CCDS Gene
 

Consensus CDS Gene CCDS82748.1

GeneSLC4A7
Descriptionsodium bicarbonate cotransporter 3 isoform f
SequencesCDS,  protein,  genomic
CCDS database CCDS82748.1

Associated Sequences

 mRNAProtein
UCSC GenesENST00000445684.5 
RefSeqNM_001321105.1 NP_001308034.1
VegaOTTHUMT00000341233 OTTHUMP00000208477
EnsemblENST00000445684 ENSP00000406804
MGCBC156213 
BC172463 

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


RefSeq summary of CCDS82748.1

This locus encodes a sodium bicarbonate cotransporter. The encoded transmembrane protein appears to transport sodium and bicarbonate ions in a 1:1 ratio, and is thus considered an electroneutral cotransporter. The encoded protein likely plays a critical role in regulation of intracellular pH involved in visual and auditory sensory transmission. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Apr 2012]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: EU934247.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END##


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Data last updated: 2019-10-03

Description

This track shows human genome high-confidence gene annotations from the Consensus Coding Sequence (CCDS) project. This project is a collaborative effort to identify a core set of human 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 human genome.

Collaborators include:

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

Methods

CDS annotations of the human 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