Format

Send to:

Choose Destination

PDE6D phosphodiesterase 6D [ Homo sapiens (human) ]

Gene ID: 5147, updated on 5-Aug-2018

Summary

Official Symbol
PDE6Dprovided by HGNC
Official Full Name
phosphodiesterase 6Dprovided by HGNC
Primary source
HGNC:HGNC:8788
See related
Ensembl:ENSG00000156973 MIM:602676; Vega:OTTHUMG00000153785
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PDED; JBTS22
Summary
This gene encodes the delta subunit of rod-specific photoreceptor phosphodiesterase (PDE), a key enzyme in the phototransduction cascade. A similar protein in cow functions in solubilizing membrane-bound PDE. In addition to its role in the PDE complex, the encoded protein is thought to bind to prenyl groups of proteins to target them to subcellular organelles called cilia. Mutations in this gene are associated with Joubert syndrome-22. Alternative splicing results in multiple splice variants. [provided by RefSeq, Mar 2014]
Expression
Ubiquitous expression in testis (RPKM 13.2), brain (RPKM 8.3) and 24 other tissues See more
Orthologs

Genomic context

See PDE6D in Genome Data Viewer
Location:
2q37.1
Exon count:
6
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 2 NC_000002.12 (231732425..231781327, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (232597147..232645974, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RN7SL499P-PTMA intergenic region enhancers Neighboring gene microRNA 1244-1 Neighboring gene prothymosin alpha Neighboring gene RNA, U6 small nuclear 840, pseudogene Neighboring gene COP9 signalosome subunit 7B Neighboring gene ribosomal protein L28 pseudogene 2 Neighboring gene guanidinoacetate N-methyltransferase pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Joubert syndrome 22
MedGen: C3810278 OMIM: 615665 GeneReviews: Joubert Syndrome
Compare labs

NHGRI GWAS Catalog

Description
Genetic variants associated with disordered eating.
NHGRI GWA Catalog
Many sequence variants affecting diversity of adult human height.
NHGRI GWA Catalog

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3',5'-cyclic-nucleotide phosphodiesterase activity IEA
Inferred from Electronic Annotation
more info
 
GTPase inhibitor activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Rab GTPase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
negative regulation of GTPase activity IEA
Inferred from Electronic Annotation
more info
 
response to stimulus IEA
Inferred from Electronic Annotation
more info
 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cilium TAS
Traceable Author Statement
more info
 
cytoplasmic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
cytoskeleton IEA
Inferred from Electronic Annotation
more info
 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Names
GMP-PDE delta
phosphodiesterase 6D, cGMP-specific, rod, delta
protein p17
NP_001277947.1
NP_002592.1
XP_011509644.1

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_034064.1 RefSeqGene

    Range
    5001..53903
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001291018.1NP_001277947.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta isoform 2

    See identical proteins and their annotated locations for NP_001277947.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region resulting in a frameshift compared to variant 1. The encoded protein (isoform 2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC073476, BC007831, BI754373, HY037751
    Consensus CDS
    CCDS77538.1
    UniProtKB/Swiss-Prot
    O43924
    UniProtKB/TrEMBL
    B8ZZK5
    Related
    ENSP00000387108.1, OTTHUMP00000204404, ENST00000409772.5, OTTHUMT00000332411
    Conserved Domains (1) summary
    pfam05351
    Location:1088
    GMP_PDE_delta; GMP-PDE, delta subunit
  2. NM_002601.3NP_002592.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta isoform 1

    See identical proteins and their annotated locations for NP_002592.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC007831, HY037751
    Consensus CDS
    CCDS33398.1
    UniProtKB/Swiss-Prot
    O43924
    UniProtKB/TrEMBL
    Q6IB24
    Related
    ENSP00000287600.4, OTTHUMP00000204402, ENST00000287600.8, OTTHUMT00000332407
    Conserved Domains (1) summary
    pfam05351
    Location:10149
    GMP_PDE_delta; GMP-PDE, delta subunit

RNA

  1. NR_110994.1 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks several exons and contains an alternate 3' terminal exon compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region found in variant 1.
    Source sequence(s)
    AK311623, HY037751
    Related
    ENST00000477748.1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p12 Primary Assembly

    Range
    231732425..231781327 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511342.1XP_011509644.1  retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta isoform X1

    Conserved Domains (1) summary
    pfam05351
    Location:1130
    GMP_PDE_delta; GMP-PDE, delta subunit
Support Center