9HA1 Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_9HA1_001 | 1/A/59:68 | No text annotation | homologous HL_5J7L_134 NA | |
| HL_9HA1_003 | 1/A/123:128 | No text annotation | homologous HL_5J7L_136 NA | |
| HL_9HA1_011 | 1/A/327:335 | T-loop with unstacked turn | homologous HL_5J7L_144 NA | |
| HL_9HA1_018 | 1/A/611:617 | No text annotation | homologous HL_5J7L_151 NA | |
| HL_9HA1_027 | 1/A/1324:1330 | Pseudoknot geometry with 3' bulge | homologous HL_9DFE_032 HL_49081.1 | |
| HL_9HA1_029 | 1/A/1389:1398 | No text annotation | homologous HL_5J7L_168 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_9HA1_002 | No text annotation | ||
| HL_9HA1_004 | No text annotation | ||
| HL_9HA1_005 | No text annotation | ||
| HL_9HA1_006 | No text annotation | ||
| HL_9HA1_007 | No text annotation | ||
| HL_9HA1_008 | No text annotation | ||
| HL_9HA1_009 | T-loop with 2 stacked bulged bases | ||
| HL_9HA1_010 | No text annotation | ||
| HL_9HA1_012 | No text annotation | ||
| HL_9HA1_013 | No text annotation | ||
| HL_9HA1_014 | GNRA | ||
| HL_9HA1_015 | GNRA | ||
| HL_9HA1_016 | No text annotation | ||
| HL_9HA1_017 | No text annotation | ||
| HL_9HA1_019 | No text annotation | ||
| HL_9HA1_020 | GNRA | ||
| HL_9HA1_021 | No text annotation | ||
| HL_9HA1_022 | GNRA | ||
| HL_9HA1_023 | No text annotation | ||
| HL_9HA1_024 | No text annotation | ||
| HL_9HA1_025 | GNRA | ||
| HL_9HA1_026 | T-loop with 2 stacked bulged bases | ||
| HL_9HA1_028 | GNRA | ||
| HL_9HA1_030 | Mini UNCG with extended bulge | ||
| HL_9HA1_031 | No text annotation | ||
| HL_9HA1_032 | UNCG | ||
| HL_9HA1_033 | Mini UNCG | ||
| HL_9HA1_034 | No text annotation | ||
| HL_9HA1_035 | GNRA | ||
| HL_9HA1_036 | No text annotation | ||
| HL_9HA1_037 | No text annotation | ||
| HL_9HA1_038 | No text annotation | ||
| HL_9HA1_039 | GNRA | ||
| HL_9HA1_040 | Ribsomal LSU H95 | ||
| HL_9HA1_041 | No text annotation | ||
| HL_9HA1_042 | Mini UNCG | ||
| HL_9HA1_043 | No text annotation | ||
| HL_9HA1_044 | GNRA |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_9HA1_001 | 1/A/24:30, 1/A/510:516 | Triple sheared with non-canonical cWW | homologous IL_7A0S_001 IL_22311.1 | |
| IL_9HA1_002 | 1/A/36:37, 1/A/442:444 | Single bulged A | homologous IL_5J7L_246 NA | |
| IL_9HA1_004 | 1/A/82:85, 1/A/97:104 | No text annotation | ||
| IL_9HA1_006 | 1/A/188:194, 1/A/201:208 | 8x7 Sarcin-Ricin; G-bulge | homologous IL_7A0S_006 IL_62167.3 | |
| IL_9HA1_011 | 1/A/293:295, 1/A/343:347 | No text annotation | homologous IL_5J7L_254 NA | |
| IL_9HA1_026 | 1/A/1196:1198, 1/A/1247:1250 | Isolated cWS basepair | homologous IL_7A0S_041 IL_42997.5 | |
| IL_9HA1_032 | 1/A/1320:1323, 1/A/1331:1333 | No text annotation | ||
| IL_9HA1_053 | 1/A/2636:2640, 1/A/2774:2782 | tSH-tHS-tHW | homologous IL_7A0S_093 IL_04638.4 | |
| IL_9HA1_056 | 1/A/2680:2684, 1/A/2725:2727 | C-loop | homologous IL_5J7L_347 NA | |
| IL_9HA1_057 | 1/A/2687:2691, 1/A/2718:2722 | UAA/GAN related, with intercalation | homologous IL_5J7L_348 NA | |
| IL_9HA1_064 | 1/A/2843:2846, 1/A/2870:2874 | Multiple bulged bases with non-canonical cWW | homologous IL_5J7L_353 NA | |
| IL_9HA1_065 | 1/A/2847:2852, 1/A/2865:2869 | tHS double platform | homologous IL_5J7L_354 NA |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_9HA1_003 | Minor groove platform | ||
| IL_9HA1_005 | No text annotation | ||
| IL_9HA1_007 | Single stack bend | ||
| IL_9HA1_008 | No text annotation | ||
| IL_9HA1_009 | No text annotation | ||
| IL_9HA1_010 | No text annotation | ||
| IL_9HA1_012 | No text annotation | ||
| IL_9HA1_013 | Double sheared | ||
| IL_9HA1_014 | AAA cross-strand stack | ||
| IL_9HA1_015 | Single stack bend | ||
| IL_9HA1_016 | Isolated non-canonical cWW pair | ||
| IL_9HA1_017 | No text annotation | ||
| IL_9HA1_018 | 90 degree turn | ||
| IL_9HA1_019 | No text annotation | ||
| IL_9HA1_020 | Stack outside cWW | ||
| IL_9HA1_021 | Single bulged C | ||
| IL_9HA1_022 | UAA/GAN | ||
| IL_9HA1_023 | SSU/LSU pseudoknot | ||
| IL_9HA1_024 | Single bulged U | ||
| IL_9HA1_025 | No text annotation | ||
| IL_9HA1_027 | No text annotation | ||
| IL_9HA1_028 | Kink-turn | ||
| IL_9HA1_029 | 8x7 Sarcin-Ricin; G-bulge | ||
| IL_9HA1_030 | Major groove platform; stack outside cWW | ||
| IL_9HA1_031 | Single stack bend | ||
| IL_9HA1_033 | UAA/GAN | ||
| IL_9HA1_034 | tSH-tHW-tHS | ||
| IL_9HA1_035 | No text annotation | ||
| IL_9HA1_036 | No text annotation | ||
| IL_9HA1_037 | Tandem non-canonical cWW pairs | ||
| IL_9HA1_038 | tSH-tHW | ||
| IL_9HA1_039 | Single bulged U | ||
| IL_9HA1_040 | No text annotation | ||
| IL_9HA1_041 | tSH-tHW-tHS | ||
| IL_9HA1_042 | 180 degree turn | ||
| IL_9HA1_043 | Single bulged A | ||
| IL_9HA1_044 | UAA/GAN variation | ||
| IL_9HA1_045 | No text annotation | ||
| IL_9HA1_046 | Isolated tWW turn | ||
| IL_9HA1_047 | Decoding loop related | ||
| IL_9HA1_048 | Intercalated tWH | ||
| IL_9HA1_049 | 6x5 Sarcin-Ricin; G-bulge | ||
| IL_9HA1_050 | Triple sheared | ||
| IL_9HA1_051 | Single stack bend | ||
| IL_9HA1_052 | Major groove platform | ||
| IL_9HA1_054 | Single stack bend | ||
| IL_9HA1_055 | No text annotation | ||
| IL_9HA1_058 | Multiple bulged bases | ||
| IL_9HA1_059 | UAA/GAN with extra cWW | ||
| IL_9HA1_060 | Isolated near basepair | ||
| IL_9HA1_061 | Single bulged A | ||
| IL_9HA1_062 | No text annotation | ||
| IL_9HA1_063 | Major groove intercalation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_9HA1_001 | 1/A/30:31, 1/A/474:481, 1/A/509:510 | No text annotation | homologous J3_4WF9_010 J3_68715.1 | |
| J3_9HA1_002 | 1/A/32:35, 1/A/445:461, 1/A/468:473 | No text annotation | homologous J3_5J7L_067 NA | |
| J3_9HA1_003 | 1/A/56:57, 1/A/70:76, 1/A/110:114 | No text annotation | homologous J3_5J7L_037 NA | |
| J3_9HA1_004 | 1/A/1298:1303, 1/A/1625:1627, 1/A/1639:1642 | No text annotation | homologous J3_5J7L_041 NA | |
| J3_9HA1_005 | 1/A/1306:1309, 1/A/1605:1611, 1/A/1620:1622 | No text annotation | homologous J3_5J7L_042 NA | |
| J3_9HA1_009 | 1/A/2812:2815, 1/A/2831:2836, 1/A/2882:2888 | No text annotation | homologous J3_5J7L_048 NA | |
| J6_9HA1_001 | 1/A/45:46, 1/A/179:183, 1/A/215:224, 1/A/231:235, 1/A/262:266, 1/A/426:433 | No text annotation | ||
| J7_9HA1_001 | 1/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 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| J3_9HA1_006 | No text annotation | ||
| J3_9HA1_007 | No text annotation | ||
| J3_9HA1_008 | No text annotation | ||
| J4_9HA1_001 | No text annotation | ||
| J4_9HA1_002 | No text annotation | ||
| J4_9HA1_003 | No text annotation | ||
| J4_9HA1_004 | No text annotation | ||
| J4_9HA1_005 | No text annotation | ||
| J4_9HA1_006 | No text annotation | ||
| J4_9HA1_007 | No text annotation | ||
| J4_9HA1_008 | No text annotation | ||
| J5_9HA1_001 | No text annotation | ||
| J5_9HA1_002 | No text annotation | ||
| J5_9HA1_003 | No text annotation | ||
| J5_9HA1_004 | No text annotation | ||
| J7_9HA1_002 | No text annotation |
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