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LY86 lymphocyte antigen 86 [ Homo sapiens (human) ]

Gene ID: 9450, updated on 2-Nov-2024

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
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Genomic context

See LY86 in Genome Data Viewer
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_000006.12Genomic Context describing neighboring genes Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:6361855-6363054 Neighboring gene small nuclear RNA activating complex polypeptide 5 pseudogene 1 Neighboring gene LY86 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23916 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23917 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23921 Neighboring gene calponin 3 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23922 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23923 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23924 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23925 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:6654090-6654280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:6674525-6675024 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr6:6694456-6695405 Neighboring gene uncharacterized LOC101928004 Neighboring gene uncharacterized LOC101928047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:6712197-6712986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23927 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:6725016-6725709 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:6750245-6750862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:6751483-6752100 Neighboring gene uncharacterized LOC105374901

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

Description
Genome-wide association of body fat distribution in African ancestry populations suggests new loci.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.
EBI GWAS Catalog
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
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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Component Evidence Code Pubs
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 

General protein information

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)

  1. NM_004271.4NP_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:30159
    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 ...

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    6588720..6654982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    6457947..6524157
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)