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    Ly6e lymphocyte antigen 6 family member E [ Mus musculus (house mouse) ]

    Gene ID: 17069, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Ly6eprovided by MGI
    Official Full Name
    lymphocyte antigen 6 family member Eprovided by MGI
    Primary source
    MGI:MGI:106651
    See related
    Ensembl:ENSMUSG00000022587 AllianceGenome:MGI:106651
    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
    Ly67; Tsa1; RIG-E; Sca-2; TSA-1
    Summary
    Enables acetylcholine receptor binding activity and acetylcholine receptor inhibitor activity. Involved in negative regulation of viral entry into host cell. Acts upstream of or within several processes, including acetylcholine receptor signaling pathway; epinephrine secretion; and ventricular cardiac muscle tissue morphogenesis. Predicted to be located in side of membrane and synapse. Predicted to be active in plasma membrane. Is expressed in several structures, including alimentary system; brain; extraembryonic component; genitourinary system; and immune system. Orthologous to human LY6E (lymphocyte antigen 6 family member E). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in thymus adult (RPKM 431.0), spleen adult (RPKM 360.8) and 23 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ly6e in Genome Data Viewer
    Location:
    15 D3; 15 34.29 cM
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 15 NC_000081.7 (74826874..74831753)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 15 NC_000081.6 (74955025..74959904)

    Chromosome 15 - NC_000081.7Genomic Context describing neighboring genes Neighboring gene predicted gene 6610 Neighboring gene STARR-positive B cell enhancer ABC_E1173 Neighboring gene predicted gene, 39556 Neighboring gene STARR-seq mESC enhancer starr_39002 Neighboring gene STARR-positive B cell enhancer ABC_E7383 Neighboring gene predicted gene 28068 Neighboring gene lymphocyte antigen 6 family member I Neighboring gene predicted gene 8000

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

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    Related articles in PubMed

    1. Stem cell antigen 2 expression in adult and developing mice. Antica M, et al. Immunol Lett, 1997 Jan. PMID 9093881
    2. Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks. Delgado-Chaves FM, et al. Genes (Basel), 2020 Jul 21. PMID 32708319, Free PMC Article
    3. Functional characterization of hepatoma-specific stem cell antigen-2. He J, et al. Mol Carcinog, 2004 Jun. PMID 15170814
    4. Mouse stem cell antigen Sca-2 is a member of the Ly-6 family of cell surface proteins. Classon BJ, et al. Proc Natl Acad Sci U S A, 1994 Jun 7. PMID 8202484, Free PMC Article
    5. Identification through bioinformatics of cDNAs encoding human thymic shared Ag-1/stem cell Ag-2. A new member of the human Ly-6 family. Capone MC, et al. J Immunol, 1996 Aug 1. PMID 8757598

    See all (45) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LY6E impairs coronavirus fusion and confers immune control of viral disease.
      Title: LY6E impairs coronavirus fusion and confers immune control of viral disease.
    2. Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks.
      Title: Computational Analysis of the Global Effects of Ly6E in the Immune Response to Coronavirus Infection Using Gene Networks.
    3. demonstrate that LY6E is essential for the normal fusion of syncytiotrophoblast layer I, and for the proper morphogenesis of both fetal and maternal vasculatures within the placenta
      Title: Deletion of the Syncytin A receptor Ly6e impairs syncytiotrophoblast fusion and placental morphogenesis causing embryonic lethality in mice.
    4. Knocking down Ly6e greatly reduced SynA-induced cell fusion, thus suggesting that Ly6e is the sole receptor for SynA in vivo.
      Title: A Cell Fusion-Based Screening Method Identifies Glycosylphosphatidylinositol-Anchored Protein Ly6e as the Receptor for Mouse Endogenous Retroviral Envelope Syncytin-A.
    5. Sca-2 -- a signal transducer situated at the nexus of surface molecules regulating death receptor-mediated apoptosis in hepatoma
      Title: Functional characterization of hepatoma-specific stem cell antigen-2.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (4) 
    • Targeted (3)  1 citation

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables acetylcholine receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables acetylcholine receptor binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables acetylcholine receptor inhibitor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables acetylcholine receptor inhibitor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in acetylcholine receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within acetylcholine receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within adrenal gland development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within epinephrine secretion IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within in utero embryonic development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of viral entry into host cell IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of viral entry into host cell ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within norepinephrine metabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within organ growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within ventricular cardiac muscle tissue morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lymphocyte antigen 6E
    Names
    lymphocyte antigen 6 complex, locus E
    stem cell antigen 2
    thymic shared antigen 1

    NCBI Reference Sequences (RefSeq)

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    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_001164036.2 → NP_001157508.2  lymphocyte antigen 6E precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1 to 7 all encode the same protein.
      Source sequence(s)
      AC124637
      Consensus CDS
      CCDS27538.1
      UniProtKB/TrEMBL
      A0A087WNT2, A0A087WPY4
      Related
      ENSMUSP00000139482.3, ENSMUST00000190810.8
      Conserved Domains (1) summary
      smart00134
      Location:21 → 105
      LU; Ly-6 antigen / uPA receptor -like domain

    2. NM_001164037.2 → NP_001157509.2  lymphocyte antigen 6E precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1 to 7 all encode the same protein.
      Source sequence(s)
      AC124637
      Consensus CDS
      CCDS27538.1
      UniProtKB/TrEMBL
      A0A087WNT2, A0A087WPY4
      Related
      ENSMUSP00000141145.3, ENSMUST00000185861.8
      Conserved Domains (1) summary
      smart00134
      Location:21 → 105
      LU; Ly-6 antigen / uPA receptor -like domain

    3. NM_001164038.2 → NP_001157510.2  lymphocyte antigen 6E precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1 to 7 all encode the same protein.
      Source sequence(s)
      AC124637, U04268
      Consensus CDS
      CCDS27538.1
      UniProtKB/TrEMBL
      A0A087WNT2, A0A087WPY4
      Related
      ENSMUSP00000140145.3, ENSMUST00000188866.7
      Conserved Domains (1) summary
      smart00134
      Location:21 → 105
      LU; Ly-6 antigen / uPA receptor -like domain

    4. NM_001164039.2 → NP_001157511.2  lymphocyte antigen 6E precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 1. Variants 1 to 7 all encode the same protein.
      Source sequence(s)
      AC124637
      Consensus CDS
      CCDS27538.1
      UniProtKB/TrEMBL
      A0A087WNT2, A0A087WPY4
      Conserved Domains (1) summary
      smart00134
      Location:21 → 105
      LU; Ly-6 antigen / uPA receptor -like domain

    5. NM_001164040.2 → NP_001157512.2  lymphocyte antigen 6E precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1. Variants 1 to 7 all encode the same protein.
      Source sequence(s)
      AC124637
      Consensus CDS
      CCDS27538.1
      UniProtKB/TrEMBL
      A0A087WNT2, A0A087WPY4
      Related
      ENSMUSP00000139471.3, ENSMUST00000187606.8
      Conserved Domains (1) summary
      smart00134
      Location:21 → 105
      LU; Ly-6 antigen / uPA receptor -like domain

    6. NM_001374138.1 → NP_001361067.1  lymphocyte antigen 6E precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR, compared to variant 1. Variants 1 to 7 all encode the same protein.
      Source sequence(s)
      AC124637
      UniProtKB/TrEMBL
      A0A087WNT2, A0A087WPY4
      Related
      ENSMUSP00000140553.3, ENSMUST00000187284.8
      Conserved Domains (1) summary
      smart00134
      Location:21 → 105
      LU; Ly-6 antigen / uPA receptor -like domain

    7. NM_008529.4 → NP_032555.2  lymphocyte antigen 6E precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. Variants 1 to 7 all encode the same protein.
      Source sequence(s)
      AC124637
      Consensus CDS
      CCDS27538.1
      UniProtKB/TrEMBL
      A0A087WNT2, A0A087WPY4
      Related
      ENSMUSP00000139549.3, ENSMUST00000191436.8
      Conserved Domains (1) summary
      smart00134
      Location:21 → 105
      LU; Ly-6 antigen / uPA receptor -like domain

    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_000081.7 Reference GRCm39 C57BL/6J

      Range
      74826874..74831753
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036159201.1 → XP_036015094.1  lymphocyte antigen 6E isoform X1

      UniProtKB/Swiss-Prot
      Q61128, Q64253, Q99JA5
      Related
      ENSMUSP00000141059.3, ENSMUST00000188042.3
      Conserved Domains (1) summary
      smart00134
      Location:27 → 111
      LU; Ly-6 antigen / uPA receptor -like domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q64253.3 GenPept UniProtKB/Swiss-Prot:Q64253

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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