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Pld3 phospholipase D family member 3 [ Mus musculus (house mouse) ]

Gene ID: 18807, updated on 5-Mar-2024

Summary

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Official Symbol
Pld3provided by MGI
Official Full Name
phospholipase D family member 3provided by MGI
Primary source
MGI:MGI:1333782
See related
Ensembl:ENSMUSG00000003363 AllianceGenome:MGI:1333782
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
Sam-9
Summary
Enables single-stranded DNA 5'-3' exodeoxyribonuclease activity. Involved in regulation of cytokine production involved in inflammatory response. Located in late endosome membrane and lysosomal membrane. Is expressed in several structures, including alimentary system; cardiovascular system; genitourinary system; nervous system; and sensory organ. Human ortholog(s) of this gene implicated in spinocerebellar ataxia 46. Orthologous to human PLD3 (phospholipase D family member 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in cortex adult (RPKM 194.3), frontal lobe adult (RPKM 152.9) and 28 other tissues See more
Orthologs
human all
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Genomic context

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See Pld3 in Genome Data Viewer
Location:
7 A3; 7 15.92 cM
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 7 NC_000073.7 (27231090..27252511, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 7 NC_000073.6 (27531367..27553229, complement)

Chromosome 7 - NC_000073.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E4910 Neighboring gene predicted gene 15541 Neighboring gene periaxin Neighboring gene homeodomain interacting protein kinase 4 Neighboring gene CapStarr-seq enhancer MGSCv37_chr7:28326448-28326635 Neighboring gene CapStarr-seq enhancer MGSCv37_chr7:28330144-28330331 Neighboring gene RIKEN cDNA 2310022A10 gene Neighboring gene predicted gene, 45975 Neighboring gene STARR-seq mESC enhancer starr_18371 Neighboring gene STARR-seq mESC enhancer starr_18372 Neighboring gene ribosomal protein L17 pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. PLD3 affects axonal spheroids and network defects in Alzheimer's disease. Yuan P, et al. Nature, 2022 Dec. PMID 36450991, Free PMC Article
  2. Cleavage of DNA and RNA by PLD3 and PLD4 limits autoinflammatory triggering by multiple sensors. Gavin AL, et al. Nat Commun, 2021 Oct 7. PMID 34620855, Free PMC Article
  3. PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer's disease. Nackenoff AG, et al. PLoS Genet, 2021 Apr. PMID 33830999, Free PMC Article
  4. PLD3 and spinocerebellar ataxia. Gonzalez AC, et al. Brain, 2018 Nov 1. PMID 30312375, Free PMC Article
  5. PLD3 gene and processing of APP. Fazzari P, et al. Nature, 2017 Jan 25. PMID 28128235

See all (37) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PLD3 affects axonal spheroids and network defects in Alzheimer's disease.
    Title: PLD3 affects axonal spheroids and network defects in Alzheimer's disease.
  2. Cleavage of DNA and RNA by PLD3 and PLD4 limits autoinflammatory triggering by multiple sensors.
    Title: Cleavage of DNA and RNA by PLD3 and PLD4 limits autoinflammatory triggering by multiple sensors.
  3. PLD3 is a neuronal lysosomal phospholipase D associated with beta-amyloid plaques and cognitive function in Alzheimer's disease.
    Title: PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer's disease.
  4. this study shows that PLD3 and PLD4 are single-stranded acid exonucleases that regulate endosomal nucleic-acid sensing
    Title: PLD3 and PLD4 are single-stranded acid exonucleases that regulate endosomal nucleic-acid sensing.
  5. PLD3 plays a role in myogenesis during myotube formation, potentially in the events surrounding ER reorganization.
    Title: A role for phospholipase D3 in myotube formation.
  6. Pld3 expression is associated with hematopoietic stem cells that have durable self-renewal potential.
    Title: Prospective isolation and molecular characterization of hematopoietic stem cells with durable self-renewal potential.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Targeted (4) 
  • Endonuclease-mediated (5)  1 citation

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables catalytic activity IEA
Inferred from Electronic Annotation
more info
  
enables exonuclease activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables nuclease activity IEA
Inferred from Electronic Annotation
more info
  
NOT enables phospholipase D activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables phospholipase D activity ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 
enables phospholipase D activity TAS
Traceable Author Statement
more info
  
enables single-stranded DNA 5'-3' DNA exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables single-stranded DNA 5'-3' DNA exonuclease activity ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within immune system process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within inflammatory response IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in myotube differentiation ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of cytokine production involved in inflammatory response IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi membrane ISO
Inferred from Sequence Orthology
more info
  
located_in early endosome membrane ISO
Inferred from Sequence Orthology
more info
  
located_in endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
located_in endoplasmic reticulum membrane ISO
Inferred from Sequence Orthology
more info
  
located_in endoplasmic reticulum membrane TAS
Traceable Author Statement
more info
  
located_in endosome IEA
Inferred from Electronic Annotation
more info
  
located_in late endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in late endosome membrane ISO
Inferred from Sequence Orthology
more info
  
located_in lysosomal lumen ISO
Inferred from Sequence Orthology
more info
  
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in lysosome IEA
Inferred from Electronic Annotation
more info
  
located_in membrane ISS
Inferred from Sequence or Structural Similarity
more info
 PubMed 

General protein information

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Preferred Names
5'-3' exonuclease PLD3
Names
PLD 3
choline phosphatase 3
phosphatidylcholine-hydrolyzing phospholipase D3
phospholipase D3
schwannoma-associated protein 9
NP_001304284.1
NP_001404025.1
NP_001404026.1
NP_001404027.1
NP_001404028.1
NP_001404029.1
NP_035246.1
XP_017177531.1
XP_030098079.1

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_001317355.2 → NP_001304284.1  5'-3' exonuclease PLD3 isoform a

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1-4 all encode the same isoform (a).
    Source sequence(s)
    AC158304
    Consensus CDS
    CCDS21025.1
    UniProtKB/Swiss-Prot
    O35405, Q3U5M5
    Related
    ENSMUSP00000112942.2, ENSMUST00000117611.8
    Conserved Domains (1) summary
    PHA02820
    Location:77 → 488
    PHA02820; phospholipase-D-like protein; Provisional

  2. NM_001417096.1 → NP_001404025.1  5'-3' exonuclease PLD3 isoform a

    Status: VALIDATED

    Source sequence(s)
    AC158304
    UniProtKB/Swiss-Prot
    O35405, Q3U5M5

  3. NM_001417097.1 → NP_001404026.1  5'-3' exonuclease PLD3 isoform a

    Status: VALIDATED

    Source sequence(s)
    AC158304
    UniProtKB/Swiss-Prot
    O35405, Q3U5M5

  4. NM_001417098.1 → NP_001404027.1  5'-3' exonuclease PLD3 isoform b

    Status: VALIDATED

    Source sequence(s)
    AC158304

  5. NM_001417099.1 → NP_001404028.1  5'-3' exonuclease PLD3 isoform b

    Status: VALIDATED

    Source sequence(s)
    AC158304

  6. NM_001417100.1 → NP_001404029.1  5'-3' exonuclease PLD3 isoform b

    Status: VALIDATED

    Source sequence(s)
    AC158304

  7. NM_011116.3 → NP_035246.1  5'-3' exonuclease PLD3 isoform a

    See identical proteins and their annotated locations for NP_035246.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-4 all encode the same isoform (a).
    Source sequence(s)
    AC158304
    Consensus CDS
    CCDS21025.1
    UniProtKB/Swiss-Prot
    O35405, Q3U5M5
    Related
    ENSMUSP00000113820.2, ENSMUST00000117095.8
    Conserved Domains (1) summary
    PHA02820
    Location:77 → 488
    PHA02820; phospholipase-D-like protein; Provisional

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

  1. NC_000073.7 Reference GRCm39 C57BL/6J

    Range
    27231090..27252511 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017322042.3 → XP_017177531.1  5'-3' exonuclease PLD3 isoform X2

    Conserved Domains (1) summary
    PHA02820
    Location:24 → 435
    PHA02820; phospholipase-D-like protein; Provisional

  2. XM_030242219.2 → XP_030098079.1  5'-3' exonuclease PLD3 isoform X3

    Conserved Domains (1) summary
    PHA02820
    Location:11 → 417
    PHA02820; phospholipase-D-like protein; Provisional
Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O35405.1 GenPept UniProtKB/Swiss-Prot:O35405

Gene LinkOut

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