RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_6XDQ_0071/D/12:22No text annotation
homologous
HL_4LFB_001
HL_73535.1
HL_6XDQ_0231/D/786:796No text annotation
homologous
HL_5J7L_017
NA
HL_6XDQ_0251/D/862:867GNRA
homologous
HL_5J7L_019
NA
HL_6XDQ_0261/D/897:902GNRA
homologous
HL_4LFB_020
HL_34789.2
HL_6XDQ_0291/D/1076:1081GNRA
homologous
HL_5J7L_023
NA
HL_6XDQ_0431/a/194:201No text annotation
geometric
HL_5J7L_139
NA
HL_6XDQ_0511/a/462:467GNRA
homologous
HL_5J7L_147
NA
HL_6XDQ_0541/a/566:575T-loop with 2 stacked bulged bases
geometric
HL_5J7L_150
NA
HL_6XDQ_0601/a/779:785No text annotation
homologous
HL_5J7L_156
NA
HL_6XDQ_0641/a/978:985No text annotation
homologous
HL_5J7L_160
NA
HL_6XDQ_0701/a/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_6XDQ_0821/a/1777:1787No text annotation
homologous
HL_5J7L_178
NA
HL_6XDQ_1001/a/2594:2599GNRA
homologous
HL_5J7L_196
NA
HL_6XDQ_1081/d/86:90Mini UNCG
homologous
HL_5J7L_204
NA

Problematic loops

#loop idProblemSequence
HL_6XDQ_001No text annotation
HL_6XDQ_002tRNA anticodon loop
HL_6XDQ_003T-loop with 2 stacked bulged bases
HL_6XDQ_004No text annotation
HL_6XDQ_005No text annotation
HL_6XDQ_006T-loop with 2 stacked bulged bases
HL_6XDQ_008No text annotation
HL_6XDQ_009GNRA
HL_6XDQ_010GNRA
HL_6XDQ_109No text annotation
HL_6XDQ_011No text annotation
HL_6XDQ_012GNRA related
HL_6XDQ_013GNRA
HL_6XDQ_014No text annotation
HL_6XDQ_015UNCG
HL_6XDQ_016GNRA
HL_6XDQ_017UNCG
HL_6XDQ_018GNRA wlth extra near cWW
HL_6XDQ_019No text annotation
HL_6XDQ_020GNRA-like with tWH
HL_6XDQ_021No text annotation
HL_6XDQ_022GNRA
HL_6XDQ_024No text annotation
HL_6XDQ_027No text annotation
HL_6XDQ_028GNRA
HL_6XDQ_030T-loop related
HL_6XDQ_110No text annotation
HL_6XDQ_031No text annotation
HL_6XDQ_032GNRA
HL_6XDQ_033GNRA
HL_6XDQ_034T-loop with 3 stacked bulged bases
HL_6XDQ_035No text annotation
HL_6XDQ_036UNCG
HL_6XDQ_037GNRA
HL_6XDQ_038No text annotation
HL_6XDQ_039No text annotation
HL_6XDQ_040No text annotation
HL_6XDQ_041UNCG
HL_6XDQ_042No text annotation
HL_6XDQ_044No text annotation
HL_6XDQ_045No text annotation
HL_6XDQ_046T-loop with 2 stacked bulged bases
HL_6XDQ_047No text annotation
HL_6XDQ_048T-loop with unstacked turn
HL_6XDQ_049No text annotation
HL_6XDQ_050Pseudoknot geometry
HL_6XDQ_052GNRA
HL_6XDQ_053No text annotation
HL_6XDQ_055No text annotation
HL_6XDQ_056GNRA
HL_6XDQ_057No text annotation
HL_6XDQ_058GNRA wlth tandem sheared
HL_6XDQ_059No text annotation
HL_6XDQ_061No text annotation
HL_6XDQ_111No text annotation
HL_6XDQ_062No text annotation
HL_6XDQ_063No text annotation
HL_6XDQ_065No text annotation
HL_6XDQ_066GNRA wlth tandem sheared
HL_6XDQ_067No text annotation
HL_6XDQ_068GNRA
HL_6XDQ_069T-loop with 2 stacked bulged bases
HL_6XDQ_071GNRA
HL_6XDQ_072No text annotation
HL_6XDQ_073Mini UNCG with extended bulge
HL_6XDQ_074Pseudoknot geometry with 3' bulge
HL_6XDQ_075UNCG
HL_6XDQ_076Mini UNCG
HL_6XDQ_077No text annotation
HL_6XDQ_078GNRA
HL_6XDQ_079UNCG
HL_6XDQ_112No text annotation
HL_6XDQ_080No text annotation
HL_6XDQ_081No text annotation
HL_6XDQ_083GNRA related
HL_6XDQ_084GNRA variation
HL_6XDQ_085No text annotation
HL_6XDQ_086No text annotation
HL_6XDQ_087No text annotation
HL_6XDQ_088No text annotation
HL_6XDQ_089No text annotation
HL_6XDQ_090No text annotation
HL_6XDQ_091No text annotation
HL_6XDQ_092No text annotation
HL_6XDQ_114No text annotation
HL_6XDQ_093Pseudoknot geometry
HL_6XDQ_094GNRA
HL_6XDQ_095GNRA
HL_6XDQ_096No text annotation
HL_6XDQ_097No text annotation
HL_6XDQ_098GNRA variation
HL_6XDQ_099No text annotation
HL_6XDQ_101GNRA
HL_6XDQ_102Ribsomal LSU H95
HL_6XDQ_103No text annotation
HL_6XDQ_104No text annotation
HL_6XDQ_115UNCG variation
HL_6XDQ_105No text annotation
HL_6XDQ_106GNRA
HL_6XDQ_113No text annotation
HL_6XDQ_107No text annotation

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_6XDQ_0011/D/30:32,
1/D/552:553		Single bulged G
homologous
IL_4LFB_001
IL_28408.2
IL_6XDQ_0141/D/242:247,
1/D/277:284		Kink-turn with non-sequential stacking
homologous
IL_5J7L_014
NA
IL_6XDQ_0241/D/504:511,
1/D/540:541		SSU/LSU pseudoknot
homologous
IL_5J7L_024
NA
IL_6XDQ_0261/D/569:575,
1/D/880:881		No text annotation
homologous
IL_5J7L_026
NA
IL_6XDQ_0361/D/774:778,
1/D/804:805		Left turn
homologous
IL_4LFB_032
IL_29346.3
IL_6XDQ_0381/D/887:894,
1/D/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
homologous
IL_5J7L_038
NA
IL_6XDQ_0391/D/922:923,
1/D/1393:1395		Single bulged A
homologous
IL_5J7L_039
NA
IL_6XDQ_0401/D/925:927,
1/D/1390:1391		Single bulged G
homologous
IL_5J7L_040
NA
IL_6XDQ_0411/D/933:935,
1/D/1380:1384		Minor groove platform
homologous
IL_5J7L_041
NA
IL_6XDQ_0511/D/1061:1063,
1/D/1193:1195		Isolated non-canonical cWW pair
homologous
IL_4LFB_047
IL_68118.2
IL_6XDQ_0591/D/1399:1401,
1/D/1501:1504		No text annotation
geometric
IL_5J7L_058
NA
IL_6XDQ_0621/D/1412:1414,
1/D/1486:1488		Isolated non-canonical cWW pair
homologous
IL_5J7L_061
NA
IL_6XDQ_0631/D/1416:1419,
1/D/1481:1484		Double sheared
homologous
IL_5J7L_062
NA
IL_6XDQ_0721/a/188:194,
1/a/201:208		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_250
NA
IL_6XDQ_0771/a/481:484,
1/a/496:509		No text annotation
geometric
IL_5J7L_255
NA
IL_6XDQ_0791/a/564:566,
1/a/575:577		Isolated non-canonical cWW pair
homologous
IL_5J7L_257
NA
IL_6XDQ_0811/a/672:674,
1/a/806:808		No text annotation
homologous
IL_7RQB_017
NA
IL_6XDQ_0821/a/674:678,
1/a/799:806		tHW-tHW cross-strand stack
geometric
IL_7RQB_018
NA
IL_6XDQ_0871/a/741:742,
1/a/754:756		Single stack bend
geometric
IL_4LFB_041
IL_15011.2
IL_6XDQ_0881/a/742:744,
1/a/753:754		Single stack bend
geometric
IL_4V83_236
IL_15011.2
IL_6XDQ_0891/a/775:777,
1/a/787:791		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_6XDQ_1131/a/1262:1269,
1/a/2011:2017		8x7 Sarcin-Ricin; G-bulge
homologous
IL_5J7L_289
NA
IL_6XDQ_1301/a/1651:1656,
1/a/2004:2006		No text annotation
homologous
IL_5J7L_304
NA
IL_6XDQ_1971/a/1666:1674,
1/a/1990:1994		No text annotation
homologous
IL_5J7L_386
NA
IL_6XDQ_1331/a/1669:1674,
1/a/1990:1993		Intercalated tWH
geometric
IL_5J7L_307
NA
IL_6XDQ_1441/a/1933:1934,
1/a/1964:1967		Bulged stacked bases
geometric
IL_7RQB_076
NA
IL_6XDQ_1461/a/2050:2052,
1/a/2617:2618		Major groove platform
homologous
IL_5J7L_320
NA
IL_6XDQ_1471/a/2054:2056,
1/a/2612:2615		No text annotation
homologous
IL_5J7L_321
NA
IL_6XDQ_1501/a/2070:2071,
1/a/2438:2441		Minor groove platform
geometric
IL_5J7L_324
NA
IL_6XDQ_1661/a/2510:2512,
1/a/2574:2578		Isolated non-canonical cWW with bulges
geometric
IL_5J7L_340
NA
IL_6XDQ_1671/a/2512:2513,
1/a/2571:2574		No text annotation
homologous
IL_5J7L_341
NA
IL_6XDQ_1701/a/2591:2592,
1/a/2601:2603		Single bulged A
homologous
IL_7RQB_101
NA

Problematic loops

#loop idProblemSequence
IL_6XDQ_186No text annotation
IL_6XDQ_187No text annotation
IL_6XDQ_188No text annotation
IL_6XDQ_002Single bulged A
IL_6XDQ_003No text annotation
IL_6XDQ_004Minor groove platform
IL_6XDQ_005Multiple bulged bases
IL_6XDQ_006Minor groove platform with extra cWW
IL_6XDQ_007Minor groove platform
IL_6XDQ_189Single bulged G
IL_6XDQ_008Single bulged G, near cWW
IL_6XDQ_009Isolated non-canonical cWW pair
IL_6XDQ_010Minor groove platform related
IL_6XDQ_011Isolated cWH basepair
IL_6XDQ_190No text annotation
IL_6XDQ_012tWH-tWH-tHW-tHW
IL_6XDQ_013No text annotation
IL_6XDQ_015No text annotation
IL_6XDQ_016C-loop
IL_6XDQ_017Single bulged U
IL_6XDQ_018C-loop
IL_6XDQ_019Single bulged G
IL_6XDQ_020No text annotation
IL_6XDQ_021No text annotation
IL_6XDQ_022tSH-tHW-tWW
IL_6XDQ_023No text annotation
IL_6XDQ_025Kink-turn related
IL_6XDQ_027tSH-tHW-tHS
IL_6XDQ_028Major groove platform
IL_6XDQ_029Major groove minor groove platform; mini C-loop
IL_6XDQ_030No text annotation
IL_6XDQ_031Major groove platform; stack outside cWW
IL_6XDQ_032Single stack bend
IL_6XDQ_033Tandem non-canonical cWW pairs
IL_6XDQ_034No text annotation
IL_6XDQ_035Kink-turn
IL_6XDQ_037tSH-tHW-tHS
IL_6XDQ_042No text annotation
IL_6XDQ_043Minor groove platform
IL_6XDQ_044No text annotation
IL_6XDQ_045No text annotation
IL_6XDQ_046Single bulged U
IL_6XDQ_047Not an internal loop
IL_6XDQ_048Isolated cWS basepair
IL_6XDQ_049Minor groove platform
IL_6XDQ_050Single bulged A
IL_6XDQ_052No text annotation
IL_6XDQ_053Minor groove platform
IL_6XDQ_054No text annotation
IL_6XDQ_055No text annotation
IL_6XDQ_056180 degree turn
IL_6XDQ_191No text annotation
IL_6XDQ_057Double sheared with non-canonical cWW
IL_6XDQ_058No text annotation
IL_6XDQ_060No text annotation
IL_6XDQ_061No text annotation
IL_6XDQ_064Triple sheared related
IL_6XDQ_065Single bulged A
IL_6XDQ_066No text annotation
IL_6XDQ_067Triple sheared with non-canonical cWW
IL_6XDQ_068Single bulged A
IL_6XDQ_069Minor groove platform
IL_6XDQ_070No text annotation
IL_6XDQ_071Single stack bend
IL_6XDQ_0737x6 Sarcin-Ricin; G-bulge
IL_6XDQ_074No text annotation
IL_6XDQ_075No text annotation
IL_6XDQ_076No text annotation
IL_6XDQ_078Double sheared
IL_6XDQ_080AAA cross-strand stack
IL_6XDQ_083Single bulged A
IL_6XDQ_084Single bulged G
IL_6XDQ_085Triple sheared
IL_6XDQ_086Major groove platform
IL_6XDQ_09090 degree turn
IL_6XDQ_192No text annotation
IL_6XDQ_091Stack outside cWW
IL_6XDQ_092Single stack bend
IL_6XDQ_193No text annotation
IL_6XDQ_0937x7 Sarcin-Ricin with intercalated A; G-bulge
IL_6XDQ_094Single bulged G
IL_6XDQ_095C-loop with bulged stacked A's
IL_6XDQ_096Isolated non-canonical cWW pair
IL_6XDQ_097Double sheared with non-canonical cWW
IL_6XDQ_194No text annotation
IL_6XDQ_098No text annotation
IL_6XDQ_099Single bulged C
IL_6XDQ_100UAA/GAN
IL_6XDQ_101SSU/LSU pseudoknot
IL_6XDQ_102Single bulged U
IL_6XDQ_103Kink-turn related
IL_6XDQ_104No text annotation
IL_6XDQ_105Isolated non-canonical cWW pair
IL_6XDQ_106Tandem non-canonical cWW pairs
IL_6XDQ_107Kink-turn
IL_6XDQ_195No text annotation
IL_6XDQ_108No text annotation
IL_6XDQ_109Major groove platform
IL_6XDQ_110Isolated cWS basepair
IL_6XDQ_111No text annotation
IL_6XDQ_112Kink-turn
IL_6XDQ_114Major groove platform; stack outside cWW
IL_6XDQ_115C-loop
IL_6XDQ_116UAA/GAN
IL_6XDQ_117tSH-tHW-tHS
IL_6XDQ_118Single stack bend
IL_6XDQ_119Single stack bend
IL_6XDQ_196No text annotation
IL_6XDQ_120No text annotation
IL_6XDQ_121UAA/GAN
IL_6XDQ_122Tandem non-canonical cWW pairs
IL_6XDQ_123tSH-tHW
IL_6XDQ_124Single bulged U
IL_6XDQ_125No text annotation
IL_6XDQ_126tSH-tHW-tHS
IL_6XDQ_127No text annotation
IL_6XDQ_200180 degree turn
IL_6XDQ_128Single bulged A
IL_6XDQ_129UAA/GAN variation
IL_6XDQ_131Isolated tWW turn
IL_6XDQ_132Major groove platform; stack outside cWW
IL_6XDQ_134tSH-tSH-tHH-tHS
IL_6XDQ_1356x5 Sarcin-Ricin; G-bulge
IL_6XDQ_136Triple sheared
IL_6XDQ_137Single bulged C
IL_6XDQ_138Single bulged A
IL_6XDQ_139Kink-turn related
IL_6XDQ_140Minor groove platform, major groove intercalation
IL_6XDQ_141Major groove intercalation
IL_6XDQ_142Major groove minor groove platform; mini C-loop
IL_6XDQ_198No text annotation
IL_6XDQ_143UAA/GAN related
IL_6XDQ_145No text annotation
IL_6XDQ_148No text annotation
IL_6XDQ_149No text annotation
IL_6XDQ_151Isolated tHS basepair with bulges
IL_6XDQ_152Isolated non-canonical cWW pair
IL_6XDQ_153Isolated non-canonical cWW pair
IL_6XDQ_154Isolated non-canonical cWW pair
IL_6XDQ_155Isolated non-canonical cWW pair
IL_6XDQ_156No text annotation
IL_6XDQ_199No text annotation
IL_6XDQ_157Kink-turn
IL_6XDQ_158Single bulged U
IL_6XDQ_159Double sheared
IL_6XDQ_160No text annotation
IL_6XDQ_161No text annotation
IL_6XDQ_162No text annotation
IL_6XDQ_163Major groove minor groove platform with extra cWW
IL_6XDQ_164Double sheared with non-canonical cWW
IL_6XDQ_165No text annotation
IL_6XDQ_168Major groove platform with intercalation
IL_6XDQ_169No text annotation
IL_6XDQ_171tSH-tHS-tHW
IL_6XDQ_172Sarcin-Ricin target in LSU H95; G-bulge
IL_6XDQ_173C-loop
IL_6XDQ_174UAA/GAN related, with intercalation
IL_6XDQ_175Multiple bulged bases
IL_6XDQ_176UAA/GAN with extra cWW
IL_6XDQ_177No text annotation
IL_6XDQ_178Major groove intercalation
IL_6XDQ_179Multiple bulged bases with non-canonical cWW
IL_6XDQ_180tHS double platform
IL_6XDQ_181Major groove intercalation
IL_6XDQ_182No text annotation
IL_6XDQ_183Major groove minor groove platform; mini C-loop
IL_6XDQ_184Symmetric double minor groove platform
IL_6XDQ_185Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_6XDQ_0041/D/826:829,
1/D/857:861,
1/D/868:874		No text annotation
homologous
J3_5J7L_004
NA
J3_6XDQ_0091/D/1063:1068,
1/D/1107:1113,
1/D/1187:1193		No text annotation
homologous
J3_5J7L_008
NA
J3_6XDQ_0131/a/30:31,
1/a/474:481,
1/a/509:510		No text annotation
homologous
J3_7RQB_001
NA
J3_6XDQ_0321/a/30:31,
1/a/474:484,
1/a/496:510		No text annotation
homologous
J3_9DFE_002
J3_17917.1
J3_6XDQ_0331/a/32:35,
1/a/445:461,
1/a/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_6XDQ_0151/a/683:689,
1/a/773:775,
1/a/791:794		No text annotation
homologous
J3_5J7L_038
NA
J3_6XDQ_0191/a/1306:1309,
1/a/1605:1611,
1/a/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_47341.1
J4_6XDQ_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_6XDQ_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_6XDQ_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_6XDQ_0131/a/1772:1776,
1/a/1788:1792,
1/a/1827:1830,
1/a/1975:1979		No text annotation
homologous
J4_5J7L_025
NA
J5_6XDQ_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_6XDQ_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_6XDQ_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_6XDQ_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

Problematic loops

#loop idProblemSequence
J3_6XDQ_001No text annotation
J3_6XDQ_027No text annotation
J3_6XDQ_002No text annotation
J3_6XDQ_028No text annotation
J3_6XDQ_003No text annotation
J3_6XDQ_005No text annotation
J3_6XDQ_006No text annotation
J3_6XDQ_029No text annotation
J3_6XDQ_007No text annotation
J3_6XDQ_008No text annotation
J3_6XDQ_030No text annotation
J3_6XDQ_010No text annotation
J3_6XDQ_011No text annotation
J3_6XDQ_031No text annotation
J3_6XDQ_012No text annotation
J3_6XDQ_014No text annotation
J3_6XDQ_034No text annotation
J3_6XDQ_016No text annotation
J3_6XDQ_017No text annotation
J3_6XDQ_018No text annotation
J3_6XDQ_020No text annotation
J3_6XDQ_035No text annotation
J3_6XDQ_021Kink-turn 3-way junction
J3_6XDQ_036No text annotation
J3_6XDQ_022No text annotation
J3_6XDQ_023No text annotation
J3_6XDQ_024No text annotation
J3_6XDQ_025No text annotation
J3_6XDQ_026No text annotation
J4_6XDQ_001tRNA junction
J4_6XDQ_002tRNA junction
J4_6XDQ_004No text annotation
J4_6XDQ_006No text annotation
J4_6XDQ_007No text annotation
J4_6XDQ_008No text annotation
J4_6XDQ_010No text annotation
J4_6XDQ_011No text annotation
J4_6XDQ_012No text annotation
J4_6XDQ_014No text annotation
J4_6XDQ_015No text annotation
J5_6XDQ_001No text annotation
J5_6XDQ_002No text annotation
J5_6XDQ_003No text annotation
J5_6XDQ_004No text annotation
J6_6XDQ_001No text annotation
J7_6XDQ_002No text annotation

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