hg19 CCDS Gene
 

Consensus CDS Gene CCDS6214.1

GeneSTAU2
Descriptiondouble-stranded RNA-binding protein Staufen homolog 2 isoform e
SequencesCDS,  protein,  genomic
CCDS database CCDS6214.1

Associated Sequences

 mRNAProtein
UCSC Genesuc003xzp.3 
uc010lzk.3 
RefSeqNM_001164384.1 NP_001157856.1
NM_014393.2 NP_055208.2
VegaOTTHUMT00000379003 OTTHUMP00000226836
OTTHUMT00000379008 OTTHUMP00000226841
EnsemblENST00000355780 ENSP00000348026
ENST00000522509 ENSP00000427977
MGCBC110447 
BC008369 

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

RefSeq summary of CCDS6214.1

Staufen homolog 2 is a member of the family of double-stranded RNA (dsRNA)-binding proteins involved in the transport and/or localization of mRNAs to different subcellular compartments and/or organelles. These proteins are characterized by the presence of multiple dsRNA-binding domains which are required to bind RNAs having double-stranded secondary structures. Staufen homolog 2 shares 48.5% and 59.9% similarity with drosophila and human staufen, respectively. The exact function of Staufen homolog 2 is not known, but since it contains 3 copies of conserved dsRNA binding domain, it could be involved in double-stranded RNA binding events. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009].

Data schema/format description and download

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Data last updated at UCSC: 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