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

Gene ID: 5159, updated on 17-Dec-2019

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

Genomic context

See PDGFRB in Genome Data Viewer
Location:
5q32
Exon count:
24
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (150113839..150155845, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (149493402..149535447, 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
ATP binding IEA
Inferred from Electronic Annotation
more info
 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
phosphatidylinositol 3-kinase binding IEA
Inferred from Electronic Annotation
more info
 
platelet activating factor receptor activity TAS
Traceable Author Statement
more info
PubMed 
platelet-derived growth factor beta-receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
platelet-derived growth factor beta-receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
platelet-derived growth factor beta-receptor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
platelet-derived growth factor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
platelet-derived growth factor binding IDA
Inferred from Direct Assay
more info
PubMed 
platelet-derived growth factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
platelet-derived growth factor receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
platelet-derived growth factor-activated receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein tyrosine kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
signaling receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
transmembrane receptor protein tyrosine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
vascular endothelial growth factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
G protein-coupled receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
MAPK cascade TAS
Traceable Author Statement
more info
 
aging IEA
Inferred from Electronic Annotation
more info
 
aorta morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cardiac myofibril assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
cell chemotaxis IDA
Inferred from Direct Assay
more info
PubMed 
cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell migration involved in coronary angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cell migration involved in vasculogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
cellular response to platelet-derived growth factor stimulus IEA
Inferred from Electronic Annotation
more info
 
glycosaminoglycan biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
hematopoietic progenitor cell differentiation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
inner ear development IEA
Inferred from Electronic Annotation
more info
 
lung growth IEA
Inferred from Electronic Annotation
more info
 
male gonad development IEA
Inferred from Electronic Annotation
more info
 
metanephric S-shaped body morphogenesis IEA
Inferred from Electronic Annotation
more info
 
metanephric comma-shaped body morphogenesis IEA
Inferred from Electronic Annotation
more info
 
metanephric glomerular capillary formation ISS
Inferred from Sequence or Structural Similarity
more info
 
metanephric glomerular mesangial cell proliferation involved in metanephros development ISS
Inferred from Sequence or Structural Similarity
more info
 
metanephric mesenchymal cell migration IEA
Inferred from Electronic Annotation
more info
 
metanephric mesenchyme development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
peptidyl-tyrosine phosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
phosphatidylinositol metabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
phosphatidylinositol-mediated signaling IMP
Inferred from Mutant Phenotype
more info
PubMed 
platelet-derived growth factor receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
platelet-derived growth factor receptor-beta signaling pathway IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of DNA biosynthetic process ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of ERK1 and ERK2 cascade IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of ERK1 and ERK2 cascade ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of MAP kinase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of Rho protein signal transduction IEA
Inferred from Electronic Annotation
more info
 
positive regulation of apoptotic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of calcium ion import ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of cell migration IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of collagen biosynthetic process IEA
Inferred from Electronic Annotation
more info
 
positive regulation of fibroblast proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of hepatic stellate cell activation IEA
Inferred from Electronic Annotation
more info
 
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
 
positive regulation of mitotic nuclear division ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of phosphatidylinositol 3-kinase activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of phosphatidylinositol 3-kinase signaling ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of phospholipase C activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of phosphoprotein phosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of protein kinase B signaling TAS
Traceable Author Statement
more info
 
positive regulation of reactive oxygen species metabolic process ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of smooth muscle cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of smooth muscle cell migration IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of smooth muscle cell migration ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of smooth muscle cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of smooth muscle cell proliferation ISS
Inferred from Sequence or Structural Similarity
more info
 
protein autophosphorylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of actin cytoskeleton organization ISS
Inferred from Sequence or Structural Similarity
more info
 
response to estradiol IEA
Inferred from Electronic Annotation
more info
 
response to estrogen IEA
Inferred from Electronic Annotation
more info
 
response to fluid shear stress IEA
Inferred from Electronic Annotation
more info
 
response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
 
response to hyperoxia IEA
Inferred from Electronic Annotation
more info
 
response to retinoic acid IEA
Inferred from Electronic Annotation
more info
 
retina vasculature development in camera-type eye ISS
Inferred from Sequence or Structural Similarity
more info
 
signal transduction IDA
Inferred from Direct Assay
more info
PubMed 
smooth muscle cell chemotaxis ISS
Inferred from Sequence or Structural Similarity
more info
 
transmembrane receptor protein tyrosine kinase signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
wound healing IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
apical plasma membrane ISS
Inferred from Sequence or Structural Similarity
more info
 
cell surface IEA
Inferred from Electronic Annotation
more info
 
cytoplasm ISS
Inferred from Sequence or Structural Similarity
more info
 
cytoplasmic vesicle IEA
Inferred from Electronic Annotation
more info
 
focal adhesion HDA PubMed 
integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
intrinsic component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal lumen IEA
Inferred from Electronic Annotation
more info
 
membrane HDA PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISS
Inferred from Sequence or Structural Similarity
more info
 
plasma membrane TAS
Traceable Author Statement
more info
 
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)

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 (4) summary
    cd05107
    Location:498889
    PTKc_PDGFR_beta; Catalytic domain of the Protein Tyrosine Kinase, Platelet Derived Growth Factor Receptor beta
    cd05859
    Location:250351
    Ig4_PDGFR; Fourth immunoglobulin (Ig)-like domain of platelet-derived growth factor receptor (PDGFR)
    cd05861
    Location:164248
    Ig_PDGFR-alphabeta; Immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b)
    cl11960
    Location:361459
    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 109.20191205

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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