U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

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

    Gene ID: 10803, updated on 27-Nov-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: 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

    Related articles in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001256369.2NP_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:37316
      7tmA_CCR9; CC chemokine receptor type 9, member of the class A family of seven-transmembrane G protein-coupled receptors
    2. NM_001386447.1NP_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:49328
      7tmA_CCR9; CC chemokine receptor type 9, member of the class A family of seven-transmembrane G protein-coupled receptors
    3. NM_001386448.1NP_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:49328
      7tmA_CCR9; CC chemokine receptor type 9, member of the class A family of seven-transmembrane G protein-coupled receptors
    4. NM_006641.4NP_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:37316
      7tmA_CCR9; CC chemokine receptor type 9, member of the class A family of seven-transmembrane G protein-coupled receptors
    5. NM_031200.3NP_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:49328
      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)