Human Gene CXCR6 (uc003cpc.1) Description and Page Index
  Description: Homo sapiens chemokine (C-X-C motif) receptor 6 (CXCR6), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr3:45,984,973-45,989,845 Size: 4,873 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr3:45,987,974-45,989,002 Size: 1,029 Coding Exon Count: 1 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:45,984,973-45,989,845)mRNA (may differ from genome)Protein (342 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkHGNCHPRDLynxMGIneXtProt
OMIMPubMedReactomeStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: CXCR6_HUMAN
DESCRIPTION: RecName: Full=C-X-C chemokine receptor type 6; Short=CXC-R6; Short=CXCR-6; AltName: Full=CDw186; AltName: Full=G-protein coupled receptor STRL33; AltName: Full=G-protein coupled receptor bonzo; AltName: CD_antigen=CD186;
FUNCTION: Receptor for the C-X-C chemokine CXCL16. Used as a coreceptor by SIVs and by strains of HIV-2 and m-tropic HIV-1.
SUBCELLULAR LOCATION: Cell membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Expressed in lymphoid tissues and activated T cells.
SIMILARITY: Belongs to the G-protein coupled receptor 1 family.
WEB RESOURCE: Name=Wikipedia; Note=CXC chemokine receptors entry; URL="http://en.wikipedia.org/wiki/CXC_chemokine_receptors";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CXCR6
CDC HuGE Published Literature: CXCR6
Positive Disease Associations: HIV; pneumocystis carinii pneumonia , monocyte chemoattractant protein 1 (66-77)
Related Studies:
  1. HIV; pneumocystis carinii pneumonia
    Duggal, P. et al. 2003, Genetic influence of CXCR6 chemokine receptor alleles on PCP-mediated AIDS progression among African Americans., Genes and immunity. 2003 Jun;4(4):245-50. [PubMed 12761559]
    We suggest that CXCR6 may play a role in late-stage HIV-1 infection and may alter the progression to death after initial infection with PCP.
  2. monocyte chemoattractant protein 1 (66-77)
    , , . [PubMed 0]

-  MalaCards Disease Associations
  MalaCards Gene Search: CXCR6
Diseases sorted by gene-association score: xanthogranulomatous cholecystitis (1)

-  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: 5.88 RPKM in Spleen
Total median expression: 23.79 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 -21.9081-0.270 Picture PostScript Text
3' UTR -260.10843-0.309 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
IPR002235 - Chemokine_CXCR6
IPR000355 - Chemokine_rcpt
IPR017452 - GPCR_Rhodpsn_supfam

Pfam Domains:
PF00001 - 7 transmembrane receptor (rhodopsin family)
PF10320 - Serpentine type 7TM GPCR chemoreceptor Srsx

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

ModBase Predicted Comparative 3D Structure on O00574
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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 orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  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:0015026 coreceptor activity
GO:0016494 C-X-C chemokine receptor activity
GO:0019958 C-X-C chemokine binding

Biological Process:
GO:0006935 chemotaxis
GO:0006954 inflammatory response
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0019079 viral genome replication
GO:0070098 chemokine-mediated signaling pathway

Cellular Component:
GO:0005886 plasma membrane
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  JC209412 - Sequence 1 from Patent WO2012025759.
Y13248 - Homo sapiens mRNA for orphan chemokine receptor TYMSTR.
U73531 - Human G protein-coupled receptor STRL33.3 (STRL33) mRNA, complete cds.
AK313754 - Homo sapiens cDNA, FLJ94355, Homo sapiens chemokine (C-X-C motif) receptor 6 (CXCR6), mRNA.
U73530 - Human G protein-coupled receptor (STRL33) mRNA, alternative 5'UTR sequence.
BC033584 - Homo sapiens chemokine (C-X-C motif) receptor 6, mRNA (cDNA clone MGC:34420 IMAGE:5225727), complete cds.
U73529 - Human G protein-coupled receptor STRL33.1 (STRL33) mRNA, complete cds.
DQ895294 - Synthetic construct Homo sapiens clone IMAGE:100009754; FLH183034.01L; RZPDo839F02139D chemokine (C-X-C motif) receptor 6 (CXCR6) gene, encodes complete protein.
DQ892101 - Synthetic construct clone IMAGE:100004731; FLH183038.01X; RZPDo839F02140D chemokine (C-X-C motif) receptor 6 (CXCR6) gene, encodes complete protein.
AB464489 - Synthetic construct DNA, clone: pF1KB8800, Homo sapiens CXCR6 gene for chemokine (C-X-C motif) receptor 6, without stop codon, in Flexi system.
CU689658 - Synthetic construct Homo sapiens gateway clone IMAGE:100019019 5' read CXCR6 mRNA.
KJ893104 - Synthetic construct Homo sapiens clone ccsbBroadEn_02498 CXCR6 gene, encodes complete protein.
AF007545 - Homo sapiens SIV/HIV receptor Bonzo (Bonzo) mRNA, complete cds.
JD025454 - Sequence 6478 from Patent EP1572962.
JD030501 - Sequence 11525 from Patent EP1572962.
JD023255 - Sequence 4279 from Patent EP1572962.
JD030906 - Sequence 11930 from Patent EP1572962.
JD192538 - Sequence 173562 from Patent EP1572962.
JD218184 - Sequence 199208 from Patent EP1572962.
JD058959 - Sequence 39983 from Patent EP1572962.
JD074537 - Sequence 55561 from Patent EP1572962.
JD305193 - Sequence 286217 from Patent EP1572962.
JD182790 - Sequence 163814 from Patent EP1572962.
JD119573 - Sequence 100597 from Patent EP1572962.
JD314219 - Sequence 295243 from Patent EP1572962.
JD121258 - Sequence 102282 from Patent EP1572962.
JD052011 - Sequence 33035 from Patent EP1572962.
JD297202 - Sequence 278226 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04060 - Cytokine-cytokine receptor interaction
hsa04062 - Chemokine signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein O00574 (Reactome details) participates in the following event(s):

R-HSA-373358 Receptor CXCR6 binds CXCL16 ligand
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-418594 G alpha (i) signalling events
R-HSA-375276 Peptide ligand-binding receptors
R-HSA-388396 GPCR downstream signalling
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-372790 Signaling by GPCR
R-HSA-500792 GPCR ligand binding
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: BONZO, CXCR6_HUMAN, NM_006564, NP_006555, O00574, O00575, Q9HCA5, STRL33, TYMSTR
UCSC ID: uc003cpc.1
RefSeq Accession: NM_006564
Protein: O00574 (aka CXCR6_HUMAN or CCR6_HUMAN)
CCDS: CCDS2735.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_006564.1
exon count: 2CDS single in 3' UTR: no RNA size: 1953
ORF size: 1029CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2224.50frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.