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

Gene ID: 5155, updated on 18-Sep-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
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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 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