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

Gene ID: 71785, updated on 22-Jan-2023

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
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Genomic context

See Pdgfd in Genome Data Viewer
Location:
9; 9 A1
Exon count:
10
Annotation release Status Assembly Chr Location
109 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_000075.7Genomic Context describing neighboring genes Neighboring gene heat shock protein 90 alpha (cytosolic), class B member 1 pseudogene Neighboring gene non-POU-domain-containing, octamer binding protein pseudogene Neighboring gene DNA-damage inducible 1 Neighboring gene predicted gene, 21089 Neighboring gene predicted gene, 23097

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

General gene information

Markers

Homology

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
PubMed 
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
PubMed 
involved_in positive regulation of ERK1 and ERK2 cascade IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of MAP kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
involved_in positive regulation of cell population proliferation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of protein autophosphorylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 PubMed 
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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

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)

  1. NM_001357397.1NP_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:49163
    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 ...
  2. NM_001357398.1NP_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:55169
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
  3. NM_027924.3NP_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
    Q925I7, Q9D1L8
    Related
    ENSMUSP00000128388.2, ENSMUST00000168039.8
    Conserved Domains (2) summary
    cd00041
    Location:55169
    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 ...

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000075.7 Reference GRCm39 C57BL/6J

    Range
    6168377..6534284
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    Conserved Domains (2) summary
    cd00041
    Location:55169
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
    cl02885
    Location:297326
    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)
  2. XM_036155304.1XP_036011197.1  platelet-derived growth factor D isoform X4

    Conserved Domains (1) summary
    cd00041
    Location:55169
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
  3. XM_036155303.1XP_036011196.1  platelet-derived growth factor D isoform X3

    Conserved Domains (1) summary
    cd00041
    Location:49163
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.
  4. XM_006509887.5XP_006509950.1  platelet-derived growth factor D isoform X2

    Conserved Domains (1) summary
    cd00041
    Location:55169
    CUB; CUB domain; extracellular domain; present in proteins mostly known to be involved in development; not found in prokaryotes, plants and yeast.