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

    Gene ID: 110855, updated on 11-Apr-2024

    Summary

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    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
    human all
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. HDAC inhibition in the cpfl1 mouse protects degenerating cone photoreceptors in vivo. Trifunović D, et al. Hum Mol Genet, 2016 Oct 15. PMID 28172811
    2. Structural and functional phenotyping in the cone-specific photoreceptor function loss 1 (cpfl1) mouse mutant - a model of cone dystrophies. Fischer MD, et al. Adv Exp Med Biol, 2010. PMID 20238063
    3. An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas. Bachu VS, et al. Dev Biol, 2022 Aug. PMID 35644251, Free PMC Article
    4. Single AAV-mediated mutation replacement genome editing in limited number of photoreceptors restores vision in mice. Nishiguchi KM, et al. Nat Commun, 2020 Jan 24. PMID 31980606, Free PMC Article
    5. Systematic spatiotemporal mapping reveals divergent cell death pathways in three mouse models of hereditary retinal degeneration. Power MJ, et al. J Comp Neurol, 2020 May. PMID 31710697

    See all (49) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Reconstitution of the phosphodiesterase 6 maturation process important for photoreceptor cell function.
      Title: Reconstitution of the phosphodiesterase 6 maturation process important for photoreceptor cell function.
    2. An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas.
      Title: An enhancer located in a Pde6c intron drives transient expression in the cone photoreceptors of developing mouse and human retinas.
    3. AIPL1-mediated production of folded PDE6C is markedly elevated in the presence of the inhibitory Pgamma-subunit of PDE6.
      Title: Aryl Hydrocarbon Receptor-interacting Protein-like 1 Is an Obligate Chaperone of Phosphodiesterase 6 and Is Assisted by the γ-Subunit of Its Client.
    4. A comprehensive in vivo assessment of retinal morphology and function was performed in cpfl1 (cone photoreceptor function loss 1) mice to better define the disease process in this model of cone dystrophies.
      Title: Structural and functional phenotyping in the cone-specific photoreceptor function loss 1 (cpfl1) mouse mutant - a model of cone dystrophies.
    5. the spontaneous mouse mutant cpfl1 that features a lack of cone function and rapid degeneration of the cone photoreceptors represents a homologous mouse model for PDE6C associated achromatopsia.
      Title: A homologous genetic basis of the murine cpfl1 mutant and human achromatopsia linked to mutations in the PDE6C gene.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    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

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    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_001170959.2 → NP_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:81 → 232
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      pfam00233
      Location:561 → 781
      PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

    2. NM_033614.3 → NP_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:81 → 232
      GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
      pfam00233
      Location:561 → 806
      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)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q91ZQ1.1 GenPept UniProtKB/Swiss-Prot:Q91ZQ1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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