LOCUS       NM_212836               2245 bp    mRNA    linear   VRT 16-APR-2022
DEFINITION  Danio rerio caudal type homeobox 1a (cdx1a), mRNA.
ACCESSION   NM_212836
VERSION     NM_212836.3
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 2245)
  AUTHORS   Ye Z, Braden CR, Wills A and Kimelman D.
  TITLE     Identification of in vivo Hox13-binding sites reveals an essential
            locus controlling zebrafish brachyury expression
  JOURNAL   Development 148 (11) (2021)
   PUBMED   34061173
REFERENCE   2  (bases 1 to 2245)
  AUTHORS   Quintanilla CA and Ho RK.
  TITLE     The Cdx transcription factors and retinoic acid play parallel roles
            in antero-posterior position of the pectoral fin field during
            gastrulation
  JOURNAL   Mech Dev 164, 103644 (2020)
   PUBMED   32911082
REFERENCE   3  (bases 1 to 2245)
  AUTHORS   Li J, Dedloff MR, Stevens K, Maney L, Prochaska M, Hongay CF and
            Wallace KN.
  TITLE     A novel group of secretory cells regulates development of the
            immature intestinal stem cell niche through repression of the main
            signaling pathways driving proliferation
  JOURNAL   Dev Biol 456 (1), 47-62 (2019)
   PUBMED   31398318
REFERENCE   4  (bases 1 to 2245)
  AUTHORS   Warga RM, Mueller RL, Ho RK and Kane DA.
  TITLE     Zebrafish Tbx16 regulates intermediate mesoderm cell fate by
            attenuating Fgf activity
  JOURNAL   Dev Biol 383 (1), 75-89 (2013)
   PUBMED   24008197
REFERENCE   5  (bases 1 to 2245)
  AUTHORS   Warner CM, Gust KA, Stanley JK, Habib T, Wilbanks MS, Garcia-Reyero
            N and Perkins EJ.
  TITLE     A systems toxicology approach to elucidate the mechanisms involved
            in RDX species-specific sensitivity
  JOURNAL   Environ Sci Technol 46 (14), 7790-7798 (2012)
   PUBMED   22697906
REFERENCE   6  (bases 1 to 2245)
  AUTHORS   Skromne I, Thorsen D, Hale M, Prince VE and Ho RK.
  TITLE     Repression of the hindbrain developmental program by Cdx factors is
            required for the specification of the vertebrate spinal cord
  JOURNAL   Development 134 (11), 2147-2158 (2007)
   PUBMED   17507415
  REMARK    GeneRIF: Repression of the hindbrain developmental program by Cdx
            factors is required for the specification of the vertebrate spinal
            cord.
REFERENCE   7  (bases 1 to 2245)
  AUTHORS   Lin X, Rinaldo L, Fazly AF and Xu X.
  TITLE     Depletion of Med10 enhances Wnt and suppresses Nodal signaling
            during zebrafish embryogenesis
  JOURNAL   Dev Biol 303 (2), 536-548 (2007)
   PUBMED   17208216
REFERENCE   8  (bases 1 to 2245)
  AUTHORS   Shimizu T, Bae YK and Hibi M.
  TITLE     Cdx-Hox code controls competence for responding to Fgfs and
            retinoic acid in zebrafish neural tissue
  JOURNAL   Development 133 (23), 4709-4719 (2006)
   PUBMED   17079270
REFERENCE   9  (bases 1 to 2245)
  AUTHORS   Davidson AJ and Zon LI.
  TITLE     The caudal-related homeobox genes cdx1a and cdx4 act redundantly to
            regulate hox gene expression and the formation of putative
            hematopoietic stem cells during zebrafish embryogenesis
  JOURNAL   Dev Biol 292 (2), 506-518 (2006)
   PUBMED   16457800
  REMARK    GeneRIF: The expression and function of cdx1a are reported.
REFERENCE   10 (bases 1 to 2245)
  AUTHORS   Shimizu T, Bae YK, Muraoka O and Hibi M.
  TITLE     Interaction of Wnt and caudal-related genes in zebrafish posterior
            body formation
  JOURNAL   Dev Biol 279 (1), 125-141 (2005)
   PUBMED   15708563
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC115217.1.
            
            On Mar 25, 2007 this sequence version replaced NM_212836.2.
            
            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 :: BC115217.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505372, SAMEA3505376
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2245
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="14"
                     /map="14"
     gene            1..2245
                     /gene="cdx1a"
                     /gene_synonym="cdx2"
                     /note="caudal type homeobox 1a"
                     /db_xref="GeneID:405762"
                     /db_xref="ZFIN:ZDB-GENE-050510-1"
     exon            1..372
                     /gene="cdx1a"
                     /gene_synonym="cdx2"
                     /inference="alignment:Splign:2.1.0"
     CDS             6..692
                     /gene="cdx1a"
                     /gene_synonym="cdx2"
                     /note="homeobox protein Cdx2; caudal type homeo box
                     transcription factor 1 a"
                     /codon_start=1
                     /product="homeobox protein CDX-1a"
                     /protein_id="NP_998001.2"
                     /db_xref="GeneID:405762"
                     /db_xref="ZFIN:ZDB-GENE-050510-1"
                     /translation="

MSVSYLLDTAMYGNPARHLNLSQPHLNVYPSAPYPDYSGYHPGPALGNDLHHTGSSWSPGFGPGSRDDWPPLYGHGTGHSLPANGVEVSVLPSVDQGLLSGAPVDREEPQDWMRRSAVPTNPGGKTRTKDKYRVVYSDVQRLELEKEFHFSRYITIRRKAELAGTLNLSERQVKIWFQNRRAKERKMNKKRLQQVQQSSSGLANTTTVSSSDSGLMTDNISSSIKEEY"

     misc_feature    36..374
                     /gene="cdx1a"
                     /gene_synonym="cdx2"
                     /note="Caudal like protein activation region; Region:
                     Caudal_act; pfam04731"
                     /db_xref="CDD:428094"
     misc_feature    order(396..407,411..413,462..464,480..482,519..521,
                     525..530,537..542,546..554,558..563)
                     /gene="cdx1a"
                     /gene_synonym="cdx2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(399..401,408..410,528..530,537..542,549..551)
                     /gene="cdx1a"
                     /gene_synonym="cdx2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    402..560
                     /gene="cdx1a"
                     /gene_synonym="cdx2"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            373..521
                     /gene="cdx1a"
                     /gene_synonym="cdx2"
                     /inference="alignment:Splign:2.1.0"
     exon            522..2211
                     /gene="cdx1a"
                     /gene_synonym="cdx2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggaaaatgtccgtgagctacctgctggacacggccatgtacggcaaccccgcgagacacctgaacctcagccagcctcacctgaacgtctacccgtccgccccgtacccggactacagcggataccatccgggaccggcgctcggcaatgacctgcatcacaccggcagctcatggagtccggggttcgggcccggttcgcgcgatgattggcccccgctgtacggccacgggacgggtcactctctgccggctaacggggtggaggtcagcgtgctgccatctgtggatcaggggctgctgagcggagcgccggtggacagagaggagccgcaggactggatgaggcgcagcgcggtgccgaccaaccctggagggaaaacacggacgaaggacaagtacagagtggtgtacagtgacgtccagcgcctggagctggagaaagagtttcatttcagccgctacatcaccatcagaaggaaggcggagcttgcaggaacactcaacctatcagaacgccaggtcaagatctggtttcagaacagacgagccaaagaaaggaagatgaacaaaaagcgtctccagcaggttcagcagagctccagcggtctggcaaacaccaccacggttagcagctccgacagcggcttgatgacagacaatatctccagctccatcaaagaggaatactgaaaactctcagatttcagagaaacagttcatgtttacacagtttcagcgacacggagcaatggaccacttcatattgcactatattacactaatgacacgcagtgttgggggaaacgcatttcaagtgatgtgagttactttgttataatattacttttctaagtaacaagtaaagtaatgagttactattaaagctacgtaataatatttgagtttttcccagtactgggttgcagctggaagggcatccactgcttaaaacatatgacagaatagttggtggttgattccactgtggtgacccctgataaataaggaaaataatcctccgagttctgaaatagaggtaagaaaaagtaacgcgcaaaataactctaaagtaacgctttcctcaccatacaaagaacctaatgctgtttacaccagacgcggaacgcatgaaaaaaatctcactattcgcacgcaagttgccacttgaacaattgagtttaatcgcttgattcgtgcatcaaatccgcttcattcccgtgtcaaattcacttcaaaacagacgcggattcgcgtgttgggcagggcttctgtctgcccggtgactctagcttcattgctgaatggctaacttggatcttatgaaggaaataacagtgtttatgtgttttataaaggctgaaaaacagcgtcgatacagttagggtcgtgtctgagtccactacatccttggagaggtgcatccaggtctgtgagcgcataaactcctccagaaactgaacatggatgacggaggttttcagctatgcttctgactgagcccagcccagtttgatgaactgtcgcctggaggatttcccccggaacacggacaacaggcgatacgtcacaatcacgcccccacaagagcaagctcctgattggttaacacagcgcaaaacgctcaattggcgctgcaccattcacgtgtatcgcgctattcgcgccgcacaattcgcgtcattcacaccgtgccattcacgcgtatcgtgccgcaggatgtctatttgcgcgtttgcattgacttaacatgtaaatcactcgtgcttgacgtgcgttccgcgtctggtgtgaacgcagcatcacacaactatagtgtcttctttgcagagtaactcaataatttaatgcattacttactatctttccccaacactgcacacacgtttattgtgaacgaagcgcacagtatttcaatgttttgtagaaagcgatgatctcagagaatgtggatcgacacacatcattattcttcctcaatggttttgcgctctgctgttgatatgacctcacttcactttactcctgatttgatgactttttttacctgtggcgcctctttatcactactgattttgctttatgtaagatatttcacacttactggatcatggaaaactgactttttcgtttttaaagtagccaacttgtgccttcgtgtaattattcattcaataaagtgtataattttaataaaaataaaaatatttgaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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