LOCUS       NM_010456               2048 bp    mRNA    linear   ROD 28-JAN-2025
DEFINITION  Mus musculus homeobox A9 (Hoxa9), transcript variant 1, mRNA.
ACCESSION   NM_010456
VERSION     NM_010456.4
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 2048)
  AUTHORS   Frenette,B., Gueno,J., Houde,N., Landry-Truchon,K., Giguere,A.,
            Ashok,T., Ryckman,A., Morton,B.R., Mansfield,J.H. and Jeannotte,L.
  TITLE     Loss of Hoxa5 function affects Hox gene expression in different
            biological contexts
  JOURNAL   Sci Rep 14 (1), 30903 (2024)
   PUBMED   39730789
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2048)
  AUTHORS   Fu,X., Fu,P., Yang,T. and Niu,T.
  TITLE     Homeobox A9 is a novel mediator of vascular smooth muscle cell
            phenotypic switching and proliferation by regulating methyl-CpG
            binding protein 2
  JOURNAL   Cell Signal 108, 110695 (2023)
   PUBMED   37127144
  REMARK    GeneRIF: Homeobox A9 is a novel mediator of vascular smooth muscle
            cell phenotypic switching and proliferation by regulating
            methyl-CpG binding protein 2.
REFERENCE   3  (bases 1 to 2048)
  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   4  (bases 1 to 2048)
  AUTHORS   Popovic,R., Erfurth,F. and Zeleznik-Le,N.
  TITLE     Transcriptional complexity of the HOXA9 locus
  JOURNAL   Blood Cells Mol Dis 40 (2), 156-159 (2008)
   PUBMED   17916434
  REMARK    Review article
REFERENCE   5  (bases 1 to 2048)
  AUTHORS   Fujimoto,S., Araki,K., Chisaka,O., Araki,M., Takagi,K. and
            Yamamura,K.
  TITLE     Analysis of the murine Hoxa-9 cDNA: an alternatively spliced
            transcript encodes a truncated protein lacking the homeodomain
  JOURNAL   Gene 209 (1-2), 77-85 (1998)
   PUBMED   9524228
REFERENCE   6  (bases 1 to 2048)
  AUTHORS   Lawrence,H.J., Helgason,C.D., Sauvageau,G., Fong,S., Izon,D.J.,
            Humphries,R.K. and Largman,C.
  TITLE     Mice bearing a targeted interruption of the homeobox gene HOXA9
            have defects in myeloid, erythroid, and lymphoid hematopoiesis
  JOURNAL   Blood 89 (6), 1922-1930 (1997)
   PUBMED   9058712
REFERENCE   7  (bases 1 to 2048)
  AUTHORS   Rijli,F.M., Matyas,R., Pellegrini,M., Dierich,A., Gruss,P.,
            Dolle,P. and Chambon,P.
  TITLE     Cryptorchidism and homeotic transformations of spinal nerves and
            vertebrae in Hoxa-10 mutant mice
  JOURNAL   Proc Natl Acad Sci U S A 92 (18), 8185-8189 (1995)
   PUBMED   7667266
REFERENCE   8  (bases 1 to 2048)
  AUTHORS   Satokata,I., Benson,G. and Maas,R.
  TITLE     Sexually dimorphic sterility phenotypes in Hoxa10-deficient mice
  JOURNAL   Nature 374 (6521), 460-463 (1995)
   PUBMED   7700356
REFERENCE   9  (bases 1 to 2048)
  AUTHORS   Scott,M.P.
  TITLE     Vertebrate homeobox gene nomenclature
  JOURNAL   Cell 71 (4), 551-553 (1992)
   PUBMED   1358459
REFERENCE   10 (bases 1 to 2048)
  AUTHORS   Rubin,M.R., King,W., Toth,L.E., Sawczuk,I.S., Levine,M.S.,
            D'Eustachio,P. and Nguyen-Huu,M.C.
  TITLE     Murine Hox-1.7 homeo-box gene: cloning, chromosomal location, and
            expression
  JOURNAL   Mol Cell Biol 7 (10), 3836-3841 (1987)
   PUBMED   2891029
  REMARK    Erratum:[Mol Cell Biol 1988 Dec;8(12):5593]
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AC015583.34.
            
            On Mar 31, 2023 this sequence version replaced NM_010456.3.
            
            Summary: This gene is located in a cluster of developmentally and
            temporally regulated genes on chromosome 6 encoding proteins
            involved in pattern formation. These proteins contain a
            characteristic DNA-binding motif called a homeodomain and function
            in transcriptional regulation. There are four distinct clusters of
            similar genes on chromosomes 2, 6, 11, and 15. The protein encoded
            by this gene is important for hematopoeisis. Alternative splicing
            results in multiple transcript variants. [provided by RefSeq, Mar
            2013].
            
            Sequence Note:.
            
            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 :: BC055059.1, SRR13948564.229620.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849382, SAMN00849389
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-662               AC015583.34        87177-87838
            663-2048            AC015583.34        88884-90269
FEATURES             Location/Qualifiers
     source          1..2048
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="6"
                     /map="6 25.4 cM"
     gene            1..2048
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="homeobox A9"
                     /db_xref="GeneID:15405"
                     /db_xref="MGI:MGI:96180"
     exon            1..662
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /inference="alignment:Splign:2.1.0"
     CDS             86..901
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="isoform 1 is encoded by transcript variant 1;
                     homeobox protein Hox-A9; homeobox protein Hox-1.7; homeo
                     box A9"
                     /codon_start=1
                     /product="homeobox protein Hox-A9 isoform 1"
                     /protein_id="NP_034586.1"
                     /db_xref="CCDS:CCDS20146.1"
                     /db_xref="GeneID:15405"
                     /db_xref="MGI:MGI:96180"
                     /translation="MATTGALGNYYVDSFLLGADAADELGAGRYAPGTLGQPPRQAAA
                     LAEHPDFSPCSFQSKAAVFGASWNPVHAAGANAVPAAVYHHHHHPYVHPQAPVAAAAP
                     DGRYMRSWLEPTPGALSFAGLPSSRPYGIKPEPLSARRGDCPTLDTHTLSLTDYACGS
                     PPVDREKQPSEGAFSENNAENESGGDKPPIDPNNPAANWLHARSTRKKRCPYTKHQTL
                     ELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDRAKDE"
     exon            663..2048
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /inference="alignment:Splign:2.1.0"
     regulatory      1696..1701
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="hexamer: ATTAAA"
     regulatory      1700..1705
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="hexamer: AAGAAA"
     polyA_site      1717
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="major polyA site"
     polyA_site      1721
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="major polyA site"
     regulatory      1866..1871
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="hexamer: AATAAA"
     polyA_site      1890
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="major polyA site"
     regulatory      2026..2031
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="hexamer: AATAAA"
     polyA_site      2048
                     /gene="Hoxa9"
                     /gene_synonym="D6a9; Hox-1.7"
                     /note="major polyA site"
ORIGIN      
        1 ctggtgccac caagttgtta catgaaatct gcagtttcat aatttcggcg ggtcgggctg
       61 ggccggccag gcgcgggcta ctgcaatggc caccaccggg gccctgggca actactatgt
      121 ggactccttc ctgctgggcg ccgacgctgc tgatgagctg ggtgcgggac gctacgctcc
      181 agggaccctg ggtcaacccc caaggcaggc ggcagctctg gccgaacacc ccgacttcag
      241 tccttgcagc ttccagtcca aggcggcggt gtttggtgcc tcgtggaacc cagtgcacgc
      301 ggcgggcgcc aatgcggtgc ctgctgcagt gtatcatcac caccaccacc cctacgtgca
      361 tccccaggcg cccgtggcgg cggcggcgcc ggacggcagg tatatgcgct cctggctgga
      421 acccacgccc ggtgcgctct ccttcgcggg cttaccctcc agccggcctt atggcattaa
      481 acctgaaccg ctctcggcca gaaggggtga ctgtcccacg cttgacactc acactttgtc
      541 cctgactgac tatgcttgtg gttctcctcc agttgataga gaaaaacaac ccagcgaagg
      601 cgccttctcc gaaaacaatg ccgagaatga gagcggcgga gacaagcccc ccatcgatcc
      661 caataacccg gctgccaact ggctacatgc tcgctccact cggaagaagc gatgccccta
      721 cacaaaacac cagacgctgg aactggagaa ggagtttctg tttaacatgt acctcacacg
      781 ggaccgcagg tacgaggtgg cccggctgct caacctcacc gaaaggcagg tcaagatctg
      841 gttccagaac cgcaggatga aaatgaagaa aatcaacaag gaccgagcaa aagacgagtg
      901 agccttttag gggctcattt aaaaagagag caagctagaa agaaaaagaa aggactgtcc
      961 gtctccctct gtctcctctc ccccaaaccc agcctccacc cgcacaaagg ggctctaaat
     1021 cccaggcctc atctccccac tggcagtccg tgctcaggct ggctcttagg cctgcggctt
     1081 tgatggagga ggtattgtaa gctttccatt ttatagaagg cacacacaca cacaagggag
     1141 ggcattagcg ctattggctg tatgtgctag cttgtatata tatatatata tttaaaaaaa
     1201 atctacctgc ttctgacttt aagcaaaagg aaagaaaact acctttttat ataatgcaca
     1261 actgttgatg actggctgta tagtttttag tctctgtagc taatttaatt tgctcttcgt
     1321 gtggcagatc attctgccaa aatacttgaa cactgtgttt tattgtggta attatgtttt
     1381 gtgactcaaa cttctgtgct gggtgaagta cccattgtga ttgtggaagc tagaattcaa
     1441 tttgaactca ggttgtttat ggggggagag aagctgtggc ataatgtata gctctgtagt
     1501 cttctgtgta gctagactgt taacctacga ttgtaaacta gctgtaagga tttcccagtg
     1561 aaatcagatt tggaaagaaa agagagatag ttctccggga tgcatagatt catgatttat
     1621 ctacttttga aatgtgggct tcttcatctt tacgttctag actccaattt tgtccaatgt
     1681 atatagaatc tccatattaa agaaatattc ataatcagaa agcttgaata ttgtttttgc
     1741 accagaggag aagtgaggaa attcggagct atacgtgtgt gcagagggtt gctacctatg
     1801 ggtttacgct taattttaat tgggagaaag tgagtgctta ttgtaatgga gttaatttta
     1861 ttgataataa attatacacc atgaaactgc tcttgggcta ctgtagattt gtatccttgg
     1921 tgaatttggg gttcccatcg gattgaacat acactgtata ttttgcaata gttacctcaa
     1981 ggcctactga ccaaattgtt gtgtcgagat atttaacttt tgccaaataa aatatattga
     2041 ttctttta
//
