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Chicken assembly and gene annotation


The Gallus_gallus-5.0 assembly of the chicken genome was released in December 2015 by the International Chicken Genome Consortium. It consists of 34 chromosomes, 1 linkage group and 15,411 unplaced scaffolds.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000002315.3

Gene annotation

Gallus_gallus-5.0 was annotated using a standard Ensembl genebuild pipeline, incorporating RNASeq data (PRJEB12891) and PacBio long read data (PRJEB13248, PRJEB13246) provided by the Roslin Institute. The annotation process is described in the document below.

PacBio long read data set

Two tissue samples were sequenced using the PacBio long read sequencing technology, embryo and brain. Both sets were used to add UTR to gene models and as input source for our lincRNA discovery pipeline. The embryo set was sequenced using 5' and 3' capping, therefore all the sequences were considered as full length cDNAs and incorporated into the gene models.

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. 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
Breast muscle6132
Caecal tonsil10421
Gizzard fat8892
Harderian gland6544
Heart muscle7746
Left optic lobe7616

More information

General information about this species can be found in Wikipedia.



AssemblyGallus_gallus-5.0, INSDC Assembly GCA_000002315.3, Dec 2015
Base Pairs1,285,637,921
Golden Path Length1,230,258,557
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJun 2016
Genebuild releasedOct 2016
Genebuild last updated/patchedDec 2016
Database version94.5

Gene counts

Coding genes18,346
Non coding genes6,492
Small non coding genes1,705
Long non coding genes4,643
Misc non coding genes144
Gene transcripts38,118


Genscan gene predictions50,996
Short Variants23,873,479
Structural variants3

About this species