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PDE6B phosphodiesterase 6B [ Homo sapiens (human) ]

Gene ID: 5158, updated on 4-Jun-2020

Summary

Official Symbol
PDE6Bprovided by HGNC
Official Full Name
phosphodiesterase 6Bprovided by HGNC
Primary source
HGNC:HGNC:8786
See related
Ensembl:ENSG00000133256 MIM:180072
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

Genomic context

See PDE6B in Genome Data Viewer
Location:
4p16.3
Exon count:
28
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 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 uncharacterized LOC105374338 Neighboring gene transmembrane protein 271 Neighboring gene PDE6B antisense RNA 1 Neighboring gene ATP synthase membrane subunit e Neighboring gene solute carrier family 49 member 3 Neighboring gene myosin light chain 5

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 Functions

What's a GeneRIF?

Pathways from PubChem

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 
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 
Wnt signaling pathway, calcium modulating pathway TAS
Traceable Author Statement
more info
 
entrainment of circadian clock by photoperiod ISS
Inferred from Sequence or Structural Similarity
more info
 
phototransduction, visible light TAS
Traceable Author Statement
more info
PubMed 
regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
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
 
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 beta
Names
GMP-PDE beta
phosphodiesterase 6B, cGMP-specific, rod, beta
rod cGMP-phosphodiesterase beta-subunit
NP_000274.3
NP_001138763.2
NP_001138764.2
NP_001337083.1
NP_001337084.1
NP_001366175.1
NP_001366176.1
XP_011511775.1
XP_011511776.1
XP_011511777.1
XP_011511778.1
XP_011511780.1
XP_016863773.1

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_009839.1 RefSeqGene

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

mRNA and Protein(s)

  1. NM_000283.4NP_000274.3  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
    Consensus CDS
    CCDS33932.1
    Related
    ENSP00000420295.1, ENST00000496514.5
  2. NM_001145291.2NP_001138763.2  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
    Consensus CDS
    CCDS54703.1
    Related
    ENSP00000255622.6, ENST00000255622.10
  3. NM_001145292.2NP_001138764.2  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 3

    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)
    AC107464
    Consensus CDS
    CCDS46993.1
    Related
    ENSP00000406334.2, ENST00000429163.6
  4. NM_001350154.3NP_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
    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_001350155.3NP_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
    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
  6. NM_001379246.1NP_001366175.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC107464
  7. NM_001379247.1NP_001366176.1  rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC107464

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 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_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
  6. 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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