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    Pld4 phospholipase D family, member 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 362792, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Pld4provided by RGD
    Official Full Name
    phospholipase D family, member 4provided by RGD
    Primary source
    RGD:1598308
    See related
    EnsemblRapid:ENSRNOG00000028566 AllianceGenome:RGD:1598308
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to enable single-stranded DNA 5'-3' DNA exonuclease activity. Predicted to be involved in hematopoietic progenitor cell differentiation; phagocytosis; and regulation of cytokine production involved in inflammatory response. Predicted to act upstream of or within establishment of localization in cell. Predicted to be located in early endosome and endoplasmic reticulum membrane. Predicted to be active in several cellular components, including endoplasmic reticulum; phagocytic vesicle; and trans-Golgi network membrane. Orthologous to human PLD4 (phospholipase D family member 4). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Spleen (RPKM 228.3), Thymus (RPKM 75.4) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pld4 in Genome Data Viewer
    Location:
    6q32
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 6 NC_086024.1 (137639948..137647462)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 6 NC_051341.1 (131818860..131827457)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 6 NC_005105.4 (137323713..137331231)

    Chromosome 6 - NC_086024.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC134479262 Neighboring gene centrosomal protein 170B Neighboring gene uncharacterized LOC134479263 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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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    Related articles in PubMed

    1. 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
    2. Phospholipase D family member 4, a transmembrane glycoprotein with no phospholipase D activity, expression in spleen and early postnatal microglia. Yoshikawa F, et al. PLoS One, 2010 Nov 11. PMID 21085684, Free PMC Article
    3. Haploinsufficiency of SAMD9L, an endosome fusion facilitator, causes myeloid malignancies in mice mimicking human diseases with monosomy 7. Nagamachi A, et al. Cancer Cell, 2013 Sep 9. PMID 24029230
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    NOT enables phospholipase D activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded DNA 5'-3' DNA exonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within establishment of localization in cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in hematopoietic progenitor cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within hematopoietic progenitor cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in phagocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within phagocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cytokine production involved in inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in phagocytic vesicle IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in phagocytic vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in trans-Golgi network membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    5'-3' exonuclease PLD4
    Names
    phospholipase D4
    NP_001119760.1
    XP_038968522.2

    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_001126288.1 → NP_001119760.1  5'-3' exonuclease PLD4

      See identical proteins and their annotated locations for NP_001119760.1

      Status: PROVISIONAL

      Source sequence(s)
      CH474034
      UniProtKB/TrEMBL
      A6KBW2, B1WBV8, G3V904
      Related
      ENSRNOP00000107901.1, ENSRNOT00000122215.1
      Conserved Domains (2) summary
      PHA02820
      Location:120 → 527
      PHA02820; phospholipase-D-like protein; Provisional
      cl15239
      Location:328 → 515
      PLDc_SF; Catalytic domain of phospholipase D superfamily proteins

    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

    1. NC_086024.1 Reference GRCr8

      Range
      137639948..137647462
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039112594.2 → XP_038968522.2  5'-3' exonuclease PLD4 isoform X1

      Related
      ENSRNOP00000032119.4, ENSRNOT00000029017.5
    Nucleotide Protein Strain
    Heading Accession and Version

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