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    Pld4 phospholipase D family member 4 [ Mus musculus (house mouse) ]

    Gene ID: 104759, updated on 21-Apr-2024

    Summary

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    Official Symbol
    Pld4provided by MGI
    Official Full Name
    phospholipase D family member 4provided by MGI
    Primary source
    MGI:MGI:2144765
    See related
    Ensembl:ENSMUSG00000052160 AllianceGenome:MGI:2144765
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    thss
    Summary
    Enables single-stranded DNA 5'-3' exodeoxyribonuclease activity. Involved in regulation of cytokine production involved in inflammatory response. Acts upstream of or within hematopoietic progenitor cell differentiation and phagocytosis. Located in several cellular components, including cytoplasmic vesicle; endoplasmic reticulum membrane; and trans-Golgi network membrane. Is expressed in brain and hemolymphoid system. Used to study systemic lupus erythematosus. Orthologous to human PLD4 (phospholipase D family member 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in spleen adult (RPKM 135.8), mammary gland adult (RPKM 57.0) and 14 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    12 F1; 12 61.2 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (112727089..112735420)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (112760446..112768986)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene centrosomal protein 170B Neighboring gene microRNA 6940 Neighboring gene transmembrane protein 11 pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E5361 Neighboring gene AHNAK nucleoprotein 2 Neighboring gene clathrin binding box of aftiphilin containing 1

    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. Microglial phospholipase D4 deficiency influences myelination during brain development. Chiba T, et al. Proc Jpn Acad Ser B Phys Biol Sci, 2016. PMID 27477458, 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. PLD4 is a genetic determinant to systemic lupus erythematosus and involved in murine autoimmune phenotypes. Akizuki S, et al. Ann Rheum Dis, 2019 Apr. PMID 30679154
    4. Targeting Phospholipase D4 Attenuates Kidney Fibrosis. Trivedi P, et al. J Am Soc Nephrol, 2017 Dec. PMID 28814511, Free PMC Article
    5. PLD$ is involved in phagocytosis of microglia: expression and localization changes of PLD4 are correlated with activation state of microglia. Otani Y, et al. PLoS One, 2011. PMID 22102906, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. Pld4 mutant mice revealed autoimmune phenotypes suggesting functional involvement of PLD4 with the basics of systemic lupus erythematosus.
      Title: PLD4 is a genetic determinant to systemic lupus erythematosus and involved in murine autoimmune phenotypes.
    3. 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.
    4. Phospholipase D4 has a role in kidney fibrosis
      Title: Targeting Phospholipase D4 Attenuates Kidney Fibrosis.
    5. microglia may have a transient role in myelination via a PLD4-related mechanism during development.
      Title: Microglial phospholipase D4 deficiency influences myelination during brain development.
    6. Results showed that PLD4 is a non-PLD, HKD motif-carrying, transmembrane glycoprotein localized in the endoplasmic reticulum and Golgi apparatus.
      Title: Phospholipase D family member 4, a transmembrane glycoprotein with no phospholipase D activity, expression in spleen and early postnatal microglia.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Spontaneous (1) 
    • Targeted (2)  1 citation
    • Chemically induced (ENU) (1)  1 citation
    • Endonuclease-mediated (3) 

    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 TAS
    Traceable Author Statement
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables single-stranded DNA 5'-3' DNA exonuclease activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within establishment of localization in cell IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in hematopoietic progenitor cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within hematopoietic progenitor cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 phagocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within phagocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 cytoplasmic vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane TAS
    Traceable Author Statement
    more info
    		  
    located_in endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in phagocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in phagocytic vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in trans-Golgi network membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    5'-3' exonuclease PLD4
    Names
    PLD 4
    choline phosphatase 4
    phosphatidylcholine-hydrolyzing phospholipase D4
    phospholipase D4
    NP_849242.1
    XP_017170415.1

    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_178911.4 → NP_849242.1  5'-3' exonuclease PLD4

      See identical proteins and their annotated locations for NP_849242.1

      Status: PROVISIONAL

      Source sequence(s)
      AC124353, MF597757
      Consensus CDS
      CCDS26195.1
      UniProtKB/Swiss-Prot
      Q3TD59, Q3UA19, Q6PDR0, Q8BG07, Q8BR69
      Related
      ENSMUSP00000067002.4, ENSMUST00000063888.5
      Conserved Domains (2) summary
      PHA02820
      Location:94 → 501
      PHA02820; phospholipase-D-like protein; Provisional
      cl15239
      Location:302 → 489
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

    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_000078.7 Reference GRCm39 C57BL/6J

      Range
      112727089..112735420
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017314926.3 → XP_017170415.1  5'-3' exonuclease PLD4 isoform X1

      Conserved Domains (1) summary
      cl15239
      Location:96 → 237
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BG07.1 GenPept UniProtKB/Swiss-Prot:Q8BG07

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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