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

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: mouse all
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Genomic context

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_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Exploring the impact of PDGFD in osteosarcoma metastasis through single-cell sequencing analysis.
Title: Exploring the impact of PDGFD in osteosarcoma metastasis through single-cell sequencing analysis.
MicroRNA miR-145-5p Inhibits Cutaneous Wound Healing by Targeting PDGFD in Diabetic Foot Ulcer.
Title: MicroRNA miR-145-5p Inhibits Cutaneous Wound Healing by Targeting PDGFD in Diabetic Foot Ulcer.
The role of THBS1 and PDGFD in the immune microenvironment of Helicobacter pylori-associated gastric cancer.
Title: The role of THBS1 and PDGFD in the immune microenvironment of Helicobacter pylori-associated gastric cancer.
Reversible promoter demethylation of PDGFD confers gemcitabine resistance through STAT3 activation and RRM1 upregulation.
Title: Reversible promoter demethylation of PDGFD confers gemcitabine resistance through STAT3 activation and RRM1 upregulation.
lncRNA PITPNA-AS1 promotes cell proliferation and metastasis in hepatocellular carcinoma by upregulating PDGFD.
Title: lncRNA PITPNA-AS1 promotes cell proliferation and metastasis in hepatocellular carcinoma by upregulating PDGFD.
Combination therapy with chitosan/siRNA nanoplexes targeting PDGF-D and PDGFR-beta reveals anticancer effect in breast cancer.
Title: Combination therapy with chitosan/siRNA nanoplexes targeting PDGF-D and PDGFR-β reveals anticancer effect in breast cancer.
Platelet-derived growth factor D expression in adrenal cells is modulated by corticosteroids: putative role in adrenal suppression.
Title: Platelet-derived growth factor D expression in adrenal cells is modulated by corticosteroids: putative role in adrenal suppression.
ZNF561 antisense RNA 1 contributes to angiogenesis in hepatocellular carcinoma through upregulation of platelet-derived growth Factor-D.
Title: ZNF561 antisense RNA 1 contributes to angiogenesis in hepatocellular carcinoma through upregulation of platelet-derived growth Factor-D.
E3 ligase HUWE1 promotes PDGF D-mediated osteoblastic differentiation of mesenchymal stem cells by effecting polyubiquitination of beta-PDGFR.
Title: E3 ligase HUWE1 promotes PDGF D-mediated osteoblastic differentiation of mesenchymal stem cells by effecting polyubiquitination of β-PDGFR.
PDGF-D-PDGFRbeta signaling enhances IL-15-mediated human natural killer cell survival.
Title: PDGF-D-PDGFRβ signaling enhances IL-15-mediated human natural killer cell survival.

Submit: New GeneRIF Correction See all GeneRIFs (65)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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 EBI GWAS CatalogPubMed
Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of coronary heart disease and its risk factors in 8,090 African Americans: the NHLBI CARe Project. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of selenium concentrations. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S4670 (e-PCR)
- UniSTS:66818

D11S2909 (e-PCR)
- UniSTS:152070

RH99280 (e-PCR)
- UniSTS:86620

RH92113 (e-PCR)
- UniSTS:84848

SHGC-146711 (e-PCR)
- UniSTS:172664

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables growth factor activity	IEA Inferred from Electronic Annotation more info
enables platelet-derived growth factor receptor binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cellular response to amino acid stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hydrogen peroxide	IEA Inferred from Electronic Annotation more info
involved_in cellular response to platelet-derived growth factor stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to transforming growth factor beta stimulus	IEA Inferred from Electronic Annotation more info
involved_in platelet-derived growth factor receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of ERK1 and ERK2 cascade	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell division	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of cell population proliferation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of fibroblast proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of glomerular mesangial cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of monocyte extravasation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of smooth muscle cell chemotaxis	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of smooth muscle cell proliferation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi membrane	TAS Traceable Author Statement more info
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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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)

NM_025208.5 → NP_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:55 → 168

CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.

cd00135
Location:270 → 365

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 ...
NM_033135.4 → NP_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:49 → 162

CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.

cd00135
Location:264 → 359

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 ...