LOCUS       NM_204085               3214 bp    mRNA    linear   VRT 03-APR-2024
DEFINITION  Xenopus tropicalis caudal type homeobox 1 (cdx1), mRNA.
ACCESSION   NM_204085
VERSION     NM_204085.1
KEYWORDS    RefSeq.
SOURCE      Xenopus tropicalis (tropical clawed frog)
  ORGANISM  Xenopus tropicalis
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae;
            Xenopus; Silurana.
REFERENCE   1  (bases 1 to 3214)
  AUTHORS   Kumar,S., Umair,Z., Kumar,V., Lee,U., Choi,S.C. and Kim,J.
  TITLE     Ventx1.1 competes with a transcriptional activator Xcad2 to
            regulate negatively its own expression
  JOURNAL   BMB Rep 52 (6), 403-408 (2019)
   PUBMED   31068250
  REMARK    GeneRIF: Results suggest that Ventx1.1 negatively regulates its own
            transcription in competition with Xcad2, thereby fine-tuning its
            own expression levels during dorsoventral patterning of Xenopus
            early embryo.
REFERENCE   2  (bases 1 to 3214)
  AUTHORS   Faas,L. and Isaacs,H.V.
  TITLE     Overlapping functions of Cdx1, Cdx2, and Cdx4 in the development of
            the amphibian Xenopus tropicalis
  JOURNAL   Dev Dyn 238 (4), 835-852 (2009)
   PUBMED   19301404
  REMARK    GeneRIF: during amphibian development the overall landscape of Cdx
            activity in the embryo is more important than the specific function
            of individual Cdx proteins
REFERENCE   3  (bases 1 to 3214)
  AUTHORS   Klein,S.L., Strausberg,R.L., Wagner,L., Pontius,J., Clifton,S.W.
            and Richardson,P.
  TITLE     Genetic and genomic tools for Xenopus research: The NIH Xenopus
            initiative
  JOURNAL   Dev Dyn 225 (4), 384-391 (2002)
   PUBMED   12454917
REFERENCE   4  (bases 1 to 3214)
  AUTHORS   Reece-Hoyes,J.S., Keenan,I.D. and Isaacs,H.V.
  TITLE     Cloning and expression of the Cdx family from the frog Xenopus
            tropicalis
  JOURNAL   Dev Dyn 223 (1), 134-140 (2002)
   PUBMED   11803576
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AF417198.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AF417198.1, BC171326.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMD00028290, SAMD00028291
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..3214
                     /organism="Xenopus tropicalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:8364"
                     /chromosome="3"
                     /map="3"
     gene            1..3214
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /note="caudal type homeobox 1"
                     /db_xref="GeneID:395055"
                     /db_xref="Xenbase:XB-GENE-485396"
     exon            1..549
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    102..104
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /note="upstream in-frame stop codon"
     CDS             120..908
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /note="caudal type homeobox transcription factor 1; cad2;
                     caudal type homeo box transcription factor 1"
                     /codon_start=1
                     /product="homeobox protein CDX-1"
                     /protein_id="NP_989416.1"
                     /db_xref="GeneID:395055"
                     /db_xref="Xenbase:XB-GENE-485396"
                     /translation="

MYVGYLLDKDNNMYPNPVRHPGLNLNPQNYVPAPPQYSDFPSYHHVPGINSDPHHGQPGGTWSSYTPSREDWHPYGPGPGASSANPAQISFSPSDYNPVQPPGPGLLPPSLNSSVSPLSPSAQRRNLYEWMRRTGVPTSTNSNGKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAASLALTERQVKIWFQNRRAKERKVNKKKMQQQSQQASTTTPTPPSVGTTAGMGGLCSSSSSNSNLVSPSSMPIKEEYLS"

     misc_feature    156..542
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /note="Caudal like protein activation region; Region:
                     Caudal_act; pfam04731"
                     /db_xref="CDD:461413"
     misc_feature    243..479
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90X89.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    570..737
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    573..638
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90X89.1);
                     Region: Interaction with DNA.
                     /evidence=ECO:0000250|UniProtKB:P47902"
     misc_feature    690..725
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90X89.1);
                     Region: Interaction with 5-mCpG DNA.
                     /evidence=ECO:0000250|UniProtKB:P47902"
     misc_feature    726..905
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90X89.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            550..695
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /inference="alignment:Splign:2.1.0"
     exon            696..3191
                     /gene="cdx1"
                     /gene_synonym="cdx-1; xcad2; xtcad2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

caaggcaaggtgaagggaatcagacaaccaggaagaagtggctcagtgctgaaggaaactccacagactcaggagattgttacccgggcacattatgtgcataggacttcttggcaaagatgtacgtgggttatcttttggataaggacaacaacatgtaccccaatcctgtcaggcaccctggccttaatttgaatcctcagaactatgtaccggcgccccctcagtattctgatttccccagctatcatcatgtccctgggattaacagtgatccacaccatggccagcctggtggcacctggagctcttatacccccagcagagaagattggcacccctatggaccgggacctggagcttcatccgctaacccagcacagatctctttcagtccctctgattataaccctgttcagcccccaggacctggacttctgcctccttctttaaattcctctgtttcccctctgtcccccagcgcacaaaggcgcaatctctatgaatggatgaggcgcacaggggtccccaccagcaccaacagcaatggtaagacaagaacaaaagacaagtatcgtgtggtttatacagaccaccagcgccttgaattagaaaaggaattccattacagccgctatataaccatccgcagaaaggcagaactggcagcttcactggcgctaacggaacggcaggtaaaaatttggttccaaaatcgtagagcaaaagaaaggaaggttaacaagaaaaaaatgcagcagcaaagtcaacaggcctcaacaaccactccaaccccaccatcagtgggtacgactgctggaatgggagggctttgcagtagcagcagcagcaacagcaatttggtatctccatcctcaatgcctatcaaggaagaatatctttcgtaagctatctgcaattagtgaaccattccaaaggacattcttccatacagttttcccaagggaggaccaccaaattcatttcctcgctacaggatcctgcaagaccggactggcgaattacaatgcaggatctagcagcagtaatgggattacagctgtaggcatatatctgccaactgtatcactgcagaacagccagtatcatgccctccatgtacaaatacagaaaaacggctctgcgtgtgctttattgccaagaattggactttatgttatcgtcattattgttactgtatatttaaacgaaagtcctaatctaaaagacgtatttttatgtgccacgtagtggtatatattttttttctatttgataaaacaggtgtttttgtataattttcaagtagggcatcttcacaagtgatagagttttatttcttgatcgcaggggacaaccttgtctagtattatatctccaatcaaagaattattccagatgaaccaacgccactcccaaagctttggaaaaacaagactggttcctgaaacaatatgtaagaaatgaaggagtgttaagatgtgctccaaactcttctgttgcttgtacttgtatatataaagtttagtttatagttactgtttataaagcgcatctaggctgattccaaatgtgcagtcatgtttggactgagaaggcaaagggggtaaggtcactttcatatgatgagcaaagttggcgtacatgttatcctaatggagtctggatctctcagtttacccttcacacagagtaacacatttcttacaagccaatcccccaaagcccagagctgtcacaggttttgatgggccaacactagtttgaatattcataaaaaatactttctcctttttattccttacatttcaattcagtcacacacaaacaaatagggttggtcatttttgaccacactcaaacattggtctgcctgagctagtggtaggcaacattaaccagcttgttattgtacaggttaagaaatggatgattgcattggttggtgtaagtagtcattagccattcactctgcttgcaaacccagtgaactctgtgctgaactaatagatctatttctttagtgtctagtttggctttgaatatgagtggctaatggaagcagacctgaattaagcccagctgtttttgccatgagtagccacctttagagcaggctcaaatgtcctttgtttgaccagaattcatcaaaataaaatagtagtgctgtataaacagtggtaaatagtatatgatgacattatacctttatattatattttaaccatttatttacctatcggaattattgagagctaaatgtatatttattttccttgtgctttattttgccagtcttctgtgaaggtattactggctcaataagcagccattgtccctttagcagcctggccaccagttcattttcattatcatgtcccacaagccttttattgtgtttgtagctatttaaggcaaaaagaggcatggcctagccatccagggggtgaatcatggcatcactggagctgtttatggccaaactaagacataaatggtactctttggtgcaggggaaattttcctagctttttgctatacttgagtaggtttgttctcctgctctgtgccaaaatacagaatactgtacattctgcatacagaatgaagcagccatacatagcatgatgggccatctgtgtgcagcgggcaatgatgacctaatatacgctcccaattgggtcatgggtctgcatagagattatatcattgttttaggagccatatcgcacagtatataaatatcctacagtctatgtgtaaattacctgtatgtaaattctgtacatgtatgactagctaaataagtcaacctttcaacctgaaaaggcattattattaaaaatgaaccctcttaatattttccaaatgtaaatgttaatcatagagaagaaccatttcaatttatttaacagatggtttgtgaatacacatgaccatttaagacccattaaatatcagtaatatggaacaaccatattcctaataataactcatatccgctaactttataaaccagaaacagttttgttcatatgttttatggtctaaaactttaagagggtattttttgggagggggggggggatttactctgcattataaatgttaatttttgtgattgctttttctttgctaccatctggacctttttaggtcagagaataaatctatttattttttggtgtaaaaaaaaaaaaaaaaaaaaaaaaaa

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