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

Gene ID: 18582, updated on 21-Apr-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 sensory perception of light stimulus. 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, Apr 2022]
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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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. Mechanism and dynamics of INPP5E transport into and inside the ciliary compartment. Kösling SK, et al. Biol Chem, 2018 Feb 23. PMID 29140789
  2. Photoreceptor cGMP phosphodiesterase delta subunit (PDEdelta) functions as a prenyl-binding protein. Zhang H, et al. J Biol Chem, 2004 Jan 2. PMID 14561760
  3. 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
  4. 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
  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 (36) 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)
  • Targeted (2)  1 citation
  • Chemically induced (ENU) (1) 
  • Endonuclease-mediated (1) 

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 ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within phototransduction TAS
Traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within response to stimulus IEA
Inferred from Electronic Annotation
more info
  
involved_in sensory perception of light stimulus IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within 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 cytoskeleton IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
more info
  
located_in membrane IEA
Inferred from Electronic Annotation
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

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