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    Pld3 phospholipase D family, member 3 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 361527, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Pld3provided by RGD
    Official Full Name
    phospholipase D family, member 3provided by RGD
    Primary source
    RGD:1308248
    See related
    EnsemblRapid:ENSRNOG00000018390 AllianceGenome:RGD:1308248
    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 myotube differentiation and regulation of cytokine production involved in inflammatory response. Predicted to be located in bounding membrane of organelle; endoplasmic reticulum membrane; and lysosomal lumen. 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, Nov 2024]
    Expression
    Biased expression in Brain (RPKM 308.3), Spleen (RPKM 235.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Pld3 in Genome Data Viewer
    Location:
    1q21
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (91949465..91971834, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (82821863..82844280, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (84339269..84361686, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene transmembrane protein 258, pseudogene 4 Neighboring gene periaxin Neighboring gene homeodomain interacting protein kinase 4 Neighboring gene similar to human chromosome 19 open reading frame 47 Neighboring gene large ribosomal subunit protein uL22-like Neighboring gene AKT serine/threonine kinase 2 Neighboring gene uncharacterized LOC103691074

    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. Hu-K4 is a ubiquitously expressed type 2 transmembrane protein associated with the endoplasmic reticulum. Munck A, et al. FEBS J, 2005 Apr. PMID 15794758
    2. PLD3 and spinocerebellar ataxia. Gonzalez AC, et al. Brain, 2018 Nov 1. PMID 30312375, Free PMC Article
    3. Analysis of novel endosome-to-Golgi retrieval genes reveals a role for PLD3 in regulating endosomal protein sorting and amyloid precursor protein processing. Mukadam AS, et al. Cell Mol Life Sci, 2018 Jul. PMID 29368044, Free PMC Article
    4. PLD3 gene and processing of APP. Fazzari P, et al. Nature, 2017 Jan 25. PMID 28128235
    5. A role for phospholipase D3 in myotube formation. Osisami M, et al. PLoS One, 2012. PMID 22428023, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC109410

    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables single-stranded DNA 5'-3' DNA exonuclease activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables single-stranded DNA 5'-3' DNA exonuclease activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in DNA metabolic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in immune system process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in myotube differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in myotube differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in myotube differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of cytokine production involved in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of cytokine production involved in inflammatory response ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of cytokine production involved in inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in Golgi membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in early endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in early endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in late endosome membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in late endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in lysosomal lumen IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal lumen ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in lysosomal lumen ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in lysosomal membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in lysosomal membrane ISO
    Inferred from Sequence Orthology
    more info
    		  

    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
    NP_001012167.1
    XP_006228640.1
    XP_006228642.1
    XP_006228643.1
    XP_038937789.1
    XP_063122470.1
    XP_063122475.1

    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_001012167.1 → NP_001012167.1  5'-3' exonuclease PLD3

      See identical proteins and their annotated locations for NP_001012167.1

      Status: PROVISIONAL

      Source sequence(s)
      BC089987
      UniProtKB/Swiss-Prot
      Q5FVH2
      UniProtKB/TrEMBL
      A0A8I5ZPG5, A6J9D6
      Related
      ENSRNOP00000054004.2, ENSRNOT00000057177.5
      Conserved Domains (1) summary
      PHA02820
      Location:77 → 488
      PHA02820; phospholipase-D-like protein; Provisional

    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_086019.1 Reference GRCr8

      Range
      91949465..91971834 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006228578.5 → XP_006228640.1  5'-3' exonuclease PLD3 isoform X1

      See identical proteins and their annotated locations for XP_006228640.1

      UniProtKB/Swiss-Prot
      Q5FVH2
      UniProtKB/TrEMBL
      A0A8I5ZPG5, A6J9D6
      Conserved Domains (1) summary
      PHA02820
      Location:77 → 488
      PHA02820; phospholipase-D-like protein; Provisional

    2. XM_063266400.1 → XP_063122470.1  5'-3' exonuclease PLD3 isoform X1

      UniProtKB/Swiss-Prot
      Q5FVH2
      UniProtKB/TrEMBL
      A6J9D6

    3. XM_006228581.5 → XP_006228643.1  5'-3' exonuclease PLD3 isoform X1

      See identical proteins and their annotated locations for XP_006228643.1

      UniProtKB/Swiss-Prot
      Q5FVH2
      UniProtKB/TrEMBL
      A0A8I5ZPG5, A6J9D6
      Conserved Domains (1) summary
      PHA02820
      Location:77 → 488
      PHA02820; phospholipase-D-like protein; Provisional

    4. XM_039081861.2 → XP_038937789.1  5'-3' exonuclease PLD3 isoform X1

      UniProtKB/Swiss-Prot
      Q5FVH2
      UniProtKB/TrEMBL
      A0A8I5ZPG5, A6J9D6
      Conserved Domains (1) summary
      PHA02820
      Location:77 → 488
      PHA02820; phospholipase-D-like protein; Provisional

    5. XM_063266405.1 → XP_063122475.1  5'-3' exonuclease PLD3 isoform X1

      UniProtKB/Swiss-Prot
      Q5FVH2
      UniProtKB/TrEMBL
      A6J9D6

    6. XM_006228580.3 → XP_006228642.1  5'-3' exonuclease PLD3 isoform X1

      See identical proteins and their annotated locations for XP_006228642.1

      UniProtKB/Swiss-Prot
      Q5FVH2
      UniProtKB/TrEMBL
      A0A8I5ZPG5, A6J9D6
      Conserved Domains (1) summary
      PHA02820
      Location:77 → 488
      PHA02820; phospholipase-D-like protein; Provisional
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5FVH2.1 GenPept UniProtKB/Swiss-Prot:Q5FVH2

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