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    PDGFB platelet derived growth factor subunit B [ Homo sapiens (human) ]

    Gene ID: 5155, updated on 9-Dec-2024

    Summary

    Official Symbol
    PDGFBprovided by HGNC
    Official Full Name
    platelet derived growth factor subunit Bprovided by HGNC
    Primary source
    HGNC:HGNC:8800
    See related
    Ensembl:ENSG00000100311 MIM:190040; AllianceGenome:HGNC:8800
    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
    SIS; SSV; IBGC5; PDGF2; c-sis; PDGF-2
    Summary
    This gene encodes a member of the protein family comprised of both platelet-derived growth factors (PDGF) and vascular endothelial growth factors (VEGF). The encoded preproprotein is proteolytically processed to generate platelet-derived growth factor subunit B, which can homodimerize, or alternatively, heterodimerize with the related platelet-derived growth factor subunit A. These proteins bind and activate PDGF receptor tyrosine kinases, which play a role in a wide range of developmental processes. Mutations in this gene are associated with meningioma. Reciprocal translocations between chromosomes 22 and 17, at sites where this gene and that for collagen type 1, alpha 1 are located, are associated with dermatofibrosarcoma protuberans, a rare skin tumor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2015]
    Expression
    Broad expression in placenta (RPKM 18.6), fat (RPKM 12.7) and 23 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PDGFB in Genome Data Viewer
    Location:
    22q13.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (39223359..39244982, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (39694033..39715652, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (39619364..39640987, complement)

    Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39527431-39527992 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39529632-39530316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39530317-39531000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39531107-39532084 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39540727-39541516 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39544030-39544628 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39544629-39545227 Neighboring gene chromobox 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39548263-39548844 Neighboring gene FUN14 domain containing 2 pseudogene 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39567703-39568508 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39569521-39570190 Neighboring gene Sharpr-MPRA regulatory region 8665 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39601000-39601939 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:39605384-39605884 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39609067-39609686 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39609687-39610305 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr22:39610322-39611521 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39612165-39612782 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39632330-39633224 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39633225-39634119 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19036 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13747 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13748 Neighboring gene H3K4me1 hESC enhancers GRCh37_chr22:39650154-39650932 and GRCh37_chr22:39650933-39651711 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39658425-39658924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19039 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39664844-39665376 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:39673716-39673890 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39673875-39674634 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39677709-39678208 Neighboring gene uncharacterized LOC124905119 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:39690515-39691375 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39692677-39693342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39693343-39694006 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr22:39704579-39705778 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13749 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:39706697-39707237 Neighboring gene small nucleolar RNA, C/D box 83B Neighboring gene ribosomal protein L3

    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
    Envelope surface glycoprotein gp120 env Human primary pulmonary arterial endothelial cells (HPAEC) are treated with both HIV-1 Tat and gp120 resulting in increased ROS generation and PDGF-B expression PubMed
    env PDGFB protects neurons from gp120-induced cytotoxicity through an increased phosphorylation of both GSK-3beta and Bad, the downregulation of the proapoptotic protein Bax, and inhibition of gp120-induced release of mitochondrial cytochrome C PubMed
    env Gp120-mediated activation of caspase-3 is significantly reduced in cells pretreated with PDGF-B. PDGF-mediated protection against gp120 involves the phosphoinositide (PI)3-kinase/Akt pathway PubMed
    env Pretreatment with PDGFB reduces gp120-associated neurotoxicity and rescues neurite outgrowth PubMed
    Tat 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
    tat HIV-1-Tat-mediated upregulation of platelet-derived growth factor (PDGF) B chain in astrocytes is regulated by activation of ERK1/2 and JNK MAPK signaling pathways and the downstream transcription factor early growth response 1 (Egr1) PubMed
    tat Human primary pulmonary arterial endothelial cells (HPAEC) are treated with both HIV-1 Tat and gp120 resulting in increased ROS generation and PDGF-B expression PubMed
    tat PDGF-BB-mediated protection against HIV-1 Tat and morphine-induced neuron apoptosis involves Akt activation PubMed
    tat PDGF-BB prevents mitochondria depolarization in human neurons exposed to HIV-1 Tat and morphine PubMed
    tat PDGF-BB inhibits NADPH oxidase-mediated reactive oxygen species production induced by HIV-1 Tat and morphine treatment in neuroblastoma cells PubMed
    tat PDGF-BB prevents caspase-3 activation induced by HIV-1 Tat and morphine in neuroblastoma cells PubMed
    tat PDGF-BB protects neurons against HIV-1 Tat and morphine-induced apoptosis by promoting Bcl2 and inhibiting Bax expression 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

    Clone Names

    • FLJ12858

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in angiogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to growth factor stimulus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular response to mycophenolic acid ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in cellular response to platelet-derived growth factor stimulus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in embryonic placenta development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in heart development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    NOT involved_in hemopoiesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in interleukin-18-mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in intracellular signal transduction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in metanephric glomerular mesangial cell development ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in monocyte chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of miRNA transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of phosphatidylinositol biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of platelet activation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in negative regulation of vascular associated smooth muscle cell differentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in paracrine signaling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in peptidyl-tyrosine phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in platelet-derived growth factor receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in platelet-derived growth factor receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in platelet-derived growth factor receptor signaling pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of ERK1 and ERK2 cascade IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of ERK1 and ERK2 cascade IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of MAP kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of MAPK cascade IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of blood vessel endothelial cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of calcium ion import IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of cell-substrate adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of endothelial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of fibroblast proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of gene expression IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of gene expression ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of glomerular filtration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of glomerular mesangial cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of hyaluronan biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of metanephric mesenchymal cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of miRNA transcription IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of mitotic nuclear division IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction IBA
    Inferred from Biological aspect of Ancestor
    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 protein autophosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of reactive oxygen species metabolic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of smooth muscle cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of smooth muscle cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of smooth muscle cell proliferation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of vascular associated smooth muscle cell dedifferentiation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of vascular associated smooth muscle cell migration IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of vascular associated smooth muscle cell proliferation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in reactive oxygen species metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to wounding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to wounding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in Golgi lumen TAS
    Traceable Author Statement
    more info
     
    located_in Golgi membrane TAS
    Traceable Author Statement
    more info
     
    located_in basolateral plasma membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in platelet alpha granule lumen TAS
    Traceable Author Statement
    more info
     
    part_of platelet-derived growth factor complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 

    General protein information

    Preferred Names
    platelet-derived growth factor subunit B
    Names
    PDGF subunit B
    PDGF, B chain
    becaplermin
    epididymis secretory sperm binding protein
    platelet-derived growth factor 2
    platelet-derived growth factor B chain
    platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog)
    platelet-derived growth factor, beta polypeptide (oncogene SIS)
    proto-oncogene c-Sis

    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_012111.1 RefSeqGene

      Range
      4971..26594
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_002608.4NP_002599.1  platelet-derived growth factor subunit B isoform 1 preproprotein

      See identical proteins and their annotated locations for NP_002599.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1), which contains a signal peptide.
      Source sequence(s)
      BC029822, BC077725, CD386140, M12783, X02811, Z81010
      Consensus CDS
      CCDS13987.1
      UniProtKB/Swiss-Prot
      G3XAG8, P01127, P78431, Q15354, Q6FHE7, Q9UF23
      UniProtKB/TrEMBL
      A0A384NYY3
      Related
      ENSP00000330382.6, ENST00000331163.11
      Conserved Domains (2) summary
      pfam00341
      Location:97180
      PDGF; PDGF/VEGF domain
      pfam04692
      Location:2193
      PDGF_N; Platelet-derived growth factor, N terminal region
    2. NM_033016.3NP_148937.1  platelet-derived growth factor subunit B isoform 2

      See identical proteins and their annotated locations for NP_148937.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' terminal exon, resulting in the use of an alternate start codon compared to variant (1). The encoded isoform (2) has a shorter and distinct N-terminus, and lacks a signal peptide compared to isoform 1. It is not known whether this isoform (2) is proteolytically processed in the same manner as isoform (1).
      Source sequence(s)
      BC029822, M12783, X83705, Z81010
      Consensus CDS
      CCDS33650.1
      UniProtKB/Swiss-Prot
      P01127
      Related
      ENSP00000370963.4, ENST00000381551.8
      Conserved Domains (2) summary
      pfam00341
      Location:82165
      PDGF; PDGF/VEGF domain
      pfam04692
      Location:778
      PDGF_N; Platelet-derived growth factor, N terminal region

    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_000022.11 Reference GRCh38.p14 Primary Assembly

      Range
      39223359..39244982 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047441394.1XP_047297350.1  platelet-derived growth factor subunit B isoform X1

    2. XM_047441393.1XP_047297349.1  platelet-derived growth factor subunit B isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060946.1 Alternate T2T-CHM13v2.0

      Range
      39694033..39715652 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054325676.1XP_054181651.1  platelet-derived growth factor subunit B isoform X1

    2. XM_054325675.1XP_054181650.1  platelet-derived growth factor subunit B isoform X1