CCDS Gene
 

Consensus CDS Gene CCDS1946.2

GenePCGF1
Descriptionpolycomb group RING finger protein 1
SequencesCDS,  protein,  genomic
CCDS database CCDS1946.2

Associated Sequences

 mRNAProtein
UCSC Genesuc002slz.3 
RefSeqNM_032673.2 NP_116062.2
VegaOTTHUMT00000252216 OTTHUMP00000160412
EnsemblENST00000233630 ENSP00000233630
MGCBC004952 

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


RefSeq summary of CCDS1946.2

PCGF1 is a mammalian homolog of the Drosophila polycomb group genes, which act as transcriptional repressors to regulate anterior-posterior patterning in early embryonic development (Nunes et al., 2001 [PubMed 11287196]). See also PCGF2 (MIM 600346).[supplied by OMIM, Aug 2008]. 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 :: SRR5189667.331340.1, SRR1163655.595382.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000233630.11/ ENSP00000233630.6 RefSeq Select criteria :: based on conservation, expression, longest protein ##RefSeq-Attributes-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