RNA 3D Hub //

9H3R Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9H3R_0011/A/59:68No text annotation
homologous
HL_5J7L_134
NA
HL_9H3R_0101/A/327:335T-loop with unstacked turn
homologous
HL_5J7L_144
NA
HL_9H3R_0131/A/462:467GNRA
homologous
HL_4WF9_015
HL_34789.1
HL_9H3R_0171/A/611:617No text annotation
geometric
HL_5J7L_151
NA
HL_9H3R_0231/A/978:985No text annotation
homologous
HL_9DFE_026
HL_47171.1

Problematic loops

#loop idProblemSequence
HL_9H3R_002No text annotation
HL_9H3R_003No text annotation
HL_9H3R_004Externally structured
HL_9H3R_005No text annotation
HL_9H3R_006No text annotation
HL_9H3R_007No text annotation
HL_9H3R_008No text annotation
HL_9H3R_009T-loop with 2 stacked bulged bases
HL_9H3R_011No text annotation
HL_9H3R_012Pseudoknot geometry
HL_9H3R_014GNRA
HL_9H3R_015No text annotation
HL_9H3R_016T-loop with 2 stacked bulged bases
HL_9H3R_018GNRA
HL_9H3R_019No text annotation
HL_9H3R_020GNRA wlth tandem sheared
HL_9H3R_021No text annotation
HL_9H3R_022GNRA
HL_9H3R_024No text annotation
HL_9H3R_025GNRA wlth tandem sheared
HL_9H3R_026No text annotation
HL_9H3R_027GNRA
HL_9H3R_028T-loop with 2 stacked bulged bases
HL_9H3R_029Pseudoknot geometry with 3' bulge
HL_9H3R_030GNRA
HL_9H3R_031No text annotation
HL_9H3R_032Mini UNCG with extended bulge
HL_9H3R_033Pseudoknot geometry with 3' bulge
HL_9H3R_034No text annotation
HL_9H3R_035Mini UNCG
HL_9H3R_036No text annotation
HL_9H3R_037GNRA
HL_9H3R_038No text annotation
HL_9H3R_039No text annotation
HL_9H3R_040No text annotation
HL_9H3R_041No text annotation
HL_9H3R_042No text annotation
HL_9H3R_043No text annotation
HL_9H3R_044No text annotation
HL_9H3R_045Pseudoknot geometry
HL_9H3R_046GNRA
HL_9H3R_047GNRA
HL_9H3R_048No text annotation
HL_9H3R_049No text annotation
HL_9H3R_050GNRA variation
HL_9H3R_051No text annotation
HL_9H3R_052No text annotation
HL_9H3R_053GNRA
HL_9H3R_054Ribsomal LSU H95
HL_9H3R_055No text annotation
HL_9H3R_056No text annotation
HL_9H3R_057No text annotation
HL_9H3R_058Externally structured
HL_9H3R_059No text annotation
HL_9H3R_060Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9H3R_0021/A/36:37,
1/A/442:444		Single bulged A
homologous
IL_5J7L_246
NA
IL_9H3R_0041/A/82:85,
1/A/97:104		No text annotation
IL_9H3R_0061/A/188:194,
1/A/201:208		8x7 Sarcin-Ricin; G-bulge
homologous
IL_7A0S_006
IL_62167.1
IL_9H3R_0121/A/481:484,
1/A/496:509		No text annotation
homologous
IL_9DFE_012
IL_44923.1
IL_9H3R_0211/A/844:848,
1/A/930:934		No text annotation
homologous
IL_5J7L_399
NA
IL_9H3R_0221/A/847:848,
1/A/930:933		Stack outside cWW
homologous
IL_5J7L_268
NA
IL_9H3R_0291/A/994:996,
1/A/1159:1160		Single bulged C
homologous
IL_4WF9_035
IL_05642.1
IL_9H3R_0341/A/1024:1030,
1/A/1124:1140		No text annotation
homologous
IL_5J7L_281
NA

Problematic loops

#loop idProblemSequence
IL_9H3R_001Triple sheared with non-canonical cWW
IL_9H3R_003Minor groove platform
IL_9H3R_005Single stack bend
IL_9H3R_0077x6 Sarcin-Ricin; G-bulge
IL_9H3R_008No text annotation
IL_9H3R_009Single stack bend
IL_9H3R_010No text annotation
IL_9H3R_011No text annotation
IL_9H3R_013Double sheared
IL_9H3R_014Isolated non-canonical cWW pair
IL_9H3R_015AAA cross-strand stack
IL_9H3R_016Isolated non-canonical cWW pair
IL_9H3R_017tHW-tHW cross-strand stack
IL_9H3R_018No text annotation
IL_9H3R_019No text annotation
IL_9H3R_02090 degree turn
IL_9H3R_023Single stack bend
IL_9H3R_024No text annotation
IL_9H3R_025Single bulged G
IL_9H3R_026C-loop
IL_9H3R_027Isolated non-canonical cWW pair
IL_9H3R_028Double sheared with non-canonical cWW
IL_9H3R_030UAA/GAN
IL_9H3R_031SSU/LSU pseudoknot
IL_9H3R_032Single bulged U
IL_9H3R_033Kink-turn related
IL_9H3R_035Isolated non-canonical cWW pair
IL_9H3R_036Tandem non-canonical cWW pairs
IL_9H3R_037Kink-turn
IL_9H3R_038Isolated cWS basepair
IL_9H3R_039No text annotation
IL_9H3R_040Kink-turn
IL_9H3R_041Major groove platform; stack outside cWW
IL_9H3R_042C-loop
IL_9H3R_043Single stack bend
IL_9H3R_044UAA/GAN
IL_9H3R_045No text annotation
IL_9H3R_046tSH-tHW-tHS
IL_9H3R_047No text annotation
IL_9H3R_048UAA/GAN
IL_9H3R_049Tandem non-canonical cWW pairs
IL_9H3R_050tSH-tHW
IL_9H3R_051Single bulged U
IL_9H3R_052No text annotation
IL_9H3R_053tSH-tHW-tHS
IL_9H3R_054180 degree turn
IL_9H3R_055Single bulged A
IL_9H3R_056UAA/GAN variation
IL_9H3R_0576x5 Sarcin-Ricin; G-bulge
IL_9H3R_058Triple sheared with non-canonical cWW
IL_9H3R_059Major groove platform
IL_9H3R_060No text annotation
IL_9H3R_061Single bulged U
IL_9H3R_062Minor groove platform
IL_9H3R_063Isolated tHS basepair with bulges
IL_9H3R_064Tandem non-canonical cWW pairs
IL_9H3R_065Isolated non-canonical cWW pair
IL_9H3R_066No text annotation
IL_9H3R_067No text annotation
IL_9H3R_068No text annotation
IL_9H3R_069No text annotation
IL_9H3R_070Single bulged U
IL_9H3R_071Double sheared
IL_9H3R_072No text annotation
IL_9H3R_073No text annotation
IL_9H3R_074Major groove platform
IL_9H3R_075No text annotation
IL_9H3R_076Double sheared with non-canonical cWW
IL_9H3R_077Major groove platform
IL_9H3R_078No text annotation
IL_9H3R_079No text annotation
IL_9H3R_080Single bulged A
IL_9H3R_081No text annotation
IL_9H3R_082Sarcin-Ricin target in LSU H95; G-bulge
IL_9H3R_083C-loop
IL_9H3R_084UAA/GAN related, with intercalation
IL_9H3R_085Multiple bulged bases
IL_9H3R_086UAA/GAN with extra cWW
IL_9H3R_087Single bulged A
IL_9H3R_088No text annotation
IL_9H3R_089Major groove intercalation
IL_9H3R_090Multiple bulged bases with non-canonical cWW
IL_9H3R_091tHS double platform
IL_9H3R_092Major groove intercalation
IL_9H3R_093No text annotation
IL_9H3R_094Major groove minor groove platform; mini C-loop
IL_9H3R_095Symmetric double minor groove platform
IL_9H3R_096Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9H3R_0011/A/30:31,
1/A/474:481,
1/A/509:510		No text annotation
homologous
J3_5J7L_036
NA
J3_9H3R_0021/A/32:35,
1/A/445:461,
1/A/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_9H3R_0041/A/297:301,
1/A/316:325,
1/A/337:341		No text annotation
homologous
J3_5J7L_068
NA
J3_9H3R_0071/A/1306:1309,
1/A/1605:1611,
1/A/1620:1622		No text annotation
homologous
J3_5J7L_042
NA
J3_9H3R_0111/A/2282:2284,
1/A/2384:2395,
1/A/2421:2427		No text annotation
homologous
J3_9DFE_015
J3_04772.1
J3_9H3R_0131/A/2517:2520,
1/A/2545:2547,
1/A/2561:2567		No text annotation
homologous
J3_4WF9_009
J3_32601.6
J5_9H3R_0011/A/47:54,
1/A/116:121,
1/A/130:131,
1/A/148:152,
1/A/174:178		No text annotation
J5_9H3R_0031/A/584:589,
1/A/668:671,
1/A/809:812,
1/A/1195:1196,
1/A/1250:1256		No text annotation
J6_9H3R_0011/A/45:46,
1/A/179:183,
1/A/214:224,
1/A/231:235,
1/A/262:266,
1/A/426:433		No text annotation
J6_9H3R_0021/A/2074:2077,
1/A/2243:2246,
1/A/2258:2259,
1/A/2281:2284,
1/A/2384:2395,
1/A/2421:2435		No text annotation
J7_9H3R_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_9H3R_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_9H3R_003No text annotation
J3_9H3R_005No text annotation
J3_9H3R_006No text annotation
J3_9H3R_008No text annotation
J3_9H3R_009No text annotation
J3_9H3R_010Kink-turn 3-way junction
J3_9H3R_012No text annotation
J3_9H3R_014No text annotation
J3_9H3R_015No text annotation
J3_9H3R_016No text annotation
J4_9H3R_001No text annotation
J4_9H3R_002No text annotation
J4_9H3R_003No text annotation
J4_9H3R_004No text annotation
J4_9H3R_005No text annotation
J4_9H3R_006No text annotation
J4_9H3R_007No text annotation
J4_9H3R_008No text annotation
J5_9H3R_002No text annotation
J5_9H3R_004No text annotation
J5_9H3R_005No text annotation

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