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MR1 major histocompatibility complex, class I-related [ Homo sapiens (human) ]

Gene ID: 3140, updated on 11-Apr-2024

Summary

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Official Symbol
MR1provided by HGNC
Official Full Name
major histocompatibility complex, class I-relatedprovided by HGNC
Primary source
HGNC:HGNC:4975
See related
Ensembl:ENSG00000153029 MIM:600764; AllianceGenome:HGNC:4975
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HLALS
Summary
MAIT (mucosal-associated invariant T-cells) lymphocytes represent a small population of T-cells primarily found in the gut. The protein encoded by this gene is an antigen-presenting molecule that presents metabolites of microbial vitamin B to MAITs. This presentation may activate the MAITs to regulate the amounts of specific types of bacteria in the gut. Several transcript variants encoding different isoforms have been found for this gene, and a pseudogene of it has been detected about 36 kbp upstream on the same chromosome. [provided by RefSeq, Jul 2015]
Expression
Ubiquitous expression in urinary bladder (RPKM 6.3), thyroid (RPKM 5.6) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
1q25.3
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (181033387..181061938)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (180388622..180417159)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (181002523..181031074)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene major histocompatibility complex, class I-related pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1598 Neighboring gene syntaxin 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:180959945-180960105 Neighboring gene MPRA-validated peak491 silencer Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:180991746-180992529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2167 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2168 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2169 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2170 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:181014030-181014179 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:181015297-181015799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2171 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2172 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:181046610-181047144 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:181047145-181047678 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1601 Neighboring gene uncharacterized LOC124904465 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1602 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1603 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1604 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2173 Neighboring gene Sharpr-MPRA regulatory region 8031 Neighboring gene immediate early response 5

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Suppression of MR1 by human cytomegalovirus inhibits MAIT cell activation. Ashley CL, et al. Front Immunol, 2023. PMID 36845106, Free PMC Article
  2. A specialized tyrosine-based endocytosis signal in MR1 controls antigen presentation to MAIT cells. Lim HJ, et al. J Cell Biol, 2022 Dec 5. PMID 36129434, Free PMC Article
  3. Recognition of the antigen-presenting molecule MR1 by a Vδ3(+) γδ T cell receptor. Rice MT, et al. Proc Natl Acad Sci U S A, 2021 Dec 7. PMID 34845016, Free PMC Article
  4. MR1 encompasses at least six allele groups with coding region alterations. Rozemuller E, et al. HLA, 2021 Dec. PMID 34351076
  5. T cell receptor diversity, specificity and promiscuity of functionally heterogeneous human MR1-restricted T cells. Lepore M, et al. Mol Immunol, 2021 Feb. PMID 33360378, Free PMC Article

See all (69) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. MR1 antigen presentation to MAIT cells and other MR1-restricted T cells.
    Title: MR1 antigen presentation to MAIT cells and other MR1-restricted T cells.
  2. The MR1/MAIT cell axis in CNS diseases.
    Title: The MR1/MAIT cell axis in CNS diseases.
  3. Characterization of the TCRbeta repertoire of peripheral MR1-restricted MAIT cells in psoriasis vulgaris patients.
    Title: Characterization of the TCRβ repertoire of peripheral MR1-restricted MAIT cells in psoriasis vulgaris patients.
  4. Control of the temporal development of Alzheimer's disease pathology by the MR1/MAIT cell axis.
    Title: Control of the temporal development of Alzheimer's disease pathology by the MR1/MAIT cell axis.
  5. Suppression of MR1 by human cytomegalovirus inhibits MAIT cell activation.
    Title: Suppression of MR1 by human cytomegalovirus inhibits MAIT cell activation.
  6. Role of MR1-driven signals and amphiregulin on the recruitment and repair function of MAIT cells during skin wound healing.
    Title: Role of MR1-driven signals and amphiregulin on the recruitment and repair function of MAIT cells during skin wound healing.
  7. A specialized tyrosine-based endocytosis signal in MR1 controls antigen presentation to MAIT cells.
    Title: A specialized tyrosine-based endocytosis signal in MR1 controls antigen presentation to MAIT cells.
  8. MR1 encompasses at least six allele groups with coding region alterations.
    Title: MR1 encompasses at least six allele groups with coding region alterations.
  9. The P5-type ATPase ATP13A1 modulates major histocompatibility complex I-related protein 1 (MR1)-mediated antigen presentation.
    Title: The P5-type ATPase ATP13A1 modulates major histocompatibility complex I-related protein 1 (MR1)-mediated antigen presentation.
  10. Recognition of the antigen-presenting molecule MR1 by a Vdelta3(+) gammadelta T cell receptor.
    Title: Recognition of the antigen-presenting molecule MR1 by a Vδ3(+) γδ T cell receptor.
Submit: New GeneRIF Correction See all GeneRIFs (48)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of major histocompatibility complex, class I-related (MR1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed
Knockdown of major histocompatibility complex, class I-related, isoform 4 (MR1) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ31593

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables MHC class I receptor activity TAS
Traceable Author Statement
more info
 PubMed 
enables T cell receptor binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables beta-2-microglobulin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in T cell differentiation in thymus ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in antigen processing and presentation of exogenous antigen IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in defense response to Gram-negative bacterium IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in defense response to Gram-positive bacterium IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in innate immune response IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of T cell mediated cytotoxicity directed against tumor cell target IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
part_of MHC class I protein complex IEA
Inferred from Electronic Annotation
more info
  
located_in early endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in extracellular space IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in late endosome membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
major histocompatibility complex class I-related gene protein
Names
MHC class I-like antigen MR-1
MHC class I-related protein
MHC class-I related-gene protein
major histocompatibility complex, class I-like sequence

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.

Genomic

  1. NG_042221.1 RefSeqGene

    Range
    5559..33514
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001194999.2 → NP_001181928.1  major histocompatibility complex class I-related gene protein isoform 2 precursor

    See identical proteins and their annotated locations for NP_001181928.1

    Status: REVIEWED

    Source sequence(s)
    AL356267
    Consensus CDS
    CCDS53442.1
    UniProtKB/Swiss-Prot
    Q95460
    Related
    ENSP00000356551.3, ENST00000367579.7
    Conserved Domains (2) summary
    cd07698
    Location:157 → 249
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:25 → 153
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  2. NM_001195000.2 → NP_001181929.1  major histocompatibility complex class I-related gene protein isoform 3 precursor

    See identical proteins and their annotated locations for NP_001181929.1

    Status: REVIEWED

    Source sequence(s)
    AL356267
    Consensus CDS
    CCDS53440.1
    UniProtKB/Swiss-Prot
    Q95460
    Conserved Domains (1) summary
    cl08246
    Location:25 → 198
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  3. NM_001195035.2 → NP_001181964.1  major histocompatibility complex class I-related gene protein isoform 4 precursor

    See identical proteins and their annotated locations for NP_001181964.1

    Status: REVIEWED

    Source sequence(s)
    AL356267
    Consensus CDS
    CCDS53441.1
    UniProtKB/Swiss-Prot
    Q95460
    Related
    ENSP00000388504.2, ENST00000434571.7
    Conserved Domains (1) summary
    cl08246
    Location:25 → 198
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  4. NM_001310213.2 → NP_001297142.1  major histocompatibility complex class I-related gene protein isoform 5

    Status: REVIEWED

    Source sequence(s)
    AL356267
    Conserved Domains (1) summary
    cl08246
    Location:6 → 127
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  5. NM_001385161.1 → NP_001372090.1  major histocompatibility complex class I-related gene protein isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AL356267
    Consensus CDS
    CCDS1342.1
    UniProtKB/Swiss-Prot
    A8K2V9, B4E3B1, O97985, O97986, Q53GM1, Q95460, Q95HB8, Q9MY23, Q9NPL2, Q9TQB3, Q9TQB9, Q9TQK3
    Related
    ENSP00000356552.5, ENST00000367580.6
    Conserved Domains (2) summary
    cd07698
    Location:202 → 292
    IgC1_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains
    cl08246
    Location:25 → 198
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  6. NM_001385162.1 → NP_001372091.1  major histocompatibility complex class I-related gene protein isoform 6 precursor

    Status: REVIEWED

    Source sequence(s)
    AL356267
    Consensus CDS
    CCDS91120.1
    UniProtKB/TrEMBL
    A0A8C8PVM5
    Related
    ENSP00000478976.2, ENST00000617803.5
    Conserved Domains (3) summary
    cd00096
    Location:203 → 208
    Ig; Ig strand C [structural motif]
    cl08246
    Location:25 → 198
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2
    cl11960
    Location:202 → 263
    Ig; Immunoglobulin domain

  7. NM_001385163.1 → NP_001372092.1  major histocompatibility complex class I-related gene protein isoform 7 precursor

    Status: REVIEWED

    Source sequence(s)
    AL356267
    Conserved Domains (1) summary
    cl08246
    Location:25 → 198
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  8. NM_001385164.1 → NP_001372093.1  major histocompatibility complex class I-related gene protein isoform 3 precursor

    Status: REVIEWED

    Source sequence(s)
    AL356267
    Consensus CDS
    CCDS53440.1
    Related
    ENSP00000282990.6, ENST00000282990.10
    Conserved Domains (1) summary
    cl08246
    Location:25 → 198
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

  9. NM_001531.3 → NP_001522.1  major histocompatibility complex class I-related gene protein isoform 1 precursor

    See identical proteins and their annotated locations for NP_001522.1

    Status: REVIEWED

    Source sequence(s)
    AL356267
    Consensus CDS
    CCDS1342.1
    UniProtKB/Swiss-Prot
    A8K2V9, B4E3B1, O97985, O97986, Q53GM1, Q95460, Q95HB8, Q9MY23, Q9NPL2, Q9TQB3, Q9TQB9, Q9TQK3
    Related
    ENSP00000477563.1, ENST00000614012.5
    Conserved Domains (2) summary
    cd07698
    Location:202 → 292
    IgC1_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain, alpha3 immunoglobulin domain; member of the C1-set of Ig superfamily (IgSF) domains
    cl08246
    Location:25 → 198
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    181033387..181061938
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047418899.1 → XP_047274855.1  major histocompatibility complex class I-related gene protein isoform X1

    UniProtKB/TrEMBL
    A0A8C8PVM5

  2. XM_011509463.3 → XP_011507765.1  major histocompatibility complex class I-related gene protein isoform X2

    Conserved Domains (2) summary
    cd07698
    Location:115 → 207
    IgC_MHC_I_alpha3; Class I major histocompatibility complex (MHC) alpha chain immunoglobulin domain
    cl08246
    Location:20 → 111
    MHC_I; Class I Histocompatibility antigen, domains alpha 1 and 2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    180388622..180417159
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054336224.1 → XP_054192199.1  major histocompatibility complex class I-related gene protein isoform X1

    UniProtKB/TrEMBL
    A0A8C8PVM5

  2. XM_054336225.1 → XP_054192200.1  major histocompatibility complex class I-related gene protein isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q95460.1 GenPept UniProtKB/Swiss-Prot:Q95460

Gene LinkOut

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