LOCUS       NM_008272               1719 bp    mRNA    linear   ROD 28-JAN-2025
DEFINITION  Mus musculus homeobox C9 (Hoxc9), mRNA.
ACCESSION   NM_008272
VERSION     NM_008272.3
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Mus musculus (house mouse)
  ORGANISM  Mus musculus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE   1  (bases 1 to 1719)
  AUTHORS   Hung,Y.S., Lin,W.M., Wang,Y.C., Kuo,W.C., Chen,Y.Y., Fann,M.J.,
            Yu,J.Y. and Wong,Y.H.
  TITLE     Protogenin facilitates trunk-to-tail HOX code transition via
            modulating GDF11/SMAD2 signaling in mammalian embryos
  JOURNAL   Commun Biol 7 (1), 1669 (2024)
   PUBMED   39702818
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1719)
  AUTHORS   Song,L., Li,Q., Xia,L., Sahay,A.E., Qiu,Q., Li,Y., Li,H.,
            Sasaki,K., Susztak,K., Wu,H. and Wan,L.
  TITLE     Single-cell multiomics reveals ENL mutation perturbs kidney
            developmental trajectory by rewiring gene regulatory landscape
  JOURNAL   Nat Commun 15 (1), 5937 (2024)
   PUBMED   39009564
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1719)
  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   4  (bases 1 to 1719)
  AUTHORS   Kumar,S., Alam,S.S., Bareke,E., Beauchamp,M.C., Dong,Y., Chan,W.,
            Majewski,J. and Jerome-Majewska,L.A.
  TITLE     Sf3b4 regulates chromatin remodeler splicing and Hox expression
  JOURNAL   Differentiation 131, 59-73 (2023)
   PUBMED   37167859
REFERENCE   5  (bases 1 to 1719)
  AUTHORS   Sawai,A., Pfennig,S., Bulajic,M., Miller,A., Khodadadi-Jamayran,A.,
            Mazzoni,E.O. and Dasen,J.S.
  TITLE     PRC1 sustains the integrity of neural fate in the absence of PRC2
            function
  JOURNAL   Elife 11, e72769 (2022)
   PUBMED   34994686
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1719)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
REFERENCE   7  (bases 1 to 1719)
  AUTHORS   Hameister,H., Schulz,W.A., Meyer,J., Thoma,S., Adolph,S., Gaa,A.
            and von Deimling,O.
  TITLE     Gene order and genetic distance of 13 loci spanning murine
            chromosome 15
  JOURNAL   Genomics 14 (2), 417-422 (1992)
   PUBMED   1358803
REFERENCE   8  (bases 1 to 1719)
  AUTHORS   Peterson,R.L., Jacobs,D.F. and Awgulewitsch,A.
  TITLE     Hox-3.6: isolation and characterization of a new murine homeobox
            gene located in the 5' region of the Hox-3 cluster
  JOURNAL   Mech Dev 37 (3), 151-166 (1992)
   PUBMED   1353983
REFERENCE   9  (bases 1 to 1719)
  AUTHORS   Erselius,J.R., Goulding,M.D. and Gruss,P.
  TITLE     Structure and expression pattern of the murine Hox-3.2 gene
  JOURNAL   Development 110 (2), 629-642 (1990)
   PUBMED   1723949
REFERENCE   10 (bases 1 to 1719)
  AUTHORS   Awgulewitsch,A., Bieberich,C., Bogarad,L., Shashikant,C. and
            Ruddle,F.H.
  TITLE     Structural analysis of the Hox-3.1 transcription unit and the
            Hox-3.2--Hox-3.1 intergenic region
  JOURNAL   Proc Natl Acad Sci U S A 87 (16), 6428-6432 (1990)
   PUBMED   1696731
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AC021667.21.
            
            On Nov 17, 2006 this sequence version replaced NM_008272.2.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            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 :: BC050838.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN04095723 [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-70                AC021667.21        79858-79927
            71-1169             AC021667.21        83915-85013
            1170-1719           AC021667.21        86718-87267
FEATURES             Location/Qualifiers
     source          1..1719
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="15"
                     /map="15 58.04 cM"
     gene            1..1719
                     /gene="Hoxc9"
                     /gene_synonym="Hox-3.2"
                     /note="homeobox C9"
                     /db_xref="GeneID:15427"
                     /db_xref="MGI:MGI:96199"
     exon            1..70
                     /gene="Hoxc9"
                     /gene_synonym="Hox-3.2"
                     /inference="alignment:Splign:2.1.0"
     exon            71..1169
                     /gene="Hoxc9"
                     /gene_synonym="Hox-3.2"
                     /inference="alignment:Splign:2.1.0"
     CDS             632..1414
                     /gene="Hoxc9"
                     /gene_synonym="Hox-3.2"
                     /note="homeobox protein Hox-3.2; homeo box C9"
                     /codon_start=1
                     /product="homeobox protein Hox-C9"
                     /protein_id="NP_032298.1"
                     /db_xref="CCDS:CCDS27893.1"
                     /db_xref="GeneID:15427"
                     /db_xref="MGI:MGI:96199"
                     /translation="MSATGPISNYYVDSLISHDNEDLLASRFPATGAHPAAARPSGLV
                     PDCSDFPSCSFAPKPAVFSTSWAPVPSQSSVVYHPYGPQPHLGADTRYMRTWLEPLSG
                     AVSFPSFPAGGRHYALKPDAYPGRRADCGPGDGRSYPDYMYGSPGELRDRAPQTLPSP
                     EADALAGSKHKEEKADLDPSNPVANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLT
                     RDRRYEVARVLNLTERQVKIWFQNRRMKMKKMNKEKTDKEQS"
     exon            1170..1719
                     /gene="Hoxc9"
                     /gene_synonym="Hox-3.2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1695..1700
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxc9"
                     /gene_synonym="Hox-3.2"
                     /note="hexamer: AATAAA"
     polyA_site      1719
                     /gene="Hoxc9"
                     /gene_synonym="Hox-3.2"
                     /note="major polyA site"
ORIGIN      
        1 cgcttcctca gtctgggctc caaagtcact gcaaatttcc ttgcgataca tacatcacac
       61 aaaagatcag agactgcagg agcgtcggag ccgacagaga cagattacgt caagaaatag
      121 ttcctccacc tacctcgtcc ggcctccccg cccctgaggg gctccccgag cccatctcag
      181 ctctgggggt ccaggaaccc tggcttctgg gactggcatt ttcatcttgt tttttttttt
      241 ttttttaatc ctcatggtag ggggagccat ctgcttttgg ctgcacatgg tcaagggggg
      301 ggggtccctg atgagatatg attcgtccgg ggaggggggg ctgtctggcg ccttgggtcc
      361 agagttgcaa atcgccagga aaacgcaggt cgcggggatc agcaaagaga agggggcggt
      421 aaagggggga aaaagcaagg gggaaaaaaa gcccctgcgc attgatccgc gccgtatttt
      481 tgggtaaata cgatcacgtg ggggctgggg aaccaatgag ctgccgggaa aaggctggaa
      541 aaataattac ctgccttgat tgttctgtga gcagataaaa agtacatata cagttcatac
      601 aataatctta tgtatgtaaa accctgttac gatgtcggcg acggggccca tcagtaacta
      661 ttacgtggac tcgctcatct ctcacgacaa tgaagacctc ctagcgtcca ggtttccggc
      721 caccggggct caccctgccg ccgccagacc cagcggcttg gtgccggact gtagcgattt
      781 tccgtcctgt agcttcgcgc ccaagccggc tgtattcagt acgtcgtggg cgccggtgcc
      841 ctcgcagtcg tctgtggtct atcaccctta cggcccccag ccccacctcg gcgccgacac
      901 gcgctacatg cggacttggc tcgagccgct gtccggcgcc gtctccttcc ccagcttccc
      961 ggccgggggc cgtcactacg ccctcaagcc cgacgcctac ccggggcgcc gcgccgactg
     1021 cggcccgggc gacggccgca gctacccgga ctacatgtac ggctcgcccg gggaactgcg
     1081 cgaccgcgcc ccgcagacgc tgccctcgcc cgaggcggac gcgctggccg gcagcaagca
     1141 caaagaggag aaggccgacc tggaccctag caaccccgtg gccaactgga tccacgcccg
     1201 ttccacaagg aagaagcgct gcccctacac caagtaccag acgctggaac tggagaagga
     1261 gtttctcttc aatatgtatt taaccaggga ccgtcggtac gaggtggccc gtgttctcaa
     1321 tctcactgag cggcaggtca aaatctggtt tcagaaccgg aggatgaaga tgaaaaagat
     1381 gaataaagag aaaaccgaca aggaacaatc ctaagccctg ccccagcctg ctgcctcggc
     1441 acagccaagg gaaacacaaa aacccccaca aaaaatgccc caacccaggc gggagaaagc
     1501 acgaaaagaa aaggaaagaa caagatagag aaaagcccac cgtcttaaaa agaaaagaaa
     1561 aaaaaggaag gggaaaaatg caaactcttg cgatgtggga gggttaagtg ttgagaaatt
     1621 ggtgtttaga gttagttcta tccatcgagg aggaggcagg agagaaactg cgttctcttc
     1681 cccagcgcaa ctgaaataaa tgacacacac aaatgtgaa
//
