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    XCR1 X-C motif chemokine receptor 1 [ Homo sapiens (human) ]

    Gene ID: 2829, updated on 2-Nov-2024

    Summary

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    Official Symbol
    XCR1provided by HGNC
    Official Full Name
    X-C motif chemokine receptor 1provided by HGNC
    Primary source
    HGNC:HGNC:1625
    See related
    Ensembl:ENSG00000173578 MIM:600552; AllianceGenome:HGNC:1625
    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
    GPR5; CCXCR1
    Summary
    The protein encoded by this gene is a chemokine receptor belonging to the G protein-coupled receptor superfamily. The family members are characterized by the presence of 7 transmembrane domains. The encoded protein transduces a signal by increasing the intracellular calcium ion level. The viral macrophage inflammatory protein-II is an antagonist of this receptor and blocks signaling. Some studies have implicated a cluster of genes at 3p21.31, including this gene, as associated with COVID-19 risk. The encoded protein may also play a role in cell proliferation and migration in several types of cancer. [provided by RefSeq, Jan 2023]
    Annotation information
    Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
    Expression
    Biased expression in lymph node (RPKM 2.0), spleen (RPKM 1.4) and 12 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See XCR1 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (46017007..46085844, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (46032885..46101714, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (46058499..46127336, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene FYVE and coiled-coil domain autophagy adaptor 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45989039-45989208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19787 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009167-46009806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009807-46010446 Neighboring gene Sharpr-MPRA regulatory region 2695 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46029541-46030041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46034569-46035069 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46037115-46037614 Neighboring gene uncharacterized LOC105377063 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14287 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46072313-46072813 Neighboring gene nuclear receptor binding factor 2 pseudogene 2 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_70191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19791 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19792 Neighboring gene Sharpr-MPRA regulatory region 1914 Neighboring gene uncharacterized LOC105377067 Neighboring gene FLT1 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46211627-46212128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46212129-46212628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19794

    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 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. The herpesvirus 8 encoded chemokines vCCL2 (vMIP-II) and vCCL3 (vMIP-III) target the human but not the murine lymphotactin receptor. Lüttichau HR. Virol J, 2008 Apr 21. PMID 18426556, Free PMC Article
    2. XCR1 promotes cell growth and migration and is correlated with bone metastasis in non-small cell lung cancer. Wang T, et al. Biochem Biophys Res Commun, 2015 Aug 21. PMID 26166822
    3. The lymphotactin receptor is expressed in epithelial ovarian carcinoma and contributes to cell migration and proliferation. Kim M, et al. Mol Cancer Res, 2012 Nov. PMID 22964431
    4. Transcriptomic analyses of chemokines reveal that down-regulation of XCR1 is associated with advanced hepatocellular carcinoma. Yanru W, et al. Biochem Biophys Res Commun, 2018 Feb 19. PMID 29408492
    5. XCL1 and XCR1 in the immune system. Lei Y, et al. Microbes Infect, 2012 Mar. PMID 22100876

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Systematic Pan-Cancer Analysis Reveals X-C Motif Chemokine Receptor 1 as a Prognostic and Immunological Biomarker.
      Title: Systematic Pan-Cancer Analysis Reveals X-C Motif Chemokine Receptor 1 as a Prognostic and Immunological Biomarker.
    2. Overexpression of chemokine receptor lymphotactin receptor 1 has prognostic value in clear cell renal cell carcinoma.
      Title: Overexpression of chemokine receptor lymphotactin receptor 1 has prognostic value in clear cell renal cell carcinoma.
    3. Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1.
      Title: Structure-function guided modeling of chemokine-GPCR specificity for the chemokine XCL1 and its receptor XCR1.
    4. XCL1-XCR1 chemokine pathway promotes trophoblast invasion by increasing matrix metalloproteinase activity in human first-trimester placenta
      Title: XCL1-XCR1 pathway promotes trophoblast invasion at maternal-fetal interface by inducing MMP-2/MMP-9 activity.
    5. Our study provides the basis for further investigation of the molecular mechanism by which down-regulation of XCR1 promotes the development and progression of HCC.
      Title: Transcriptomic analyses of chemokines reveal that down-regulation of XCR1 is associated with advanced hepatocellular carcinoma.
    6. Demonstrate equivalence between human and mouse XCR1(+) dendritic cells and human and mouse Langerhans cells.
      Title: Comparative genomics analysis of mononuclear phagocyte subsets confirms homology between lymphoid tissue-resident and dermal XCR1(+) DCs in mouse and human and distinguishes them from Langerhans cells.
    7. results indicate that XCR1 is a new potential therapeutic target for the treatment of lung cancer bone metastasis
      Title: XCR1 promotes cell growth and migration and is correlated with bone metastasis in non-small cell lung cancer.
    8. Induction of potent CD8 T cell cytotoxicity by specific targeting of antigen to cross-presenting dendritic cells in vivo via murine or human XCR1.
      Title: Induction of potent CD8 T cell cytotoxicity by specific targeting of antigen to cross-presenting dendritic cells in vivo via murine or human XCR1.
    9. XCR1 is expressed early during the course of tumorigenic transformation and contributes towards increased cell migration and proliferation, which can facilitate the prometastatic behavior of epithelial ovarian cancer cells.
      Title: The lymphotactin receptor is expressed in epithelial ovarian carcinoma and contributes to cell migration and proliferation.
    10. CD8alpha-positive dendritic cells (DCs) and CD103-positive DCs belong to a common DC subset which is unequivocally identified by XCR1 transgene expression despite their different anatomical locations.
      Title: Cutting edge: expression of XCR1 defines mouse lymphoid-tissue resident and migratory dendritic cells of the CD8α+ type.
    Submit: New GeneRIF Correction See all GeneRIFs (18)

    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

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables C-C chemokine binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables C-C chemokine receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chemokine receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in G protein-coupled receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in calcium-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in chemokine-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chemotaxis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in inflammatory response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in positive regulation of cytosolic calcium ion concentration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in release of sequestered calcium ion into cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in external side of plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    chemokine XC receptor 1
    Names
    G protein-coupled receptor 5
    XC chemokine receptor 1
    chemokine (C motif) XC receptor 1
    chemokine (C motif) receptor 1
    lymphotactin receptor

    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_001024644.2 → NP_001019815.1  chemokine XC receptor 1

      See identical proteins and their annotated locations for NP_001019815.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 3. All three variants encode the same protein.
      Source sequence(s)
      AB189435, AC099782, BC069075, BC095533
      Consensus CDS
      CCDS2736.1
      UniProtKB/Swiss-Prot
      P46094
      UniProtKB/TrEMBL
      B2RAP0, Q502V0
      Related
      ENSP00000310405.3, ENST00000309285.4
      Conserved Domains (1) summary
      cd15182
      Location:32 → 298
      7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors

    2. NM_001381860.1 → NP_001368789.1  chemokine XC receptor 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) represents the longest transcript. All three variants encode the same protein.
      Source sequence(s)
      AC099782, AC104439, AC133140
      Consensus CDS
      CCDS2736.1
      UniProtKB/Swiss-Prot
      P46094
      UniProtKB/TrEMBL
      B2RAP0, Q502V0
      Related
      ENSP00000507745.1, ENST00000683768.1
      Conserved Domains (1) summary
      cd15182
      Location:32 → 298
      7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors

    3. NM_005283.3 → NP_005274.1  chemokine XC receptor 1

      See identical proteins and their annotated locations for NP_005274.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 3. All three variants encode the same protein.
      Source sequence(s)
      AB189434, AC099782, BC069075, BC095533
      Consensus CDS
      CCDS2736.1
      UniProtKB/Swiss-Prot
      P46094
      UniProtKB/TrEMBL
      B2RAP0, Q502V0
      Related
      ENSP00000379277.3, ENST00000395946.3
      Conserved Domains (1) summary
      cd15182
      Location:32 → 298
      7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors

    RNA

    1. NR_170111.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC104439, AC133140

    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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      46017007..46085844 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      46032885..46101714 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P46094.1 GenPept UniProtKB/Swiss-Prot:P46094

    Gene LinkOut

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

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