LOCUS       NM_204311               1468 bp    mRNA    linear   VRT 24-SEP-2023
DEFINITION  Gallus gallus caudal type homeobox 2 (CDX2), mRNA.
ACCESSION   NM_204311
VERSION     NM_204311.2
KEYWORDS    RefSeq.
SOURCE      Gallus gallus (chicken)
  ORGANISM  Gallus gallus
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda;
            Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes;
            Phasianidae; Phasianinae; Gallus.
REFERENCE   1  (bases 1 to 1468)
  AUTHORS   Tang H, Finn RD and Thomas PD.
  TITLE     TreeGrafter: phylogenetic tree-based annotation of proteins with
            Gene Ontology terms and other annotations
  JOURNAL   Bioinformatics 35 (3), 518-520 (2019)
   PUBMED   30032202
REFERENCE   2  (bases 1 to 1468)
  AUTHORS   Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C,
            Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N and Hunter S.
  TITLE     Manual GO annotation of predictive protein signatures: the InterPro
            approach to GO curation
  JOURNAL   Database (Oxford) 2012, bar068 (2012)
   PUBMED   22301074
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1468)
  AUTHORS   Pernaute B, Canon S, Crespo M, Fernandez-Tresguerres B, Rayon T and
            Manzanares M.
  TITLE     Comparison of extraembryonic expression of Eomes and Cdx2 in
            pregastrulation chick and mouse embryo unveils regulatory changes
            along evolution
  JOURNAL   Dev Dyn 239 (2), 620-629 (2010)
   PUBMED   20014105
  REMARK    GeneRIF: expressed in extraembryonic tissues, but temporal pattern
            of expression differs from what occurs in mouse
REFERENCE   4  (bases 1 to 1468)
  AUTHORS   Marom K, Shapira E and Fainsod A.
  TITLE     The chicken caudal genes establish an anterior-posterior gradient
            by partially overlapping temporal and spatial patterns of
            expression
  JOURNAL   Mech Dev 64 (1-2), 41-52 (1997)
   PUBMED   9232595
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000027.1.
            
            On Nov 9, 2021 this sequence version replaced NM_204311.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: U80614.1, SRR12888491.331455.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992323, SAMEA103992484
                                           [ECO:0000348]
            ##Evidence-Data-END##
            COMPLETENESS: full length.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-767               JAENSK010000027.1  23068699-23069465
            768-913             JAENSK010000027.1  23071240-23071385
            914-1468            JAENSK010000027.1  23071617-23072171
FEATURES             Location/Qualifiers
     source          1..1468
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="1"
                     /map="1"
     gene            1..1468
                     /gene="CDX2"
                     /note="caudal type homeobox 2"
                     /db_xref="CGNC:12839"
                     /db_xref="GeneID:374205"
     exon            1..767
                     /gene="CDX2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    50..52
                     /gene="CDX2"
                     /note="upstream in-frame stop codon"
     CDS             251..1084
                     /gene="CDX2"
                     /note="caudal type homeo box transcription factor 2;
                     caudal type homeobox transcription factor 2"
                     /codon_start=1
                     /product="homeobox protein CDX-2"
                     /protein_id="NP_989642.2"
                     /db_xref="CGNC:12839"
                     /db_xref="GeneID:374205"
                     /translation="

MYVSYLLDKDGPMYPGPVRHSGGLNLAAQNFVGAAQYADYGGYHVNLDGAQSPGPAWPAPYAAPLRDDWGAYGQGAPPPAAAAAVHGLNGGSPAAAMAYSPADFHHHHHHHPHAHHHAGPAPHCSAGGMQPLGAAPAAAAASAAPEPLSPGGQRRGLCEWVRKPAQAPLGSQVKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELASSLGLSERQVKIWFQNRRAKERKINKKKLQQAQPGAAEPLSPTAPPLPGPAAAPPPAGLGPAAPQ"

     misc_feature    287..751
                     /gene="CDX2"
                     /note="Caudal like protein activation region; Region:
                     Caudal_act; pfam04731"
                     /db_xref="CDD:428094"
     misc_feature    order(788..799,803..805,854..856,872..874,911..913,
                     917..922,929..934,938..946,950..955)
                     /gene="CDX2"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(791..793,800..802,920..922,929..934,941..943)
                     /gene="CDX2"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    794..952
                     /gene="CDX2"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:425441"
     exon            768..913
                     /gene="CDX2"
                     /inference="alignment:Splign:2.1.0"
     exon            914..1468
                     /gene="CDX2"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

gcctttggtgtgtctgggccattactaatagagccttgtaaacaatcgttaatcatgtaagcgctgccggccatcgccttcggaccgggagcgctcggcggcggcgaactgcgcggggccgcggcccctccgcctgccccctccccgccgcgggagcccggccccgggcggcggcgctccgacggccccggcagcggcgctccgacggccccagcagcatgccgagagcggccgccggggccccgccagcatgtacgtgagctacctcctggacaaggacgggcccatgtaccccggccccgttcgccactcgggggggctcaacctggcggcgcagaacttcgtgggcgccgcgcaatacgcggactacggcggctaccatgtgaacctcgacggcgcgcagtcccccgggccggcctggcccgcgccctacgccgctcctctccgcgacgactggggggcctacgggcagggagcccctccgcccgccgccgccgccgccgtgcacggcctcaacggcggctcccccgccgcagcgatggcctacagccccgccgacttccaccaccaccaccaccaccacccgcacgcccaccaccacgccggccccgcgccgcactgctccgccggggggatgcagcctctcggcgccgcccccgccgccgccgccgcctccgccgcccccgagccgctgtcccccggcgggcagcgccgcggcctctgcgagtgggtgaggaaaccggcgcaggccccgctcggtagccaagtcaaaaccaggacgaaggacaaataccgcgtggtgtacacggaccaccagcggttggagctggagaaggagttccactacagccgctatatcaccatccggaggaaagctgagctggcctccagcctggggctgtcggagaggcaggtgaaaatctggttccagaaccgtcgggcgaaggagaggaagatcaacaagaagaagctgcagcaggcgcagcccggcgccgcggagccgctcagccccaccgcccctccgcttcccggccccgcggccgcaccgccacccgccgggctgggccccgccgccccgcagtgacagcggccccggccgagcgcagggactgcacggaccgcggagggacggccgggccgggccggggccggaggggccccgcggccacagcgggagcggccccaatgcactgcagcgccgtgtgtacagatgtacagtgagcgcgtctcgtccggggaaccgcggcttcggtgttattaatgttattatggttttctttcgtcggtatttttccttttattttttatttttattttttttaccctggcctttgttaggtgtaaggggagcgtggcactccccagtgaatctcagggatcggcgcgaaggtctgagcgatgctgttgggctgacgatgaattttattgggaaagaaagaaagaaaaaattaaagcacattggtttttt

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