LOCUS       NM_001173469            1834 bp    mRNA    linear   ROD 30-MAR-2024
DEFINITION  Rattus norvegicus homeo box D9 (Hoxd9), mRNA.
ACCESSION   NM_001173469 XM_002726192
VERSION     NM_001173469.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 1834)
  AUTHORS   Hong,Q., Li,X.D., Xie,P. and Du,S.X.
  TITLE     All-trans-retinoic acid suppresses rat embryo hindlimb bud
            mesenchymal chondrogenesis by modulating HoxD9 expression
  JOURNAL   Bioengineered 12 (1), 3900-3911 (2021)
   PUBMED   34288810
  REMARK    GeneRIF: All-trans-retinoic acid suppresses rat embryo hindlimb bud
            mesenchymal chondrogenesis by modulating HoxD9 expression.
REFERENCE   2  (bases 1 to 1834)
  AUTHORS   Raines,A.M., Adam,M., Magella,B., Meyer,S.E., Grimes,H.L., Dey,S.K.
            and Potter,S.S.
  TITLE     Recombineering-based dissection of flanking and paralogous Hox gene
            functions in mouse reproductive tracts
  JOURNAL   Development 140 (14), 2942-2952 (2013)
   PUBMED   23760953
REFERENCE   3  (bases 1 to 1834)
  AUTHORS   McIntyre,D.C., Rakshit,S., Yallowitz,A.R., Loken,L., Jeannotte,L.,
            Capecchi,M.R. and Wellik,D.M.
  TITLE     Hox patterning of the vertebrate rib cage
  JOURNAL   Development 134 (16), 2981-2989 (2007)
   PUBMED   17626057
REFERENCE   4  (bases 1 to 1834)
  AUTHORS   de la Cruz,C.C., Der-Avakian,A., Spyropoulos,D.D., Tieu,D.D. and
            Carpenter,E.M.
  TITLE     Targeted disruption of Hoxd9 and Hoxd10 alters locomotor behavior,
            vertebral identity, and peripheral nervous system development
  JOURNAL   Dev Biol 216 (2), 595-610 (1999)
   PUBMED   10642795
REFERENCE   5  (bases 1 to 1834)
  AUTHORS   Chen,F. and Capecchi,M.R.
  TITLE     Paralogous mouse Hox genes, Hoxa9, Hoxb9, and Hoxd9, function
            together to control development of the mammary gland in response to
            pregnancy
  JOURNAL   Proc Natl Acad Sci U S A 96 (2), 541-546 (1999)
   PUBMED   9892669
REFERENCE   6  (bases 1 to 1834)
  AUTHORS   Fromental-Ramain,C., Warot,X., Lakkaraju,S., Favier,B., Haack,H.,
            Birling,C., Dierich,A., Doll e,P. and Chambon,P.
  TITLE     Specific and redundant functions of the paralogous Hoxa-9 and
            Hoxd-9 genes in forelimb and axial skeleton patterning
  JOURNAL   Development 122 (2), 461-472 (1996)
   PUBMED   8625797
REFERENCE   7  (bases 1 to 1834)
  AUTHORS   Zappavigna,V., Renucci,A., Izpisua-Belmonte,J.C., Urier,G.,
            Peschle,C. and Duboule,D.
  TITLE     HOX4 genes encode transcription factors with potential auto- and
            cross-regulatory capacities
  JOURNAL   EMBO J 10 (13), 4177-4187 (1991)
   PUBMED   1756725
REFERENCE   8  (bases 1 to 1834)
  AUTHORS   Oliver,G., Sidell,N., Fiske,W., Heinzmann,C., Mohandas,T.,
            Sparkes,R.S. and De Robertis,E.M.
  TITLE     Complementary homeo protein gradients in developing limb buds
  JOURNAL   Genes Dev 3 (5), 641-650 (1989)
   PUBMED   2568311
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAXUCZ010000003.1.
            
            On Nov 27, 2020 this sequence version replaced NM_001173469.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC169092.1, SRR26643287.8141.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760383, SAMEA5760389
                                           [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
            1-859               JAXUCZ010000003.1  80008006-80008864
            860-1834            JAXUCZ010000003.1  80009212-80010186
FEATURES             Location/Qualifiers
     source          1..1834
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="3"
                     /map="3q23"
     gene            1..1834
                     /gene="Hoxd9"
                     /note="homeo box D9"
                     /db_xref="GeneID:688999"
                     /db_xref="RGD:1582908"
     exon            1..859
                     /gene="Hoxd9"
                     /inference="alignment:Splign:2.1.0"
     CDS             70..1101
                     /gene="Hoxd9"
                     /note="homeobox Hox-D9"
                     /codon_start=1
                     /product="homeobox protein Hox-D9"
                     /protein_id="NP_001166940.1"
                     /db_xref="GeneID:688999"
                     /db_xref="RGD:1582908"
                     /translation="MSSSGTLSNYYVDSLIGHEGDEVFAARFGPPGPGTQGRPAGVAD
                     GPAAAAEFASCSFAPKSSVFSASWSAVAAQPPAAATMSGLYHPYVSPPPLAAAEPGRY
                     VRSWMEPLPGFPGGAGGGGGSGGGGGGGSGGPGPVPSPGGPANGRHYGIKPETGAAPA
                     PSAASTSSSTSSSSSSKRTECSAARESQGSGGPEFPCNSFLRDKAAAAAAAAAGNGPG
                     VGIGTGPGTGGSSEPSACSDHPSPGCPLKEEEKQPPQPPQQQLDPNNPAANWIHARST
                     RKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARILNLTERQVKIWFQNRRMKMKKM
                     SKEKCPKGD"
     exon            860..1834
                     /gene="Hoxd9"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 cgggcgccgg cgaggagccg ctcggcggtg ggcagtgtaa ccttgggtgg gagcgcgcgg
       61 tgcctcaaca tgtcgtccag tggcaccctc agcaactact acgtggactc gctcataggc
      121 catgagggcg acgaggtgtt cgccgcgcgc tttgggccac cggggccggg gacacagggt
      181 cggcccgcag gtgtggccga tggcccggcc gccgccgccg agttcgcctc gtgtagtttt
      241 gcccccaaat cgtccgtgtt ctccgcctcg tggtccgcgg tggccgccca gcccccggcg
      301 gcggcgacga tgagcggcct gtaccacccg tacgtgtccc cgccgcccct ggccgccgcc
      361 gagccgggcc gctacgtacg ctcctggatg gagccgctgc ccggcttccc cggcggcgcg
      421 ggcggtggcg gtggcagtgg tggcggcggt ggcggaggta gcggaggccc gggtcccgtt
      481 cccagccccg gcggtccagc caacgggcgc cactacggga ttaagcctga aaccggagca
      541 gccccggccc cctctgcagc ctccacttcc tcctccacct cctcgtcctc ctcctccaaa
      601 aggactgagt gctccgcggc ccgcgagtcc caggggagcg gcggcccaga attcccgtgc
      661 aactcgttcc tgcgggacaa ggcggcagcg gcggcggcgg cggcggcagg gaacgggccc
      721 ggggtgggaa tcgggaccgg gcctgggacg ggaggctcgt ccgagccctc agcttgcagc
      781 gatcacccga gcccgggctg cccgctgaag gaggaggaga agcagccgcc gcagccgccg
      841 cagcagcaac ttgacccaaa caaccctgca gcgaactgga tccacgctcg ctccacccgg
      901 aaaaagcgct gtccctacac caaataccag acgctagagc tggagaagga attcctcttc
      961 aacatgtacc tcacccggga ccggcgctac gaggtggcca ggattctgaa ccttacagag
     1021 agacaagtca aaatctggtt ccagaaccgt aggatgaaaa tgaaaaagat gagcaaggag
     1081 aaatgtccta aaggagactg acccagtgcg ggtcaggcct gcagcgctca aaaggcagcg
     1141 ggttttggtt ttttgttgtt gattgttttc tttgtgggtg cttgattcag aaactctgca
     1201 gcgattcgga cattcttctt ttttttttag gtagaagtga ctgtgtggtt ggtctctgtg
     1261 agttatttgg gggacgctgt atttgctcgc atatgtattg gagaatccaa gtggctttgg
     1321 agtcttgtcc tatctcactc cctccctttc ccactccctt ggttccttag gaaatgcttt
     1381 attttgtgag tgcacgcagg cttgatggag ccctatcctg tgtaaatgtt cctcatgttt
     1441 ctggaaagtg ctgtagtgta gtctcacccc atccagcctc ccaaacaggg ccaactatct
     1501 aattccgaga atctgaaaga agagaaagac tgtggacaca caccccctcc cccaaaaaac
     1561 ccagctcagc tgcaggaaaa cccctatcct cagggagccc gcggactgac ttccagagag
     1621 gcctaccaag aagccctggg ccctgggaca cgaggttggg gtggggttga ggagaggctt
     1681 agtccttgga gcacggggaa gctactttct ccccaggagg gctgggctcc ctggggcggc
     1741 ctcgggaggt ggccctccat attcctgcct gaggaccagt tgtaaatgtt accgcttcct
     1801 acaaataaat gctgatctga acaaatggag ccca
//
