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This site presents an annotation of the first draft chicken
genome assembly, March 2004 [NIH press release].
The chicken genome sequence was determined by whole genome shotgun at
the Genome Sequencing Center at Washington University, St Louis. The analysis
of the chicken sequence involves an international group of scientists
including individuals from the US, UK, Europe and China.
The gene set for Chicken was built using a modified version of the standard Ensembl genebuild pipeline. The majority of gene models are based on genewise alignments of proteins from other species. Most of the proteins being aligned were from species genetically distant to chicken. To improve the accuracy of models generated from these proteins, the Genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. The gene models were assessed by generating sets of potential orthologs to genes from other mammalian species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, and exonerate used to build new gene models for these based on the human ortholog peptide sequence.
This release of G. gallus GGAW contains some sequence that is not specific to chromosome W. A large portion of the sequence assigned to W was done so based on the presence of W-specific repeats. These repeats have now been shown to be not specific to chromosome W. Thus, the only portions of GGAW which should currently be considered specific to W are:
The following updates have been made to ensembl_compara.
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ContigView navigation has been enhanced with new popup menus and navigation features.
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The following xrefs have been added/updated.
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| Assembly: | WASHUC 1, Mar 2004 |
| Genebuild: | Ensembl, Dec 2005 |
| Database version: | 38.1n |
| Known genes: | 12,960 |
| Novel genes: | 5,672 |
| Pseudogenes: | 94 |
| RNA genes: | 634 |
| Genscan gene predictions: | 76,146 |
| Gene exons: | 187,568 |
| Gene transcripts: | 24,262 |
| Base Pairs: | 1,054,197,620 |
| Golden Path Length: | 1,053,973,890 |
| Most common InterPro domains: | Top 40 Top 500 |
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