LOCUS       NM_023963               2049 bp    mRNA    linear   ROD 03-APR-2024
DEFINITION  Rattus norvegicus caudal type homeo box 2 (Cdx2), mRNA.
ACCESSION   NM_023963
VERSION     NM_023963.2
KEYWORDS    RefSeq; RefSeq Select.
SOURCE      Rattus norvegicus (Norway rat)
  ORGANISM  Rattus norvegicus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
            Muroidea; Muridae; Murinae; Rattus.
REFERENCE   1  (bases 1 to 2049)
  AUTHORS   Yin,Y., Morgunova,E., Jolma,A., Kaasinen,E., Sahu,B.,
            Khund-Sayeed,S., Das,P.K., Kivioja,T., Dave,K., Zhong,F.,
            Nitta,K.R., Taipale,M., Popov,A., Ginno,P.A., Domcke,S., Yan,J.,
            Schubeler,D., Vinson,C. and Taipale,J.
  TITLE     Impact of cytosine methylation on DNA binding specificities of
            human transcription factors
  JOURNAL   Science 356 (6337) (2017)
   PUBMED   28473536
REFERENCE   2  (bases 1 to 2049)
  AUTHORS   Wang,C., Chen,Y., Deng,H., Gao,S. and Li,L.
  TITLE     Rbm46 regulates trophectoderm differentiation by stabilizing Cdx2
            mRNA in early mouse embryos
  JOURNAL   Stem Cells Dev 24 (7), 904-915 (2015)
   PUBMED   25397698
REFERENCE   3  (bases 1 to 2049)
  AUTHORS   Walsh,M.F., Hermann,R., Lee,J.H., Chaturvedi,L. and Basson,M.D.
  TITLE     Schlafen 3 Mediates the Differentiating Effects of Cdx2 in Rat
            IEC-Cdx2L1 Enterocytes
  JOURNAL   J Invest Surg 28 (4), 202-207 (2015)
   PUBMED   26268420
  REMARK    GeneRIF: Cdx2 expression levels, elevated by IPTG treatment, are
            not affected by Slfn3-specific siRNA, suggesting that Cdx2 lies
            upstream of Slfn3 in IEC-Cdx1-L1 enterocytes.
REFERENCE   4  (bases 1 to 2049)
  AUTHORS   Payer,B., Rosenberg,M., Yamaji,M., Yabuta,Y., Koyanagi-Aoi,M.,
            Hayashi,K., Yamanaka,S., Saitou,M. and Lee,J.T.
  TITLE     Tsix RNA and the germline factor, PRDM14, link X reactivation and
            stem cell reprogramming
  JOURNAL   Mol Cell 52 (6), 805-818 (2013)
   PUBMED   24268575
REFERENCE   5  (bases 1 to 2049)
  AUTHORS   Wang,L., Miao,Y.L., Zheng,X., Lackford,B., Zhou,B., Han,L., Yao,C.,
            Ward,J.M., Burkholder,A., Lipchina,I., Fargo,D.C., Hochedlinger,K.,
            Shi,Y., Williams,C.J. and Hu,G.
  TITLE     The THO complex regulates pluripotency gene mRNA export and
            controls embryonic stem cell self-renewal and somatic cell
            reprogramming
  JOURNAL   Cell Stem Cell 13 (6), 676-690 (2013)
   PUBMED   24315442
REFERENCE   6  (bases 1 to 2049)
  AUTHORS   Liu,J., Puscheck,E.E., Wang,F., Trostinskaia,A., Barisic,D.,
            Maniere,G., Wygle,D., Zhong,W., Rings,E.H. and Rappolee,D.A.
  TITLE     Serine-threonine kinases and transcription factors active in signal
            transduction are detected at high levels of phosphorylation during
            mitosis in preimplantation embryos and trophoblast stem cells
  JOURNAL   Reproduction 128 (5), 643-654 (2004)
   PUBMED   15509711
REFERENCE   7  (bases 1 to 2049)
  AUTHORS   Uesaka,T., Kageyama,N. and Watanabe,H.
  TITLE     Identifying target genes regulated downstream of Cdx2 by microarray
            analysis
  JOURNAL   J Mol Biol 337 (3), 647-660 (2004)
   PUBMED   15019784
  REMARK    GeneRIF: Cdx2-regulated genes were elucidated,which suggested the
            functions of Cdx2 in cell fate decision and maintenance of
            intestinal epithelium
REFERENCE   8  (bases 1 to 2049)
  AUTHORS   Uesaka,T., Lu,H., Katoh,O. and Watanabe,H.
  TITLE     Heparin-binding EGF-like growth factor gene transcription regulated
            by Cdx2 in the intestinal epithelium
  JOURNAL   Am J Physiol Gastrointest Liver Physiol 283 (4), G840-G847 (2002)
   PUBMED   12223343
  REMARK    GeneRIF: data indicate HB-EGF gene expression can be regulated by
            Cdx2 in intestinal epithelial (IEC-6) cells
REFERENCE   9  (bases 1 to 2049)
  AUTHORS   van den Akker,E., Forlani,S., Chawengsaksophak,K., de Graaff,W.,
            Beck,F., Meyer,B.I. and Deschamps,J.
  TITLE     Cdx1 and Cdx2 have overlapping functions in anteroposterior
            patterning and posterior axis elongation
  JOURNAL   Development 129 (9), 2181-2193 (2002)
   PUBMED   11959827
REFERENCE   10 (bases 1 to 2049)
  AUTHORS   Chawengsaksophak,K., James,R., Hammond,V.E., Kontgen,F. and Beck,F.
  TITLE     Homeosis and intestinal tumours in Cdx2 mutant mice
  JOURNAL   Nature 386 (6620), 84-87 (1997)
   PUBMED   9052785
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from
            JAXUCZ010000012.1.
            
            On Nov 27, 2020 this sequence version replaced NM_023963.1.
            
            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 :: AJ278466.1, SRR26643291.31870.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN11044071, SAMN16093043
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on conservation, expression,
                                      longest protein
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-647               JAXUCZ010000012.1  12762904-12763550
            648-793             JAXUCZ010000012.1  12766695-12766840
            794-2049            JAXUCZ010000012.1  12767991-12769246
FEATURES             Location/Qualifiers
     source          1..2049
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="12"
                     /map="12p11"
     gene            1..2049
                     /gene="Cdx2"
                     /note="caudal type homeo box 2"
                     /db_xref="GeneID:66019"
                     /db_xref="RGD:621234"
     exon            1..647
                     /gene="Cdx2"
                     /inference="alignment:Splign:2.1.0"
     CDS             110..1042
                     /gene="Cdx2"
                     /codon_start=1
                     /product="homeobox protein CDX-2"
                     /protein_id="NP_076453.1"
                     /db_xref="GeneID:66019"
                     /db_xref="RGD:621234"
                     /translation="MYVSYLLDKDVSMYPSSVRHSGGLNLAPQNFVSPPQYPDYGGYH
                     VAAAAAAAANLDSAQSPGPSWPTAYGAPLREDWNGYAPGGAAAANAVAHGLNGGSPAA
                     AMGYSSPAEYHAHHHPHHHPHHPAAAPSCASGLLQTLNPGPPGPAATAAAEQLSPSGQ
                     RRNLCEWMRKPAQPSLGSQVKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAEL
                     AATLGLSERQVKIWFQNRRAKERKINKKKLQQQQQQQPPAPPPPQPSQPQSGALRSVP
                     EPLSPVTSLQGSVPGSVPGVLGPAGGVLNSTVTQ"
     exon            648..793
                     /gene="Cdx2"
                     /inference="alignment:Splign:2.1.0"
     exon            794..2049
                     /gene="Cdx2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      
        1 cagtaatcag ctacctttat ccctagcccc ctgcgccccg cgcccttggc agccttcaac
       61 gcttgtcccc aggcagtatg gtgaggtctg ctctgggtcc ctcgccacca tgtacgtgag
      121 ctaccttctg gacaaggacg tgagcatgta ccctagctcc gtgcgccact ccggcggcct
      181 caacctggcg ccgcagaact ttgtcagtcc cccgcagtac ccggactacg gtggttacca
      241 cgtggcggcc gccgctgctg cggcggcgaa cttggatagc gctcagtccc cagggccatc
      301 ctggcccacc gcgtacggcg cccctctccg cgaggactgg aatggctacg cacccggggg
      361 cgctgccgca gccaacgcgg tagcccacgg cctcaatggt ggctccccgg ccgccgctat
      421 gggctacagc agccccgccg aataccacgc acaccatcac ccgcatcatc accctcacca
      481 tccggccgct gcgccgtcct gcgcctccgg attgctgcag acgctcaacc ccggccctcc
      541 agggcccgca gccaccgccg ccgcagaaca gctgtccccc agcggccagc ggcgaaacct
      601 ttgtgaatgg atgaggaagc cagctcagcc gtccctagga agccaagtga aaaccaggac
      661 gaaagacaaa taccgggtgg tgtacacaga ccatcagcgg ctggagctgg agaaggaatt
      721 tcactatagt cgatacatca ccatcaggag gaaagctgag ttggccgcca cactcgggct
      781 ctcggagagg caggttaaaa tttggtttca gaaccgcaga gccaaggaaa ggaaaatcaa
      841 caaaaagaag ttgcaacagc agcagcagca gcagcctccc gcaccgccgc caccacagcc
      901 ttcccagcct cagtccggtg cattgcggag cgtgccggag cccttgagtc ctgtgacctc
      961 cttgcaaggc tcggtgcctg gttctgttcc tggggttctg gggccagctg gaggggtttt
     1021 aaactccact gtcacccagt gacccctcct gtggcctgaa gtggcggtgg ctcagcaatc
     1081 ccaggctgag ccatgaggag cacggacact gtgagaaacc tcagaagaga cccctcttct
     1141 cctacccaca aacaacacct acagatggag atcgaggaca gagggcagaa gacgagtggg
     1201 attgtggacc tcaggagaag atatggttta gatttttttt tttaaatttt tcccgttctg
     1261 acttttcctg tcagcaaagg aagtgattcc tggggcttct tcattcatgc tccttgccag
     1321 gactggctac aggcaccaag ctttcagctt cttttgcctc agctctttgc ctccaaaaaa
     1381 aaagagactg tatttctgtt tggagctgag gagagataga gtgtgaggcc ggagttgggg
     1441 gttggggcgg gcggggcaag caacacttga gccaagatgg ctgtttcctg ctgactgctt
     1501 tctgagaacc agctggccat cctgcctcag gggcagggac tgttgaaact actgagccag
     1561 aggcagctaa gacagaaagc tggattgacc gaagtctgca gaaccttccc cccctcaggt
     1621 ggtctgtgct ttcttctctg tccacagatc aggaaggggt ggtgggttca gggaccatcg
     1681 tgtgagagga gggggggtgg ttagccaact ccaggcccct gcgacaaggg cttgtttaga
     1741 aagcctgtca ccagagctgc tgtaggctga atgtatgtct gtgtcgtaaa tgccagagcc
     1801 aacctggact tcctgtccct tccctcgtct ttggctgaag aagaccggaa ttgctgctgt
     1861 tcgagtcact ggtctgtgta acaagccaaa caagcctttt aaaaagcctt ctggatccat
     1921 gggtagagag agagagtgag agacgttgta tggtgaaggg aagtggggag ggggatatct
     1981 gaacacagtt gacttttatt ttgtaaaaag acaaaagata taaaaggagc tttacagatt
     2041 tcagatcct
//
