Pld3 phospholipase D family member 3 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Pld3provided by MGI
Official Full Name: phospholipase D family member 3provided by MGI
Primary source: MGI:MGI:1333782
See related: Ensembl:ENSMUSG00000003363 AllianceGenome:MGI:1333782
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Sam-9
Summary: Enables single-stranded DNA 5'-3' DNA exonuclease activity. Involved in regulation of cytokine production involved in inflammatory response. Located in late endosome membrane and lysosomal membrane. Is expressed in several structures, including alimentary system; cardiovascular system; genitourinary system; nervous system; and sensory organ. 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, Dec 2024]
Expression: Ubiquitous expression in cortex adult (RPKM 194.3), frontal lobe adult (RPKM 152.9) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 7 A3; 7 15.92 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	7	NC_000073.7 (27231090..27252511, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	7	NC_000073.6 (27531367..27553229, complement)

Chromosome 7 - NC_000073.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PLD3 affects axonal spheroids and network defects in Alzheimer's disease.
Title: PLD3 affects axonal spheroids and network defects in Alzheimer's disease.
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.
PLD3 is a neuronal lysosomal phospholipase D associated with beta-amyloid plaques and cognitive function in Alzheimer's disease.
Title: PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer's disease.
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.
PLD3 plays a role in myogenesis during myotube formation, potentially in the events surrounding ER reorganization.
Title: A role for phospholipase D3 in myotube formation.
Pld3 expression is associated with hematopoietic stem cells that have durable self-renewal potential.
Title: Prospective isolation and molecular characterization of hematopoietic stem cells with durable self-renewal potential.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (5) 1 citation
Targeted (4)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Pld3 (e-PCR), detects polymorphism
- UniSTS:507160

AF026124 (e-PCR)
- UniSTS:185699

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
NOT enables phospholipase D activity	IDA Inferred from Direct Assay more info	PubMed
enables phospholipase D activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables phospholipase D activity	TAS Traceable Author Statement more info
enables single-stranded DNA 5'-3' DNA exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
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
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune 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 regulation of cytokine production involved in inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
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 endoplasmic reticulum membrane	ISO Inferred from Sequence Orthology more info
located_in endoplasmic reticulum membrane	TAS Traceable Author Statement more info
located_in late endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in late endosome membrane	ISO Inferred from Sequence Orthology 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 membrane	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	ISS Inferred from Sequence or Structural Similarity more info	PubMed

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; schwannoma-associated protein 9

NP_001304284.1

EC 3.1.16.1

NP_001404025.1

EC 3.1.16.1

NP_001404026.1

EC 3.1.16.1

NP_001404027.1

EC 3.1.16.1

NP_001404028.1

EC 3.1.16.1

NP_001404029.1

EC 3.1.16.1

NP_035246.1

EC 3.1.16.1

XP_017177531.1

EC 3.1.16.1

XP_030098079.1

EC 3.1.16.1

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)

NM_001317355.2 → NP_001304284.1 5'-3' exonuclease PLD3 isoform a

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longer isoform (a). Variants 1-4 all encode the same isoform (a).

Source sequence(s)

AC158304

Consensus CDS

CCDS21025.1

UniProtKB/Swiss-Prot

O35405, Q3U5M5

Related

ENSMUSP00000112942.2, ENSMUST00000117611.8

Conserved Domains (1) summary

PHA02820
Location:77 → 488

PHA02820; phospholipase-D-like protein; Provisional
NM_001417096.1 → NP_001404025.1 5'-3' exonuclease PLD3 isoform a

Status: VALIDATED

Source sequence(s)

AC158304

UniProtKB/Swiss-Prot

O35405, Q3U5M5
NM_001417097.1 → NP_001404026.1 5'-3' exonuclease PLD3 isoform a

Status: VALIDATED

Source sequence(s)

AC158304

UniProtKB/Swiss-Prot

O35405, Q3U5M5
NM_001417098.1 → NP_001404027.1 5'-3' exonuclease PLD3 isoform b

Status: VALIDATED

Source sequence(s)

AC158304
NM_001417099.1 → NP_001404028.1 5'-3' exonuclease PLD3 isoform b

Status: VALIDATED

Source sequence(s)

AC158304
NM_001417100.1 → NP_001404029.1 5'-3' exonuclease PLD3 isoform b

Status: VALIDATED

Source sequence(s)

AC158304
NM_011116.3 → NP_035246.1 5'-3' exonuclease PLD3 isoform a

See identical proteins and their annotated locations for NP_035246.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-4 all encode the same isoform (a).

Source sequence(s)

AC158304

Consensus CDS

CCDS21025.1

UniProtKB/Swiss-Prot

O35405, Q3U5M5

Related

ENSMUSP00000113820.2, ENSMUST00000117095.8

Conserved Domains (1) summary

PHA02820
Location:77 → 488

PHA02820; phospholipase-D-like protein; Provisional

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

NC_000073.7 Reference GRCm39 C57BL/6J

Range

27231090..27252511 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017322042.3 → XP_017177531.1 5'-3' exonuclease PLD3 isoform X2

Conserved Domains (1) summary

PHA02820
Location:24 → 435

PHA02820; phospholipase-D-like protein; Provisional
XM_030242219.2 → XP_030098079.1 5'-3' exonuclease PLD3 isoform X3

Conserved Domains (1) summary

PHA02820
Location:11 → 417

PHA02820; phospholipase-D-like protein; Provisional