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Chicken assembly and gene annotation


The GRCg6a assembly was submitted by Genome Reference Consortium on April 2018. The assembly is on chromosome level, consisting of 1,403 contigs assembled into 525 scaffolds. From these sequences, 34 chromosomes have been built. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 17,655,422 while the scaffold N50 is 20,785,086.

Gene annotation

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 gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments. Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold. Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome. lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.



AssemblyGRCg6a, INSDC Assembly GCA_000002315.5, Mar 2018
Base Pairs1,065,365,425
Golden Path Length1,065,365,425
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedApr 2018
Genebuild releasedApr 2018
Genebuild last updated/patchedMar 2018
Database version104.6

Gene counts

Coding genes16,878
Non coding genes7,166
Small non coding genes1,525
Long non coding genes5,506
Misc non coding genes135
Gene transcripts39,288


Genscan gene predictions36,703
Short Variants23,768,870

About this species