LY96 Gene (Protein Coding)

Lymphocyte Antigen 96

GC08P073991
GIFtS:
44
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
  • MD2 3 4
  • Myeloid Differentiation Protein-2 3
  • ESOP1 4
  • MD-2 3

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 Intestinal Botulism and Wound Botulism. Among its related pathways are Bacterial infections in CF airways and Regulation by c-FLIP. 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

Additional gene information 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 for LY96 Gene

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 750.6 +1.2 1167 3.8 SP1 ZBTB40 ETV6 ELF1 RELA L3MBTL2 ZNF121 NKRF ELF3 TFE3 LY96 TMEM70 ELOC piR-60140-024
GH08J073967 Enhancer 0.5 ENCODE 10.6 -24.8 -24848 0.2 HLF CEBPG PRDM1 IKZF1 CEBPA CEBPB NFE2 FOS IRF9 LY96 UBE2W TMEM70 ELOC piR-57461-258
GH08J073966 Promoter 0.4 Ensembl 10.6 -24.4 -24428 0.2 CEBPB LY96 UBE2W ELOC piR-57461-258
GH08J074056 Enhancer 0.3 Ensembl 10.8 +66.0 65972 1.4 MAFK ZNF316 RPS3AP32 lnc-LY96-5 TMEM70 ELOC LY96 GDAP1 ENSG00000253596 ENSG00000254288 lnc-LY96-4 RF00026-1084
GH08J074033 Enhancer 0.3 Ensembl ENCODE 11 +42.0 41972 2.2 piR-56133-221 TMEM70 LY96 ELOC GDAP1 piR-60112-009
- 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 UCSC Golden Path with GeneCards custom track

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

Genomic Locations for LY96 Gene
chr8:73,991,329-74,032,562
(GRCh38/hg38)
Size:
41,234 bases
Orientation:
Plus strand
chr8:74,903,564-74,941,322
(GRCh37/hg19)
Size:
37,759 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 Structure • Gene Density

RefSeq DNA sequence for LY96 Gene

Proteins for LY96 Gene

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  • 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

Protein Expression for LY96 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for LY96 Gene

Other Protein References for LY96 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for LY96
  • Boster Bio Antibodies for LY96

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

Blocks:
InterPro:
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

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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 IDA,IBA 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>

Animal Model Products

CRISPR Products

Clone Products

  • Addgene plasmids 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 4
endosome 4
nucleus 2
endoplasmic reticulum 1
cytosol 1
lysosome 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Vesicles (2)
See all subcellular structures

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
Toll Like Receptor 9 (TLR9) Cascade
.94
TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation
.94
Activated TLR4 signalling
.91
Toll Like Receptor 4 (TLR4) Cascade
.91
MyD88 dependent cascade initiated on endosome
.86
Toll Like Receptor 7/8 (TLR7/8) Cascade
.86
MyD88-independent TLR3/TLR4 cascade
.86
Toll Like Receptor 3 (TLR3) Cascade
.86
TRIF-mediated TLR3/TLR4 signaling
.86
MyD88-Mal cascade initiated on plasma membrane
.85
Toll Like Receptor 2 (TLR2) Cascade
.85
Toll Like Receptor TLR1-TLR2 Cascade
.85
Toll Like Receptor TLR6-TLR2 Cascade
.85
Toll-Like Receptors Cascades
.82
Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon
.01
IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation
.01
Regulation of TLR by endogenous ligand
.01
TRAF6 mediated induction of TAK1 complex
.01
TRIF-mediated programmed cell death
.01
2 Diseases associated with the TLR signaling cascade
Diseases associated with the TLR signaling cascade
.46
Diseases of Immune System
.46
IRAK4 deficiency (TLR2/4)
.46
MyD88 deficiency (TLR2/4)
.01
3 Toll-like Receptor Signaling Pathway
Toll-like receptor signaling pathway
.92
Toll-like Receptor Signaling Pathway
.92
Regulation of toll-like receptor signaling pathway
.71
4 Bacterial infections in CF airways
Bacterial infections in CF airways
.78
Immune response Bacterial infections in normal airways
.78
Immune response TLR signaling pathways
.46
5 PEDF Induced Signaling
MIF Mediated Glucocorticoid Regulation
.94
MIF Regulation of Innate Immune Cells
.94
genes like me logo Genes that share pathways with LY96: view

Pathways by source for LY96 Gene

1 Sino Biological pathway for LY96 Gene
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

Products:

  1. Drug

(8) 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 Agonist, Target 0
Methadone Approved, Illicit Pharma Target 383
Morphine Approved, Investigational Pharma Full agonist, Agonist, Partial agonist, Target, activator 1307
3-Hydroxy-Myristic Acid Experimental Pharma Target 0
Myristic acid Experimental Pharma Target 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

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
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mRNA/cDNA for LY96 Gene

(2) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(18) Selected AceView cDNA sequences:
(2) Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Clone Products

  • Addgene plasmids 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
ECgene alternative splicing isoforms for
LY96

Expression for LY96 Gene

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  1. Primer
  2. Gene Expression Assay

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

mRNA expression in normal human tissues for LY96 Gene
mRNA expression by BioGPS for LY96 GenemRNA expression by GTEx 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

NURSA nuclear receptor signaling pathways regulating expression of LY96 Gene:

LY96

SOURCE GeneReport for Unigene cluster for LY96 Gene:

Hs.726603

Evidence on tissue expression from TISSUES for LY96 Gene

  • Liver(4.4)
  • Blood(3.1)
  • Spleen(2.8)
  • Intestine(2.5)
  • Lymph node(2.5)
  • Lung(2.3)
  • Heart(2.2)
genes like me logo Genes that share expression patterns with LY96: view

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 32
  • 100 (n)
MD2 33
  • 99 (a)
 OneToOne
dog
(Canis familiaris)
 Mammalia LY96 33 32
  • 81.25 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia LY96 32
  • 77.08 (n)
MD2 33
  • 64 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Ly96 17 33 32
  • 75.62 (n)
rat
(Rattus norvegicus)
 Mammalia Ly96 32
  • 74.73 (n)
oppossum
(Monodelphis domestica)
 Mammalia LY96 33
  • 49 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves LY96 33
  • 32 (a)
 OneToOne
Species where no ortholog for LY96 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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

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  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for LY96 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs1000003109 -- 74,030,296(+) T/C genic_downstream_transcript_variant, intron_variant
rs1000035964 -- 74,024,718(+) T/A/C intron_variant
rs1000057015 -- 74,024,286(+) G/A intron_variant
rs1000060019 -- 74,063,638(+) A/C/G genic_downstream_transcript_variant, intron_variant
rs1000082970 -- 74,036,049(+) G/A genic_downstream_transcript_variant, intron_variant

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 Assay Products

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

Disorders for LY96 Gene

MalaCards: The human disease database

(16) MalaCards diseases for LY96 Gene - From: HGMD, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
intestinal botulism
  • intestinal colonization botulism
wound botulism
  • cutaneous infectious botulism
interstitial emphysema
parametritis
  • pelvic cellulitis
neurotic disorder
  • depressive neurosis
- 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 of Genetics and Cytogenetics in Oncology and Haematology
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. Crystal structure of the TLR4-MD-2 complex with bound endotoxin antagonist Eritoran. (PMID: 17803912) Kim HM … Lee JO (Cell 2007) 3 4 23 56
  2. 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 56
  3. Decreased expression of Toll-like receptor-4 and MD-2 correlates with intestinal epithelial cell protection against dysregulated proinflammatory gene expression in response to bacterial lipopolysaccharide. (PMID: 11466383) Abreu MT … Arditi M (Journal of immunology (Baltimore, Md. : 1950) 2001) 2 3 23 56
  4. MD-2 enables Toll-like receptor 2 (TLR2)-mediated responses to lipopolysaccharide and enhances TLR2-mediated responses to Gram-positive and Gram-negative bacteria and their cell wall components. (PMID: 11160242) Dziarski R … Gupta D (Journal of immunology (Baltimore, Md. : 1950) 2001) 3 4 23 56
  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 56

ExternalLinks

View latest publications for LY96 gene in Mastermind

Products for LY96 Gene

  • Addgene plasmids for LY96

Sources for LY96 Gene