Human Gene PLA2G4D (uc001zox.3)
  Description: Homo sapiens phospholipase A2, group IVD (cytosolic) (PLA2G4D), mRNA.
RefSeq Summary (NM_178034): The phospholipase A2 enzyme family, including PLA2G4D, catalyze the hydrolysis of glycerophospholipids at the sn-2 position and then liberate free fatty acids and lysophospholipids (Chiba et al., 2004 [PubMed 14709560]).[supplied by OMIM, Jun 2009].
Transcript (Including UTRs)
   Position: hg19 chr15:42,359,881-42,386,752 Size: 26,872 Total Exon Count: 20 Strand: -
Coding Region
   Position: hg19 chr15:42,360,913-42,386,657 Size: 25,745 Coding Exon Count: 20 

Page IndexSequence and LinksUniProtKB CommentsPrimersGenetic AssociationsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr15:42,359,881-42,386,752)mRNA (may differ from genome)Protein (818 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PA24D_HUMAN
DESCRIPTION: RecName: Full=Cytosolic phospholipase A2 delta; Short=cPLA2-delta; EC=3.1.1.4; AltName: Full=Phospholipase A2 group IVD;
FUNCTION: Calcium-dependent phospholipase A2 that selectively hydrolyzes glycerophospholipids in the sn-2 position. Not arachidonic acid-specific but has linoleic acid-specific activity. May play a role in inflammation in psoriatic lesions.
CATALYTIC ACTIVITY: Phosphatidylcholine + H(2)O = 1- acylglycerophosphocholine + a carboxylate.
ENZYME REGULATION: Stimulated by cytosolic Ca(2+).
SUBCELLULAR LOCATION: Cytoplasm, cytosol. Cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side (By similarity). Note=Translocates to membrane vesicles in a calcium- dependent fashion. Translocates to perinuclear regions upon ionomycin stimulation (By similarity).
TISSUE SPECIFICITY: Expressed in stratified squamous epithelia, such as those in skin and cervix, but not in other tissues. Strongly expressed in the upper spinous layer of the psoriatic epidermis, expressed weakly and discontinuously in atopic dermatitis and mycosis fungoides, and not detected in the epidermis of normal skin.
DOMAIN: The N-terminal C2 domain associates with lipid membranes upon calcium binding. It modulates enzyme activity by presenting the active site to its substrate in response to elevations of cytosolic Ca(2+) (By similarity).
SIMILARITY: Contains 1 C2 domain.
SIMILARITY: Contains 1 PLA2c domain.
SEQUENCE CAUTION: Sequence=AAH34571.1; Type=Erroneous initiation; Note=Translation N-terminally extended;

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): PLA2G4D
CDC HuGE Published Literature: PLA2G4D
Positive Disease Associations: Stroke
Related Studies:
  1. Stroke
    , , . [PubMed 0]
  2. Stroke
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 13.96 RPKM in Skin - Not Sun Exposed (Suprapubic)
Total median expression: 34.94 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 -43.4095-0.457 Picture PostScript Text
3' UTR -319.431032-0.310 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
IPR016035 - Acyl_Trfase/lysoPLipase
IPR000008 - C2_Ca-dep
IPR008973 - C2_Ca/lipid-bd_dom_CaLB
IPR018029 - C2_membr_targeting
IPR002642 - LysoPLipase_cat_dom

Pfam Domains:
PF00168 - C2 domain
PF01735 - Lysophospholipase catalytic domain

SCOP Domains:
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
52151 - FabD/lysophospholipase-like

ModBase Predicted Comparative 3D Structure on Q86XP0
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 Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004620 phospholipase activity
GO:0004622 lysophospholipase activity
GO:0004623 phospholipase A2 activity
GO:0008970 phosphatidylcholine 1-acylhydrolase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0047498 calcium-dependent phospholipase A2 activity

Biological Process:
GO:0006629 lipid metabolic process
GO:0006644 phospholipid metabolic process
GO:0006654 phosphatidic acid biosynthetic process
GO:0008152 metabolic process
GO:0009395 phospholipid catabolic process
GO:0016042 lipid catabolic process
GO:0036148 phosphatidylglycerol acyl-chain remodeling
GO:0036149 phosphatidylinositol acyl-chain remodeling
GO:0036150 phosphatidylserine acyl-chain remodeling
GO:0036151 phosphatidylcholine acyl-chain remodeling
GO:0036152 phosphatidylethanolamine acyl-chain remodeling
GO:0046475 glycerophospholipid catabolic process

Cellular Component:
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane


-  Descriptions from all associated GenBank mRNAs
  KJ904112 - Synthetic construct Homo sapiens clone ccsbBroadEn_13506 PLA2G4D gene, encodes complete protein.
BC034571 - Homo sapiens phospholipase A2, group IVD (cytosolic), mRNA (cDNA clone IMAGE:5167964), complete cds.
AB090876 - Homo sapiens cPLA2 delta mRNA for cytosolic phospholipase A2 delta, complete cds.
JD500421 - Sequence 481445 from Patent EP1572962.
JD556630 - Sequence 537654 from Patent EP1572962.
JD547525 - Sequence 528549 from Patent EP1572962.
JD403521 - Sequence 384545 from Patent EP1572962.
JD400060 - Sequence 381084 from Patent EP1572962.
JD555801 - Sequence 536825 from Patent EP1572962.
JD249342 - Sequence 230366 from Patent EP1572962.
JD398405 - Sequence 379429 from Patent EP1572962.
JD254527 - Sequence 235551 from Patent EP1572962.
JD536947 - Sequence 517971 from Patent EP1572962.
JD342913 - Sequence 323937 from Patent EP1572962.
JD340507 - Sequence 321531 from Patent EP1572962.
JD170960 - Sequence 151984 from Patent EP1572962.
JD455373 - Sequence 436397 from Patent EP1572962.
JD164337 - Sequence 145361 from Patent EP1572962.
JD525354 - Sequence 506378 from Patent EP1572962.
JD248674 - Sequence 229698 from Patent EP1572962.
JD103325 - Sequence 84349 from Patent EP1572962.
BC140416 - Synthetic construct Homo sapiens clone IMAGE:100014453, MGC:173165 phospholipase A2, group IVD (cytosolic) (PLA2G4D) mRNA, encodes complete protein.
BC146533 - Synthetic construct Homo sapiens clone IMAGE:100014896, MGC:180155 phospholipase A2, group IVD (cytosolic) (PLA2G4D) mRNA, encodes complete protein.
AB527201 - Synthetic construct DNA, clone: pF1KE0351, Homo sapiens PLA2G4D gene for phospholipase A2, group IVD, without stop codon, in Flexi system.
JD086526 - Sequence 67550 from Patent EP1572962.
JD319173 - Sequence 300197 from Patent EP1572962.
JD173824 - Sequence 154848 from Patent EP1572962.
JD250898 - Sequence 231922 from Patent EP1572962.
JD045312 - Sequence 26336 from Patent EP1572962.
JD371002 - Sequence 352026 from Patent EP1572962.
JD192314 - Sequence 173338 from Patent EP1572962.
CU689918 - Synthetic construct Homo sapiens gateway clone IMAGE:100016793 5' read PLA2G4D mRNA.
DQ891792 - Synthetic construct clone IMAGE:100004422; FLH179968.01X; RZPDo839E06132D phospholipase A2, group IVD (cytosolic) (PLA2G4D) gene, encodes complete protein.
DQ894974 - Synthetic construct Homo sapiens clone IMAGE:100009434; FLH179964.01L; RZPDo839E06131D phospholipase A2, group IVD (cytosolic) (PLA2G4D) gene, encodes complete protein.
JD224583 - Sequence 205607 from Patent EP1572962.
JD076306 - Sequence 57330 from Patent EP1572962.
JD474858 - Sequence 455882 from Patent EP1572962.
JD218443 - Sequence 199467 from Patent EP1572962.
JD454862 - Sequence 435886 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04666 - Fc gamma R-mediated phagocytosis

BioCyc Knowledge Library
LIPASYN-PWY - phospholipases

Reactome (by CSHL, EBI, and GO)

Protein Q86XP0 (Reactome details) participates in the following event(s):

R-HSA-1482604 PA is hydrolyzed to 1-acyl LPA by PLA2[1] (OM)
R-HSA-1482656 PA is hydrolysed to 1-acyl LPA by PLA2[1]
R-HSA-1482900 PG is hydrolyzed to 1-acyl LPG by PLA2[1]
R-HSA-1482612 2-acyl LPC is hydrolyzed to GPCho by PLA2[8]
R-HSA-1482685 1-acyl LPC is hydrolyzed to GPCho by PLA2[8]
R-HSA-1482862 PC is hydrolysed to 2-acyl LPC by PLA2[7]
R-HSA-1482856 PC is hydrolyzed to 1-acyl LPC by PLA2[5]
R-HSA-1482828 PE is hydrolyzed to 2-acyl LPE by PLA2[4]
R-HSA-1482884 PE is hydrolyzed to 1-acyl LPE by PLA2[2]
R-HSA-1482920 PG is hydrolyzed to 2-acyl LPG by PLA2[14]
R-HSA-1482932 PI is hydrolyzed to 2-acyl LPI by PLA2[13]
R-HSA-1482825 PI is hydrolyzed to 1-acyl LPI by PLA2[11]
R-HSA-1482897 PS is hydrolyzed to 2-acyl LPS by PLA2[10]
R-HSA-1482771 PS is hydrolyzed to 1-acyl LPS by PLA2[9]
R-HSA-1482745 PG is hydrolyzed to 1-acyl LPG by PLA2G4B (IM)
R-HSA-1482847 PG is hydrolysed to 2-acyl LPG by PLA2G4B (IM)
R-HSA-1483166 Synthesis of PA
R-HSA-1482925 Acyl chain remodelling of PG
R-HSA-1483115 Hydrolysis of LPC
R-HSA-1482788 Acyl chain remodelling of PC
R-HSA-1482839 Acyl chain remodelling of PE
R-HSA-1482922 Acyl chain remodelling of PI
R-HSA-1482801 Acyl chain remodelling of PS
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-1483257 Phospholipid metabolism
R-HSA-556833 Metabolism of lipids
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: NM_178034, NP_828848, PA24D_HUMAN, Q86XP0, Q8N176
UCSC ID: uc001zox.3
RefSeq Accession: NM_178034
Protein: Q86XP0 (aka PA24D_HUMAN)
CCDS: CCDS32203.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_178034.3
exon count: 20CDS single in 3' UTR: no RNA size: 3584
ORF size: 2457CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 5111.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.