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    PDGFRB platelet derived growth factor receptor beta [ Homo sapiens (human) ]

    Gene ID: 5159, updated on 11-Jul-2021

    Summary

    Official Symbol
    PDGFRBprovided by HGNC
    Official Full Name
    platelet derived growth factor receptor betaprovided by HGNC
    Primary source
    HGNC:HGNC:8804
    See related
    Ensembl:ENSG00000113721 MIM:173410
    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
    IMF1; KOGS; IBGC4; JTK12; PDGFR; PENTT; CD140B; PDGFR1; PDGFR-1
    Summary
    The protein encoded by this gene is a cell surface tyrosine kinase receptor for members of the platelet-derived growth factor family. These growth factors are mitogens for cells of mesenchymal origin. The identity of the growth factor bound to a receptor monomer determines whether the functional receptor is a homodimer (PDGFB or PDGFD) or a heterodimer (PDGFA and PDGFB). This gene is essential for normal development of the cardiovascular system and aids in rearrangement of the actin cytoskeleton. This gene is flanked on chromosome 5 by the genes for granulocyte-macrophage colony-stimulating factor and macrophage-colony stimulating factor receptor; all three genes may be implicated in the 5-q syndrome. A translocation between chromosomes 5 and 12, that fuses this gene to that of the ETV6 gene, results in chronic myeloproliferative disorder with eosinophilia. [provided by RefSeq, Aug 2017]
    Expression
    Broad expression in gall bladder (RPKM 79.5), placenta (RPKM 61.0) and 21 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PDGFRB in Genome Data Viewer
    Location:
    5q32
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    109.20210514 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (150113839..150155845, complement)
    105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149493402..149535408, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene colony stimulating factor 1 receptor Neighboring gene LTR-CSF1R promoter Neighboring gene ribosomal protein L7 pseudogene 1 Neighboring gene CSF1R promoter E1 Neighboring gene caudal type homeobox 1 Neighboring gene solute carrier family 6 member 7

    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?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat and cocaine treatment induces phosphorylation of PDGFR-beta at position Y934 without the requirement of PDGF binding in human pulmonary arterial smooth muscle cells PubMed
    tat HIV-1 Tat upregulates the expression of platelet-derived growth factor subunit B homodimer through activation of the PDGFR-B/MEK/NF-kappaB pathway in human brain microvascular pericytes PubMed

    Go to the HIV-1, Human Interaction Database

    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
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables growth factor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables phosphatidylinositol 3-kinase binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables platelet activating factor receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables platelet-derived growth factor beta-receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables platelet-derived growth factor beta-receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables platelet-derived growth factor beta-receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables platelet-derived growth factor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables platelet-derived growth factor binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables platelet-derived growth factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables platelet-derived growth factor receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables platelet-derived growth factor-activated receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein tyrosine kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables signaling receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables transmembrane receptor protein tyrosine kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    enables vascular endothelial growth factor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in G protein-coupled receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in aging IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in aorta morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cardiac myofibril assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell migration involved in coronary angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cell migration involved in vasculogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to platelet-derived growth factor stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in glycosaminoglycan biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in inner ear development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lung growth IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in male gonad development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in metanephric S-shaped body morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in metanephric comma-shaped body morphogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in metanephric glomerular capillary formation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in metanephric glomerular mesangial cell proliferation involved in metanephros development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in metanephric mesenchymal cell migration IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in metanephric mesenchyme development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in multicellular organism development IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in peptidyl-tyrosine phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in phosphatidylinositol metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in phosphatidylinositol-mediated signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in platelet-derived growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in platelet-derived growth factor receptor-beta signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of DNA biosynthetic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of ERK1 and ERK2 cascade IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of ERK1 and ERK2 cascade ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of MAP kinase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of Rho protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of calcium ion import ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of collagen biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of fibroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of hepatic stellate cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of mitotic nuclear division ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of phosphatidylinositol 3-kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of phosphatidylinositol 3-kinase signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of phospholipase C activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of phosphoprotein phosphatase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of reactive oxygen species metabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of smooth muscle cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in positive regulation of smooth muscle cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of smooth muscle cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of smooth muscle cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of smooth muscle cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein autophosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of actin cytoskeleton organization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in response to estradiol IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to estrogen IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to fluid shear stress IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to hydrogen peroxide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to hyperoxia IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to retinoic acid IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to toxic substance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in retina vasculature development in camera-type eye ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in smooth muscle cell chemotaxis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in transmembrane receptor protein tyrosine kinase signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    involved_in wound healing IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
     
    located_in apical plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    located_in focal adhesion HDA PubMed 
    is_active_in integral component of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    located_in intrinsic component of plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosomal lumen IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane HDA PubMed 
    located_in membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    part_of receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    platelet-derived growth factor receptor beta
    Names
    Activated tyrosine kinase PDGFRB
    CD140 antigen-like family member B
    NDEL1-PDGFRB
    PDGF-R-beta
    PDGFR-beta
    beta-type platelet-derived growth factor receptor
    platelet-derived growth factor receptor 1
    platelet-derived growth factor receptor, beta polypeptide
    NP_001341945.1
    NP_001341946.1
    NP_002600.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_023367.1 RefSeqGene

      Range
      5001..47021
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001355016.2NP_001341945.1  platelet-derived growth factor receptor beta isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AC005895, AC011382
      Conserved Domains (5) summary
      cd05107
      Location:498889
      PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta
      cd00096
      Location:367375
      Ig; Ig strand B [structural motif]
      cd05859
      Location:250351
      Ig4_PDGFR; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR)
      cd05861
      Location:148247
      IgI_PDGFR-alphabeta; Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha and beta; member of the I-set of IgSF domains
      cl11960
      Location:367455
      Ig; Immunoglobulin domain
    2. NM_001355017.2NP_001341946.1  platelet-derived growth factor receptor beta isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice junction compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1.
      Source sequence(s)
      AC005895, AC011382
      Conserved Domains (4) summary
      cd05107
      Location:401792
      PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta
      cd05859
      Location:153254
      Ig4_PDGFR; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR)
      cd05861
      Location:67151
      Ig_PDGFR-alphabeta; Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b)
      cl11960
      Location:264362
      Ig; Immunoglobulin domain
    3. NM_002609.4NP_002600.1  platelet-derived growth factor receptor beta isoform 1 precursor

      See identical proteins and their annotated locations for NP_002600.1

      Status: REVIEWED

      Source sequence(s)
      AC005895, AC011382
      Consensus CDS
      CCDS4303.1
      UniProtKB/Swiss-Prot
      P09619
      UniProtKB/TrEMBL
      Q59F04
      Related
      ENSP00000261799.4, ENST00000261799.9
      Conserved Domains (8) summary
      cd05107
      Location:562953
      PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta
      cd05859
      Location:314415
      Ig4_PDGFR-alpha; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR) alpha
      cd05861
      Location:228312
      Ig1_PDGFR-alphabeta; Frst immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b)
      smart00409
      Location:40110
      IG; Immunoglobulin
      smart00410
      Location:222310
      IG_like; Immunoglobulin like
      pfam00047
      Location:37114
      ig; Immunoglobulin domain
      pfam07714
      Location:600953
      Pkinase_Tyr; Protein tyrosine kinase
      cl11960
      Location:425523
      Ig; Immunoglobulin domain

    RNA

    1. NR_149150.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks most of the exons found in variant 1. This variant is represented as non-coding because it lacks the entire coding region found in variant 1.
      Source sequence(s)
      AC005895

    RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20210514

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

      Range
      150113839..150155845 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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