Dog assembly and gene annotation

Assembly

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
Blood17589
Brain21402
Heart19034
Kidney20738
Liver19824
Lung20331
Ovary22191
Skin20205
Skeletal muscle18173
Testis32652

Vega logo Additional manual annotation of this genome can be found in Vega

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyCanFam3.1, INSDC Assembly GCA_000002285.2, Sep 2011
Database version78.31
Base Pairs2,392,715,236
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).

2,410,976,875
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedNov 2011
Genebuild releasedJul 2012
Genebuild last updated/patchedJul 2012

Gene counts

Coding genes

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

19,856
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.

3,774
Pseudogenes

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.

950
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.29,884

Other

Genscan gene predictions46,687
Short Variants3,466,982
Structural variants470