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

Gene ID: 361527, updated on 17-Aug-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' exodeoxyribonuclease 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, Apr 2022]
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
    A0A8I5ZPG5, 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
    A0A8I5ZPG5, 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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