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Aliases for PDGFD Gene

Aliases for PDGFD Gene

  • Platelet Derived Growth Factor D 2 3
  • SCDGFB 3 4 6
  • IEGF 3 4 6
  • 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
  • Spinal Cord-Derived Growth Factor-B 3
  • 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. Among its related pathways are PI3K-Akt signaling pathway and Signaling by FGFR. 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, 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 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

Genomic Location for PDGFD Gene

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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 Lys160
  • Glycosylation at Asn276
  • Modification sites at PhosphoSitePlus

Other Protein References for PDGFD Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for PDGFD Gene

Domains 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 :
  • Q9GZP0
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 --
GO:0008083 growth factor activity IEA --
genes like me logo Genes that share ontologies with PDGFD: view

miRNA for PDGFD Gene

miRTarBase miRNAs that target PDGFD

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting 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
extracellular 5
endoplasmic reticulum 4
golgi apparatus 4
plasma membrane 2
cytoskeleton 1
endosome 1
lysosome 1
mitochondrion 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:0005788 endoplasmic reticulum lumen TAS --
GO:0016020 membrane --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with PDGFD: view

Pathways 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 organismal development IEA --
GO:0048008 platelet-derived growth factor receptor signaling pathway IEA --
GO:0050730 regulation of peptidyl-tyrosine phosphorylation IEA --
GO:0051781 positive regulation of cell division IEA --
GO:0071230 cellular response to amino acid stimulus IEA --
genes like me logo Genes that share ontologies with PDGFD: view

Compounds for PDGFD Gene

(14) ApexBio Compounds for PDGFD Gene

Compound Action Cas Number
Amuvatinib (MP-470, HPK 56) Multi-kinase inhibitor, inhibits PDGFR, c-Kit, and Flt3 [850879-09-3]
Crenolanib (CP-868596) Potent and selective PDGFR-beta inhibitor [670220-88-9]
Flumatinib mesylate multi-kinase inhibitor for c-Abl, PDGFRbeta and c-Kit [895519-91-2]
Imatinib Mesylate (STI571) Multi-target kinase inhibitor of abl, c-kit, and PDGFR [220127-57-1]
Masitinib (AB1010) tyrosine kinase, c-Kit, PDGFR, FGFR3, the FAK pathway inhibitor [790299-79-5]
MK-2461 potent inhibitor of Met, Ron, Flt1, Flt 3, PDGFRbeta, and Mer with IC50 of 2.5 nM, 7 nM, 10 nM, 22 nM, 22 nM and 24 nM, respectively. [917879-39-1]
Nintedanib (BIBF 1120) Multi-target kinase inhibitor, inhibits VEGFR, PDGFR, and FGFR [928326-83-4]
Pazopanib (GW-786034) Multi-target kinase inhibitor, inhibits VEGFR, PDGFR, and FGFR [635702-64-6]
Ponatinib (AP24534) pan-BCR-ABL inhibitor [943319-70-8]
Regorafenib Multi-kinase inhibitor, inhibits VEGFR, PDGFR, FGFR, mutant kit, RET, and Raf-1 [755037-03-7]
SKLB610 Potent VEGFR inhibitor [1125780-41-7]
Sorafenib Multi-target kinase inhibitor of Raf kinases and tyrosine kinases [284461-73-0]
Sorafenib Tosylate Multi-target kinase inhibitor of Raf kinases and tyrosine kinases [475207-59-1]
Sunitinib malate ATP-competitive multi-target kinase inhibitor, inhibits VEGFR, PDGFR, and KIT [341031-54-7]

(4) Tocris Compounds for PDGFD 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]
genes like me logo Genes that share compounds with PDGFD: view

Transcripts for PDGFD Gene

mRNA/cDNA 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 (7.4) and Artery - Aorta (6.5).

Integrated Proteomics: protein expression 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 expressions with PDGFD: view

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 35
  • 99.55 (n)
  • 100 (a)
PDGFD 36
  • 100 (a)
OneToOne
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
oppossum
(Monodelphis domestica)
Mammalia PDGFD 36
  • 84 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDGFD 36
  • 84 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Pdgfd 35
  • 86.04 (n)
  • 86.76 (a)
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 CABZ01114098.1 36
  • 60 (a)
OneToOne
LOC100535718 35
  • 66.15 (n)
  • 69.37 (a)
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

Selected 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 MAF
rs166350 -- 104,001,280(+) tgtac(C/T)agcag intron-variant
rs168636 -- 104,111,105(+) TGATT(A/G)TAACT intron-variant
rs173413 -- 104,120,009(+) ttaat(A/G)ttatc intron-variant
rs181733 -- 104,109,306(+) tgtgt(G/T)attcg intron-variant
rs183122 -- 104,116,778(-) agacc(A/G)gcccc 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

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

MalaCards: The human disease database. (1) Diseases for PDGFD Gene including...

Search for PDGFD Gene in MalaCards »

Relevant External Links for PDGFD

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

No data available for UniProtKB/Swiss-Prot 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
  2. 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 23
  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 23
  4. 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
  5. Expressed sequence tag analysis of adult human iris for the NEIBank project: steroid-response factors and similarities with retinal pigment epithelium. (PMID: 12107412) Wistow G. … Peterson K. (Mol. Vis. 2002) 3 4

Products for PDGFD Gene

Sources for PDGFD Gene

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