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This site displays the 2.1 (May 2006) release of the chicken genome. The analysis of the chicken sequence involves an international group of scientists including individuals from the US, UK, Europe and China, headed by the Genome Sequencing Center at Washington University School of Medicine, St. Louis.
Of the 1.05 Gb genome, approximately 95% of the sequence has been anchored to chromosomes, which include autosomes 1-28 and 32, two additional linkage groups, and sex chromosomes W and Z. (In contrast to mammals, the female chicken is heterogametic (ZW) and the male is homogametic (ZZ).) The remaining unanchored contigs have been concatenated into the virtual chromosome "chrUn", separated by gaps of 100 bp. All unknown gap sizes have been set to 100 bp. The N50 ultracontig size is 15.5Mb (n=19); the longest ultracontig is 80.3Mb on chicken chromosome 3. The N50 supercontig size is 11.1Mb (n=26); the longest supercontig is 52Mb on chr2. The N50 contig size is 45kb (n=5863); the longest contig is 625kb. Q20 base redundancy: 7.1X
The gene set for Chicken was built using a modified version of the standard Ensembl genebuild pipeline. Gene models are based on genewise alignments of chicken proteins as well as genetically distant proteins from other species. To improve the accuracy of models generated from distant species, the Genewise alignments were made to stretches of genomic sequence rather than to 'miniseqs'. The protein based gene models were then extended using Chicken cDNA and EST alignments, the cDNAs were added to models made from chicken proteins and the ESTs to models based on proteins from other species. The resulting gene models were then assessed by generating sets of potential orthologs to genes from other vertebrate species. Potentially missing predictions and partial gene predictions were identified by examining the orthologs, which were then used to build new gene models.
The multiple alignments are being extended with new species and 2X genomes.
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Canonical transcripts have been defined for all genes in the core databases.
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| Assembly: | WASHUC2, May 2006 |
| Genebuild: | Ensembl, Aug 2006 |
| Database version: | 50.2h |
| Known protein-coding genes: | 4,782 |
| Projected protein-coding genes: | 7,569 |
| Novel protein-coding genes: | 4,385 |
| Pseudogenes: | 96 |
| RNA genes: | 655 |
| Genscan gene predictions: | 40,505 |
| Gene exons: | 182,183 |
| Gene transcripts: | 22,291 |
| SNPs: | 2,960,841 |
| Base Pairs: | 1,050,947,331 |
| Golden Path Length: | 1,100,480,441 |
| Most common InterPro domains: | Top 40 Top 500 |
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