Human Gene PLD1 (ENST00000356327.9) from GENCODE V44
  Description: Homo sapiens phospholipase D1 (PLD1), transcript variant 2, mRNA. (from RefSeq NM_001130081)
RefSeq Summary (NM_001130081): This gene encodes a phosphatidylcholine-specific phospholipase which catalyzes the hydrolysis of phosphatidylcholine in order to yield phosphatidic acid and choline. The enzyme may play a role in signal transduction and subcellular trafficking. Alternative splicing results in multiple transcript variants with both catalytic and regulatory properties. [provided by RefSeq, Sep 2011].
Gencode Transcript: ENST00000356327.9
Gencode Gene: ENSG00000075651.17
Transcript (Including UTRs)
   Position: hg38 chr3:171,600,405-171,810,438 Size: 210,034 Total Exon Count: 26 Strand: -
Coding Region
   Position: hg38 chr3:171,603,078-171,738,051 Size: 134,974 Coding Exon Count: 25 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:171,600,405-171,810,438)mRNA (may differ from genome)Protein (1036 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCLynxMalacardsMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PLD1_HUMAN
DESCRIPTION: RecName: Full=Phospholipase D1; Short=PLD 1; Short=hPLD1; EC=3.1.4.4; AltName: Full=Choline phosphatase 1; AltName: Full=Phosphatidylcholine-hydrolyzing phospholipase D1;
FUNCTION: Implicated as a critical step in numerous cellular pathways, including signal transduction, membrane trafficking, and the regulation of mitosis. May be involved in the regulation of perinuclear intravesicular membrane traffic (By similarity).
CATALYTIC ACTIVITY: A phosphatidylcholine + H(2)O = choline + a phosphatidate.
ENZYME REGULATION: Stimulated by phosphatidylinositol 4,5- bisphosphate and phosphatidylinositol 3,4,5-trisphosphate, activated by the phosphokinase C-alpha, by the ADP-ribosylation factor-1 (ARF-1), and to a lesser extent by GTP-binding proteins: RHO A, RAC-1 and CDC42. Inhibited by oleate.
SUBUNIT: Interacts with PIP5K1B.
SUBCELLULAR LOCATION: Cytoplasm, perinuclear region (By similarity). Endoplasmic reticulum membrane; Lipid-anchor; Cytoplasmic side (By similarity). Golgi apparatus membrane; Lipid- anchor; Cytoplasmic side (By similarity). Late endosome membrane; Lipid-anchor; Cytoplasmic side (By similarity).
TISSUE SPECIFICITY: Expressed abundantly in the pancreas and heart and at high levels in brain, placenta, spleen, uterus and small intestine.
SIMILARITY: Belongs to the phospholipase D family.
SIMILARITY: Contains 1 PH domain.
SIMILARITY: Contains 2 PLD phosphodiesterase domains.
SIMILARITY: Contains 1 PX (phox homology) domain.
WEB RESOURCE: Name=Wikipedia; Note=Phospholipase D entry; URL="http://en.wikipedia.org/wiki/Phospholipase_D";

-  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: PLD1
Diseases sorted by gene-association score: cardiac valvular defect, developmental* (1219), coffin-lowry syndrome (7)
* = Manually curated disease association

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.26 RPKM in Adrenal Gland
Total median expression: 175.07 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 -15.9071-0.224 Picture PostScript Text
3' UTR -671.802673-0.251 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
IPR011993 - PH_like_dom
IPR001683 - Phox
IPR025202 - PLD-like_dom
IPR001849 - Pleckstrin_homology
IPR001736 - PLipase_D/transphosphatidylase
IPR016555 - PLipase_D_euk
IPR015679 - PLipase_D_fam

Pfam Domains:
PF00169 - PH domain
PF00614 - Phospholipase D Active site motif
PF13091 - PLD-like domain
PF00787 - PX domain

ModBase Predicted Comparative 3D Structure on Q13393
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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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  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:0035091 phosphatidylinositol binding
GO:0070290 N-acylphosphatidylethanolamine-specific phospholipase D activity

Biological Process:
GO:0006629 lipid metabolic process
GO:0006654 phosphatidic acid biosynthetic process
GO:0006935 chemotaxis
GO:0007264 small GTPase mediated signal transduction
GO:0007265 Ras protein signal transduction
GO:0016042 lipid catabolic process
GO:0032534 regulation of microvillus assembly
GO:0043312 neutrophil degranulation
GO:0048017 inositol lipid-mediated signaling
GO:0048870 cell motility

Cellular Component:
GO:0000139 Golgi membrane
GO:0005737 cytoplasm
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0030139 endocytic vesicle
GO:0031902 late endosome membrane
GO:0035579 specific granule membrane
GO:0048471 perinuclear region of cytoplasm
GO:0070821 tertiary granule membrane


-  Descriptions from all associated GenBank mRNAs
  AB209907 - Homo sapiens mRNA for phospholipase D1 variant protein.
BC068976 - Homo sapiens phospholipase D1, phosphatidylcholine-specific, mRNA (cDNA clone MGC:70810 IMAGE:6068382), complete cds.
U38545 - Human ARF-activated phosphatidylcholine-specific phospholipase D1a (hPLD1) mRNA, complete cds.
KJ891822 - Synthetic construct Homo sapiens clone ccsbBroadEn_01216 PLD1 gene, encodes complete protein.
HQ257981 - Synthetic construct Homo sapiens clone IMAGE:100072290 phospholipase D1, phosphatidylcholine-specific (PLD1) gene, encodes complete protein.
AB385136 - Synthetic construct DNA, clone: pF1KB5631, Homo sapiens PLD1 gene for phospholipase D1, complete cds, without stop codon, in Flexi system.
BX648900 - Homo sapiens mRNA; cDNA DKFZp686P22252 (from clone DKFZp686P22252).
JD485703 - Sequence 466727 from Patent EP1572962.
JD501861 - Sequence 482885 from Patent EP1572962.
JD067233 - Sequence 48257 from Patent EP1572962.
JD060744 - Sequence 41768 from Patent EP1572962.
JD114880 - Sequence 95904 from Patent EP1572962.
AJ276230 - Homo sapiens mRNA for partial phospholipase D1, splice variant PLD1a/b2.
AK091897 - Homo sapiens cDNA FLJ34578 fis, clone KIDNE2008404, highly similar to PHOSPHOLIPASE D1 (EC 3.1.4.4).
AX747241 - Sequence 766 from Patent EP1308459.
AK026225 - Homo sapiens cDNA: FLJ22572 fis, clone HSI02313.
JD178229 - Sequence 159253 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00564 - Glycerophospholipid metabolism
hsa00565 - Ether lipid metabolism
hsa01100 - Metabolic pathways
hsa04144 - Endocytosis
hsa04666 - Fc gamma R-mediated phagocytosis
hsa04912 - GnRH signaling pathway
hsa05200 - Pathways in cancer
hsa05212 - Pancreatic cancer

BioCarta from NCI Cancer Genome Anatomy Project
h_rasPathway - Ras Signaling Pathway
h_rac1Pathway - Rac 1 cell motility signaling pathway
h_cb1rPathway - Metabolism of Anandamide, an Endogenous Cannabinoid

Reactome (by CSHL, EBI, and GO)

Protein Q13393 (Reactome details) participates in the following event(s):

R-HSA-6799350 Exocytosis of specific granule membrane proteins
R-HSA-6798747 Exocytosis of tertiary granule membrane proteins
R-HSA-1483182 PC is hydrolyzed to PA and choline by PLD1/2
R-HSA-1483142 PC is transphosphatidylated to PG by PLD1-4/6
R-HSA-2029471 Hydrolysis of PC to PA by PLD
R-HSA-6798695 Neutrophil degranulation
R-HSA-1483166 Synthesis of PA
R-HSA-1483148 Synthesis of PG
R-HSA-168249 Innate Immune System
R-HSA-2029485 Role of phospholipids in phagocytosis
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-168256 Immune System
R-HSA-2029480 Fcgamma receptor (FCGR) dependent phagocytosis
R-HSA-1483257 Phospholipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000356327.1, ENST00000356327.2, ENST00000356327.3, ENST00000356327.4, ENST00000356327.5, ENST00000356327.6, ENST00000356327.7, ENST00000356327.8, NM_001130081, PLD1_HUMAN, Q13393, uc003fht.1, uc003fht.2, uc003fht.3, uc003fht.4
UCSC ID: ENST00000356327.9
RefSeq Accession: NM_001130081
Protein: Q13393 (aka PLD1_HUMAN)
CCDS: CCDS3216.1, CCDS46957.1

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