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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 2 3
  • 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 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 proliferative glomerulonephritis. Among its related pathways are Phospholipase D signaling pathway and Focal Adhesion. 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 Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

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

ENSRs around PDGFD on UCSC Golden Path with GeneCards custom track

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

Proteomics data for PDGFD Gene at MOPED

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

No data available for DME Specific Peptides for PDGFD Gene

Domains & Families for PDGFD Gene

Protein Domains 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).
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

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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

No data available for Gene Ontology (GO) - Cellular Components for PDGFD Gene

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:0007596 blood coagulation IBA --
GO:0031954 positive regulation of protein autophosphorylation IBA --
GO:0043406 positive regulation of MAP kinase activity IBA --
GO:0048008 platelet-derived growth factor receptor signaling pathway IEA,IBA --
GO:0048146 positive regulation of fibroblast proliferation IEA --
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

(3) 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 490
CR002 Investigational Pharma Target 0
MLN-518 Investigational Pharma Target 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
AG 18
118409-57-7
DMPQ dihydrochloride
1123491-15-5
SU 16f
251356-45-3
SU 6668
252916-29-3

(5) Tocris Compounds for PDGFD Gene

Compound Action Cas Number
AG 18 EGFR/PDGFR-kinase inhibitor 118409-57-7
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
Sunitinib malate Potent VEGFR, PDGFRbeta and KIT inhibitor 341031-54-7
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:

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



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

Protein tissue co-expression partners for PDGFD Gene

- Elite partner

Primer Products

In Situ Assay 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
cow
(Bos Taurus)
Mammalia PDGFD 35
  • 88.92 (n)
  • 91.21 (a)
PDGFD 36
  • 91 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PDGFD 35
  • 87.93 (n)
  • 88.92 (a)
PDGFD 36
  • 89 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Pdgfd 35
  • 85.86 (n)
  • 85.14 (a)
Pdgfd 16
Pdgfd 36
  • 85 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PDGFD 35
  • 99.55 (n)
  • 100 (a)
PDGFD 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdgfd 35
  • 86.04 (n)
  • 86.76 (a)
oppossum
(Monodelphis domestica)
Mammalia PDGFD 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDGFD 36
  • 84 (a)
OneToOne
chicken
(Gallus gallus)
Aves PDGFD 35
  • 79.14 (n)
  • 81.15 (a)
PDGFD 36
  • 75 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia PDGFD 36
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100492060 35
  • 70.42 (n)
  • 71.7 (a)
zebrafish
(Danio rerio)
Actinopterygii LOC100535718 35
  • 66.15 (n)
  • 69.37 (a)
CABZ01114098.1 36
  • 60 (a)
OneToOne
Species with no ortholog for PDGFD:
  • 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
rs35045740 - 103,947,667(+) TGAAA(C/T)AGAGC reference, missense
rs537824 -- 104,069,199(-) cctgt(A/G)ctctt intron-variant
rs539028 -- 103,992,402(+) ATTGT(C/T)ATCAT intron-variant
rs540673 -- 103,919,710(+) CCCCA(C/T)GTTGG intron-variant

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

Variant ID Type Subtype PubMed ID
esv2750977 CNV Gain 17911159
esv271193 CNV Insertion 20981092
esv273423 CNV Insertion 20981092
nsv38514 CNV Loss 16902084
esv2671461 CNV Deletion 23128226
esv270422 CNV Insertion 20981092
esv2676733 CNV Deletion 23128226
nsv819791 CNV Loss 19587683
esv22062 CNV Loss 19812545
dgv237n67 CNV Loss 20364138
esv2666036 CNV Deletion 23128226
nsv526709 CNV Loss 19592680
esv2477876 CNV Insertion 19546169
esv2205640 CNV Deletion 18987734
esv2745011 CNV Deletion 23290073
esv3147 CNV Deletion 18987735
esv2666677 CNV Deletion 23128226
esv2745012 CNV Deletion 23290073
nsv826068 CNV Loss 20364138
esv2750978 CNV Gain 17911159
nsv519705 CNV Loss 19592680
esv1297071 CNV Insertion 17803354
esv29047 CNV Gain 19812545
esv2597532 CNV Deletion 19546169
esv2037427 CNV Deletion 18987734
esv3736 CNV Deletion 18987735
esv2745013 CNV Deletion 23290073
esv9653 CNV Loss 19470904
esv991768 CNV Deletion 20482838
esv1417082 CNV Deletion 17803354

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

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

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

Disorders for PDGFD Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
mesangial proliferative glomerulonephritis
  • glomerulonephritis - mesangial proliferative
proliferative glomerulonephritis
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 23 67
  2. Human umbilical cord blood stem cells show PDGF-D-dependent glioma cell tropism in vitro and in vivo. (PMID: 20406896) Gondi C.S. … Rao J.S. (Neuro-oncology 2010) 3 23
  3. Identification of platelet-derived growth factor D in human chronic allograft nephropathy. (PMID: 18187181) Liu G. … Alpers C.E. (Hum. Pathol. 2008) 3 23
  4. [Expression and clinical implication of platelet-derived growth factor-D and platelet-derived growth factor-beta in childhood IgA nephropathy]. (PMID: 18471357) Rong Z.H. … Duan H.J. (Zhongguo Wei Zhong Bing Ji Jiu Yi Xue 2008) 3 23
  5. Inducible platelet-derived growth factor D-chain expression by angiotensin II and hydrogen peroxide involves transcriptional regulation by Ets-1 and Sp1. (PMID: 16189269) Liu M.Y. … Khachigian L.M. (Blood 2006) 3 23

Products for PDGFD Gene

Sources for PDGFD Gene

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