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Aliases for EFNB1 Gene

Aliases for EFNB1 Gene

  • Ephrin B1 2 3 5
  • ELK Ligand 3 4
  • Ephrin-B1 2 3
  • Elk-L 3 4
  • EPLG2 3 4
  • LERK2 3 4
  • EFL3 3 4
  • Craniofrontonasal Syndrome (Craniofrontonasal Dysplasia) 2
  • Eph-Related Receptor Tyrosine Kinase Ligand 2 3
  • EPH-Related Receptor Tyrosine Kinase Ligand 2 4
  • LERK-2 4
  • EFL-3 4
  • CFND 3
  • EFB1 3
  • CFNS 3

External Ids for EFNB1 Gene

Previous HGNC Symbols for EFNB1 Gene

  • EPLG2
  • CFNS

Previous GeneCards Identifiers for EFNB1 Gene

  • GC0XP064226
  • GC0XP065526
  • GC0XP066282
  • GC0XP066915
  • GC0XP067831
  • GC0XP067965
  • GC0XP068048
  • GC0XP061874

Summaries for EFNB1 Gene

Entrez Gene Summary for EFNB1 Gene

  • The protein encoded by this gene is a type I membrane protein and a ligand of Eph-related receptor tyrosine kinases. It may play a role in cell adhesion and function in the development or maintenance of the nervous system. [provided by RefSeq, Jul 2008]

GeneCards Summary for EFNB1 Gene

EFNB1 (Ephrin B1) is a Protein Coding gene. Diseases associated with EFNB1 include Craniofrontonasal Syndrome and Hypertelorism. Among its related pathways are EPH-Ephrin signaling and Developmental Biology. Gene Ontology (GO) annotations related to this gene include ephrin receptor binding. An important paralog of this gene is EFNB2.

UniProtKB/Swiss-Prot for EFNB1 Gene

  • Binds to the receptor tyrosine kinases EPHB1 and EPHA1. 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).

  • 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. Binds to the receptor tyrosine kinases EPHB3 (preferred), EPHB1 and EPHA1. 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).

Gene Wiki entry for EFNB1 Gene

Additional gene information for EFNB1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EFNB1 Gene

Genomics for EFNB1 Gene

GeneHancer (GH) Regulatory Elements for EFNB1 Gene

Promoters and enhancers for EFNB1 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
GH0XI068827 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 +2.6 2644 8.1 ARID4B SIN3A IRF4 YY1 GLIS2 ARID2 ZNF143 SP3 RXRA SP5 EFNB1 LOC102723911
GH0XI069613 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 4.3 +787.1 787122 5.1 ELF3 PKNOX1 FOXA2 ARID4B KLF17 DMAP1 THRB RARA ZNF335 GLIS2 EDA EFNB1 GC0XP069675
GH0XI068989 Enhancer 0.8 Ensembl ENCODE 10.1 +161.2 161208 1.6 ZNF449 ZIC2 SP1 HIC1 ZNF791 ZNF512B GLIS2 ZNF366 ZNF512 CTBP2 EFNB1 LOC102723911
GH0XI069551 Enhancer 1 Ensembl ENCODE 4 +725.9 725922 7.3 ELF3 PKNOX1 FOXA2 MLX NFIB DMAP1 RARA ZNF335 FOS CREM EDA EFNB1 STARD8 ENSG00000228160 FAM155B
GH0XI069602 Enhancer 0.4 ENCODE 5 +775.5 775471 3.1 SIX4 HLF EFNB1 EDA ENSG00000228160
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around EFNB1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EFNB1 gene promoter:

Genomic Locations for EFNB1 Gene

Genomic Locations for EFNB1 Gene
chrX:68,828,997-68,842,164
(GRCh38/hg38)
Size:
13,168 bases
Orientation:
Plus strand
chrX:68,048,840-68,062,007
(GRCh37/hg19)

Genomic View for EFNB1 Gene

Genes around EFNB1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EFNB1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EFNB1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EFNB1 Gene

Proteins for EFNB1 Gene

  • Protein details for EFNB1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P98172-EFNB1_HUMAN
    Recommended name:
    Ephrin-B1
    Protein Accession:
    P98172
    Secondary Accessions:
    • D3DVU0

    Protein attributes for EFNB1 Gene

    Size:
    346 amino acids
    Molecular mass:
    38007 Da
    Quaternary structure:
    • Interacts with GRIP1 and GRIP2. Interacts with TLE1.

neXtProt entry for EFNB1 Gene

Post-translational modifications for EFNB1 Gene

  • Inducible phosphorylation of tyrosine residues in the cytoplasmic domain.
  • Ubiquitination at posLast=289289
  • Glycosylation at posLast=139139, posLast=179179, Ser201, and posLast=211211
  • Modification sites at PhosphoSitePlus

Other Protein References for EFNB1 Gene

ENSEMBL proteins:
REFSEQ proteins:

Protein Products

No data available for DME Specific Peptides for EFNB1 Gene

Domains & Families for EFNB1 Gene

Gene Families for EFNB1 Gene

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

Protein Domains for EFNB1 Gene

Suggested Antigen Peptide Sequences for EFNB1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P98172

UniProtKB/Swiss-Prot:

EFNB1_HUMAN :
  • Belongs to the ephrin family.
Family:
  • Belongs to the ephrin family.
genes like me logo Genes that share domains with EFNB1: view

Function for EFNB1 Gene

Molecular function for EFNB1 Gene

GENATLAS Biochemistry:
ephrin B-1,eph-related receptor tyrosine kinase,class B,ligand,high affinity,involved in short-range contact-mediated axonal guidance
UniProtKB/Swiss-Prot Function:
Binds to the receptor tyrosine kinases EPHB1 and EPHA1. 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:
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. Binds to the receptor tyrosine kinases EPHB3 (preferred), EPHB1 and EPHA1. 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 Induction:
By TNF.

LifeMap Function Summary for EFNB1 Gene

It affects the following cells:
EFNB1 as growth factor is involved in stem cell differentiation protocols towards the derivation of the following cells:

Gene Ontology (GO) - Molecular Function for EFNB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 9883737
GO:0046875 ephrin receptor binding TAS,IBA --
genes like me logo Genes that share ontologies with EFNB1: view
genes like me logo Genes that share phenotypes with EFNB1: view

Human Phenotype Ontology for EFNB1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for EFNB1 Gene

MGI Knock Outs for EFNB1:

miRNA for EFNB1 Gene

miRTarBase miRNAs that target EFNB1

Clone Products

  • Addgene plasmids for EFNB1

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Transcription Factor Targets and HOMER Transcription for EFNB1 Gene

Localization for EFNB1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EFNB1 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 EFNB1 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytoskeleton 3
nucleus 2
endoplasmic reticulum 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EFNB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005737 cytoplasm IEA --
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 8660976
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with EFNB1: view

Pathways & Interactions for EFNB1 Gene

genes like me logo Genes that share pathways with EFNB1: view

Pathways by source for EFNB1 Gene

2 Qiagen pathways for EFNB1 Gene
2 Cell Signaling Technology pathways for EFNB1 Gene

SIGNOR curated interactions for EFNB1 Gene

Activates:

Gene Ontology (GO) - Biological Process for EFNB1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001755 neural crest cell migration IEA --
GO:0007155 cell adhesion TAS 8798744
GO:0007267 cell-cell signaling TAS 8798744
GO:0007275 multicellular organism development IEA --
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with EFNB1: view

Drugs & Compounds for EFNB1 Gene

(1) Drugs for EFNB1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with EFNB1: view

Transcripts for EFNB1 Gene

mRNA/cDNA for EFNB1 Gene

(1) REFSEQ mRNAs :
(6) Additional mRNA sequences :
(270) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for EFNB1 Gene

Ephrin-B1:
Representative Sequences:

Clone Products

  • Addgene plasmids for EFNB1

Alternative Splicing Database (ASD) splice patterns (SP) for EFNB1 Gene

No ASD Table

Relevant External Links for EFNB1 Gene

GeneLoc Exon Structure for
EFNB1
ECgene alternative splicing isoforms for
EFNB1

Expression for EFNB1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EFNB1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for EFNB1 Gene

This gene is overexpressed in Bone (31.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for EFNB1 Gene



NURSA nuclear receptor signaling pathways regulating expression of EFNB1 Gene:

EFNB1

SOURCE GeneReport for Unigene cluster for EFNB1 Gene:

Hs.144700

mRNA Expression by UniProt/SwissProt for EFNB1 Gene:

P98172-EFNB1_HUMAN
Tissue specificity: Heart, placenta, lung, liver, skeletal muscle, kidney, pancreas.

Evidence on tissue expression from TISSUES for EFNB1 Gene

  • Nervous system(4.6)
  • Eye(4.3)
  • Skin(4.2)
  • Liver(4.1)
  • Intestine(2.7)

Phenotype-based relationships between genes and organs from Gene ORGANizer for EFNB1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cranial nerve
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • scalp
  • skull
  • tooth
Thorax:
  • breast
  • chest wall
  • clavicle
  • diaphragm
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
Abdomen:
  • abdominal wall
  • intestine
  • large intestine
  • liver
  • small intestine
  • stomach
Pelvis:
  • pelvis
  • penis
  • testicle
  • urethra
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • nail
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • hair
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with EFNB1: view

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for EFNB1 Gene

Orthologs for EFNB1 Gene

This gene was present in the common ancestor of animals.

Orthologs for EFNB1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EFNB1 33 34
  • 99.62 (n)
cow
(Bos Taurus)
Mammalia EFNB1 33 34
  • 92.29 (n)
dog
(Canis familiaris)
Mammalia EFNB1 33 34
  • 91.52 (n)
mouse
(Mus musculus)
Mammalia Efnb1 33 16 34
  • 90.72 (n)
rat
(Rattus norvegicus)
Mammalia Efnb1 33
  • 90.43 (n)
oppossum
(Monodelphis domestica)
Mammalia EFNB1 34
  • 77 (a)
OneToOne
chicken
(Gallus gallus)
Aves EFNB1 33 34
  • 77.45 (n)
lizard
(Anolis carolinensis)
Reptilia EFNB1 34
  • 67 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100494328 33
  • 72.94 (n)
African clawed frog
(Xenopus laevis)
Amphibia efnb1-A 33
zebrafish
(Danio rerio)
Actinopterygii efnb1 33 34
  • 66.77 (n)
fruit fly
(Drosophila melanogaster)
Insecta Ephrin 34
  • 10 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea efn-2 34
  • 28 (a)
ManyToMany
efn-3 34
  • 27 (a)
ManyToMany
vab-2 34
  • 22 (a)
ManyToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.7000 34
  • 24 (a)
OneToMany
Species where no ortholog for EFNB1 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)
  • 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 EFNB1 Gene

ENSEMBL:
Gene Tree for EFNB1 (if available)
TreeFam:
Gene Tree for EFNB1 (if available)

Paralogs for EFNB1 Gene

Paralogs for EFNB1 Gene

(2) SIMAP similar genes for EFNB1 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with EFNB1: view

Variants for EFNB1 Gene

Sequence variations from dbSNP and Humsavar for EFNB1 Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs104894796 pathogenic, Craniofrontonasal dysplasia, Craniofrontonasal syndrome (CFNS) [MIM:304110] 68,838,820(+) C/T coding_sequence_variant, missense_variant
rs104894801 likely-pathogenic, pathogenic, not provided, Craniofrontonasal dysplasia, Craniofrontonasal syndrome (CFNS) [MIM:304110] 68,838,649(+) C/A/G/T coding_sequence_variant, missense_variant
rs104894802 pathogenic, Craniofrontonasal dysplasia 68,829,885(+) T/G coding_sequence_variant, missense_variant
rs104894803 pathogenic, Craniofrontonasal dysplasia 68,829,886(+) G/A coding_sequence_variant, stop_gained
rs104894804 pathogenic, Craniofrontonasal dysplasia, not provided 68,838,684(+) C/T coding_sequence_variant, stop_gained

Structural Variations from Database of Genomic Variants (DGV) for EFNB1 Gene

Variant ID Type Subtype PubMed ID
esv1584074 OTHER inversion 17803354
nsv516469 CNV gain 19592680

Variation tolerance for EFNB1 Gene

Residual Variation Intolerance Score: 17% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.50; 29.14% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EFNB1 Gene

Human Gene Mutation Database (HGMD)
EFNB1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
EFNB1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EFNB1 Gene

Disorders for EFNB1 Gene

MalaCards: The human disease database

(8) MalaCards diseases for EFNB1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search EFNB1 in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

EFNB1_HUMAN
  • Craniofrontonasal syndrome (CFNS) [MIM:304110]: X-linked inherited syndrome characterized by hypertelorism, coronal synostosis with brachycephaly, downslanting palpebral fissures, clefting of the nasal tip, joint anomalies, longitudinally grooved fingernails and other digital anomalies. {ECO:0000269 PubMed:15124102, ECO:0000269 PubMed:15166289, ECO:0000269 PubMed:15959873}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for EFNB1

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 EFNB1: view

No data available for Genatlas for EFNB1 Gene

Publications for EFNB1 Gene

  1. A novel mutation in EFNB1, probably with a dominant negative effect, underlying craniofrontonasal syndrome. (PMID: 16526919) Shotelersuk V … Ausavarat S (The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association 2006) 2 3 22 58
  2. Twenty-six novel EFNB1 mutations in familial and sporadic craniofrontonasal syndrome (CFNS). (PMID: 15959873) Wieland I … Wieacker P (Human mutation 2005) 3 4 22 58
  3. Ephrin-B1 reverse signaling controls a posttranscriptional feedback mechanism via miR-124. (PMID: 20308325) Arvanitis DN … Davy A (Molecular and cellular biology 2010) 3 22 58
  4. Prevalence and complications of single-gene and chromosomal disorders in craniosynostosis. (PMID: 20643727) Wilkie AO … Wall SA (Pediatrics 2010) 3 44 58
  5. A novel combination of factors, termed SPIE, which promotes dopaminergic neuron differentiation from human embryonic stem cells. (PMID: 19672298) Vazin T … Freed WJ (PloS one 2009) 3 22 58

Products for EFNB1 Gene

  • Addgene plasmids for EFNB1

Sources for EFNB1 Gene

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