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LY96 lymphocyte antigen 96 [ Homo sapiens (human) ]

Gene ID: 23643, updated on 12-Sep-2020

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
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

Genomic context

See LY96 in Genome Data Viewer
Location:
8q21.11
Exon count:
7
Annotation release Status Assembly Chr Location
109.20200815 current GRCh38.p13 (GCF_000001405.39) 8 NC_000008.11 (73991275..74099807)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (74903564..74941314)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene ribosomal protein S20 pseudogene 21 Neighboring gene transmembrane protein 70 Neighboring gene DSTN pseudogene 3 Neighboring gene RNA, U6 small nuclear 1300, pseudogene Neighboring gene RPS3A pseudogene 32 Neighboring gene RNA, U6 small nuclear 1197, pseudogene Neighboring gene uncharacterized LOC105375903 Neighboring gene junctophilin 1

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

Associated conditions

Description Tests
Novel genetic variants modify the effect of smoking on carotid plaque burden in Hispanics.
GeneReviews: Not available

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
Toll-like receptor 4 binding IEA
Inferred from Electronic Annotation
more info
 
coreceptor activity TAS
Traceable Author Statement
more info
PubMed 
lipopolysaccharide binding IEA
Inferred from Electronic Annotation
more info
 
lipopolysaccharide receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lipopolysaccharide receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
I-kappaB kinase/NF-kappaB signaling TAS
Traceable Author Statement
more info
 
MyD88-dependent toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
MyD88-independent toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
TRIF-dependent toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
apoptotic signaling pathway TAS
Traceable Author Statement
more info
 
cell surface receptor signaling pathway TAS
Traceable Author Statement
more info
PubMed 
cellular defense response TAS
Traceable Author Statement
more info
PubMed 
cellular response to lipopolysaccharide IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
detection of lipopolysaccharide IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
detection of lipopolysaccharide IDA
Inferred from Direct Assay
more info
PubMed 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
lipopolysaccharide-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
necroptotic process TAS
Traceable Author Statement
more info
 
negative regulation of MyD88-independent toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
positive regulation of lipopolysaccharide-mediated signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of tumor necrosis factor production ISS
Inferred from Sequence or Structural Similarity
more info
 
response to lipopolysaccharide IDA
Inferred from Direct Assay
more info
PubMed 
toll-like receptor 4 signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
toll-like receptor 4 signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
 
toll-like receptor 4 signaling pathway TAS
Traceable Author Statement
more info
 
toll-like receptor signaling pathway TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
endosome membrane TAS
Traceable Author Statement
more info
 
extracellular space IEA
Inferred from Electronic Annotation
more info
 
intrinsic component of plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
lipopolysaccharide receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lipopolysaccharide receptor complex IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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

NCBI Reference Sequences (RefSeq)

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
    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: Homo sapiens Updated Annotation Release 109.20200815

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p13 Primary Assembly

    Range
    73991275..74099807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017013300.1XP_016868789.1  lymphocyte antigen 96 isoform X2

  2. XM_017013299.1XP_016868788.1  lymphocyte antigen 96 isoform X1

  3. XM_011517508.2XP_011515810.1  lymphocyte antigen 96 isoform X3

    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 ...
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