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    PDE6B phosphodiesterase 6B [ Homo sapiens (human) ]

    Gene ID: 5158, updated on 22-May-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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