Gallus gallus
Photo courtesy of Bill Payne,
Michigan State University
(NHGRI Press Photos)

The May 2006 chicken (Gallus gallus) draft assembly was produced by the Genome Sequencing Center at the Washington University School of Medicine in St. Louis.

Sample position queries

A genome position can be specified by the accession number of a sequenced genomic supercontig, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid position queries for the chicken genome. See the User's Guide for more information.

Request:   Genome Browser Response:
chrZ   Displays all of chromosome Z
chr3:1-1000000   Displays first million bases of chr 3
chr3:1000000+2000 Displays a region of chr 3 that spans 2000 bases, starting with position 1000000
Contig44   Displays region of assembly for the supercontig with ID contig44
Contig44.48   Displays region of assembly for the contig with ID contig44.48
BX950328   Displays region of mRNA with GenBank accession number BX950328
BU335953   Displays region of EST with GenBank accession BU335953 on chr Z
chr13_3.145   Displays region of genome containing Genscan gene prediction chr13_3.145
CWNT-8C   Displays region of genome with gene symbol CWNT-8C
NM_204735   Displays the region of genome with RefSeq identifier NM_204735
374180   Displays the region of genome with LocusLink identifier 374180
CWNT-8C   Displays region of genome with gene symbol CWNT-8C
ENSGALT00000023622   Displays the region of genome with Ensembl identifier ENSGALT00000023622. NOTE: Due to space constraints, the Genome Browser displays abridged Ensembl identifiers, but the full ID name must be used in searches. For example, the ENSGALT00000023622 identifier displays as ENSGAL23622 in the Genome Browser.
pseudogene mRNA   Lists transcribed pseudogenes, but not cDNAs
homeobox caudal   Lists mRNAs for caudal homeobox genes
zinc finger   Lists many zinc finger mRNAs
kruppel zinc finger   Lists only kruppel-like zinc fingers
zhang   Lists mRNAs deposited by scientist named Zhang
Taguchi,T.   Lists mRNAs deposited by co-author T. Taguchi
Use this last format for author queries. Although GenBank requires the search format Taguchi T, internally it uses the format Taguchi,T..

Assembly details

198,000 additional reads covering all contig ends and regions of low quality have been added to the original assembly's 6.6X coverage. Approximately 95% of the sequence has been anchored to chromosomes, which include autosomes 1-24, 26-28, and 32, 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 that could be localized to a chromosome have been concatenated into the virtual chromosomes "chr*_random", separated by gaps of 10,000 bp. Unanchored contigs that could not be localized to a chromosome have been concatenated into the virtual chromosome "chrUn_random", separated by gaps of 100 bp in order to reduce the total size of chrUn_random. The chicken mitochondrial sequence is also available as the virtual chromosome "chrM".

The following two paragraphs are quoted directly from the assembly release notes.

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.

Although centromere positions are indicated on the chicken draft sequence, little is known of their exact sequence. The centromeres of 18 chromosomes were tentatively localized based on FISH hybridization using BAC clones, genetic markers flanking the centromeres in coordination with mapping gaps in the physical map, repetitive sequence content, and analysis of proximity to the constrictions of the mitotic metaphase chromosomes. In three cases those centromere assignments were confirmed by sequence identification, utilizing the CNM repeats on GGA11, 23 and 28. In 10 cases (GGA2, GGA3, GGA4, GGA5, GGA7, GGA9, GGA11, GGA23, GGA28 GGA25) XhoI-like repetitive sequences (similar to the CNM repeats) were identified near the centromere boundaries adding confidence as to those centromere locations. Macrochromosome centromere sizes were assigned arbitrarily to be 1.5 Mb and those of microchromosomes to be 0.5 Mb lengths in absence of any evidence as to their true lengths.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page. These data have specific conditions for use. The chicken browser annotation tracks were generated by UCSC and collaborators worldwide. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release.