LOCUS       NM_031200               2527 bp    mRNA    linear   PRI 05-APR-2024
DEFINITION  Homo sapiens C-C motif chemokine receptor 9 (CCR9), transcript
            variant A, mRNA.
ACCESSION   NM_031200
VERSION     NM_031200.3
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 2527)
  AUTHORS   Hinrichs,A.C., Kruize,A.A., Lafeber,F.P.J.G., Leavis,H.L. and van
            Roon,J.A.G.
  TITLE     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
  JOURNAL   Int J Mol Sci 24 (15), 11952 (2023)
   PUBMED   37569326
  REMARK    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.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2527)
  AUTHORS   Zeng,X., Lei,Y., Pan,S., Sun,J., He,H., Xiao,D., Jamal,M., Shen,H.,
            Zhou,F., Shao,L. and Zhang,Q.
  TITLE     LncRNA15691 promotes T-ALL infiltration by upregulating CCR9 via
            increased MATR3 stability
  JOURNAL   J Leukoc Biol 113 (2), 203-215 (2023)
   PUBMED   36822174
  REMARK    GeneRIF: LncRNA15691 promotes T-ALL infiltration by upregulating
            CCR9 via increased MATR3 stability.
REFERENCE   3  (bases 1 to 2527)
  AUTHORS   Hinrichs,A.C., Kruize,A.A., Leavis,H.L. and van Roon,J.A.G.
  TITLE     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
  JOURNAL   Front Immunol 13, 1017157 (2022)
   PUBMED   36505431
  REMARK    GeneRIF: 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.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2527)
  AUTHORS   Xu,B., Deng,C., Wu,X., Ji,T., Zhao,L., Han,Y., Yang,W., Qi,Y.,
            Wang,Z., Yang,Z. and Yang,Y.
  TITLE     CCR9 and CCL25: A review of their roles in tumor promotion
  JOURNAL   J Cell Physiol 235 (12), 9121-9132 (2020)
   PUBMED   32401349
  REMARK    Review article
REFERENCE   5  (bases 1 to 2527)
  AUTHORS   Sumida,H.
  TITLE     Recent advances in roles of G-protein coupled receptors in
            intestinal intraepithelial lymphocytes
  JOURNAL   Biosci Microbiota Food Health 39 (3), 77-82 (2020)
   PUBMED   32775124
  REMARK    Review article
REFERENCE   6  (bases 1 to 2527)
  AUTHORS   Biswas,S., Bryant,R.V. and Travis,S.
  TITLE     Interfering with leukocyte trafficking in Crohn's disease
  JOURNAL   Best Pract Res Clin Gastroenterol 38-39, 101617 (2019)
   PUBMED   31327399
  REMARK    Review article
REFERENCE   7  (bases 1 to 2527)
  AUTHORS   Hernandez-Ruiz,M. and Zlotnik,A.
  TITLE     Mucosal Chemokines
  JOURNAL   J Interferon Cytokine Res 37 (2), 62-70 (2017)
   PUBMED   28207301
  REMARK    Review article
REFERENCE   8  (bases 1 to 2527)
  AUTHORS   Tu,Z., Xiao,R., Xiong,J., Tembo,K.M., Deng,X., Xiong,M., Liu,P.,
            Wang,M. and Zhang,Q.
  TITLE     CCR9 in cancer: oncogenic role and therapeutic targeting
  JOURNAL   J Hematol Oncol 9, 10 (2016)
   PUBMED   26879872
  REMARK    GeneRIF: Studies indicate important roles played by chemokine
            ligand 25 (CCL25)/chemokine receptor 9 (CCR9) in tumorigenesis,
            tumor chemoresistance and metastasis.
            Review article
            Publication Status: Online-Only
REFERENCE   9  (bases 1 to 2527)
  AUTHORS   Zaballos,A., Gutierrez,J., Varona,R., Ardavin,C. and Marquez,G.
  TITLE     Cutting edge: identification of the orphan chemokine receptor
            GPR-9-6 as CCR9, the receptor for the chemokine TECK
  JOURNAL   J Immunol 162 (10), 5671-5675 (1999)
   PUBMED   10229797
REFERENCE   10 (bases 1 to 2527)
  AUTHORS   Itoh,H., Toyama,R., Kozasa,T., Tsukamoto,T., Matsuoka,M. and
            Kaziro,Y.
  TITLE     Presence of three distinct molecular species of Gi protein alpha
            subunit. Structure of rat cDNAs and human genomic DNAs
  JOURNAL   J Biol Chem 263 (14), 6656-6664 (1988)
   PUBMED   2834384
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AF145439.1.
            This sequence is a reference standard in the RefSeqGene project.
            
            On Nov 23, 2018 this sequence version replaced NM_031200.2.
            
            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].
            
            Transcript Variant: This variant (A) encodes the longer isoform
            (A).
            
            Publication Note:  This RefSeq record includes a subset of the
            publications that are available for this gene. Please see the Gene
            record to access additional publications.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC069678.1, AF145439.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2144835, SAMEA2146236
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000357632.7/ ENSP00000350256.2
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-2527              AF145439.1         17-2543
FEATURES             Location/Qualifiers
     source          1..2527
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="3"
                     /map="3p21.31"
     gene            1..2527
                     /gene="CCR9"
                     /gene_synonym="CC-CKR-9; CDw199; GPR-9-6; GPR28"
                     /note="C-C motif chemokine receptor 9"
                     /db_xref="GeneID:10803"
                     /db_xref="HGNC:HGNC:1610"
                     /db_xref="MIM:604738"
     exon            1..113
                     /gene="CCR9"
                     /gene_synonym="CC-CKR-9; CDw199; GPR-9-6; GPR28"
                     /inference="alignment:Splign:2.1.0"
     exon            114..162
                     /gene="CCR9"
                     /gene_synonym="CC-CKR-9; CDw199; GPR-9-6; GPR28"
                     /inference="alignment:Splign:2.1.0"
     CDS             142..1251
                     /gene="CCR9"
                     /gene_synonym="CC-CKR-9; CDw199; GPR-9-6; GPR28"
                     /note="isoform A is encoded by transcript variant A; G
                     protein-coupled receptor 28; C-C chemokine receptor type
                     9; chemokine (C-C motif) receptor 9"
                     /codon_start=1
                     /product="C-C chemokine receptor type 9 isoform A"
                     /protein_id="NP_112477.1"
                     /db_xref="CCDS:CCDS2732.1"
                     /db_xref="GeneID:10803"
                     /db_xref="HGNC:HGNC:1610"
                     /db_xref="MIM:604738"
                     /translation="MTPTDFTSPIPNMADDYGSESTSSMEDYVNFNFTDFYCEKNNVR
                     QFASHFLPPLYWLVFIVGALGNSLVILVYWYCTRVKTMTDMFLLNLAIADLLFLVTLP
                     FWAIAAADQWKFQTFMCKVVNSMYKMNFYSCVLLIMCISVDRYIAIAQAMRAHTWREK
                     RLLYSKMVCFTIWVLAAALCIPEILYSQIKEESGIAICTMVYPSDESTKLKSAVLTLK
                     VILGFFLPFVVMACCYTIIIHTLIQAKKSSKHKALKVTITVLTVFVLSQFPYNCILLV
                     QTIDAYAMFISNCAVSTNIDICFQVTQTIAFFHSCLNPVLYVFVGERFRRDLVKTLKN
                     LGCISQAQWVSFTRREGSLKLSSMLLETTSGALSL"
     exon            163..2527
                     /gene="CCR9"
                     /gene_synonym="CC-CKR-9; CDw199; GPR-9-6; GPR28"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2506..2511
                     /regulatory_class="polyA_signal_sequence"
                     /gene="CCR9"
                     /gene_synonym="CC-CKR-9; CDw199; GPR-9-6; GPR28"
                     /note="hexamer: ATTAAA"
     polyA_site      2526
                     /gene="CCR9"
                     /gene_synonym="CC-CKR-9; CDw199; GPR-9-6; GPR28"
                     /note="major polyA site"
ORIGIN      
        1 agaacccaca aagcctgccc ctcatcccag gcagagagca acccagctct ttccccagac
       61 actgagagct ggtggtgcct gctgtcccag ggagagttgc atcgccctcc acagagcagg
      121 cttgcatctg actgacccac catgacaccc acagacttca caagccctat tcctaacatg
      181 gctgatgact atggctctga atccacatct tccatggaag actacgttaa cttcaacttc
      241 actgacttct actgtgagaa aaacaatgtc aggcagtttg cgagccattt cctcccaccc
      301 ttgtactggc tcgtgttcat cgtgggtgcc ttgggcaaca gtcttgttat ccttgtctac
      361 tggtactgca caagagtgaa gaccatgacc gacatgttcc ttttgaattt ggcaattgct
      421 gacctcctct ttcttgtcac tcttcccttc tgggccattg ctgctgctga ccagtggaag
      481 ttccagacct tcatgtgcaa ggtggtcaac agcatgtaca agatgaactt ctacagctgt
      541 gtgttgctga tcatgtgcat cagcgtggac aggtacattg ccattgccca ggccatgaga
      601 gcacatactt ggagggagaa aaggcttttg tacagcaaaa tggtttgctt taccatctgg
      661 gtattggcag ctgctctctg catcccagaa atcttataca gccaaatcaa ggaggaatcc
      721 ggcattgcta tctgcaccat ggtttaccct agcgatgaga gcaccaaact gaagtcagct
      781 gtcttgaccc tgaaggtcat tctggggttc ttccttccct tcgtggtcat ggcttgctgc
      841 tataccatca tcattcacac cctgatacaa gccaagaagt cttccaagca caaagcccta
      901 aaagtgacca tcactgtcct gaccgtcttt gtcttgtctc agtttcccta caactgcatt
      961 ttgttggtgc agaccattga cgcctatgcc atgttcatct ccaactgtgc cgtttccacc
     1021 aacattgaca tctgcttcca ggtcacccag accatcgcct tcttccacag ttgcctgaac
     1081 cctgttctct atgtttttgt gggtgagaga ttccgccggg atctcgtgaa aaccctgaag
     1141 aacttgggtt gcatcagcca ggcccagtgg gtttcattta caaggagaga gggaagcttg
     1201 aagctgtcgt ctatgttgct ggagacaacc tcaggagcac tctccctctg aggggtcttc
     1261 tctgaggtgc atggttcttt tggaagaaat gagaaataca gaaacagttt ccccactgat
     1321 gggaccagag agagtgaaag agaaaagaaa actcagaaag ggatgaatct gaactatatg
     1381 attacttgta gtcagaattt gccaaagcaa atatttcaaa atcaactgac tagtgcagga
     1441 ggctgttgat tggctcttga ctgtgatgcc cgcaattctc aaaggaggac taaggaccgg
     1501 cactgtggag caccctggct ttgccactcg ccggagcatc aatgccgctg cctctggagg
     1561 agcccttgga ttttctccat gcactgtgaa cttctgtggc ttcagttctc atgctgcctc
     1621 ttccaaaagg ggacacagaa gcactggctg ctgctacaga ccgcaaaagc agaaagtttc
     1681 gtgaaaatgt ccatctttgg gaaattttct accctgctct tgagcctgat aacccatgcc
     1741 aggtcttata gattcctgat ctagaacctt tccaggcaat ctcagaccta atttccttct
     1801 gttctccttg ttctgttctg ggccagtgaa ggtccttgtt ctgattttga aacgatctgc
     1861 aggtcttgcc agtgaacccc tggacaactg accacaccca caaggcatcc aaagtctgtt
     1921 ggcttccaat ccatttctgt gtcctgctgg aggttttaac ctagacaagg attccgctta
     1981 ttccttggta tggtgacagt gtctctccat ggcctgagca gggagattat aacagctggg
     2041 ttcgcaggag ccagccttgg ccctgttgta ggcttgttct gttgagtggc acttgctttg
     2101 ggtccaccgt ctgtctgctc cctagaaaat gggctggttc ttttggccct cttctttctg
     2161 aggcccactt tattctgagg aatacagtga gcagatatgg gcagcagcca ggtagggcaa
     2221 aggggtgaag cgcaggcctt gctggaaggc tatttacttc catgcttctc cttttcttac
     2281 tctatagtgg caacatttta aaagctttta acttagagat taggctgaaa aaaataagta
     2341 atggaattca cctttgcatc ttttgtgtct ttcttatcat gatttggcaa aatgcatcac
     2401 ctttgaaaat atttcacata ttggaaaagt gctttttaat gtgtatatga agcattaatt
     2461 acttgtcact ttctttaccc tgtctcaata ttttaagtgt gtgcaattaa agatcaaata
     2521 gatacat
//
