Human Gene GNPAT (uc009xfp.3)
  Description: Homo sapiens glyceronephosphate O-acyltransferase (GNPAT), mRNA.
RefSeq Summary (NM_014236): This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015].
Transcript (Including UTRs)
   Position: hg19 chr1:231,376,919-231,413,719 Size: 36,801 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr1:231,377,125-231,413,288 Size: 36,164 Coding Exon Count: 15 

Page IndexSequence and LinksPrimersGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:231,376,919-231,413,719)mRNA (may differ from genome)Protein (619 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
OMIMPubMedTreefamUniProtKBBioGrid CRISPR DB

-  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): GNPAT
CDC HuGE Published Literature: GNPAT

-  MalaCards Disease Associations
  MalaCards Gene Search: GNPAT
Diseases sorted by gene-association score: rhizomelic chondrodysplasia punctata, type 2* (1689), rhizomelic chondrodysplasia punctata (42), peroxisomal disease (25), peroxisome disorders (21), chondrodysplasia punctata syndrome (17), chondrodysplasia punctata, x-linked dominant (12), rhizomelic chondrodysplasia punctata, type 3 (10), zellweger syndrome (9), child syndrome (9), rhizomelic chondrodysplasia punctata, type 5 (8), rhizomelic chondrodysplasia punctata, type 1 (7), refsum disease (6), peroxisome biogenesis disorder 1b (4)
* = Manually curated disease association

-  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: 30.25 RPKM in Muscle - Skeletal
Total median expression: 750.53 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 -88.10206-0.428 Picture PostScript Text
3' UTR -98.40431-0.228 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
IPR022284 - G3P_O-AcylTrfase

Pfam Domains:
PF01553 - Acyltransferase

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

ModBase Predicted Comparative 3D Structure on B4DNM9
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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  AK023953 - Homo sapiens cDNA FLJ13891 fis, clone THYRO1001617, highly similar to Dihydroxyacetone phosphate acyltransferase (EC 2.3.1.42).
AK314181 - Homo sapiens cDNA, FLJ94903, highly similar to Homo sapiens glyceronephosphate O-acyltransferase (GNPAT), mRNA.
AK297982 - Homo sapiens cDNA FLJ53146 complete cds, highly similar to Dihydroxyacetone phosphate acyltransferase(EC 2.3.1.42).
AK223304 - Homo sapiens mRNA for glyceronephosphate O-acyltransferase variant, clone: TMS03217.
AK309994 - Homo sapiens cDNA, FLJ17036.
AK222773 - Homo sapiens mRNA for glyceronephosphate O-acyltransferase variant, clone: HEP01035.
AJ002190 - Homo sapiens cDNA for dihydroxyacetone phosphate acyltransferase (DAP-AT).
AB209882 - Homo sapiens mRNA for glyceronephosphate O-acyltransferase variant protein.
JD476385 - Sequence 457409 from Patent EP1572962.
AF043937 - Homo sapiens peroxisomal acyl-CoA:dihydroxyacetonephosphate acyltransferase (DHAPAT) mRNA, complete cds.
BC000450 - Homo sapiens glyceronephosphate O-acyltransferase, mRNA (cDNA clone MGC:8450 IMAGE:2821393), complete cds.
AK311386 - Homo sapiens cDNA, FLJ18428.
JD019295 - Sequence 319 from Patent EP1572962.
JD030584 - Sequence 11608 from Patent EP1572962.
JD020838 - Sequence 1862 from Patent EP1572962.
AF035285 - Homo sapiens clone 23729 dihydroxyacetone phosphate acyltransferase mRNA, partial cds.
JD022694 - Sequence 3718 from Patent EP1572962.
JD023843 - Sequence 4867 from Patent EP1572962.
JD433804 - Sequence 414828 from Patent EP1572962.
JD094551 - Sequence 75575 from Patent EP1572962.
JD254248 - Sequence 235272 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00564 - Glycerophospholipid metabolism
hsa04146 - Peroxisome

-  Other Names for This Gene
  Alternate Gene Symbols: AK297982, B4DNM9, B4DNM9_HUMAN, NM_014236, NP_055051
UCSC ID: uc009xfp.3
RefSeq Accession: NM_014236
Protein: B4DNM9

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: AK297982.1
exon count: 15CDS single in 3' UTR: no RNA size: 2076
ORF size: 1860CDS single in intron: no Alignment % ID: 99.86
txCdsPredict score: 3786.50frame 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.