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CCR9 Gene(Protein Coding)

C-C Motif Chemokine Receptor 9

GCID:
GC03P045903
GIFtS:
47
Genes Participants
UDN Logo

Aliases for CCR9 Gene

Aliases for CCR9 Gene

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

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 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]

GeneCards Summary for CCR9 Gene

CCR9 (C-C Motif Chemokine Receptor 9) is a Protein Coding gene. Diseases associated with CCR9 include Celiac Disease 1 and Cd45 Deficiency. Among its related pathways are Akt Signaling and Peptide ligand-binding receptors. 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 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 , fRNAdb sequence ontologies and piRNA Summary for CCR9 Gene

Genomics for CCR9 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for CCR9 Gene

Promoters and enhancers for CCR9 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH03J045886 Promoter/Enhancer 0.7 EPDnew dbSUPER 650.7 +0.0 27 0.1 CCR9 GC03P045904 LZTFL1
GH03J045887 Enhancer 0.5 dbSUPER 650.7 +1.6 1635 1.5 ZBED1 JUNB ZFP36 ZMYM3 CCR9 FYCO1 CXCR6 GC03P045904 LZTFL1
GH03J045864 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 55.6 -21.2 -21239 1.7 HDGF PKNOX1 SMAD1 STAT5A BMI1 BATF KLF5 IRF4 ATF7 ETV6 CCR9 LZTFL1 FYCO1 EXOSC7 XCR1 GC03P045849 GC03M045883
GH03J045841 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 11.3 -44.5 -44549 1.7 PKNOX1 ARNT ARID4B SIN3A IRF4 YY1 ZNF766 E2F8 FOS NFYC LZTFL1 CCR9 SDHDP4 CXCR6 LARS2 GC03P045849 PIR58059
GH03J045687 Promoter/Enhancer 2.5 EPDnew Ensembl ENCODE dbSUPER 8.9 -194.6 -194608 8.2 ZFP64 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC SACM1L RN7SL145P LIMD1 ZDHHC3 ZNF502 ZNF501 EXOSC7 LARS2-AS1 XCR1 CCR9
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CCR9 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CCR9 gene promoter:

Genomic Locations for CCR9 Gene

Genomic Locations for CCR9 Gene
chr3:45,886,504-45,903,177
(GRCh38/hg38)
Size:
16,674 bases
Orientation:
Plus strand
chr3:45,927,996-45,944,667
(GRCh37/hg19)

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

Products:

  1. Antibody
  2. Protein
  3. Assay

  • 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
    Miscellaneous:
    • EC50 of SCYA25/TECK for isoform 1 is lower than for isoform 2.
    SequenceCaution:
    • Sequence=AAH95516.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305};

    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:

Antibody Products

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

Blocks:
InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for CCR9 Gene

GenScript: Design optimal peptide antigens:

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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  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

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:0004871 obsolete signal transducer activity IEA --
GO:0004930 G-protein coupled receptor activity IEA --
GO:0004950 chemokine receptor activity TAS 10229797
GO:0016493 C-C chemokine receptor activity IEA --
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 Model Products

CRISPR Products

miRNA for CCR9 Gene

miRTarBase miRNAs that target CCR9

Inhibitory RNA Products

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

Clone Products

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 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:0009986 cell surface IDA 18308860
GO:0016020 membrane IEA --
GO:0016021 integral component of 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

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 IEA,TAS --
GO:0006955 immune response IEA,TAS --
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

Products:

  1. Drug

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
calcium Approved Nutra 0
CCX282 Investigational Pharma Target 0
CCL25 Pharma Agonist, Full agonist 0
[<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
Full agonist, Agonist
genes like me logo Genes that share compounds with CCR9: view

Transcripts for CCR9 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for CCR9 Gene

(10) Selected AceView cDNA sequences:
(8) Additional mRNA sequences :
(4) REFSEQ mRNAs :
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for CCR9 Gene

Chemokine (C-C motif) receptor 9:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

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

Clone Products

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

No ASD Table

Relevant External Links for CCR9 Gene

GeneLoc Exon Structure for
CCR9
ECgene alternative splicing isoforms for
CCR9

Expression for CCR9 Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CCR9 Gene

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

NURSA nuclear receptor signaling pathways regulating expression of CCR9 Gene:

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(2.8)
  • Spleen(2.7)
  • Blood(2.6)
  • Lymph node(2.2)
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 34 33
  • 99.37 (n)
 OneToOne
dog
(Canis familiaris)
 Mammalia CCR9 34 33
  • 86.61 (n)
 OneToOne
cow
(Bos Taurus)
 Mammalia CCR9 34 33
  • 86.07 (n)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Ccr9 33
  • 85.64 (n)
mouse
(Mus musculus)
 Mammalia Ccr9 16 34 33
  • 84.73 (n)
oppossum
(Monodelphis domestica)
 Mammalia CCR9 34
  • 79 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves CCR9 34 33
  • 60.85 (n)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia CCR9 34
  • 49 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia LOC100489281 33
  • 55.78 (n)
zebrafish
(Danio rerio)
 Actinopterygii LOC100334253 33
  • 53.75 (n)
ccr9a 34
  • 44 (a)
 OneToMany
ccr9b 34 34
  • 39 (a)
 OneToMany
Species where no ortholog for CCR9 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 squirt (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

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

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for CCR9 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1000247122 -- 45,889,107(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000298349 -- 45,902,442(+) C/T 3_prime_UTR_variant
rs1001108102 -- 45,891,037(+) G/A/C genic_upstream_transcript_variant, intron_variant
rs1001275860 -- 45,890,817(+) T/A genic_upstream_transcript_variant, intron_variant
rs1001288822 -- 45,890,461(+) A/G genic_upstream_transcript_variant, intron_variant

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for CCR9 Gene

MalaCards: The human disease database

(4) MalaCards diseases for CCR9 Gene - From: DISEASES and Novoseek

Disorder Aliases PubMed IDs
celiac disease 1
  • celiac disease, susceptibility to, 1
cd45 deficiency
precursor t-cell acute lymphoblastic leukemia
  • precursor t-cell acute lymphoblastic leukemia/lymphoma
cholangitis, primary sclerosing
  • psc
- 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

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
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 58
  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 44 58
  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 58
  4. Intracellular allosteric antagonism of the CCR9 receptor. (PMID: 27926729) Oswald C … Marshall FH (Nature 2016) 3 4 58
  5. Polymorphisms in innate immunity genes and patients response to dendritic cell-based HIV immuno-treatment. (PMID: 20056178) Segat L … Crovella S (Vaccine 2010) 3 44 58

Products for CCR9 Gene

Sources for CCR9 Gene

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