Human Gene PAFAH1B3 (ENST00000262890.8_7) from GENCODE V47lift37
  Description: platelet activating factor acetylhydrolase 1b catalytic subunit 3, transcript variant 2 (from RefSeq NM_002573.4)
Gencode Transcript: ENST00000262890.8_7
Gencode Gene: ENSG00000079462.8_12
Transcript (Including UTRs)
   Position: hg19 chr19:42,801,187-42,806,776 Size: 5,590 Total Exon Count: 5 Strand: -
Coding Region
   Position: hg19 chr19:42,801,230-42,806,461 Size: 5,232 Coding Exon Count: 5 

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 (chr19:42,801,187-42,806,776)mRNA (may differ from genome)Protein (231 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: PA1B3_HUMAN
DESCRIPTION: RecName: Full=Platelet-activating factor acetylhydrolase IB subunit gamma; EC=3.1.1.47; AltName: Full=PAF acetylhydrolase 29 kDa subunit; Short=PAF-AH 29 kDa subunit; AltName: Full=PAF-AH subunit gamma; Short=PAFAH subunit gamma;
FUNCTION: Inactivates paf by removing the acetyl group at the sn-2 position. This is a catalytic subunit. Plays an important role during the development of brain.
CATALYTIC ACTIVITY: 1-alkyl-2-acetyl-sn-glycero-3-phosphocholine + H(2)O = 1-alkyl-sn-glycero-3-phosphocholine + acetate.
SUBUNIT: Cytosolic PAF-AH IB is formed of three subunits of 45 kDa (alpha), 30 kDa (beta) and 29 kDa (gamma). The catalytic activity of the enzyme resides in the beta and gamma subunits, whereas the alpha subunit has regulatory activity. Trimer formation is not essential for the catalytic activity.
INTERACTION: Q8TBB1:LNX1; NbExp=2; IntAct=EBI-711522, EBI-739832;
SUBCELLULAR LOCATION: Cytoplasm.
TISSUE SPECIFICITY: In the adult, expressed in brain, skeletal muscle, kidney, thymus, spleen, colon, testis, ovary and peripheral blood leukocytes. In the fetus, highest expression occurs in brain.
SIMILARITY: Belongs to the 'GDSL' lipolytic enzyme family. Platelet-activating factor acetylhydrolase IB beta/gamma subunits subfamily.

-  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: PAFAH1B3
Diseases sorted by gene-association score: miller-dieker lissencephaly syndrome (1)

-  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: 40.81 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 582.95 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 -145.10315-0.461 Picture PostScript Text
3' UTR -1.2043-0.028 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
IPR013830 - Esterase_SGNH_hydro-type
IPR013831 - Esterase_SGNH_hydro-type_subgr

Pfam Domains:
PF13472 - GDSL-like Lipase/Acylhydrolase family

SCOP Domains:
52266 - SGNH hydrolase

ModBase Predicted Comparative 3D Structure on Q15102
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    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003847 1-alkyl-2-acetylglycerophosphocholine esterase activity
GO:0004623 phospholipase A2 activity
GO:0005515 protein binding
GO:0016787 hydrolase activity
GO:0042802 identical protein binding
GO:0046982 protein heterodimerization activity
GO:0047179 platelet-activating factor acetyltransferase activity

Biological Process:
GO:0006629 lipid metabolic process
GO:0007283 spermatogenesis
GO:0007399 nervous system development
GO:0007420 brain development
GO:0016042 lipid catabolic process

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


-  Descriptions from all associated GenBank mRNAs
  BC003016 - Homo sapiens platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa, mRNA (cDNA clone MGC:4046 IMAGE:2822228), complete cds.
GQ900969 - Homo sapiens clone HEL-T-81 epididymis secretory sperm binding protein mRNA, complete cds.
D63391 - Homo sapiens mRNA for platelet activating factor acetylhydrolase IB gamma-subunit, complete cds.
BC007863 - Homo sapiens platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa, mRNA (cDNA clone MGC:14395 IMAGE:4301185), complete cds.
JD424013 - Sequence 405037 from Patent EP1572962.
JD391792 - Sequence 372816 from Patent EP1572962.
KJ891749 - Synthetic construct Homo sapiens clone ccsbBroadEn_01143 PAFAH1B3 gene, encodes complete protein.
AB528706 - Synthetic construct DNA, clone: pF1KB6944, Homo sapiens PAFAH1B3 gene for platelet-activating factor acetylhydrolase, isoform Ib, subunit 3, without stop codon, in Flexi system.
CR407626 - Homo sapiens full open reading frame cDNA clone RZPDo834D022D for gene PAFAH1B3, platelet-activating factor acetylhydrolase, isoform Ib, gamma subunit 29kDa complete cds, without stopcodon.
JD452765 - Sequence 433789 from Patent EP1572962.
JD219317 - Sequence 200341 from Patent EP1572962.
JD555739 - Sequence 536763 from Patent EP1572962.

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

Protein Q15102 (Reactome details) participates in the following event(s):

R-HSA-8848484 PLA2s hydrolyze phospholipids at the Golgi membrane
R-HSA-6811436 COPI-independent Golgi-to-ER retrograde traffic
R-HSA-8856688 Golgi-to-ER retrograde transport
R-HSA-6811442 Intra-Golgi and retrograde Golgi-to-ER traffic
R-HSA-199991 Membrane Trafficking
R-HSA-5653656 Vesicle-mediated transport

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000262890.1, ENST00000262890.2, ENST00000262890.3, ENST00000262890.4, ENST00000262890.5, ENST00000262890.6, ENST00000262890.7, NM_002573, PA1B3_HUMAN, PAFAH1B3 , PAFAHG, Q15102, Q53X88, uc317hej.1, uc317hej.2
UCSC ID: ENST00000262890.8_7
RefSeq Accession: NM_002573.4
Protein: Q15102 (aka PA1B3_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.