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    LY96 lymphocyte antigen 96 [ Homo sapiens (human) ]

    Gene ID: 23643, updated on 9-Dec-2024

    Summary

    Official Symbol
    LY96provided by HGNC
    Official Full Name
    lymphocyte antigen 96provided by HGNC
    Primary source
    HGNC:HGNC:17156
    See related
    Ensembl:ENSG00000154589 MIM:605243; AllianceGenome:HGNC:17156
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MD2; MD-2; ly-96; ESOP-1
    Summary
    This gene encodes a protein which associates with toll-like receptor 4 on the cell surface and confers responsiveness to lipopolysaccyaride (LPS), thus providing a link between the receptor and LPS signaling. Studies of the mouse ortholog suggest that this gene may be involved in endotoxin neutralization. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2010]
    Expression
    Broad expression in spleen (RPKM 8.6), appendix (RPKM 8.4) and 22 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See LY96 in Genome Data Viewer
    Location:
    8q21.11
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (73991392..74099857)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (74420655..74529114)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (74903627..74941314)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr8:74897195-74897777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27538 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27539 Neighboring gene ribosomal protein S20 pseudogene 21 Neighboring gene transmembrane protein 70 Neighboring gene DSTN pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19298 Neighboring gene RNA, U6 small nuclear 1300, pseudogene Neighboring gene RPS3A pseudogene 32 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:74990404-74990904 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:74990905-74991405 Neighboring gene RNA, U6 small nuclear 1197, pseudogene Neighboring gene uncharacterized LOC105375903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27541 Neighboring gene MPRA-validated peak7074 silencer Neighboring gene junctophilin 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr8:75193255-75194454 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19299 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:75213303-75213804 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:75232842-75233732

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    Novel genetic variants modify the effect of smoking on carotid plaque burden in Hispanics.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat interacts physically with the TLR4-MD2 complex and the N-terminal region (residues 1-29) of Tat is involved in the interation with TLR4-MD2 PubMed
    Vif vif HIV-1 Vif upregulates the expression of lymphocyte antigen 96 (LY96) in Vif-expression T cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables Toll-like receptor 4 binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables coreceptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables lipopolysaccharide binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables lipopolysaccharide immune receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables lipopolysaccharide immune receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cell surface receptor signaling pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cellular defense response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cellular response to lipopolysaccharide IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in detection of lipopolysaccharide IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in detection of lipopolysaccharide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in innate immune response NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in lipopolysaccharide-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of lipopolysaccharide-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of tumor necrosis factor production ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within response to lipopolysaccharide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in response to lipopolysaccharide IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in toll-like receptor 4 signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in toll-like receptor 4 signaling pathway ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in toll-like receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    part_of lipopolysaccharide receptor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of lipopolysaccharide receptor complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    part_of receptor complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 

    General protein information

    Preferred Names
    lymphocyte antigen 96
    Names
    myeloid differentiation protein-2
    protein MD-2

    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_001195797.2NP_001182726.1  lymphocyte antigen 96 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001182726.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      BC020690, BG435728
      Consensus CDS
      CCDS56540.1
      UniProtKB/Swiss-Prot
      Q9Y6Y9
      Related
      ENSP00000430533.1, ENST00000518893.1
      Conserved Domains (1) summary
      cl00274
      Location:22123
      ML; The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of ...
    2. NM_015364.5NP_056179.4  lymphocyte antigen 96 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC022868, AC087672
      Consensus CDS
      CCDS6216.1
      UniProtKB/Swiss-Prot
      B3Y6A5, E5RJJ7, Q9Y6Y9
      Related
      ENSP00000284818.2, ENST00000284818.7
      Conserved Domains (1) summary
      cl00274
      Location:22153
      ML; The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      73991392..74099857
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017013299.2XP_016868788.1  lymphocyte antigen 96 isoform X2

    2. XM_017013300.2XP_016868789.1  lymphocyte antigen 96 isoform X3

    3. XM_011517508.3XP_011515810.1  lymphocyte antigen 96 isoform X4

      Conserved Domains (1) summary
      cl00274
      Location:22130
      ML; The ML (MD-2-related lipid-recognition) domain is present in MD-1, MD-2, GM2 activator protein, Niemann-Pick type C2 (Npc2) protein, phosphatidylinositol/phosphatidylglycerol transfer protein (PG/PI-TP), mite allergen Der p 2 and several proteins of ...
    4. XM_047421662.1XP_047277618.1  lymphocyte antigen 96 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      74420655..74529114
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054360237.1XP_054216212.1  lymphocyte antigen 96 isoform X2

    2. XM_054360238.1XP_054216213.1  lymphocyte antigen 96 isoform X3

    3. XM_054360239.1XP_054216214.1  lymphocyte antigen 96 isoform X4

    4. XM_054360236.1XP_054216211.1  lymphocyte antigen 96 isoform X1