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

Gene ID: 10803, updated on 1-Aug-2020

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 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]
Expression
Biased expression in small intestine (RPKM 2.0), duodenum (RPKM 1.6) and 6 other tissues See more
Orthologs

Genomic context

See CCR9 in Genome Data Viewer
Location:
3p21.31
Exon count:
5
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 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 uncharacterized LOC107986083 Neighboring gene leucine zipper transcription factor like 1 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 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

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
C-C chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
C-C chemokine receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chemokine receptor activity TAS
Traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
CD8-positive, gamma-delta intraepithelial T cell differentiation IEA
Inferred from Electronic Annotation
more info
 
G protein-coupled receptor signaling pathway TAS
Traceable Author Statement
more info
 
calcium-mediated signaling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cell chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cellular defense response TAS
Traceable Author Statement
more info
PubMed 
chemokine-mediated signaling pathway IEA
Inferred from Electronic Annotation
more info
 
chemotaxis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
immune response IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cytosolic calcium ion concentration IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cell surface IDA
Inferred from Direct Assay
more info
PubMed 
external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
integral component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
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)

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_001256369.1NP_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
    ENSP00000348260.2, ENST00000355983.3
    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_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
  3. 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 Annotation Release 109.20200522

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

mRNA and Protein(s)

  1. XM_011533312.2XP_011531614.1  C-C chemokine receptor type 9 isoform X1

    See identical proteins and their annotated locations for XP_011531614.1

    UniProtKB/Swiss-Prot
    P51686
    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
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