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Aliases for PDGFB Gene

Aliases for PDGFB Gene

  • Platelet-Derived Growth Factor Beta Polypeptide 2 3 4
  • Becaplermin 2 3 4
  • SIS 3 4 6
  • Platelet-Derived Growth Factor Beta Polypeptide (Simian Sarcoma Viral (V-Sis) Oncogene Homolog) 2 3
  • Platelet-Derived Growth Factor B Chain 3 4
  • Proto-Oncogene C-Sis 3 4
  • PDGF Subunit B 3 4
  • PDGF-2 3 4
  • IBGC5 3 6
  • PDGF2 3 4
  • Platelet-Derived Growth Factor, Beta Polypeptide (Oncogene SIS) 3
  • Platelet-Derived Growth Factor Subunit B 3
  • Platelet-Derived Growth Factor 2 3
  • PDGF, B Chain 3
  • Oncogene SIS 2
  • C-Sis 3
  • SSV 3

External Ids for PDGFB Gene

Previous HGNC Symbols for PDGFB Gene

  • SIS

Previous GeneCards Identifiers for PDGFB Gene

  • GC22M036234
  • GC22M037862
  • GC22M037944
  • GC22M039619
  • GC22M022587

Summaries for PDGFB Gene

Entrez Gene Summary for PDGFB Gene

  • The protein encoded by this gene is a member of the platelet-derived growth factor family. The four members of this family are mitogenic factors for cells of mesenchymal origin and are characterized by a motif of eight cysteines. This gene product can exist either as a homodimer (PDGF-BB) or as a heterodimer with the platelet-derived growth factor alpha polypeptide (PDGF-AB), where the dimers are connected by disulfide bonds. 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 a particular type of skin tumor called dermatofibrosarcoma protuberans resulting from unregulated expression of growth factor. Two alternatively spliced transcript variants encoding different isoforms have been identified for this gene. [provided by RefSeq, Feb 2013]

GeneCards Summary for PDGFB Gene

PDGFB (Platelet-Derived Growth Factor Beta Polypeptide) is a Protein Coding gene. Diseases associated with PDGFB include dermatofibrosarcoma protuberans and basal ganglia calcification, idiopathic, 5. Among its related pathways are PI3K-Akt signaling pathway and PI-3K cascade. GO annotations related to this gene include protein homodimerization activity and growth factor activity. An important paralog of this gene is PDGFA.

UniProtKB/Swiss-Prot for PDGFB Gene

  • Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).

Tocris Summary for PDGFB Gene

  • Platelet-derived growth factor receptors (PDGFRs) are catalytic receptors that have intracellular tyrosine kinase activity. They have roles in the regulation of many biological processes including embryonic development, angiogenesis, cell proliferation and differentiation, and contribute to the pathophysiology of some diseases, including cancer. There are two isoforms of the PDGFR receptor; PDGFRalpha and PDGFRbeta, which can form homo- or heterodimers. The endogenous PDGFR ligands are PDGF-A, -B, -C and -D, which induce receptor dimerization and transphosphorylation at specific tyrosine residues upon binding. This activates the intracellular kinase activity, initiating intracellular signaling through the MAPK, PI 3-K and PKCgamma pathways.

Gene Wiki entry for PDGFB Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDGFB Gene

Genomics for PDGFB Gene

Regulatory Elements for PDGFB Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for PDGFB Gene

Start:
39,223,359 bp from pter
End:
39,244,952 bp from pter
Size:
21,594 bases
Orientation:
Minus strand

Genomic View for PDGFB Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PDGFB Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDGFB Gene

Proteins for PDGFB Gene

  • Protein details for PDGFB Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P01127-PDGFB_HUMAN
    Recommended name:
    Platelet-derived growth factor subunit B
    Protein Accession:
    P01127
    Secondary Accessions:
    • G3XAG8
    • P78431
    • Q15354
    • Q6FHE7
    • Q9UF23

    Protein attributes for PDGFB Gene

    Size:
    241 amino acids
    Molecular mass:
    27283 Da
    Quaternary structure:
    • Homodimer; antiparallel disulfide-linked dimer. Heterodimer with PDGFA; antiparallel disulfide-linked dimer. The PDGFB homodimer interacts with PDGFRA and PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB. The heterodimer composed of PDGFA and PDGFB interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB. Interacts with XLKD1 (By similarity).

    Three dimensional structures from OCA and Proteopedia for PDGFB Gene

    Alternative splice isoforms for PDGFB Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDGFB Gene

Proteomics data for PDGFB Gene at MOPED

Post-translational modifications for PDGFB Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PDGFB Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

Antibody Products

Protein Products

No data available for DME Specific Peptides for PDGFB Gene

Domains for PDGFB Gene

Suggested Antigen Peptide Sequences for PDGFB Gene

Graphical View of Domain Structure for InterPro Entry

P01127

UniProtKB/Swiss-Prot:

PDGFB_HUMAN :
  • P01127
Family:
  • Belongs to the PDGF/VEGF growth factor family.
genes like me logo Genes that share domains with PDGFB: view

No data available for Gene Families for PDGFB Gene

Function for PDGFB Gene

Molecular function for PDGFB Gene

GENATLAS Biochemistry: platelet-derived growth factor,beta polypeptide,27.3kDa,(simian sarcoma viral (v-sis) oncogene homolog),potent mitogen for cells of mesenchymal origin,also involved in transformation process
UniProtKB/Swiss-Prot Function: Growth factor that plays an essential role in the regulation of embryonic development, cell proliferation, cell migration, survival and chemotaxis. Potent mitogen for cells of mesenchymal origin. Required for normal proliferation and recruitment of pericytes and vascular smooth muscle cells in the central nervous system, skin, lung, heart and placenta. Required for normal blood vessel development, and for normal development of kidney glomeruli. Plays an important role in wound healing. Signaling is modulated by the formation of heterodimers with PDGFA (By similarity).

Gene Ontology (GO) - Molecular Function for PDGFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005102 receptor binding --
GO:0005161 platelet-derived growth factor receptor binding NAS 1661670
GO:0005515 protein binding IPI 10806482
GO:0005518 collagen binding IDA 8900172
GO:0008083 growth factor activity IDA 12070119
genes like me logo Genes that share ontologies with PDGFB: view
genes like me logo Genes that share phenotypes with PDGFB: view

Animal Models for PDGFB Gene

MGI Knock Outs for PDGFB:

Animal Model Products

CRISPR Products

miRNA for PDGFB Gene

miRTarBase miRNAs that target PDGFB

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PDGFB

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targeting and HOMER Transcription for PDGFB Gene

Localization for PDGFB Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDGFB Gene

Secreted. Note=Released by platelets upon wounding.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDGFB Gene COMPARTMENTS Subcellular localization image for PDGFB gene
Compartment Confidence
extracellular 5
endoplasmic reticulum 4
golgi apparatus 4
plasma membrane 4
cytoskeleton 2
nucleus 2
cytosol 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PDGFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane TAS --
GO:0005576 extracellular region TAS --
GO:0005615 extracellular space IBA --
GO:0005737 cytoplasm ISS --
GO:0005788 endoplasmic reticulum lumen TAS --
genes like me logo Genes that share ontologies with PDGFB: view

Pathways for PDGFB Gene

SuperPathways for PDGFB Gene

Superpath Contained pathways
1 Apoptotic Pathways in Synovial Fibroblasts
2 PI-3K cascade
3 Signaling by FGFR
4 GPCR Pathway
5 ERK Signaling
genes like me logo Genes that share pathways with PDGFB: view

PCR Array Products

Gene Ontology (GO) - Biological Process for PDGFB Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001568 blood vessel development --
GO:0001666 response to hypoxia IEA --
GO:0001892 embryonic placenta development ISS --
GO:0001938 positive regulation of endothelial cell proliferation IDA 9685360
GO:0002548 monocyte chemotaxis IDA 17991872
genes like me logo Genes that share ontologies with PDGFB: view

Compounds for PDGFB Gene

UniProtKB/Swiss-Prot:

P01127-PDGFB_HUMAN
Pharmaceutical: Available under the name Regranex (Ortho-McNeil). Used to promote healing in diabetic neuropathic foot ulcers

(4) Tocris Compounds for PDGFB Gene

Compound Action Cas Number
DMPQ dihydrochloride Potent, selective inhibitor of PDGFRbeta [1123491-15-5]
SU 16f Potent and selective PDGFRbeta inhibitor [251356-45-3]
SU 6668 PDGFR, VEGFR and FGFR inhibitor [252916-29-3]
Toceranib Potent PDGFR and VEGFR inhibitor [356068-94-5]

(34) Novoseek inferred chemical compound relationships for PDGFB Gene

Compound -log(P) Hits PubMed IDs
regranex 89.4 8
imatinib 59.6 5
vegf 55.5 36
tgf beta1 36.4 7
tyrosine 34.5 5
genes like me logo Genes that share compounds with PDGFB: view

Transcripts for PDGFB Gene

mRNA/cDNA for PDGFB Gene

Unigene Clusters for PDGFB Gene

Platelet-derived growth factor beta polypeptide:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PDGFB

Primer Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDGFB Gene

No ASD Table

Relevant External Links for PDGFB Gene

GeneLoc Exon Structure for
PDGFB
ECgene alternative splicing isoforms for
PDGFB

Expression for PDGFB Gene

mRNA expression in normal human tissues for PDGFB Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, and MOPED for PDGFB Gene

SOURCE GeneReport for Unigene cluster for PDGFB Gene Hs.1976

mRNA Expression by UniProt/SwissProt for PDGFB Gene

P01127-PDGFB_HUMAN
Tissue specificity: Expressed at high levels in the heart, brain (sustantia nigra), placenta and fetal kidney. Expressed at moderate levels in the brain (hippocampus), skeletal muscle, kidney and lung.
genes like me logo Genes that share expressions with PDGFB: view

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for PDGFB Gene

Orthologs for PDGFB Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDGFB Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDGFB 35
  • 99.45 (n)
  • 99.59 (a)
PDGFB 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia PDGFB 35
  • 88.75 (n)
  • 91.67 (a)
PDGFB 36
  • 90 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDGFB 35
  • 91.42 (n)
  • 93.36 (a)
PDGFB 36
  • 93 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdgfb 35
  • 86.31 (n)
  • 89.63 (a)
Pdgfb 16
Pdgfb 36
  • 90 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PDGFB 36
  • 75 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDGFB 36
  • 45 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdgfb 35
  • 85.48 (n)
  • 87.97 (a)
chicken
(Gallus gallus)
Aves PDGFB 35
  • 65.67 (n)
  • 57.26 (a)
PDGFB 36
  • 51 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDGFB 36
  • 51 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdgfb 35
  • 52.78 (n)
  • 48.25 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC796490 35
  • 50.47 (n)
  • 45.25 (a)
pdgfb 36
  • 15 (a)
OneToMany
PDGFB (1 of 3) 36
  • 17 (a)
OneToMany
PDGFB (2 of 3) 36
  • 15 (a)
OneToMany
Species with no ortholog for PDGFB:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for PDGFB Gene

ENSEMBL:
Gene Tree for PDGFB (if available)
TreeFam:
Gene Tree for PDGFB (if available)

Paralogs for PDGFB Gene

Paralogs for PDGFB Gene

Selected SIMAP similar genes for PDGFB Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with PDGFB: view

Variants for PDGFB Gene

Sequence variations from dbSNP and Humsavar for PDGFB Gene

SNP ID Clin Chr 22 pos Sequence Context AA Info Type MAF
rs17565 - 39,231,816(-) TGACC(A/G)TTGCT reference, missense
rs130653 -- 39,246,735(-) GAAGG(A/T)TCCAG upstream-variant-2KB
rs130654 -- 39,246,649(-) AGGAG(C/G)AGGGT upstream-variant-2KB
rs739014 -- 39,233,856(-) TGCCC(C/T)AGGTC intron-variant
rs879180 -- 39,235,542(+) ACCCT(C/T)GGCAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PDGFB Gene

Variant ID Type Subtype PubMed ID
dgv4974n71 CNV Loss 21882294
nsv834198 CNV Loss 17160897
esv2724248 CNV Deletion 23290073
nsv915095 CNV Loss 21882294

Relevant External Links for PDGFB Gene

HapMap Linkage Disequilibrium report
PDGFB
Human Gene Mutation Database (HGMD)
PDGFB

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDGFB Gene

Disorders for PDGFB Gene

(3) OMIM Diseases for PDGFB Gene (190040)

UniProtKB/Swiss-Prot

PDGFB_HUMAN
  • Basal ganglia calcification, idiopathic, 5 (IBGC5) [MIM:615483]: A form of basal ganglia calcification, an autosomal dominant condition characterized by symmetric calcification in the basal ganglia and other brain regions. Affected individuals can either be asymptomatic or show a wide spectrum of neuropsychiatric symptoms, including parkinsonism, dystonia, tremor, ataxia, dementia, psychosis, seizures, and chronic headache. Serum levels of calcium, phosphate, alkaline phosphatase and parathyroid hormone are normal. The neuropathological hallmark of the disease is vascular and pericapillary calcification, mainly of calcium phosphate, in the affected brain areas. {ECO:0000269 PubMed:23913003}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB. {ECO:0000269 PubMed:12660034}.

(85) Novoseek inferred disease relationships for PDGFB Gene

Disease -log(P) Hits PubMed IDs
dermatofibrosarcoma protuberans 83.7 12
diabetic foot 61.9 15
dermatofibrosarcoma 59.8 2
foot ulcer 56.7 5
ulcer 53.7 35

Relevant External Links for PDGFB

Genetic Association Database (GAD)
PDGFB
Human Genome Epidemiology (HuGE) Navigator
PDGFB
genes like me logo Genes that share disorders with PDGFB: view

Publications for PDGFB Gene

  1. PDGF-B gene single-nucleotide polymorphisms are not predictive for disease onset or progression of IgA nephropathy. (PMID: 17338425) Bicanski B. … Floege J. (Clin. Nephrol. 2007) 3 23 48
  2. Two PDGF-B chain residues, arginine 27 and isoleucine 30, mediate receptor binding and activation. (PMID: 1661670) Clements J.M. … Winslow D. (EMBO J. 1991) 2 3 4
  3. Nucleotide sequence of transforming human c-sis cDNA clones with homology to platelet-derived growth factor. (PMID: 2991848) Ratner L. … Wong-Staal F. (Nucleic Acids Res. 1985) 2 3 4
  4. Assignment of interchain disulfide bonds in platelet-derived growth factor (PDGF) and evidence for agonist activity of monomeric PDGF. (PMID: 1317862) Andersson M. … Heldin C.-H. (J. Biol. Chem. 1992) 3 4
  5. Crystal structure of human platelet-derived growth factor BB. (PMID: 1396586) Oefner C. … Hosang M. (EMBO J. 1992) 3 4

Products for PDGFB Gene

  • Addgene plasmids for PDGFB

Sources for PDGFB Gene

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