Pdgfd platelet derived growth factor D [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Pdgfdprovided by RGD
Official Full Name: platelet derived growth factor Dprovided by RGD
Primary source: RGD:621880
See related: Ensembl:ENSRNOG00000029148 AllianceGenome:RGD:621880
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Scdgfb; rSCDGF-B
Summary: Predicted to enable platelet-derived growth factor receptor binding activity. Involved in several processes, including cellular response to growth factor stimulus; positive regulation of cell migration; and positive regulation of cell population proliferation. Located in extracellular space. Used to study glomerulonephritis and mesangial proliferative glomerulonephritis. Biomarker of liver cirrhosis; mesangial proliferative glomerulonephritis; and myocardial infarction. Human ortholog(s) of this gene implicated in prostatic hypertrophy. Orthologous to human PDGFD (platelet derived growth factor D). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 96.1), Kidney (RPKM 64.3) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 8q11

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	8	NC_086026.1 (11773335..12007277)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	8	NC_051343.1 (3488448..3722395)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	8	NC_005107.4 (4441010..4666754)

Chromosome 8 - NC_086026.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PDGFD promotes the angiogenic capacity of EPCs.
Title: Platelet‑derived growth factor D promotes the angiogenic capacity of endothelial progenitor cells.
observations indicated that PDGF can contribute to the development of cardiac interstitial fibrosis in the noninfarcted myocardium, but does not alter scar formation in the infarcted myocardium.
Title: Platelet-derived growth factor blockade on cardiac remodeling following infarction.
Activities of PI3K/PKB and PKCs are critical for the Pdgfd - induced COX-2 expression in rat mesangial cells.
Title: Platelet-derived growth factor-D induces expression of cyclooxygenase-2 in rat mesangial cells through activation of PI3K/PKB and PKCs.
Podocyte-specific PDGF-D overexpression caused mesangioproliferative disease, glomerulosclerosis, and crescentic glomerulonephritis. Podocyte-specific PDGF-D overexpression induced paracrine mesangial cell proliferation upstream of the filtration flow.
Title: Induction of progressive glomerulonephritis by podocyte-specific overexpression of platelet-derived growth factor-D.
alloimmune response induces PDGF-A, PDGF-C, and PDGF-D expression in the graft vasculature;PDGF-D mediated profibrotic and proarteriosclerotic effects in transplanted hearts involving the TGF-[beta]1 pathway
Title: PDGF-A, -C, and -D but not PDGF-B increase TGF-beta1 and chronic rejection in rat cardiac allografts.
All 3 residues in Sp1 (Thr668, Ser670, and Thr681) are required for Sp1-dependent platelet-derived growth factor-D activation in response to angiotensin II
Title: Angiotensin II-inducible platelet-derived growth factor-D transcription requires specific Ser/Thr residues in the second zinc finger region of Sp1.
The expression of SCDGF/PDGF-C/fallotein and SCDGF-B/PDGF-D in the rat central nervous system
Title: The expression of SCDGF/PDGF-C/fallotein and SCDGF-B/PDGF-D in the rat central nervous system.
These results support the fact that PDGF-D is involved in the formation of neointimal hyperplasia induced by balloon catheter injury and may serve as a target in preventing vascular restenosis after coronary angioplasty.
Title: PDGF-D contributes to neointimal hyperplasia in rat model of vessel injury.
analysis of expression of PDGF-A, -B, -C and -D and the PDGF-receptors alpha and beta in activated rat hepatic stellate cells
Title: Expression patterns of PDGF-A, -B, -C and -D and the PDGF-receptors alpha and beta in activated rat hepatic stellate cells (HSC).
PDGFD is expressed in the eye and has a key role in control of lens epithelial cell proliferation
Title: Platelet-derived growth factor D, tissue-specific expression in the eye, and a key role in control of lens epithelial cell proliferation.

Submit: New GeneRIF Correction See all GeneRIFs (11)

General gene information

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Gene Ontology Provided by RGD

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
acts_upstream_of_or_within cellular response to amino acid stimulus	ISO Inferred from Sequence Orthology more info
involved_in cellular response to hydrogen peroxide	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to platelet-derived growth factor stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to transforming growth factor beta stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
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 MAP kinase activity	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	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of glomerular mesangial cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of monocyte extravasation	IMP Inferred from Mutant Phenotype more info	PubMed
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 protein autophosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of smooth muscle cell chemotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of smooth muscle cell proliferation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of peptidyl-tyrosine phosphorylation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: platelet-derived growth factor D

Names: iris-expressed growth factor; platelet-derived growth factor, D polypeptide; spinal cord-derived growth factor B; spinal-cord derived growth factor-B protein

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_023962.3 → NP_076452.1 platelet-derived growth factor D precursor

See identical proteins and their annotated locations for NP_076452.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000008

UniProtKB/Swiss-Prot

Q9EQT1

UniProtKB/TrEMBL

A6JN21

Conserved Domains (2) summary

cd00041
Location:55 → 169

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 ...

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086026.1 Reference GRCr8

Range

11773335..12007277

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039082130.2 → XP_038938058.1 platelet-derived growth factor D isoform X1

Related

ENSRNOP00000068187.2

Conserved Domains (2) summary

cd00041
Location:49 → 163

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 ...