Human Gene PLD3 (ENST00000409735.9_5) from GENCODE V47lift37
  Description: phospholipase D family member 3, transcript variant 2 (from RefSeq NM_012268.4)
Gencode Transcript: ENST00000409735.9_5
Gencode Gene: ENSG00000105223.21_16
Transcript (Including UTRs)
   Position: hg19 chr19:40,854,602-40,884,392 Size: 29,791 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr19:40,872,391-40,884,080 Size: 11,690 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:40,854,602-40,884,392)mRNA (may differ from genome)Protein (490 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PLD3_HUMAN
DESCRIPTION: RecName: Full=Phospholipase D3; Short=PLD 3; EC=3.1.4.4; AltName: Full=Choline phosphatase 3; AltName: Full=HindIII K4L homolog; AltName: Full=Hu-K4; AltName: Full=Phosphatidylcholine-hydrolyzing phospholipase D3;
CATALYTIC ACTIVITY: A phosphatidylcholine + H(2)O = choline + a phosphatidate.
INTERACTION: P19838:NFKB1; NbExp=2; IntAct=EBI-2689908, EBI-300010;
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type II membrane protein.
TISSUE SPECIFICITY: Widely expressed. Expressed at higher level in brain. Expressed at low level in corpus callosum, suggesting that it is highly expressed in neurons.
PTM: Glycosylated.
SIMILARITY: Belongs to the phospholipase D family.
SIMILARITY: Contains 2 PLD phosphodiesterase domains.
SEQUENCE CAUTION: Sequence=AAB16799.1; Type=Frameshift; Positions=52;

-  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


-  MalaCards Disease Associations
  MalaCards Gene Search: PLD3
Diseases sorted by gene-association score: acute conjunctivitis (18), acute hemorrhagic conjunctivitis (18), conjunctival folliculosis (17), shipyard eye (13), conjunctival disease (10), inclusion conjunctivitis (8), alzheimer disease (5)

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

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 490.02 RPKM in Pituitary
Total median expression: 4611.15 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -178.00352-0.506 Picture PostScript Text
3' UTR -134.30312-0.430 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 Q8IV08
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003824 catalytic activity
GO:0004630 phospholipase D activity
GO:0005515 protein binding
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
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  JF432185 - Synthetic construct Homo sapiens clone IMAGE:100073344 phospholipase D family, member 3 (PLD3) gene, encodes complete protein.
KJ893427 - Synthetic construct Homo sapiens clone ccsbBroadEn_02821 PLD3 gene, encodes complete protein.
BC036327 - Homo sapiens phospholipase D family, member 3, mRNA (cDNA clone MGC:35422 IMAGE:5189261), complete cds.
AK293690 - Homo sapiens cDNA FLJ59669 complete cds, highly similar to Homo sapiens phospholipase D family, member 3 (PLD3), transcript variant 1, mRNA.
BC096820 - Homo sapiens phospholipase D family, member 3, mRNA (cDNA clone MGC:111351 IMAGE:30558682), complete cds.
U60644 - Human HU-K4 mRNA, complete cds.
JD124758 - Sequence 105782 from Patent EP1572962.
JD391822 - Sequence 372846 from Patent EP1572962.
AY927565 - Homo sapiens mRNA sequence.
JD261148 - Sequence 242172 from Patent EP1572962.
JD538400 - Sequence 519424 from Patent EP1572962.
CU690326 - Synthetic construct Homo sapiens gateway clone IMAGE:100019641 5' read PLD3 mRNA.
AB529100 - Synthetic construct DNA, clone: pF1KB4417, Homo sapiens PLD3 gene for phospholipase D family, member 3, without stop codon, in Flexi system.
JD089817 - Sequence 70841 from Patent EP1572962.
JD180053 - Sequence 161077 from Patent EP1572962.
BC000553 - Homo sapiens phospholipase D family, member 3, mRNA (cDNA clone IMAGE:3163199), partial cds.
MS906548 - Sequence 102 from Patent WO2017059902.
MS909354 - Sequence 102 from Patent WO2017060314.
MS906549 - Sequence 103 from Patent WO2017059902.
MS909355 - Sequence 103 from Patent WO2017060314.
MS906546 - Sequence 100 from Patent WO2017059902.
MS909352 - Sequence 100 from Patent WO2017060314.
MS906547 - Sequence 101 from Patent WO2017059902.
MS909353 - Sequence 101 from Patent WO2017060314.
MS906550 - Sequence 104 from Patent WO2017059902.
MS909356 - Sequence 104 from Patent WO2017060314.
MS906536 - Sequence 90 from Patent WO2017059902.
MS909342 - Sequence 90 from Patent WO2017060314.
MS906537 - Sequence 91 from Patent WO2017059902.
MS909343 - Sequence 91 from Patent WO2017060314.
MS906543 - Sequence 97 from Patent WO2017059902.
MS906544 - Sequence 98 from Patent WO2017059902.
MS909349 - Sequence 97 from Patent WO2017060314.
MS909350 - Sequence 98 from Patent WO2017060314.
MS906542 - Sequence 96 from Patent WO2017059902.
MS909348 - Sequence 96 from Patent WO2017060314.
MS906545 - Sequence 99 from Patent WO2017059902.
MS909351 - Sequence 99 from Patent WO2017060314.
MS906538 - Sequence 92 from Patent WO2017059902.
MS909344 - Sequence 92 from Patent WO2017060314.
MS906539 - Sequence 93 from Patent WO2017059902.
MS909345 - Sequence 93 from Patent WO2017060314.
MS906540 - Sequence 94 from Patent WO2017059902.
MS909346 - Sequence 94 from Patent WO2017060314.
MS906541 - Sequence 95 from Patent WO2017059902.
MS909347 - Sequence 95 from Patent WO2017060314.
JD131834 - Sequence 112858 from Patent EP1572962.
JD131835 - Sequence 112859 from Patent EP1572962.
JD418443 - Sequence 399467 from Patent EP1572962.
JD525498 - Sequence 506522 from Patent EP1572962.
JD271889 - Sequence 252913 from Patent EP1572962.
JD418370 - Sequence 399394 from Patent EP1572962.
JD417539 - Sequence 398563 from Patent EP1572962.
JD282795 - Sequence 263819 from Patent EP1572962.
JD191310 - Sequence 172334 from Patent EP1572962.
JD215082 - Sequence 196106 from Patent EP1572962.
JD387212 - Sequence 368236 from Patent EP1572962.
JD327525 - Sequence 308549 from Patent EP1572962.
MP573215 - Sequence 102 from Patent EP3636764.
MP573216 - Sequence 103 from Patent EP3636764.
MP573213 - Sequence 100 from Patent EP3636764.
MP573214 - Sequence 101 from Patent EP3636764.
MP573217 - Sequence 104 from Patent EP3636764.
MP573203 - Sequence 90 from Patent EP3636764.
MP573204 - Sequence 91 from Patent EP3636764.
MP573210 - Sequence 97 from Patent EP3636764.
MP573211 - Sequence 98 from Patent EP3636764.
MP573209 - Sequence 96 from Patent EP3636764.
MP573212 - Sequence 99 from Patent EP3636764.
MP573205 - Sequence 92 from Patent EP3636764.
MP573206 - Sequence 93 from Patent EP3636764.
MP573207 - Sequence 94 from Patent EP3636764.
MP573208 - Sequence 95 from Patent EP3636764.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
LIPASYN-PWY - phospholipases

BioCarta from NCI Cancer Genome Anatomy Project
h_cb1rPathway - Metabolism of Anandamide, an Endogenous Cannabinoid

Reactome (by CSHL, EBI, and GO)

Protein Q8IV08 (Reactome details) participates in the following event(s):

R-HSA-1483142 PC is transphosphatidylated to PG by PLD1-4/6
R-HSA-2029471 Hydrolysis of PC to PA by PLD
R-HSA-1483148 Synthesis of PG
R-HSA-2029485 Role of phospholipids in phagocytosis
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-2029480 Fcgamma receptor (FCGR) dependent phagocytosis
R-HSA-1483257 Phospholipid metabolism
R-HSA-168249 Innate Immune System
R-HSA-556833 Metabolism of lipids
R-HSA-168256 Immune System
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000409735.1, ENST00000409735.2, ENST00000409735.3, ENST00000409735.4, ENST00000409735.5, ENST00000409735.6, ENST00000409735.7, ENST00000409735.8, NM_012268, PLD3_HUMAN, Q8IV08, Q92853, Q9BW87, uc319gcn.1, uc319gcn.2
UCSC ID: ENST00000409735.9_5
RefSeq Accession: NM_012268.4
Protein: Q8IV08 (aka PLD3_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene PLD3:
ataxias (Hereditary Ataxia Overview)

-  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.