Human Gene EFNA1 (ENST00000368407.8_4) from GENCODE V47lift37
  Description: ephrin A1, transcript variant 1 (from RefSeq NM_004428.3)
Gencode Transcript: ENST00000368407.8_4
Gencode Gene: ENSG00000169242.12_7
Transcript (Including UTRs)
   Position: hg19 chr1:155,100,352-155,107,375 Size: 7,024 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr1:155,100,454-155,106,543 Size: 6,090 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:155,100,352-155,107,375)mRNA (may differ from genome)Protein (205 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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-  Comments and Description Text from UniProtKB
  ID: EFNA1_HUMAN
DESCRIPTION: RecName: Full=Ephrin-A1; AltName: Full=EPH-related receptor tyrosine kinase ligand 1; Short=LERK-1; AltName: Full=Immediate early response protein B61; AltName: Full=Tumor necrosis factor alpha-induced protein 4; Short=TNF alpha-induced protein 4; Contains: RecName: Full=Ephrin-A1, secreted form; 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. Plays an important role in angiogenesis and tumor neovascularization. The recruitment of VAV2, VAV3 and PI3-kinase p85 subunit by phosphorylated EPHA2 is critical for EFNA1-induced RAC1 GTPase activation and vascular endothelial cell migration and assembly. Exerts anti-oncogenic effects in tumor cells through activation and down-regulation of EPHA2. Activates EPHA2 by inducing tyrosine phosphorylation which leads to its internalization and degradation. Acts as a negative regulator in the tumorigenesis of gliomas by down-regulating EPHA2 and FAK. Can evoke collapse of embryonic neuronal growth cone and regulates dendritic spine morphogenesis.
SUBUNIT: Monomer. Homodimer. Forms heterodimers with EPHA2. Binds to the receptor tyrosine kinases EPHA2, EPHA3, EPHA4, EPHA5, EPHA6 and EPHA7. Also binds with low affinity to EPHA1.
INTERACTION: P29317:EPHA2; NbExp=5; IntAct=EBI-715194, EBI-702104;
SUBCELLULAR LOCATION: Cell membrane; Lipid-anchor, GPI-anchor.
SUBCELLULAR LOCATION: Ephrin-A1, secreted form: Secreted.
TISSUE SPECIFICITY: Brain. Down-regulated in primary glioma tissues compared to the normal tissues. The soluble monomeric form is expressed in the glioblastoma multiforme (GBM) and breast cancer cells (at protein level).
INDUCTION: By TNF and IL1B/interleukin-1 beta.
PTM: Undergoes proteolysis by a metalloprotease to give rise to a soluble monomeric form.
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


-  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: 116.97 RPKM in Liver
Total median expression: 1002.34 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 -35.30102-0.346 Picture PostScript Text
3' UTR -297.60832-0.358 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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3CZU - X-ray MuPIT 3HEI - X-ray MuPIT 3MBW - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P20827
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:0005102 receptor binding
GO:0005515 protein binding
GO:0046875 ephrin receptor binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0001525 angiogenesis
GO:0001934 positive regulation of protein phosphorylation
GO:0003180 aortic valve morphogenesis
GO:0003183 mitral valve morphogenesis
GO:0003199 endocardial cushion to mesenchymal transition involved in heart valve formation
GO:0007267 cell-cell signaling
GO:0007411 axon guidance
GO:0010719 negative regulation of epithelial to mesenchymal transition
GO:0014028 notochord formation
GO:0016477 cell migration
GO:0030182 neuron differentiation
GO:0033628 regulation of cell adhesion mediated by integrin
GO:0034446 substrate adhesion-dependent cell spreading
GO:0043409 negative regulation of MAPK cascade
GO:0043410 positive regulation of MAPK cascade
GO:0043535 regulation of blood vessel endothelial cell migration
GO:0045765 regulation of angiogenesis
GO:0048013 ephrin receptor signaling pathway
GO:0050730 regulation of peptidyl-tyrosine phosphorylation
GO:0050731 positive regulation of peptidyl-tyrosine phosphorylation
GO:0050770 regulation of axonogenesis
GO:0050821 protein stabilization
GO:0061002 negative regulation of dendritic spine morphogenesis
GO:0061098 positive regulation of protein tyrosine kinase activity
GO:0070244 negative regulation of thymocyte apoptotic process
GO:1902004 positive regulation of beta-amyloid formation
GO:1902961 positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process
GO:1903051 negative regulation of proteolysis involved in cellular protein catabolic process

Cellular Component:
GO:0005576 extracellular region
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0031225 anchored component of membrane
GO:0046658 anchored component of plasma membrane


-  Descriptions from all associated GenBank mRNAs
  KJ896749 - Synthetic construct Homo sapiens clone ccsbBroadEn_06143 EFNA1 gene, encodes complete protein.
AK057845 - Homo sapiens cDNA FLJ25116 fis, clone CBR05731, highly similar to EPHRIN-A1 PRECURSOR.
AK313117 - Homo sapiens cDNA, FLJ93602, highly similar to Homo sapiens ephrin-A1 (EFNA1), mRNA.
AK308965 - Homo sapiens cDNA, FLJ99006.
AK289589 - Homo sapiens cDNA FLJ75959 complete cds, highly similar to Homo sapiens ephrin-A1 (EFNA1), transcript variant 2, mRNA.
AL833641 - Homo sapiens mRNA; cDNA DKFZp686M0979 (from clone DKFZp686M0979).
AK311677 - Homo sapiens cDNA, FLJ18719.
BC032698 - Homo sapiens ephrin-A1, mRNA (cDNA clone MGC:45272 IMAGE:5402648), complete cds.
GQ901005 - Homo sapiens clone HEL-T-117 epididymis secretory sperm binding protein mRNA, complete cds.
BC095432 - Homo sapiens ephrin-A1, mRNA (cDNA clone MGC:111106 IMAGE:30376031), complete cds.
M57730 - Human B61 mRNA, complete cds.
CR457416 - Homo sapiens full open reading frame cDNA clone RZPDo834E1110D for gene EFNA1, ephrin-A1; complete cds, incl. stopcodon.
DQ890722 - Synthetic construct clone IMAGE:100003352; FLH165465.01X; RZPDo839C08160D ephrin-A1 (EFNA1) gene, encodes complete protein.
DQ893900 - Synthetic construct Homo sapiens clone IMAGE:100008360; FLH165461.01L; RZPDo839C08159D ephrin-A1 (EFNA1) gene, encodes complete protein.
BC150578 - Homo sapiens cDNA clone IMAGE:40133066.
JD496142 - Sequence 477166 from Patent EP1572962.
JD189084 - Sequence 170108 from Patent EP1572962.
JD502647 - Sequence 483671 from Patent EP1572962.
JD445400 - Sequence 426424 from Patent EP1572962.
JD342916 - Sequence 323940 from Patent EP1572962.
JD297038 - Sequence 278062 from Patent EP1572962.
JD387546 - Sequence 368570 from Patent EP1572962.
JD387547 - Sequence 368571 from Patent EP1572962.
JD340201 - Sequence 321225 from Patent EP1572962.
JD127556 - Sequence 108580 from Patent EP1572962.
JD137225 - Sequence 118249 from Patent EP1572962.
JD508235 - Sequence 489259 from Patent EP1572962.
JD467265 - Sequence 448289 from Patent EP1572962.
JD485733 - Sequence 466757 from Patent EP1572962.
JD137077 - Sequence 118101 from Patent EP1572962.

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

Protein P20827 (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: D3DV86, EFNA1_HUMAN, ENST00000368407.1, ENST00000368407.2, ENST00000368407.3, ENST00000368407.4, ENST00000368407.5, ENST00000368407.6, ENST00000368407.7, EPLG1, LERK1, NM_004428, P20827, Q5SR60, Q5SR61, Q6I9T9, Q8N578, TNFAIP4, uc318gsw.1, uc318gsw.2
UCSC ID: ENST00000368407.8_4
RefSeq Accession: NM_004428.3
Protein: P20827 (aka EFNA1_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.