CCDS Gene
 

Consensus CDS Gene CCDS57181.1

GenePax6
Descriptionpaired box protein Pax-6 isoform 2
SequencesCDS,  protein,  genomic
CCDS database CCDS57181.1

Associated Sequences

 mRNAProtein
UCSC GenesENSMUST00000090397.12 
ENSMUST00000111082.7 
ENSMUST00000111083.9 
ENSMUST00000111087.9 
RefSeqNM_001244201.2 NP_001231130.1
NM_001244202.2 NP_001231131.1
NM_001310144.1 NP_001297073.1
VegaOTTMUST00000035641 OTTMUSP00000015973
OTTMUST00000035646 OTTMUSP00000015976
OTTMUST00000035648 OTTMUSP00000015978
OTTMUST00000035649 OTTMUSP00000015979
EnsemblENSMUST00000090397 ENSMUSP00000087878
ENSMUST00000111082 ENSMUSP00000106711
ENSMUST00000111083 ENSMUSP00000106712
ENSMUST00000111087 ENSMUSP00000106716
MGCBC011272 
BC036957 

Note: mRNA and protein sequences in other gene collections may differ from the CCDS sequences.


RefSeq summary of CCDS57181.1

This gene encodes a homeobox-containing protein that functions as a regulator of transcription. It plays a key role in the development of neural tissues, particularly the eye. Activity of this protein is also required for expression of glucagon in the pancreas. This gene is regulated by multiple enhancers located up to tens or hundreds of kilobases upstream and downstream of the transcription start sites. Mutations in this gene or deletion of these regulatory elements results in severe defects in eye development. Alternative splicing and the use of alternative promoters results in multiple transcript variants, some of which encode proteins that lack the N-terminal paired domain. [provided by RefSeq, Jul 2015].


View table schema

Go to CCDS track controls

Data last updated at UCSC: 2019-10-03

Description

This track shows mouse genome high-confidence gene annotations from the Consensus 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.

Collaborators include:

For more information on the different gene tracks, see our Genes FAQ.

Methods

CDS annotations of the mouse genome were obtained from two sources: NCBI RefSeq and a union of the gene annotations from Ensembl and Vega, collectively known as Hinxton.

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 gene:

  • 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.

Credits

This track was produced at UCSC from data downloaded from the CCDS project web site.

References

Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. 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 and proteins. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4. PMID: 15608248; PMC: PMC539979