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PDGFD platelet derived growth factor D [ Homo sapiens (human) ]

Gene ID: 80310, updated on 1-Jun-2020

Summary

Official Symbol
PDGFDprovided by HGNC
Official Full Name
platelet derived growth factor Dprovided by HGNC
Primary source
HGNC:HGNC:30620
See related
Ensembl:ENSG00000170962 MIM:609673
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
IEGF; SCDGFB; MSTP036; SCDGF-B
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, 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]
Expression
Biased expression in adrenal (RPKM 66.8), ovary (RPKM 41.5) and 13 other tissues See more
Orthologs

Genomic context

See PDGFD in Genome Data Viewer
Location:
11q22.3
Exon count:
7
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (103907189..104164147, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (103777914..104035027, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723862 Neighboring gene uncharacterized LOC105369464 Neighboring gene microRNA 4693 Neighboring gene DNA damage inducible 1 homolog 1 Neighboring gene RNA, 5S ribosomal pseudogene 348 Neighboring gene uncharacterized LOC102723879

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 association study in Europeans and South Asians identifies five new loci for coronary artery disease.
NHGRI GWA Catalog
Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women.
NHGRI GWA Catalog
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project.
NHGRI GWA Catalog
Genome-wide association study of selenium concentrations.
NHGRI GWA Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC26867

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 
Process Evidence Code Pubs
cellular response to amino acid stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to hydrogen peroxide IEA
Inferred from Electronic Annotation
more info
 
cellular response to platelet-derived growth factor stimulus IEA
Inferred from Electronic Annotation
more info
 
cellular response to transforming growth factor beta stimulus IEA
Inferred from Electronic Annotation
more info
 
multicellular organism 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 
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 fibroblast proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of glomerular mesangial cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of monocyte extravasation IEA
Inferred from Electronic Annotation
more info
 
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 
positive regulation of smooth muscle cell chemotaxis IEA
Inferred from Electronic Annotation
more info
 
positive regulation of smooth muscle cell proliferation IEA
Inferred from Electronic Annotation
more info
 
regulation of peptidyl-tyrosine phosphorylation IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi membrane TAS
Traceable Author Statement
more info
 
endoplasmic reticulum lumen TAS
Traceable Author Statement
more info
 
extracellular region TAS
Traceable Author Statement
more info
 
extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
platelet-derived growth factor D
Names
PDGF-D
iris-expressed growth factor
spinal cord-derived growth factor B

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_025208.5NP_079484.1  platelet-derived growth factor D isoform 1 precursor

    See identical proteins and their annotated locations for NP_079484.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AF113216, AI962915, BC030645
    Consensus CDS
    CCDS41703.1
    UniProtKB/Swiss-Prot
    Q9GZP0
    Related
    ENSP00000376865.2, ENST00000393158.7
    Conserved Domains (2) summary
    cd00041
    Location:55168
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    cd00135
    Location:270365
    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 ...
  2. NM_033135.4NP_149126.1  platelet-derived growth factor D isoform 2 precursor

    See identical proteins and their annotated locations for NP_149126.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AF113216, AI962915, BC030645
    Consensus CDS
    CCDS8326.1
    UniProtKB/Swiss-Prot
    Q9GZP0
    Related
    ENSP00000302193.5, ENST00000302251.9
    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:264359
    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 ...

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    103907189..104164147 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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