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    CCR6 C-C motif chemokine receptor 6 [ Homo sapiens (human) ]

    Gene ID: 1235, updated on 10-Dec-2024

    Summary

    Official Symbol
    CCR6provided by HGNC
    Official Full Name
    C-C motif chemokine receptor 6provided by HGNC
    Primary source
    HGNC:HGNC:1607
    See related
    Ensembl:ENSG00000112486 MIM:601835; AllianceGenome:HGNC:1607
    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
    BN-1; DCR2; DRY6; CCR-6; CD196; CKRL3; GPR29; CKR-L3; CMKBR6; GPRCY4; STRL22; CC-CKR-6; C-C CKR-6
    Summary
    This gene encodes a member of the beta chemokine receptor family, which is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. The gene is preferentially expressed by immature dendritic cells and memory T cells. The ligand of this receptor is macrophage inflammatory protein 3 alpha (MIP-3 alpha). This receptor has been shown to be important for B-lineage maturation and antigen-driven B-cell differentiation, and it may regulate the migration and recruitment of dentritic and T cells during inflammatory and immunological responses. Alternatively spliced transcript variants that encode the same protein have been described for this gene. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in lymph node (RPKM 8.0), appendix (RPKM 6.0) and 13 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CCR6 in Genome Data Viewer
    Location:
    6q27
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (167111795..167139141)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (168494454..168521816)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (167525283..167552629)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25444 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17787 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17788 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17789 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17790 Neighboring gene microRNA 3939 Neighboring gene centrosomal protein 43 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25446 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25447 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25448 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:167493737-167494237 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25449 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25450 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25451 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25452 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25453 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25454 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25455 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:167532493-167532993 Neighboring gene uncharacterized LOC107986672 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25456 Neighboring gene uncharacterized LOC112267970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:167556216-167557144 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:167557145-167558073 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:167576665-167577653 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:167578457-167579656 Neighboring gene uncharacterized LOC105378123 Neighboring gene G protein-coupled receptor 31

    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
    A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility.
    EBI GWAS Catalog
    Amerindian-specific regions under positive selection harbour new lipid variants in Latinos.
    EBI GWAS Catalog
    Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease.
    EBI GWAS Catalog
    Genetics of rheumatoid arthritis contributes to biology and drug discovery.
    EBI GWAS Catalog
    Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.
    EBI GWAS Catalog
    Genome-wide association study for vitiligo identifies susceptibility loci at 6q27 and the MHC.
    EBI GWAS Catalog
    Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
    EBI GWAS Catalog
    Genome-wide association study of autistic-like traits in a general population study of young adults.
    EBI GWAS Catalog
    Genome-wide association study of Crohn's disease in Koreans revealed three new susceptibility loci and common attributes of genetic susceptibility across ethnic populations.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Novel risk loci for rheumatoid arthritis in Han Chinese and congruence with risk variants in Europeans.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of chemokine (C-C motif) receptor 6 (CCR6) in human B cells PubMed
    env HIV-1 gp120 interactions with CXCR4 and CCR5 lead to the cross-desensitization of CCR6 and CCR7; this gp120-induced inhibition is strictly dependent on CXCR4 or CCR5 and lipid rafts but not on CD4 or V(H)3-expressing BCR 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

    Potential readthrough

    Included gene: CEP43

    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 binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables C-C chemokine binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables C-C chemokine receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables C-C chemokine receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables C-C chemokine receptor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables chemokine receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables signaling receptor activity TAS
    Traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in DN2 thymocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in DN3 thymocyte differentiation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in T cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in calcium-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in calcium-mediated signaling IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in cell chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in cellular defense response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in chemokine-mediated signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chemotaxis IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in chemotaxis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in dendritic cell chemotaxis TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in humoral immune response TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in isotype switching to IgA isotypes ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in leukocyte migration involved in inflammatory response ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in lymphocyte migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of cytosolic calcium ion concentration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of dendritic cell chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of flagellated sperm motility involved in capacitation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in regulation of T cell migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in signal transduction TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in thymocyte migration IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in thymocyte migration ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Component Evidence Code Pubs
    located_in cell surface 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
     
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
     
    located_in sperm flagellum IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in sperm midpiece IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in sperm plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in sperm principal piece IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    C-C chemokine receptor type 6
    Names
    G protein-coupled receptor 29
    LARC receptor
    chemokine (C-C motif) receptor 6
    chemokine (C-C) receptor 6
    chemokine receptor-like 3
    seven-transmembrane receptor, lymphocyte, 22

    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_001394582.1NP_001381511.1  C-C chemokine receptor type 6

      Status: REVIEWED

      Source sequence(s)
      AL121935
      Consensus CDS
      CCDS5298.1
      UniProtKB/Swiss-Prot
      E1P5C6, P51684, P78553, Q92846
      UniProtKB/TrEMBL
      A8KAF0
      Related
      ENSP00000339393.4, ENST00000349984.6
      Conserved Domains (1) summary
      cd15172
      Location:47327
      7tmA_CCR6; CC chemokine receptor type 6, member of the class A family of seven-transmembrane G protein-coupled receptors
    2. NM_004367.6NP_004358.2  C-C chemokine receptor type 6

      See identical proteins and their annotated locations for NP_004358.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 2. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL121935, CD692892, DN996219
      Consensus CDS
      CCDS5298.1
      UniProtKB/Swiss-Prot
      E1P5C6, P51684, P78553, Q92846
      UniProtKB/TrEMBL
      A8KAF0
      Related
      ENSP00000383715.2, ENST00000400926.5
      Conserved Domains (1) summary
      cd15172
      Location:47327
      7tmA_CCR6; CC chemokine receptor type 6, member of the class A family of seven-transmembrane G protein-coupled receptors
    3. NM_031409.4NP_113597.2  C-C chemokine receptor type 6

      See identical proteins and their annotated locations for NP_113597.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) is the longer transcript. Variants 1 and 2 encode the same protein.
      Source sequence(s)
      AL121935, BC037960, DA645096
      Consensus CDS
      CCDS5298.1
      UniProtKB/Swiss-Prot
      E1P5C6, P51684, P78553, Q92846
      UniProtKB/TrEMBL
      A8KAF0
      Related
      ENSP00000343952.5, ENST00000341935.10
      Conserved Domains (1) summary
      cd15172
      Location:47327
      7tmA_CCR6; CC chemokine receptor type 6, member of the class A family of seven-transmembrane G protein-coupled receptors

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      167111795..167139141
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      168494454..168521816
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)