-canonical cWW
IL_6VZJ_165No text annotation
IL_6VZJ_168Major groove platform with intercalation
IL_6VZJ_169No text annotation
IL_6VZJ_171tSH-tHS-tHW
IL_6VZJ_172Sarcin-Ricin target in LSU H95; G-bulge
IL_6VZJ_173C-loop
IL_6VZJ_174UAA/GAN related, with intercalation
IL_6VZJ_175Multiple bulged bases
IL_6VZJ_176UAA/GAN with extra cWW
IL_6VZJ_177No text annotation
IL_6VZJ_178Major groove intercalation
IL_6VZJ_179Multiple bulged bases with non-canonical cWW
IL_6VZJ_180tHS double platform
IL_6VZJ_181Major groove intercalation
IL_6VZJ_182No text annotation
IL_6VZJ_183Major groove minor groove platform; mini C-loop
IL_6VZJ_184Symmetric double minor groove platform
IL_6VZJ_185Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6VZJ_0011/D/46:47,
1/D/361:367,
1/D/393:395		No text annotation
homologous
J3_5J7L_001
NA
J3_6VZJ_0271/D/46:52,
1/D/359:367,
1/D/393:395		No text annotation
homologous
J3_5J7L_050
NA
J3_6VZJ_0031/D/672:673,
1/D/717:725,
1/D/732:734		No text annotation
homologous
J3_5J7L_003
NA
J3_6VZJ_0041/D/826:829,
1/D/857:861,
1/D/868:874		No text annotation
homologous
J3_5J7L_004
NA
J3_6VZJ_0091/D/1063:1068,
1/D/1107:1113,
1/D/1187:1193		No text annotation
homologous
J3_5J7L_008
NA
J3_6VZJ_0101/D/1073:1074,
1/D/1083:1087,
1/D/1098:1102		No text annotation
homologous
J3_5J7L_009
NA
J3_6VZJ_0321/a/30:31,
1/a/474:484,
1/a/496:510		No text annotation
homologous
J3_9DFE_002
J3_17917.1
J3_6VZJ_0331/a/32:35,
1/a/445:461,
1/a/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_6VZJ_0151/a/683:689,
1/a/773:775,
1/a/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_6VZJ_0181/a/1298:1303,
1/a/1625:1627,
1/a/1639:1642		No text annotation
homologous
J3_5J7L_041
NA
J3_6VZJ_0191/a/1306:1309,
1/a/1605:1611,
1/a/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_47341.1
J3_6VZJ_0231/a/2517:2520,
1/a/2545:2547,
1/a/2561:2567		No text annotation
homologous
J3_5J7L_046
NA
J4_6VZJ_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_6VZJ_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_6VZJ_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_6VZJ_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_6VZJ_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_6VZJ_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_6VZJ_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_6VZJ_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_6VZJ_002No text annotation
J3_6VZJ_028No text annotation
J3_6VZJ_005No text annotation
J3_6VZJ_006No text annotation
J3_6VZJ_029No text annotation
J3_6VZJ_007No text annotation
J3_6VZJ_008No text annotation
J3_6VZJ_030No text annotation
J3_6VZJ_011No text annotation
J3_6VZJ_031No text annotation
J3_6VZJ_012No text annotation
J3_6VZJ_013No text annotation
J3_6VZJ_014No text annotation
J3_6VZJ_034No text annotation
J3_6VZJ_016No text annotation
J3_6VZJ_017No text annotation
J3_6VZJ_020No text annotation
J3_6VZJ_035No text annotation
J3_6VZJ_021Kink-turn 3-way junction
J3_6VZJ_036No text annotation
J3_6VZJ_022No text annotation
J3_6VZJ_024No text annotation
J3_6VZJ_025No text annotation
J3_6VZJ_026No text annotation
J4_6VZJ_001tRNA junction
J4_6VZJ_002tRNA junction
J4_6VZJ_003No text annotation
J4_6VZJ_004No text annotation
J4_6VZJ_006No text annotation
J4_6VZJ_007No text annotation
J4_6VZJ_008No text annotation
J4_6VZJ_010No text annotation
J4_6VZJ_011No text annotation
J4_6VZJ_012No text annotation
J4_6VZJ_013No text annotation
J4_6VZJ_014No text annotation
J5_6VZJ_001No text annotation
J5_6VZJ_002No text annotation
J5_6VZJ_003No text annotation
J5_6VZJ_004No text annotation
J6_6VZJ_001No text annotation

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