LOCUS       NM_001110759             926 bp    mRNA    linear   VRT 30-JAN-2022
DEFINITION  Danio rerio homeobox C12a (hoxc12a), mRNA.
ACCESSION   NM_001110759 XM_685980
VERSION     NM_001110759.1
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 926)
  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 926)
  AUTHORS   Fouchecourt S, Picolo F, Elis S, Lecureuil C, Thelie A, Govoroun M,
            Bregeon M, Papillier P, Lareyre JJ 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 926)
  AUTHORS   Malmstrom M, Britz R, Matschiner M, Torresen OK, Hadiaty RK, Yaakob
            N, Tan HH, Jakobsen KS, 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 926)
  AUTHORS   Jimenez L, Wang J, Morrison MA, Whatcott C, Soh KK, Warner S,
            Bearss D, Jette CA and Stewart RA.
  TITLE     Phenotypic chemical screening using a zebrafish neural crest EMT
            reporter identifies retinoic acid as an inhibitor of epithelial
            morphogenesis
  JOURNAL   Dis Model Mech 9 (4), 389-400 (2016)
   PUBMED   26794130
REFERENCE   5  (bases 1 to 926)
  AUTHORS   Junker JP, Noel ES, Guryev V, Peterson KA, Shah G, Huisken J,
            McMahon AP, Berezikov E, Bakkers J and van Oudenaarden A.
  TITLE     Genome-wide RNA Tomography in the zebrafish embryo
  JOURNAL   Cell 159 (3), 662-675 (2014)
   PUBMED   25417113
REFERENCE   6  (bases 1 to 926)
  AUTHORS   Zou SM, Jiang XY, He ZZ, Yuan J, Yuan XN and Li SF.
  TITLE     Hox gene clusters in blunt snout bream, Megalobrama amblycephala
            and comparison with those of zebrafish, fugu and medaka genomes
  JOURNAL   Gene 400 (1-2), 60-70 (2007)
   PUBMED   17618068
REFERENCE   7  (bases 1 to 926)
  AUTHORS   Kurosawa G, Takamatsu N, Takahashi M, Sumitomo M, Sanaka E, Yamada
            K, Nishii K, Matsuda M, Asakawa S, Ishiguro H, Miura K, Kurosawa Y,
            Shimizu N, Kohara Y and Hori H.
  TITLE     Organization and structure of hox gene loci in medaka genome and
            comparison with those of pufferfish and zebrafish genomes
  JOURNAL   Gene 370, 75-82 (2006)
   PUBMED   16472944
  REMARK    Erratum:[Gene. 2006 Jul;376(2):298-9]
REFERENCE   8  (bases 1 to 926)
  AUTHORS   Corredor-Adamez M, Welten MC, Spaink HP, Jeffery JE, Schoon RT, de
            Bakker MA, Bagowski CP, Meijer AH, Verbeek FJ and Richardson MK.
  TITLE     Genomic annotation and transcriptome analysis of the zebrafish
            (Danio rerio) hox complex with description of a novel member, hox b
            13a
  JOURNAL   Evol Dev 7 (5), 362-375 (2005)
   PUBMED   16174031
REFERENCE   9  (bases 1 to 926)
  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   10 (bases 1 to 926)
  AUTHORS   Amores A, Force A, Yan YL, Joly L, Amemiya C, Fritz A, Ho RK,
            Langeland J, Prince V, Wang YL, Westerfield M, Ekker M and
            Postlethwait JH.
  TITLE     Zebrafish hox clusters and vertebrate genome evolution
  JOURNAL   Science 282 (5394), 1711-1714 (1998)
   PUBMED   9831563
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC162849.1.
            
            On Sep 9, 2008 this sequence version replaced XM_685980.3.
            
            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 :: BC162849.1, DQ060559.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505370, SAMEA3505371
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..926
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="23"
                     /map="23"
     gene            1..926
                     /gene="hoxc12a"
                     /gene_synonym="si:dkey-81p22.1"
                     /note="homeobox C12a"
                     /db_xref="GeneID:562600"
                     /db_xref="ZFIN:ZDB-GENE-000822-6"
     exon            1..612
                     /gene="hoxc12a"
                     /gene_synonym="si:dkey-81p22.1"
                     /inference="alignment:Splign:2.1.0"
     CDS             27..851
                     /gene="hoxc12a"
                     /gene_synonym="si:dkey-81p22.1"
                     /note="homeo box C12a"
                     /codon_start=1
                     /product="homeobox protein Hox-C12a"
                     /protein_id="NP_001104229.1"
                     /db_xref="GeneID:562600"
                     /db_xref="ZFIN:ZDB-GENE-000822-6"
                     /translation="

MGEHNLLNPGFVGPLVNIHTGDRFYFPNFRASGGQLAGLPSLSYPRRDNVCSLPWNPSESCNGYPQSYFSSPVSINPSFNRSCEITRLEESKCYYGNSSSTRDSCSDNNSLKREERARDTSVSSDHGMHNGMGNSGTFSKYDYGTEHLTQDPPSCQSLESDSSSSVLNEGGKTSASDPQTLVSQGNHASNIAGGGGAPWYPMHTRTRKKRKPYSKLQLAELEGEFMLNEFITRQRRRELSDRLNLSDQQVKIWFQNRRMKKKRLLLREQALSFF"

     misc_feature    order(645..659,663..665,714..716,732..734,771..773,
                     777..782,789..794,798..806,810..815)
                     /gene="hoxc12a"
                     /gene_synonym="si:dkey-81p22.1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    651..812
                     /gene="hoxc12a"
                     /gene_synonym="si:dkey-81p22.1"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     misc_feature    order(651..653,660..662,780..782,789..794,801..803)
                     /gene="hoxc12a"
                     /gene_synonym="si:dkey-81p22.1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            613..926
                     /gene="hoxc12a"
                     /gene_synonym="si:dkey-81p22.1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agaagctgttggtctggcccgcggaaatgggcgagcataatcttcttaatcctgggtttgtgggacctttggtaaacatccacactggagacaggttttacttcccgaattttagagcctcagggggacagctggcggggctaccgtctctctcgtaccctagaagggacaatgtttgctctctcccgtggaatccatcggagtcgtgcaatggatatcctcagtcttactttagcagtcccgtatctattaacccctcttttaatcgatcttgtgaaataacccgactggaggaaagcaagtgttattatggcaattccagcagcaccagagattcgtgttcagacaacaacagtctcaaacgagaggagcgagcaagagatacatcagtatcgtctgatcacgggatgcacaatgggatgggcaacagtggcaccttctcaaagtatgattatggcaccgaacatctgacccaagacccgccatcctgtcagtctttggagtccgactccagttcttcggtgctaaacgaaggaggaaagacttcagcaagcgacccacaaaccctggtatcgcaaggaaaccacgcaagcaatatcgccggtggaggaggtgccccgtggtacccgatgcacacccggacccgcaagaaacgaaaaccctattccaaactgcaactggccgagcttgaaggagaattcatgctgaacgagttcatcaccagacagcgacgtagagagctgtctgacaggctcaatctcagcgaccaacaggttaaaatttggttccaaaatcggcggatgaagaaaaagagactgttgctgagggaacaggctttgtccttcttttaaggaggcacaaaatatacattgcttaatggtagcccaacaacagtatttagttaatggtaatctgccattggccca

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