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Aliases for PDGFD Gene

Aliases for PDGFD Gene

  • Platelet Derived Growth Factor D 2 3 5
  • Spinal Cord-Derived Growth Factor B 3 4
  • Iris-Expressed Growth Factor 3 4
  • SCDGF-B 3 4
  • PDGF-D 3 4
  • SCDGFB 3 4
  • IEGF 3 4
  • Spinal Cord Derived Growth Factor B 2
  • Platelet-Derived Growth Factor D 3
  • MSTP036 3

External Ids for PDGFD Gene

Previous GeneCards Identifiers for PDGFD Gene

  • GC11M103315
  • GC11M103283
  • GC11M103777
  • GC11M099706

Summaries for PDGFD Gene

Entrez Gene Summary for PDGFD 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 core motif of eight cysteines, seven of which are found in this factor. This gene product only forms homodimers and, therefore, does not dimerize with the other three family members. It differs from alpha and beta members of this family in having an unusual N-terminal domain, the CUB domain. Two splice variants have been identified for this gene. [provided by RefSeq, Jul 2008]

GeneCards Summary for PDGFD Gene

PDGFD (Platelet Derived Growth Factor D) is a Protein Coding gene. Diseases associated with PDGFD include Mesangial Proliferative Glomerulonephritis and Prostate Cancer. Among its related pathways are RET signaling and Cytoskeleton remodeling_Role of PDGFs in cell migration. GO annotations related to this gene include growth factor activity and platelet-derived growth factor receptor binding. An important paralog of this gene is PDGFC.

UniProtKB/Swiss-Prot for PDGFD 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. Plays an important role in wound healing. Induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix (By similarity).

Tocris Summary for PDGFD 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.

Gene Wiki entry for PDGFD Gene

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

Genomics for PDGFD Gene

Regulatory Elements for PDGFD Gene

Enhancers for PDGFD Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH11F104064 0.2 Ensembl 11.4 +99.8 99779 0.4 HLF DDI1 PDGFD ENSG00000255548
GH11F104001 0.4 ENCODE 11.2 +162.5 162521 1.4 CEBPB TBX21 DDI1 PDGFD ENSG00000255548
GH11F104073 1.3 Ensembl ENCODE 11.1 +90.1 90079 1.0 SPI1 DDI1 PDGFD
GH11F103960 0.6 ENCODE 11 +203.1 203103 1.1 FOS ZNF433 NFE2L2 DDI1 PDGFD ENSG00000255548
GH11F103958 0.5 ENCODE 11 +205.2 205195 1.1 PKNOX1 MXI1 TBL1XR1 BMI1 RELA CBX5 MTA2 TRIM22 JUNB CHD1 DDI1 PDGFD ENSG00000255548
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PDGFD on UCSC Golden Path with GeneCards custom track

Promoters for PDGFD Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001573007 678 2200 ELF3 SIN3A FEZF1 ZNF2 RAD21 GLIS2 SCRT2 EGR2 NFYC CEBPB

Genomic Location for PDGFD Gene

Chromosome:
11
Start:
103,907,186 bp from pter
End:
104,164,379 bp from pter
Size:
257,194 bases
Orientation:
Minus strand

Genomic View for PDGFD Gene

Genes around PDGFD on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDGFD Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDGFD Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDGFD Gene

Proteins for PDGFD Gene

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

    Protein Symbol:
    Q9GZP0-PDGFD_HUMAN
    Recommended name:
    Platelet-derived growth factor D
    Protein Accession:
    Q9GZP0
    Secondary Accessions:
    • A8K9T6
    • Q9BWV5

    Protein attributes for PDGFD Gene

    Size:
    370 amino acids
    Molecular mass:
    42848 Da
    Quaternary structure:
    • Homodimer; disulfide-linked. Interacts with PDGFRB homodimers, and with heterodimers formed by PDGFRA and PDGFRB.

    Alternative splice isoforms for PDGFD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDGFD Gene

Post-translational modifications for PDGFD Gene

  • Activated by proteolytic cleavage. Proteolytic removal of the N-terminal CUB domain releasing the core domain is necessary for unmasking the receptor-binding epitopes of the core domain. Cleavage after Arg-247 or Arg-249 by urokinase plasminogen activator gives rise to the active form.
  • Ubiquitination at Lys 160
  • Glycosylation at Asn 276
  • Modification sites at PhosphoSitePlus

Other Protein References for PDGFD Gene

Antibody Products

  • Abcam antibodies for PDGFD
  • Cloud-Clone Corp. Antibodies for PDGFD

No data available for DME Specific Peptides for PDGFD Gene

Domains & Families for PDGFD Gene

Suggested Antigen Peptide Sequences for PDGFD Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9GZP0

UniProtKB/Swiss-Prot:

PDGFD_HUMAN :
  • Contains 1 CUB domain.
  • Belongs to the PDGF/VEGF growth factor family.
Domain:
  • Contains 1 CUB domain.
Family:
  • Belongs to the PDGF/VEGF growth factor family.
genes like me logo Genes that share domains with PDGFD: view

No data available for Gene Families for PDGFD Gene

Function for PDGFD Gene

Molecular function for PDGFD Gene

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. Plays an important role in wound healing. Induces macrophage recruitment, increased interstitial pressure, and blood vessel maturation during angiogenesis. Can initiate events that lead to a mesangial proliferative glomerulonephritis, including influx of monocytes and macrophages and production of extracellular matrix (By similarity).

Gene Ontology (GO) - Molecular Function for PDGFD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005161 platelet-derived growth factor receptor binding IEA,IBA --
GO:0008083 growth factor activity IEA --
genes like me logo Genes that share ontologies with PDGFD: view
genes like me logo Genes that share phenotypes with PDGFD: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PDGFD

miRNA for PDGFD Gene

miRTarBase miRNAs that target PDGFD

Inhibitory RNA Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDGFD Gene

Localization for PDGFD Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDGFD Gene

Secreted. Note=Released by platelets upon wounding.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for PDGFD Gene COMPARTMENTS Subcellular localization image for PDGFD gene
Compartment Confidence
endoplasmic reticulum 5
extracellular 5
golgi apparatus 4
plasma membrane 2
cytoskeleton 1
endosome 1
lysosome 1
mitochondrion 1
vacuole 1

Gene Ontology (GO) - Cellular Components for PDGFD 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:0005788 endoplasmic reticulum lumen TAS --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with PDGFD: view

Pathways & Interactions for PDGFD Gene

genes like me logo Genes that share pathways with PDGFD: view

Gene Ontology (GO) - Biological Process for PDGFD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007596 blood coagulation IBA --
GO:0008284 positive regulation of cell proliferation IBA --
GO:0014068 positive regulation of phosphatidylinositol 3-kinase signaling IBA --
GO:0030335 positive regulation of cell migration IBA --
genes like me logo Genes that share ontologies with PDGFD: view

No data available for SIGNOR curated interactions for PDGFD Gene

Drugs & Compounds for PDGFD Gene

(6) Drugs for PDGFD Gene - From: DrugBank, DGIdb, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Sunitinib Approved, Investigational Pharma inhibitor VEGFR/PDGFRβ/ KIT/ FLT3/RET/CSF-1R inhibitor, RTK inhibitor, Kinase Inhibitors, Vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) inhibitors, Potent VEGFR, PDGFRbeta and KIT inhibitor 500
CR002 Investigational Pharma Target 0
MLN-518 Investigational Pharma Target 0
DMPQ dihydrochloride Pharma Potent, selective inhibitor of PDGFRbeta 0
SU 16f Pharma Potent and selective PDGFRbeta inhibitor 0

(2) Additional Compounds for PDGFD Gene - From: Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
AC 710
1351522-04-7
SU 6668
252916-29-3

(5) Tocris Compounds for PDGFD Gene

Compound Action Cas Number
AC 710 Potent and selective PDGFR family inhibitor 1351522-04-7
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
genes like me logo Genes that share compounds with PDGFD: view

Transcripts for PDGFD Gene

Unigene Clusters for PDGFD Gene

Platelet derived growth factor D:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b
SP1:
SP2: -

Relevant External Links for PDGFD Gene

GeneLoc Exon Structure for
PDGFD
ECgene alternative splicing isoforms for
PDGFD

Expression for PDGFD Gene

mRNA expression in normal human tissues for PDGFD Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PDGFD Gene

This gene is overexpressed in Adrenal Gland (x7.4) and Artery - Aorta (x6.5).

Protein differential expression in normal tissues from HIPED for PDGFD Gene

This gene is overexpressed in Serum (42.0) and Peripheral blood mononuclear cells (16.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PDGFD Gene



Protein tissue co-expression partners for PDGFD Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDGFD Gene:

PDGFD

SOURCE GeneReport for Unigene cluster for PDGFD Gene:

Hs.352298

mRNA Expression by UniProt/SwissProt for PDGFD Gene:

Q9GZP0-PDGFD_HUMAN
Tissue specificity: Expressed at high levels in the heart, pancreas, adrenal gland and ovary and at low levels in placenta, liver, kidney, prostate, testis, small intestine, spleen and colon. In the kidney, expressed by the visceral epithelial cells of the glomeruli. A widespread expression is also seen in the medial smooth muscle cells of arteries and arterioles, as well as in smooth muscle cells of vasa rectae in the medullary area. Expressed in the adventitial connective tissue surrounding the suprarenal artery. In chronic obstructive nephropathy, a persistent expression is seen in glomerular visceral epithelial cells and vascular smooth muscle cells, as well as de novo expression by periglomerular interstitial cells and by some neointimal cells of atherosclerotic vessels. Expression in normal prostate is seen preferentially in the mesenchyme of the gland while expression is increased and more profuse in prostate carcinoma. Expressed in many ovarian, lung, renal and brain cancer-derived cell lines.
genes like me logo Genes that share expression patterns with PDGFD: view

Primer Products

Orthologs for PDGFD Gene

This gene was present in the common ancestor of chordates.

Orthologs for PDGFD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PDGFD 34 35
  • 99.55 (n)
cow
(Bos Taurus)
Mammalia PDGFD 34 35
  • 88.92 (n)
dog
(Canis familiaris)
Mammalia PDGFD 34 35
  • 87.93 (n)
rat
(Rattus norvegicus)
Mammalia Pdgfd 34
  • 86.04 (n)
mouse
(Mus musculus)
Mammalia Pdgfd 34 16 35
  • 85.86 (n)
oppossum
(Monodelphis domestica)
Mammalia PDGFD 35
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDGFD 35
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDGFD 34 35
  • 79.14 (n)
lizard
(Anolis carolinensis)
Reptilia PDGFD 35
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492060 34
  • 70.42 (n)
zebrafish
(Danio rerio)
Actinopterygii LOC100535718 34
  • 66.15 (n)
CABZ01114098.1 35
  • 60 (a)
OneToOne
Species where no ortholog for PDGFD was found in the sources mined by GeneCards:
  • 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 PDGFD Gene

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

Paralogs for PDGFD Gene

Paralogs for PDGFD Gene

(3) SIMAP similar genes for PDGFD Gene using alignment to 2 proteins:

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

Variants for PDGFD Gene

Sequence variations from dbSNP and Humsavar for PDGFD Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
VAR_036418 A colorectal cancer sample
rs10160779 -- 103,934,685(+) ggaac(G/T)gccct intron-variant
rs1021290 -- 103,971,814(+) TGTAA(C/T)ATTGA intron-variant
rs1021291 -- 103,972,257(+) cctcc(A/G)cccac intron-variant
rs1027619 -- 104,099,456(-) CACCA(C/T)GTTGC intron-variant

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

Variant ID Type Subtype PubMed ID
dgv2143n54 CNV loss 21841781
dgv2144n54 CNV loss 21841781
dgv2145n54 CNV loss 21841781
dgv2146n54 CNV loss 21841781
dgv2147n54 CNV loss 21841781
dgv237n67 CNV loss 20364138
dgv713n106 CNV deletion 24896259
dgv714n106 CNV deletion 24896259
dgv71e215 CNV deletion 23714750
esv1297071 CNV insertion 17803354
esv1417082 CNV deletion 17803354
esv2037427 CNV deletion 18987734
esv2205640 CNV deletion 18987734
esv22062 CNV loss 19812545
esv2477876 CNV insertion 19546169
esv2597532 CNV deletion 19546169
esv2666036 CNV deletion 23128226
esv2666677 CNV deletion 23128226
esv2671461 CNV deletion 23128226
esv2676733 CNV deletion 23128226
esv2745011 CNV deletion 23290073
esv2745012 CNV deletion 23290073
esv2745013 CNV deletion 23290073
esv2750977 CNV gain 17911159
esv2750978 CNV gain 17911159
esv2760322 CNV loss 21179565
esv29047 CNV gain 19812545
esv3147 CNV loss 18987735
esv3255384 CNV deletion 24192839
esv3306145 CNV mobile element insertion 20981092
esv3306917 CNV mobile element insertion 20981092
esv3309150 CNV mobile element insertion 20981092
esv3327429 CNV insertion 20981092
esv3375835 CNV insertion 20981092
esv3440419 CNV insertion 20981092
esv3548276 CNV deletion 23714750
esv3627567 CNV loss 21293372
esv3627568 CNV gain 21293372
esv3627571 CNV loss 21293372
esv3627575 CNV loss 21293372
esv3736 CNV loss 18987735
esv9653 CNV loss 19470904
esv991768 CNV deletion 20482838
nsv1043976 CNV gain 25217958
nsv1052674 CNV loss 25217958
nsv1069619 CNV deletion 25765185
nsv1070984 CNV deletion 25765185
nsv1113431 CNV deletion 24896259
nsv1143550 CNV deletion 24896259
nsv1152736 CNV deletion 26484159
nsv38514 CNV deletion 16902084
nsv519705 CNV loss 19592680
nsv526709 CNV loss 19592680
nsv819791 CNV loss 19587683
nsv826068 CNV loss 20364138
nsv957226 CNV deletion 24416366
nsv958608 CNV deletion 24416366

Variation tolerance for PDGFD Gene

Residual Variation Intolerance Score: 70.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.56; 55.95% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PDGFD Gene

Human Gene Mutation Database (HGMD)
PDGFD
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDGFD

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

Disorders for PDGFD Gene

MalaCards: The human disease database

(2) MalaCards diseases for PDGFD Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
mesangial proliferative glomerulonephritis
  • glomerulonephritis - mesangial proliferative
prostate cancer
  • prostate cancer, hereditary, 5
- elite association - COSMIC cancer census association via MalaCards
Search PDGFD in MalaCards View complete list of genes associated with diseases

Relevant External Links for PDGFD

Genetic Association Database (GAD)
PDGFD
Human Genome Epidemiology (HuGE) Navigator
PDGFD
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDGFD
genes like me logo Genes that share disorders with PDGFD: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDGFD Gene

Publications for PDGFD Gene

  1. Molecular cloning of SCDGF-B, a novel growth factor homologous to SCDGF/PDGF-C/fallotein. (PMID: 11162582) Hamada T. … Miyata Y. (Biochem. Biophys. Res. Commun. 2001) 2 3 4 22 64
  2. Platelet-derived growth factor D: tumorigenicity in mice and dysregulated expression in human cancer. (PMID: 11980634) LaRochelle W.J. … Lichenstein H.S. (Cancer Res. 2002) 2 3 4 64
  3. Platelet-derived growth factor-D expression in developing and mature human kidneys. (PMID: 12427128) Changsirikulchai S. … Alpers C.E. (Kidney Int. 2002) 3 4 22 64
  4. Chromosomal location, exon structure, and vascular expression patterns of the human PDGFC and PDGFC genes. (PMID: 11342471) Uutela M. … Alitalo K. (Circulation 2001) 3 4 22 64
  5. Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. (PMID: 21347282) Lettre G. … Boerwinkle E. (PLoS Genet. 2011) 3 46 64

Products for PDGFD Gene

Sources for PDGFD Gene

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