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    CXCR5 C-X-C motif chemokine receptor 5 [ Homo sapiens (human) ]

    Gene ID: 643, updated on 3-Dec-2024

    Summary

    Official Symbol
    CXCR5provided by HGNC
    Official Full Name
    C-X-C motif chemokine receptor 5provided by HGNC
    Primary source
    HGNC:HGNC:1060
    See related
    Ensembl:ENSG00000160683 MIM:601613; AllianceGenome:HGNC:1060
    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
    BLR1; CD185; MDR15
    Summary
    This gene encodes a multi-pass membrane protein that belongs to the CXC chemokine receptor family. It is expressed in mature B-cells and Burkitt's lymphoma. This cytokine receptor binds to B-lymphocyte chemoattractant (BLC), and is involved in B-cell migration into B-cell follicles of spleen and Peyer patches. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Aug 2011]
    Expression
    Biased expression in lymph node (RPKM 22.1), spleen (RPKM 17.8) and 3 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CXCR5 in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    2
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (118883892..118897787)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (118902950..118918023)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118754601..118768496)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene COX7C pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5603 Neighboring gene SET pseudogene 16 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3955 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5605 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5607 Neighboring gene uncharacterized LOC124902767 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118758848-118759465 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118766473-118767231 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118768851-118769358 Neighboring gene BCL9 like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5608 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118779970-118780511 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118781595-118782134 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr11:118782402-118783601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5609 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118784843-118785382 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118785383-118785924 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118787549-118788090 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118788631-118789172 Neighboring gene microRNA 4492 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118792419-118792959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118794043-118794583 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118794584-118795123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5610 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118795793-118796294 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3957 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3958 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3959 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118798447-118798948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5611 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5613 Neighboring gene RNA, 7SL, cytoplasmic 688, pseudogene

    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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Association analyses identify three susceptibility Loci for vitiligo in the Chinese Han population.
    EBI GWAS Catalog
    Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
    EBI GWAS Catalog
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.
    EBI GWAS Catalog
    Genome-wide Association Study Identifies Five Susceptibility Loci for Follicular Lymphoma outside the HLA Region.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    HIV-1 infection downregulates CXCR5 and PDCD1 (PD1) expression in primary germinal center T follicular helper cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef HIV-1 Nef induces variable levels of CXCR5 downregulation in different cell types PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC117347

    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 C-X-C chemokine receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables G protein-coupled 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 B cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in G protein-coupled receptor signaling pathway 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 immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in leukocyte chemotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lymph node development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of cytokinesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cytosolic calcium ion concentration IBA
    Inferred from Biological aspect of Ancestor
    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

    Preferred Names
    C-X-C chemokine receptor type 5
    Names
    Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)
    Burkitt lymphoma receptor 1, GTP-binding protein
    CXC-R5
    CXCR-5
    MDR-15
    chemokine (C-X-C motif) receptor 5
    monocyte-derived receptor 15

    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_001716.5NP_001707.1  C-X-C chemokine receptor type 5 isoform 1

      See identical proteins and their annotated locations for NP_001707.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript, and encodes the longer isoform (1).
      Source sequence(s)
      AK291512, AP004609, AW575330, BC110352
      Consensus CDS
      CCDS8402.1
      UniProtKB/Swiss-Prot
      P32302, Q14811
      UniProtKB/TrEMBL
      A0N0R2, A8K647, Q2YD84
      Related
      ENSP00000292174.4, ENST00000292174.5
      Conserved Domains (1) summary
      pfam00001
      Location:68322
      7tm_1; 7 transmembrane receptor (rhodopsin family)
    2. NM_032966.2NP_116743.1  C-X-C chemokine receptor type 5 isoform 2

      See identical proteins and their annotated locations for NP_116743.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs at the 5' end compared to variant 1. This results in translation initiation from an in-frame downstream AUG, and an isoform (2) with a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AW575330, BC110352, CO958128, X68829
      UniProtKB/TrEMBL
      A8K647, Q2YD84
      Conserved Domains (1) summary
      pfam00001
      Location:23277
      7tm_1; 7 transmembrane receptor (rhodopsin family)

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      118883892..118897787
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      118902950..118918023
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369641.1XP_054225616.1  C-X-C chemokine receptor type 5 isoform X1

      UniProtKB/Swiss-Prot
      P32302, Q14811
      UniProtKB/TrEMBL
      A0N0R2, A8K647, Q2YD84