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

Gene ID: 1235, updated on 1-Jun-2020

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
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

Genomic context

See CCR6 in Genome Data Viewer
Location:
6q27
Exon count:
4
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (167111807..167139141)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (167525295..167554168)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene microRNA 3939 Neighboring gene centrosomal protein 43 Neighboring gene uncharacterized LOC105378122 Neighboring gene uncharacterized LOC107986672 Neighboring gene uncharacterized LOC112267970 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

NHGRI GWAS Catalog

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

Homology

Gene Ontology Provided by GOA

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

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_004367.5NP_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
    P51684
    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
  2. NM_031409.3NP_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
    P51684
    Related
    ENSP00000343952.5, ENST00000341935.9
    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: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    167111807..167139141
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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