LOCUS       NM_131109               1653 bp    mRNA    linear   VRT 16-AUG-2023
DEFINITION  Danio rerio caudal type homeobox 4 (cdx4), mRNA.
ACCESSION   NM_131109 XM_001336183 XM_001336267
VERSION     NM_131109.3
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 1653)
  AUTHORS   Prummel KD, Crowell HL, Nieuwenhuize S, Brombacher EC, Daetwyler S,
            Soneson C, Kresoja-Rakic J, Kocere A, Ronner M, Ernst A, Labbaf Z,
            Clouthier DE, Firulli AB, Sanchez-Iranzo H, Naganathan SR, O'Rourke
            R, Raz E, Mercader N, Burger A, Felley-Bosco E, Huisken J, Robinson
            MD and Mosimann C.
  TITLE     Hand2 delineates mesothelium progenitors and is reactivated in
            mesothelioma
  JOURNAL   Nat Commun 13 (1), 1677 (2022)
   PUBMED   35354817
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1653)
  AUTHORS   Rocha M, Kushkowski E, Schnirman R, Booth C, Singh N, Beadell A and
            Prince VE.
  TITLE     Zebrafish Cdx4 regulates neural crest cell specification and
            migratory behaviors in the posterior body
  JOURNAL   Dev Biol 480, 25-38 (2021)
   PUBMED   34389276
  REMARK    GeneRIF: Zebrafish Cdx4 regulates neural crest cell specification
            and migratory behaviors in the posterior body.
REFERENCE   3  (bases 1 to 1653)
  AUTHORS   Wang B, Rong X, Zhou Y, Liu Y, Sun J, Zhao B, Deng B, Lu L, Lu L,
            Li Y and Zhou J.
  TITLE     Eukaryotic initiation factor 4A3 inhibits Wnt/beta-catenin
            signaling and regulates axis formation in zebrafish embryos
  JOURNAL   Development 148 (9) (2021)
   PUBMED   33914867
REFERENCE   4  (bases 1 to 1653)
  AUTHORS   Ye Z and Kimelman D.
  TITLE     Hox13 genes are required for mesoderm formation and axis elongation
            during early zebrafish development
  JOURNAL   Development 147 (22) (2020)
   PUBMED   33154036
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1653)
  AUTHORS   Rogers KW, ElGamacy M, Jordan BM and Muller P.
  TITLE     Optogenetic investigation of BMP target gene expression diversity
  JOURNAL   Elife 9, e58641 (2020)
   PUBMED   33174840
  REMARK    Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1653)
  AUTHORS   Hammerschmidt M, Pelegri F, Mullins MC, Kane DA, Brand M, van Eeden
            FJ, Furutani-Seiki M, Granato M, Haffter P, Heisenberg CP, Jiang
            YJ, Kelsh RN, Odenthal J, Warga RM and Nusslein-Volhard C.
  TITLE     Mutations affecting morphogenesis during gastrulation and tail
            formation in the zebrafish, Danio rerio
  JOURNAL   Development 123, 143-151 (1996)
   PUBMED   9007236
REFERENCE   7  (bases 1 to 1653)
  AUTHORS   Griffin K, Patient R and Holder N.
  TITLE     Analysis of FGF function in normal and no tail zebrafish embryos
            reveals separate mechanisms for formation of the trunk and the tail
  JOURNAL   Development 121 (9), 2983-2994 (1995)
   PUBMED   7555724
REFERENCE   8  (bases 1 to 1653)
  AUTHORS   Kelly GM, Greenstein P, Erezyilmaz DF and Moon RT.
  TITLE     Zebrafish wnt8 and wnt8b share a common activity but are involved
            in distinct developmental pathways
  JOURNAL   Development 121 (6), 1787-1799 (1995)
   PUBMED   7600994
REFERENCE   9  (bases 1 to 1653)
  AUTHORS   Strahle U and Jesuthasan S.
  TITLE     Ultraviolet irradiation impairs epiboly in zebrafish embryos:
            evidence for a microtubule-dependent mechanism of epiboly
  JOURNAL   Development 119 (3), 909-919 (1993)
   PUBMED   8187646
REFERENCE   10 (bases 1 to 1653)
  AUTHORS   Joly JS, Maury M, Joly C, Duprey P, Boulekbache H and Condamine H.
  TITLE     Expression of a zebrafish caudal homeobox gene correlates with the
            establishment of posterior cell lineages at gastrulation
  JOURNAL   Differentiation 50 (2), 75-87 (1992)
   PUBMED   1354191
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            BX247946.6.
            
            On Aug 16, 2023 this sequence version replaced NM_131109.2.
            
            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 :: BC154241.1, GDQQ01001020.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2168448, SAMEA3505370
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-636               BX247946.6         42195-42830
            637-782             BX247946.6         44543-44688
            783-1653            BX247946.6         44791-45661
FEATURES             Location/Qualifiers
     source          1..1653
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Tuebingen"
                     /db_xref="taxon:7955"
                     /chromosome="14"
                     /map="14"
     gene            1..1653
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /note="caudal type homeobox 4"
                     /db_xref="GeneID:798281"
                     /db_xref="ZFIN:ZDB-GENE-980526-330"
     exon            1..636
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    84..86
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /note="upstream in-frame stop codon"
     CDS             201..1013
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /note="caudal homeobox 1; caudal type homeo box
                     transcription factor 4"
                     /codon_start=1
                     /product="homeobox protein CDX-4"
                     /protein_id="NP_571184.2"
                     /db_xref="GeneID:798281"
                     /db_xref="ZFIN:ZDB-GENE-980526-330"
                     /translation="

MYVGYLLEKEASMYHQGAVRRSGISLPPQNFVSTPQYSDFTGYHHVPNMETHAQSAGAWGAPYGAPREDWGAYSLGPPNSISAPMSNSSPGPVSYCSPDYNTMHGPGSAVLPPPPENIPVAQLSPERERRNSYQWMSKTVQSSSTGKTRTKEKYRVVYTDHQRLELEKEFHFNRYITIRRKSELAVNLGLSERQVKIWFQNRRAKERKLIKKKLGQSDGSGGSVHSDPGSVSPLPVPGSLSPSDIHGSLYPAQMNALPSMRNIQQVTVTQ"

     misc_feature    237..638
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /note="Caudal like protein activation region; Region:
                     Caudal_act; pfam04731"
                     /db_xref="CDD:428094"
     misc_feature    order(657..668,672..674,723..725,741..743,780..782,
                     786..791,798..803,807..815,819..824)
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(660..662,669..671,789..791,798..803,810..812)
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    663..821
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            637..782
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /inference="alignment:Splign:2.1.0"
     exon            783..1653
                     /gene="cdx4"
                     /gene_synonym="cad1; cb546; cdx1; CHUNP6923; id:ibd1215;
                     id:ibd2812; id:ibd5107; kgg; kugelig"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

agactcacatcatgtttgattgaagcacgtcaaggactacgtcgcgtgacccggagctccttttggactattacacttccagataaatagtattgaagaaaaagtttttgagtcgggccttggatccaagtgatatttggcttgatgcatggctggcatgttgccttaaaaaaagttattttaggggtttcttccaaatcatgtacgttggataccttttggagaaagaggcaagcatgtatcaccaaggagcggttcgtcgatctggcatcagtcttccaccacagaactttgtttccacacctcagtattcagattttacaggataccatcatgtgcccaatatggagacacacgcacagtcggcaggggcatggggcgctccttatggcgctccgagagaggactggggcgcctacagcctcggacctccaaattctatttctgcacctatgagcaattcatctccgggaccagtttcctattgctcgcccgattataacaccatgcacggccctggatcggcggttcttcctccaccacctgaaaatattcctgtggcccaactatccccagagagagaaaggcgtaattcctatcagtggatgagcaaaaccgtccagtcgtcatcaaccggcaaaacgagaacgaaggagaaataccgagtggtatacacagatcaccaaaggctggagctggagaaagagtttcattttaatcgctatatcacaatcagaagaaaatccgaacttgctgtaaacctcgggctttcagagagacaggttaagatctggtttcagaaccgcagagctaaggaaaggaaattaatcaaaaagaaattgggtcagtctgacggaagcggagggtcagtgcacagcgacccaggctccgtcagtcctctaccggtaccagggtcactgagtccttcagatatacacggttctctgtatccagcacaaatgaacgccttgccgtccatgaggaacatacagcaagttactgtcactcagtgaactcgaacttggaacatccaactttaactgagcactccaacacgctgaaaggacagaaccaaacgtggtcaaaaaggattacaaactattaatgaataaatgaatgaataaataaataagaggcgtgggttgtggattacaaccgaagaatcacgtctgaaatgcgacgaaatgctggaggctcttcaaatattgttttaatagaatagtttttaaaattaagaaaaaaaactacaaaaaccttgttcgtctgatccagagactaaatattttaatggtttgtgttttctcgaataagatataaatatcttttttctgtatgtggtgagtgtatctaaatgtttgtttgtatataaaatgagaactacaggtacggagtttcatgggacgtgtaatgatccttaccctggaactgttaaacttttattgtctgtgaaaaccaatgacctgcgatgtcaggctgttttatgcgccagtttgtgtccaaagcgcacgtcgttcactttcttttcacaggggtgatgtgcaggtgtcacataccagatacgggtataacgtttgatttcagcaatgtgtaaataaatgttttgcaataacttttattgtgtcttcatgtatcattaaacaaatggcaatagca

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