RNA 3D Hub //

8VOR Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8VOR_0071/D/12:22No text annotation
geometric
HL_4LFB_001
HL_73535.1
HL_8VOR_0211/D/726:731GNRA
geometric
HL_5J7L_016
NA
HL_8VOR_0221/D/786:796No text annotation
geometric
HL_5J7L_017
NA
HL_8VOR_0241/D/862:867GNRA
geometric
HL_5J7L_019
NA
HL_8VOR_0251/D/897:902GNRA
geometric
HL_4LFB_020
HL_34789.2
HL_8VOR_0271/D/1076:1081GNRA
geometric
HL_5J7L_023
NA
HL_8VOR_0401/a/194:201No text annotation
geometric
HL_5J7L_139
NA
HL_8VOR_0421/a/246:252No text annotation
geometric
HL_5J7L_141
NA
HL_8VOR_0481/a/462:467GNRA
geometric
HL_5J7L_147
NA
HL_8VOR_0511/a/566:575T-loop with 2 stacked bulged bases
geometric
HL_5J7L_150
NA
HL_8VOR_0561/a/779:785No text annotation
geometric
HL_5J7L_156
NA
HL_8VOR_0591/a/978:985No text annotation
geometric
HL_5J7L_160
NA
HL_8VOR_0651/a/1324:1330Pseudoknot geometry with 3' bulge
geometric
HL_5J7L_166
NA
HL_8VOR_0761/a/1777:1787No text annotation
geometric
HL_5J7L_178
NA
HL_8VOR_0821/a/2264:2276No text annotation
geometric
HL_5J7L_187
NA
HL_8VOR_0901/a/2594:2599GNRA
geometric
HL_4V9F_065
HL_34789.2

Problematic loops

#loop idProblemSequence
HL_8VOR_001No text annotation
HL_8VOR_002No text annotation
HL_8VOR_003T-loop with 2 stacked bulged bases
HL_8VOR_004No text annotation
HL_8VOR_005No text annotation
HL_8VOR_006T-loop with 2 stacked bulged bases
HL_8VOR_008No text annotation
HL_8VOR_009GNRA
HL_8VOR_010GNRA
HL_8VOR_011No text annotation
HL_8VOR_012GNRA related
HL_8VOR_013GNRA
HL_8VOR_014No text annotation
HL_8VOR_015UNCG
HL_8VOR_016GNRA
HL_8VOR_017UNCG
HL_8VOR_018GNRA wlth extra near cWW
HL_8VOR_019GNRA-like with tWH
HL_8VOR_020No text annotation
HL_8VOR_023No text annotation
HL_8VOR_026GNRA
HL_8VOR_028T-loop related
HL_8VOR_029No text annotation
HL_8VOR_030GNRA
HL_8VOR_031GNRA
HL_8VOR_032T-loop with 3 stacked bulged bases
HL_8VOR_033No text annotation
HL_8VOR_034UNCG
HL_8VOR_035No text annotation
HL_8VOR_036No text annotation
HL_8VOR_037No text annotation
HL_8VOR_038UNCG
HL_8VOR_039No text annotation
HL_8VOR_041No text annotation
HL_8VOR_043T-loop with 2 stacked bulged bases
HL_8VOR_044No text annotation
HL_8VOR_045T-loop with unstacked turn
HL_8VOR_046No text annotation
HL_8VOR_047Pseudoknot geometry
HL_8VOR_049GNRA
HL_8VOR_050No text annotation
HL_8VOR_052No text annotation
HL_8VOR_053GNRA
HL_8VOR_054No text annotation
HL_8VOR_055GNRA wlth tandem sheared
HL_8VOR_057No text annotation
HL_8VOR_058No text annotation
HL_8VOR_060No text annotation
HL_8VOR_061GNRA wlth tandem sheared
HL_8VOR_062No text annotation
HL_8VOR_063GNRA
HL_8VOR_064T-loop with 2 stacked bulged bases
HL_8VOR_066GNRA
HL_8VOR_067No text annotation
HL_8VOR_068Mini UNCG with extended bulge
HL_8VOR_069Pseudoknot geometry with 3' bulge
HL_8VOR_070UNCG
HL_8VOR_071Mini UNCG
HL_8VOR_072GNRA
HL_8VOR_073UNCG
HL_8VOR_074No text annotation
HL_8VOR_075No text annotation
HL_8VOR_077GNRA related
HL_8VOR_078GNRA variation
HL_8VOR_079No text annotation
HL_8VOR_080UNCG
HL_8VOR_081No text annotation
HL_8VOR_083No text annotation
HL_8VOR_084Pseudoknot geometry
HL_8VOR_085GNRA
HL_8VOR_086GNRA
HL_8VOR_087No text annotation
HL_8VOR_088No text annotation
HL_8VOR_089GNRA variation
HL_8VOR_091GNRA
HL_8VOR_092Ribsomal LSU H95
HL_8VOR_093No text annotation
HL_8VOR_094No text annotation
HL_8VOR_095No text annotation
HL_8VOR_096GNRA
HL_8VOR_097No text annotation
HL_8VOR_098No text annotation
HL_8VOR_099Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8VOR_0011/D/30:32,
1/D/552:553		Single bulged G
geometric
IL_4LFB_001
IL_28408.2
IL_8VOR_0031/D/47:52,
1/D/359:361		No text annotation
geometric
IL_5J7L_003
NA
IL_8VOR_0121/D/242:247,
1/D/277:284		Kink-turn with non-sequential stacking
geometric
IL_5J7L_014
NA
IL_8VOR_0141/D/292:293,
1/D/304:308		C-loop
geometric
IL_4LFB_013
IL_06671.1
IL_8VOR_0221/D/504:511,
1/D/540:541		SSU/LSU pseudoknot
geometric
IL_5J7L_024
NA
IL_8VOR_0231/D/569:575,
1/D/880:881		No text annotation
geometric
IL_5J7L_026
NA
IL_8VOR_0241/D/580:584,
1/D/757:761		tSH-tHW-tHS
geometric
IL_5J7L_027
NA
IL_8VOR_0331/D/774:778,
1/D/804:805		Left turn
geometric
IL_4LFB_032
IL_29346.3
IL_8VOR_0341/D/779:783,
1/D/799:803		tSH-tHW-tHS
geometric
IL_5J7L_037
NA
IL_8VOR_0351/D/887:894,
1/D/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
geometric
IL_5J7L_038
NA
IL_8VOR_0361/D/922:923,
1/D/1393:1395		Single bulged A
geometric
IL_5J7L_039
NA
IL_8VOR_0371/D/925:927,
1/D/1390:1391		Single bulged G
geometric
IL_5J7L_040
NA
IL_8VOR_0381/D/933:935,
1/D/1380:1384		Minor groove platform
geometric
IL_5J7L_041
NA
IL_8VOR_0451/D/1060:1061,
1/D/1195:1197		Single bulged A
geometric
IL_5J7L_049
NA
IL_8VOR_0461/D/1061:1063,
1/D/1193:1195		Isolated non-canonical cWW pair
geometric
IL_4LFB_047
IL_68118.2
IL_8VOR_0531/D/1399:1401,
1/D/1501:1504		No text annotation
geometric
IL_5J7L_058
NA
IL_8VOR_0541/D/1412:1414,
1/D/1486:1488		Isolated non-canonical cWW pair
geometric
IL_5J7L_061
NA
IL_8VOR_0551/D/1416:1419,
1/D/1481:1484		Double sheared
geometric
IL_5J7L_062
NA
IL_8VOR_0691/a/481:484,
1/a/496:509		No text annotation
geometric
IL_5J7L_255
NA
IL_8VOR_0711/a/564:566,
1/a/575:577		Isolated non-canonical cWW pair
geometric
IL_5J7L_257
NA
IL_8VOR_0731/a/672:674,
1/a/806:808		Isolated non-canonical cWW pair
geometric
IL_5J7L_259
NA
IL_8VOR_0741/a/674:678,
1/a/799:806		tHW-tHW cross-strand stack
geometric
IL_5J7L_260
NA
IL_8VOR_0781/a/738:740,
1/a/757:758		Major groove platform
geometric
IL_5J7L_264
NA
IL_8VOR_0791/a/741:742,
1/a/754:756		Single stack bend
geometric
IL_8P9A_328
IL_15011.2
IL_8VOR_0801/a/742:744,
1/a/753:754		Single stack bend
geometric
IL_4V84_420
NA
IL_8VOR_0811/a/775:777,
1/a/787:791		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_8VOR_1061/a/1262:1269,
1/a/2011:2017		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_289
NA
IL_8VOR_1231/a/1651:1656,
1/a/2004:2006		No text annotation
geometric
IL_5J7L_304
NA
IL_8VOR_1241/a/1663:1665,
1/a/1995:1997		Isolated tWW turn
geometric
IL_5J7L_305
NA
IL_8VOR_1261/a/1666:1674,
1/a/1990:1994		No text annotation
geometric
IL_5J7L_386
NA
IL_8VOR_1271/a/1669:1674,
1/a/1990:1993		Intercalated tWH
geometric
IL_5J7L_307
NA
IL_8VOR_1391/a/2050:2052,
1/a/2617:2618		Major groove platform
geometric
IL_5J7L_320
NA
IL_8VOR_1401/a/2054:2056,
1/a/2612:2615		No text annotation
geometric
IL_5J7L_321
NA
IL_8VOR_1411/a/2070:2071,
1/a/2438:2441		Minor groove platform
geometric
IL_9DFE_081
IL_34520.2
IL_8VOR_1541/a/2510:2512,
1/a/2574:2578		Isolated non-canonical cWW with bulges
geometric
IL_5J7L_340
NA
IL_8VOR_1551/a/2512:2513,
1/a/2571:2574		No text annotation
geometric
IL_5J7L_341
NA
IL_8VOR_1571/a/2591:2592,
1/a/2601:2603		Single bulged A
geometric
IL_1U9S_001
IL_14190.2

Problematic loops

#loop idProblemSequence
IL_8VOR_002Single bulged A
IL_8VOR_004Minor groove platform
IL_8VOR_005Multiple bulged bases
IL_8VOR_006Minor groove platform with extra cWW
IL_8VOR_007Minor groove platform
IL_8VOR_008Single bulged G
IL_8VOR_009Isolated non-canonical cWW pair
IL_8VOR_010Minor groove platform related
IL_8VOR_011No text annotation
IL_8VOR_013No text annotation
IL_8VOR_015Single bulged U
IL_8VOR_016C-loop
IL_8VOR_017Single bulged G
IL_8VOR_018No text annotation
IL_8VOR_019No text annotation
IL_8VOR_020tSH-tHW-tWW
IL_8VOR_021No text annotation
IL_8VOR_025Major groove platform
IL_8VOR_026Major groove minor groove platform; mini C-loop
IL_8VOR_027No text annotation
IL_8VOR_028Major groove platform; stack outside cWW
IL_8VOR_029Single stack bend
IL_8VOR_030Tandem non-canonical cWW pairs
IL_8VOR_031No text annotation
IL_8VOR_032Kink-turn
IL_8VOR_039Minor groove platform
IL_8VOR_040Minor groove platform
IL_8VOR_041No text annotation
IL_8VOR_042Single bulged U
IL_8VOR_043Isolated cWS basepair
IL_8VOR_044Minor groove platform
IL_8VOR_047No text annotation
IL_8VOR_048Minor groove platform
IL_8VOR_049No text annotation
IL_8VOR_050No text annotation
IL_8VOR_051No text annotation
IL_8VOR_052No text annotation
IL_8VOR_056Triple sheared related
IL_8VOR_057Single bulged A
IL_8VOR_058No text annotation
IL_8VOR_059Triple sheared with non-canonical cWW
IL_8VOR_060Single bulged A
IL_8VOR_061Minor groove platform
IL_8VOR_062No text annotation
IL_8VOR_063Single stack bend
IL_8VOR_0648x7 Sarcin-Ricin; G-bulge
IL_8VOR_0657x6 Sarcin-Ricin; G-bulge
IL_8VOR_066No text annotation
IL_8VOR_067No text annotation
IL_8VOR_068No text annotation
IL_8VOR_070Double sheared
IL_8VOR_072AAA cross-strand stack
IL_8VOR_075Single bulged A
IL_8VOR_076Single bulged G
IL_8VOR_077Triple sheared
IL_8VOR_08290 degree turn
IL_8VOR_083No text annotation
IL_8VOR_084Stack outside cWW
IL_8VOR_085Single stack bend
IL_8VOR_0867x7 Sarcin-Ricin with intercalated A; G-bulge
IL_8VOR_087Single bulged G
IL_8VOR_088C-loop with bulged stacked A's
IL_8VOR_089Isolated non-canonical cWW pair
IL_8VOR_090Double sheared with non-canonical cWW
IL_8VOR_091No text annotation
IL_8VOR_092Single bulged C
IL_8VOR_093UAA/GAN
IL_8VOR_094SSU/LSU pseudoknot
IL_8VOR_095Single bulged U
IL_8VOR_096Kink-turn related
IL_8VOR_097No text annotation
IL_8VOR_098Isolated non-canonical cWW pair
IL_8VOR_099Tandem non-canonical cWW pairs
IL_8VOR_100Kink-turn
IL_8VOR_101No text annotation
IL_8VOR_102Major groove platform
IL_8VOR_103Isolated cWS basepair
IL_8VOR_104No text annotation
IL_8VOR_105Kink-turn
IL_8VOR_107Major groove platform; stack outside cWW
IL_8VOR_108C-loop
IL_8VOR_109UAA/GAN
IL_8VOR_110tSH-tHW-tHS
IL_8VOR_111Single stack bend
IL_8VOR_112Single stack bend
IL_8VOR_113No text annotation
IL_8VOR_114UAA/GAN
IL_8VOR_115Tandem non-canonical cWW pairs
IL_8VOR_116tSH-tHW
IL_8VOR_117Single bulged U
IL_8VOR_118No text annotation
IL_8VOR_119tSH-tHW-tHS
IL_8VOR_120180 degree turn
IL_8VOR_121Single bulged A
IL_8VOR_122UAA/GAN variation
IL_8VOR_125Major groove platform; stack outside cWW
IL_8VOR_128tSH-tSH-tHH-tHS
IL_8VOR_1296x5 Sarcin-Ricin; G-bulge
IL_8VOR_130Triple sheared
IL_8VOR_131Single bulged A
IL_8VOR_132Kink-turn related
IL_8VOR_133Minor groove platform, major groove intercalation
IL_8VOR_134Major groove intercalation
IL_8VOR_135Major groove minor groove platform; mini C-loop
IL_8VOR_136No text annotation
IL_8VOR_137UAA/GAN related
IL_8VOR_138Bulged stacked bases
IL_8VOR_142Isolated tHS basepair with bulges
IL_8VOR_143Isolated non-canonical cWW pair
IL_8VOR_144Isolated non-canonical cWW pair
IL_8VOR_145Isolated non-canonical cWW pair
IL_8VOR_146No text annotation
IL_8VOR_147No text annotation
IL_8VOR_148Kink-turn
IL_8VOR_149Single bulged U
IL_8VOR_150Double sheared
IL_8VOR_151No text annotation
IL_8VOR_152Major groove minor groove platform with extra cWW
IL_8VOR_153Double sheared with non-canonical cWW
IL_8VOR_156Major groove platform with intercalation
IL_8VOR_158tSH-tHS-tHW
IL_8VOR_159Sarcin-Ricin target in LSU H95; G-bulge
IL_8VOR_160C-loop
IL_8VOR_161UAA/GAN related, with intercalation
IL_8VOR_162Multiple bulged bases
IL_8VOR_163UAA/GAN with extra cWW
IL_8VOR_164No text annotation
IL_8VOR_165Major groove intercalation
IL_8VOR_166Multiple bulged bases with non-canonical cWW
IL_8VOR_167tHS double platform
IL_8VOR_168Major groove intercalation
IL_8VOR_169No text annotation
IL_8VOR_170Major groove minor groove platform; mini C-loop
IL_8VOR_171Symmetric double minor groove platform
IL_8VOR_172Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8VOR_0021/D/46:52,
1/D/359:367,
1/D/393:395		No text annotation
geometric
J3_5J7L_050
NA
J3_8VOR_0061/D/826:829,
1/D/857:861,
1/D/868:874		No text annotation
geometric
J3_5J7L_004
NA
J3_8VOR_0121/D/1063:1068,
1/D/1107:1113,
1/D/1187:1193		No text annotation
geometric
J3_5J7L_008
NA
J3_8VOR_0131/D/1073:1074,
1/D/1083:1087,
1/D/1098:1102		No text annotation
J3_8VOR_0171/a/30:31,
1/a/474:481,
1/a/509:510		No text annotation
geometric
J3_5J7L_036
NA
J3_8VOR_0181/a/30:31,
1/a/474:484,
1/a/496:510		No text annotation
geometric
J3_5J7L_066
NA
J3_8VOR_0191/a/32:35,
1/a/445:461,
1/a/468:473		No text annotation
geometric
J3_5J7L_067
NA
J3_8VOR_0221/a/683:689,
1/a/773:775,
1/a/791:794		No text annotation
geometric
J3_5J7L_038
NA
J3_8VOR_0261/a/1306:1309,
1/a/1605:1611,
1/a/1620:1622		No text annotation
geometric
J3_7A0S_007
J3_47341.1
J4_8VOR_0051/D/575:577,
1/D/764:769,
1/D/810:821,
1/D/879:880		No text annotation
J4_8VOR_0091/a/1270:1276,
1/a/1294:1295,
1/a/1645:1648,
1/a/2009:2010		No text annotation
J5_8VOR_0051/a/531:533,
1/a/560:564,
1/a/577:579,
1/a/1261:1262,
1/a/2017:2018		No text annotation
J5_8VOR_0061/a/584:589,
1/a/668:671,
1/a/809:812,
1/a/1195:1196,
1/a/1250:1256		No text annotation
J7_8VOR_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_8VOR_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_8VOR_001No text annotation
J3_8VOR_003No text annotation
J3_8VOR_004No text annotation
J3_8VOR_005No text annotation
J3_8VOR_007No text annotation
J3_8VOR_008No text annotation
J3_8VOR_009No text annotation
J3_8VOR_010No text annotation
J3_8VOR_011No text annotation
J3_8VOR_014No text annotation
J3_8VOR_015No text annotation
J3_8VOR_016No text annotation
J3_8VOR_020No text annotation
J3_8VOR_021No text annotation
J3_8VOR_023No text annotation
J3_8VOR_024No text annotation
J3_8VOR_025No text annotation
J3_8VOR_027No text annotation
J3_8VOR_028No text annotation
J3_8VOR_029Kink-turn 3-way junction
J3_8VOR_030No text annotation
J3_8VOR_031No text annotation
J3_8VOR_032No text annotation
J3_8VOR_033No text annotation
J3_8VOR_034No text annotation
J3_8VOR_035No text annotation
J4_8VOR_001No text annotation
J4_8VOR_002No text annotation
J4_8VOR_003No text annotation
J4_8VOR_004No text annotation
J4_8VOR_006No text annotation
J4_8VOR_007No text annotation
J4_8VOR_008No text annotation
J4_8VOR_010No text annotation
J4_8VOR_011No text annotation
J4_8VOR_012No text annotation
J4_8VOR_013No text annotation
J4_8VOR_014No text annotation
J4_8VOR_015No text annotation
J5_8VOR_001No text annotation
J5_8VOR_002No text annotation
J5_8VOR_003No text annotation
J5_8VOR_004No text annotation
J5_8VOR_007No text annotation
J6_8VOR_001No text annotation

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