Human Gene CCR6 (ENST00000341935.10_6) from GENCODE V47lift37
  Description: C-C motif chemokine receptor 6, transcript variant 2 (from RefSeq NM_031409.4)
Gencode Transcript: ENST00000341935.10_6
Gencode Gene: ENSG00000112486.18_12
Transcript (Including UTRs)
   Position: hg19 chr6:167,536,584-167,552,629 Size: 16,046 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr6:167,549,623-167,550,843 Size: 1,221 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:167,536,584-167,552,629)mRNA (may differ from genome)Protein (374 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CCR6_HUMAN
DESCRIPTION: RecName: Full=C-C chemokine receptor type 6; Short=C-C CKR-6; Short=CC-CKR-6; Short=CCR-6; AltName: Full=Chemokine receptor-like 3; Short=CKR-L3; AltName: Full=DRY6; AltName: Full=G-protein coupled receptor 29; AltName: Full=GPR-CY4; Short=GPRCY4; AltName: Full=LARC receptor; AltName: CD_antigen=CD196;
FUNCTION: Receptor for a C-C type chemokine. Binds to MIP-3- alpha/LARC and subsequently transduces a signal by increasing the intracellular calcium ions level.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Spleen, lymph nodes, appendix, and fetal liver. Expressed in lymphocytes, T-cells and B-cells but not in natural killer cells, monocytes or granulocytes.
INDUCTION: By IL2/interleukin-2.
SIMILARITY: Belongs to the G-protein coupled receptor 1 family.
CAUTION: It is uncertain whether Met-1 or Met-6 is the initiator.
SEQUENCE CAUTION: Sequence=CAB02144.1; Type=Erroneous initiation;
WEB RESOURCE: Name=Wikipedia; Note=CC chemokine receptors entry; URL="http://en.wikipedia.org/wiki/CC_chemokine_receptors";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: CCR6
Diseases sorted by gene-association score: limited scleroderma* (25), diffuse cutaneous systemic sclerosis* (18), erdheim-chester disease (7), clostridium difficile colitis (6), pustulosis palmaris et plantaris (5), stromal keratitis (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.83 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 29.02 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -64.50225-0.287 Picture PostScript Text
3' UTR -511.001786-0.286 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000276 - 7TM_GPCR_Rhodpsn
IPR004067 - Chemokine_CCR6
IPR000355 - Chemokine_rcpt
IPR017452 - GPCR_Rhodpsn_supfam

Pfam Domains:
PF00001 - 7 transmembrane receptor (rhodopsin family)

SCOP Domains:
81321 - Family A G protein-coupled receptor-like

ModBase Predicted Comparative 3D Structure on P51684
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0004930 G-protein coupled receptor activity
GO:0004950 chemokine receptor activity
GO:0005515 protein binding
GO:0016493 C-C chemokine receptor activity
GO:0019957 C-C chemokine binding
GO:0038023 signaling receptor activity

Biological Process:
GO:0002407 dendritic cell chemotaxis
GO:0002523 leukocyte migration involved in inflammatory response
GO:0006935 chemotaxis
GO:0006955 immune response
GO:0006959 humoral immune response
GO:0006968 cellular defense response
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007204 positive regulation of cytosolic calcium ion concentration
GO:0010634 positive regulation of epithelial cell migration
GO:0019722 calcium-mediated signaling
GO:0048290 isotype switching to IgA isotypes
GO:0060326 cell chemotaxis
GO:0060474 positive regulation of flagellated sperm motility involved in capacitation
GO:0070098 chemokine-mediated signaling pathway
GO:0072676 lymphocyte migration
GO:0072678 T cell migration
GO:0072679 thymocyte migration
GO:1904155 DN2 thymocyte differentiation
GO:1904156 DN3 thymocyte differentiation
GO:2000404 regulation of T cell migration
GO:2000510 positive regulation of dendritic cell chemotaxis

Cellular Component:
GO:0005622 intracellular
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0009897 external side of plasma membrane
GO:0009986 cell surface
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0036126 sperm flagellum
GO:0097225 sperm midpiece
GO:0097228 sperm principal piece
GO:0097524 sperm plasma membrane


-  Descriptions from all associated GenBank mRNAs
  BX647686 - Homo sapiens mRNA; cDNA DKFZp686O1481 (from clone DKFZp686O1481).
U68031 - Human G protein-coupled receptor (STRL22) mRNA, alternatively spliced 5'UTR sequence.
U68030 - Human G protein-coupled receptor (STRL22) mRNA, complete cds.
AK293015 - Homo sapiens cDNA FLJ75538 complete cds, highly similar to Homo sapiens CCR6 chemokine receptor (CMKBR6) gene.
AK223494 - Homo sapiens mRNA for chemokine (C-C motif) receptor 6 variant, clone: FCC120B07.
BC037960 - Homo sapiens chemokine (C-C motif) receptor 6, mRNA (cDNA clone MGC:46000 IMAGE:5748098), complete cds.
JD450058 - Sequence 431082 from Patent EP1572962.
JD141798 - Sequence 122822 from Patent EP1572962.
JD530494 - Sequence 511518 from Patent EP1572962.
JD199014 - Sequence 180038 from Patent EP1572962.
JD045660 - Sequence 26684 from Patent EP1572962.
AY242126 - Homo sapiens chemokine (C-C motif) receptor 6 (CCR6) mRNA, complete cds.
U60000 - Human IL8-related receptor (DRY6) mRNA, complete cds.
AB590446 - Synthetic construct DNA, clone: pFN21AE1403, Homo sapiens CCR6 gene for chemokine (C-C motif) receptor 6, without stop codon, in Flexi system.
DQ892462 - Synthetic construct clone IMAGE:100005092; FLH186545.01X; RZPDo839F0871D chemokine (C-C motif) receptor 6 (CCR6) gene, encodes complete protein.
DQ895674 - Synthetic construct Homo sapiens clone IMAGE:100010134; FLH186541.01L; RZPDo839F0861D chemokine (C-C motif) receptor 6 (CCR6) gene, encodes complete protein.
KJ890939 - Synthetic construct Homo sapiens clone ccsbBroadEn_00333 CCR6 gene, encodes complete protein.
JD305636 - Sequence 286660 from Patent EP1572962.
JD314390 - Sequence 295414 from Patent EP1572962.
JD218593 - Sequence 199617 from Patent EP1572962.
JD283865 - Sequence 264889 from Patent EP1572962.
JD232933 - Sequence 213957 from Patent EP1572962.
JD560618 - Sequence 541642 from Patent EP1572962.
JD309689 - Sequence 290713 from Patent EP1572962.
JD456254 - Sequence 437278 from Patent EP1572962.
JD549967 - Sequence 530991 from Patent EP1572962.
JD087573 - Sequence 68597 from Patent EP1572962.
JD431795 - Sequence 412819 from Patent EP1572962.
JD095833 - Sequence 76857 from Patent EP1572962.
JD436222 - Sequence 417246 from Patent EP1572962.
JD267986 - Sequence 249010 from Patent EP1572962.
JD371648 - Sequence 352672 from Patent EP1572962.
JD053096 - Sequence 34120 from Patent EP1572962.
JD078333 - Sequence 59357 from Patent EP1572962.
JD379046 - Sequence 360070 from Patent EP1572962.
JD437045 - Sequence 418069 from Patent EP1572962.
JD410653 - Sequence 391677 from Patent EP1572962.
JD105604 - Sequence 86628 from Patent EP1572962.
JD158836 - Sequence 139860 from Patent EP1572962.
JD275690 - Sequence 256714 from Patent EP1572962.
JD208656 - Sequence 189680 from Patent EP1572962.
JD111743 - Sequence 92767 from Patent EP1572962.
JD477826 - Sequence 458850 from Patent EP1572962.
JD411921 - Sequence 392945 from Patent EP1572962.
JD301461 - Sequence 282485 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P51684 (Reactome details) participates in the following event(s):

R-HSA-373087 Receptor CCR6 binds CCL20 ligand
R-HSA-1471338 Beta-defensins 1, 4A and 103 bind CCR6
R-HSA-749454 The Ligand:GPCR:Gi complex dissociates
R-HSA-749456 Liganded Gi-activating GPCRs bind inactive heterotrimeric G-protein Gi
R-HSA-380073 Liganded Gi-activating GPCR acts as a GEF for Gi
R-HSA-380108 Chemokine receptors bind chemokines
R-HSA-1461957 Beta defensins
R-HSA-418594 G alpha (i) signalling events
R-HSA-375276 Peptide ligand-binding receptors
R-HSA-1461973 Defensins
R-HSA-388396 GPCR downstream signalling
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-6803157 Antimicrobial peptides
R-HSA-372790 Signaling by GPCR
R-HSA-500792 GPCR ligand binding
R-HSA-168249 Innate Immune System
R-HSA-162582 Signal Transduction
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: CCR6_HUMAN, CKRL3, CMKBR6, E1P5C6, ENST00000341935.1, ENST00000341935.2, ENST00000341935.3, ENST00000341935.4, ENST00000341935.5, ENST00000341935.6, ENST00000341935.7, ENST00000341935.8, ENST00000341935.9, GPR29, NM_031409, P51684, P78553, Q92846, STRL22, uc317wej.1, uc317wej.2
UCSC ID: ENST00000341935.10_6
RefSeq Accession: NM_031409.4
Protein: P51684 (aka CCR6_HUMAN or CKR6_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.