Human Gene LPCAT1 (ENST00000283415.4_8) from GENCODE V47lift37
  Description: lysophosphatidylcholine acyltransferase 1 (from RefSeq NM_024830.5)
Gencode Transcript: ENST00000283415.4_8
Gencode Gene: ENSG00000153395.11_10
Transcript (Including UTRs)
   Position: hg19 chr5:1,461,542-1,524,075 Size: 62,534 Total Exon Count: 14 Strand: -
Coding Region
   Position: hg19 chr5:1,463,766-1,523,959 Size: 60,194 Coding Exon Count: 14 

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 (chr5:1,461,542-1,524,075)mRNA (may differ from genome)Protein (534 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PCAT1_HUMAN
DESCRIPTION: RecName: Full=Lysophosphatidylcholine acyltransferase 1; Short=LPC acyltransferase 1; Short=LPCAT-1; Short=LysoPC acyltransferase 1; EC=2.3.1.-; AltName: Full=1-acylglycerophosphocholine O-acyltransferase; EC=2.3.1.23; AltName: Full=1-alkylglycerophosphocholine O-acetyltransferase; EC=2.3.1.67; AltName: Full=Acetyl-CoA:lyso-platelet-activating factor acetyltransferase; Short=Acetyl-CoA:lyso-PAF acetyltransferase; Short=Lyso-PAF acetyltransferase; Short=LysoPAFAT; AltName: Full=Acyltransferase-like 2; AltName: Full=Phosphonoformate immuno-associated protein 3;
FUNCTION: Possesses both acyltransferase and acetyltransferase activities. Activity is calcium-independent. Mediates the conversion of 1-acyl-sn-glycero-3-phosphocholine (LPC) into phosphatidylcholine (PC). Displays a clear preference for saturated fatty acyl-CoAs, and 1-myristoyl or 1-palmitoyl LPC as acyl donors and acceptors, respectively. May synthesize phosphatidylcholine in pulmonary surfactant, thereby playing a pivotal role in respiratory physiology.
CATALYTIC ACTIVITY: Acyl-CoA + 1-acyl-sn-glycero-3-phosphocholine = CoA + 1,2-diacyl-sn-glycero-3-phosphocholine.
CATALYTIC ACTIVITY: Acetyl-CoA + 1-alkyl-sn-glycero-3- phosphocholine = CoA + 2-acetyl-1-alkyl-sn-glycero-3- phosphocholine.
ENZYME REGULATION: Not activated by inflammatory stimulation. Inhibited by Cu(2+) and Fe(2+). Activity is not affected by Co(2+), Mg(2+) or Mn(2+) (By similarity).
PATHWAY: Lipid metabolism; phospholipid metabolism.
SUBCELLULAR LOCATION: Endoplasmic reticulum membrane; Single-pass type II membrane protein (By similarity). Golgi apparatus membrane; Single-pass type II membrane protein (By similarity).
DOMAIN: The HXXXXD motif is essential for acyltransferase activity and may constitute the binding site for the phosphate moiety of the glycerol-3-phosphocholine (By similarity).
DOMAIN: The di-lysine motif confers endoplasmic reticulum localization for type I membrane proteins (By similarity).
SIMILARITY: Belongs to the 1-acyl-sn-glycerol-3-phosphate acyltransferase family.
SIMILARITY: Contains 2 EF-hand domains.
SEQUENCE CAUTION: Sequence=BAB14061.1; Type=Erroneous initiation; Sequence=BAB14065.1; Type=Erroneous initiation;

-  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: LPCAT1
Diseases sorted by gene-association score: retinitis pigmentosa (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D001564 Benzo(a)pyrene
  • D013749 Tetrachlorodibenzodioxin
  • D015056 1-Methyl-3-isobutylxanthine
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide
  • D015124 8-Bromo Cyclic Adenosine Monophosphate
  • D016604 Aflatoxin B1
  • D002737 Chloroprene
  • D004390 Chlorpyrifos
  • D002794 Choline
          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: 57.81 RPKM in Lung
Total median expression: 573.97 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 -58.80116-0.507 Picture PostScript Text
3' UTR -797.602224-0.359 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
IPR002123 - Acyltransferase
IPR011992 - EF-hand-like_dom
IPR018249 - EF_HAND_2
IPR002048 - EF_hand_Ca-bd

Pfam Domains:
PF01553 - Acyltransferase
PF13833 - EF-hand domain pair

SCOP Domains:
47473 - EF-hand
69593 - Glycerol-3-phosphate (1)-acyltransferase

ModBase Predicted Comparative 3D Structure on Q8NF37
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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 Details  
Gene SorterGene Sorter Gene Sorter  
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003841 1-acylglycerol-3-phosphate O-acyltransferase activity
GO:0005509 calcium ion binding
GO:0016740 transferase activity
GO:0016746 transferase activity, transferring acyl groups
GO:0046872 metal ion binding
GO:0047144 2-acylglycerol-3-phosphate O-acyltransferase activity
GO:0047159 1-alkenylglycerophosphocholine O-acyltransferase activity
GO:0047184 1-acylglycerophosphocholine O-acyltransferase activity
GO:0047191 1-alkylglycerophosphocholine O-acyltransferase activity
GO:0047192 1-alkylglycerophosphocholine O-acetyltransferase activity

Biological Process:
GO:0006629 lipid metabolic process
GO:0006644 phospholipid metabolic process
GO:0006654 phosphatidic acid biosynthetic process
GO:0006656 phosphatidylcholine biosynthetic process
GO:0008152 metabolic process
GO:0008654 phospholipid biosynthetic process
GO:0036148 phosphatidylglycerol acyl-chain remodeling
GO:0036151 phosphatidylcholine acyl-chain remodeling
GO:0043129 surfactant homeostasis
GO:0043312 neutrophil degranulation
GO:0045732 positive regulation of protein catabolic process
GO:0060041 retina development in camera-type eye
GO:2001246 negative regulation of phosphatidylcholine biosynthetic process

Cellular Component:
GO:0000139 Golgi membrane
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0005794 Golgi apparatus
GO:0005811 lipid particle
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0035577 azurophil granule membrane


-  Descriptions from all associated GenBank mRNAs
  AK090444 - Homo sapiens mRNA for FLJ00365 protein.
BC002543 - Homo sapiens lysophosphatidylcholine acyltransferase 1, mRNA (cDNA clone IMAGE:3138846).
BC020166 - Homo sapiens lysophosphatidylcholine acyltransferase 1, mRNA (cDNA clone IMAGE:3343363), partial cds.
AK123603 - Homo sapiens cDNA FLJ41609 fis, clone CTONG3001560.
AK095552 - Homo sapiens cDNA FLJ38233 fis, clone FCBBF2005122.
AK022499 - Homo sapiens cDNA FLJ12437 fis, clone NT2RM1000118, weakly similar to CALCINEURIN B SUBUNIT.
AK022505 - Homo sapiens cDNA FLJ12443 fis, clone NT2RM1000186, weakly similar to CALCINEURIN B SUBUNIT.
AL831864 - Homo sapiens mRNA; cDNA DKFZp761J0417 (from clone DKFZp761J0417).
JD293036 - Sequence 274060 from Patent EP1572962.
JD135502 - Sequence 116526 from Patent EP1572962.
JD181494 - Sequence 162518 from Patent EP1572962.
AF052162 - Homo sapiens clone 24655 mRNA sequence.
JD204473 - Sequence 185497 from Patent EP1572962.
JD038269 - Sequence 19293 from Patent EP1572962.
JD146498 - Sequence 127522 from Patent EP1572962.
JD559962 - Sequence 540986 from Patent EP1572962.
JD315539 - Sequence 296563 from Patent EP1572962.
JD563800 - Sequence 544824 from Patent EP1572962.
JD237965 - Sequence 218989 from Patent EP1572962.
JD286937 - Sequence 267961 from Patent EP1572962.
JD429915 - Sequence 410939 from Patent EP1572962.
JD245922 - Sequence 226946 from Patent EP1572962.
JD066416 - Sequence 47440 from Patent EP1572962.
JD551695 - Sequence 532719 from Patent EP1572962.
JD474420 - Sequence 455444 from Patent EP1572962.
JD190838 - Sequence 171862 from Patent EP1572962.
JD381511 - Sequence 362535 from Patent EP1572962.
JD150609 - Sequence 131633 from Patent EP1572962.
JD325166 - Sequence 306190 from Patent EP1572962.
JD020865 - Sequence 1889 from Patent EP1572962.
JD144166 - Sequence 125190 from Patent EP1572962.
JD031331 - Sequence 12355 from Patent EP1572962.
JD329708 - Sequence 310732 from Patent EP1572962.
JD255019 - Sequence 236043 from Patent EP1572962.
JD139212 - Sequence 120236 from Patent EP1572962.
JD374021 - Sequence 355045 from Patent EP1572962.
JD374020 - Sequence 355044 from Patent EP1572962.
JD140470 - Sequence 121494 from Patent EP1572962.
JD458747 - Sequence 439771 from Patent EP1572962.
JD230519 - Sequence 211543 from Patent EP1572962.
JD060951 - Sequence 41975 from Patent EP1572962.
JD114136 - Sequence 95160 from Patent EP1572962.
JD316470 - Sequence 297494 from Patent EP1572962.
JD278900 - Sequence 259924 from Patent EP1572962.
JD515161 - Sequence 496185 from Patent EP1572962.
JD251408 - Sequence 232432 from Patent EP1572962.
JD493942 - Sequence 474966 from Patent EP1572962.
JD307244 - Sequence 288268 from Patent EP1572962.
JD158533 - Sequence 139557 from Patent EP1572962.
JD189050 - Sequence 170074 from Patent EP1572962.
JD486046 - Sequence 467070 from Patent EP1572962.
JD224241 - Sequence 205265 from Patent EP1572962.
JD280258 - Sequence 261282 from Patent EP1572962.
JD351213 - Sequence 332237 from Patent EP1572962.
AF530061 - Homo sapiens phosphonoformate immuno-associated protein 3 (PFAAP3) mRNA, complete cds.
AB244719 - Homo sapiens LPCAT1 mRNA for LPC acyltransferase, complete cds.
KJ903247 - Synthetic construct Homo sapiens clone ccsbBroadEn_12641 LPCAT1 gene, encodes complete protein.
BC140367 - Synthetic construct Homo sapiens clone IMAGE:100014325, MGC:173201 lysophosphatidylcholine acyltransferase 1 (LPCAT1) mRNA, encodes complete protein.
AB463849 - Synthetic construct DNA, clone: pF1KB7248, Homo sapiens AYTL2 gene for lysophosphatidylcholine acyltransferase 1, without stop codon, in Flexi system.
CU676500 - Synthetic construct Homo sapiens gateway clone IMAGE:100019202 5' read AYTL2 mRNA.
JD257604 - Sequence 238628 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q8NF37 (Reactome details) participates in the following event(s):

R-HSA-8873923 STARD10 binds LPCAT1 and PC
R-HSA-6798739 Exocytosis of azurophil granule membrane proteins
R-HSA-75885 1-acyl LPA is acylated to PA by AGPAT (LPAAT)
R-HSA-1482539 1-acyl LPG is acylated to PG by LPGAT
R-HSA-1482635 2-acyl LPG is acylated to PG by LPGAT
R-HSA-1482547 1-acyl LPC is acylated to PC by LPCAT
R-HSA-1482533 2-acyl LPC is acylated to PC by LPCAT
R-HSA-1483191 Synthesis of PC
R-HSA-1483206 Glycerophospholipid biosynthesis
R-HSA-6798695 Neutrophil degranulation
R-HSA-1483166 Synthesis of PA
R-HSA-1482925 Acyl chain remodelling of PG
R-HSA-1482788 Acyl chain remodelling of PC
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: AYTL2, ENST00000283415.1, ENST00000283415.2, ENST00000283415.3, NM_024830, PCAT1_HUMAN, PFAAP3, Q1HAQ1, Q7Z4G6, Q8N3U7, Q8NF37, Q8WUL8, Q9GZW6, uc317kcp.1, uc317kcp.2
UCSC ID: ENST00000283415.4_8
RefSeq Accession: NM_024830.5
Protein: Q8NF37 (aka PCAT1_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.