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2020-11-27 00:09:32, GGRNA.v2 : RefSeq release 202 (Sep, 2020)

LOCUS       NM_001124632            1497 bp    mRNA    linear   VRT 27-JUN-2020
DEFINITION  Oncorhynchus mykiss caudal-type homeobox protein 1 (cdx1), mRNA.
ACCESSION   NM_001124632
VERSION     NM_001124632.1
KEYWORDS    RefSeq.
SOURCE      Oncorhynchus mykiss (rainbow trout)
  ORGANISM  Oncorhynchus mykiss
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Protacanthopterygii;
            Salmoniformes; Salmonidae; Salmoninae; Oncorhynchus.
REFERENCE   1  (bases 1 to 1497)
  AUTHORS   Salem M, Rexroad CE 3rd, Wang J, Thorgaard GH and Yao J.
  TITLE     Characterization of the rainbow trout transcriptome using Sanger
            and 454-pyrosequencing approaches
  JOURNAL   BMC Genomics 11, 564 (2010)
   PUBMED   20942956
  REMARK    Publication Status: Online-Only
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AY434713.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: AY434713.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMN00002956, SAMN03153604
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1497
                     /organism="Oncorhynchus mykiss"
                     /mol_type="mRNA"
                     /db_xref="taxon:8022"
                     /chromosome="25"
                     /map="25"
     gene            1..1497
                     /gene="cdx1"
                     /note="caudal-type homeobox protein 1"
                     /db_xref="GeneID:100136660"
     CDS             92..901
                     /gene="cdx1"
                     /function="involved in the control of proliferation and
                     differentiation of intestine epithelial cells"
                     /codon_start=1
                     /product="caudal-type homeobox protein 1"
                     /protein_id="NP_001118104.1"
                     /db_xref="GeneID:100136660"
                     /translation="
MWDPLDKEGSMYHPGPLRRSGINIPPQNFVSTPQYSDFTGYHHVPNMDTHTQSSGAWGAPYVAPREDWGAYSLGPPNTIPTPMNNSSPGQVSYCSPEYNPMHAPGSAVLQPPTDNISVAQLSPDRERRNSSYQWMNKTVQSSSTGKTRTKEKYRVVYTDHQRLELEKEFHFNRYITIRRKSELAGNLGLSERQVKIWFQNRRAKERKLIKKKMGSDGSGGSVHSDPGSVSPLPVPGSLSPSDIHGSLYPPPGMNNLPSIRNIQQVTVTQ"
     misc_feature    128..502
                     /gene="cdx1"
                     /note="Caudal like protein activation region; Region:
                     Caudal_act; pfam04731"
                     /db_xref="CDD:282574"
     misc_feature    482..499
                     /gene="cdx1"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="Region: hexapeptide"
     misc_feature    539..718
                     /gene="cdx1"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="Region: homeobox"
     misc_feature    order(545..556,560..562,611..613,629..631,668..670,
                     674..679,686..691,695..703,707..712)
                     /gene="cdx1"
                     /note="DNA binding site [nucleotide binding]"
                     /db_xref="CDD:238039"
     misc_feature    order(548..550,557..559,677..679,686..691,698..700)
                     /gene="cdx1"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    551..709
                     /gene="cdx1"
                     /note="Homeobox domain; Region: Homeobox; pfam00046"
                     /db_xref="CDD:278475"
     misc_feature    563..607
                     /gene="cdx1"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="Region: helix 1 of homeobox"
     misc_feature    620..649
                     /gene="cdx1"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="Region: helix 2 of homeobox"
     misc_feature    662..712
                     /gene="cdx1"
                     /inference="non-experimental evidence, no additional
                     details recorded"
                     /note="Region: helix 3 of homeobox"
ORIGIN      
gcccccnnggttttttttttgttttagattacagaggggtcgcccggaaatatgtcgacttgaagtcgctttggaacttttttcaatcattatgtgggatcctctggataaggagggcagcatgtatcacccaggacctttaagacgatcgggaatcaacatccccccacagaactttgtttccacgccacaatattccgactttactggataccatcatgtgccaaacatggatactcatacacagtcttcgggggcttggggagctccttatgtcgcaccgagggaggactggggcgcctatagtctggggcctcctaacactattcctacgcccatgaacaactcctcgccgggacaagtttcatattgctcacctgaatacaatcccatgcacgcgccagggtcagcagtattgcaaccacctacagataatatttctgttgctcaactttccccggatagagaaaggcgcaattcttcttaccagtggatgaacaaaacggtacaatcatcatctacgggcaaaacaagaacgaaggagaaatacagagtggtttacaccgatcaccagagactggagctggagaaggagtttcattttaatcgttacatcactatccgaagaaagtccgaacttgcggggaacctgggcctttcagaacgacaggtgaagatctggtttcaaaatcgcagagccaaggagaggaaattaatcaaaaagaaaatggggtctgatggcagtggaggatcagtgcacagtgacccgggttcagtgagtcctctgcccgtaccaggctcactcagtccgtcggatattcacggctctctctacccaccccccggaatgaacaacttgccatctattaggaacatacagcaagttactgtcactcagtagaatcgaatttagaccattcaacacaactgagcactccaacacgctgaaaggaccgttcctcaagacttggattccaatggattattcaaacgtcctgaagaacatgttgtggattaggagatttcgagaaacaagatgatttataactgcaacgaaatgctggaggctcttgaaatattgtttttatagaatagttctaataataattccaaaaaacccatacaaaatcaacatatggttcagacatgtaatgcttaaattgtttgtttgtgtctgagttattgagatataaatataattttctgtagactatgtaatgaagtgtataagtgtttgtaaataaaataaaaaaccaggtacattttatttgaaattgatctggaatgaaaagggatatcattaatttggagcttttataatggcttgccaaactatgcattttcttctccaatttgattgcaaagcacactttcgtaacgtttttctacagggacaagtaaatcaggttttaagtgagatacgggtggaacgtttgtttgatgttcaaatgtaaataaaatgtgttttaccgttaaaaaaaaaaaaaaaaaaaaaaa
//

by @meso_cacase at DBCLS
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If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596. [Full Text]