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

    Gene ID: 2829, updated on 27-Nov-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    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 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 
    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

    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)

    NEW Try the new Transcript table

    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_001024644.2NP_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:32298
      7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors
    2. NM_001381860.1NP_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:32298
      7tmA_XCR1; XC chemokine receptor 1, member of the class A family of seven-transmembrane G protein-coupled receptors
    3. NM_005283.3NP_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:32298
      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)