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

Gene ID: 56034, updated on 1-Aug-2020

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
109.20200522 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 PubChem

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
 
growth factor receptor binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 109.20200522

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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