LOCUS       NM_013555               2100 bp    mRNA    linear   ROD 28-JAN-2025
DEFINITION  Mus musculus homeobox D9 (Hoxd9), mRNA.
ACCESSION   NM_013555
VERSION     NM_013555.4
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 2100)
  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 2100)
  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   3  (bases 1 to 2100)
  AUTHORS   Oikonomakos,I., Tedesco,M., Motamedi,F.J., Peitzsch,M., Nef,S.,
            Bornstein,S.R., Schedl,A., Steenblock,C. and Neirijnck,Y.
  TITLE     In vitro differentiation of mouse pluripotent stem cells into
            corticosteroid-producing adrenocortical cells
  JOURNAL   Stem Cell Reports 19 (9), 1289-1303 (2024)
   PUBMED   39178848
REFERENCE   4  (bases 1 to 2100)
  AUTHORS   Chen,Y., Zhou,T., Liao,Z., Gao,W., Wu,J., Zhang,S., Li,Y., Liu,H.,
            Zhou,H., Xu,C. and Su,P.
  TITLE     Hnrnpk is essential for embryonic limb bud development as a
            transcription activator and a collaborator of insulator protein
            Ctcf
  JOURNAL   Cell Death Differ 30 (10), 2293-2308 (2023)
   PUBMED   37608075
REFERENCE   5  (bases 1 to 2100)
  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   6  (bases 1 to 2100)
  AUTHORS   Nazarali,A., Kim,Y. and Nirenberg,M.
  TITLE     Hox-1.11 and Hox-4.9 homeobox genes
  JOURNAL   Proc Natl Acad Sci U S A 89 (7), 2883-2887 (1992)
   PUBMED   1348361
REFERENCE   7  (bases 1 to 2100)
  AUTHORS   Renucci,A., Zappavigna,V., Zakany,J., Izpisua-Belmonte,J.C.,
            Burki,K. and Duboule,D.
  TITLE     Comparison of mouse and human HOX-4 complexes defines conserved
            sequences involved in the regulation of Hox-4.4
  JOURNAL   EMBO J 11 (4), 1459-1468 (1992)
   PUBMED   1348690
REFERENCE   8  (bases 1 to 2100)
  AUTHORS   Dolle,P., Izpisua-Belmonte,J.C., Boncinelli,E. and Duboule,D.
  TITLE     The Hox-4.8 gene is localized at the 5' extremity of the Hox-4
            complex and is expressed in the most posterior parts of the body
            during development
  JOURNAL   Mech Dev 36 (1-2), 3-13 (1991)
   PUBMED   1685889
REFERENCE   9  (bases 1 to 2100)
  AUTHORS   Dolle,P., Izpisua-Belmonte,J.C., Brown,J.M., Tickle,C. and
            Duboule,D.
  TITLE     HOX-4 genes and the morphogenesis of mammalian genitalia
  JOURNAL   Genes Dev 5 (10), 1767-1767 (1991)
   PUBMED   1680771
REFERENCE   10 (bases 1 to 2100)
  AUTHORS   Izpisua-Belmonte,J.C., Falkenstein,H., Dolle,P., Renucci,A. and
            Duboule,D.
  TITLE     Murine genes related to the Drosophila AbdB homeotic genes are
            sequentially expressed during development of the posterior part of
            the body
  JOURNAL   EMBO J 10 (8), 2279-2289 (1991)
   PUBMED   1676674
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            AL928644.12 and AK134427.1.
            
            On Aug 4, 2012 this sequence version replaced NM_013555.3.
            
            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 :: BC019150.2, AK134427.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00849374, SAMN00849375
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-271               AL928644.12        182695-182965
            272-688             AK134427.1         62-478
            689-689             AL928644.12        183383-183383
            690-2079            AK134427.1         480-1869
            2080-2100           AL928644.12        185120-185140
FEATURES             Location/Qualifiers
     source          1..2100
                     /organism="Mus musculus"
                     /mol_type="mRNA"
                     /strain="C57BL/6"
                     /db_xref="taxon:10090"
                     /chromosome="2"
                     /map="2 44.13 cM"
     gene            1..2100
                     /gene="Hoxd9"
                     /gene_synonym="Hox-4.4; Hox-5.2"
                     /note="homeobox D9"
                     /db_xref="GeneID:15438"
                     /db_xref="MGI:MGI:96210"
     exon            1..1071
                     /gene="Hoxd9"
                     /gene_synonym="Hox-4.4; Hox-5.2"
                     /inference="alignment:Splign:2.1.0"
     CDS             294..1313
                     /gene="Hoxd9"
                     /gene_synonym="Hox-4.4; Hox-5.2"
                     /note="homeobox protein Hox-4.4; homeobox protein Hox-5.2;
                     homeo box D9"
                     /codon_start=1
                     /product="homeobox protein Hox-D9"
                     /protein_id="NP_038583.1"
                     /db_xref="CCDS:CCDS16142.1"
                     /db_xref="GeneID:15438"
                     /db_xref="MGI:MGI:96210"
                     /translation="MSSSGTLSNYYVDSLIGHEGDEVFAARFGPPGPGTQGRPAGVAD
                     GPAAATAEFASCSFAPKSSVFSASWSAVAAQPPAAATMSGLYHPYVSPPPLAAAEPGR
                     YVRSWMEPLPGFPGGAGGGGGSGGGGGGGPGPVPSPGGPANGRHYGIKPETGAAPAPA
                     AASTSSSSSTSSSSSSKRTECSAARESQGSGGPEFPCNSFLRDKAAAATGNGPGVGIG
                     TGPGAVGSSEPSACSDHPSPGCSLKEEEKQPPQPPQQQLDPNNPAANWIHARSTRKKR
                     CPYTKYQTLELEKEFLFNMYLTRDRRYEVARILNLTERQVKIWFQNRRMKMKKMSKEK
                     CPKGD"
     exon            1072..2100
                     /gene="Hoxd9"
                     /gene_synonym="Hox-4.4; Hox-5.2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      2055..2060
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxd9"
                     /gene_synonym="Hox-4.4; Hox-5.2"
                     /note="hexamer: AATAAA"
     regulatory      2071..2076
                     /regulatory_class="polyA_signal_sequence"
                     /gene="Hoxd9"
                     /gene_synonym="Hox-4.4; Hox-5.2"
                     /note="hexamer: AACAAA"
     polyA_site      2085
                     /gene="Hoxd9"
                     /gene_synonym="Hox-4.4; Hox-5.2"
                     /note="major polyA site"
     polyA_site      2100
                     /gene="Hoxd9"
                     /gene_synonym="Hox-4.4; Hox-5.2"
                     /note="major polyA site"
ORIGIN      
        1 gccgccgcca ccagggcggg ctgagccggg ccaggccggg ctggtgcgtg gacctgggcc
       61 cggcagctct aattgcaacg ctcctgttga tgatgatttt ttttttttta aatcacagca
      121 gcccccagtt tagcggactg atttactccg ggtattggta aatatgatca cgtgggccgc
      181 gcgaccaatg gtggtggctg cagcctgcga actagtcggc ggctcgggcg ccggcgagga
      241 gccgctcggc ggtgggcagt ggaaccttgg gtgggagcga gcggcgcctc accatgtcgt
      301 ccagtggcac cctcagcaac tactacgtgg actcgctcat aggccatgag ggcgacgagg
      361 tgttcgccgc gcgctttggg ccaccggggc cggggacaca gggccggccc gcaggtgtgg
      421 ccgatggccc agccgccgcc accgccgagt tcgcctcgtg tagttttgcc cccaaatcgt
      481 ccgtgttctc cgcctcgtgg tccgcggtgg ccgcccagcc cccggcggcg gcgacgatga
      541 gcggcctgta ccacccgtac gtgtccccgc cgcccctggc tgccgccgag ccgggacgct
      601 acgtacgctc ctggatggag ccgctgcccg gcttccccgg cggcgcaggc ggtggcggtg
      661 gcagtggtgg cggcggtggc ggaggcccgg gtcccgttcc cagccccggt ggcccagcca
      721 acgggcgcca ctacgggatt aagcctgaaa ccggagcggc cccggccccc gctgcagcct
      781 ccacctcctc ctcctcctcc acctcctcgt cctcctcctc caaaaggact gagtgctccg
      841 cggcccgcga gtcccagggg agcggcggcc cagaattccc gtgcaactcg ttcctgcggg
      901 acaaggcagc ggcggcgaca gggaacgggc ccggggtggg aatcgggacc gggccagggg
      961 cggtaggctc gtccgagccc tcagcttgca gcgatcaccc gagcccgggc tgctcgctga
     1021 aggaggagga gaagcagccg ccgcagccgc cgcagcagca acttgaccca aacaaccctg
     1081 cagcgaactg gatccacgct cgctccaccc ggaaaaagcg ctgtccctac accaaatacc
     1141 agacgctaga gctggagaag gaattcctct tcaacatgta cctcacccgg gaccggcgct
     1201 acgaggtggc caggattctg aaccttacag agagacaagt caaaatctgg ttccagaacc
     1261 gtaggatgaa aatgaaaaag atgagcaagg agaagtgccc taaaggagac tgacccagtg
     1321 cgggtctggc ctgcagcact caaaaggcag cgggtttttt tgtttgtttg tttgtttgtt
     1381 ttgttttttg ttttttgttg ttgtttgttt tctttgtggg tgcttgattc agaaactctg
     1441 cagcgactcg gactttcttc tttttttagg tagaagtgac tgtgtggttg gtctctgtga
     1501 gttatctggg ggacactgta tttgctcgca tatgtattgg agaaaccaag tggctttgga
     1561 gtcttgtcct gtcccactcc ctcccttccc tgctcccctg attccttagg aaatgctata
     1621 ttttgtgagt gcacgcaggc ttgatggagc cctattctat gtaaatgtcc ctcatgtttc
     1681 tgaaaagtgc tgtagtttag tctcacccta tccagcctcc caaacagggc caacgatcta
     1741 attccgagaa tctgaaggaa gacagagtgt ggacaccccc accctgctct cccaactaaa
     1801 atccaactca gctgctcaag gcaggaaaac ccctttcctc ggggagccgg cggactgact
     1861 tccacagagg cctaccgaga aaccttgggc cctggggcgc gagattgggg gtggggtggg
     1921 gataggctta gtcctcagag caccggggaa gctactttct ccccgggagg gctgagctcc
     1981 cattgggcgg cctcgggagg ttgccttcca tattcctgcc tgaggaccag ttgtaaatgt
     2041 taccgcttcc aacaaataaa tgctgatctg aacaaatgga gcccagccgc tggccctgaa
//
