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

Gene ID: 10803, updated on 8-Jul-2021

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
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

See CCR9 in Genome Data Viewer
Location:
3p21.31
Exon count:
6
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (45886064..45903174)
105.20201022 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (45927556..45944666)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986083 Neighboring gene leucine zipper transcription factor like 1 Neighboring gene CCR9 promoter region Neighboring gene succinate dehydrogenase complex subunit D pseudogene 4 Neighboring gene FYVE and coiled-coil domain autophagy adaptor 1 Neighboring gene C-X-C motif chemokine receptor 6 Neighboring gene Sharpr-MPRA regulatory region 2695

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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Multiple common variants for celiac disease influencing immune gene expression.
GeneReviews: Not available

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables C-C chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables C-C chemokine receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IEA
Inferred from Electronic Annotation
more info
 
involved_in calcium-mediated signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
involved_in positive regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
located_in integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
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)

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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_001256369.2NP_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/Swiss-Prot
    P51686
    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
    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
    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/Swiss-Prot
    P51686
    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
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

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