9HA4 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9HA4_001 | 1/A/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_9HA4_011 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_9HA4_023 | 1/A/978:985 | No text annotation | homologous HL_9DFE_026 HL_47171.1 | |
| HL_9HA4_028 | 1/A/1363:1368 | GNRA | homologous HL_5J7L_167 NA | |
| HL_9HA4_038 | 1/A/2027:2036 | No text annotation | homologous HL_5J7L_183 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9HA4_002 | No text annotation | ||
| HL_9HA4_003 | No text annotation | ||
| HL_9HA4_004 | No text annotation | ||
| HL_9HA4_005 | No text annotation | ||
| HL_9HA4_006 | No text annotation | ||
| HL_9HA4_007 | No text annotation | ||
| HL_9HA4_008 | No text annotation | ||
| HL_9HA4_009 | T-loop with 2 stacked bulged bases | ||
| HL_9HA4_010 | No text annotation | ||
| HL_9HA4_012 | No text annotation | ||
| HL_9HA4_013 | Pseudoknot geometry | ||
| HL_9HA4_014 | GNRA | ||
| HL_9HA4_015 | GNRA | ||
| HL_9HA4_016 | No text annotation | ||
| HL_9HA4_017 | T-loop with 2 stacked bulged bases | ||
| HL_9HA4_018 | No text annotation | ||
| HL_9HA4_019 | No text annotation | ||
| HL_9HA4_020 | GNRA | ||
| HL_9HA4_021 | No text annotation | ||
| HL_9HA4_022 | GNRA | ||
| HL_9HA4_024 | Externally structured | ||
| HL_9HA4_025 | GNRA | ||
| HL_9HA4_026 | T-loop with 2 stacked bulged bases | ||
| HL_9HA4_027 | Pseudoknot geometry with 3' bulge | ||
| HL_9HA4_029 | No text annotation | ||
| HL_9HA4_030 | Mini UNCG with extended bulge | ||
| HL_9HA4_031 | Pseudoknot geometry with 3' bulge | ||
| HL_9HA4_032 | UNCG | ||
| HL_9HA4_033 | Mini UNCG | ||
| HL_9HA4_034 | No text annotation | ||
| HL_9HA4_035 | GNRA | ||
| HL_9HA4_036 | Mini UNCG | ||
| HL_9HA4_037 | No text annotation | ||
| HL_9HA4_039 | No text annotation | ||
| HL_9HA4_040 | No text annotation | ||
| HL_9HA4_041 | Pseudoknot geometry | ||
| HL_9HA4_042 | GNRA | ||
| HL_9HA4_043 | GNRA | ||
| HL_9HA4_044 | No text annotation | ||
| HL_9HA4_045 | GNRA | ||
| HL_9HA4_046 | No text annotation | ||
| HL_9HA4_047 | No text annotation | ||
| HL_9HA4_048 | Mini UNCG | ||
| HL_9HA4_049 | No text annotation | ||
| HL_9HA4_050 | GNRA | ||
| HL_9HA4_051 | No text annotation | ||
| HL_9HA4_052 | Mini UNCG |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9HA4_010 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_9HA4_020 | 1/A/844:848, 1/A/930:934 | No text annotation | homologous IL_5J7L_399 NA | |
| IL_9HA4_021 | 1/A/847:848, 1/A/930:933 | Stack outside cWW | homologous IL_5J7L_268 NA | |
| IL_9HA4_025 | 1/A/994:996, 1/A/1159:1160 | Single bulged C | homologous IL_5J7L_276 NA | |
| IL_9HA4_027 | 1/A/1004:1011, 1/A/1150:1151 | SSU/LSU pseudoknot | homologous IL_4WF9_037 IL_11411.1 | |
| IL_9HA4_030 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_7A0S_041 IL_42997.5 | |
| IL_9HA4_058 | 1/A/2680:2684, 1/A/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_9HA4_059 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_9HA4_065 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9HA4_001 | Triple sheared with non-canonical cWW | ||
| IL_9HA4_002 | Single bulged A | ||
| IL_9HA4_003 | Minor groove platform | ||
| IL_9HA4_004 | No text annotation | ||
| IL_9HA4_005 | Single stack bend | ||
| IL_9HA4_006 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_9HA4_007 | 7x6 Sarcin-Ricin; G-bulge | ||
| IL_9HA4_008 | No text annotation | ||
| IL_9HA4_009 | No text annotation | ||
| IL_9HA4_011 | Single stack bend | ||
| IL_9HA4_012 | No text annotation | ||
| IL_9HA4_013 | Double sheared | ||
| IL_9HA4_014 | Isolated non-canonical cWW pair | ||
| IL_9HA4_015 | AAA cross-strand stack | ||
| IL_9HA4_016 | Single stack bend | ||
| IL_9HA4_017 | Isolated non-canonical cWW pair | ||
| IL_9HA4_018 | No text annotation | ||
| IL_9HA4_019 | 90 degree turn | ||
| IL_9HA4_022 | Single stack bend | ||
| IL_9HA4_023 | 7x7 Sarcin-Ricin with intercalated A; G-bulge | ||
| IL_9HA4_024 | Single bulged G | ||
| IL_9HA4_026 | UAA/GAN | ||
| IL_9HA4_028 | Single bulged U | ||
| IL_9HA4_029 | No text annotation | ||
| IL_9HA4_031 | No text annotation | ||
| IL_9HA4_032 | Kink-turn | ||
| IL_9HA4_033 | Major groove platform; stack outside cWW | ||
| IL_9HA4_034 | Major groove minor groove platform with tHH | ||
| IL_9HA4_035 | No text annotation | ||
| IL_9HA4_036 | UAA/GAN | ||
| IL_9HA4_037 | No text annotation | ||
| IL_9HA4_038 | tSH-tHW-tHS | ||
| IL_9HA4_039 | No text annotation | ||
| IL_9HA4_040 | No text annotation | ||
| IL_9HA4_041 | Tandem non-canonical cWW pairs | ||
| IL_9HA4_042 | tSH-tHW | ||
| IL_9HA4_043 | Single bulged U | ||
| IL_9HA4_044 | No text annotation | ||
| IL_9HA4_045 | tSH-tHW-tHS | ||
| IL_9HA4_046 | 180 degree turn | ||
| IL_9HA4_047 | Isolated non-canonical cWW pair | ||
| IL_9HA4_048 | Single bulged A | ||
| IL_9HA4_049 | UAA/GAN variation | ||
| IL_9HA4_050 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_9HA4_051 | Triple sheared | ||
| IL_9HA4_052 | Single bulged C | ||
| IL_9HA4_053 | Major groove platform | ||
| IL_9HA4_054 | Double sheared | ||
| IL_9HA4_055 | Single bulged U | ||
| IL_9HA4_056 | tSH-tHS-tHW | ||
| IL_9HA4_057 | Sarcin-Ricin target in LSU H95; G-bulge | ||
| IL_9HA4_060 | Multiple bulged bases | ||
| IL_9HA4_061 | UAA/GAN with extra cWW | ||
| IL_9HA4_062 | Single bulged A | ||
| IL_9HA4_063 | No text annotation | ||
| IL_9HA4_064 | Major groove intercalation | ||
| IL_9HA4_066 | tHS double platform | ||
| IL_9HA4_067 | Major groove intercalation | ||
| IL_9HA4_068 | No text annotation | ||
| IL_9HA4_069 | No text annotation | ||
| IL_9HA4_070 | Symmetric double minor groove platform | ||
| IL_9HA4_071 | Bacterial 5S Loop E |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9HA4_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation | homologous J3_4WF9_010 J3_68715.1 | |
| J3_9HA4_002 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_9HA4_011 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J4_9HA4_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_9HA4_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 | |
| J6_9HA4_001 | 1/A/45:46, 1/A/179:183, 1/A/214:225, 1/A/230:235, 1/A/262:266, 1/A/426:433 | No text annotation | ||
| J7_9HA4_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_9HA4_003 | No text annotation | ||
| J3_9HA4_004 | No text annotation | ||
| J3_9HA4_005 | No text annotation | ||
| J3_9HA4_006 | No text annotation | ||
| J3_9HA4_007 | No text annotation | ||
| J3_9HA4_008 | No text annotation | ||
| J3_9HA4_009 | No text annotation | ||
| J3_9HA4_010 | No text annotation | ||
| J3_9HA4_012 | No text annotation | ||
| J4_9HA4_002 | No text annotation | ||
| J4_9HA4_003 | No text annotation | ||
| J4_9HA4_004 | No text annotation | ||
| J4_9HA4_006 | No text annotation | ||
| J4_9HA4_007 | No text annotation | ||
| J4_9HA4_008 | No text annotation | ||
| J5_9HA4_001 | No text annotation | ||
| J5_9HA4_002 | No text annotation | ||
| J5_9HA4_003 | No text annotation | ||
| J7_9HA4_001 | No text annotation |
Coloring options: