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 dif... See more...

Aliases for LY96 Gene

Aliases for LY96 Gene

  • Lymphocyte Antigen 96 2 3 4 5
  • Protein MD-2 3 4
  • ESOP-1 3 4
  • Ly-96 3 4
  • MD-2 2 3
  • MD2 3 4
  • Myeloid Differentiation Protein-2 3
  • ESOP1 4
  • LY96 5

External Ids for LY96 Gene

Previous GeneCards Identifiers for LY96 Gene

  • GC08P074844
  • GC08P074626
  • GC08P074953
  • GC08P075066
  • GC08P070394

Summaries for LY96 Gene

Entrez Gene Summary for LY96 Gene

  • 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]

GeneCards Summary for LY96 Gene

LY96 (Lymphocyte Antigen 96) is a Protein Coding gene. Diseases associated with LY96 include Melioidosis and Acute Gonococcal Cervicitis. Among its related pathways are Bacterial infections in CF airways and Activated TLR4 signalling. Gene Ontology (GO) annotations related to this gene include coreceptor activity and lipopolysaccharide receptor activity.

UniProtKB/Swiss-Prot Summary for LY96 Gene

  • Binds bacterial lipopolysaccharide (LPS) (PubMed:17803912, PubMed:17569869). Cooperates with TLR4 in the innate immune response to bacterial lipopolysaccharide (LPS), and with TLR2 in the response to cell wall components from Gram-positive and Gram-negative bacteria (PubMed:11160242, PubMed:11593030). Enhances TLR4-dependent activation of NF-kappa-B (PubMed:10359581). Cells expressing both LY96 and TLR4, but not TLR4 alone, respond to LPS (PubMed:10359581).

Gene Wiki entry for LY96 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for LY96 Gene

Genomics for LY96 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for LY96 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
GH08J073990 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 250.7 +1.2 1221 3.8 SP1 BCL11A GABPA GTF2E2 FOXA2 TRIM22 ELF1 EBF1 ZNF316 ADNP HSALNG0066214 LY96 TMEM70 ELOC PCBP2P2 piR-60140-024 GDAP1
GH08J073967 Enhancer 0.6 ENCODE 10.6 -24.8 -24794 0.2 CEBPA IKZF1 CEBPB NFE2 IRF9 ZNF384 CEBPG HLF FOS RBFOX2 LY96 UBE2W TMEM70 ELOC HSALNG0066207 piR-57461-258
GH08J073966 Promoter 0.5 Ensembl 10.6 -24.4 -24374 0.2 CEBPB RBFOX2 LY96 UBE2W ELOC HSALNG0066207 piR-57461-258
GH08J073965 Promoter 0.5 Ensembl 10.6 -25.4 -25374 0.2 ZNF189 ZNF24 LY96 UBE2W ELOC HSALNG0066207 piR-57461-258
GH08J074056 Enhancer 0.3 Ensembl 10.8 +66.0 66026 1.4 ZNF316 MAFK RPS3AP32 lnc-LY96-5 TMEM70 ELOC LY96 GDAP1 ENSG00000253596 ENSG00000254288 lnc-LY96-4 RF00026-1084
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LY96 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for LY96

Top Transcription factor binding sites by QIAGEN in the LY96 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • IRF-1
  • MRF-2
  • Msx-1
  • MZF-1
  • STAT1
  • STAT1alpha
  • TBP

Genomic Locations for LY96 Gene

Latest Assembly
chr8:73,991,275-74,099,807
(GRCh38/hg38)
Size:
108,533 bases
Orientation:
Plus strand

Previous Assembly
chr8:74,903,627-74,941,314
(GRCh37/hg19 by Entrez Gene)
Size:
37,688 bases
Orientation:
Plus strand

chr8:74,903,587-74,941,322
(GRCh37/hg19 by Ensembl)
Size:
37,736 bases
Orientation:
Plus strand

Genomic View for LY96 Gene

Genes around LY96 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LY96 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LY96 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LY96 Gene

Proteins for LY96 Gene

  • Protein details for LY96 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y6Y9-LY96_HUMAN
    Recommended name:
    Lymphocyte antigen 96
    Protein Accession:
    Q9Y6Y9
    Secondary Accessions:
    • B3Y6A5
    • E5RJJ7

    Protein attributes for LY96 Gene

    Size:
    160 amino acids
    Molecular mass:
    18546 Da
    Quaternary structure:
    • Heterogeneous homopolymer formed from homodimers; disulfide-linked (PubMed:11593030, PubMed:12642668). Belongs to the lipopolysaccharide (LPS) receptor, a multi-protein complex containing at least CD14, LY96 and TLR4 (PubMed:11274165). Binds to the extracellular domains of TLR2 and TLR4 (PubMed:10359581, PubMed:11593030, PubMed:17803912). Ligand binding induces interaction with TLR4 and oligomerization of the complex.

    Three dimensional structures from OCA and Proteopedia for LY96 Gene

    Alternative splice isoforms for LY96 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for LY96 Gene

Post-translational modifications for LY96 Gene

Other Protein References for LY96 Gene

No data available for DME Specific Peptides for LY96 Gene

Domains & Families for LY96 Gene

Gene Families for LY96 Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for LY96 Gene

InterPro:
Blocks:
  • E1 protein and Def2/Der2 allergen
ProtoNet:

Suggested Antigen Peptide Sequences for LY96 Gene

GenScript: Design optimal peptide antigens:
  • MD-2 mimetic protein variant (D0VAW8_HUMAN)
  • Protein MD-2 (LY96_HUMAN)
genes like me logo Genes that share domains with LY96: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for LY96 Gene

Function for LY96 Gene

Molecular function for LY96 Gene

UniProtKB/Swiss-Prot Function:
Binds bacterial lipopolysaccharide (LPS) (PubMed:17803912, PubMed:17569869). Cooperates with TLR4 in the innate immune response to bacterial lipopolysaccharide (LPS), and with TLR2 in the response to cell wall components from Gram-positive and Gram-negative bacteria (PubMed:11160242, PubMed:11593030). Enhances TLR4-dependent activation of NF-kappa-B (PubMed:10359581). Cells expressing both LY96 and TLR4, but not TLR4 alone, respond to LPS (PubMed:10359581).

Phenotypes From GWAS Catalog for LY96 Gene

Gene Ontology (GO) - Molecular Function for LY96 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001530 lipopolysaccharide binding IEA --
GO:0001875 lipopolysaccharide receptor activity IBA,IDA 19252480
GO:0005515 protein binding IPI 15728506
GO:0015026 coreceptor activity TAS 10359581
GO:0035662 Toll-like receptor 4 binding IEA --
genes like me logo Genes that share ontologies with LY96: view
genes like me logo Genes that share phenotypes with LY96: view

Animal Models for LY96 Gene

MGI Knock Outs for LY96:
  • Ly96 Ly96<tm1Kmiy>

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LY96

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for LY96 Gene

Localization for LY96 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LY96 Gene

Secreted, extracellular space. Secreted. Note=Retained in the extracellular space at the cell surface by interaction with TLR4 (PubMed:10359581). {ECO:0000269 PubMed:10359581, ECO:0000269 PubMed:11593030}.

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 LY96 gene
Compartment Confidence
plasma membrane 5
extracellular 5
endosome 4
nucleus 3
cytoskeleton 2
mitochondrion 2
endoplasmic reticulum 2
cytosol 2
lysosome 2
golgi apparatus 2
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for LY96 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
GO:0005615 extracellular space IEA --
GO:0005886 plasma membrane TAS --
GO:0010008 endosome membrane TAS --
GO:0031226 intrinsic component of plasma membrane IDA 11274165
genes like me logo Genes that share ontologies with LY96: view

Pathways & Interactions for LY96 Gene

PathCards logo

SuperPathways for LY96 Gene

SuperPathway Contained pathways
1 Activated TLR4 signalling
2 Diseases associated with the TLR signaling cascade
3 Toll-like Receptor Signaling Pathway
4 Bacterial infections in CF airways
.78
.78
.46
5 Toll-Like receptor Signaling Pathways
.33
genes like me logo Genes that share pathways with LY96: view

Pathways by source for LY96 Gene

8 GeneGo (Thomson Reuters) pathways for LY96 Gene
  • Bacterial infections in CF airways
  • Cytokine production by Th17 cells in CF
  • Cytokine production by Th17 cells in CF (Mouse model)
  • Immune response Bacterial infections in normal airways
  • Immune response MIF in innate immunity response
5 Qiagen pathways for LY96 Gene
  • MIF Action Through Endocytic Pathway
  • MIF Mediated Glucocorticoid Regulation
  • MIF Regulation of Innate Immune Cells
  • Toll Comparative Pathway
  • Toll-Like Receptors Pathway
1 GeneTex pathway for LY96 Gene

SIGNOR curated interactions for LY96 Gene

Activates:
Is inactivated by:

Gene Ontology (GO) - Biological Process for LY96 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002224 toll-like receptor signaling pathway TAS --
GO:0002376 immune system process IEA --
GO:0002755 MyD88-dependent toll-like receptor signaling pathway TAS --
GO:0002756 MyD88-independent toll-like receptor signaling pathway TAS --
GO:0006954 inflammatory response IEA --
genes like me logo Genes that share ontologies with LY96: view

Drugs & Compounds for LY96 Gene

(7) Drugs for LY96 Gene - From: DrugBank, PharmGKB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
lauric acid Approved, Experimental Pharma Target 0
Morphine Approved, Investigational Pharma Target, activator 1486
(R)-3-hydroxytetradecanoic acid Experimental Pharma Target 0
Myristic acid Experimental Pharma Target 0
Tumor necrosis factor alpha (TNF-alpha) inhibitors Pharma 0

(3) Additional Compounds for LY96 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with LY96: view

Transcripts for LY96 Gene

mRNA/cDNA for LY96 Gene

2 REFSEQ mRNAs :
5 NCBI additional mRNA sequence :
2 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for LY96

Alternative Splicing Database (ASD) splice patterns (SP) for LY96 Gene

No ASD Table

Relevant External Links for LY96 Gene

GeneLoc Exon Structure for
LY96

Expression for LY96 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for LY96 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for LY96 Gene

This gene is overexpressed in Whole Blood (x10.3) and Spleen (x5.0).

Protein differential expression in normal tissues from HIPED for LY96 Gene

This gene is overexpressed in Gallbladder (69.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for LY96 Gene



Protein tissue co-expression partners for LY96 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for LY96

SOURCE GeneReport for Unigene cluster for LY96 Gene:

Hs.726603

Evidence on tissue expression from TISSUES for LY96 Gene

  • Liver(4.5)
  • Blood(3.4)
  • Spleen(3.3)
  • Lymph node(3)
  • Intestine(2.9)
  • Heart(2.8)
  • Lung(2.8)
  • Nervous system(2.6)
  • Kidney(2.5)
  • Bone marrow(2.4)
  • Muscle(2.2)
  • Skin(2.1)
  • Stomach(2)
genes like me logo Genes that share expression patterns with LY96: view

Primer products for research

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for LY96 Gene

Orthologs for LY96 Gene

This gene was present in the common ancestor of chordates.

Orthologs for LY96 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia LY96 30
  • 100 (n)
MD2 31
  • 99 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia LY96 30 31
  • 81.25 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia LY96 30
  • 77.08 (n)
MD2 31
  • 64 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Ly96 30 17 31
  • 75.62 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Ly96 30
  • 74.73 (n)
Oppossum
(Monodelphis domestica)
Mammalia LY96 31
  • 49 (a)
OneToOne
Chicken
(Gallus gallus)
Aves LY96 31
  • 32 (a)
OneToOne
Species where no ortholog for LY96 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Lizard (Anolis carolinensis)
  • 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 Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • 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)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)
  • Zebrafish (Danio rerio)

Evolution for LY96 Gene

ENSEMBL:
Gene Tree for LY96 (if available)
TreeFam:
Gene Tree for LY96 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LY96: view image

Paralogs for LY96 Gene

No data available for Paralogs for LY96 Gene

Variants for LY96 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for LY96 Gene

SNP ID Clinical significance and condition Chr 08 pos Variation AA Info Type
rs11466004 - p.Pro157Ser
rs6472812 - p.Arg56Gly

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for LY96 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for LY96 Gene

Variant ID Type Subtype PubMed ID
esv2668168 CNV deletion 23128226
esv3617644 CNV loss 21293372
nsv6259 CNV insertion 18451855
nsv831355 CNV loss 17160897

Variation tolerance for LY96 Gene

Residual Variation Intolerance Score: 45.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.30; 25.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LY96 Gene

Human Gene Mutation Database (HGMD)
LY96
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LY96

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LY96 Gene

Disorders for LY96 Gene

MalaCards: The human disease database

(9) MalaCards diseases for LY96 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
melioidosis
  • melioidosis, susceptibility to
acute gonococcal cervicitis
  • acute gonorrhea of cervix
acute cervicitis
pneumonia
  • acute pneumonia
cataract 30
  • cataract 30 pulverulent
- elite association - COSMIC cancer census association via MalaCards
Search LY96 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LY96

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with LY96: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LY96 Gene

Publications for LY96 Gene

  1. Gene polymorphisms of Toll-like and related recognition receptors in relation to the vaginal carriage of Gardnerella vaginalis and Atopobium vaginae. (PMID: 19200604) Verstraelen H … Temmerman M (Journal of reproductive immunology 2009) 3 23 41
  2. Natural selection in the TLR-related genes in the course of primate evolution. (PMID: 18810425) Nakajima T … Kimura A (Immunogenetics 2008) 3 4 23
  3. Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran. (PMID: 17803912) Kim HM … Lee JO (Cell 2007) 3 4 23
  4. Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa. (PMID: 17569869) Ohto U … Satow Y (Science (New York, N.Y.) 2007) 3 4 23
  5. Lipopolysaccharide is in close proximity to each of the proteins in its membrane receptor complex. transfer from CD14 to TLR4 and MD-2. (PMID: 11274165) da Silva Correia J … Ulevitch RJ (The Journal of biological chemistry 2001) 3 4 23

Products for LY96 Gene

Sources for LY96 Gene