Ly96 lymphocyte antigen 96 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Ly96provided by RGD
Full Name: lymphocyte antigen 96provided by RGD
Primary source: RGD:1302993
See related: AllianceGenome:RGD:1302993
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: MD2; MD-2
Summary: Predicted to enable lipopolysaccharide immune receptor activity. Predicted to be involved in positive regulation of tumor necrosis factor production; response to lipopolysaccharide; and toll-like receptor 4 signaling pathway. Predicted to act upstream of or within positive regulation of lipopolysaccharide-mediated signaling pathway and response to lipopolysaccharide. Predicted to be intrinsic component of plasma membrane. Predicted to be part of lipopolysaccharide receptor complex. Orthologous to human LY96 (lymphocyte antigen 96). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Adrenal (RPKM 71.2), Spleen (RPKM 67.8) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q11

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (7365536..7397864, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (2582233..2612357, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (1972212..1989448, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Evidence that angiotensin II does not directly stimulate the MD2-TLR4 innate inflammatory pathway.
Title: Evidence that angiotensin II does not directly stimulate the MD2-TLR4 innate inflammatory pathway.
MD2 is essential to obesity-related cardiac hypertrophy through activating JNK/ERK and NF-kappaB-dependent cardiac inflammatory pathways. Targeting MD2 would be a therapeutic approach to prevent obesity-induced cardiac injury and remodeling.
Title: Inhibition of myeloid differentiation factor-2 attenuates obesity-induced cardiomyopathy and fibrosis.
Up-regulation of MD-2 in alveolar macrophages was attenuated after PAI-1 gene knockdown.
Title: Plasminogen activator inhibitor-1 regulates LPS-induced TLR4/MD-2 pathway activation and inflammation in alveolar macrophages.
Data show that rifampin binds to myeloid differentiation protein 2 (MD-2), the key coreceptor for innate immune TLR4.
Title: Rifampin inhibits Toll-like receptor 4 signaling by targeting myeloid differentiation protein 2 and attenuates neuropathic pain.
LPS induced increases in TNF-alpha, IL-1 beta and IL-6 protein levels in NR8383 cell supernatants was significantly inhibited by MD-2 silencing.
Title: Myeloid differentiation protein 2 silencing decreases LPS-induced cytokine production and TLR4/MyD88 pathway activity in alveolar macrophages.
Higher dose LPS can up-regulate the gene expression of TLR4 and MD-2 in rat alveolar macrophage NR8383 cell line, and promote the secretion of TNF-alpha, IL-6 and IL-1beta.
Title: [The effect of lipopolysaccharide on gene expression of TLR4 and MD-2 in rat alveolar macrophage and its secretion of inflammation cytokines].
After LPS challenge, gene expressions of TLR4, MD-2 and TNF-alpha were significantly lower in females.
Title: [Influence of sexual difference on expression of Toll-like receptor 4 and myeloid differential protein-2 mRNA in the lung in septic rats].
high affinity interactions between the palmitoyl-oleoyl-phosphatidylglycerol and the Toll-like receptor 4-interacting proteins CD14 and MD-2.
Title: Anionic pulmonary surfactant phospholipids inhibit inflammatory responses from alveolar macrophages and U937 cells by binding the lipopolysaccharide-interacting proteins CD14 and MD-2.

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General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables Toll-like receptor 4 binding	IEA Inferred from Electronic Annotation more info
enables lipopolysaccharide binding	IEA Inferred from Electronic Annotation more info
enables lipopolysaccharide immune receptor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cellular response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in detection of lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
acts_upstream_of lipopolysaccharide-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in lipopolysaccharide-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of lipopolysaccharide-mediated signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of tumor necrosis factor production	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in response to lipopolysaccharide	ISO Inferred from Sequence Orthology more info
involved_in toll-like receptor 4 signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in toll-like receptor signaling pathway	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of lipopolysaccharide receptor complex	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of receptor complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: lymphocyte antigen 96

Names: LPS co-receptor MD-2

NCBI Reference Sequences (RefSeq)

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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)

NM_001024279.1 → NP_001019450.1 lymphocyte antigen 96 precursor

See identical proteins and their annotated locations for NP_001019450.1

Status: PROVISIONAL

Source sequence(s)

AY963291

UniProtKB/TrEMBL

Q56DL5

Conserved Domains (1) summary

cl00274
Location:23 → 153

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_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

7365536..7397864 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063288158.1 → XP_063144228.1 lymphocyte antigen 96 isoform X1

UniProtKB/TrEMBL

Q56DL5
XM_039110517.2 → XP_038966445.1 lymphocyte antigen 96 isoform X2

UniProtKB/TrEMBL

A6JF95

Conserved Domains (1) summary

cl00274
Location:6 → 114

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 ...