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

Gene ID: 10803, updated on 28-Oct-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
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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: HPA RNA-seq normal tissues 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

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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)

Genotypes

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

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