Human Gene EPHA3 (uc003dqx.1)
  Description: Homo sapiens EPH receptor A3 (EPHA3), transcript variant 2, mRNA.
RefSeq Summary (NM_182644): This gene belongs to the ephrin receptor subfamily of the protein-tyrosine kinase family. EPH and EPH-related receptors have been implicated in mediating developmental events, particularly in the nervous system. Receptors in the EPH subfamily typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. This gene encodes a protein that binds ephrin-A ligands. Two alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Jul 2008].
Transcript (Including UTRs)
   Position: hg19 chr3:89,156,674-89,449,495 Size: 292,822 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr3:89,156,899-89,448,656 Size: 291,758 Coding Exon Count: 7 

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 (chr3:89,156,674-89,449,495)mRNA (may differ from genome)Protein (539 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCLynxMalacardsMGIOMIM
PubMedReactomeUniProtKBWikipediaBioGrid 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): EPHA3
CDC HuGE Published Literature: EPHA3
Positive Disease Associations: Cholesterol, HDL , Neuroblastoma , Triglycerides
Related Studies:
  1. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
  2. Neuroblastoma
    John M Maris et al. The New England journal of medicine 2008, Chromosome 6p22 locus associated with clinically aggressive neuroblastoma., The New England journal of medicine. [PubMed 18463370]
    A common genetic variation at chromosome band 6p22 is associated with susceptibility to neuroblastoma.
  3. Neuroblastoma
    John M Maris et al. The New England journal of medicine 2008, Chromosome 6p22 locus associated with clinically aggressive neuroblastoma., The New England journal of medicine. [PubMed 18463370]
    A common genetic variation at chromosome band 6p22 is associated with susceptibility to neuroblastoma.
           more ... click here to view the complete list

-  MalaCards Disease Associations
  MalaCards Gene Search: EPHA3
Diseases sorted by gene-association score: kummell's disease (12), beriberi (12), ariboflavinosis (9), myelophthisic anemia (7), pseudohypoaldosteronism, type i (7), lung large cell carcinoma (6), colorectal cancer (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: 8.82 RPKM in Prostate
Total median expression: 80.00 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 -78.44225-0.349 Picture PostScript Text
3' UTR -202.65839-0.242 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
  Pfam Domains:
PF00041 - Fibronectin type III domain
PF01404 - Ephrin receptor ligand binding domain
PF07699 - Putative ephrin-receptor like

SCOP Domains:
49265 - Fibronectin type III
49785 - Galactose-binding domain-like
57184 - Growth factor receptor domain

ModBase Predicted Comparative 3D Structure on P29320-2
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
  AF213459 - Homo sapiens ephrin receptor EPHA3 complete form (EPHA3) mRNA, complete cds.
BC063282 - Homo sapiens EPH receptor A3, mRNA (cDNA clone MGC:71556 IMAGE:30347891), complete cds.
M83941 - Human receptor tyrosine kinase (HEK) mRNA, complete cds.
AF213460 - Homo sapiens ephrin receptor EPHA3 secreted form (EPHA3) mRNA, complete cds.
BC026247 - Homo sapiens cDNA clone IMAGE:4720840, containing frame-shift errors.
AK291411 - Homo sapiens cDNA FLJ77258 complete cds, highly similar to Homo sapiens EPH receptor A3 (EPHA3), transcript variant 1, mRNA.
HM005377 - Homo sapiens clone HTL-T-64 testicular tissue protein Li 64 mRNA, complete cds.
AB384708 - Synthetic construct DNA, clone: pF1KB1569, Homo sapiens EPHA3 gene for ephrin type-A receptor 3 precursor, complete cds, without stop codon, in Flexi system.
KJ896774 - Synthetic construct Homo sapiens clone ccsbBroadEn_06168 EPHA3 gene, encodes complete protein.
JD198932 - Sequence 179956 from Patent EP1572962.
JD436158 - Sequence 417182 from Patent EP1572962.
JD226471 - Sequence 207495 from Patent EP1572962.
JD140444 - Sequence 121468 from Patent EP1572962.
JD271735 - Sequence 252759 from Patent EP1572962.
JD464712 - Sequence 445736 from Patent EP1572962.
HM437236 - Homo sapiens ephrin type-A receptor 3 variant (EPHA3) mRNA, partial cds.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04360 - Axon guidance

Reactome (by CSHL, EBI, and GO)

Protein P29320 (Reactome details) participates in the following event(s):

R-HSA-3928646 EPHAs bind EFNAs
R-HSA-3928597 EPH:EFN dimers tetramerise
R-HSA-2682334 EPH-Ephrin signaling
R-HSA-3928665 EPH-ephrin mediated repulsion of cells
R-HSA-422475 Axon guidance
R-HSA-1266738 Developmental Biology

-  Other Names for This Gene
  Alternate Gene Symbols: ETK, ETK1, HEK, NM_182644, NP_872585, P29320-2, TYRO4
UCSC ID: uc003dqx.1
RefSeq Accession: NM_182644
Protein: P29320-2, splice isoform of P29320 CCDS: CCDS46875.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_182644.2
exon count: 7CDS single in 3' UTR: no RNA size: 2684
ORF size: 1620CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3346.00frame 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: 865# 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.