Ly96 MGI Mouse Gene Detail - MGI:1341909

Symbol

Ly96
Name

lymphocyte antigen 96
Synonyms

ESOP-1, MD-2, MD2, myeloid differentiation factor-2

Feature Type

protein coding gene
IDs

MGI:1341909
NCBI Gene: 17087
Alliance

genome feature page
Transcription Start Sites

6 TSS

Sequence Map

Chr1:16758680-16779829 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 5.10 cM
Mapping Data

1 experiment

SNPs within 2kb

765 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1341909	protein coding gene	Chr1:16758275-16779835 (+)
129S1/SvImJ	ENSMUSG00200018582	protein coding gene	Chr1:14148108-14170419 (+)
A/J	ENSMUSG00195027216	protein coding gene	Chr1:13943332-13965632 (+)
AKR/J	ENSMUSG00220008251	protein coding gene	Chr1:13991709-14014026 (+)
BALB/cJ	ENSMUSG00180023295	protein coding gene	Chr1:14009689-14031987 (+)
C3H/HeJ	ENSMUSG00175000244	protein coding gene	Chr1:13935738-13958031 (+)
C57BL/6NJ	ENSMUSG00215010500	protein coding gene	Chr1:13971781-13994096 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0013971	protein coding gene	Chr1:12626384-12647750 (+)
CAST/EiJ	ENSTCUG00005020648	protein coding gene	Chr1:14269768-14291407 (+)
CBA/J	ENSMUSG00210002624	protein coding gene	Chr1:13801473-13823771 (+)
DBA/2J	ENSMUSG00185003839	protein coding gene	Chr1:14865748-14888037 (+)
FVB/NJ	ENSMUSG00205015943	protein coding gene	Chr1:14037515-14059813 (+)
JF1/MsJ	ENSUMUG00000016680	protein coding gene	Chr1:14131010-14151667 (+)
LP/J	ENSMUSG00230017788	protein coding gene	Chr1:14849437-14871744 (+)
NOD/ShiLtJ	ENSMUSG00190027542	protein coding gene	Chr1:13911024-13933315 (+)
NZO/HlLtJ	ENSMUSG00225004511	protein coding gene	Chr1:18252261-18274545 (+)
PWK/PhJ	ENSLUMG00010020880	protein coding gene	Chr1:13721059-13741683 (+)
SPRET/EiJ	ENSMSPG00010026831	protein coding gene	Chr1:14546734-14567677 (+)
WSB/EiJ	ENSIUOG00005011652	protein coding gene	Chr1:13879231-13901551 (+)

Human Ortholog

LY96, lymphocyte antigen 96

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

LY96, lymphocyte antigen 96
Synonyms

ESOP-1, ly-96, MD-2, MD2
Links

HGNC:17156

NCBI Gene ID: 23643

UniProt: Q9Y6Y9
Chr Location

8q21.11; chr8:73991392-74099857 (+) GRCh38

MGI Vertebrate Homology

Ly96 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: LY96
Gene Tree

Ly96

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Phenotype Summary

10 phenotypes from 2 alleles in 2 genetic backgrounds
60 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

10
Chemically induced (ENU)

1
Endonuclease-mediated

6
Targeted

3
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

13 strains or lines available

Mice homozygous for a knock-out allele display impaired responsiveness to LPS, are resistant to LPS-induced lethal toxicity but show increased susceptibility to Salmonella typhimurium infection.

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All GO Annotations

46
GO References

15

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

633
Tissues

34
cDNA Data

7
Literature Summary

2

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

40
RefSeq

4
UniProt

4
CCDS

CCDS14832.1, CCDS78550.1

Ensembl

ENSMUSG00000025779 (Evidence)
NCBI Gene

17087

			Length	Strain/Species	Flank
genomic	17087	NCBI Gene Model \| MGI Sequence Detail	21150	C57BL/6J	± kb
transcript	NM_016923	RefSeq \| MGI Sequence Detail	603	C57BL/6
polypeptide	Q9JHF9	UniProt \| EBI \| MGI Sequence Detail	160	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000003296 lymphocyte antigen 96

(term hierarchy)
PDB

2Z64, 3VQ1, 3VQ2, 5IJB, 5IJC, 5IJD, 7MLM, 8WQT, 8WRY, 8WSA
InterPro Domains

IPR014756 Immunoglobulin E-set

IPR039217 Lymphocyte antigen 96

IPR003172 MD-2-related lipid-recognition domain
GlyGen

Q9JHF9 3 sites, 1 N-linked glycan (1 site)

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All nucleic 7

cDNA 7

Antibodies 2

Microarray probesets 2

Summaries

All 150

Developmental Gene Expression 2

Gene Ontology 15

Phenotypes 60
Earliest

J:55323 Shimazu R, et al., MD-2, a molecule that confers lipopolysaccharide responsiveness on Toll-like receptor 4. J Exp Med. 1999 Jun 7;189(11):1777-82
Latest

J:372177 Qian C, et al., Cyclic-di-GMP induces inflammation and acute lung injury through direct binding to MD2. Clin Transl Med. 2024 Aug;14(8):e1744

TSS for Ly96:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr6007	Chr1:16758256-16758297 (+)	-403 bp
Tssr6008	Chr1:16758629-16758682 (+)	-24 bp
Tssr6009	Chr1:16758683-16758695 (+)	9 bp
Tssr6010	Chr1:16758731-16758742 (+)	57 bp
Tssr6011	Chr1:16761955-16761972 (+)	3,284 bp
Tssr6012	Chr1:16779693-16779705 (+)	21,019 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/01/2026 MGI 6.24