Ensembl mobile site help

Things to know when navigating the Ensembl mobile site

Search box

Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more.

Top navigation

Touch MENU button to open the main menu and touch again to close.

Touch MENU

Left hand side menu

Touch the left menu icon () or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close.

The ? icon

Touch the icon to get help

And don't forget to send us your comments using the feedback link inside the main menu.

EnsemblEnsembl Home

Dog assembly and gene annotation

The domestic dog (Canis lupus familiaris) is a member of the genus Canis (canines), which forms part of the wolf-like canids, and is the most widely abundant terrestrial carnivore. The dog and the extant gray wolf are sister taxa as modern wolves are not closely related to the wolves that were first domesticated, which implies that the direct ancestor of the dog is extinct.

Unlike other domestic species which were primarily selected for production-related traits, dogs were initially selected for their behaviors. In 2016, a study found that there were only 11 fixed genes that showed variation between wolves and dogs. These genes have been shown to affect the catecholamine synthesis pathway, with the majority of the genes affecting the fight-or-flight response (i.e. selection for tameness) and emotional processing.

Assembly

The CanFam3.1 assembly was submitted by Dog Genome Sequencing Consortium on November 2011. The assembly is on chromosome level, consisting of 27,106 contigs assembled into 3,310 scaffolds. From these sequences, 39 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 267,478 while the scaffold N50 is 45,876,610.

Gene annotation

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.

Statistics

Summary

AssemblyCanFam3.1, INSDC Assembly GCA_000002285.2, Sep 2011
Base Pairs2,410,976,875
Golden Path Length2,410,976,875
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedNov 2011
Genebuild releasedJul 2012
Genebuild last updated/patchedJun 2019
Database version104.31

Gene counts

Coding genes20,257
Non coding genes10,081
Small non coding genes2,976
Long non coding genes7,083
Misc non coding genes22
Pseudogenes613
Gene transcripts60,994

Other

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

About this species

HASH(0x3ac75a78)