AgamP3.4
From VectorBase Help System
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[edit] Release
The AgamP3.4. gene set was released in July 2007. See the additional information about how this set was produced.
[edit] Change in Identifiers
A major change for the AgamP3.4 gene set in comparison to the AgamP3.3 set was the change from the Ensembl identifiers to VectorBase ones. This means that all genes are now named AGAPxxxxxx. Transcripts and peptides are indicated using the FlyBase style -R and -P suffices. Alternate isoforms are indicated by a further character in the suffix; A to Z.
Advantages of the new nomenclature are the shorter, more manageable format without the large number of leading zeros and that the relationship between gene/transcript and peptide identifiers is simple and intuitive.
[edit] Gene set statistics
| Count | % | |
| Genes | ||
| No. genes | 12,945 | - |
| No. protein-coding genes | 12,457 | 96.2 % |
| No. of other genes | 488 | 3.8 % |
| No. of tRNA genes | 450 | 3.5 % |
| No. of rRNA genes | 0 | - % |
| No. of snRNA genes | 0 | - % |
| No. of miRNA genes | 38 | 0.3 % |
| No. of misc_RNA genes | 0 | - % |
| Transcripts | ||
| No. transcripts | 13,621 | - |
| No. protein-coding transcripts | 13,133 | 96.4 % |
| No. of other transcripts | 488 | 3.6 % |
| No. of tRNA transcripts | 450 | 3.3 % |
| No. of rRNA transcripts | 0 | - % |
| No. of snRNA transcripts | 0 | - % |
| No. of miRNA transcripts | 38 | 0.3 % |
| No. of misc_RNA transcripts | 0 | - % |
| Manual annotation | ||
| Manually reviewed gene structures | 3,534 | 25.9 % |
| Community supplied gene structures | 1,441 | 10.6 % |
