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PDE6A phosphodiesterase 6A [ Homo sapiens (human) ]

Gene ID: 5145, updated on 13-Feb-2019

Summary

Official Symbol
PDE6Aprovided by HGNC
Official Full Name
phosphodiesterase 6Aprovided by HGNC
Primary source
HGNC:HGNC:8785
See related
Ensembl:ENSG00000132915 MIM:180071
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
PDEA; RP43; CGPR-A
Summary
This gene encodes the cyclic-GMP (cGMP)-specific phosphodiesterase 6A alpha subunit, expressed in cells of the retinal rod outer segment. The phosphodiesterase 6 holoenzyme is a heterotrimer composed of an alpha, beta, and two gamma subunits. cGMP is an important regulator of rod cell membrane current, and its dynamic concentration is established by phosphodiesterase 6A cGMP hydrolysis and guanylate cyclase cGMP synthesis. The protein is a subunit of a key phototransduction enzyme and participates in processes of transmission and amplification of the visual signal. Mutations in this gene have been identified as one cause of autosomal recessive retinitis pigmentosa. [provided by RefSeq, Jul 2008]
Expression
Low expression observed in reference dataset See more
Orthologs

Genomic context

See PDE6A in Genome Data Viewer
Location:
5q32
Exon count:
24
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 5 NC_000005.10 (149857956..149944793, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149237519..149324356, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PPARG coactivator 1 beta Neighboring gene microRNA 378a Neighboring gene NFE2L2 motif-containing MPRA enhancer 202 Neighboring gene mitochondrial fission factor pseudogene Neighboring gene solute carrier family 26 member 2 Neighboring gene tigger transposable element derived 6 Neighboring gene HMG-box containing 3

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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Activation of the phototransduction cascade, organism-specific biosystem (from REACTOME)
    Activation of the phototransduction cascade, organism-specific biosystemThe photoreceptor cascade starts with light isomerization of 11-cis-retinal (11cRAL) of rhodopsin (RHO) to all-trans-retinal (atRAL), inducing a conformational change in RHO to the active, metarhodop...
  • Beta-catenin independent WNT signaling, organism-specific biosystem (from REACTOME)
    Beta-catenin independent WNT signaling, organism-specific biosystemHumans and mice have 19 identified WNT proteins that were originally classified as either 'canonical' or 'non-canonical' depending upon whether they were able to transform the mouse mammary epithelia...
  • Ca2+ pathway, organism-specific biosystem (from REACTOME)
    Ca2+ pathway, organism-specific biosystemA number of so called non-canonical WNT ligands have been shown to promote intracellular calcium release upon FZD binding. This beta-catenin-independent WNT pathway acts through heterotrimeric G pro...
  • Inactivation, recovery and regulation of the phototransduction cascade, organism-specific biosystem (from REACTOME)
    Inactivation, recovery and regulation of the phototransduction cascade, organism-specific biosystemTo terminate the single photon response and restore the system to its basal state, the three activated intermediates in phototransduction, rhodopsin (MII), transducin alpha subunit with GTP bound (GN...
  • Phototransduction, organism-specific biosystem (from KEGG)
    Phototransduction, organism-specific biosystemPhototransduction is a biochemical process by which the photoreceptor cells generate electrical signals in response to captured photons. The vertebrate cascade starts with the absorption of photons b...
  • Phototransduction, conserved biosystem (from KEGG)
    Phototransduction, conserved biosystemPhototransduction is a biochemical process by which the photoreceptor cells generate electrical signals in response to captured photons. The vertebrate cascade starts with the absorption of photons b...
  • Purine metabolism, organism-specific biosystem (from KEGG)
    Purine metabolism, organism-specific biosystem
    Purine metabolism
  • Purine metabolism, conserved biosystem (from KEGG)
    Purine metabolism, conserved biosystem
    Purine metabolism
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Wnt, organism-specific biosystem (from REACTOME)
    Signaling by Wnt, organism-specific biosystemWNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Sai...
  • The phototransduction cascade, organism-specific biosystem (from REACTOME)
    The phototransduction cascade, organism-specific biosystemThe visual pigment (rhodopsin in rods) consists of an 11-cis-retinal (11cRAL) chromophore covalently attached to a GPCR opsin family member via a Schiff base linkage. Upon photon absorption, 11cRAL i...
  • Visual phototransduction, organism-specific biosystem (from REACTOME)
    Visual phototransduction, organism-specific biosystemVisual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are p...
  • Visual signal transduction: Rods, organism-specific biosystem (from Pathway Interaction Database)
    Visual signal transduction: Rods, organism-specific biosystem
    Visual signal transduction: Rods

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-GMP phosphodiesterase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
3',5'-cyclic-GMP phosphodiesterase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
G protein-coupled receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
G protein-coupled receptor signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
Wnt signaling pathway, calcium modulating pathway TAS
Traceable Author Statement
more info
 
regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of cytosolic calcium ion concentration IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of rhodopsin mediated signaling pathway TAS
Traceable Author Statement
more info
 
retina development in camera-type eye IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rhodopsin mediated signaling pathway TAS
Traceable Author Statement
more info
PubMed 
visual perception IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
photoreceptor disc membrane TAS
Traceable Author Statement
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha
Names
GMP-PDE alpha
PDE V-B1
cGMP phosphodiesterase alpha subunit
phosphodiesterase 6A, cGMP-specific, rod, alpha
rod photoreceptor cGMP phosphodiesterase alpha subunit
NP_000431.2
XP_011535952.1
XP_011535953.1
XP_011535954.1
XP_011535955.1
XP_011535956.1
XP_016865061.1

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_009102.1 RefSeqGene

    Range
    5001..91838
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000440.3NP_000431.2  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha

    See identical proteins and their annotated locations for NP_000431.2

    Status: REVIEWED

    Source sequence(s)
    AC008427, AC008545, BC035909, BU734142, M26061
    Consensus CDS
    CCDS4299.1
    UniProtKB/Swiss-Prot
    P16499
    Related
    ENSP00000255266.5, ENST00000255266.9
    Conserved Domains (2) summary
    smart00065
    Location:254441
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:558802
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p12 Primary Assembly

    Range
    149857956..149944793 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017009572.2XP_016865061.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X1

    UniProtKB/TrEMBL
    F1T0K3
    Related
    ENSP00000478060.1, ENST00000613228.1
    Conserved Domains (2) summary
    smart00065
    Location:173360
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:477721
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  2. XM_011537650.2XP_011535952.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X2

    Conserved Domains (2) summary
    smart00065
    Location:40146
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:263507
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  3. XM_011537652.1XP_011535954.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X4

    See identical proteins and their annotated locations for XP_011535954.1

    Conserved Domains (2) summary
    smart00065
    Location:1182
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:199443
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  4. XM_011537651.2XP_011535953.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X3

    Conserved Domains (2) summary
    smart00065
    Location:792
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:209453
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  5. XM_011537654.2XP_011535956.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X4

    See identical proteins and their annotated locations for XP_011535956.1

    Conserved Domains (2) summary
    smart00065
    Location:1182
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:199443
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  6. XM_011537653.2XP_011535955.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpha isoform X4

    See identical proteins and their annotated locations for XP_011535955.1

    Conserved Domains (2) summary
    smart00065
    Location:1182
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:199443
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
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