EFNB3, a member of the ephrin gene family, is important in brain development as well as in its maintenance. Moreover, since levels of EFNB3 expression were particularly high in several forebrain subregions compared to other brain subregions, it may play a pivotal role in forebrain function. The EPH and EPH-related receptors comprise the largest subfamily of receptor protein-t... See more...

Aliases for EFNB3 Gene

Aliases for EFNB3 Gene

  • Ephrin B3 2 3 5
  • Ephrin-B3 2 3 4
  • EPH-Related Receptor Transmembrane Ligand ELK-L3 3 4
  • EPH-Related Receptor Tyrosine Kinase Ligand 8 2 4
  • EPLG8 3 4
  • LERK8 3 4
  • Eph-Related Receptor Tyrosine Kinase Ligand 8 3
  • LERK-8 4
  • EFL6 3

External Ids for EFNB3 Gene

Previous HGNC Symbols for EFNB3 Gene

  • EPLG8

Previous GeneCards Identifiers for EFNB3 Gene

  • GC17U990024
  • GC17P008348
  • GC17P007551
  • GC17P007809
  • GC17P007549
  • GC17P007608
  • GC17P007501
  • GC17P007706
  • GC17P007828
  • GC17P007850
  • GC17P007879
  • GC17P007709
  • GC17P007738
  • GC17P007767
  • GC17P007795

Summaries for EFNB3 Gene

Entrez Gene Summary for EFNB3 Gene

  • EFNB3, a member of the ephrin gene family, is important in brain development as well as in its maintenance. Moreover, since levels of EFNB3 expression were particularly high in several forebrain subregions compared to other brain subregions, it may play a pivotal role in forebrain function. The EPH and EPH-related receptors comprise the largest subfamily of receptor protein-tyrosine kinases and have been implicated in mediating developmental events, particularly in the nervous system. EPH Receptors typically have a single kinase domain and an extracellular region containing a Cys-rich domain and 2 fibronectin type III repeats. The ephrin ligands and receptors have been named by the Eph Nomenclature Committee (1997). Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. The Eph family of receptors are similarly divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. [provided by RefSeq, Jul 2008]

GeneCards Summary for EFNB3 Gene

EFNB3 (Ephrin B3) is a Protein Coding gene. Diseases associated with EFNB3 include Abnormal Retinal Correspondence and Binocular Vision Disease. Among its related pathways are EPH-Ephrin signaling and EphB-EphrinB Signaling. Gene Ontology (GO) annotations related to this gene include ephrin receptor binding and transmembrane-ephrin receptor activity. An important paralog of this gene is EFNB1.

UniProtKB/Swiss-Prot Summary for EFNB3 Gene

  • Cell surface transmembrane 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. May play a pivotal role in forebrain function. Binds to, and induce the collapse of, commissural axons/growth cones in vitro. May play a role in constraining the orientation of longitudinally projecting axons (By similarity).
  • (Microbial infection) Acts as a receptor for nipah virus and hendra virus.

Gene Wiki entry for EFNB3 Gene

Additional gene information for EFNB3 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for EFNB3 Gene

Genomics for EFNB3 Gene

GeneHancer (GH) Regulatory Elements for EFNB3 Gene

Promoters and enhancers for EFNB3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J007703 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 512.2 -0.5 -519 4 ZNF217 EP300 TCF12 USF1 TEAD4 ZNF10 ZIC2 ZBTB10 ZBTB26 SAP30 EFNB3 lnc-TP53-1 WRAP53 piR-32020
GH17J007715 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE CraniofacialAtlas 19 +11.5 11540 3.3 ZNF217 EP300 CTCF TCF12 NRF1 PHF8 TEAD4 ZNF639 ZNF10 ZIC2 DNAH2 lnc-TP53-2 DVL2 CTC1 SNORD10 CNTROB SNORA48 WRAP53 PFAS POLR2A
GH17J007625 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas 11 -77.0 -76979 5.8 EP300 TCF12 USF1 POLR2G SP1 PHF8 TEAD4 ZBTB5 ZIC2 KDM6A SAT2 lnc-SAT2-2 SHBG CHRNB1 DVL2 TP53 WRAP53 CYB5D1 EFNB3 SENP3
GH17J007684 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 10.1 -18.1 -18095 6.2 RXRA FOXK2 ZBTB40 ZNF217 EP300 CTCF TCF12 SIN3A MYC USF1 TP53 WRAP53 lnc-EFNB3-1 piR-32020 lnc-SAT2-1 lnc-SAT2-3 DNAH2 ATP1B2 EFNB3 ALOX15B
GH17J007613 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 11 -90.9 -90897 3.4 EP300 CTCF ZSCAN5C MYC NRF1 POLR2G SP1 PHF8 TEAD4 ZFX FXR2 SHBG TP53 CNTROB TNFSF12 SNORD10 SNORA48 MIR324 PFAS CTC1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around EFNB3 on UCSC Golden Path with GeneCards custom track

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for EFNB3

Top Transcription factor binding sites by QIAGEN in the EFNB3 gene promoter:
  • C/EBPbeta
  • E2F
  • E2F-1
  • E2F-2
  • E2F-3a
  • Sp1

Genomic Locations for EFNB3 Gene

Genomic Locations for EFNB3 Gene
chr17:7,705,202-7,711,375
(GRCh38/hg38)
Size:
6,174 bases
Orientation:
Plus strand
chr17:7,608,520-7,614,696
(GRCh37/hg19)
Size:
6,177 bases
Orientation:
Plus strand

Genomic View for EFNB3 Gene

Genes around EFNB3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EFNB3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EFNB3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EFNB3 Gene

Proteins for EFNB3 Gene

  • Protein details for EFNB3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q15768-EFNB3_HUMAN
    Recommended name:
    Ephrin-B3
    Protein Accession:
    Q15768
    Secondary Accessions:
    • B2RBW2
    • D3DTQ6
    • O00680
    • Q8TBH7
    • Q92875

    Protein attributes for EFNB3 Gene

    Size:
    340 amino acids
    Molecular mass:
    35835 Da
    Quaternary structure:
    • Interacts with GRIP1 and GRIP2.
    • (Microbial infection) Interacts with nipah virus and hendra virus glycoprotein (PubMed:16477309, PubMed:17376907).

    Three dimensional structures from OCA and Proteopedia for EFNB3 Gene

neXtProt entry for EFNB3 Gene

Post-translational modifications for EFNB3 Gene

  • Glycosylation at Asn210
  • Modification sites at PhosphoSitePlus

Other Protein References for EFNB3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EFNB3 Gene

Domains & Families for EFNB3 Gene

Gene Families for EFNB3 Gene

HGNC:
Human Protein Atlas (HPA):
  • Cancer-related genes
  • Predicted membrane proteins

Protein Domains for EFNB3 Gene

Blocks:
  • Ephrin signature
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for EFNB3 Gene

GenScript: Design optimal peptide antigens:
  • EPH-related receptor tyrosine kinase ligand 8 (EFNB3_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q15768

UniProtKB/Swiss-Prot:

EFNB3_HUMAN :
  • Belongs to the ephrin family.
Family:
  • Belongs to the ephrin family.
genes like me logo Genes that share domains with EFNB3: view

Function for EFNB3 Gene

Molecular function for EFNB3 Gene

UniProtKB/Swiss-Prot Function:
Cell surface transmembrane 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. May play a pivotal role in forebrain function. Binds to, and induce the collapse of, commissural axons/growth cones in vitro. May play a role in constraining the orientation of longitudinally projecting axons (By similarity).
UniProtKB/Swiss-Prot Function:
(Microbial infection) Acts as a receptor for nipah virus and hendra virus.
GENATLAS Biochemistry:
ephrin B-3,eph-related receptor tyrosine kinase,class B,ligand,involved in short-range contact-mediated axonal guidance,expressed in fetal brain,and in adult forebrain

Phenotypes From GWAS Catalog for EFNB3 Gene

Gene Ontology (GO) - Molecular Function for EFNB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001618 virus receptor activity IEA --
GO:0005005 transmembrane-ephrin receptor activity TAS 9126477
GO:0005515 protein binding IPI 23812375
GO:0046875 ephrin receptor binding IDA 8808709
genes like me logo Genes that share ontologies with EFNB3: view
genes like me logo Genes that share phenotypes with EFNB3: view

Animal Models for EFNB3 Gene

MGI Knock Outs for EFNB3:

Animal Model Products

CRISPR Products

miRNA for EFNB3 Gene

miRTarBase miRNAs that target EFNB3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for EFNB3 Gene

Localization for EFNB3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EFNB3 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for EFNB3 gene
Compartment Confidence
plasma membrane 5
extracellular 3
nucleus 3
cytoskeleton 2
endoplasmic reticulum 2
mitochondrion 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for EFNB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS,IDA --
GO:0005887 integral component of plasma membrane TAS 9126477
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0098686 hippocampal mossy fiber to CA3 synapse IEA --
genes like me logo Genes that share ontologies with EFNB3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for EFNB3 Gene

Pathways & Interactions for EFNB3 Gene

PathCards logo

SuperPathways for EFNB3 Gene

SuperPathway Contained pathways
1 EPH-Ephrin signaling
.35
2 EphB-EphrinB Signaling
.58
.58
.33
3 Developmental Biology
4 Angiogenesis (CST)
5 Tyrosine Kinases / Adaptors
genes like me logo Genes that share pathways with EFNB3: view

Pathways by source for EFNB3 Gene

1 BioSystems pathway for EFNB3 Gene
1 KEGG pathway for EFNB3 Gene
2 GeneGo (Thomson Reuters) pathways for EFNB3 Gene
  • Cell adhesion Ephrins signaling
  • Cytoskeleton remodeling Reverse signaling by ephrin B
2 Qiagen pathways for EFNB3 Gene
  • EphB-EphrinB Signaling
  • Ephrin-Eph Signaling
2 Cell Signaling Technology pathways for EFNB3 Gene

SIGNOR curated interactions for EFNB3 Gene

Activates:

Gene Ontology (GO) - Biological Process for EFNB3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007267 cell-cell signaling TAS 9126477
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development TAS 9126477
GO:0007411 axon guidance IBA,IEA 21873635
GO:0007628 adult walking behavior IEA --
genes like me logo Genes that share ontologies with EFNB3: view

Drugs & Compounds for EFNB3 Gene

(1) Drugs for EFNB3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with EFNB3: view

Transcripts for EFNB3 Gene

mRNA/cDNA for EFNB3 Gene

1 REFSEQ mRNAs :
9 NCBI additional mRNA sequence :
1 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for EFNB3 Gene

No ASD Table

Relevant External Links for EFNB3 Gene

GeneLoc Exon Structure for
EFNB3

Expression for EFNB3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EFNB3 Gene

mRNA differential expression in normal tissues according to GTEx for EFNB3 Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x6.5), Brain - Anterior cingulate cortex (BA24) (x5.3), Brain - Cortex (x4.9), Brain - Hypothalamus (x4.9), Brain - Frontal Cortex (BA9) (x4.4), and Brain - Caudate (basal ganglia) (x4.1).

Protein differential expression in normal tissues from HIPED for EFNB3 Gene

This gene is overexpressed in Bone (35.7), Pancreatic juice (12.2), Fetal Brain (12.2), and Platelet (8.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for EFNB3 Gene



Protein tissue co-expression partners for EFNB3 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for EFNB3

SOURCE GeneReport for Unigene cluster for EFNB3 Gene:

Hs.26988

mRNA Expression by UniProt/SwissProt for EFNB3 Gene:

Q15768-EFNB3_HUMAN
Tissue specificity: Highly expressed in brain; expressed in embryonic floor plate, roof plate and hindbrain segments.

Evidence on tissue expression from TISSUES for EFNB3 Gene

  • Nervous system(4.8)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with EFNB3: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for EFNB3 Gene

Orthologs for EFNB3 Gene

This gene was present in the common ancestor of animals.

Orthologs for EFNB3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EFNB3 31
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia EFNB3 31 30
  • 94.71 (n)
OneToOne
dog
(Canis familiaris)
Mammalia EFNB3 31 30
  • 93.43 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Efnb3 30
  • 93.43 (n)
mouse
(Mus musculus)
Mammalia Efnb3 17 31 30
  • 91.96 (n)
oppossum
(Monodelphis domestica)
Mammalia EFNB3 31
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia EFNB3 31
  • 57 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia efnb3 30
  • 62.64 (n)
African clawed frog
(Xenopus laevis)
Amphibia efnb3-A 30
zebrafish
(Danio rerio)
Actinopterygii efnb3b 31 30
  • 60 (n)
OneToMany
efnb3a 31
  • 50 (a)
OneToMany
efnb3 30
fruit fly
(Drosophila melanogaster)
Insecta Ephrin 31
  • 10 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea efn-3 31
  • 29 (a)
ManyToMany
efn-2 31
  • 26 (a)
ManyToMany
vab-2 31
  • 24 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7000 31
  • 25 (a)
OneToMany
Species where no ortholog for EFNB3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for EFNB3 Gene

ENSEMBL:
Gene Tree for EFNB3 (if available)
TreeFam:
Gene Tree for EFNB3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for EFNB3: view image

Paralogs for EFNB3 Gene

Paralogs for EFNB3 Gene

(2) SIMAP similar genes for EFNB3 Gene using alignment to 1 proteins:

  • EFNB3_HUMAN
genes like me logo Genes that share paralogs with EFNB3: view

Variants for EFNB3 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for EFNB3 Gene

SNP ID Clinical significance and condition Chr 17 pos Variation AA Info Type
VAR_002356 - p.Arg166Gln

Additional dbSNP identifiers (rs#s) for EFNB3 Gene

Structural Variations from Database of Genomic Variants (DGV) for EFNB3 Gene

Variant ID Type Subtype PubMed ID
nsv952119 CNV deletion 24416366

Variation tolerance for EFNB3 Gene

Residual Variation Intolerance Score: 22.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.99; 36.73% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EFNB3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EFNB3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EFNB3 Gene

Disorders for EFNB3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for EFNB3 Gene - From: DISEASES and Novoseek

Disorder Aliases PubMed IDs
abnormal retinal correspondence
binocular vision disease
  • simultaneous visual perception without fusion
brain cancer
  • adult brain tumor
- elite association - COSMIC cancer census association via MalaCards
Search EFNB3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for EFNB3

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with EFNB3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EFNB3 Gene

Publications for EFNB3 Gene

  1. cDNA cloning, chromosomal localization, and expression pattern of EPLG8, a new member of the EPLG gene family encoding ligands of EPH-related protein-tyrosine kinase receptors. (PMID: 9126477) Tang XX … Ikegaki N (Genomics 1997) 2 3 4 23 54
  2. Genetic susceptibility to distinct bladder cancer subphenotypes. (PMID: 19692168) Guey LT … EPICURO/Spanish Bladder Cancer Study investigators (European urology 2010) 3 41 54
  3. Polymorphisms in innate immunity genes and lung cancer risk in Xuanwei, China. (PMID: 19170196) Shen M … Lan Q (Environmental and molecular mutagenesis 2009) 3 41 54
  4. Pathway-based evaluation of 380 candidate genes and lung cancer susceptibility suggests the importance of the cell cycle pathway. (PMID: 18676680) Hosgood HD … Lan Q (Carcinogenesis 2008) 3 41 54
  5. Two key residues in ephrinB3 are critical for its use as an alternative receptor for Nipah virus. (PMID: 16477309) Negrete OA … Lee B (PLoS pathogens 2006) 3 4 54

Products for EFNB3 Gene

  • Boster Bio Antibodies for EFNB3
  • Boster Bio ELISA Kits for EFNB3

Sources for EFNB3 Gene