Human Gene EFNA3 (ENST00000368408.4_4) from GENCODE V47lift37
  Description: ephrin A3 (from RefSeq NM_004952.5)
Gencode Transcript: ENST00000368408.4_4
Gencode Gene: ENSG00000143590.14_8
Transcript (Including UTRs)
   Position: hg19 chr1:155,051,313-155,060,014 Size: 8,702 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr1:155,051,418-155,059,019 Size: 7,602 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 (chr1:155,051,313-155,060,014)mRNA (may differ from genome)Protein (238 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: EFNA3_HUMAN
DESCRIPTION: RecName: Full=Ephrin-A3; AltName: Full=EFL-2; AltName: Full=EHK1 ligand; Short=EHK1-L; AltName: Full=EPH-related receptor tyrosine kinase ligand 3; Short=LERK-3; Flags: Precursor;
FUNCTION: Cell surface GPI-bound ligand for Eph receptors, a family of receptor tyrosine kinases which are crucial for migration, repulsion and adhesion during neuronal, vascular and epithelial development. Binds promiscuously Eph receptors residing on adjacent cells, leading to contact-dependent bidirectional signaling into neighboring cells. The signaling pathway downstream of the receptor is referred to as forward signaling while the signaling pathway downstream of the ephrin ligand is referred to as reverse signaling (By similarity).
SUBUNIT: Interacts with EPHA8; activates EPHA8.
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor, GPI-anchor.
TISSUE SPECIFICITY: Expressed in brain, skeletal muscle, spleen, thymus, prostate, testis, ovary, small intestine, and peripheral blood leukocytes.
SIMILARITY: Belongs to the ephrin family.
SIMILARITY: Contains 1 ephrin RBD (ephrin receptor-binding) domain.

-  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: EFNA3
Diseases sorted by gene-association score: androgenic alopecia (13)

-  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: 10.94 RPKM in Skin - Sun Exposed (Lower leg)
Total median expression: 38.67 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 -45.60105-0.434 Picture PostScript Text
3' UTR -386.20995-0.388 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
IPR008972 - Cupredoxin
IPR001799 - Ephrin
IPR019765 - Ephrin_CS

Pfam Domains:
PF00812 - Ephrin

SCOP Domains:
49503 - Cupredoxins

ModBase Predicted Comparative 3D Structure on P52797
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    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005005 transmembrane-ephrin receptor activity
GO:0005515 protein binding
GO:0046875 ephrin receptor binding

Biological Process:
GO:0007267 cell-cell signaling
GO:0007411 axon guidance
GO:0016525 negative regulation of angiogenesis
GO:0045664 regulation of neuron differentiation
GO:0048013 ephrin receptor signaling pathway
GO:1902961 positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0031225 anchored component of membrane


-  Descriptions from all associated GenBank mRNAs
  AK301966 - Homo sapiens cDNA FLJ57652 complete cds, highly similar to Ephrin-A3 precursor.
LF206180 - JP 2014500723-A/13683: Polycomb-Associated Non-Coding RNAs.
BC017722 - Homo sapiens ephrin-A3, mRNA (cDNA clone MGC:21335 IMAGE:4397263), complete cds.
BC110406 - Homo sapiens ephrin-A3, mRNA (cDNA clone MGC:102749 IMAGE:5732044), complete cds.
U14187 - Homo sapiens LERK-3 (EPLG3) mRNA, complete cds.
AK296030 - Homo sapiens cDNA FLJ59263 complete cds, highly similar to Ephrin-A3 precursor.
AK316248 - Homo sapiens cDNA, FLJ79147 complete cds, highly similar to Ephrin-A3 precursor.
L37360 - Homo sapiens (clone hEHK1-L) EHK1 receptor tyrosine kinase ligand (EFL-2) mRNA, complete cds.
DQ894854 - Synthetic construct Homo sapiens clone IMAGE:100009314; FLH179125.01L; RZPDo839D02129D ephrin-A3 (EFNA3) gene, encodes complete protein.
DQ891668 - Synthetic construct clone IMAGE:100004298; FLH179129.01X; RZPDo839D02130D ephrin-A3 (EFNA3) gene, encodes complete protein.
LF206181 - JP 2014500723-A/13684: Polycomb-Associated Non-Coding RNAs.
MA441757 - JP 2018138019-A/13683: Polycomb-Associated Non-Coding RNAs.
MA441758 - JP 2018138019-A/13684: Polycomb-Associated Non-Coding RNAs.
LF211907 - JP 2014500723-A/19410: Polycomb-Associated Non-Coding RNAs.
LF352221 - JP 2014500723-A/159724: Polycomb-Associated Non-Coding RNAs.
JD459038 - Sequence 440062 from Patent EP1572962.
LF352220 - JP 2014500723-A/159723: Polycomb-Associated Non-Coding RNAs.
LF352219 - JP 2014500723-A/159722: Polycomb-Associated Non-Coding RNAs.
MA587798 - JP 2018138019-A/159724: Polycomb-Associated Non-Coding RNAs.
MA587797 - JP 2018138019-A/159723: Polycomb-Associated Non-Coding RNAs.
MA587796 - JP 2018138019-A/159722: Polycomb-Associated Non-Coding RNAs.
MA447484 - JP 2018138019-A/19410: Polycomb-Associated Non-Coding RNAs.
JD485336 - Sequence 466360 from Patent EP1572962.
JD544129 - Sequence 525153 from Patent EP1572962.
JD045299 - Sequence 26323 from Patent EP1572962.
JD398426 - Sequence 379450 from Patent EP1572962.
JD081497 - Sequence 62521 from Patent EP1572962.
JD519600 - Sequence 500624 from Patent EP1572962.
JD498305 - Sequence 479329 from Patent EP1572962.
JD365657 - Sequence 346681 from Patent EP1572962.
JD061732 - Sequence 42756 from Patent EP1572962.
JD052897 - Sequence 33921 from Patent EP1572962.
JD537091 - Sequence 518115 from Patent EP1572962.
JD558120 - Sequence 539144 from Patent EP1572962.
JD301137 - Sequence 282161 from Patent EP1572962.
LF352218 - JP 2014500723-A/159721: Polycomb-Associated Non-Coding RNAs.
JD134155 - Sequence 115179 from Patent EP1572962.
JD403116 - Sequence 384140 from Patent EP1572962.
MA587795 - JP 2018138019-A/159721: Polycomb-Associated Non-Coding RNAs.

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

Protein P52797 (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: B7ZAD3, D3DV85, EFL2, EFNA3_HUMAN, ENST00000368408.1, ENST00000368408.2, ENST00000368408.3, EPLG3, LERK3, NM_004952, P52797, Q0VGC9, Q5SR70, uc318gsx.1, uc318gsx.2
UCSC ID: ENST00000368408.4_4
RefSeq Accession: NM_004952.5
Protein: P52797 (aka EFNA3_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.