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    PDE6C phosphodiesterase 6C [ Homo sapiens (human) ]

    Gene ID: 5146, updated on 27-Nov-2024

    Summary

    Official Symbol
    PDE6Cprovided by HGNC
    Official Full Name
    phosphodiesterase 6Cprovided by HGNC
    Primary source
    HGNC:HGNC:8787
    See related
    Ensembl:ENSG00000095464 MIM:600827; AllianceGenome:HGNC:8787
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    COD4; ACHM5; PDEA2
    Summary
    This gene encodes the alpha-prime subunit of cone phosphodiesterase, which is composed of a homodimer of two alpha-prime subunits and 3 smaller proteins of 11, 13, and 15 kDa. Mutations in this gene are associated with cone dystrophy type 4 (COD4). [provided by RefSeq, Mar 2010]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    NEW
    Try the new Gene table
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    Genomic context

    See PDE6C in Genome Data Viewer
    Location:
    10q23.33
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (93612537..93666010)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (94492491..94545941)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (95372294..95425767)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902485 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:95341272-95341477 Neighboring gene free fatty acid receptor 4 Neighboring gene retinol binding protein 4 Neighboring gene FRA10A associated CGG repeat 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3786 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:95474242-95474394 Neighboring gene fragile site, folic acid type, rare, fra(10)(q23.3) or fra(10)(q24.2) Neighboring gene uncharacterized LOC101927013 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:95505761-95506512 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:95508859-95509841

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Achromatopsia
    MedGen: C0152200 GeneReviews: Achromatopsia
    not available
    Cone dystrophy 4
    MedGen: C2751308 OMIM: 613093 GeneReviews: Achromatopsia
    not available

    EBI GWAS Catalog

    Description
    A genome-wide association meta-analysis of preschool internalizing problems.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 3',5'-cyclic-AMP phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables 3',5'-cyclic-GMP phosphodiesterase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables cGMP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables calmodulin-activated 3',5'-cyclic-GMP phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables calmodulin-activated dual specificity 3',5'-cyclic-GMP, 3',5'-cyclic-AMP phosphodiesterase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in cAMP-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in phototransduction, visible light IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retinal cone cell development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in visual perception IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'
    Names
    cGMP phosphodiesterase 6C
    phosphodiesterase 6C, cGMP-specific, cone, alpha prime
    NP_006195.3

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_016752.1 RefSeqGene

      Range
      4950..58423
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_006204.4NP_006195.3  cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha'

      See identical proteins and their annotated locations for NP_006195.3

      Status: REVIEWED

      Source sequence(s)
      AL157396, AL356214, BG206143, BG220856, U31973
      Consensus CDS
      CCDS7429.1
      UniProtKB/Swiss-Prot
      A6NCR6, P51160, Q5VY29
      Related
      ENSP00000360502.3, ENST00000371447.4
      Conserved Domains (2) summary
      smart00065
      Location:80231
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      pfam00233
      Location:561806
      PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      93612537..93666010
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      94492491..94545941
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)