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Pde6c phosphodiesterase 6C, cGMP specific, cone, alpha prime [ Mus musculus (house mouse) ]

Gene ID: 110855, updated on 18-Apr-2024

Summary

Official Symbol
Pde6cprovided by MGI
Official Full Name
phosphodiesterase 6C, cGMP specific, cone, alpha primeprovided by MGI
Primary source
MGI:MGI:105956
See related
Ensembl:ENSMUSG00000024992 AllianceGenome:MGI:105956
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
cpfl1
Summary
Predicted to enable 3',5'-cyclic-nucleotide phosphodiesterase activity. Acts upstream of or within phototransduction, visible light; retinal cone cell development; and visual perception. Predicted to be located in plasma membrane. Is expressed in brain and retina. Used to study achromatopsia. Human ortholog(s) of this gene implicated in cone-rod dystrophy. Orthologous to human PDE6C (phosphodiesterase 6C). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in liver E18 (RPKM 5.7), placenta adult (RPKM 4.9) and 2 other tissues See more
Orthologs
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Genomic context

Location:
19 C2; 19 32.77 cM
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 19 NC_000085.7 (38121220..38172391)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 19 NC_000085.6 (38132781..38183955)

Chromosome 19 - NC_000085.7Genomic Context describing neighboring genes Neighboring gene free fatty acid receptor 4 Neighboring gene retinol binding protein 4, plasma Neighboring gene predicted gene, 32440 Neighboring gene predicted gene, 52398 Neighboring gene STARR-seq mESC enhancer starr_46076 Neighboring gene FRA10A associated CGG repeat 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr19:38298641-38298824 Neighboring gene STARR-seq mESC enhancer starr_46077 Neighboring gene STARR-seq mESC enhancer starr_46079 Neighboring gene predicted gene, 32574 Neighboring gene predicted gene, 32491

Genomic regions, transcripts, and products

Expression

  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 
  • Spontaneous (1)  1 citation

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Gene Ontology Provided by MGI

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 3',5'-cyclic-nucleotide phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
enables cGMP binding IEA
Inferred from Electronic Annotation
more info
 
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
 
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
enables phosphoric diester hydrolase activity 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
 
acts_upstream_of_or_within phototransduction, visible light IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within response to stimulus IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within retinal cone cell development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within sensory perception of light stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in signal transduction IEA
Inferred from Electronic Annotation
more info
 
involved_in visual perception IBA
Inferred from Biological aspect of Ancestor
more info
 
acts_upstream_of_or_within visual perception IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in membrane IEA
Inferred from Electronic Annotation
more info
 
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
NP_001164430.1
NP_291092.1

NCBI Reference Sequences (RefSeq)

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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.

mRNA and Protein(s)

  1. NM_001170959.2NP_001164430.1  cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' isoform 2

    See identical proteins and their annotated locations for NP_001164430.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the coding region, compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AC112153
    Consensus CDS
    CCDS50431.1
    UniProtKB/Swiss-Prot
    Q91ZQ1
    Related
    ENSMUSP00000107948.2, ENSMUST00000112329.3
    Conserved Domains (2) summary
    smart00065
    Location:81232
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:561781
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  2. NM_033614.3NP_291092.1  cone cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha' isoform 1

    See identical proteins and their annotated locations for NP_291092.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC112153
    Consensus CDS
    CCDS37971.1
    UniProtKB/Swiss-Prot
    Q8R0D4, Q91ZQ1
    Related
    ENSMUSP00000025956.6, ENSMUST00000025956.13
    Conserved Domains (2) summary
    smart00065
    Location:81232
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:561806
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000085.7 Reference GRCm39 C57BL/6J

    Range
    38121220..38172391
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)