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CCR9 C-C motif chemokine receptor 9 [ Homo sapiens (human) ]

Gene ID: 10803, updated on 26-May-2016
Official Symbol
CCR9provided by HGNC
Official Full Name
C-C motif chemokine receptor 9provided by HGNC
Primary source
HGNC:HGNC:1610
See related
Ensembl:ENSG00000173585 HPRD:09200; MIM:604738; Vega:OTTHUMG00000133450
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
GPR28; CDw199; GPR-9-6; CC-CKR-9
Summary
The protein encoded by this gene is a member of the beta chemokine receptor family. It is predicted to be a seven transmembrane protein similar to G protein-coupled receptors. Chemokines and their receptors are key regulators of the thymocytes migration and maturation in normal and inflammation conditions. The specific ligand of this receptor is CCL25. It has been found that this gene is differentially expressed by T lymphocytes of small intestine and colon, suggested a role in the thymocytes recruitment and development that may permit functional specialization of immune responses in different segment of the gastrointestinal tract. This gene is mapped to the chemokine receptor gene cluster region. Two alternatively spliced transcript variants have been described. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]
Orthologs
Location:
3p21.3
Exon count:
5
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 3 NC_000003.12 (45886504..45903177)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45927996..45944667)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene solute carrier family 6 member 20 Neighboring gene leucine zipper transcription factor like 1 Neighboring gene succinate dehydrogenase complex subunit D pseudogene 4 Neighboring gene FYVE and coiled-coil domain containing 1 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene uncharacterized LOC105377063

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

NHGRI GWAS Catalog

Description
Multiple common variants for celiac disease influencing immune gene expression.
NHGRI GWA Catalog

Protein interactions

Protein Gene Interaction Pubs
Nef nef HIV-1 Nef induces variable levels of CCR9 downregulation in different cell types PubMed
Vif vif HIV-1 Vif downregulates the expression of chemokine (C-C motif) receptor 9 (CCR9) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

  • Chemokine receptors bind chemokines, organism-specific biosystem (from REACTOME)
    Chemokine receptors bind chemokines, organism-specific biosystemChemokine receptors are cytokine receptors found on the surface of certain cells, which interact with a type of cytokine called a chemokine. Following interaction, these receptors trigger a flux of i...
  • Chemokine signaling pathway, organism-specific biosystem (from KEGG)
    Chemokine signaling pathway, organism-specific biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
  • Chemokine signaling pathway, conserved biosystem (from KEGG)
    Chemokine signaling pathway, conserved biosystemInflammatory immune response requires the recruitment of leukocytes to the site of inflammation upon foreign insult. Chemokines are small chemoattractant peptides that provide directional cues for th...
  • Class A/1 (Rhodopsin-like receptors), organism-specific biosystem (from REACTOME)
    Class A/1 (Rhodopsin-like receptors), organism-specific biosystemRhodopsin-like receptors (class A/1) are the largest group of GPCRs and are the best studied group from a functional and structural point of view. They show great diversity at the sequence level and ...
  • Cytokine-cytokine receptor interaction, organism-specific biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, organism-specific biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • Cytokine-cytokine receptor interaction, conserved biosystem (from KEGG)
    Cytokine-cytokine receptor interaction, conserved biosystemCytokines are soluble extracellular proteins or glycoproteins that are crucial intercellular regulators and mobilizers of cells engaged in innate as well as adaptive inflammatory host defenses, cell ...
  • G alpha (i) signalling events, organism-specific biosystem (from REACTOME)
    G alpha (i) signalling events, organism-specific biosystemThe classical signalling mechanism for G alpha (i) is inhibition of the cAMP dependent pathway through inhibition of adenylate cyclase. Decreased production of cAMP from ATP results in decreased act...
  • GPCR downstream signaling, organism-specific biosystem (from REACTOME)
    GPCR downstream signaling, organism-specific biosystemG protein-coupled receptors (GPCRs) are classically defined as the receptor, G-protein and downstream effectors, the alpha subunit of the G-protein being the primary signaling molecule. However, it h...
  • GPCR ligand binding, organism-specific biosystem (from REACTOME)
    GPCR ligand binding, organism-specific biosystemThere are more than 800 G-protein coupled receptor (GPCRs) in the human genome, making it the largest receptor superfamily. GPCRs are also the largest class of drug targets, involved in virtually all...
  • GPCRs, Class A Rhodopsin-like, organism-specific biosystem (from WikiPathways)
    GPCRs, Class A Rhodopsin-like, organism-specific biosystemThis pathway was created using the GPCRDB (Horn et al., 1998), http://www.cmbi.kun.nl/7tm/. The groupings are based on the GPCR phylogenetic tree available from the GPCRDB and the training sets used ...
  • Intestinal immune network for IgA production, organism-specific biosystem (from KEGG)
    Intestinal immune network for IgA production, organism-specific biosystemThe intestine is the largest lymphoid tissue in the body. One striking feature of intestinal immunity is its ability to generate great amounts of noninflammatory immunoglobulin A (IgA) antibodies tha...
  • Intestinal immune network for IgA production, conserved biosystem (from KEGG)
    Intestinal immune network for IgA production, conserved biosystemThe intestine is the largest lymphoid tissue in the body. One striking feature of intestinal immunity is its ability to generate great amounts of noninflammatory immunoglobulin A (IgA) antibodies tha...
  • Peptide GPCRs, organism-specific biosystem (from WikiPathways)
    Peptide GPCRs, organism-specific biosystem
    Peptide GPCRs
  • Peptide ligand-binding receptors, organism-specific biosystem (from REACTOME)
    Peptide ligand-binding receptors, organism-specific biosystemThese receptors, a subset of the Class A/1 (Rhodopsin-like) family, all bind peptide ligands which include the chemokines, opioids and somatostatins.
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by GPCR, organism-specific biosystem (from REACTOME)
    Signaling by GPCR, organism-specific biosystemG protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors i...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
C-C chemokine receptor activity IEA
Inferred from Electronic Annotation
more info
 
chemokine receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
G-protein coupled receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
cellular defense response TAS
Traceable Author Statement
more info
PubMed 
chemokine-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
chemotaxis IEA
Inferred from Electronic Annotation
more info
 
immune response IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cytosolic calcium ion concentration TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
Preferred Names
C-C chemokine receptor type 9
Names
G protein-coupled receptor 28
chemokine (C-C motif) receptor 9

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.

Genomic

  1. NG_029472.1 RefSeqGene

    Range
    5001..21672
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001256369.1NP_001243298.1  C-C chemokine receptor type 9 isoform B

    See identical proteins and their annotated locations for NP_001243298.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (C) includes an alternate internal exon and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants B and C encode the same isoform (B), which has a shorter N-terminus compared to isoform A.
    Source sequence(s)
    AF145439, AK312824, BC069678, DB103756
    Consensus CDS
    CCDS2733.1
    UniProtKB/Swiss-Prot
    P51686
    UniProtKB/TrEMBL
    B2R734
    Related
    ENSP00000348260, ENST00000355983
    Conserved Domains (1) summary
    pfam00001
    Location:59305
    7tm_1; 7 transmembrane receptor (rhodopsin family)
  2. NM_006641.3NP_006632.2  C-C chemokine receptor type 9 isoform B

    See identical proteins and their annotated locations for NP_006632.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (B) lacks an internal exon and initiates translation at a downstream, in-frame start codon, compared to variant 1. Variants B and C encode the same isoform (B), which has a shorter N-terminus compared to isoform A.
    Source sequence(s)
    AF145439, DB103756, DB132476
    Consensus CDS
    CCDS2733.1
    UniProtKB/Swiss-Prot
    P51686
    Related
    ENSP00000379292, OTTHUMP00000164654, ENST00000395963, OTTHUMT00000257324
    Conserved Domains (1) summary
    pfam00001
    Location:59305
    7tm_1; 7 transmembrane receptor (rhodopsin family)
  3. NM_031200.2NP_112477.1  C-C chemokine receptor type 9 isoform A

    See identical proteins and their annotated locations for NP_112477.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (A) encodes the longer isoform (A).
    Source sequence(s)
    AF145439, DB103756
    Consensus CDS
    CCDS2732.1
    UniProtKB/Swiss-Prot
    P51686
    Related
    ENSP00000350256, OTTHUMP00000164653, ENST00000357632, OTTHUMT00000257323
    Conserved Domains (1) summary
    pfam00001
    Location:71317
    7tm_1; 7 transmembrane receptor (rhodopsin family)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p2 Primary Assembly

    Range
    45886504..45903177
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533312.1XP_011531614.1  

    See identical proteins and their annotated locations for XP_011531614.1

    UniProtKB/Swiss-Prot
    P51686
    Conserved Domains (1) summary
    pfam00001
    Location:71317
    7tm_1; 7 transmembrane receptor (rhodopsin family)

Alternate CHM1_1.1

Genomic

  1. NC_018914.2 Alternate CHM1_1.1

    Range
    45877982..45894642
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)