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Dog assembly and gene annotation


The CanFam3.1 assembly of the dog genome was produced in September 2011 by the Broad Institute of MIT and Harvard. It consists of 39 chromosomes (1-38 and X) and 15 unplaced scaffolds.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000002285.2

Gene annotation

CanFam3.1 was annotated using a standard Ensembl mammalian genebuild pipeline, incorporating RNA-Seq data provided by the Broad Institute. 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 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. 8,968 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
Skeletal muscle18173

More information

General information about this species can be found in Wikipedia.



AssemblyCanFam3.1, INSDC Assembly GCA_000002285.2, Sep 2011
Base Pairs2,392,715,236
Golden Path Length2,410,976,875
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2011
Genebuild releasedJul 2012
Genebuild last updated/patchedMay 2016
Database version94.31

Gene counts

Coding genes19,856
Non coding genes11,898
Small non coding genes3,348
Long non coding genes8,124
Misc non coding genes426
Gene transcripts39,074


Genscan gene predictions46,687
Short Variants6,136,915
Structural variants104,982

About this species