4GMA Hairpin, Internal, and multi-helix Junction Loop Motifs
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| HL_4GMA_002 | 1/Z/58:66 | T-loop with 2 bulged bases not stacked | geometric HL_4FRN_005 HL_01609.1 | |
| HL_4GMA_003 | 1/Z/74:81 | Pseudoknot geometry | geometric HL_6UFJ_003 HL_93324.2 | |
| HL_4GMA_004 | 1/Z/119:124 | GNRA | geometric HL_4Y1M_003 HL_37824.3 | |
| HL_4GMA_005 | 1/Z/193:201 | Pseudoknot geometry | geometric HL_6R47_001 HL_93324.2 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| HL_4GMA_001 | No text annotation |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| IL_4GMA_001 | 1/Z/7:9, 1/Z/176:177 | Single stack bend | geometric IL_4LFB_041 IL_06586.1 | |
| IL_4GMA_002 | 1/Z/86:90, 1/Z/153:158 | No text annotation | geometric IL_6VMY_002 IL_70627.3 | |
| IL_4GMA_003 | 1/Z/93:97, 1/Z/143:150 | Kink-turn | ||
| IL_4GMA_004 | 1/Z/97:102, 1/Z/138:143 | Triple sheared with non-canonical cWW | geometric IL_7A0S_018 IL_06136.2 | |
| IL_4GMA_007 | 1/Z/113:115, 1/Z/128:132 | Major groove minor groove platform with extra cWW | geometric IL_4GXY_009 IL_80823.1 |
Problematic loops
| # | loop id | Problem | Sequence |
|---|---|---|---|
| IL_4GMA_009 | Kink-turn | ||
| IL_4GMA_005 | Isolated non-canonical cWW pair | ||
| IL_4GMA_006 | No text annotation | ||
| IL_4GMA_008 | Tandem non-canonical cWW pairs |
Valid loops
| 3D | Loop id | Location | Annotation; motif group | Mapped info |
|---|---|---|---|---|
| J3_4GMA_001 | 1/Z/17:18, 1/Z/41:47, 1/Z/167:168 | No text annotation | geometric J3_6VMY_001 NA | |
| J4_4GMA_001 | 1/Z/48:55, 1/Z/69:73, 1/Z/82:84, 1/Z/160:166 | No text annotation |
Problematic loops
No problematic loops
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