The red junglefowl (Gallus gallus) is a tropical member of the family Phasianidae. It is the primary progenitor of the domestic chicken (though genetic evidence strongly suggests some past hybridisation with the grey junglefowl, as well). The red junglefowl was first domesticated at least 5000 years ago in Asia. Since then, it has spread around the world, and the domestic form is kept globally as a very productive food source of both meat and eggs.
The Gallus_gallus-4.0 assembly of the chicken genome was produced in November 2011 by the International Chicken Genome Consortium. It consists of 31 chromosomes, 2 linkage groups and 14,093 unplaced scaffolds.
The genome assembly represented here corresponds to GenBank Assembly ID GCA_000002315.2
Gallus_gallus-4.0 was annotated using a standard Ensembl genebuild pipeline, incorporating RNASeq data provided by a number of sources. The annotation process is described in the document below.
RNASeq data set
In addition to the main set, we have predicted gene models for each tissue type using the RNA-Seq pipeline. We did a BLASTp of these models against UniProt proteins of vertabrate species with protein existence level 1 and 2 in order to confirm the open reading frame (ORF). The best BLAST hit is displayed as a transcript supporting evidence. 5139 gene models were made exclusively from RNASeq data. The data was also used to add UTR to gene models.
The tissue-specific sets of transcript models built using our RNAseq pipeline are as follows:
|Tissue||Number of gene models|
General information about this species can be found in Wikipedia.
|Assembly||Galgal4, INSDC Assembly GCA_000002315.2, Nov 2011|
|Golden Path Length||1,046,932,099|
|Annotation method||Full genebuild|
|Genebuild started||Dec 2011|
|Genebuild released||Apr 2013|
|Genebuild last updated/patched||Dec 2013|
|Genscan gene predictions||40,572|