RNA 3D Hub //

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

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_8VOS_0071/D/12:22No text annotation
geometric
HL_4LFB_001
HL_31940.1
HL_8VOS_0221/D/786:796No text annotation
geometric
HL_5J7L_017
NA
HL_8VOS_0251/D/897:902GNRA
geometric
HL_4LFB_020
HL_34789.1
HL_8VOS_0271/D/1076:1081GNRA
geometric
HL_5J7L_023
NA
HL_8VOS_0511/a/566:575T-loop with 2 stacked bulged bases
geometric
HL_5J7L_150
NA
HL_8VOS_0561/a/779:785No text annotation
geometric
HL_5J7L_156
NA
HL_8VOS_0651/a/1324:1330Pseudoknot geometry with 3' bulge
geometric
HL_5J7L_166
NA
HL_8VOS_0761/a/1777:1787No text annotation
geometric
HL_5J7L_178
NA
HL_8VOS_0901/a/2594:2599GNRA
geometric
HL_4V9F_065
HL_34789.1

Problematic loops

#loop idProblemSequence
HL_8VOS_001No text annotation
HL_8VOS_002No text annotation
HL_8VOS_003T-loop with 2 stacked bulged bases
HL_8VOS_004No text annotation
HL_8VOS_005No text annotation
HL_8VOS_006T-loop with 2 stacked bulged bases
HL_8VOS_008No text annotation
HL_8VOS_009GNRA
HL_8VOS_010GNRA
HL_8VOS_011No text annotation
HL_8VOS_012GNRA related
HL_8VOS_013GNRA
HL_8VOS_014No text annotation
HL_8VOS_015UNCG
HL_8VOS_016GNRA
HL_8VOS_017UNCG
HL_8VOS_018GNRA wlth extra near cWW
HL_8VOS_019GNRA-like with tWH
HL_8VOS_020No text annotation
HL_8VOS_021GNRA
HL_8VOS_023No text annotation
HL_8VOS_024GNRA
HL_8VOS_026GNRA
HL_8VOS_028T-loop related
HL_8VOS_029No text annotation
HL_8VOS_030GNRA
HL_8VOS_031GNRA
HL_8VOS_032T-loop with 3 stacked bulged bases
HL_8VOS_033No text annotation
HL_8VOS_034UNCG
HL_8VOS_035No text annotation
HL_8VOS_036No text annotation
HL_8VOS_037No text annotation
HL_8VOS_038UNCG
HL_8VOS_039No text annotation
HL_8VOS_040No text annotation
HL_8VOS_041No text annotation
HL_8VOS_042No text annotation
HL_8VOS_043T-loop with 2 stacked bulged bases
HL_8VOS_044No text annotation
HL_8VOS_045T-loop with unstacked turn
HL_8VOS_046No text annotation
HL_8VOS_047Pseudoknot geometry
HL_8VOS_048GNRA
HL_8VOS_049GNRA
HL_8VOS_050No text annotation
HL_8VOS_052No text annotation
HL_8VOS_053GNRA
HL_8VOS_054No text annotation
HL_8VOS_055GNRA wlth tandem sheared
HL_8VOS_057No text annotation
HL_8VOS_058No text annotation
HL_8VOS_059No text annotation
HL_8VOS_060No text annotation
HL_8VOS_061GNRA wlth tandem sheared
HL_8VOS_062No text annotation
HL_8VOS_063GNRA
HL_8VOS_064T-loop with 2 stacked bulged bases
HL_8VOS_066GNRA
HL_8VOS_067No text annotation
HL_8VOS_068Mini UNCG with extended bulge
HL_8VOS_069Pseudoknot geometry with 3' bulge
HL_8VOS_070UNCG
HL_8VOS_071Mini UNCG
HL_8VOS_072GNRA
HL_8VOS_073UNCG
HL_8VOS_074No text annotation
HL_8VOS_075No text annotation
HL_8VOS_077GNRA related
HL_8VOS_078GNRA variation
HL_8VOS_079No text annotation
HL_8VOS_080UNCG
HL_8VOS_081No text annotation
HL_8VOS_082No text annotation
HL_8VOS_083No text annotation
HL_8VOS_084Pseudoknot geometry
HL_8VOS_085GNRA
HL_8VOS_086GNRA
HL_8VOS_087No text annotation
HL_8VOS_088No text annotation
HL_8VOS_089GNRA variation
HL_8VOS_091GNRA
HL_8VOS_092Ribsomal LSU H95
HL_8VOS_093No text annotation
HL_8VOS_094No text annotation
HL_8VOS_095No text annotation
HL_8VOS_096GNRA
HL_8VOS_097No text annotation
HL_8VOS_098No text annotation
HL_8VOS_099Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_8VOS_0121/D/242:247,
1/D/277:284		Kink-turn with non-sequential stacking
geometric
IL_5J7L_014
NA
IL_8VOS_0231/D/569:575,
1/D/880:881		No text annotation
geometric
IL_5J7L_026
NA
IL_8VOS_0331/D/774:778,
1/D/804:805		Left turn
geometric
IL_4LFB_032
IL_29346.3
IL_8VOS_0351/D/887:894,
1/D/905:910		8x6 Sarcin-Ricin with inserted Y; G-bulge
geometric
IL_5J7L_038
NA
IL_8VOS_0361/D/922:923,
1/D/1393:1395		Single bulged A
geometric
IL_5J7L_039
NA
IL_8VOS_0381/D/933:935,
1/D/1380:1384		Minor groove platform
geometric
IL_5J7L_041
NA
IL_8VOS_0531/D/1399:1401,
1/D/1501:1504		No text annotation
geometric
IL_5J7L_058
NA
IL_8VOS_0541/D/1412:1414,
1/D/1486:1488		Isolated non-canonical cWW pair
geometric
IL_5J7L_061
NA
IL_8VOS_0551/D/1416:1419,
1/D/1481:1484		Double sheared
geometric
IL_5J7L_062
NA
IL_8VOS_0691/a/481:484,
1/a/496:509		No text annotation
geometric
IL_5J7L_255
NA
IL_8VOS_0711/a/564:566,
1/a/575:577		Isolated non-canonical cWW pair
geometric
IL_5J7L_257
NA
IL_8VOS_0731/a/672:674,
1/a/806:808		Isolated non-canonical cWW pair
geometric
IL_5J7L_259
NA
IL_8VOS_0741/a/674:678,
1/a/799:806		tHW-tHW cross-strand stack
geometric
IL_5J7L_260
NA
IL_8VOS_0791/a/741:742,
1/a/754:756		Single stack bend
geometric
IL_8P9A_328
IL_15011.1
IL_8VOS_0801/a/742:744,
1/a/753:754		Single stack bend
geometric
IL_4V84_420
NA
IL_8VOS_0811/a/775:777,
1/a/787:791		Multiple bulged bases
geometric
IL_5J7L_265
NA
IL_8VOS_1061/a/1262:1269,
1/a/2011:2017		8x7 Sarcin-Ricin; G-bulge
geometric
IL_5J7L_289
NA
IL_8VOS_1261/a/1666:1674,
1/a/1990:1994		No text annotation
geometric
IL_5J7L_386
NA
IL_8VOS_1271/a/1669:1674,
1/a/1990:1993		Intercalated tWH
geometric
IL_5J7L_307
NA
IL_8VOS_1391/a/2050:2052,
1/a/2617:2618		Major groove platform
geometric
IL_5J7L_320
NA
IL_8VOS_1401/a/2054:2056,
1/a/2612:2615		No text annotation
geometric
IL_5J7L_321
NA
IL_8VOS_1411/a/2070:2071,
1/a/2438:2441		Minor groove platform
geometric
IL_9DFE_081
IL_34520.1
IL_8VOS_1541/a/2510:2512,
1/a/2574:2578		Isolated non-canonical cWW with bulges
geometric
IL_5J7L_340
NA
IL_8VOS_1551/a/2512:2513,
1/a/2571:2574		No text annotation
geometric
IL_5J7L_341
NA
IL_8VOS_1571/a/2591:2592,
1/a/2601:2603		Single bulged A
geometric
IL_1U9S_001
NA

Problematic loops

#loop idProblemSequence
IL_8VOS_001Single bulged G
IL_8VOS_002Single bulged A
IL_8VOS_003No text annotation
IL_8VOS_004Minor groove platform
IL_8VOS_005Multiple bulged bases
IL_8VOS_006Minor groove platform with extra cWW
IL_8VOS_007Minor groove platform
IL_8VOS_008Single bulged G
IL_8VOS_009Isolated non-canonical cWW pair
IL_8VOS_010Minor groove platform related
IL_8VOS_011No text annotation
IL_8VOS_013No text annotation
IL_8VOS_014C-loop
IL_8VOS_015Single bulged U
IL_8VOS_016C-loop
IL_8VOS_017Single bulged G
IL_8VOS_018No text annotation
IL_8VOS_019No text annotation
IL_8VOS_020tSH-tHW-tWW
IL_8VOS_021No text annotation
IL_8VOS_022SSU/LSU pseudoknot
IL_8VOS_024tSH-tHW-tHS
IL_8VOS_025Major groove platform
IL_8VOS_026Major groove minor groove platform; mini C-loop
IL_8VOS_027No text annotation
IL_8VOS_028Major groove platform; stack outside cWW
IL_8VOS_029Single stack bend
IL_8VOS_030Tandem non-canonical cWW pairs
IL_8VOS_031No text annotation
IL_8VOS_032Kink-turn
IL_8VOS_034tSH-tHW-tHS
IL_8VOS_037Single bulged G
IL_8VOS_039Minor groove platform
IL_8VOS_040Minor groove platform
IL_8VOS_041No text annotation
IL_8VOS_042Single bulged U
IL_8VOS_043Isolated cWS basepair
IL_8VOS_044Minor groove platform
IL_8VOS_045Single bulged A
IL_8VOS_046Isolated non-canonical cWW pair
IL_8VOS_047No text annotation
IL_8VOS_048Minor groove platform
IL_8VOS_049No text annotation
IL_8VOS_050No text annotation
IL_8VOS_051No text annotation
IL_8VOS_052No text annotation
IL_8VOS_056Triple sheared related
IL_8VOS_057Single bulged A
IL_8VOS_058No text annotation
IL_8VOS_059Triple sheared with non-canonical cWW
IL_8VOS_060Single bulged A
IL_8VOS_061Minor groove platform
IL_8VOS_062No text annotation
IL_8VOS_063Single stack bend
IL_8VOS_0648x7 Sarcin-Ricin; G-bulge
IL_8VOS_0657x6 Sarcin-Ricin; G-bulge
IL_8VOS_066No text annotation
IL_8VOS_067No text annotation
IL_8VOS_068No text annotation
IL_8VOS_070Double sheared
IL_8VOS_072AAA cross-strand stack
IL_8VOS_075Single bulged A
IL_8VOS_076Single bulged G
IL_8VOS_077Triple sheared
IL_8VOS_078Major groove platform
IL_8VOS_08290 degree turn
IL_8VOS_083No text annotation
IL_8VOS_084Stack outside cWW
IL_8VOS_085Single stack bend
IL_8VOS_0867x7 Sarcin-Ricin with intercalated A; G-bulge
IL_8VOS_087Single bulged G
IL_8VOS_088C-loop with bulged stacked A's
IL_8VOS_089Isolated non-canonical cWW pair
IL_8VOS_090Double sheared with non-canonical cWW
IL_8VOS_091No text annotation
IL_8VOS_092Single bulged C
IL_8VOS_093UAA/GAN
IL_8VOS_094SSU/LSU pseudoknot
IL_8VOS_095Single bulged U
IL_8VOS_096Kink-turn related
IL_8VOS_097No text annotation
IL_8VOS_098Isolated non-canonical cWW pair
IL_8VOS_099Tandem non-canonical cWW pairs
IL_8VOS_100Kink-turn
IL_8VOS_101No text annotation
IL_8VOS_102Major groove platform
IL_8VOS_103Isolated cWS basepair
IL_8VOS_104No text annotation
IL_8VOS_105Kink-turn
IL_8VOS_107Major groove platform; stack outside cWW
IL_8VOS_108C-loop
IL_8VOS_109UAA/GAN
IL_8VOS_110tSH-tHW-tHS
IL_8VOS_111Single stack bend
IL_8VOS_112Single stack bend
IL_8VOS_113No text annotation
IL_8VOS_114UAA/GAN
IL_8VOS_115Tandem non-canonical cWW pairs
IL_8VOS_116tSH-tHW
IL_8VOS_117Single bulged U
IL_8VOS_118No text annotation
IL_8VOS_119tSH-tHW-tHS
IL_8VOS_120180 degree turn
IL_8VOS_121Single bulged A
IL_8VOS_122UAA/GAN variation
IL_8VOS_123No text annotation
IL_8VOS_124Isolated tWW turn
IL_8VOS_125Major groove platform; stack outside cWW
IL_8VOS_128tSH-tSH-tHH-tHS
IL_8VOS_1296x5 Sarcin-Ricin; G-bulge
IL_8VOS_130Triple sheared
IL_8VOS_131Single bulged A
IL_8VOS_132Kink-turn related
IL_8VOS_133Minor groove platform, major groove intercalation
IL_8VOS_134Major groove intercalation
IL_8VOS_135Major groove minor groove platform; mini C-loop
IL_8VOS_136No text annotation
IL_8VOS_137UAA/GAN related
IL_8VOS_138Bulged stacked bases
IL_8VOS_142Isolated tHS basepair with bulges
IL_8VOS_143Isolated non-canonical cWW pair
IL_8VOS_144Isolated non-canonical cWW pair
IL_8VOS_145Isolated non-canonical cWW pair
IL_8VOS_146No text annotation
IL_8VOS_147No text annotation
IL_8VOS_148Kink-turn
IL_8VOS_149Single bulged U
IL_8VOS_150Double sheared
IL_8VOS_151No text annotation
IL_8VOS_152Major groove minor groove platform with extra cWW
IL_8VOS_153Double sheared with non-canonical cWW
IL_8VOS_156Major groove platform with intercalation
IL_8VOS_158tSH-tHS-tHW
IL_8VOS_159Sarcin-Ricin target in LSU H95; G-bulge
IL_8VOS_160C-loop
IL_8VOS_161UAA/GAN related, with intercalation
IL_8VOS_162Multiple bulged bases
IL_8VOS_163UAA/GAN with extra cWW
IL_8VOS_164No text annotation
IL_8VOS_165Major groove intercalation
IL_8VOS_166Multiple bulged bases with non-canonical cWW
IL_8VOS_167tHS double platform
IL_8VOS_168Major groove intercalation
IL_8VOS_169No text annotation
IL_8VOS_170Major groove minor groove platform; mini C-loop
IL_8VOS_171Symmetric double minor groove platform
IL_8VOS_172Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_8VOS_0061/D/826:829,
1/D/857:861,
1/D/868:874		No text annotation
geometric
J3_5J7L_004
NA
J3_8VOS_0121/D/1063:1068,
1/D/1107:1113,
1/D/1187:1193		No text annotation
geometric
J3_5J7L_008
NA
J3_8VOS_0171/a/30:31,
1/a/474:481,
1/a/509:510		No text annotation
geometric
J3_5J7L_036
NA
J3_8VOS_0181/a/30:31,
1/a/474:484,
1/a/496:510		No text annotation
geometric
J3_5J7L_066
NA
J3_8VOS_0191/a/32:35,
1/a/445:461,
1/a/468:473		No text annotation
geometric
J3_5J7L_067
NA
J3_8VOS_0221/a/683:689,
1/a/773:775,
1/a/791:794		No text annotation
geometric
J3_5J7L_038
NA
J3_8VOS_0261/a/1306:1309,
1/a/1605:1611,
1/a/1620:1622		No text annotation
geometric
J3_7A0S_007
J3_47341.1
J4_8VOS_0031/D/115:122,
1/D/239:240,
1/D/286:289,
1/D/311:312		No text annotation
J4_8VOS_0051/D/575:577,
1/D/764:769,
1/D/810:821,
1/D/879:880		No text annotation
J4_8VOS_0091/a/1270:1276,
1/a/1294:1295,
1/a/1645:1648,
1/a/2009:2010		No text annotation
J4_8VOS_0131/a/1772:1776,
1/a/1788:1792,
1/a/1827:1830,
1/a/1975:1979		No text annotation
J5_8VOS_0051/a/531:533,
1/a/560:564,
1/a/577:579,
1/a/1261:1262,
1/a/2017:2018		No text annotation
J5_8VOS_0061/a/584:589,
1/a/668:671,
1/a/809:812,
1/a/1195:1196,
1/a/1250:1256		No text annotation
J7_8VOS_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_8VOS_001No text annotation
J3_8VOS_002No text annotation
J3_8VOS_003No text annotation
J3_8VOS_004No text annotation
J3_8VOS_005No text annotation
J3_8VOS_007No text annotation
J3_8VOS_008No text annotation
J3_8VOS_009No text annotation
J3_8VOS_010No text annotation
J3_8VOS_011No text annotation
J3_8VOS_013No text annotation
J3_8VOS_014No text annotation
J3_8VOS_015No text annotation
J3_8VOS_016No text annotation
J3_8VOS_020No text annotation
J3_8VOS_021No text annotation
J3_8VOS_023No text annotation
J3_8VOS_024No text annotation
J3_8VOS_025No text annotation
J3_8VOS_027No text annotation
J3_8VOS_028No text annotation
J3_8VOS_029Kink-turn 3-way junction
J3_8VOS_030No text annotation
J3_8VOS_031No text annotation
J3_8VOS_032No text annotation
J3_8VOS_033No text annotation
J3_8VOS_034No text annotation
J3_8VOS_035No text annotation
J4_8VOS_001No text annotation
J4_8VOS_002No text annotation
J4_8VOS_004No text annotation
J4_8VOS_006No text annotation
J4_8VOS_007No text annotation
J4_8VOS_008No text annotation
J4_8VOS_010No text annotation
J4_8VOS_011No text annotation
J4_8VOS_012No text annotation
J4_8VOS_014No text annotation
J4_8VOS_015No text annotation
J5_8VOS_001No text annotation
J5_8VOS_002No text annotation
J5_8VOS_003No text annotation
J5_8VOS_004No text annotation
J5_8VOS_007No text annotation
J6_8VOS_001No text annotation
J7_8VOS_002No text annotation

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