Ensembl Chicken

Karyotype

Click on a chromosome for a closer view

About the Chicken genome

Assembly

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.

• Full list of credits

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

Annotation

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.

What's New in Ensembl 44

Gallus gallus News

• Patch for Ensembl Chicken database
  Ensembl Gallus gallus has been patched with a small number of additional gene predictions, and the corresponding xrefs and variation databases updated.
• Variation updates
  All species with variation data now have a failed_variation table. Also, in species that have duplicate variations (with the same mapping but different IDs), these have been put into the variation_synonym table.

General News

• ncRNAs for Ensembl chordates
  All Ensembl genebuild databases (i.e. excluding the imported invertebrate databases for mosquitoes, fruit fly, worm and yeast) have been updated with new ncRNA data.
• Compara updates
  

  Pairwise alignments

  • Platypus (Ornithorhynchus anatinus) OANA5 BLASTZ_NET vs Mus musculus (NCBIM36)
  • Cat (Felis catus) BLASTZ_NET vs Canis familiaris (BROADD2)
  • Treeshrew (Tupaia belangeri) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Hedgehog (Erinaceus europaeus) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Opossum (Monodelphis domestica) BROAD5 (new assembly) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Bushbaby (Otolemur garnetti) (2X genome, new species) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Ground squirrel (Spermophilus tridecemlineatus) (2X genome, new species) BLASTZ_NET vs Homo sapiens (NCBI36)
  • Little brown bat (Myotis lucifugus) (2X genome, new species) BLASTZ_NET vs Homo sapiens (NCBI36)

  Multiple alignments

  PECAN (vertebrates) 10 ways.
  Read more...

• Schema changes
  There have been no major schema changes this release, however we are starting to systematically work through the schema to make sure that all column types are appropriate for the data they are likely to hold.
  Read more...

More news...

Statistics

* Total number of base pairs = sum of lengths of DNA table

** Reference assembly (Golden path) length = sum of non-redundant top level seq regions