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PDE6B phosphodiesterase 6B [ Homo sapiens (human) ]

Gene ID: 5158, updated on 3-Jun-2018
Official Symbol
PDE6Bprovided by HGNC
Official Full Name
phosphodiesterase 6Bprovided by HGNC
Primary source
HGNC:HGNC:8786
See related
Ensembl:ENSG00000133256 MIM:180072; Vega:OTTHUMG00000159909
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
rd1; PDEB; RP40; CSNB3; CSNBAD2; GMP-PDEbeta
Summary
Photon absorption triggers a signaling cascade in rod photoreceptors that activates cGMP phosphodiesterase (PDE), resulting in the rapid hydrolysis of cGMP, closure of cGMP-gated cation channels, and hyperpolarization of the cell. PDE is a peripheral membrane heterotrimeric enzyme made up of alpha, beta, and gamma subunits. This gene encodes the beta subunit. Mutations in this gene result in retinitis pigmentosa and autosomal dominant congenital stationary night blindness. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2009]
Expression
Broad expression in brain (RPKM 2.0), thyroid (RPKM 1.1) and 19 other tissues See more
Orthologs
See PDE6B in Genome Data Viewer
Location:
4p16.3
Exon count:
28
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 4 NC_000004.12 (587325..670892)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (619363..664681)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene phosphatidylinositol glycan anchor biosynthesis class G Neighboring gene uncharacterized LOC105374338 Neighboring gene uncharacterized LOC101928521 Neighboring gene ATP synthase membrane subunit e Neighboring gene solute carrier family 49 member 3 Neighboring gene myosin light chain 5

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

  • 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
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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
GMP metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
phototransduction, visible light TAS
Traceable Author Statement
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 IEA
Inferred from Electronic Annotation
more info
 
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
 
Preferred Names
rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
Names
GMP-PDE beta
phosphodiesterase 6B, cGMP-specific, rod, beta
rod cGMP-phosphodiesterase beta-subunit
NP_000274.2
NP_001138763.1
NP_001138764.1
NP_001337083.1
NP_001337084.1
XP_011511775.1
XP_011511776.1
XP_011511777.1
XP_011511778.1
XP_011511780.1
XP_016863773.1
XP_016863774.1
XP_016863775.1

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_009839.1 RefSeqGene

    Range
    5001..50319
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000283.3NP_000274.2  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC107464, AI131517, BC000249, S41458
    Consensus CDS
    CCDS33932.1
    UniProtKB/Swiss-Prot
    P35913
    Related
    ENSP00000420295.1, OTTHUMP00000216948, ENST00000496514.5, OTTHUMT00000358109
    Conserved Domains (2) summary
    smart00065
    Location:71230
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:556801
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  2. NM_001145291.1NP_001138763.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. The resulting isoform (2) lacks one amino acid near the C-terminus, compared to isoform 1.
    Source sequence(s)
    AC107464, AI131517, BC000249, X66142
    Consensus CDS
    CCDS54703.1
    UniProtKB/Swiss-Prot
    P35913
    Related
    ENSP00000255622.6, OTTHUMP00000216947, ENST00000255622.10, OTTHUMT00000358108
    Conserved Domains (2) summary
    smart00065
    Location:71230
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:556801
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  3. NM_001145292.1NP_001138764.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 3

    See identical proteins and their annotated locations for NP_001138764.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) represents use of an alternate promoter and 5' UTR, and uses a downstream start codon, compared to variant 1. The resulting isoform (3) has a substantially shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AI131517, AK295285, BC000249, BX487988
    Consensus CDS
    CCDS46993.1
    UniProtKB/Swiss-Prot
    P35913
    UniProtKB/TrEMBL
    B4DHV7
    Related
    ENSP00000406334.2, OTTHUMP00000216949, ENST00000429163.6, OTTHUMT00000358110
    Conserved Domains (2) summary
    smart00065
    Location:52160
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:277522
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  4. NM_001350154.1NP_001337083.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) represents the use of an alternate promoter. It differs in the 5' UTR, uses a downstream start codon and contains multiple coding region differences, compared to variant 1. It encodes isoform 4, which is shorter than isoform 1.
    Source sequence(s)
    AC107464, AI131517
    Conserved Domains (2) summary
    smart00065
    Location:52160
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:277517
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  5. NM_001350155.1NP_001337084.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) represents the use of an alternate promoter. It differs in the 5' UTR, uses a downstream start codon and contains multiple coding region differences, resulting in a frameshift and an early stop codon, compared to variant 1. It encodes isoform 5, which is shorter and has a distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AC107464, AI131517
    Conserved Domains (2) summary
    smart00065
    Location:154
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:171411
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase

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_000004.12 Reference GRCh38.p12 Primary Assembly

    Range
    587325..670892
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011513474.3XP_011511776.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X2

    Conserved Domains (2) summary
    smart00065
    Location:144303
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:629874
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  2. XM_011513473.3XP_011511775.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X1

    Conserved Domains (2) summary
    smart00065
    Location:144303
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:629874
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  3. XM_011513476.3XP_011511778.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X4

    Conserved Domains (2) summary
    smart00065
    Location:144303
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:629857
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  4. XM_011513475.2XP_011511777.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X3

    Conserved Domains (2) summary
    smart00065
    Location:71230
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:556801
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  5. XM_017008286.1XP_016863775.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X6

    UniProtKB/Swiss-Prot
    P35913
  6. XM_017008284.1XP_016863773.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X5

    Conserved Domains (2) summary
    smart00065
    Location:52160
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:277517
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
  7. XM_017008285.1XP_016863774.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X6

    UniProtKB/Swiss-Prot
    P35913
  8. XM_011513478.2XP_011511780.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform X7

    Conserved Domains (2) summary
    smart00065
    Location:1182
    GAF; Domain present in phytochromes and cGMP-specific phosphodiesterases
    pfam00233
    Location:199444
    PDEase_I; 3'5'-cyclic nucleotide phosphodiesterase
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