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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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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