LOCUS       NM_131215               1656 bp    mRNA    linear   VRT 23-MAR-2025
DEFINITION  Danio rerio orthodenticle homeobox 2a (otx2a), mRNA.
ACCESSION   NM_131215
VERSION     NM_131215.3
KEYWORDS    RefSeq.
SOURCE      Danio rerio (zebrafish)
  ORGANISM  Danio rerio
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Actinopterygii; Neopterygii; Teleostei; Ostariophysi;
            Cypriniformes; Danionidae; Danioninae; Danio.
REFERENCE   1  (bases 1 to 1656)
  AUTHORS   Zhao,S., Wang,C., Luo,H., Li,F., Wang,Q., Xu,J., Huang,Z., Liu,W.
            and Zhang,W.
  TITLE     A role for Retinoblastoma 1 in hindbrain morphogenesis by
            regulating GBX family
  JOURNAL   J Genet Genomics 51 (9), 900-910 (2024)
   PUBMED   38570112
REFERENCE   2  (bases 1 to 1656)
  AUTHORS   Ulhaq,Z.S., Ogino,Y. and Tse,W.K.F.
  TITLE     FGF8 rescues motor deficits in zebrafish model of limb-girdle
            muscular dystrophy R18
  JOURNAL   Biochem Biophys Res Commun 652, 76-83 (2023)
   PUBMED   36827861
REFERENCE   3  (bases 1 to 1656)
  AUTHORS   Qiu,Y., Fung,L., Schilling,T.F. and Nie,Q.
  TITLE     Multiple morphogens and rapid elongation promote segmental
            patterning during development
  JOURNAL   PLoS Comput Biol 17 (6), e1009077 (2021)
   PUBMED   34161317
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1656)
  AUTHORS   Bando,H., Gergics,P., Bohnsack,B.L., Toolan,K.P., Richter,C.E.,
            Shavit,J.A. and Camper,S.A.
  TITLE     Otx2b mutant zebrafish have pituitary, eye and mandible defects
            that model mammalian disease
  JOURNAL   Hum Mol Genet 29 (10), 1648-1657 (2020)
   PUBMED   32277752
REFERENCE   5  (bases 1 to 1656)
  AUTHORS   Farnsworth,D.R., Saunders,L.M. and Miller,A.C.
  TITLE     A single-cell transcriptome atlas for zebrafish development
  JOURNAL   Dev Biol 459 (2), 100-108 (2020)
   PUBMED   31782996
REFERENCE   6  (bases 1 to 1656)
  AUTHORS   Kassahn,K.S., Dang,V.T., Wilkins,S.J., Perkins,A.C. and Ragan,M.A.
  TITLE     Evolution of gene function and regulatory control after
            whole-genome duplication: comparative analyses in vertebrates
  JOURNAL   Genome Res 19 (8), 1404-1418 (2009)
   PUBMED   19439512
REFERENCE   7  (bases 1 to 1656)
  AUTHORS   Scholpp,S., Foucher,I., Staudt,N., Peukert,D., Lumsden,A. and
            Houart,C.
  TITLE     Otx1l, Otx2 and Irx1b establish and position the ZLI in the
            diencephalon
  JOURNAL   Development 134 (17), 3167-3176 (2007)
   PUBMED   17670791
  REMARK    GeneRIF: The Zona limitans intrathalamica is induced within the
            competence area established by Otx1l/2, and is posteriorly
            restricted by Irx1b.
REFERENCE   8  (bases 1 to 1656)
  AUTHORS   Foucher,I., Mione,M., Simeone,A., Acampora,D., Bally-Cuif,L. and
            Houart,C.
  TITLE     Differentiation of cerebellar cell identities in absence of Fgf
            signalling in zebrafish Otx morphants
  JOURNAL   Development 133 (10), 1891-1900 (2006)
   PUBMED   16611693
REFERENCE   9  (bases 1 to 1656)
  AUTHORS   Woods,I.G., Wilson,C., Friedlander,B., Chang,P., Reyes,D.K.,
            Nix,R., Kelly,P.D., Chu,F., Postlethwait,J.H. and Talbot,W.S.
  TITLE     The zebrafish gene map defines ancestral vertebrate chromosomes
  JOURNAL   Genome Res 15 (9), 1307-1314 (2005)
   PUBMED   16109975
REFERENCE   10 (bases 1 to 1656)
  AUTHORS   Hauptmann,G., Soll,I. and Gerster,T.
  TITLE     The early embryonic zebrafish forebrain is subdivided into
            molecularly distinct transverse and longitudinal domains
  JOURNAL   Brain Res Bull 57 (3-4), 371-375 (2002)
   PUBMED   11922991
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC076432.1.
            
            On Aug 31, 2012 this sequence version replaced NM_131215.2.
            
            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 :: BC076432.1, D26174.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505376, SAMEA3505378
                                           [ECO:0000348]
            ##Evidence-Data-END##
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-1656              BC076432.1         5-1660
FEATURES             Location/Qualifiers
     source          1..1656
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /strain="Singapore"
                     /db_xref="taxon:7955"
                     /chromosome="1"
                     /map="1"
     gene            1..1656
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /note="orthodenticle homeobox 2a"
                     /db_xref="GeneID:30462"
                     /db_xref="ZFIN:ZDB-GENE-980526-27"
     exon            1..245
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    33..35
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /note="upstream in-frame stop codon"
     exon            246..363
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /inference="alignment:Splign:2.1.0"
     CDS             267..1283
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /note="homeobox protein Otx1l; orthodenticle homolog 1a;
                     zOTX3; orthodenticle homolog 1 like; orthodenticle homolog
                     3; orthodenticle homeobox 1a"
                     /codon_start=1
                     /product="homeobox protein OTX1 A"
                     /protein_id="NP_571290.1"
                     /db_xref="GeneID:30462"
                     /db_xref="ZFIN:ZDB-GENE-980526-27"
                     /translation="

MMSYLKQAPYAMNGLGLGGATMDLLHPSVGYPTNPRKQRRERTTFTRTQLDILESLFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQSSTNSKIRPAKKKPSPSRESPGSESSGHFTPPAVSSSSSSSSSSSGSNPSALSGVGLISSSSSGTPVPSIWSPAPVSPVPAPPSLPDISPPASASCMQRAMSSGGGTTGVPSYPMPYNQAPSYAQGYPTSNAASYFGGMDCGSYLAPMTGHAHHHPHAHHSQLSTAAAVSGHHHPHHIGQSSGHHPHHQGYGGTALPFSSSDCLDYKEQVASSWKLNFSSAAADCLDYKDQAAWRFQVL"

     misc_feature    411..548
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /note="Region: Homeodomain; pfam00046"
                     /db_xref="CDD:459649"
     misc_feature    537..884
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90267.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     misc_feature    816..1091
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /note="Otx1 transcription factor; Region: TF_Otx;
                     pfam03529"
                     /db_xref="CDD:427350"
     misc_feature    1047..1136
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /note="propagated from UniProtKB/Swiss-Prot (Q90267.1);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            364..515
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /inference="alignment:Splign:2.1.0"
     exon            516..1629
                     /gene="otx2a"
                     /gene_synonym="otx1a; otx1l; otx3"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

aatctcaatccgtcagcattgcttatcagcgataatattacgtttggatacaaggatcctctttagacagcgcatatgcgtggactttaagcaaattgggaacttgttgtgaagtttggctaatttgtttttggctaatcagctggagtcgcctttctctcaaaagtaaaaaggtgtttcttggctttgtggattttcagtttacggatctcaaagaaaatatcacagaagatcaagacaaaaaggtgtctctctggggctcagcaatgatgtcatacctcaagcaggccccgtatgccatgaacgggctggggctcggcggggcaaccatggacctcctgcatccctctgtgggatatcccacgaatcctcgtaaacaaagaagagagaggacgacatttacacgcactcagctggacatcttggagagtctgttcgctaaaacccgctatcctgacattttcatgcgcgaggaggtcgccctgaagattaatttgcccgagtcaagagtgcaggtttggtttaaaaacagaagagcaaagtgtcgccagcagcagcagcagagcagcaccaactcaaagatccgtccggcaaagaagaaaccgtctccgtcccgcgagagcccggggtctgagagcagcggccacttcactccccctgccgtctcttcatcatcctcatcctcgtcttcatcctcgggctccaacccgtctgctcttagcggagttggtctgatcagcagctcgtcctcaggaacacctgtcccgtccatctggagtcccgcaccagtctctccagtccccgcacctccctccctccctgatatctcgcctccagccagcgcatcctgcatgcagagggctatgtctagtggaggggggacaactggcgtcccgtcgtaccccatgccctacaatcaggctcccagctacgcccagggctacccgacctcaaacgctgcttcttatttcggaggcatggactgcggatcctacttggcacccatgaccggccacgcccaccatcacccgcatgcccatcactcacagctgagcaccgccgctgcagtctcaggacaccatcatcctcaccatattgggcagagcagcgggcaccaccctcatcaccaggggtacggtggcaccgcgctgcctttcagctcttcagactgtctggattacaaagagcaagtggcgtcatcatggaaactcaacttcagctctgcggcggccgactgcttggactataaagaccaggccgcctggcgctttcaggttttgtaagaatgtttcccccgatgtttacttgtttgtttttcttcccgaacaagtgtgttttcctcaccatttgggaaaaagcagtgactgttttgggccagctttttttccagagcttaccaaagtgtgtttctaaatggaggcgggttctccgtggcccctcagtcggactgagttgaaagcgagggctgcatttgacgtgacgcactcaaggaatggtgttttgaaactatgaaggcaataataattttatatataactctttccgttggcgaaggtggcctacagctcatgtgagatgttacacactaatttgcattcatgttcatttaataaatataaagctgaaaatcaaaaaaaaaaaaaaaaaaaaaaaaaa

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