Pdgfd platelet-derived growth factor, D polypeptide [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pdgfdprovided by MGI
Official Full Name: platelet-derived growth factor, D polypeptideprovided by MGI
Primary source: MGI:MGI:1919035
See related: Ensembl:ENSMUSG00000032006 AllianceGenome:MGI:1919035
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: 1110003I09Rik
Summary: Predicted to enable platelet-derived growth factor receptor binding activity. Acts upstream of or within cellular response to amino acid stimulus and regulation of peptidyl-tyrosine phosphorylation. Located in extracellular space. Is expressed in bladder; brain; and urethra of male. 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 bladder adult (RPKM 9.0), subcutaneous fat pad adult (RPKM 2.8) and 13 other tissues See more
Orthologs: human all
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Genomic context

Location:: 9 A1; 9 2.46 cM

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (6168377..6534284)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (6168363..6534284)

Chromosome 9 - NC_000075.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Molecular mechanisms of coronary artery disease risk at the PDGFD locus.
Title: Molecular mechanisms of coronary artery disease risk at the PDGFD locus.
PDGFD switches on stem cell endothelial commitment.
Title: PDGFD switches on stem cell endothelial commitment.
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.
Inhibiting PDGF-D alleviates the symptoms of HELLP by suppressing NF-kappaB activation.
Title: Inhibiting PDGF-D alleviates the symptoms of HELLP by suppressing NF-κB activation.
PDGF-D activation by macrophage-derived uPA promotes AngII-induced cardiac remodeling in obese mice.
Title: PDGF-D activation by macrophage-derived uPA promotes AngII-induced cardiac remodeling in obese mice.
Data (including data from studies using transgenic/mutant mice and cells from such mice) suggest that Pdgfd promotes cell proliferation, cell migration, and expression of inflammatory factors in adventitial fibroblasts; in obese mice, inhibition of Pdgfd significantly reduces aortic aneurysm formation (induced by infusion of angiotensin II).
Title: Perivascular Adipose Tissue-Derived PDGF-D Contributes to Aortic Aneurysm Formation During Obesity.
upregulated in kidney fibrosis, may mediate renal scarring, and is dispensable for normal kidney development and physiological functions
Title: The role of PDGF-D in healthy and fibrotic kidneys.
Inactivation of the Pdgfd gene resulted in a mild phenotype in C57BL/6 mice, and the offspring was viable, fertile and generally in good health.
Title: Mice Lacking Platelet-Derived Growth Factor D Display a Mild Vascular Phenotype.
PDGF-D intensifies fibrogenesis by interfering with the fibrolytic activity of the TIMP-1/MMP-2/MMP-9 system, and PDGF-D signaling is mediated through both PDGF-alpha and -beta receptors.
Title: Platelet-derived growth factor-D modulates extracellular matrix homeostasis and remodeling through TIMP-1 induction and attenuation of MMP-2 and MMP-9 gelatinase activities.
Radial glia require PDGFD-PDGFRbeta signalling in human but not mouse neocortex
Title: Radial glia require PDGFD-PDGFRβ signalling in human but not mouse neocortex.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (2) 1 citation
Endonuclease-mediated (5) 1 citation

General gene information

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Markers

RH126547 (e-PCR)
- UniSTS:208786

D9Mit186 (e-PCR), detects polymorphism
- UniSTS:131742

Gene Ontology Provided by MGI

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
enables platelet-derived growth factor receptor binding	ISO Inferred from Sequence Orthology more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cellular response to amino acid stimulus	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to transforming growth factor beta stimulus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism development	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 MAP kinase activity	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within 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	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of glomerular mesangial cell proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of monocyte extravasation	ISO Inferred from Sequence Orthology 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 protein autophosphorylation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of smooth muscle cell chemotaxis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of smooth muscle cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of peptidyl-tyrosine phosphorylation	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular space	HDA more info	PubMed
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info
located_in extracellular space	ISO Inferred from Sequence Orthology 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: PDGF-D; SCDGF-B; 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_001357397.1 → NP_001344326.1 platelet-derived growth factor D isoform 2 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AC115825, AC154302, AC168218

Consensus CDS

CCDS90490.1

Related

ENSMUSP00000056240.7, ENSMUST00000058692.9

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 ...
NM_001357398.1 → NP_001344327.1 platelet-derived growth factor D isoform 3 precursor

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate exon in the 3' coding sequence compared to variant 1, that causes a frameshift. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AC115825, AC154302, AC168218

Consensus CDS

CCDS90489.1

Related

ENSMUSP00000149162.2, ENSMUST00000214892.2

Conserved Domains (1) 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.
NM_027924.3 → NP_082200.1 platelet-derived growth factor D isoform 1 precursor

See identical proteins and their annotated locations for NP_082200.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AK003359, AK141551, DV045274

Consensus CDS

CCDS22801.1

UniProtKB/Swiss-Prot

Q3URF6, Q8K2L3, Q925I7, Q9D1L8

Related

ENSMUSP00000128388.2, ENSMUST00000168039.8

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_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000075.7 Reference GRCm39 C57BL/6J

Range

6168377..6534284

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011242370.4 → XP_011240672.1 platelet-derived growth factor D isoform X1

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.

cl02885
Location:297 → 326

Ebola_HIV-1-like_HR1-HR2; heptad repeat 1-heptad repeat 2 region (ectodomain) of the transmembrane subunit of various endogenous retroviruses (ERVs) and infectious retroviruses, including Ebola virus and human immunodeficiency virus type 1 (HIV-1)
XM_036155304.1 → XP_036011197.1 platelet-derived growth factor D isoform X4

Conserved Domains (1) 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.
XM_036155303.1 → XP_036011196.1 platelet-derived growth factor D isoform X3

Conserved Domains (1) 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.
XM_006509887.5 → XP_006509950.1 platelet-derived growth factor D isoform X2

Conserved Domains (1) 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.