LOCUS       NM_204676               2415 bp    mRNA    linear   VRT 12-JUN-2024
DEFINITION  Gallus gallus caudal type homeobox 1 (CDX1), mRNA.
ACCESSION   NM_204676
VERSION     NM_204676.3
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 2415)
  AUTHORS   Tang,H., Finn,R.D. and Thomas,P.D.
  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 2415)
  AUTHORS   Burge,S., Kelly,E., Lonsdale,D., Mutowo-Muellenet,P., McAnulla,C.,
            Mitchell,A., Sangrador-Vegas,A., Yong,S.Y., 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 2415)
  AUTHORS   Gaunt,S.J., Drage,D. and Cockley,A.
  TITLE     Vertebrate caudal gene expression gradients investigated by use of
            chick cdx-A/lacZ and mouse cdx-1/lacZ reporters in transgenic mouse
            embryos: evidence for an intron enhancer
  JOURNAL   Mech Dev 120 (5), 573-586 (2003)
   PUBMED   12782274
REFERENCE   4  (bases 1 to 2415)
  AUTHORS   Doll,U. and Niessing,J.
  TITLE     Continued expression of the chicken caudal homologue in
            endodermally derived organs
  JOURNAL   Dev Biol 156 (1), 155-163 (1993)
   PUBMED   7680627
REFERENCE   5  (bases 1 to 2415)
  AUTHORS   Frumkin,A., Rangini,Z., Ben-Yehuda,A., Gruenbaum,Y. and Fainsod,A.
  TITLE     A chicken caudal homologue, CHox-cad, is expressed in the epiblast
            with posterior localization and in the early endodermal lineage
  JOURNAL   Development 112 (1), 207-219 (1991)
   PUBMED   1685114
COMMENT     VALIDATED REFSEQ: This record has undergone validation or
            preliminary review. The reference sequence was derived from
            JAENSK010000256.1.
            
            On Sep 23, 2021 this sequence version replaced NM_204676.2.
            
            Sequence Note: The RefSeq transcript and protein were derived from
            genomic sequence to make the sequence consistent with the reference
            genome assembly. The genomic coordinates used for the transcript
            record were based on alignments.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AB046532.1, SRR12888524.311001.1
                                           [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA103992290, SAMEA103992323
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-572               JAENSK010000256.1  11442638-11443209   c
            573-718             JAENSK010000256.1  11434726-11434871   c
            719-2415            JAENSK010000256.1  11432898-11434594   c
FEATURES             Location/Qualifiers
     source          1..2415
                     /organism="Gallus gallus"
                     /mol_type="mRNA"
                     /db_xref="taxon:9031"
                     /chromosome="13"
                     /map="13"
     gene            1..2415
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /note="caudal type homeobox 1"
                     /db_xref="CGNC:4232"
                     /db_xref="GeneID:395397"
     exon            1..572
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    119..121
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /note="upstream in-frame stop codon"
     CDS             143..925
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /note="homeobox protein CHOX-CAD; caudal-type homeodomain
                     protein A; caudal type homeo box transcription factor 1;
                     caudal type homeobox transcription factor 1; caudal-type
                     homeodomain protein, CdxA"
                     /codon_start=1
                     /product="homeobox protein CDX-1"
                     /protein_id="NP_990007.2"
                     /db_xref="CGNC:4232"
                     /db_xref="GeneID:395397"
                     /translation="

MYVGYLLDKDTNMYPSPVRHPSLNLNPQNYVPGPPQYSDFASYHHVPGINNDPHHGQPAAAWGSPYTPAKEDWHSYGTAAASAATNPGQFGFSPPDFNPMQPHAGSGLLPPAISSSVPQLSPNAQRRTPYEWMRRSIPSTSSSGKTRTKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAAALGLTERQVKIWFQNRRAKERKVNKKKLQQQSQPTSTTTPTPPAVGTPGPMGTLCSGSAPSLVSSSPLTIKEEFMP"

     misc_feature    179..571
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /note="Caudal like protein activation region; Region:
                     Caudal_act; pfam04731"
                     /db_xref="CDD:461413"
     misc_feature    593..760
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    596..661
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9DEB6.2);
                     Region: Interaction with DNA.
                     /evidence=ECO:0000250|UniProtKB:P47902"
     misc_feature    713..748
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9DEB6.2);
                     Region: Interaction with 5-mCpG DNA.
                     /evidence=ECO:0000250|UniProtKB:P47902"
     misc_feature    752..922
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /note="propagated from UniProtKB/Swiss-Prot (Q9DEB6.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            573..718
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /inference="alignment:Splign:2.1.0"
     exon            719..2415
                     /gene="CDX1"
                     /gene_synonym="CDX-A; CDXA; CHox-cad; CHOX-CAD1"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

ggccccgggacacagctccccaaggcgcccaggtgagcgcggtgaaggaggggcggccgctgcgtgacacccggccgcttcggcacggagcggcgcagcgcggtgcatcggcacagcatgagcacagagccaggtggagaagatgtatgtaggctatcttttggataaggacaccaacatgtatcccagtcccgtccggcatcccagcctcaacctcaacccccagaactacgtgccggggccaccccagtactcggacttcgccagctaccaccatgtgccagggattaacaacgacccgcaccatgggcagcccgcagctgcctggggctcaccctacacccctgccaaggaggactggcactcatacggcaccgctgccgcctccgccgccaccaacccggggcagtttggatttagccccccggattttaaccccatgcagccccatgcgggctctggactcctgcctccagccatcagcagctcggtgccacagctgtcccctaatgcacagaggcgcaccccgtacgaatggatgaggcgcagtattcccagcaccagcagcagcggcaagacgaggacaaaggacaagtaccgggtggtgtacacggaccaccaacgcctggagctggagaaggaatttcactacagccgctacatcaccatccgccgtaaggccgagctggctgctgccctggggctcactgaacggcaggtgaaaatctggtttcagaaccggagggcgaaagagaggaaggtgaataaaaagaagctgcagcagcagagccagcccaccagcaccaccacgccaacccccccagccgtgggcacgccagggcccatggggaccctctgcagtggcagtgccccaagccttgtctcctcatctccgctcaccatcaaggaggagttcatgccttagccccctccaccagccatagacactgagagataagcactacacggcagagcttgttgctgagcgcccaaagacaccacgtcctctggggcatggtggctctgttgccttcccaagaggctgatgagctctgtcctacacaaagcccatacgttaggtagtgctgttctcctgtaggaaacgtgcgctggtctccggtattggtagcccaaaaccagtgggatgagtctttaagtggtgctggaggaccctttctgtggcacatcagaatgagccggtgggatgcttcctgcacggtcttcctggtgatccagctgcctgctgctttggagcagctttagtgaggctgaactaggggaaagtcttggctggactcgaggcagaataaatctcagctgagattgtctgcaggatctgccacacctggagcgagttggacaacaggagctgggtaggaccctcagcagtggggctggagggggaaagggggctccttaaactgagacaatgacagtgagtgtcccccatgtcccccagccaccatccccagctccatccctgcagcaactcagggccatcgcgagacctgcagacatctgtcccacagatggaccaccctgcggaggttttgagaccaccttccagcatggaggaacaagaacaaggtttgcagttaggacactggacagctctaggttgcccagaggggccgctcacctacccatggcactgcagaacctgcacagctccgtgctgcaccaaggcactgccagctgccgggaccatcatggtgatgggacatgtcctggcacaagatgatggatagctggcttccatagagagggatgggtggatttgtgctgttttctctgaaacacaaaaggctctgggttttgcccactttgtactcctccatgtgctgcaccattggtaaccaatggcttttttttcctgctggaaatccacagttaaaattccccttaatcctgctgactcctgggatctctactggcccagctaccttacagcccagttttggatgccccaaagggcgtgctgggacacaggagggtttgaggctcctgcttgggtctgtggcttcccaagaccaaggtgagggtgcagaggctctgatggttctctcctagcaccatcatgctgagccccagcaggaacaagaagtggaggtgtccctgttgcctgcagagcccctcacccattcccagcccattctggcccagaactcacagtgttaggggtttaatactgggatttaagctccttgacacccactgcacctacagccccttaatagggtctgcatcccccaccatggggaccagtgacacctccctggggccaccactgctactttgcagcaaaggcagacaccggtgttggcttgggacttcagctcagggcttgtgtacagaaggcagaacgttttattttctaggctttggtcaaaataaaagtgagcaggagccctgtga

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