Human Gene PDGFB (ENST00000331163.11_7) from GENCODE V47lift37
  Description: platelet derived growth factor subunit B, transcript variant 1 (from RefSeq NM_002608.4)
Gencode Transcript: ENST00000331163.11_7
Gencode Gene: ENSG00000100311.17_12
Transcript (Including UTRs)
   Position: hg19 chr22:39,619,364-39,640,987 Size: 21,624 Total Exon Count: 7 Strand: -
Coding Region
   Position: hg19 chr22:39,621,728-39,639,968 Size: 18,241 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:39,619,364-39,640,987)mRNA (may differ from genome)Protein (241 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PDGFB_HUMAN
DESCRIPTION: RecName: Full=Platelet-derived growth factor subunit B; Short=PDGF subunit B; AltName: Full=PDGF-2; AltName: Full=Platelet-derived growth factor B chain; AltName: Full=Platelet-derived growth factor beta polypeptide; AltName: Full=Proto-oncogene c-Sis; AltName: INN=Becaplermin; Flags: Precursor;
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).
SUBUNIT: 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).
SUBCELLULAR LOCATION: Secreted. Note=Released by platelets upon wounding.
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.
DISEASE: Note=A chromosomal aberration involving PDGFB is found in dermatofibrosarcoma protuberans. Translocation t(17;22)(q22;q13) with PDGFB.
PHARMACEUTICAL: Available under the name Regranex (Ortho-McNeil). Used to promote healing in diabetic neuropathic foot ulcers.
SIMILARITY: Belongs to the PDGF/VEGF growth factor family.
WEB RESOURCE: Name=R&D Systems' cytokine source book: PDGF; URL="http://www.rndsystems.com/molecule_detail.aspx?m=1967";
WEB RESOURCE: Name=Regranex; Note=Clinical information on Regranex; URL="http://www.regranex.com/";
WEB RESOURCE: Name=Atlas of Genetics and Cytogenetics in Oncology and Haematology; URL="http://atlasgeneticsoncology.org/Genes/PDGFBID155.html";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: PDGFB
Diseases sorted by gene-association score: dermatofibrosarcoma protuberans* (1418), basal ganglia calcification, idiopathic, 5* (1230), meningioma, familial* (672), primary familial brain calcification 5* (500), meningioma, radiation-induced* (400), spinal meningioma* (283), primary familial brain calcification* (184), diabetic foot ulcers (19), bednar tumor (18), basal ganglia calcification (18), skin sarcoma (15), gingival overgrowth (13), ring chromosome 4 (12), kaposi sarcoma (12), intracranial berry aneurysm (11), liver rhabdomyosarcoma (11), sarcoma (10), bronchiolitis obliterans (10), lateral sinus thrombosis (10), cutaneous fibrous histiocytoma (9), asbestos-related lung carcinoma (9), shoulder impingement syndrome (9), clear cell adenofibroma (8), liver sarcoma (7), dermis tumor (7), malignant histiocytosis (7), adult fibrosarcoma (7), mixed liposarcoma (6), sciatic neuropathy (6), brain stem cancer (6), connective tissue cancer (6), retinal detachment (6), brain stem glioma (6), focal hand dystonia (4), bone ewing's sarcoma (4), vitreous disease (4), glioma (4), nominal aphasia (4), arteriosclerosis (3), renal cell carcinoma (2), esophageal cancer (2), pulmonary fibrosis, idiopathic (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 19.39 RPKM in Adipose - Subcutaneous
Total median expression: 302.76 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -490.501019-0.481 Picture PostScript Text
3' UTR -751.301983-0.379 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000072 - PD_growth_factor
IPR023581 - PD_growth_factor_CS
IPR006782 - PDGF_N

Pfam Domains:
PF00341 - PDGF/VEGF domain
PF04692 - Platelet-derived growth factor, N terminal region

SCOP Domains:
57501 - Cystine-knot cytokines

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1PDG - X-ray MuPIT 3MJG - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P01127
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005088 Ras guanyl-nucleotide exchange factor activity
GO:0005161 platelet-derived growth factor receptor binding
GO:0005515 protein binding
GO:0005518 collagen binding
GO:0008083 growth factor activity
GO:0016176 superoxide-generating NADPH oxidase activator activity
GO:0042056 chemoattractant activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046934 phosphatidylinositol-4,5-bisphosphate 3-kinase activity
GO:0046982 protein heterodimerization activity
GO:0048407 platelet-derived growth factor binding

Biological Process:
GO:0000165 MAPK cascade
GO:0001892 embryonic placenta development
GO:0001938 positive regulation of endothelial cell proliferation
GO:0002548 monocyte chemotaxis
GO:0002576 platelet degranulation
GO:0003104 positive regulation of glomerular filtration
GO:0006468 protein phosphorylation
GO:0007275 multicellular organism development
GO:0007507 heart development
GO:0008284 positive regulation of cell proliferation
GO:0009611 response to wounding
GO:0010469 regulation of receptor activity
GO:0010512 negative regulation of phosphatidylinositol biosynthetic process
GO:0010544 negative regulation of platelet activation
GO:0010628 positive regulation of gene expression
GO:0010629 negative regulation of gene expression
GO:0014068 positive regulation of phosphatidylinositol 3-kinase signaling
GO:0014911 positive regulation of smooth muscle cell migration
GO:0018105 peptidyl-serine phosphorylation
GO:0018108 peptidyl-tyrosine phosphorylation
GO:0030198 extracellular matrix organization
GO:0030335 positive regulation of cell migration
GO:0031954 positive regulation of protein autophosphorylation
GO:0032091 negative regulation of protein binding
GO:0032147 activation of protein kinase activity
GO:0032148 activation of protein kinase B activity
GO:0035655 interleukin-18-mediated signaling pathway
GO:0035793 positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway
GO:0038001 paracrine signaling
GO:0043406 positive regulation of MAP kinase activity
GO:0043410 positive regulation of MAPK cascade
GO:0043536 positive regulation of blood vessel endothelial cell migration
GO:0043552 positive regulation of phosphatidylinositol 3-kinase activity
GO:0045737 positive regulation of cyclin-dependent protein serine/threonine kinase activity
GO:0045840 positive regulation of mitotic nuclear division
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045893 positive regulation of transcription, DNA-templated
GO:0046854 phosphatidylinositol phosphorylation
GO:0048008 platelet-derived growth factor receptor signaling pathway
GO:0048146 positive regulation of fibroblast proliferation
GO:0048661 positive regulation of smooth muscle cell proliferation
GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation
GO:0050918 positive chemotaxis
GO:0050921 positive regulation of chemotaxis
GO:0051781 positive regulation of cell division
GO:0051897 positive regulation of protein kinase B signaling
GO:0060326 cell chemotaxis
GO:0061098 positive regulation of protein tyrosine kinase activity
GO:0070374 positive regulation of ERK1 and ERK2 cascade
GO:0070528 protein kinase C signaling
GO:0071363 cellular response to growth factor stimulus
GO:0071506 cellular response to mycophenolic acid
GO:0072126 positive regulation of glomerular mesangial cell proliferation
GO:0072255 metanephric glomerular mesangial cell development
GO:0072593 reactive oxygen species metabolic process
GO:0090280 positive regulation of calcium ion import
GO:1900127 positive regulation of hyaluronan biosynthetic process
GO:1902894 negative regulation of pri-miRNA transcription from RNA polymerase II promoter
GO:1902895 positive regulation of pri-miRNA transcription from RNA polymerase II promoter
GO:1904707 positive regulation of vascular smooth muscle cell proliferation
GO:1904754 positive regulation of vascular associated smooth muscle cell migration
GO:1905064 negative regulation of vascular smooth muscle cell differentiation
GO:1905176 positive regulation of vascular smooth muscle cell dedifferentiation
GO:2000379 positive regulation of reactive oxygen species metabolic process
GO:2000573 positive regulation of DNA biosynthetic process
GO:2000591 positive regulation of metanephric mesenchymal cell migration
GO:0030097 hemopoiesis

Cellular Component:
GO:0000139 Golgi membrane
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005737 cytoplasm
GO:0005788 endoplasmic reticulum lumen
GO:0005796 Golgi lumen
GO:0009986 cell surface
GO:0016020 membrane
GO:0016323 basolateral plasma membrane
GO:0031012 extracellular matrix
GO:0031093 platelet alpha granule lumen


-  Descriptions from all associated GenBank mRNAs
  FW340092 - Screening.
M12783 - Human c-sis/platelet-derived growth factor 2 (SIS/PDGF2) mRNA, complete cds.
AK022920 - Homo sapiens cDNA FLJ12858 fis, clone NT2RP2003517, highly similar to Human c-sis/platelet-derived growth factor 2 (SIS/PDGF2) mRNA.
BC029822 - Homo sapiens platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog), mRNA (cDNA clone MGC:34575 IMAGE:5174750), complete cds.
GQ901040 - Homo sapiens clone HEL-T-152 epididymis secretory sperm binding protein mRNA, complete cds.
X02744 - Human mRNA for c-sis gene (clone pSM-1).
M32009 - Human c-sis oncogene mRNA, 3' flank.
JD394010 - Sequence 375034 from Patent EP1572962.
JD130476 - Sequence 111500 from Patent EP1572962.
JD206974 - Sequence 187998 from Patent EP1572962.
JD054706 - Sequence 35730 from Patent EP1572962.
JD544264 - Sequence 525288 from Patent EP1572962.
JD144435 - Sequence 125459 from Patent EP1572962.
JD148940 - Sequence 129964 from Patent EP1572962.
JD262888 - Sequence 243912 from Patent EP1572962.
JD045911 - Sequence 26935 from Patent EP1572962.
JD093842 - Sequence 74866 from Patent EP1572962.
JD340299 - Sequence 321323 from Patent EP1572962.
JD543793 - Sequence 524817 from Patent EP1572962.
JD204152 - Sequence 185176 from Patent EP1572962.
JD480724 - Sequence 461748 from Patent EP1572962.
JD225678 - Sequence 206702 from Patent EP1572962.
X03702 - Human osteosarcoma cell line U-2 OS mRNA fragment for PDGF-B chain (PDGF= platelet-derived growth factor).
JD050106 - Sequence 31130 from Patent EP1572962.
JD535853 - Sequence 516877 from Patent EP1572962.
JD353824 - Sequence 334848 from Patent EP1572962.
JD470259 - Sequence 451283 from Patent EP1572962.
JD054517 - Sequence 35541 from Patent EP1572962.
JD254493 - Sequence 235517 from Patent EP1572962.
JD378983 - Sequence 360007 from Patent EP1572962.
JD321705 - Sequence 302729 from Patent EP1572962.
JD258331 - Sequence 239355 from Patent EP1572962.
JD166732 - Sequence 147756 from Patent EP1572962.
JD527341 - Sequence 508365 from Patent EP1572962.
JD325697 - Sequence 306721 from Patent EP1572962.
JD536791 - Sequence 517815 from Patent EP1572962.
JD150966 - Sequence 131990 from Patent EP1572962.
JD495487 - Sequence 476511 from Patent EP1572962.
JD291809 - Sequence 272833 from Patent EP1572962.
JD150680 - Sequence 131704 from Patent EP1572962.
JD099597 - Sequence 80621 from Patent EP1572962.
JD157850 - Sequence 138874 from Patent EP1572962.
JD256334 - Sequence 237358 from Patent EP1572962.
JD099482 - Sequence 80506 from Patent EP1572962.
JD178912 - Sequence 159936 from Patent EP1572962.
JD533530 - Sequence 514554 from Patent EP1572962.
JD421801 - Sequence 402825 from Patent EP1572962.
X02811 - Human mRNA for platelet-derived growth factor B chain (PDGF-B).
JD554853 - Sequence 535877 from Patent EP1572962.
JD401168 - Sequence 382192 from Patent EP1572962.
JD556026 - Sequence 537050 from Patent EP1572962.
JD236885 - Sequence 217909 from Patent EP1572962.
JD206539 - Sequence 187563 from Patent EP1572962.
JD294301 - Sequence 275325 from Patent EP1572962.
JD456908 - Sequence 437932 from Patent EP1572962.
BC077725 - Homo sapiens platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog), mRNA (cDNA clone MGC:78575 IMAGE:6379783), complete cds.
JD116062 - Sequence 97086 from Patent EP1572962.
JD058409 - Sequence 39433 from Patent EP1572962.
JD116691 - Sequence 97715 from Patent EP1572962.
JD231400 - Sequence 212424 from Patent EP1572962.
CR456538 - Homo sapiens PDGFB full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.PDGFB.V2).
JD146276 - Sequence 127300 from Patent EP1572962.
CR541807 - Homo sapiens full open reading frame cDNA clone RZPDo834G0631D for gene PDGFB, platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog); complete cds, incl. stopcodon.
CU013138 - Homo sapiens PDGFB, mRNA (cDNA clone IMAGE:100000491), complete cds, with stop codon, in Gateway system.
KJ891768 - Synthetic construct Homo sapiens clone ccsbBroadEn_01162 PDGFB gene, encodes complete protein.
AB587368 - Synthetic construct DNA, clone: pF1KB3608, Homo sapiens PDGFB gene for platelet-derived growth factor beta polypeptide, without stop codon, in Flexi system.
CU013426 - Homo sapiens PDGFB, mRNA (cDNA clone IMAGE:100000395), complete cds, without stop codon, in Gateway system.
AB590092 - Synthetic construct DNA, clone: pFN21AE1495, Homo sapiens PDGFB gene for platelet-derived growth factor beta polypeptide, without stop codon, in Flexi system.
X83705 - H.sapiens mRNA for c-sis proto-oncogene.
Y08643 - H.sapiens mRNA for COL1A1 and PDGFB chimaeric transcript.
Y15920 - Homo sapiens mRNA for chimaeric transcript of collagen type 1 alpha 1 and platelet derived growth factor beta, 464 bp.
Y15921 - Homo sapiens mRNA for chimaeric transcript of collagen type 1 alpha 1 and platelet derived growth factor beta, 431 bp.
JD195971 - Sequence 176995 from Patent EP1572962.
JD195970 - Sequence 176994 from Patent EP1572962.
JD217638 - Sequence 198662 from Patent EP1572962.
JD496845 - Sequence 477869 from Patent EP1572962.
JD144292 - Sequence 125316 from Patent EP1572962.
JD134996 - Sequence 116020 from Patent EP1572962.
JD556194 - Sequence 537218 from Patent EP1572962.
JD522214 - Sequence 503238 from Patent EP1572962.
JD336005 - Sequence 317029 from Patent EP1572962.
JD182066 - Sequence 163090 from Patent EP1572962.
JD055018 - Sequence 36042 from Patent EP1572962.
JD336755 - Sequence 317779 from Patent EP1572962.
JD222700 - Sequence 203724 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_dbpbPathway - Transcriptional activation of dbpb from mRNA

Reactome (by CSHL, EBI, and GO)

Protein P01127 (Reactome details) participates in the following event(s):

R-HSA-8865276 PDGF-AB clevage by Furin
R-HSA-8865275 PDGF-BB clevage by Furin
R-HSA-382054 PDGF binds to extracellular matrix proteins
R-HSA-2396337 HSPG2 binds FGF2(10-155), Fibronectn matrix, Transthyretin tetramer, PDGFA homodimer, PDGFB homodimer
R-HSA-382053 Translocation of PDGF from ER to Golgi
R-HSA-481007 Exocytosis of platelet alpha granule contents
R-HSA-186765 PLC-gamma binds to the active receptor
R-HSA-186778 SHP2 binds to the active receptor
R-HSA-186780 PI3-kinase binds to the active receptor
R-HSA-186819 SH2 domain of Src binds to the active receptor
R-HSA-186826 Grb2/Sos1 complex binds to the active receptor
R-HSA-380782 STAT binds to the active receptor
R-HSA-382055 Grb7 binds to the active PDGF receptor
R-HSA-382056 Crk binds to the active PDGF receptor
R-HSA-382058 Nck binds to the active PDGF receptor
R-HSA-1524182 Activated PLC gamma dissociates from the PDGF receptor
R-HSA-380780 Activation of Src
R-HSA-389083 Autophosphorylation of PDGF alpha receptors
R-HSA-389086 Autophosphorylation of PDGF alpha/beta receptors
R-HSA-186798 GAP binds to PDGF-beta receptors only
R-HSA-186786 Autophosphorylation of PDGF beta receptors
R-HSA-1524186 Phosphorylation of PLCgamma by PDGFR
R-HSA-382052 p130Cas and C3G bind PDGFR bound Crk
R-HSA-8864036 PTPN12 dephosphorylates PDGFRB at Y1021
R-HSA-186800 PI3K catalyses the phosphorylation of PIP2 to PIP3
R-HSA-186834 Sos-mediated nucleotide exchange of Ras (PDGF receptor:Grb2:Sos)
R-HSA-2400009 PI3K inhibitors block PI3K catalytic activity
R-HSA-2316434 PI3K phosphorylates PIP2 to PIP3
R-HSA-5672965 RAS GEFs promote RAS nucleotide exchange
R-HSA-186797 Signaling by PDGF
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-3000171 Non-integrin membrane-ECM interactions
R-HSA-114608 Platelet degranulation
R-HSA-186763 Downstream signal transduction
R-HSA-162582 Signal Transduction
R-HSA-1474244 Extracellular matrix organization
R-HSA-76005 Response to elevated platelet cytosolic Ca2+
R-HSA-76002 Platelet activation, signaling and aggregation
R-HSA-109582 Hemostasis
R-HSA-2219530 Constitutive Signaling by Aberrant PI3K in Cancer
R-HSA-1257604 PIP3 activates AKT signaling
R-HSA-6811558 PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
R-HSA-5673001 RAF/MAP kinase cascade
R-HSA-2219528 PI3K/AKT Signaling in Cancer
R-HSA-9006925 Intracellular signaling by second messengers
R-HSA-199418 Negative regulation of the PI3K/AKT network
R-HSA-5684996 MAPK1/MAPK3 signaling
R-HSA-5663202 Diseases of signal transduction
R-HSA-5683057 MAPK family signaling cascades
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000331163.1, ENST00000331163.10, ENST00000331163.2, ENST00000331163.3, ENST00000331163.4, ENST00000331163.5, ENST00000331163.6, ENST00000331163.7, ENST00000331163.8, ENST00000331163.9, G3XAG8, NM_002608, P01127, P78431, PDGF2, PDGFB_HUMAN, Q15354, Q6FHE7, Q9UF23, SIS, uc317tdj.1, uc317tdj.2
UCSC ID: ENST00000331163.11_7
RefSeq Accession: NM_002608.4
Protein: P01127 (aka PDGFB_HUMAN or PDGB_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PDGFB:
bgc (Primary Familial Brain Calcification)
dystonia-ov (Hereditary Dystonia Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.