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

    Gene ID: 5159, updated on 28-Oct-2024

    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; AllianceGenome:HGNC:8804
    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
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (150113839..150155845, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (150650431..150692448, complement)
    RS_2024_09 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 HMG-box containing 3 Neighboring gene small nucleolar RNA U13 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23395 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23396 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149439174-149439376 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:149444398-149444573 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23397 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149447500-149448210 Neighboring gene colony stimulating factor 1 receptor Neighboring gene RORalpha allelically-responsive CSF1R enhancer Neighboring gene CSF1R promoter/intronic regulatory region Neighboring gene LTR-CSF1R promoter Neighboring gene Sharpr-MPRA regulatory region 12786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149490949-149491461 Neighboring gene ribosomal protein L7 pseudogene 1 Neighboring gene CSF1R promoter E1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149497723-149498310 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149499971-149500878 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149507353-149507854 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149509491-149510101 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82275 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149515109-149515620 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149515621-149516130 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149516131-149516642 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149517153-149517664 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149526270-149526796 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149532128-149532648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149532649-149533168 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149537326-149538114 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23399 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149540489-149541398 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr5:149565453-149566393 Neighboring gene caudal type homeobox 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149585404-149586030 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:149587985-149589184 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:149589159-149589702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:149590543-149591114 Neighboring gene solute carrier family 6 member 7

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables GTPase activator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables enzyme binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables phospholipase C activator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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
     
    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
     
    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 activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables platelet-derived growth factor receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein kinase activity IDA
    Inferred from Direct Assay
    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 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 angiogenesis IBA
    Inferred from Biological aspect of Ancestor
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell chemotaxis IDA
    Inferred from Direct Assay
    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 cell surface receptor protein tyrosine kinase signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cellular response to platelet-derived growth factor stimulus 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 multicellular organism development IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in peptidyl-tyrosine phosphorylation IDA
    Inferred from Direct Assay
    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 calcium ion import ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of calcium-mediated signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell migration IMP
    Inferred from Mutant Phenotype
    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 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/protein kinase B signal transduction IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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
     
    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 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
     
    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 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 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
     
    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
     
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    part_of receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    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_023367.2 RefSeqGene

      Range
      5000..47006
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001355016.2 → NP_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
      UniProtKB/TrEMBL
      A8KAM8
      Conserved Domains (5) summary
      cd05107
      Location:498 → 889
      PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta
      cd00096
      Location:367 → 375
      Ig; Ig strand B [structural motif]
      cd05859
      Location:250 → 351
      Ig4_PDGFR; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR)
      cd05861
      Location:148 → 247
      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:367 → 455
      Ig; Immunoglobulin domain
    2. NM_001355017.2 → NP_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
      UniProtKB/TrEMBL
      A8KAM8
      Conserved Domains (4) summary
      cd05107
      Location:401 → 792
      PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta
      cd05859
      Location:153 → 254
      Ig4_PDGFR; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR)
      cd05861
      Location:67 → 151
      Ig_PDGFR-alphabeta; Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b)
      cl11960
      Location:264 → 362
      Ig; Immunoglobulin domain
    3. NM_002609.4 → NP_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
      B5A957, P09619, Q8N5L4
      UniProtKB/TrEMBL
      A8KAM8
      Related
      ENSP00000261799.4, ENST00000261799.9
      Conserved Domains (8) summary
      cd05107
      Location:562 → 953
      PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta
      cd05859
      Location:314 → 415
      Ig4_PDGFR-alpha; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR) alpha
      cd05861
      Location:228 → 312
      Ig1_PDGFR-alphabeta; Frst immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b)
      smart00409
      Location:40 → 110
      IG; Immunoglobulin
      smart00410
      Location:222 → 310
      IG_like; Immunoglobulin like
      pfam00047
      Location:37 → 114
      ig; Immunoglobulin domain
      pfam07714
      Location:600 → 953
      Pkinase_Tyr; Protein tyrosine kinase
      cl11960
      Location:425 → 523
      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: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

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

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      150650431..150692448 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)