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

Summary

Official Symbol: Pld3provided by RGD
Official Full Name: phospholipase D family, member 3provided by RGD
Primary source: RGD:1308248
See related: Ensembl: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
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

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_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Submit: New GeneRIF Correction

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

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

Go to the top of the page Help

Preferred Names: 5'-3' exonuclease PLD3

Names: PLD 3; choline phosphatase 3; phosphatidylcholine-hydrolyzing phospholipase D3; phospholipase D3

NP_001012167.1

EC 3.1.16.1

XP_006228640.1

EC 3.1.16.1

XP_006228642.1

EC 3.1.16.1

XP_006228643.1

EC 3.1.16.1

XP_038937789.1

EC 3.1.16.1

XP_063122470.1

EC 3.1.16.1

XP_063122475.1

EC 3.1.16.1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_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

ENSRNOP00000080374.1, ENSRNOT00000102599.1

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

NC_086019.1 Reference GRCr8

Range

91949465..91971834 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q5FVH2

UniProtKB/TrEMBL

A6J9D6
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
XM_039081861.2 → XP_038937789.1 5'-3' exonuclease PLD3 isoform X1

UniProtKB/Swiss-Prot

Q5FVH2

UniProtKB/TrEMBL

A0A8I5ZPG5, A6J9D6

Related

ENSRNOP00000054004.2

Conserved Domains (1) summary

PHA02820
Location:77 → 488

PHA02820; phospholipase-D-like protein; Provisional
XM_063266405.1 → XP_063122475.1 5'-3' exonuclease PLD3 isoform X1

UniProtKB/Swiss-Prot

Q5FVH2

UniProtKB/TrEMBL

A6J9D6
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