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

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: mouse all
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Genomic context

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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
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 EBI GWAS CatalogPubMed

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-U45982 (e-PCR)
- UniSTS:15396

CCR9_300 (e-PCR)
- UniSTS:277067

RH70643 (e-PCR)
- UniSTS:48749

CCR9_mf (e-PCR)
- UniSTS:510344

PMC135988P11 (e-PCR)
- UniSTS:270783

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

NG_029472.1 RefSeqGene

Range

5040..21671

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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
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
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