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

Summary

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
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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

Go to the top of the page Help

Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (1)
Endonuclease-mediated (1)
Targeted (2) 1 citation

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH128201 (e-PCR)
- UniSTS:211509

AI841218 (e-PCR)
- UniSTS:165087

Pde6d (e-PCR), detects polymorphism
- UniSTS:507127

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

Go to the top of the page Help

Preferred Names: retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta

Names: GMP-PDE delta

NP_001347745.1

EC 3.1.4.17

NP_001347746.1

EC 3.1.4.17

NP_032827.1

EC 3.1.4.17

XP_030108092.1

EC 3.1.4.17

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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.

mRNA and Protein(s)

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
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
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

NC_000067.7 Reference GRCm39 C57BL/6J

Range

86470735..86510260 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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