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

Gene ID: 362792, updated on 10-Oct-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' exodeoxyribonuclease activity. Predicted to be involved in hematopoietic progenitor cell differentiation; phagocytosis; and regulation of cytokine production involved in inflammatory response. 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, Apr 2022]
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

Gene LinkOut

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