CCR9 Gene (Protein Coding)

C-C Motif Chemokine Receptor 9

GC03P045903
GIFtS:
41
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 intera... See more...

Aliases for CCR9 Gene

Aliases for CCR9 Gene

  • C-C Motif Chemokine Receptor 9 2 3 5
  • GPR-9-6 2 3 4
  • Chemokine (C-C Motif) Receptor 9 2 3
  • C-C Chemokine Receptor Type 9 3 4
  • CC-CKR-9 3 4
  • CDw199 2 3
  • GPR28 3 4
  • G Protein-Coupled Receptor 28 3
  • G-Protein Coupled Receptor 28 4
  • CDw199 Antigen 4
  • C-C CKR-9 4
  • CCR-9 4
  • CCR9 5

External Ids for CCR9 Gene

Previous HGNC Symbols for CCR9 Gene

  • GPR28

Previous GeneCards Identifiers for CCR9 Gene

  • GC03P045168
  • GC03P045747
  • GC03P045888

Summaries for CCR9 Gene

Entrez Gene Summary for CCR9 Gene

  • 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]

GeneCards Summary for CCR9 Gene

CCR9 (C-C Motif Chemokine Receptor 9) is a Protein Coding gene. Diseases associated with CCR9 include Ileitis and Celiac Disease 1. Among its related pathways are Peptide ligand-binding receptors and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include G protein-coupled receptor activity and C-C chemokine receptor activity. An important paralog of this gene is CCR7.

UniProtKB/Swiss-Prot Summary for CCR9 Gene

  • Receptor for chemokine SCYA25/TECK. Subsequently transduces a signal by increasing the intracellular calcium ions level.
  • (Microbial infection) Alternative coreceptor with CD4 for HIV-1 infection.

Gene Wiki entry for CCR9 Gene

Additional gene information for CCR9 Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for CCR9 Gene

Genomics for CCR9 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for CCR9 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CCR9 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for CCR9

Top Transcription factor binding sites by QIAGEN in the CCR9 gene promoter:
  • c-Rel
  • HTF
  • Nkx2-2
  • oct-B2
  • oct-B3
  • RFX1

Genomic Locations for CCR9 Gene

Latest Assembly
chr3:45,886,064-45,903,175
(GRCh38/hg38)
Size:
17,112 bases
Orientation:
Plus strand

Previous Assembly
chr3:45,927,556-45,944,666
(GRCh37/hg19 by Entrez Gene)
Size:
17,111 bases
Orientation:
Plus strand

chr3:45,927,996-45,944,667
(GRCh37/hg19 by Ensembl)
Size:
16,672 bases
Orientation:
Plus strand

Genomic View for CCR9 Gene

Genes around CCR9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CCR9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CCR9 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for CCR9 Gene

Proteins for CCR9 Gene

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  • Protein details for CCR9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P51686-CCR9_HUMAN
    Recommended name:
    C-C chemokine receptor type 9
    Protein Accession:
    P51686
    Secondary Accessions:
    • Q4VBM3
    • Q549E0
    • Q9UQQ6

    Protein attributes for CCR9 Gene

    Size:
    369 amino acids
    Molecular mass:
    42016 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH95516.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
    Miscellaneous:
    • EC50 of SCYA25/TECK for isoform 1 is lower than for isoform 2.

    Three dimensional structures from OCA and Proteopedia for CCR9 Gene

    Alternative splice isoforms for CCR9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CCR9 Gene

Post-translational modifications for CCR9 Gene

  • Glycosylation at Asn32
  • Modification sites at PhosphoSitePlus

Other Protein References for CCR9 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibodies for research

  • Abcam antibodies for CCR9

No data available for DME Specific Peptides for CCR9 Gene

Domains & Families for CCR9 Gene

Gene Families for CCR9 Gene

HGNC:
IUPHAR :
Human Protein Atlas (HPA):
  • CD markers
  • G-protein coupled receptors
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for CCR9 Gene

InterPro:
Blocks:
  • Chemokine receptor signature
  • C-C chemokine receptor type 9 signature

Suggested Antigen Peptide Sequences for CCR9 Gene

GenScript: Design optimal peptide antigens:
  • GPR-9-6 (CCR9_HUMAN)
  • CCR9 chemokine receptor (Q9UN87_HUMAN)

Graphical View of Domain Structure for InterPro Entry

P51686

UniProtKB/Swiss-Prot:

CCR9_HUMAN :
  • Belongs to the G-protein coupled receptor 1 family.
Family:
  • Belongs to the G-protein coupled receptor 1 family.
genes like me logo Genes that share domains with CCR9: view

Function for CCR9 Gene

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  6. Cell Lines for research

Molecular function for CCR9 Gene

UniProtKB/Swiss-Prot Function:
Receptor for chemokine SCYA25/TECK. Subsequently transduces a signal by increasing the intracellular calcium ions level.
UniProtKB/Swiss-Prot Function:
(Microbial infection) Alternative coreceptor with CD4 for HIV-1 infection.
GENATLAS Biochemistry:
chemokine CC,beta receptor 9,G protein coupled receptor superfamily,highly expressed in thymus,receptor for the chemokine TECK

Phenotypes From GWAS Catalog for CCR9 Gene

Gene Ontology (GO) - Molecular Function for CCR9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004930 G protein-coupled receptor activity IEA --
GO:0004950 chemokine receptor activity TAS 10229797
GO:0016493 C-C chemokine receptor activity IBA 21873635
GO:0019957 C-C chemokine binding IBA 21873635
genes like me logo Genes that share ontologies with CCR9: view
genes like me logo Genes that share phenotypes with CCR9: view

Animal Models for CCR9 Gene

MGI Knock Outs for CCR9:

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCR9

Clone products for research

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CCR9 Gene

Localization for CCR9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CCR9 Gene

Cell membrane. Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CCR9 gene
Compartment Confidence
plasma membrane 5
extracellular 2
nucleus 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
endosome 1
cytosol 1
lysosome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CCR9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005886 plasma membrane TAS --
GO:0005887 integral component of plasma membrane TAS 10229797
GO:0009897 external side of plasma membrane IBA 21873635
GO:0009986 cell surface IDA 18308860
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with CCR9: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CCR9 Gene

Pathways & Interactions for CCR9 Gene

genes like me logo Genes that share pathways with CCR9: view

Pathways by source for CCR9 Gene

2 BioSystems pathways for CCR9 Gene
8 Qiagen pathways for CCR9 Gene
  • Akt Signaling
  • Antioxidant Action of Vitamin-C
  • Chemokine Signaling
  • Molecular Mechanisms of Cancer
  • p38 Signaling

SIGNOR curated interactions for CCR9 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for CCR9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002305 CD8-positive, gamma-delta intraepithelial T cell differentiation IEA --
GO:0006935 chemotaxis TAS 10640743
GO:0006955 immune response TAS,IBA 21873635
GO:0006968 cellular defense response TAS 10544196
GO:0007165 signal transduction IEA --
genes like me logo Genes that share ontologies with CCR9: view

Drugs & Compounds for CCR9 Gene

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(6) Drugs for CCR9 Gene - From: DrugBank, DGIdb, IUPHAR, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Vercirnon Investigational Pharma Target 0
CCL25 Pharma Agonist, Full agonist 0
Calcium Nutra 6959
[<SUP>125</SUP>I]CCL25 (HUMAN) Pharma 0
CCX025 Pharma 0

(4) Additional Compounds for CCR9 Gene - From: Novoseek and IUPHAR

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
[<sup>125</sup>I]CCL25
Agonist, Full agonist
genes like me logo Genes that share compounds with CCR9: view

Transcripts for CCR9 Gene

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mRNA/cDNA for CCR9 Gene

5 REFSEQ mRNAs :
10 NCBI additional mRNA sequence :
5 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for CCR9

Clone products for research

Alternative Splicing Database (ASD) splice patterns (SP) for CCR9 Gene

No ASD Table

Relevant External Links for CCR9 Gene

GeneLoc Exon Structure for
CCR9

Expression for CCR9 Gene

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  1. Primer products for research
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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for CCR9 Gene

mRNA expression in normal human tissues for CCR9 Gene
mRNA expression by GTEx for CCR9 GenemRNA expression by BioGPS for CCR9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CCR9 Gene

This gene is overexpressed in Small Intestine - Terminal Ileum (x26.8), Spleen (x5.1), and Whole Blood (x4.3).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for CCR9

SOURCE GeneReport for Unigene cluster for CCR9 Gene:

Hs.225946

mRNA Expression by UniProt/SwissProt for CCR9 Gene:

P51686-CCR9_HUMAN
Tissue specificity: Highly expressed in the thymus and low in lymph nodes and spleen.

Evidence on tissue expression from TISSUES for CCR9 Gene

  • Intestine(3)
  • Spleen(3)
  • Blood(2.8)
  • Liver(2.6)
  • Lymph node(2.5)
  • Bone marrow(2.5)
  • Heart(2.4)
  • Lung(2.4)
  • Kidney(2.2)
  • Stomach(2.1)
  • Muscle(2)
genes like me logo Genes that share expression patterns with CCR9: view

No data available for Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CCR9 Gene

Orthologs for CCR9 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CCR9 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia CCR9 29 30
  • 99.37 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia CCR9 29 30
  • 86.61 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia CCR9 29 30
  • 86.07 (n)
 OneToOne
Rat
(Rattus norvegicus)
 Mammalia Ccr9 29
  • 85.64 (n)
Mouse
(Mus musculus)
 Mammalia Ccr9 29 16 30
  • 84.73 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia CCR9 30
  • 79 (a)
 OneToOne
Chicken
(Gallus gallus)
 Aves CCR9 29 30
  • 60.85 (n)
 OneToOne
Lizard
(Anolis carolinensis)
 Reptilia CCR9 30
  • 49 (a)
 OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia LOC100489281 29
  • 55.78 (n)
Zebrafish
(Danio rerio)
 Actinopterygii LOC100334253 29
  • 53.75 (n)
ccr9a 30
  • 44 (a)
 OneToMany
ccr9b 30 30
  • 39 (a)
 OneToMany
Species where no ortholog for CCR9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Platypus (Ornithorhynchus anatinus)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for CCR9 Gene

ENSEMBL:
Gene Tree for CCR9 (if available)
TreeFam:
Gene Tree for CCR9 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CCR9: view image
Alliance of Genome Resources:
Additional Orthologs for CCR9

Paralogs for CCR9 Gene

Paralogs for CCR9 Gene

(41) SIMAP similar genes for CCR9 Gene using alignment to 3 proteins:

  • CCR9_HUMAN
  • C9JWC0_HUMAN
  • Q9UN87_HUMAN
genes like me logo Genes that share paralogs with CCR9: view

Variants for CCR9 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for CCR9 Gene

SNP ID Clinical significance and condition Chr 03 pos Variation AA Info Type
rs1553617019 Uncertain Significance: Hirschsprung disease 1 45,894,936(+) G/T
NM_031200.3(CCR9):c.3G>T (p.Met1Ile) 		INITIATIOR_CODON_VARIANT,MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON
rs35423527 Benign: not provided 45,901,194(+) C/T
NM_031200.3(CCR9):c.406C>T (p.Leu136=) 		SYNONYMOUS_VARIANT,INTRON
rs12721497 -- p.Met284Val
rs45530037 -- p.Ile92Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for CCR9 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for CCR9 Gene

Variant ID Type Subtype PubMed ID
esv2462115 CNV insertion 19546169
nsv834678 CNV gain 17160897

Variation tolerance for CCR9 Gene

Residual Variation Intolerance Score: 60.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.47; 28.76% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CCR9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CCR9
Leiden Open Variation Database (LOVD)
CCR9

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CCR9 Gene

Disorders for CCR9 Gene

MalaCards: The human disease database

(9) MalaCards diseases for CCR9 Gene - From: COP and GCD

Disorder Aliases PubMed IDs
ileitis
  • crohn's ileitis
celiac disease 1
  • celiac disease, susceptibility to, 1
food allergy
  • food hypersensitivity
crohn's disease
  • crohn disease
ascending cholangitis
- elite association - COSMIC cancer census association via MalaCards
Search CCR9 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CCR9

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with CCR9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CCR9 Gene

Publications for CCR9 Gene

  1. Cutting edge: identification of the orphan chemokine receptor GPR-9-6 as CCR9, the receptor for the chemokine TECK. (PMID: 10229797) Zaballos A … Márquez G (Journal of immunology (Baltimore, Md. : 1950) 1999) 2 3 4 22
  2. Donor single nucleotide polymorphism in the CCR9 gene affects the incidence of skin GVHD. (PMID: 19525985) Inamoto Y … Naoe T (Bone marrow transplantation 2010) 3 22 40
  3. CCR9A and CCR9B: two receptors for the chemokine CCL25/TECK/Ck beta-15 that differ in their sensitivities to ligand. (PMID: 10640743) Yu CR … Farber JM (Journal of immunology (Baltimore, Md. : 1950) 2000) 3 4 22
  4. Intracellular allosteric antagonism of the CCR9 receptor. (PMID: 27926729) Oswald C … Marshall FH (Nature 2016) 3 4
  5. Abnormal regulation of chemokine TECK and its receptor CCR9 in the endometriotic milieu is involved in pathogenesis of endometriosis by way of enhancing invasiveness of endometrial stromal cells. (PMID: 20081876) Wang Y … Li D (Cellular & molecular immunology 2010) 3 22

ExternalLinks

View latest publications for CCR9 gene in Mastermind

Products for CCR9 Gene

Sources for CCR9 Gene