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

Gene ID: 80310, updated on 4-Jan-2025

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; AllianceGenome:HGNC:30620
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
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Genomic context

See PDGFD in Genome Data Viewer
Location:
11q22.3
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (103907189..104164147, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (103910709..104168067, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (103777917..104034875, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene microRNA 4693 Neighboring gene MPRA-validated peak1441 silencer Neighboring gene PDGFD downstream neighbor Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5455 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5456 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:103854885-103855078 Neighboring gene DNA damage inducible 1 homolog 1 Neighboring gene RNA, 5S ribosomal pseudogene 348 Neighboring gene uncharacterized LOC102723879 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:104208910-104210109

Genomic regions, transcripts, and products

Expression

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

General gene information

Clone Names

  • MGC26867

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables growth factor activity  
enables platelet-derived growth factor receptor binding  
Process Evidence Code Pubs
involved_in cellular response to amino acid stimulus  
involved_in cellular response to hydrogen peroxide  
involved_in cellular response to platelet-derived growth factor stimulus  
involved_in cellular response to transforming growth factor beta stimulus  
involved_in platelet-derived growth factor receptor signaling pathway  
involved_in positive regulation of ERK1 and ERK2 cascade  
involved_in positive regulation of cell division  
involved_in positive regulation of cell migration  
involved_in positive regulation of cell population proliferation  
involved_in positive regulation of fibroblast proliferation  
involved_in positive regulation of glomerular mesangial cell proliferation  
involved_in positive regulation of monocyte extravasation  
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction  
involved_in positive regulation of smooth muscle cell chemotaxis  
involved_in positive regulation of smooth muscle cell proliferation  
Component Evidence Code Pubs
located_in Golgi membrane  
located_in endoplasmic reticulum lumen  
located_in extracellular region  
is_active_in extracellular space  

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)

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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
    A8K9T6, Q9BWV5, 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: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

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

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    103910709..104168067 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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