LOCUS       NM_131528               1405 bp    mRNA    linear   VRT 04-APR-2024
DEFINITION  Danio rerio homeobox C9a (hoxc9a), mRNA.
ACCESSION   NM_131528
VERSION     NM_131528.3
KEYWORDS    RefSeq.
SOURCE      Danio rerio (zebrafish)
  ORGANISM  Danio rerio
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
            Cypriniformes; Danionidae; Danioninae; Danio.
REFERENCE   1  (bases 1 to 1405)
  AUTHORS   Yamada,K., Maeno,A., Araki,S., Kikuchi,M., Suzuki,M., Ishizaka,M.,
            Satoh,K., Akama,K., Kawabe,Y., Suzuki,K., Kobayashi,D., Hamano,N.
            and Kawamura,A.
  TITLE     An atlas of seven zebrafish hox cluster mutants provides insights
            into sub/neofunctionalization of vertebrate Hox clusters
  JOURNAL   Development 148 (11) (2021)
   PUBMED   34096572
REFERENCE   2  (bases 1 to 1405)
  AUTHORS   Fouchecourt,S., Picolo,F., Elis,S., Lecureuil,C., Thelie,A.,
            Govoroun,M., Bregeon,M., Papillier,P., Lareyre,J.J. and Monget,P.
  TITLE     An evolutionary approach to recover genes predominantly expressed
            in the testes of the zebrafish, chicken and mouse
  JOURNAL   BMC Evol Biol 19 (1), 137 (2019)
   PUBMED   31269894
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1405)
  AUTHORS   Malmstrom,M., Britz,R., Matschiner,M., Torresen,O.K., Hadiaty,R.K.,
            Yaakob,N., Tan,H.H., Jakobsen,K.S., Salzburger,W. and Ruber,L.
  TITLE     The Most Developmentally Truncated Fishes Show Extensive Hox Gene
            Loss and Miniaturized Genomes
  JOURNAL   Genome Biol Evol 10 (4), 1088-1103 (2018)
   PUBMED   29684203
REFERENCE   4  (bases 1 to 1405)
  AUTHORS   Hayward,A.G. 2nd, Joshi,P. and Skromne,I.
  TITLE     Spatiotemporal analysis of zebrafish hox gene regulation by Cdx4
  JOURNAL   Dev Dyn 244 (12), 1564-1573 (2015)
   PUBMED   26335559
REFERENCE   5  (bases 1 to 1405)
  AUTHORS   Muto,A., Ikeda,S., Lopez-Burks,M.E., Kikuchi,Y., Calof,A.L.,
            Lander,A.D. and Schilling,T.F.
  TITLE     Nipbl and mediator cooperatively regulate gene expression to
            control limb development
  JOURNAL   PLoS Genet 10 (9), e1004671 (2014)
   PUBMED   25255084
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1405)
  AUTHORS   Woods,I.G., Wilson,C., Friedlander,B., Chang,P., Reyes,D.K.,
            Nix,R., Kelly,P.D., Chu,F., Postlethwait,J.H. and Talbot,W.S.
  TITLE     The zebrafish gene map defines ancestral vertebrate chromosomes
  JOURNAL   Genome Res 15 (9), 1307-1314 (2005)
   PUBMED   16109975
REFERENCE   7  (bases 1 to 1405)
  AUTHORS   Plessy,C., Dickmeis,T., Chalmel,F. and Strahle,U.
  TITLE     Enhancer sequence conservation between vertebrates is favoured in
            developmental regulator genes
  JOURNAL   Trends Genet 21 (4), 207-210 (2005)
   PUBMED   15797614
REFERENCE   8  (bases 1 to 1405)
  AUTHORS   Santini,S. and Bernardi,G.
  TITLE     Organization and base composition of tilapia Hox genes:
            implications for the evolution of Hox clusters in fish
  JOURNAL   Gene 346, 51-61 (2005)
   PUBMED   15716008
REFERENCE   9  (bases 1 to 1405)
  AUTHORS   Yekta,S., Shih,I.H. and Bartel,D.P.
  TITLE     MicroRNA-directed cleavage of HOXB8 mRNA
  JOURNAL   Science 304 (5670), 594-596 (2004)
   PUBMED   15105502
REFERENCE   10 (bases 1 to 1405)
  AUTHORS   Ahn,D.G. and Gibson,G.
  TITLE     Expression patterns of threespine stickleback hox genes and
            insights into the evolution of the vertebrate body axis
  JOURNAL   Dev Genes Evol 209 (8), 482-494 (1999)
   PUBMED   10415325
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BX005254.9 and EH591454.1.
            
            On May 15, 2015 this sequence version replaced NM_131528.2.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript 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 :: BC095014.1, GFIL01012819.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505370, SAMEA3505371
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-27                BX005254.9         118860-118886       c
            28-826              EH591454.1         27-825
            827-1405            BX005254.9         116423-117001       c
FEATURES             Location/Qualifiers
     source          1..1405
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="23"
                     /map="23"
     gene            1..1405
                     /gene="hoxc9a"
                     /gene_synonym="BZ-39; bz39; hoxc9; zgc:109844"
                     /note="homeobox C9a"
                     /db_xref="GeneID:58043"
                     /db_xref="ZFIN:ZDB-GENE-000328-5"
     exon            1..601
                     /gene="hoxc9a"
                     /gene_synonym="BZ-39; bz39; hoxc9; zgc:109844"
                     /inference="alignment:Splign:2.1.0"
     CDS             34..846
                     /gene="hoxc9a"
                     /gene_synonym="BZ-39; bz39; hoxc9; zgc:109844"
                     /note="hox-C9; homeobox gene C-9; homeo box C9a"
                     /codon_start=1
                     /product="homeobox protein Hox-C9a"
                     /protein_id="NP_571603.3"
                     /db_xref="GeneID:58043"
                     /db_xref="ZFIN:ZDB-GENE-000328-5"
                     /translation="

MHVKEKGNIAMSATGPISNYYVDSLINHESEDVLASRFTATGPISSSSRPTPLVPECADYPSCSFAPKPPVFTTSWAPVHSQSSVVYHPYTHQPHLGTDSRYVRSWLEPIPGTVSFPGYAGNSRHYGLKPDTFQDPRAGDCLGSNGRTYTDYLYCSAVDIREKQQNTPSPETESLSSGKHKDDKAELDPNNPVANWIHARSTRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMNKEKNDSKEQ"

     misc_feature    64..600
                     /gene="hoxc9a"
                     /gene_synonym="BZ-39; bz39; hoxc9; zgc:109844"
                     /note="Hox9 activation region; Region: Hox9_act;
                     pfam04617"
                     /db_xref="CDD:461369"
     misc_feature    640..786
                     /gene="hoxc9a"
                     /gene_synonym="BZ-39; bz39; hoxc9; zgc:109844"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            602..1405
                     /gene="hoxc9a"
                     /gene_synonym="BZ-39; bz39; hoxc9; zgc:109844"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

aaaaagtacacatacactccatataataatcggatgcatgtaaaagagaagggaaacatcgccatgtcggctacgggtcccataagtaattattatgtggattccttgatcaaccatgagagcgaggatgttctggcgagtcgtttcacagccactggtccgatatcctccagctcacgcccgacgcccctggtaccggaatgcgcggattacccgtcctgcagctttgccccgaaaccaccagtctttactacctcgtgggcccctgttcactcccagtcgtcagtagtttaccatccatacactcaccaacctcacctaggcacagactcaaggtacgttcgctcttggctggagcccatccccggtaccgtgtcttttccaggatatgcagggaatagcaggcactacgggctgaagcccgacaccttccaggatccccgcgccggagactgtttgggctcgaacggacgtacttatacggattatctctactgttcagccgtcgacattagagaaaagcaacagaatacaccatcgccagagacggagagcctgtcttccgggaagcacaaagacgacaaggctgaattagacccaaataatcctgtggcaaactggatccatgcgcgctcaactcgaaagaaacgttgtccgtacaccaagtatcaaacactcgaactcgaaaaggaatttttattcaatatgtacctcacaagagaccggcgatatgaggtagcaagggtgctgaacctaacggagcgacaagtcaaaatctggttccagaaccgacggatgaagatgaagaaaatgaacaaggaaaaaaacgacagtaaagaacaatagaccaaatgtcattaatcggacacagactgaaggaaaatcatcatttagaacggtcatgagtcttaacatttgcaccttcggcccataaaaggaacagagaaaacgaatatcctttatggatatctttaaaacgtgttgttattagtatggtttaatataaatgtaatttttaccatcctggattgagtcatattaatattatacgtagtttggatttacataacgtttctttactcacaaacacaaacgtggactctgaagagagactaccccgaagtttcagagaaaaatatacttgaactactttattttgaaattcctaatttatgctatatcttcgtggttgtttcttttctatgcttccatttatttgtagaaggtttgaaagccaagtattttataaagattaacaattctgtagttaagaatacgtgtttgcgtcgatgtacttagtttgtttttgatgtacctgtttgtgtattttacattctttaaactgtaaatgagtttcattatagattgtagatatatccaaatatatacaaccatgttaatatga

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