RNA 3D Hub //

9H3S Hairpin, Internal, and multi-helix Junction Loop Motifs

Download loops

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
HL_9H3S_0031/A/123:128No text annotation
homologous
HL_5J7L_136
NA
HL_9H3S_0301/A/1324:1330Pseudoknot geometry with 3' bulge
homologous
HL_5J7L_166
NA
HL_9H3S_0431/A/2027:2036No text annotation
homologous
HL_5J7L_183
NA
HL_9H3S_0451/A/2209:2215No text annotation
homologous
HL_4WF9_048
HL_81964.1

Problematic loops

#loop idProblemSequence
HL_9H3S_001No text annotation
HL_9H3S_002No text annotation
HL_9H3S_004Externally structured
HL_9H3S_005No text annotation
HL_9H3S_006No text annotation
HL_9H3S_007No text annotation
HL_9H3S_008No text annotation
HL_9H3S_009T-loop with 2 stacked bulged bases
HL_9H3S_010T-loop with unstacked turn
HL_9H3S_011No text annotation
HL_9H3S_012Pseudoknot geometry
HL_9H3S_013GNRA
HL_9H3S_014GNRA
HL_9H3S_015Mini UNCG with extended bulge
HL_9H3S_016T-loop with 2 stacked bulged bases
HL_9H3S_017No text annotation
HL_9H3S_018GNRA
HL_9H3S_019No text annotation
HL_9H3S_020GNRA wlth tandem sheared
HL_9H3S_021No text annotation
HL_9H3S_022UNCG variation
HL_9H3S_023No text annotation
HL_9H3S_024GNRA
HL_9H3S_025No text annotation
HL_9H3S_026GNRA wlth tandem sheared
HL_9H3S_027No text annotation
HL_9H3S_028GNRA
HL_9H3S_029T-loop with 2 stacked bulged bases
HL_9H3S_031GNRA
HL_9H3S_032No text annotation
HL_9H3S_033Mini UNCG with extended bulge
HL_9H3S_034Pseudoknot geometry with 3' bulge
HL_9H3S_035UNCG
HL_9H3S_036Mini UNCG
HL_9H3S_037No text annotation
HL_9H3S_038GNRA
HL_9H3S_039UNCG
HL_9H3S_040No text annotation
HL_9H3S_041No text annotation
HL_9H3S_042No text annotation
HL_9H3S_044No text annotation
HL_9H3S_046No text annotation
HL_9H3S_047No text annotation
HL_9H3S_048No text annotation
HL_9H3S_049Pseudoknot geometry
HL_9H3S_050GNRA
HL_9H3S_051GNRA
HL_9H3S_052No text annotation
HL_9H3S_053No text annotation
HL_9H3S_054GNRA variation
HL_9H3S_055No text annotation
HL_9H3S_056GNRA
HL_9H3S_057GNRA
HL_9H3S_058Ribsomal LSU H95
HL_9H3S_059No text annotation
HL_9H3S_060Mini UNCG
HL_9H3S_061No text annotation
HL_9H3S_062GNRA
HL_9H3S_063No text annotation
HL_9H3S_064Mini UNCG

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
IL_9H3S_0051/A/183:184,
1/A/212:214		Single stack bend
homologous
IL_7A0S_005
IL_15011.1
IL_9H3S_0141/A/606:610,
1/A/618:622		AAA cross-strand stack
homologous
IL_5J7L_258
NA
IL_9H3S_0361/A/1024:1030,
1/A/1124:1140		No text annotation
homologous
IL_5J7L_281
NA
IL_9H3S_0411/A/1196:1198,
1/A/1247:1250		Isolated cWS basepair
homologous
IL_7A0S_041
IL_42997.4
IL_9H3S_0461/A/1319:1323,
1/A/1331:1333		C-loop
homologous
IL_5J7L_291
NA
IL_9H3S_0571/A/1489:1491,
1/A/1499:1500		Single bulged A
homologous
IL_9DFE_061
IL_14190.1
IL_9H3S_0911/A/2636:2640,
1/A/2774:2782		tSH-tHS-tHW
homologous
IL_5J7L_345
NA
IL_9H3S_0951/A/2695:2696,
1/A/2711:2714		Multiple bulged bases
homologous
IL_5J7L_349
NA
IL_9H3S_0991/A/2838:2839,
1/A/2878:2880		Major groove intercalation
homologous
IL_5J7L_352
NA

Problematic loops

#loop idProblemSequence
IL_9H3S_001Triple sheared with non-canonical cWW
IL_9H3S_002Single bulged A
IL_9H3S_003Minor groove platform
IL_9H3S_004No text annotation
IL_9H3S_0068x7 Sarcin-Ricin; G-bulge
IL_9H3S_0077x6 Sarcin-Ricin; G-bulge
IL_9H3S_008No text annotation
IL_9H3S_009No text annotation
IL_9H3S_010No text annotation
IL_9H3S_011No text annotation
IL_9H3S_012Double sheared
IL_9H3S_013Isolated non-canonical cWW pair
IL_9H3S_015Isolated non-canonical cWW pair
IL_9H3S_016tHW-tHW cross-strand stack
IL_9H3S_017Single bulged A
IL_9H3S_018Single bulged G
IL_9H3S_019Triple sheared
IL_9H3S_020Major groove platform
IL_9H3S_021Multiple bulged bases
IL_9H3S_02290 degree turn
IL_9H3S_023No text annotation
IL_9H3S_024Stack outside cWW
IL_9H3S_025Single stack bend
IL_9H3S_0267x7 Sarcin-Ricin with intercalated A; G-bulge
IL_9H3S_027Single bulged G
IL_9H3S_028C-loop with bulged stacked A's
IL_9H3S_029Isolated non-canonical cWW pair
IL_9H3S_030Double sheared with non-canonical cWW
IL_9H3S_031Single bulged C
IL_9H3S_032UAA/GAN
IL_9H3S_033SSU/LSU pseudoknot
IL_9H3S_034Single bulged U
IL_9H3S_035Kink-turn related
IL_9H3S_037Isolated non-canonical cWW pair
IL_9H3S_038Tandem non-canonical cWW pairs
IL_9H3S_039Kink-turn
IL_9H3S_040No text annotation
IL_9H3S_042No text annotation
IL_9H3S_043Kink-turn
IL_9H3S_0448x7 Sarcin-Ricin; G-bulge
IL_9H3S_045Major groove platform; stack outside cWW
IL_9H3S_047UAA/GAN
IL_9H3S_048tSH-tHW-tHS
IL_9H3S_049No text annotation
IL_9H3S_050UAA/GAN
IL_9H3S_051Tandem non-canonical cWW pairs
IL_9H3S_052tSH-tHW
IL_9H3S_053Single bulged U
IL_9H3S_054No text annotation
IL_9H3S_055tSH-tHW-tHS
IL_9H3S_056180 degree turn
IL_9H3S_058UAA/GAN variation
IL_9H3S_059No text annotation
IL_9H3S_060Isolated tWW turn
IL_9H3S_061Major groove platform; stack outside cWW
IL_9H3S_062No text annotation
IL_9H3S_063Intercalated tWH
IL_9H3S_064tSH-tSH-tHH-tHS
IL_9H3S_0656x5 Sarcin-Ricin; G-bulge
IL_9H3S_066Triple sheared
IL_9H3S_067Single bulged A
IL_9H3S_068Major groove platform
IL_9H3S_069No text annotation
IL_9H3S_070Single bulged U
IL_9H3S_071Minor groove platform
IL_9H3S_072Isolated tHS basepair with bulges
IL_9H3S_073Isolated non-canonical cWW pair
IL_9H3S_074Single stack bend
IL_9H3S_075No text annotation
IL_9H3S_076No text annotation
IL_9H3S_077Single bulged U
IL_9H3S_078No text annotation
IL_9H3S_079Double sheared
IL_9H3S_080Single bulged U
IL_9H3S_081Single stack bend
IL_9H3S_082Major groove platform
IL_9H3S_083Major groove platform
IL_9H3S_084Major groove minor groove platform with extra cWW
IL_9H3S_085Double sheared with non-canonical cWW
IL_9H3S_086Major groove platform
IL_9H3S_087Isolated non-canonical cWW with bulges
IL_9H3S_088No text annotation
IL_9H3S_089Major groove platform with intercalation
IL_9H3S_090Single bulged A
IL_9H3S_092Sarcin-Ricin target in LSU H95; G-bulge
IL_9H3S_093C-loop
IL_9H3S_094UAA/GAN related, with intercalation
IL_9H3S_096UAA/GAN with extra cWW
IL_9H3S_097Single bulged A
IL_9H3S_098No text annotation
IL_9H3S_100Multiple bulged bases with non-canonical cWW
IL_9H3S_101tHS double platform
IL_9H3S_102Major groove intercalation
IL_9H3S_103No text annotation
IL_9H3S_104Major groove minor groove platform; mini C-loop
IL_9H3S_105Symmetric double minor groove platform
IL_9H3S_106Bacterial 5S Loop E

Valid loops

3DLoop idLocationAnnotation; motif groupMapped info
J3_9H3S_0011/A/30:31,
1/A/474:481,
1/A/509:510		No text annotation
homologous
J3_5J7L_036
NA
J3_9H3S_0021/A/32:35,
1/A/445:461,
1/A/468:473		No text annotation
homologous
J3_5J7L_067
NA
J3_9H3S_0031/A/56:57,
1/A/70:76,
1/A/110:114		No text annotation
homologous
J3_5J7L_037
NA
J3_9H3S_0071/A/1298:1303,
1/A/1625:1627,
1/A/1639:1642		No text annotation
homologous
J3_7A0S_006
J3_32852.7
J3_9H3S_0081/A/1306:1309,
1/A/1605:1611,
1/A/1620:1622		No text annotation
homologous
J3_7A0S_007
J3_47341.1
J3_9H3S_0091/A/1344:1349,
1/A/1382:1385,
1/A/1402:1403		No text annotation
homologous
J3_5J7L_043
NA
J4_9H3S_0011/A/268:269,
1/A/370:375,
1/A/399:406,
1/A/421:424		No text annotation
homologous
J4_5J7L_018
NA
J4_9H3S_0041/A/1310:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1604		No text annotation
homologous
J4_5J7L_022
NA
J4_9H3S_0051/A/1313:1314,
1/A/1338:1343,
1/A/1404:1405,
1/A/1597:1603		No text annotation
homologous
J4_5J7L_023
NA
J4_9H3S_0071/A/2285:2289,
1/A/2343:2347,
1/A/2370:2372,
1/A/2381:2383		No text annotation
homologous
J4_5J7L_027
NA
J5_9H3S_0011/A/47:54,
1/A/116:121,
1/A/130:131,
1/A/148:150,
1/A/176:178		No text annotation
homologous
J5_5J7L_013
NA
J5_9H3S_0021/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_9H3S_0031/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
J7_9H3S_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_9H3S_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_9H3S_004No text annotation
J3_9H3S_005No text annotation
J3_9H3S_006No text annotation
J3_9H3S_010No text annotation
J3_9H3S_011Kink-turn 3-way junction
J3_9H3S_012No text annotation
J3_9H3S_013No text annotation
J3_9H3S_014No text annotation
J3_9H3S_015No text annotation
J3_9H3S_016No text annotation
J3_9H3S_017No text annotation
J3_9H3S_018No text annotation
J4_9H3S_002No text annotation
J4_9H3S_003No text annotation
J4_9H3S_006No text annotation
J4_9H3S_008No text annotation
J5_9H3S_004No text annotation
J5_9H3S_005No text annotation
J5_9H3S_006No text annotation
J6_9H3S_001No text annotation
J6_9H3S_002No text annotation

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