Human Gene ETNK1 (uc001rfs.3)
  Description: Homo sapiens ethanolamine kinase 1 (ETNK1), transcript variant 2, mRNA.
RefSeq Summary (NM_001039481): This gene encodes an ethanolamine kinase, which functions in the first committed step of the phosphatidylethanolamine synthesis pathway. This cytosolic enzyme is specific for ethanolamine and exhibits negligible kinase activity on choline. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr12:22,778,076-22,797,349 Size: 19,274 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr12:22,778,098-22,797,238 Size: 19,141 Coding Exon Count: 3 

Page IndexSequence and LinksPrimersGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:22,778,076-22,797,349)mRNA (may differ from genome)Protein (258 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
H-INVHGNCLynxMGIOMIMPubMed
TreefamUniProtKBBioGrid 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): ETNK1
CDC HuGE Published Literature: ETNK1
Positive Disease Associations: von Willebrand Factor
Related Studies:
  1. von Willebrand Factor
    Qiong Yang et al. BMC medical genetics 2007, Genome-wide association and linkage analyses of hemostatic factors and hematological phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903294]
    Using genome-wide association methodology, we have successfully identified a SNP in complete LD with a sequence variant previously shown to be strongly associated with factor VII, providing proof of principle for this approach. Further study of additional strongly associated SNPs and linked regions may identify novel variants that influence the inter-individual variability in hemostatic factors and hematological phenotypes.

-  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: 15.32 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 388.91 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 -2.8022-0.127 Picture PostScript Text
3' UTR -13.30111-0.120 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
IPR026712 - Cho/Etha_kinase
IPR011009 - Kinase-like_dom

Pfam Domains:
PF01633 - Choline/ethanolamine kinase

SCOP Domains:
56112 - Protein kinase-like (PK-like)

ModBase Predicted Comparative 3D Structure on G5E969
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     
      
      
      

-  Descriptions from all associated GenBank mRNAs
  AF207600 - Homo sapiens ethanolamine kinase (EKI1) mRNA, complete cds.
BC066907 - Homo sapiens ethanolamine kinase 1, mRNA (cDNA clone MGC:87084 IMAGE:5260109), complete cds.
JF432382 - Synthetic construct Homo sapiens clone IMAGE:100073582 ethanolamine kinase 1 (ETNK1) gene, encodes complete protein.
KJ894197 - Synthetic construct Homo sapiens clone ccsbBroadEn_03591 ETNK1 gene, encodes complete protein.
KJ905497 - Synthetic construct Homo sapiens clone ccsbBroadEn_15099 ETNK1 gene, encodes complete protein.
AL137750 - Homo sapiens mRNA; cDNA DKFZp434E1212 (from clone DKFZp434E1212).
AK074425 - Homo sapiens cDNA FLJ23845 fis, clone KAT08096, highly similar to Homo sapiens ethanolamine kinase (EKI1) mRNA.
CU688188 - Synthetic construct Homo sapiens gateway clone IMAGE:100021204 5' read ETNK1 mRNA.
BC006111 - Homo sapiens ethanolamine kinase 1, mRNA (cDNA clone IMAGE:3163490), partial cds.
KJ906228 - Synthetic construct Homo sapiens clone ccsbBroadEn_15898 ETNK1 gene, encodes complete protein.
BT007084 - Homo sapiens ethanolamine kinase mRNA, complete cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00564 - Glycerophospholipid metabolism
hsa01100 - Metabolic pathways

-  Other Names for This Gene
  Alternate Gene Symbols: G5E969, G5E969_HUMAN, hCG_22726, NM_001039481, NP_001034570
UCSC ID: uc001rfs.3
RefSeq Accession: NM_001039481
Protein: G5E969 CCDS: CCDS41760.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001039481.1
exon count: 3CDS single in 3' UTR: no RNA size: 910
ORF size: 777CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1250.00frame 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.