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    Efnb3 ephrin B3 [ Mus musculus (house mouse) ]

    Gene ID: 13643, updated on 27-Nov-2024

    Summary

    Official Symbol
    Efnb3provided by MGI
    Official Full Name
    ephrin B3provided by MGI
    Primary source
    MGI:MGI:109196
    See related
    Ensembl:ENSMUSG00000003934 AllianceGenome:MGI:109196
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    Epl8; EFL-6; ELF-3; Elk-L3; LERK-8; NLERK-2
    Summary
    Predicted to enable ephrin receptor binding activity. Involved in negative regulation of axonogenesis and trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission. Acts upstream of or within T cell costimulation; adult walking behavior; and axon choice point recognition. Is active in glutamatergic synapse; hippocampal mossy fiber to CA3 synapse; and presynaptic membrane. Is expressed in several structures, including alimentary system; central nervous system; genitourinary system; integumental system; and sensory organ. Used to study movement disease. Orthologous to human EFNB3 (ephrin B3). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in CNS E18 (RPKM 44.0), whole brain E14.5 (RPKM 38.6) and 9 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Efnb3 in Genome Data Viewer
    Location:
    11 B3; 11 42.8 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (69444918..69452428, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (69554092..69561150, complement)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene KDM1 lysine (K)-specific demethylase 6B Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:69231989-69232098 Neighboring gene predicted gene, 51903 Neighboring gene dynein, axonemal, heavy chain 2 Neighboring gene STARR-seq mESC enhancer starr_29847 Neighboring gene STARR-seq mESC enhancer starr_29849 Neighboring gene STARR-seq mESC enhancer starr_29852 Neighboring gene WD repeat containing, antisense to Trp53 Neighboring gene ribosomal protein S27, pseudogene 2 Neighboring gene transformation related protein 53

    Genomic regions, transcripts, and products

    Expression

    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Chemically induced (ENU) (1) 
    • Endonuclease-mediated (1) 
    • Spontaneous (1) 
    • Targeted (9)  1 citation

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables ephrin receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ephrin receptor binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    acts_upstream_of_or_within T cell costimulation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    acts_upstream_of_or_within adult walking behavior IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within axon choice point recognition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in axon guidance IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within axon guidance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in ephrin receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within ephrin receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of axonogenesis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of presynapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of presynapse assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of synaptic transmission IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of synaptic transmission ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in trans-synaptic signaling by trans-synaptic complex, modulating synaptic transmission IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    is_active_in glutamatergic synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in glutamatergic synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in glutamatergic synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in hippocampal mossy fiber to CA3 synapse IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in hippocampal mossy fiber to CA3 synapse IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    located_in postsynaptic density membrane IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in postsynaptic density membrane ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in presynaptic membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    is_active_in presynaptic membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_007911.5 → NP_031937.1  ephrin-B3 precursor

      See identical proteins and their annotated locations for NP_031937.1

      Status: VALIDATED

      Source sequence(s)
      BC058617, BE955272, CJ065252
      Consensus CDS
      CCDS24896.1
      UniProtKB/Swiss-Prot
      O35393
      UniProtKB/TrEMBL
      Q543Q7
      Related
      ENSMUSP00000004036.6, ENSMUST00000004036.6
      Conserved Domains (1) summary
      cl19115
      Location:29 → 168
      Cupredoxin; Cupredoxin superfamily

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      69444918..69452428 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006532160.5 → XP_006532223.1  ephrin-B3 isoform X1

      Conserved Domains (1) summary
      cl19115
      Location:51 → 179
      Cupredoxin; Cupredoxin superfamily