LOCUS       NM_006897               1474 bp    mRNA    linear   PRI 08-JUN-2024
DEFINITION  Homo sapiens homeobox C9 (HOXC9), mRNA.
ACCESSION   NM_006897
VERSION     NM_006897.3
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 1474)
  AUTHORS   Liu,L., Zhang,Z., Jiang,C., Zhu,Y., Han,R., Wu,L. and Xu,Y.
  TITLE     HOXC9 characterizes a suppressive tumor immune microenvironment and
            integration with multiple immune biomarkers predicts response to
            PD-1 blockade plus chemotherapy in lung adenocarcinoma
  JOURNAL   Aging (Albany NY) 16 (5), 4841-4861 (2024)
   PUBMED   38446596
  REMARK    GeneRIF: HOXC9 characterizes a suppressive tumor immune
            microenvironment and integration with multiple immune biomarkers
            predicts response to PD-1 blockade plus chemotherapy in lung
            adenocarcinoma.
REFERENCE   2  (bases 1 to 1474)
  AUTHORS   Liu,Y., Jing,L. and Zhang,J.
  TITLE     circRNA-mediated upregulation of HOXC9 is correlated with poor
            outcome and immune microenvironment infiltrates in LUAD
  JOURNAL   Biochem Biophys Res Commun 635, 128-135 (2022)
   PUBMED   36272177
  REMARK    GeneRIF: circRNA-mediated upregulation of HOXC9 is correlated with
            poor outcome and immune microenvironment infiltrates in LUAD.
REFERENCE   3  (bases 1 to 1474)
  AUTHORS   Tang,Y., Wang,T., Yu,Y., Yan,Y. and Wu,C.
  TITLE     Upregulation of HOXC9 generates interferon-gamma resistance in
            gastric cancer by inhibiting the DAPK1/RIG1/STAT1 axis
  JOURNAL   Cancer Sci 112 (9), 3455-3468 (2021)
   PUBMED   34159686
  REMARK    GeneRIF: Upregulation of HOXC9 generates interferon-gamma
            resistance in gastric cancer by inhibiting the DAPK1/RIG1/STAT1
            axis.
REFERENCE   4  (bases 1 to 1474)
  AUTHORS   Zhao,X.F., Yang,Y.S. and Park,Y.K.
  TITLE     HOXC9 overexpression is associated with gastric cancer progression
            and a prognostic marker for poor survival in gastric cancer
            patients
  JOURNAL   Int J Clin Oncol 25 (12), 2044-2054 (2020)
   PUBMED   32816159
  REMARK    GeneRIF: HOXC9 overexpression is associated with gastric cancer
            progression and a prognostic marker for poor survival in gastric
            cancer patients.
REFERENCE   5  (bases 1 to 1474)
  AUTHORS   Luck,K., Kim,D.K., Lambourne,L., Spirohn,K., Begg,B.E., Bian,W.,
            Brignall,R., Cafarelli,T., Campos-Laborie,F.J., Charloteaux,B.,
            Choi,D., Cote,A.G., Daley,M., Deimling,S., Desbuleux,A., Dricot,A.,
            Gebbia,M., Hardy,M.F., Kishore,N., Knapp,J.J., Kovacs,I.A.,
            Lemmens,I., Mee,M.W., Mellor,J.C., Pollis,C., Pons,C.,
            Richardson,A.D., Schlabach,S., Teeking,B., Yadav,A., Babor,M.,
            Balcha,D., Basha,O., Bowman-Colin,C., Chin,S.F., Choi,S.G.,
            Colabella,C., Coppin,G., D'Amata,C., De Ridder,D., De Rouck,S.,
            Duran-Frigola,M., Ennajdaoui,H., Goebels,F., Goehring,L., Gopal,A.,
            Haddad,G., Hatchi,E., Helmy,M., Jacob,Y., Kassa,Y., Landini,S.,
            Li,R., van Lieshout,N., MacWilliams,A., Markey,D., Paulson,J.N.,
            Rangarajan,S., Rasla,J., Rayhan,A., Rolland,T., San-Miguel,A.,
            Shen,Y., Sheykhkarimli,D., Sheynkman,G.M., Simonovsky,E., Tasan,M.,
            Tejeda,A., Tropepe,V., Twizere,J.C., Wang,Y., Weatheritt,R.J.,
            Weile,J., Xia,Y., Yang,X., Yeger-Lotem,E., Zhong,Q., Aloy,P.,
            Bader,G.D., De Las Rivas,J., Gaudet,S., Hao,T., Rak,J.,
            Tavernier,J., Hill,D.E., Vidal,M., Roth,F.P. and Calderwood,M.A.
  TITLE     A reference map of the human binary protein interactome
  JOURNAL   Nature 580 (7803), 402-408 (2020)
   PUBMED   32296183
REFERENCE   6  (bases 1 to 1474)
  AUTHORS   Miano,J.M., Firulli,A.B., Olson,E.N., Hara,P., Giachelli,C.M. and
            Schwartz,S.M.
  TITLE     Restricted expression of homeobox genes distinguishes fetal from
            adult human smooth muscle cells
  JOURNAL   Proc Natl Acad Sci U S A 93 (2), 900-905 (1996)
   PUBMED   8570656
REFERENCE   7  (bases 1 to 1474)
  AUTHORS   Redline,R.W., Hudock,P., MacFee,M. and Patterson,P.
  TITLE     Expression of AbdB-type homeobox genes in human tumors
  JOURNAL   Lab Invest 71 (5), 663-670 (1994)
   PUBMED   7967520
REFERENCE   8  (bases 1 to 1474)
  AUTHORS   Acampora,D., D'Esposito,M., Faiella,A., Pannese,M., Migliaccio,E.,
            Morelli,F., Stornaiuolo,A., Nigro,V., Simeone,A. and Boncinelli,E.
  TITLE     The human HOX gene family
  JOURNAL   Nucleic Acids Res 17 (24), 10385-10402 (1989)
   PUBMED   2574852
REFERENCE   9  (bases 1 to 1474)
  AUTHORS   Boncinelli,E., Acampora,D., Pannese,M., D'Esposito,M., Somma,R.,
            Gaudino,G., Stornaiuolo,A., Cafiero,M., Faiella,A. and Simeone,A.
  TITLE     Organization of human class I homeobox genes
  JOURNAL   Genome 31 (2), 745-756 (1989)
   PUBMED   2576652
REFERENCE   10 (bases 1 to 1474)
  AUTHORS   Rabin,M., Ferguson-Smith,A., Hart,C.P. and Ruddle,F.H.
  TITLE     Cognate homeo-box loci mapped on homologous human and mouse
            chromosomes
  JOURNAL   Proc Natl Acad Sci U S A 83 (23), 9104-9108 (1986)
   PUBMED   2878432
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from BC053894.1 and AC012531.11.
            
            On Nov 22, 2018 this sequence version replaced NM_006897.2.
            
            Summary: This gene belongs to the homeobox family of genes. The
            homeobox genes encode a highly conserved family of transcription
            factors that play an important role in morphogenesis in all
            multicellular organisms. Mammals possess four similar homeobox gene
            clusters, HOXA, HOXB, HOXC and HOXD, which are located on different
            chromosomes and consist of 9 to 11 genes arranged in tandem. This
            gene is one of several homeobox HOXC genes located in a cluster on
            chromosome 12. [provided by RefSeq, Jul 2008].
            
            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 :: BC053894.1, BC021265.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1968968
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000303450.5/ ENSP00000302836.4
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-552               BC053894.1         43-594
            553-553             AC012531.11        138317-138317
            554-1323            BC053894.1         596-1365
            1324-1324           AC012531.11        140791-140791
            1325-1474           BC053894.1         1367-1516
FEATURES             Location/Qualifiers
     source          1..1474
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="12"
                     /map="12q13.13"
     gene            1..1474
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="homeobox C9"
                     /db_xref="GeneID:3225"
                     /db_xref="HGNC:HGNC:5130"
                     /db_xref="MIM:142971"
     exon            1..566
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /inference="alignment:Splign:2.1.0"
     CDS             29..811
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="homeo box C9; homeobox protein Hox-3B"
                     /codon_start=1
                     /product="homeobox protein Hox-C9"
                     /protein_id="NP_008828.1"
                     /db_xref="CCDS:CCDS8869.1"
                     /db_xref="GeneID:3225"
                     /db_xref="HGNC:HGNC:5130"
                     /db_xref="MIM:142971"
                     /translation="MSATGPISNYYVDSLISHDNEDLLASRFPATGAHPAAARPSGLV
                     PDCSDFPSCSFAPKPAVFSTSWAPVPSQSSVVYHPYGPQPHLGADTRYMRTWLEPLSG
                     AVSFPSFPAGGRHYALKPDAYPGRRADCGPGEGRSYPDYMYGSPGELRDRAPQTLPSP
                     EADALAGSKHKEEKADLDPSNPVANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLT
                     RDRRYEVARVLNLTERQVKIWFQNRRMKMKKMNKEKTDKEQS"
     exon            567..1474
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1084..1089
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="hexamer: AATAAA"
     polyA_site      1107
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="major polyA site"
     regulatory      1448..1453
                     /regulatory_class="polyA_signal_sequence"
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
                     /note="hexamer: AATATA"
     polyA_site      1474
                     /gene="HOXC9"
                     /gene_synonym="HOX3; HOX3B"
ORIGIN      
        1 aatcttatgt atgtaaaacc ccgttacgat gtcggcgacg gggcccatca gtaactatta
       61 cgtggactcg ctcatctctc acgacaatga agacctccta gcgtccaggt ttccggccac
      121 cggggctcat cccgccgccg ccagacccag cggtttggtg ccggactgta gcgattttcc
      181 gtcctgtagc ttcgcgccca agccggcagt gttcagcacg tcgtgggcgc ccgtgccctc
      241 tcagtcgtcc gtggtatatc acccgtacgg cccccagccc cacctcggcg ccgacacgcg
      301 ctacatgcgg acttggctcg agccgctgtc cggcgccgtc tccttcccca gcttcccggc
      361 cgggggccgt cactacgccc tcaagccgga cgcctacccc gggcgccgcg cggactgcgg
      421 cccaggggag ggccgcagct acccggacta catgtacggc tcgcccgggg agctgcgcga
      481 ccgcgccccg cagacactgc cctcgcccga ggcggacgcg ctcgccggca gcaagcacaa
      541 agaggagaag gccgacctgg accccagcaa ccccgtggcc aactggattc acgcccgctc
      601 cacgaggaag aagcgctgcc cctacaccaa gtaccagacg ctggaactgg agaaggagtt
      661 tctcttcaat atgtatttaa ccagggaccg tcggtatgag gtggcccggg ttctcaatct
      721 caccgagcgg caggtcaaaa tctggtttca gaatcgaagg atgaagatga aaaagatgaa
      781 taaagagaaa accgacaagg agcagtccta aaccctaccc agcctgctgc ctcagcacag
      841 ccaagggaaa aacaaaaacc ccacaaaata ccccaacaca ggcgggggag agacgaaaaa
      901 gaaaaggaaa gagcaagata gacaaaagcc aatcagctta aaaagaaaaa caaggaaggg
      961 gaaaagaaaa ctcttgcgat ttgggagggt tcagtgttga gatattggtg ttttagagtt
     1021 agttctaccc agcgaggagg aggcggggag agaaactgcg ttctctttcc ccagcgcaac
     1081 cgaaataaat gacacataca aatgtgattt ttttcctcct ttcttcagag aagccagtac
     1141 ttgaatcgct atatttctat ttttttttcc ctgtatcgta tttggtccag gtcatccctc
     1201 cccgggcctg gggcgctctg cgtgcagatt ttgtacaaaa aaaaaaaaga cacacacaca
     1261 tacatgataa tgattcccag cccaggagct gaggggtgag ggctggggac catgccgcgg
     1321 gctaggtcgg gcccgtgcag gccggcgcct tgggctgtac atagtgttcc ctctcatccc
     1381 cagggttcgt ccccagcgtc cgtcctgtaa cgtgcttctg tttgttatgg tagaacagcc
     1441 ctgtgttaat atattgaagt cacttaacca gaaa
//
