Human Gene PLD2 (ENST00000263088.11_6) from GENCODE V47lift37
  Description: phospholipase D2, transcript variant 1 (from RefSeq NM_002663.5)
Gencode Transcript: ENST00000263088.11_6
Gencode Gene: ENSG00000129219.14_11
Transcript (Including UTRs)
   Position: hg19 chr17:4,710,447-4,726,725 Size: 16,279 Total Exon Count: 25 Strand: +
Coding Region
   Position: hg19 chr17:4,711,068-4,726,159 Size: 15,092 Coding Exon Count: 24 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:4,710,447-4,726,725)mRNA (may differ from genome)Protein (933 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PLD2_HUMAN
DESCRIPTION: RecName: Full=Phospholipase D2; Short=PLD 2; Short=hPLD2; EC=3.1.4.4; AltName: Full=Choline phosphatase 2; AltName: Full=PLD1C; AltName: Full=Phosphatidylcholine-hydrolyzing phospholipase D2;
FUNCTION: May have a role in signal-induced cytoskeletal regulation and/or endocytosis (By similarity).
CATALYTIC ACTIVITY: A phosphatidylcholine + H(2)O = choline + a phosphatidate.
ENZYME REGULATION: Stimulated by phosphatidylinositol 4,5- bisphosphate and activated by the ADP-ribosylation factor-1 (ARF- 1).
SUBUNIT: Interacts with EGFR (By similarity). Interacts with PIP5K1B.
INTERACTION: P62993:GRB2; NbExp=4; IntAct=EBI-1053996, EBI-401755;
SUBCELLULAR LOCATION: Membrane; Peripheral membrane protein (By similarity).
TISSUE SPECIFICITY: Ubiquitous.
PTM: Phosphorylated by FGR (By similarity).
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: PLD2
Diseases sorted by gene-association score: tooth agenesis (2)

-  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: 40.87 RPKM in Esophagus - Mucosa
Total median expression: 605.29 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 -29.4075-0.392 Picture PostScript Text
3' UTR -208.70566-0.369 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:
PF00614 - Phospholipase D Active site motif
PF00787 - PX domain
PF13091 - PLD-like domain

SCOP Domains:
89009 - GAT-like domain
50729 - PH domain-like
56024 - Phospholipase D/nuclease
64268 - PX domain

ModBase Predicted Comparative 3D Structure on O14939
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 orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  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:0007010 cytoskeleton organization
GO:0007264 small GTPase mediated signal transduction
GO:0016042 lipid catabolic process
GO:0036465 synaptic vesicle recycling
GO:0038096 Fc-gamma receptor signaling pathway involved in phagocytosis
GO:0048017 inositol lipid-mediated signaling
GO:0048870 cell motility

Cellular Component:
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0098793 presynapse


-  Descriptions from all associated GenBank mRNAs
  AF033850 - Homo sapiens phospholipase D2 (PLD2) mRNA, complete cds.
BC015033 - Homo sapiens phospholipase D2, mRNA (cDNA clone MGC:9152 IMAGE:3907928), complete cds.
AF038441 - Homo sapiens phospholipase D2 (PLD2) mRNA, splice variant hPLD2b, complete cds.
AF038440 - Homo sapiens phospholipase D2 (PLD2) mRNA, splice variant hPLD2a, complete cds.
AK304246 - Homo sapiens cDNA FLJ53960 complete cds, highly similar to Phospholipase D2 (EC 3.1.4.4).
AK314797 - Homo sapiens cDNA, FLJ95669.
BC056871 - Homo sapiens phospholipase D2, mRNA (cDNA clone MGC:64872 IMAGE:5526564), complete cds.
AB209374 - Homo sapiens mRNA for phospholipase D2 variant protein.
AB463172 - Synthetic construct DNA, clone: pF1KB8432, Homo sapiens PLD2 gene for phospholipase D2, without stop codon, in Flexi system.
AM393149 - Synthetic construct Homo sapiens clone IMAGE:100002893 for hypothetical protein (PLD2 gene).
AM393150 - Synthetic construct Homo sapiens clone IMAGE:100002623 for hypothetical protein (PLD2 gene).
AM393159 - Synthetic construct Homo sapiens clone IMAGE:100002892 for hypothetical protein (PLD2 gene).
AM393603 - Synthetic construct Homo sapiens clone IMAGE:100002622 for hypothetical protein (PLD2 gene).
AF035483 - Homo sapiens phospholipase D2 (PLD2) mRNA, complete cds.
AY178289 - Homo sapiens phospholipase D2 (PLD2) mRNA, partial cds.
JD273227 - Sequence 254251 from Patent EP1572962.
JD549416 - Sequence 530440 from Patent EP1572962.
JD095182 - Sequence 76206 from Patent EP1572962.
JD184842 - Sequence 165866 from Patent EP1572962.
JD038880 - Sequence 19904 from Patent EP1572962.
JD068774 - Sequence 49798 from Patent EP1572962.
JD210730 - Sequence 191754 from Patent EP1572962.
JD555164 - Sequence 536188 from Patent EP1572962.
JD255157 - Sequence 236181 from Patent EP1572962.
JD290980 - Sequence 272004 from Patent EP1572962.
JD248749 - Sequence 229773 from Patent EP1572962.
JD104485 - Sequence 85509 from Patent EP1572962.
JD124406 - Sequence 105430 from Patent EP1572962.
JD284482 - Sequence 265506 from Patent EP1572962.

-  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 O14939 (Reactome details) participates in the following event(s):

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-1483166 Synthesis of PA
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: ENST00000263088.1, ENST00000263088.10, ENST00000263088.2, ENST00000263088.3, ENST00000263088.4, ENST00000263088.5, ENST00000263088.6, ENST00000263088.7, ENST00000263088.8, ENST00000263088.9, I3L2C9, NM_002663, O14939, O43540, O43579, O43580, PLD2 , PLD2_HUMAN, Q6PGR0, Q96BY3, uc317hgl.1, uc317hgl.2
UCSC ID: ENST00000263088.11_6
RefSeq Accession: NM_002663.5
Protein: O14939 (aka PLD2_HUMAN)

-  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.