Mouse Gene Pld3 (ENSMUST00000117095.7) from GENCODE VM23 Comprehensive Transcript Set (only Basic displayed by default)
  Description: Mus musculus phospholipase D family, member 3 (Pld3), transcript variant 2, mRNA. (from RefSeq NM_011116)
Gencode Transcript: ENSMUST00000117095.7
Gencode Gene: ENSMUSG00000003363.15
Transcript (Including UTRs)
   Position: mm10 chr7:27,532,000-27,553,212 Size: 21,213 Total Exon Count: 14 Strand: -
Coding Region
   Position: mm10 chr7:27,532,298-27,542,115 Size: 9,818 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA Structure
Protein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathwaysOther Names
Model InformationMethods
Data last updated at UCSC: 2019-09-19

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:27,532,000-27,553,212)mRNA (may differ from genome)Protein (488 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsMGI
PubMedReactomeSOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: PLD3_MOUSE
DESCRIPTION: RecName: Full=Phospholipase D3; Short=PLD 3; EC=3.1.4.4; AltName: Full=Choline phosphatase 3; AltName: Full=Phosphatidylcholine-hydrolyzing phospholipase D3; AltName: Full=Schwannoma-associated protein 9; Short=SAM-9;
CATALYTIC ACTIVITY: A phosphatidylcholine + H(2)O = choline + a phosphatidate.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type II membrane protein (By similarity).
TISSUE SPECIFICITY: Expressed at higher level in brain than in non-nervous tissue. Probably highly expressed in neurons. Expressed in mature neurons of the forebrain and appears to be turned on at late stages of neurogenesis. Expressed during late neuronal development in the forebrain.
PTM: Glycosylated (By similarity).
SIMILARITY: Belongs to the phospholipase D family.
SIMILARITY: Contains 2 PLD phosphodiesterase domains.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -200.20517-0.387 Picture PostScript Text
3' UTR -102.60298-0.344 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001736 - PLipase_D/transphosphatidylase

Pfam Domains:
PF00614 - Phospholipase D Active site motif
PF13091 - PLD-like domain
PF13918 - PLD-like domain

SCOP Domains:
56024 - Phospholipase D/nuclease

ModBase Predicted Comparative 3D Structure on O35405
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
HumanRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
GenBankRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004630 phospholipase D activity
GO:0016787 hydrolase activity
GO:0070290 N-acylphosphatidylethanolamine-specific phospholipase D activity

Biological Process:
GO:0006629 lipid metabolic process
GO:0016042 lipid catabolic process

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK003045 - Mus musculus adult male brain cDNA, RIKEN full-length enriched library, clone:0710008I03 product:phospholipase D3, full insert sequence.
BC068170 - Mus musculus cDNA clone IMAGE:30540708, containing frame-shift errors.
AK203458 - Mus musculus cDNA, clone:Y1G0144P05, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
BC076586 - Mus musculus phospholipase D family, member 3, mRNA (cDNA clone MGC:100011 IMAGE:30604186), complete cds.
AK200311 - Mus musculus cDNA, clone:Y1G0134C14, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
AK219313 - Mus musculus cDNA, clone:Y2G0148B09, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
AF026124 - Mus musculus schwannoma-associated protein (SAM9) mRNA, complete cds.
AK153508 - Mus musculus bone marrow macrophage cDNA, RIKEN full-length enriched library, clone:I830168M23 product:phospholipase D3, full insert sequence.
AK181419 - Mus musculus cDNA, clone:Y0G0118A22, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
AK182880 - Mus musculus cDNA, clone:Y0G0124A17, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
AK188372 - Mus musculus cDNA, clone:Y0G0144P03, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
AK184950 - Mus musculus cDNA, clone:Y0G0132B09, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
AK196865 - Mus musculus cDNA, clone:Y1G0123E03, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
AK188069 - Mus musculus cDNA, clone:Y0G0143P18, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
AK188215 - Mus musculus cDNA, clone:Y0G0144H02, strand:minus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.
AK209515 - Mus musculus cDNA, clone:Y2G0115F20, strand:plus, reference:ENSEMBL:Mouse-Transcript-ENST:ENSMUST00000003453, based on BLAT search.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
m_cb1rPathway - Metabolism of Anandamide, an Endogenous Cannabinoid

Reactome (by CSHL, EBI, and GO)

Protein O35405 (Reactome details) participates in the following event(s):

R-MMU-1483172 PC is transphosphatidylated to PG by Pld1-4/6
R-MMU-2029471 Hydrolysis of PC to PA by PLD
R-MMU-2029485 Role of phospholipids in phagocytosis
R-MMU-2029480 Fcgamma receptor (FCGR) dependent phagocytosis
R-MMU-168249 Innate Immune System
R-MMU-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: NM_011116, O35405, PLD3_MOUSE, Q3U5M5, Sam9, uc009fwm.1, uc009fwm.2, uc009fwm.3
UCSC ID: uc009fwm.3
RefSeq Accession: NM_011116
Protein: O35405 (aka PLD3_MOUSE)
CCDS: CCDS21025.1

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.