LY86 lymphocyte antigen 86 [Homo sapiens (human)] - Gene

Summary

Official Symbol: LY86provided by HGNC
Official Full Name: lymphocyte antigen 86provided by HGNC
Primary source: HGNC:HGNC:16837
See related: Ensembl:ENSG00000112799 MIM:605241; AllianceGenome:HGNC:16837
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MD1; MD-1; MMD-1; dJ80N2.1
Summary: Acts upstream of or within positive regulation of lipopolysaccharide-mediated signaling pathway. Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in lymph node (RPKM 17.5), spleen (RPKM 16.2) and 13 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p25.1

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (6588720..6654982)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (6457947..6524157)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (6588953..6655215)

Chromosome 6 - NC_000006.12 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: 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Higher expression of PLEK and LY86 as the potential biomarker of carotid atherosclerosis.
Title: Higher expression of PLEK and LY86 as the potential biomarker of carotid atherosclerosis.
Genetic variability of immune-related lncRNAs: polymorphisms in LINC-PINT and LY86-AS1 are associated with pemphigus foliaceus susceptibility.
Title: Genetic variability of immune-related lncRNAs: polymorphisms in LINC-PINT and LY86-AS1 are associated with pemphigus foliaceus susceptibility.
LY86 knockdown results in reduced monocyte migration towards the chemokine MCP-1, thereby implying that this reduced migration may underlie the increased susceptibility to candidemia.
Title: Integrating GWAS with bulk and single-cell RNA-sequencing reveals a role for LY86 in the anti-Candida host response.
our results reveal that MD-1 deficiency is of critical importance in down-regulating induction and progression of colitis, thereby suggesting that MD-1 might be a target for future interventional therapies of inflammatory bowel disease.
Title: MD-1 deficiency attenuates dextran sodium sulfate (DSS)-induced colitis through modulating the function of colonic lamina propria dendritic cells.
DNA methylation of the LY86 gene is associated with obesity, insulin resistance, and inflammation.
Title: DNA methylation of the LY86 gene is associated with obesity, insulin resistance, and inflammation.
MD-1 may be a disease susceptibility gene for adult asthma in a Southern Han population in China.
Title: [Association of single nucleotide polymorphisms of MD-1 gene with asthma in adults of Han Nationality in Southern China].
Both mouse and human RP105/MD-1 exhibit dimerization of the 1:1 RP105/MD-1 complex, demonstrating a novel organization.
Title: Crystal structures of mouse and human RP105/MD-1 complexes reveal unique dimer organization of the toll-like receptor family.
In this study, we produced variants of MD-1 and MD-2 in Pichia pastoris. Contrary to previous reports, this study suggests that MD-1 can bind to LPS.
Title: LPS ligand and culture additives improve production of monomeric MD-1 and 2 in Pichia pastoris by decreasing aggregation and intermolecular disulfide bonding.
Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
Title: Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.
Identified MD-1 SNP (rs7740529) association with asthma in Taiwanese children and adults.
Title: Association of single nucleotide polymorphisms of MD-1 gene with pediatric and adult asthma in the Taiwanese population.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association of body fat distribution in African ancestry populations suggests new loci. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel loci for major depression identified by genome-wide association study of Sequenced Treatment Alternatives to Relieve Depression and meta-analysis of three studies. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S1442 (e-PCR)
- UniSTS:26911

RH68066 (e-PCR)
- UniSTS:34351

SHGC-59926 (e-PCR)
- UniSTS:44361

SHGC-33709 (e-PCR)
- UniSTS:12891

LY86__7346 (e-PCR)
- UniSTS:466288

SHGC-59953 (e-PCR)
- UniSTS:44665

RH93579 (e-PCR)
- UniSTS:85213

D6S1668 (e-PCR)
- UniSTS:56560

AL035199 (e-PCR)
- UniSTS:94707

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in lipopolysaccharide-mediated signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of lipopolysaccharide-mediated signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of lipopolysaccharide-mediated signaling pathway	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: lymphocyte antigen 86

Names: MD-1, RP105-associated; ly-86; protein MD-1

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_004271.4 → NP_004262.1 lymphocyte antigen 86 precursor

See identical proteins and their annotated locations for NP_004262.1

Status: VALIDATED

Source sequence(s)

BC038846, CD695164

Consensus CDS

CCDS4498.1

UniProtKB/Swiss-Prot

O95711, Q9UQC4

Related

ENSP00000230568.3, ENST00000230568.5

Conserved Domains (1) summary

cd00915
Location:30 → 159

MD-1_MD-2; MD-1 and MD-2 are cofactors required for LPS signaling through cell surface receptors. MD-2 and its binding partner, Toll-like receptor 4 (TLR4), are essential for the innate immune responses of mammalian cells to bacterial lipopolysaccharide (LPS); MD-2 ...