LOCUS       NM_001419633            1778 bp    mRNA    linear   ROD 27-JUN-2025
DEFINITION  Rattus norvegicus caudal type homeo box 1 (Cdx1), mRNA.
ACCESSION   NM_001419633 XM_006254816
VERSION     NM_001419633.1
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 1778)
  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 1778)
  AUTHORS   Tang,X.B., Zhang,T., Wang,W.L., Yuan,Z.W. and Bai,Y.Z.
  TITLE     Temporal and spatial expression of caudal-type homeobox gene-2
            during hindgut development in rat embryos with
            ethylenethiourea-induced anorectal malformations
  JOURNAL   Cell Tissue Res 357 (1), 83-90 (2014)
   PUBMED   24744267
  REMARK    GeneRIF: Downregulation of Cdx2 at the time of cloacal separation
            into the primitive rectum and UGS might thus be related to the
            development of ARM.
REFERENCE   3  (bases 1 to 1778)
  AUTHORS   Serra,R.W., Fang,M., Park,S.M., Hutchinson,L. and Green,M.R.
  TITLE     A KRAS-directed transcriptional silencing pathway that mediates the
            CpG island methylator phenotype
  JOURNAL   Elife 3, e02313 (2014)
   PUBMED   24623306
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1778)
  AUTHORS   Lalles,J.P., Orozco-Solis,R., Bolanos-Jimenez,F., de Coppet,P., Le
            Drean,G. and Segain,J.P.
  TITLE     Perinatal undernutrition alters intestinal alkaline phosphatase and
            its main transcription factors KLF4 and Cdx1 in adult offspring fed
            a high-fat diet
  JOURNAL   J Nutr Biochem 23 (11), 1490-1497 (2012)
   PUBMED   22405696
  REMARK    GeneRIF: Perinatal undernutrition associated with reduced gene
            expression of Cdx1 in adult offspring fed a high-fat diet.
REFERENCE   5  (bases 1 to 1778)
  AUTHORS   Grainger,S., Lam,J., Savory,J.G., Mears,A.J., Rijli,F.M. and
            Lohnes,D.
  TITLE     Cdx regulates Dll1 in multiple lineages
  JOURNAL   Dev Biol 361 (1), 1-11 (2012)
   PUBMED   22015720
REFERENCE   6  (bases 1 to 1778)
  AUTHORS   Patterson,A.P., Chen,Z., Rubin,D.C., Moucadel,V., Iovanna,J.L.,
            Brewer,H.B. Jr. and Eggerman,T.L.
  TITLE     Developmental regulation of apolipoprotein B mRNA editing is an
            autonomous function of small intestine involving homeobox gene Cdx1
  JOURNAL   J Biol Chem 278 (9), 7600-7606 (2003)
   PUBMED   12493769
  REMARK    GeneRIF: Cdx1 has a role in apoB mrna editing, which is part of the
            cytodifferentiation function of the small intestine
REFERENCE   7  (bases 1 to 1778)
  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   8  (bases 1 to 1778)
  AUTHORS   Allan,D., Houle,M., Bouchard,N., Meyer,B.I., Gruss,P. and Lohnes,D.
  TITLE     RARgamma and Cdx1 interactions in vertebral patterning
  JOURNAL   Dev Biol 240 (1), 46-60 (2001)
   PUBMED   11784046
REFERENCE   9  (bases 1 to 1778)
  AUTHORS   Subramanian,V., Meyer,B.I. and Gruss,P.
  TITLE     Disruption of the murine homeobox gene Cdx1 affects axial skeletal
            identities by altering the mesodermal expression domains of Hox
            genes
  JOURNAL   Cell 83 (4), 641-653 (1995)
   PUBMED   7585967
REFERENCE   10 (bases 1 to 1778)
  AUTHORS   Freund,J.N., Boukamel,R. and Benazzouz,A.
  TITLE     Gradient expression of Cdx along the rat intestine throughout
            postnatal development
  JOURNAL   FEBS Lett 314 (2), 163-166 (1992)
   PUBMED   1360907
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAXUCZ010000018.1.
            
            On Apr 13, 2023 this sequence version replaced XM_006254816.3.
            
            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 :: SRR26643288.59713.1,
                                           SRR26643291.40696.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA5760393, SAMN06621351
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            RefSeq Select criteria :: based on single protein-coding transcript
            ##RefSeq-Attributes-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-544               JAXUCZ010000018.1  56760756-56761299   c
            545-690             JAXUCZ010000018.1  56744531-56744676   c
            691-1778            JAXUCZ010000018.1  56742970-56744057   c
FEATURES             Location/Qualifiers
     source          1..1778
                     /organism="Rattus norvegicus"
                     /mol_type="mRNA"
                     /strain="BN"
                     /db_xref="taxon:10116"
                     /chromosome="18"
                     /map="18q12.1"
     gene            1..1778
                     /gene="Cdx1"
                     /note="caudal type homeo box 1"
                     /db_xref="GeneID:364883"
                     /db_xref="RGD:621233"
     exon            1..544
                     /gene="Cdx1"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    19..21
                     /gene="Cdx1"
                     /note="upstream in-frame stop codon"
     CDS             100..921
                     /gene="Cdx1"
                     /note="caudal type homeobox transcription factor 1;
                     caudal-type homeobox protein 1"
                     /codon_start=1
                     /product="homeobox protein CDX-1"
                     /protein_id="NP_001406562.1"
                     /db_xref="GeneID:364883"
                     /db_xref="RGD:621233"
                     /translation="

MYVGYVLDKDSPVYPGPARPSSLGLGPPTYAPPGPAPAPPQYPDFAGYTHVEPAPAPPPTWAAPFPAPKDDWAAAYGPGPAVPAASPAPLAFGPPPDFSPVPAPPGPGPGILAQSLGGPGAPSSPGVQRRTPYEWMRRNVAAAGGGGSGKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKSELAANLGLTERQVKIWFQNRRAKERKVNKKKQQQQQQQQQQPMPPTQLPLPLDGTPTPSGPPLGSLCPTNAGLLGTPSPVPVKEEFLP"

     misc_feature    136..519
                     /gene="Cdx1"
                     /note="Caudal like protein activation region; Region:
                     Caudal_act; pfam04731"
                     /db_xref="CDD:461413"
     misc_feature    565..732
                     /gene="Cdx1"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     exon            545..690
                     /gene="Cdx1"
                     /inference="alignment:Splign:2.1.0"
     exon            691..1778
                     /gene="Cdx1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggcggccgcgggtccaggtgagcagtcgctggtcgtcggggcggccggccggcgcggcggctccagggcccagcatgcgcgggggaccctgcggtcaccatgtacgtgggctatgtgctggacaaggactcccccgtgtacccaggccccgccaggccctccagcctcggcttgggccctccgacctacgcgcccccgggcccggcgcccgcgcccccgcagtaccccgacttcgcgggttacacgcacgtggagccggcacccgcgccccctccgacctgggctgcgcccttccctgcgcccaaggacgactgggcagctgcctatggtccgggccccgcggtccccgccgccagcccggccccgctggccttcgggccccctccggactttagcccagtgcccgcgcctcccggtcctggtcctggcatcctggcgcagtccctcgggggtccgggagcaccgtcctcgccaggagtgcaaaggcggacgccctacgaatggatgcggcgcaacgtggcagctgcaggcggcggtggcagcggtaagactcggaccaaggacaagtaccgcgtggtctatacagaccaccaacgtctagagctggaaaaggagtttcactacagtcggtacatcaccattcggcgcaagtcagagctggctgctaacttgggtctcacagagcggcaggtaaagatctggttccagaaccgtcgggccaaggagcgtaaagtaaacaagaagaaacagcagcagcagcagcagcaacagcagcagcccatgcctcccacacagttgcccctgcccctggatggcacccccacaccatcggggccacccctggggagtctatgccccaccaatgctggtcttctgggcaccccctccccagtgccggtcaaggaggagtttttaccctagccccttccagcctggggtccagggatctagggacttgaatgttggacacctggctatgctggggcccagggagcctgagttccagccctgctgctgacctttggggtcactgtggacaaactgcctacctaggaccaagtagcttgcccactccctgccttccgttggctgggtcgtgtgatgagctggttggacaagcgcttgtgtcctaggccacagggtcatggggaggcccagtgagaagtctcaatcacctggagattttgcaagattcagagagctcagtgagctgtcaagacaaggttgaggctccactgtctcctccaagggttccagagtgaggtgggaggctggtgcatgggccagactggcctggggaggagtcagcattgagagagggtggtacacaggagagtagactcccacatgaagcacaaggaagatatctgtcccgcctgtcccctcttccagcctcaactttgctagccctgtcatcccctgctctggctctccccagcctggaggtagccacaaagccatcaagactgggcatgaggtggaggcgattggccatgctcttgccccctccttagcactccaaggaggcctgcggatggaaaggaggaagcctctctgggaagactatgagtcaaccttcccgttcacacccaccttcccacaggccaccatcacacctcgggagcccccagaccatggagaactcatacctgtacgggggttaagtagagtggaatctcttggatgcagcttcaggaataagatttttttttccccttttaaacaatttatgaaaatcagacatagcattaaaggaatttttttaaaaaaaagtttaa

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