Chicken assembly and gene annotation


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

Other assemblies

Gene annotation

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:

TissueNumber of gene models

More information

General information about this species can be found in Wikipedia.



AssemblyGalgal4, INSDC Assembly GCA_000002315.2, Nov 2011
Database version80.4
Base Pairs1,072,544,763
Golden Path Length

The golden path is the length of the reference assembly. It consists of the sum of all top-level sequences in the seq_region table, omitting any redundant regions such as haplotypes and PARs (pseudoautosomal regions).

Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedDec 2011
Genebuild releasedApr 2013
Genebuild last updated/patchedDec 2013

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

Non coding genes1,558
Small non coding genes

Small non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as small non coding genes: miRNA, miscRNA, rRNA, scRNA, snlRNA, snoRNA, snRNA, and also the pseudogenic form of these biotypes. The majority of the small non coding genes in Ensembl are annotated automatically by our ncRNA pipeline. Please note that tRNAs are annotated separately using tRNAscan. tRNAs are included as 'simple fetaures', not genes, because they are not annotated using aligned sequence evidence.

Misc non coding genes150

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

Gene transcriptsNucleotide sequence resulting from the transcription of the genomic DNA to mRNA. One gene can have different transcripts or splice variants resulting from the alternative splicing of different exons in genes.17,954


Genscan gene predictions40,572
Short Variants9,534,437