9H3Q Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9H3Q_003 | 1/A/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_9H3Q_010 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_9H3Q_017 | 1/A/611:617 | No text annotation | geometric HL_5J7L_151 NA | |
| HL_9H3Q_025 | 1/A/978:985 | No text annotation | homologous HL_9DFE_026 HL_47171.1 | |
| HL_9H3Q_031 | 1/A/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_9H3Q_043 | 1/A/2264:2276 | No text annotation | homologous HL_5J7L_187 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9H3Q_001 | No text annotation | ||
| HL_9H3Q_002 | No text annotation | ||
| HL_9H3Q_004 | No text annotation | ||
| HL_9H3Q_005 | No text annotation | ||
| HL_9H3Q_006 | No text annotation | ||
| HL_9H3Q_007 | No text annotation | ||
| HL_9H3Q_008 | No text annotation | ||
| HL_9H3Q_009 | T-loop with 2 stacked bulged bases | ||
| HL_9H3Q_011 | No text annotation | ||
| HL_9H3Q_012 | Pseudoknot geometry | ||
| HL_9H3Q_013 | GNRA | ||
| HL_9H3Q_014 | GNRA | ||
| HL_9H3Q_015 | No text annotation | ||
| HL_9H3Q_016 | T-loop with 2 stacked bulged bases | ||
| HL_9H3Q_018 | GNRA | ||
| HL_9H3Q_019 | GNRA | ||
| HL_9H3Q_020 | GNRA wlth tandem sheared | ||
| HL_9H3Q_021 | No text annotation | ||
| HL_9H3Q_022 | UNCG variation | ||
| HL_9H3Q_023 | No text annotation | ||
| HL_9H3Q_024 | GNRA | ||
| HL_9H3Q_026 | No text annotation | ||
| HL_9H3Q_027 | No text annotation | ||
| HL_9H3Q_028 | GNRA | ||
| HL_9H3Q_029 | T-loop with 2 stacked bulged bases | ||
| HL_9H3Q_030 | Pseudoknot geometry with 3' bulge | ||
| HL_9H3Q_032 | No text annotation | ||
| HL_9H3Q_033 | Mini UNCG with extended bulge | ||
| HL_9H3Q_034 | Pseudoknot geometry with 3' bulge | ||
| HL_9H3Q_035 | No text annotation | ||
| HL_9H3Q_036 | Mini UNCG | ||
| HL_9H3Q_037 | No text annotation | ||
| HL_9H3Q_038 | GNRA | ||
| HL_9H3Q_039 | No text annotation | ||
| HL_9H3Q_040 | No text annotation | ||
| HL_9H3Q_041 | No text annotation | ||
| HL_9H3Q_042 | No text annotation | ||
| HL_9H3Q_044 | No text annotation | ||
| HL_9H3Q_045 | Pseudoknot geometry | ||
| HL_9H3Q_046 | GNRA | ||
| HL_9H3Q_047 | GNRA | ||
| HL_9H3Q_048 | No text annotation | ||
| HL_9H3Q_049 | No text annotation | ||
| HL_9H3Q_050 | GNRA variation | ||
| HL_9H3Q_051 | No text annotation | ||
| HL_9H3Q_052 | No text annotation | ||
| HL_9H3Q_053 | GNRA | ||
| HL_9H3Q_054 | Ribsomal LSU H95 | ||
| HL_9H3Q_055 | No text annotation | ||
| HL_9H3Q_056 | No text annotation | ||
| HL_9H3Q_057 | No text annotation | ||
| HL_9H3Q_058 | GNRA | ||
| HL_9H3Q_059 | No text annotation | ||
| HL_9H3Q_060 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9H3Q_010 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_9DFE_011 IL_76658.1 | |
| IL_9H3Q_011 | 1/A/481:484, 1/A/496:509 | No text annotation | homologous IL_9DFE_012 IL_44923.1 | |
| IL_9H3Q_016 | 1/A/674:678, 1/A/799:806 | tHW-tHW cross-strand stack | homologous IL_7A0S_015 IL_73855.1 | |
| IL_9H3Q_021 | 1/A/844:847, 1/A/933:934 | 90 degree turn | geometric IL_5J7L_267 NA | |
| IL_9H3Q_022 | 1/A/844:848, 1/A/930:934 | No text annotation | geometric IL_5J7L_399 NA | |
| IL_9H3Q_023 | 1/A/847:848, 1/A/930:933 | Stack outside cWW | homologous IL_5J7L_268 NA | |
| IL_9H3Q_025 | 1/A/856:862, 1/A/915:921 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | homologous IL_5J7L_270 NA | |
| IL_9H3Q_030 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_4WF9_035 IL_05642.2 | |
| IL_9H3Q_031 | 1/A/998:1002, 1/A/1153:1157 | UAA/GAN | homologous IL_5J7L_277 NA | |
| IL_9H3Q_032 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | homologous IL_5J7L_278 NA | |
| IL_9H3Q_041 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_9H3Q_042 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_9H3Q_048 | 1/A/1417:1421, 1/A/1577:1581 | UAA/GAN | homologous IL_5J7L_295 NA | |
| IL_9H3Q_079 | 1/A/2636:2640, 1/A/2774:2782 | tSH-tHS-tHW | homologous IL_7A0S_093 IL_04638.4 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9H3Q_001 | Triple sheared with non-canonical cWW | ||
| IL_9H3Q_002 | Single bulged A | ||
| IL_9H3Q_003 | Minor groove platform | ||
| IL_9H3Q_004 | No text annotation | ||
| IL_9H3Q_005 | Single stack bend | ||
| IL_9H3Q_006 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_9H3Q_007 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_9H3Q_008 | No text annotation | ||
| IL_9H3Q_009 | No text annotation | ||
| IL_9H3Q_012 | Double sheared | ||
| IL_9H3Q_013 | Isolated non-canonical cWW pair | ||
| IL_9H3Q_014 | AAA cross-strand stack | ||
| IL_9H3Q_015 | Isolated non-canonical cWW pair | ||
| IL_9H3Q_017 | Single bulged A | ||
| IL_9H3Q_018 | Quadruple sheared | ||
| IL_9H3Q_019 | Major groove platform | ||
| IL_9H3Q_020 | No text annotation | ||
| IL_9H3Q_024 | Single stack bend | ||
| IL_9H3Q_026 | Single bulged G | ||
| IL_9H3Q_027 | C-loop with bulged stacked A's | ||
| IL_9H3Q_028 | Isolated non-canonical cWW pair | ||
| IL_9H3Q_029 | Double sheared with non-canonical cWW | ||
| IL_9H3Q_033 | Single bulged U | ||
| IL_9H3Q_034 | Kink-turn related | ||
| IL_9H3Q_035 | No text annotation | ||
| IL_9H3Q_036 | Isolated non-canonical cWW pair | ||
| IL_9H3Q_037 | Tandem non-canonical cWW pairs | ||
| IL_9H3Q_038 | No text annotation | ||
| IL_9H3Q_039 | No text annotation | ||
| IL_9H3Q_040 | Isolated cWS basepair | ||
| IL_9H3Q_043 | Major groove platform; stack outside cWW | ||
| IL_9H3Q_044 | C-loop | ||
| IL_9H3Q_045 | UAA/GAN | ||
| IL_9H3Q_046 | tSH-tHW-tHS | ||
| IL_9H3Q_047 | No text annotation | ||
| IL_9H3Q_049 | Tandem non-canonical cWW pairs | ||
| IL_9H3Q_050 | tSH-tHW | ||
| IL_9H3Q_051 | Single bulged U | ||
| IL_9H3Q_052 | No text annotation | ||
| IL_9H3Q_053 | 180 degree turn | ||
| IL_9H3Q_054 | No text annotation | ||
| IL_9H3Q_055 | No text annotation | ||
| IL_9H3Q_056 | Single stack bend | ||
| IL_9H3Q_057 | Major groove platform | ||
| IL_9H3Q_058 | Single bulged U | ||
| IL_9H3Q_059 | Minor groove platform | ||
| IL_9H3Q_060 | Isolated tHS basepair with bulges | ||
| IL_9H3Q_061 | Isolated non-canonical cWW pair | ||
| IL_9H3Q_062 | No text annotation | ||
| IL_9H3Q_063 | No text annotation | ||
| IL_9H3Q_064 | No text annotation | ||
| IL_9H3Q_065 | No text annotation | ||
| IL_9H3Q_066 | Single bulged U | ||
| IL_9H3Q_067 | No text annotation | ||
| IL_9H3Q_068 | Double sheared | ||
| IL_9H3Q_069 | Single bulged U | ||
| IL_9H3Q_070 | Major groove platform | ||
| IL_9H3Q_071 | No text annotation | ||
| IL_9H3Q_072 | Double sheared with non-canonical cWW | ||
| IL_9H3Q_073 | Major groove platform | ||
| IL_9H3Q_074 | Isolated non-canonical cWW with bulges | ||
| IL_9H3Q_075 | No text annotation | ||
| IL_9H3Q_076 | Major groove platform with intercalation | ||
| IL_9H3Q_077 | Isolated non-canonical cWW pair | ||
| IL_9H3Q_078 | Single bulged A | ||
| IL_9H3Q_080 | Single stack bend | ||
| IL_9H3Q_081 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_9H3Q_082 | C-loop | ||
| IL_9H3Q_083 | UAA/GAN related, with intercalation | ||
| IL_9H3Q_084 | Multiple bulged bases | ||
| IL_9H3Q_085 | UAA/GAN with extra cWW | ||
| IL_9H3Q_086 | Single bulged A | ||
| IL_9H3Q_087 | No text annotation | ||
| IL_9H3Q_088 | Major groove intercalation | ||
| IL_9H3Q_089 | Multiple bulged bases with non-canonical cWW | ||
| IL_9H3Q_090 | tHS double platform | ||
| IL_9H3Q_091 | Major groove intercalation | ||
| IL_9H3Q_092 | No text annotation | ||
| IL_9H3Q_093 | Major groove minor groove platform; mini C-loop | ||
| IL_9H3Q_094 | Symmetric double minor groove platform | ||
| IL_9H3Q_095 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9H3Q_002 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_9H3Q_003 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J4_9H3Q_001 | 1/A/268:269, 1/A/370:375, 1/A/399:406, 1/A/421:424 | No text annotation | homologous J4_5J7L_018 NA | |
| J4_9H3Q_004 | 1/A/1310:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1604 | No text annotation | homologous J4_5J7L_022 NA | |
| J4_9H3Q_005 | 1/A/1313:1314, 1/A/1338:1343, 1/A/1404:1405, 1/A/1597:1603 | No text annotation | homologous J4_5J7L_023 NA | |
| J4_9H3Q_007 | 1/A/2285:2289, 1/A/2343:2347, 1/A/2370:2372, 1/A/2381:2383 | No text annotation | homologous J4_5J7L_027 NA | |
| J5_9H3Q_002 | 1/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_9H3Q_003 | 1/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_9H3Q_001 | 1/A/8:15, 1/A/525:531, 1/A/2018:2023, 1/A/2040:2043, 1/A/2625:2631, 1/A/2787:2789, 1/A/2894:2895 | No text annotation | ||
| J7_9H3Q_002 | 1/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 id | Problem | Sequence |
|---|---|---|---|
| J3_9H3Q_001 | No text annotation | ||
| J3_9H3Q_004 | No text annotation | ||
| J3_9H3Q_005 | No text annotation | ||
| J3_9H3Q_006 | No text annotation | ||
| J3_9H3Q_007 | No text annotation | ||
| J3_9H3Q_008 | No text annotation | ||
| J3_9H3Q_009 | No text annotation | ||
| J3_9H3Q_010 | No text annotation | ||
| J3_9H3Q_011 | Kink-turn 3-way junction | ||
| J3_9H3Q_012 | No text annotation | ||
| J3_9H3Q_013 | No text annotation | ||
| J3_9H3Q_014 | No text annotation | ||
| J3_9H3Q_015 | No text annotation | ||
| J3_9H3Q_016 | No text annotation | ||
| J3_9H3Q_017 | No text annotation | ||
| J4_9H3Q_002 | No text annotation | ||
| J4_9H3Q_003 | No text annotation | ||
| J4_9H3Q_006 | No text annotation | ||
| J4_9H3Q_008 | No text annotation | ||
| J5_9H3Q_001 | No text annotation | ||
| J5_9H3Q_004 | No text annotation | ||
| J6_9H3Q_001 | No text annotation | ||
| J6_9H3Q_002 | No text annotation |
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