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    Pde6d phosphodiesterase 6D, cGMP-specific, rod, delta [ Mus musculus (house mouse) ]

    Gene ID: 18582, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Pde6dprovided by MGI
    Official Full Name
    phosphodiesterase 6D, cGMP-specific, rod, deltaprovided by MGI
    Primary source
    MGI:MGI:1270843
    See related
    Ensembl:ENSMUSG00000026239 AllianceGenome:MGI:1270843
    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
    PrBP/delta
    Summary
    Enables GTPase inhibitor activity. Predicted to be involved in visual perception. Predicted to act upstream of or within phototransduction. Predicted to be located in cytoplasmic vesicle and cytosol. Predicted to be active in cytoplasm. Is expressed in several structures, including alimentary system; genitourinary system; nervous system; respiratory system; and sensory organ. Human ortholog(s) of this gene implicated in Joubert syndrome 22. Orthologous to human PDE6D (phosphodiesterase 6D). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in CNS E18 (RPKM 26.2), testis adult (RPKM 22.8) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Pde6d in Genome Data Viewer
    Location:
    1 C5; 1 43.96 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 1 NC_000067.7 (86470735..86510260, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (86543012..86582785, complement)

    Chromosome 1 - NC_000067.7Genomic Context describing neighboring genes Neighboring gene ribosomal protein L30, pseudogene 6 Neighboring gene STARR-seq mESC enhancer starr_01585 Neighboring gene STARR-seq mESC enhancer starr_01588 Neighboring gene STARR-positive B cell enhancer ABC_E11078 Neighboring gene STARR-positive B cell enhancer ABC_E5780 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:88406107-88406370 Neighboring gene STARR-seq mESC enhancer starr_01595 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:88421790-88421979 Neighboring gene STARR-positive B cell enhancer mm9_chr1:88422932-88423233 Neighboring gene STARR-positive B cell enhancer mm9_chr1:88428991-88429292 Neighboring gene prothymosin alpha Neighboring gene STARR-positive B cell enhancer ABC_E2552 Neighboring gene CapStarr-seq enhancer MGSCv37_chr1:88483544-88483727 Neighboring gene COP9 signalosome subunit 7B Neighboring gene STARR-seq mESC enhancer starr_01597 Neighboring gene predicted gene, 41908

    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. Photoreceptor cGMP phosphodiesterase delta subunit (PDEdelta) functions as a prenyl-binding protein. Zhang H, et al. J Biol Chem, 2004 Jan 2. PMID 14561760
    2. Mechanism and dynamics of INPP5E transport into and inside the ciliary compartment. Kösling SK, et al. Biol Chem, 2018 Feb 23. PMID 29140789
    3. Characterization of human and mouse rod cGMP phosphodiesterase delta subunit (PDE6D) and chromosomal localization of the human gene. Li N, et al. Genomics, 1998 Apr 1. PMID 9570951
    4. Cloning and gene structure of the rod cGMP phosphodiesterase delta subunit gene (PDED) in man and mouse. Lorenz B, et al. Eur J Hum Genet, 1998 May-Jun. PMID 9781033
    5. Unc119 gene deletion partially rescues the GRK1 transport defect of Pde6d (- /-) cones. Zhang H, et al. Adv Exp Med Biol, 2014. PMID 24664735, Free PMC Article

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. It postulates a three-step mechanism regulating ciliary localization of INPP5E, consisting of farnesylation- and PDE6delta-mediated targeting, INPP5E-PDE6delta complex diffusion into the cilium with transfer to the IFT system, and retention inside cilia.
      Title: Mechanism and dynamics of INPP5E transport into and inside the ciliary compartment.
    2. the affinity to PDE6delta and the release by Arl2/3 in addition to a retention signal are the determinants for cargo sorting and enrichment at its destination.
      Title: PDE6δ-mediated sorting of INPP5E into the cilium is determined by cargo-carrier affinity.
    3. Knockout of Unc119 partially reversed the transport defect of GRK1 in cone photoreceptors caused by deletion of Pde6d.
      Title: Unc119 gene deletion partially rescues the GRK1 transport defect of Pde6d (- /-) cones.
    4. absence of PrBP/delta in retina impairs transport of prenylated proteins, particularly rhodopsin kinase 1 and cone PDE, to rod and cone outer segments
      Title: Deletion of PrBP/delta impedes transport of GRK1 and PDE6 catalytic subunits to photoreceptor outer segments.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Chemically induced (ENU) (1) 
    • Endonuclease-mediated (1) 
    • Targeted (2)  1 citation

    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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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables 3',5'-cyclic-GMP phosphodiesterase activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables GTPase inhibitor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables small GTPase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within phototransduction TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic vesicle ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasmic vesicle membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoskeleton IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
    Names
    GMP-PDE delta
    NP_001347745.1
    NP_001347746.1
    NP_032827.1
    XP_030108092.1

    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_001360816.2 → NP_001347745.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC158132
      Conserved Domains (1) summary
      pfam05351
      Location:10 → 88
      GMP_PDE_delta; GMP-PDE, delta subunit

    2. NM_001360817.2 → NP_001347746.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC158132
      Conserved Domains (1) summary
      pfam05351
      Location:1 → 79
      GMP_PDE_delta; GMP-PDE, delta subunit

    3. NM_008801.4 → NP_032827.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta isoform 1

      See identical proteins and their annotated locations for NP_032827.1

      Status: VALIDATED

      Source sequence(s)
      AC158132
      Consensus CDS
      CCDS15121.1
      UniProtKB/Swiss-Prot
      O55057
      UniProtKB/TrEMBL
      Q3TDQ8, Q3URU9
      Related
      ENSMUSP00000027444.9, ENSMUST00000027444.15
      Conserved Domains (1) summary
      pfam05351
      Location:10 → 149
      GMP_PDE_delta; GMP-PDE, delta subunit

    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_000067.7 Reference GRCm39 C57BL/6J

      Range
      86470735..86510260 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_030252232.1 → XP_030108092.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta isoform X1

      Conserved Domains (1) summary
      pfam05351
      Location:1 → 79
      GMP_PDE_delta; GMP-PDE, delta subunit
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O55057.1 GenPept UniProtKB/Swiss-Prot:O55057

    Gene LinkOut

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

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