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PDGFC platelet derived growth factor C [ Homo sapiens (human) ]

Gene ID: 56034, updated on 12-Oct-2019

Summary

Official Symbol
PDGFCprovided by HGNC
Official Full Name
platelet derived growth factor Cprovided by HGNC
Primary source
HGNC:HGNC:8801
See related
Ensembl:ENSG00000145431 MIM:608452
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SCDGF; FALLOTEIN
Summary
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. This gene product appears to form only homodimers. It differs from the platelet-derived growth factor alpha and beta polypeptides in having an unusual N-terminal domain, the CUB domain. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2010]
Expression
Ubiquitous expression in endometrium (RPKM 16.6), prostate (RPKM 13.9) and 24 other tissues See more
Orthologs

Genomic context

See PDGFC in Genome Data Viewer
Location:
4q32.1
Exon count:
9
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (156760454..156971799, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (157682763..157892546, complement)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377508 Neighboring gene long intergenic non-protein coding RNA 2272 Neighboring gene Sharpr-MPRA regulatory region 10686 Neighboring gene ribonuclease P RNA component H1, 3 pseudogene Neighboring gene glycine receptor beta

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.
NHGRI GWA Catalog
First genome-wide association scan on neurophysiological endophenotypes points to trans-regulation effects on SLC2A3 in dyslexic children.
NHGRI GWA Catalog
Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat Treatment of human neuroblastoma cells or rat primary neurons with HIV-1 Tat downregulates PDGF-C expression PubMed
tat PDGF-C mediated neuroprotection against HIV-1 Tat results from inactivation of the downstream mediator GSK3 beta by its phosphorylation at Ser-9 in human neuroblastoma cells PubMed
tat PI3K/Akt, TRPC, and GSK3 beta signaling pathways are all involved in PDGF-C mediated neuroprotection against HIV-1 Tat in human neuroblastoma cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Choline metabolism in cancer, organism-specific biosystem (from KEGG)
    Choline metabolism in cancer, organism-specific biosystemAbnormal choline metabolism is emerging as a metabolic hallmark that is associated with oncogenesis and tumour progression. Following transformation, oncogenic signalling via pathways such as the RAS...
  • Choline metabolism in cancer, conserved biosystem (from KEGG)
    Choline metabolism in cancer, conserved biosystemAbnormal choline metabolism is emerging as a metabolic hallmark that is associated with oncogenesis and tumour progression. Following transformation, oncogenic signalling via pathways such as the RAS...
  • Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • EGFR tyrosine kinase inhibitor resistance, organism-specific biosystem (from KEGG)
    EGFR tyrosine kinase inhibitor resistance, organism-specific biosystemEGFR is a tyrosine kinase that participates in the regulation of cellular homeostasis. EGFR also serves as a stimulus for cancer growth. EGFR gene mutations and protein overexpression, both of which ...
  • EGFR tyrosine kinase inhibitor resistance, conserved biosystem (from KEGG)
    EGFR tyrosine kinase inhibitor resistance, conserved biosystemEGFR is a tyrosine kinase that participates in the regulation of cellular homeostasis. EGFR also serves as a stimulus for cancer growth. EGFR gene mutations and protein overexpression, both of which ...
  • Focal Adhesion, organism-specific biosystem (from WikiPathways)
    Focal Adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, organism-specific biosystem (from KEGG)
    Focal adhesion, organism-specific biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Focal adhesion, conserved biosystem (from KEGG)
    Focal adhesion, conserved biosystemCell-matrix adhesions play essential roles in important biological processes including cell motility, cell proliferation, cell differentiation, regulation of gene expression and cell survival. At the...
  • Gap junction, organism-specific biosystem (from KEGG)
    Gap junction, organism-specific biosystemGap junctions contain intercellular channels that allow direct communication between the cytosolic compartments of adjacent cells. Each gap junction channel is formed by docking of two 'hemichannels'...
  • Gap junction, conserved biosystem (from KEGG)
    Gap junction, conserved biosystemGap junctions contain intercellular channels that allow direct communication between the cytosolic compartments of adjacent cells. Each gap junction channel is formed by docking of two 'hemichannels'...
  • Melanoma, organism-specific biosystem (from KEGG)
    Melanoma, organism-specific biosystemMelanoma is a form of skin cancer that has a poor prognosis and which is on the rise in Western populations. Melanoma arises from the malignant transformation of pigment-producing cells, melanocytes...
  • Melanoma, conserved biosystem (from KEGG)
    Melanoma, conserved biosystemMelanoma is a form of skin cancer that has a poor prognosis and which is on the rise in Western populations. Melanoma arises from the malignant transformation of pigment-producing cells, melanocytes...
  • PI3K-Akt signaling pathway, organism-specific biosystem (from KEGG)
    PI3K-Akt signaling pathway, organism-specific biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • PI3K-Akt signaling pathway, conserved biosystem (from KEGG)
    PI3K-Akt signaling pathway, conserved biosystemThe phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, tra...
  • Phospholipase D signaling pathway, organism-specific biosystem (from KEGG)
    Phospholipase D signaling pathway, organism-specific biosystemPhospholipase D (PLD) is an essential enzyme responsible for the production of the lipid second messenger phosphatidic acid (PA), which is involved in fundamental cellular processes, including membra...
  • Phospholipase D signaling pathway, conserved biosystem (from KEGG)
    Phospholipase D signaling pathway, conserved biosystemPhospholipase D (PLD) is an essential enzyme responsible for the production of the lipid second messenger phosphatidic acid (PA), which is involved in fundamental cellular processes, including membra...
  • Prostate cancer, organism-specific biosystem (from KEGG)
    Prostate cancer, organism-specific biosystemProstate cancer constitutes a major health problem in Western countries. It is the most frequently diagnosed cancer among men and the second leading cause of male cancer deaths. The identification of...
  • Prostate cancer, conserved biosystem (from KEGG)
    Prostate cancer, conserved biosystemProstate cancer constitutes a major health problem in Western countries. It is the most frequently diagnosed cancer among men and the second leading cause of male cancer deaths. The identification of...
  • Rap1 signaling pathway, organism-specific biosystem (from KEGG)
    Rap1 signaling pathway, organism-specific biosystemRap1 is a small GTPase that controls diverse processes, such as cell adhesion, cell-cell junction formation and cell polarity. Like all G proteins, Rap1 cycles between an inactive GDP-bound and an ac...
  • Rap1 signaling pathway, conserved biosystem (from KEGG)
    Rap1 signaling pathway, conserved biosystemRap1 is a small GTPase that controls diverse processes, such as cell adhesion, cell-cell junction formation and cell polarity. Like all G proteins, Rap1 cycles between an inactive GDP-bound and an ac...
  • Ras signaling pathway, organism-specific biosystem (from KEGG)
    Ras signaling pathway, organism-specific biosystemThe Ras proteins are GTPases that function as molecular switches for signaling pathways regulating cell proliferation, survival, growth, migration, differentiation or cytoskeletal dynamism. Ras prote...
  • Regulation of actin cytoskeleton, organism-specific biosystem (from KEGG)
    Regulation of actin cytoskeleton, organism-specific biosystem
    Regulation of actin cytoskeleton
  • Regulation of actin cytoskeleton, conserved biosystem (from KEGG)
    Regulation of actin cytoskeleton, conserved biosystem
    Regulation of actin cytoskeleton
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by PDGF, organism-specific biosystem (from REACTOME)
    Signaling by PDGF, organism-specific biosystemPlatelet-derived Growth Factor (PDGF) is a potent stimulator of growth and motility of connective tissue cells such as fibroblasts and smooth muscle cells as well as other cells such as capillary end...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
growth factor activity IEA
Inferred from Electronic Annotation
more info
 
platelet-derived growth factor receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
platelet-derived growth factor receptor binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
activation of transmembrane receptor protein tyrosine kinase activity IEA
Inferred from Electronic Annotation
more info
 
animal organ morphogenesis IEA
Inferred from Electronic Annotation
more info
 
bone development IEA
Inferred from Electronic Annotation
more info
 
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
central nervous system development TAS
Traceable Author Statement
more info
PubMed 
digestive tract development IEA
Inferred from Electronic Annotation
more info
 
embryonic organ development IEA
Inferred from Electronic Annotation
more info
 
platelet-derived growth factor receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
platelet-derived growth factor receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of ERK1 and ERK2 cascade IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of MAP kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cell division IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cell migration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cell proliferation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cold-induced thermogenesis ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
positive regulation of fibroblast proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of phosphatidylinositol 3-kinase signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of protein autophosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of peptidyl-tyrosine phosphorylation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi membrane TAS
Traceable Author Statement
more info
 
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
extracellular space IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
platelet-derived growth factor C
Names
PDGF-C
VEGF-E
secretory growth factor-like protein
spinal cord-derived growth factor

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_016205.3NP_057289.1  platelet-derived growth factor C precursor

    See identical proteins and their annotated locations for NP_057289.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript and encodes the functional protein.
    Source sequence(s)
    AC092608, AC093325, AF091434, AI446155
    Consensus CDS
    CCDS3795.1
    UniProtKB/Swiss-Prot
    Q9NRA1
    Related
    ENSP00000422464.1, ENST00000502773.6
    Conserved Domains (2) summary
    cd00041
    Location:49162
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    cd00135
    Location:248340
    PDGF; Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and ...

RNA

  1. NR_036641.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as PDGF-Cb) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC092608, AC093325, AF091434, AI446155, AM922296

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    156760454..156971799 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017008456.2XP_016863945.1  platelet-derived growth factor C isoform X3

    UniProtKB/Swiss-Prot
    Q9NRA1
    Related
    ENSP00000410048.2, ENST00000422544.2
  2. XM_011532124.2XP_011530426.1  platelet-derived growth factor C isoform X1

    Conserved Domains (2) summary
    cd00041
    Location:38151
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    cd00135
    Location:237329
    PDGF; Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family domain; PDGF is a potent activator for cells of mesenchymal origin; PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer; VEGF is a potent mitogen in embryonic and ...
  3. XM_017008455.1XP_016863944.1  platelet-derived growth factor C isoform X2

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