9HA7 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9HA7_001 | 1/A/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_9HA7_002 | 1/A/87:95 | No text annotation | homologous HL_5J7L_135 NA | |
| HL_9HA7_010 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_9HA7_016 | 1/A/566:575 | T-loop with 2 stacked bulged bases | homologous HL_5J7L_150 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9HA7_003 | No text annotation | ||
| HL_9HA7_004 | No text annotation | ||
| HL_9HA7_005 | No text annotation | ||
| HL_9HA7_006 | No text annotation | ||
| HL_9HA7_007 | No text annotation | ||
| HL_9HA7_008 | No text annotation | ||
| HL_9HA7_009 | T-loop with 2 stacked bulged bases | ||
| HL_9HA7_011 | No text annotation | ||
| HL_9HA7_012 | Pseudoknot geometry | ||
| HL_9HA7_013 | GNRA | ||
| HL_9HA7_014 | GNRA | ||
| HL_9HA7_015 | No text annotation | ||
| HL_9HA7_017 | No text annotation | ||
| HL_9HA7_018 | GNRA | ||
| HL_9HA7_019 | GNRA | ||
| HL_9HA7_020 | No text annotation | ||
| HL_9HA7_021 | GNRA | ||
| HL_9HA7_022 | No text annotation | ||
| HL_9HA7_023 | No text annotation | ||
| HL_9HA7_024 | GNRA | ||
| HL_9HA7_025 | T-loop with 2 stacked bulged bases | ||
| HL_9HA7_026 | Pseudoknot geometry with 3' bulge | ||
| HL_9HA7_027 | GNRA | ||
| HL_9HA7_028 | No text annotation | ||
| HL_9HA7_029 | Mini UNCG with extended bulge | ||
| HL_9HA7_030 | Pseudoknot geometry with 3' bulge | ||
| HL_9HA7_031 | No text annotation | ||
| HL_9HA7_032 | Mini UNCG | ||
| HL_9HA7_033 | No text annotation | ||
| HL_9HA7_034 | GNRA | ||
| HL_9HA7_035 | No text annotation | ||
| HL_9HA7_036 | No text annotation | ||
| HL_9HA7_037 | No text annotation | ||
| HL_9HA7_038 | No text annotation | ||
| HL_9HA7_039 | Pseudoknot geometry | ||
| HL_9HA7_040 | GNRA | ||
| HL_9HA7_041 | GNRA | ||
| HL_9HA7_042 | No text annotation | ||
| HL_9HA7_043 | GNRA | ||
| HL_9HA7_044 | Ribsomal LSU H95 | ||
| HL_9HA7_045 | No text annotation | ||
| HL_9HA7_046 | No text annotation | ||
| HL_9HA7_047 | No text annotation | ||
| HL_9HA7_048 | GNRA | ||
| HL_9HA7_049 | No text annotation | ||
| HL_9HA7_050 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9HA7_003 | 1/A/43:44, 1/A/434:436 | Minor groove platform | homologous IL_5J7L_247 NA | |
| IL_9HA7_005 | 1/A/183:184, 1/A/212:214 | Single stack bend | homologous IL_7A0S_005 IL_15011.3 | |
| IL_9HA7_013 | 1/A/564:566, 1/A/575:577 | Isolated non-canonical cWW pair | homologous IL_4WF9_017 IL_71625.3 | |
| IL_9HA7_018 | 1/A/844:848, 1/A/930:934 | No text annotation | geometric IL_5J7L_399 NA | |
| IL_9HA7_019 | 1/A/847:848, 1/A/930:933 | Stack outside cWW | homologous IL_5J7L_268 NA | |
| IL_9HA7_023 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_4WF9_035 IL_05642.3 | |
| IL_9HA7_029 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_7A0S_041 IL_42997.5 | |
| IL_9HA7_030 | 1/A/1202:1206, 1/A/1240:1243 | No text annotation | homologous IL_5J7L_287 NA | |
| IL_9HA7_031 | 1/A/1208:1215, 1/A/1234:1238 | Kink-turn | homologous IL_5J7L_288 NA | |
| IL_9HA7_033 | 1/A/1319:1323, 1/A/1331:1333 | C-loop | homologous IL_5J7L_291 NA | |
| IL_9HA7_050 | 1/A/2636:2640, 1/A/2774:2782 | tSH-tHS-tHW | homologous IL_7A0S_093 IL_04638.4 | |
| IL_9HA7_054 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9HA7_001 | Triple sheared with non-canonical cWW | ||
| IL_9HA7_002 | Single bulged A | ||
| IL_9HA7_004 | No text annotation | ||
| IL_9HA7_006 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_9HA7_007 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_9HA7_008 | No text annotation | ||
| IL_9HA7_009 | No text annotation | ||
| IL_9HA7_010 | No text annotation | ||
| IL_9HA7_011 | No text annotation | ||
| IL_9HA7_012 | Double sheared | ||
| IL_9HA7_014 | AAA cross-strand stack | ||
| IL_9HA7_015 | Isolated non-canonical cWW pair | ||
| IL_9HA7_016 | tHW-tHW cross-strand stack | ||
| IL_9HA7_017 | 90 degree turn | ||
| IL_9HA7_020 | Single stack bend | ||
| IL_9HA7_021 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_9HA7_022 | Single bulged G | ||
| IL_9HA7_024 | UAA/GAN | ||
| IL_9HA7_025 | SSU/LSU pseudoknot | ||
| IL_9HA7_026 | Single bulged U | ||
| IL_9HA7_027 | Kink-turn related | ||
| IL_9HA7_028 | No text annotation | ||
| IL_9HA7_032 | Major groove platform; stack outside cWW | ||
| IL_9HA7_034 | UAA/GAN | ||
| IL_9HA7_035 | tSH-tHW-tHS | ||
| IL_9HA7_036 | No text annotation | ||
| IL_9HA7_037 | UAA/GAN | ||
| IL_9HA7_038 | Tandem non-canonical cWW pairs | ||
| IL_9HA7_039 | tSH-tHW | ||
| IL_9HA7_040 | Single bulged U | ||
| IL_9HA7_041 | No text annotation | ||
| IL_9HA7_042 | 180 degree turn | ||
| IL_9HA7_043 | No text annotation | ||
| IL_9HA7_044 | No text annotation | ||
| IL_9HA7_045 | Single stack bend | ||
| IL_9HA7_046 | Major groove platform | ||
| IL_9HA7_047 | No text annotation | ||
| IL_9HA7_048 | Double sheared | ||
| IL_9HA7_049 | Single bulged U | ||
| IL_9HA7_051 | Single stack bend | ||
| IL_9HA7_052 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_9HA7_053 | C-loop | ||
| IL_9HA7_055 | Multiple bulged bases | ||
| IL_9HA7_056 | UAA/GAN with extra cWW | ||
| IL_9HA7_057 | Single bulged A | ||
| IL_9HA7_058 | No text annotation | ||
| IL_9HA7_059 | Major groove intercalation | ||
| IL_9HA7_060 | Multiple bulged bases with non-canonical cWW | ||
| IL_9HA7_061 | tHS double platform | ||
| IL_9HA7_062 | Major groove intercalation | ||
| IL_9HA7_063 | No text annotation | ||
| IL_9HA7_064 | Major groove minor groove platform; mini C-loop | ||
| IL_9HA7_065 | No text annotation | ||
| IL_9HA7_066 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9HA7_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation | homologous J3_4WF9_010 J3_68715.1 | |
| J3_9HA7_002 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_9HA7_003 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J7_9HA7_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_9HA7_004 | No text annotation | ||
| J3_9HA7_005 | No text annotation | ||
| J3_9HA7_006 | No text annotation | ||
| J3_9HA7_007 | No text annotation | ||
| J3_9HA7_008 | No text annotation | ||
| J3_9HA7_009 | No text annotation | ||
| J3_9HA7_010 | No text annotation | ||
| J3_9HA7_011 | No text annotation | ||
| J3_9HA7_012 | No text annotation | ||
| J3_9HA7_013 | No text annotation | ||
| J4_9HA7_001 | No text annotation | ||
| J4_9HA7_002 | No text annotation | ||
| J4_9HA7_003 | No text annotation | ||
| J4_9HA7_004 | No text annotation | ||
| J4_9HA7_005 | No text annotation | ||
| J4_9HA7_006 | No text annotation | ||
| J4_9HA7_007 | No text annotation | ||
| J4_9HA7_008 | No text annotation | ||
| J5_9HA7_001 | No text annotation | ||
| J5_9HA7_002 | No text annotation | ||
| J5_9HA7_003 | No text annotation | ||
| J6_9HA7_001 | No text annotation | ||
| J7_9HA7_001 | No text annotation |
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