This track shows mouse genome high-confidence gene annotations from the
Coding Sequence (CCDS) project. This project is a collaborative effort
to identify a core set of
mouse protein-coding regions that are consistently annotated and of high
quality. The long-term goal is to support convergence towards a standard set
of gene annotations on the mouse genome.
For more information on the different gene tracks, see our Genes FAQ.
CDS annotations of the mouse genome were obtained from two sources:
RefSeq and a union of the gene annotations from
Vega, collectively known
Genes with identical CDS genomic coordinates in both sets become CCDS
candidates. The genes undergo a quality evaluation, which must be approved by
all collaborators. The following criteria are currently used to assess each
- an initiating ATG (Exception: a non-ATG translation start codon is
annotated if it has sufficient experimental support), a valid stop codon, and
no in-frame stop codons (Exception: selenoproteins, which contain a TGA codon
that is known to be translated to a selenocysteine instead of functioning as
a stop codon)
- ability to be translated from the genome reference sequence without frameshifts
- recognizable splicing sites
- no intersection with putative pseudogene predictions
- supporting transcripts and protein homology
- conservation evidence with other species
A unique CCDS ID is assigned to the CCDS, which links together all gene
annotations with the same CDS. CCDS gene annotations are under continuous
review, with periodic updates to this track.
This track was produced at UCSC from data downloaded from the
Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et
The Ensembl genome database project.
Nucleic Acids Res. 2002 Jan 1;30(1):38-41.
PMID: 11752248; PMC: PMC99161
Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE,
Ruef BJ et al.
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the
human and mouse genomes.
Genome Res. 2009 Jul;19(7):1316-23.
PMID: 19498102; PMC: PMC2704439
Pruitt KD, Tatusova T, Maglott DR.
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4.
PMID: 15608248; PMC: PMC539979