LOCUS       NM_001016177            2047 bp    mRNA    linear   VRT 03-APR-2024
DEFINITION  Xenopus tropicalis orthodenticle homeobox 2 (otx2), mRNA.
ACCESSION   NM_001016177
VERSION     NM_001016177.2
KEYWORDS    RefSeq.
SOURCE      Xenopus tropicalis (tropical clawed frog)
  ORGANISM  Xenopus tropicalis
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Amphibia; Batrachia; Anura; Pipoidea; Pipidae; Xenopodinae;
            Xenopus; Silurana.
REFERENCE   1  (bases 1 to 2047)
  AUTHORS   Yasuoka,Y., Suzuki,Y., Takahashi,S., Someya,H., Sudou,N.,
            Haramoto,Y., Cho,K.W., Asashima,M., Sugano,S. and Taira,M.
  TITLE     Occupancy of tissue-specific cis-regulatory modules by Otx2 and
            TLE/Groucho for embryonic head specification
  JOURNAL   Nat Commun 5, 4322 (2014)
   PUBMED   25005894
  REMARK    GeneRIF: Otx2 upregulate or downregulate a large battery of target
            genes in the head organizer.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 2047)
  AUTHORS   Ogino,H., Fisher,M. and Grainger,R.M.
  TITLE     Convergence of a head-field selector Otx2 and Notch signaling: a
            mechanism for lens specification
  JOURNAL   Development 135 (2), 249-258 (2008)
   PUBMED   18057103
  REMARK    GeneRIF: The obligate integration of inputs of a field-selector
            (Otx2) and localized signaling (Notch) within target cis-regulatory
            elements might be a general mechanism of organ-field specification
            in vertebrates (as it is in Drosophila).
REFERENCE   3  (bases 1 to 2047)
  AUTHORS   Onorati,M., Cremisi,F., Liu,Y., He,R.Q., Barsacchi,G. and
            Vignali,R.
  TITLE     A specific box switches the cell fate determining activity of XOTX2
            and XOTX5b in the Xenopus retina
  JOURNAL   Neural Dev 2, 12 (2007)
   PUBMED   17597530
  REMARK    GeneRIF: A small 'specificity box' is necessary to confer on XOTX2
            and XOTX5b their distinct activities in the developing frog retina
            and to convert the neutral orthologous OTD protein of Drosophila
            into a positive and specific XOTX-like retinal regulator.
            Publication Status: Online-Only
REFERENCE   4  (bases 1 to 2047)
  AUTHORS   Klein,S.L., Strausberg,R.L., Wagner,L., Pontius,J., Clifton,S.W.
            and Richardson,P.
  TITLE     Genetic and genomic tools for Xenopus research: The NIH Xenopus
            initiative
  JOURNAL   Dev Dyn 225 (4), 384-391 (2002)
   PUBMED   12454917
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from CR761863.2.
            
            On Oct 14, 2005 this sequence version replaced NM_001016177.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: CR761863.2, CR414285.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMD00028290, SAMD00028291
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..2047
                     /organism="Xenopus tropicalis"
                     /mol_type="mRNA"
                     /db_xref="taxon:8364"
                     /chromosome="8"
                     /map="8"
     gene            1..2047
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /note="orthodenticle homeobox 2"
                     /db_xref="GeneID:548931"
                     /db_xref="Xenbase:XB-GENE-485220"
     exon            1..222
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    114..116
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /note="upstream in-frame stop codon"
     CDS             126..995
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /note="orthodenticle 2"
                     /codon_start=1
                     /product="homeobox protein OTX2"
                     /protein_id="NP_001016177.1"
                     /db_xref="GeneID:548931"
                     /db_xref="Xenbase:XB-GENE-485220"
                     /translation="

MMSYLKQPPYAVNGLSLTTSGMDLLHPSVGYPATPRKQRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQQNGGQNKVRPSKKKPSPAREVSSESGTSGQFSPPCSTSVPVISSSTAPVSIWSPASISPLSDPLSTSSSCMQRSYPMTYTQASGYSQGYAGSTSYFGGMDCGSYLTPMHHQLSGAGATLSPMGTNAVTSHLNQSPAALSSQAYGASSLGFNSTADCLDYKDQTASWKLNFNADCLDYKDQTSSWKFQVL"

     misc_feature    240..407
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    384..386
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /note="Determines DNA-binding specificity.
                     /evidence=ECO:0000250; propagated from
                     UniProtKB/Swiss-Prot (Q28FN6.1); other site"
     misc_feature    402..536
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /note="propagated from UniProtKB/Swiss-Prot (Q28FN6.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    582..827
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /note="Otx1 transcription factor; Region: TF_Otx;
                     pfam03529"
                     /db_xref="CDD:427350"
     exon            223..374
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /inference="alignment:Splign:2.1.0"
     exon            375..2031
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
                     /inference="alignment:Splign:2.1.0"
     polyA_site      2028
                     /gene="otx2"
                     /gene_synonym="mcops5; otx-2; otx2-a; otx2-b; otxA;
                     Xotx-2; Xotx2"
ORIGIN      

cttgtagaccattgtgtgcaaaggaagagcgggatcaagaagcacacactacactgatcgcccgacttgctgcaacgattttctgattttctttcgcggattgtgctccctgataaaacactagcatgatgtcttatctcaagcaaccgccatatgccgtgaatgggctcagcctgactacctccgggatggatttgttacatccgtcggtgggatatcccgcgacccccaggaaacagaggagggaaaggaccactttcaccagagcccaactggatgtcctcgaagcactttttgccaaaactcgttaccccgatatcttcatgagagaagaagtggctctaaaaatcaacttgccggagtccagagtccaggtttggttcaaaaaccgccgagccaagtgccggcagcagcaacagcagcagcagaatggggggcaaaacaaagtgagaccctctaagaagaagccctccccggccagggaagtgagctctgagagcggcaccagcggccagttcagccccccctgcagcacctcagttccagtcatatcgagcagcacagcccctgtgtccatctggagcccggcctccatctctcccctctcagacccactctccacatcatcctcatgcatgcagaggtcttaccccatgacctacacacaggcatcaggctacagccagggatatgcaggctctacatcctactttgggggcatggactgtggatcttacttgaccccaatgcaccatcaactctctggagctggggctactctcagcccaatgggcaccaacgcagtgacaagccaccttaaccagtccccagctgccctctcttcccaggcctatggggcctctagcttgggttttaactccaccgctgactgcctggattacaaagaccaaacggcctcctggaagctgaacttcaatgctgactgcttggattataaagaccaaacctcttcatggaagttccaggttttgtgaagaactttcccctctccctctctatctgcgtcaggtggaaaactttgctgagacattcccagctctggcccagtctggttgaacaagtaggaagcaaaacacacaaagaccatttatttcatccacatagaaccctgggctgactggctctggactggatctggagacatctccatgcaatgggaaaacaaaggacacatctctatccagtgaccaggaaccacatgaagtctttatcttgttagattttagcaggtggatgaaagatggagaagaactaagtgcagctgagcagcacaggagccaggctgcagagtaatttggggctgtgtgtgtattggctgcagactcaagctctgctctttcatggctgccttctggcttagaaagaacatttcaggatttgagtgaattgtgcaactgattgtcctagatgcactactttatttaaagaaaacaaattaataataatgtttataagaagtcattatgtagtttttaaaagacaatcagtgtgtgtcttatataaatggtaaatctgtggtttttaatctgtgctagacatcaaaactgtgatctcttgtattgtatgcaactgtgaactccacaccagcggggggtcgtactgtgatttaataacaggtttattattagcaggaagattcaggatttagcgcaaaaccgatgccccttaatattattcaaagcgagcgaatggggcctctaaggaactgcggttaaacctttcttttcctccaccaactcctcctgagtttattttatattcgaccccgcaacgaacgcagggaccggaatccgcaatatagaaaggaacaggacagaggattatttaataactaaaggacttgtctgttgtcactgaccctgatatattcattgcaagaaggaatcccttatgcgtttatgcttgcctttgtgaattaagatataaatatatatatatacacaccataaaccttttcccctggatctggcaaatatgtataaaaaatttattaaatgactctagcacaaaaaaaaaaaaaaaaaaa

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