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

    Gene ID: 10803, updated on 10-Dec-2024

    Summary

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    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 MIM:604738; AllianceGenome:HGNC:1610
    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 G protein-coupled receptor with seven transmembrane domains that belongs to the beta chemokine receptor family. Chemokines and their receptors are key regulators of thymocyte migration and maturation in normal and inflammation conditions. This gene is differentially expressed in T lymphocytes of the small intestine and colon, and its interaction with chemokine 25 contributes to intestinal intra-epithelial lymphocyte homing to the small intestine. This suggests a role for this gene in directing immune responses to different segments of the gastrointestinal tract. This gene and its exclusive ligand, chemokine 25, are overexpressed in a variety of malignant tumors and are closely associated with tumor proliferation, apoptosis, invasion, migration and drug resistance. This gene maps to the chemokine receptor gene cluster. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2020]
    Expression
    Biased expression in small intestine (RPKM 2.0), duodenum (RPKM 1.6) and 6 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CCR9 in Genome Data Viewer
    Location:
    3p21.31
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (45886064..45903174)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (45901704..45919057)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45927556..45944666)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene leucine zipper transcription factor like 1 Neighboring gene uncharacterized LOC124909374 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45921781-45921937 Neighboring gene CCR9 promoter region Neighboring gene succinate dehydrogenase complex subunit D pseudogene 4 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr3:45956761-45957960 Neighboring gene FYVE and coiled-coil domain autophagy adaptor 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:45979037-45980236 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:45989039-45989208 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19787 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009167-46009806 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:46009807-46010446 Neighboring gene Sharpr-MPRA regulatory region 2695 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46029541-46030041 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:46034569-46035069 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:46037115-46037614 Neighboring gene uncharacterized LOC105377063

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Recent advances in roles of G-protein coupled receptors in intestinal intraepithelial lymphocytes. Sumida H. Biosci Microbiota Food Health, 2020. PMID 32775124, Free PMC Article
    2. Intracellular allosteric antagonism of the CCR9 receptor. Oswald C, et al. Nature, 2016 Dec 15. PMID 27926729
    3. Structural Analysis of Chemokine Receptor-Ligand Interactions. Arimont M, et al. J Med Chem, 2017 Jun 22. PMID 28165741, Free PMC Article
    4. Mucosal Chemokines. Hernández-Ruiz M, et al. J Interferon Cytokine Res, 2017 Feb. PMID 28207301, Free PMC Article
    5. CC chemokine receptor 9 enhances proliferation in pancreatic intraepithelial neoplasia and pancreatic cancer cells. Shen X, et al. J Gastrointest Surg, 2009 Nov. PMID 19756884

    See all (86) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CCR9/CXCR5 Co-Expressing CD4 T Cells Are Increased in Primary Sjogren's Syndrome and Are Enriched in PD-1/ICOS-Expressing Effector T Cells.
      Title: CCR9/CXCR5 Co-Expressing CD4 T Cells Are Increased in Primary Sjögren's Syndrome and Are Enriched in PD-1/ICOS-Expressing Effector T Cells.
    2. LncRNA15691 promotes T-ALL infiltration by upregulating CCR9 via increased MATR3 stability.
      Title: LncRNA15691 promotes T-ALL infiltration by upregulating CCR9 via increased MATR3 stability.
    3. In patients with primary Sjogren's syndrome innate-like MAIT cells display upregulated IL-7R, IFN-gamma, and IL-21 expression and have increased proportions of CCR9 and CXCR5-expressing cells.
      Title: In patients with primary Sjögren's syndrome innate-like MAIT cells display upregulated IL-7R, IFN-γ, and IL-21 expression and have increased proportions of CCR9 and CXCR5-expressing cells.
    4. CCL5 Release by CCR9+ CD8 T Cells: A Potential Contributor to Immunopathology of Primary Sjogren's Syndrome.
      Title: CCL5 Release by CCR9+ CD8 T Cells: A Potential Contributor to Immunopathology of Primary Sjögren's Syndrome.
    5. Potential for CCR9+ IL-17+ Regulatory T Cell as a Predictor of Early Necrotizing Enterocolitis.
      Title: Potential for CCR9+ IL-17+ Regulatory T Cell as a Predictor of Early Necrotizing Enterocolitis.
    6. Role of CC chemokine receptor 9 in the progression of murine and human non-alcoholic steatohepatitis.
      Title: Role of CC chemokine receptor 9 in the progression of murine and human non-alcoholic steatohepatitis.
    7. Development of Anti-Human CC Chemokine Receptor 9 Monoclonal Antibodies for Flow Cytometry.
      Title: Development of Anti-Human CC Chemokine Receptor 9 Monoclonal Antibodies for Flow Cytometry.
    8. LINC00853 restrains T cell acute lymphoblastic leukemia invasion and infiltration by regulating CCR9/CCL25.
      Title: LINC00853 restrains T cell acute lymphoblastic leukemia invasion and infiltration by regulating CCR9/CCL25.
    9. CCL25 and CCR9 is a unique pathway that potentiates pannus formation by remodeling RA macrophages into mature osteoclasts.
      Title: CCL25 and CCR9 is a unique pathway that potentiates pannus formation by remodeling RA macrophages into mature osteoclasts.
    10. The Regulatory Function of CCR9(+) Dendritic Cells in Inflammation and Autoimmunity.
      Title: The Regulatory Function of CCR9(+) Dendritic Cells in Inflammation and Autoimmunity.
    Submit: New GeneRIF Correction See all GeneRIFs (58)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Multiple common variants for celiac disease influencing immune gene expression.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chemokine receptor activity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in CD8-positive, gamma-delta intraepithelial T cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in G protein-coupled receptor signaling pathway TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in calcium-mediated signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cell chemotaxis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of cytosolic calcium ion concentration IBA
    Inferred from Biological aspect of Ancestor
    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
    		  

    General protein information

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    Preferred Names
    C-C chemokine receptor type 9
    Names
    G protein-coupled receptor 28
    chemokine (C-C motif) receptor 9

    NCBI Reference Sequences (RefSeq)

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    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
      5040..21671
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001256369.2 → NP_001243298.1  C-C chemokine receptor type 9 isoform B

      See identical proteins and their annotated locations for NP_001243298.1

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Consensus CDS
      CCDS2733.1
      UniProtKB/TrEMBL
      B2R734
      Conserved Domains (1) summary
      cd15174
      Location:37 → 316
      7tmA_CCR9; CC chemokine receptor type 9, member of the class A family of seven-transmembrane G protein-coupled receptors

    2. NM_001386447.1 → NP_001373376.1  C-C chemokine receptor type 9 isoform A

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Consensus CDS
      CCDS2732.1
      UniProtKB/Swiss-Prot
      P51686, Q4VBM3, Q549E0, Q9UQQ6
      UniProtKB/TrEMBL
      B2R8G9
      Conserved Domains (1) summary
      cd15174
      Location:49 → 328
      7tmA_CCR9; CC chemokine receptor type 9, member of the class A family of seven-transmembrane G protein-coupled receptors

    3. NM_001386448.1 → NP_001373377.1  C-C chemokine receptor type 9 isoform A

      Status: REVIEWED

      Source sequence(s)
      AC099782
      Consensus CDS
      CCDS2732.1
      UniProtKB/Swiss-Prot
      P51686, Q4VBM3, Q549E0, Q9UQQ6
      UniProtKB/TrEMBL
      B2R8G9
      Conserved Domains (1) summary
      cd15174
      Location:49 → 328
      7tmA_CCR9; CC chemokine receptor type 9, member of the class A family of seven-transmembrane G protein-coupled receptors

    4. NM_006641.4 → NP_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, DB132476
      Consensus CDS
      CCDS2733.1
      UniProtKB/TrEMBL
      B2R734
      Related
      ENSP00000379292.2, ENST00000395963.2
      Conserved Domains (1) summary
      cd15174
      Location:37 → 316
      7tmA_CCR9; CC chemokine receptor type 9, member of the class A family of seven-transmembrane G protein-coupled receptors

    5. NM_031200.3 → NP_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
      Consensus CDS
      CCDS2732.1
      UniProtKB/Swiss-Prot
      P51686, Q4VBM3, Q549E0, Q9UQQ6
      UniProtKB/TrEMBL
      B2R8G9
      Related
      ENSP00000350256.2, ENST00000357632.7
      Conserved Domains (1) summary
      cd15174
      Location:49 → 328
      7tmA_CCR9; CC chemokine receptor type 9, 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_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      45886064..45903174
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      45901704..45919057
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P51686.2 GenPept UniProtKB/Swiss-Prot:P51686

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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