LOCUS       NM_131362               1914 bp    mRNA    linear   VRT 16-SEP-2024
DEFINITION  Danio rerio SIX homeobox 3a (six3a), mRNA.
ACCESSION   NM_131362
VERSION     NM_131362.1
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 1914)
  AUTHORS   Letelier,J., Buono,L., Almuedo-Castillo,M., Zang,J., Mounieres,C.,
            Gonzalez-Diaz,S., Polvillo,R., Sanabria-Reinoso,E., Corbacho,J.,
            Sousa-Ortega,A., Diez Del Corral,R., Neuhauss,S.C.F. and
            Martinez-Morales,J.R.
  TITLE     Mutation of vsx genes in zebrafish highlights the robustness of the
            retinal specification network
  JOURNAL   Elife 12, e85594 (2023)
   PUBMED   37227126
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1914)
  AUTHORS   Ellingsen,S., Narawane,S., Fjose,A., Verri,T. and Ronnestad,I.
  TITLE     The zebrafish cationic amino acid
            transporter/glycoprotein-associated family: sequence and
            spatiotemporal distribution during development of the transport
            system b0,+ (slc3a1/slc7a9)
  JOURNAL   Fish Physiol Biochem 47 (5), 1507-1525 (2021)
   PUBMED   34338990
REFERENCE   3  (bases 1 to 1914)
  AUTHORS   Bengani,H., Grozeva,D., Moyon,L., Bhatia,S., Louros,S.R., Hope,J.,
            Jackson,A., Prendergast,J.G., Owen,L.J., Naville,M., Rainger,J.,
            Grimes,G., Halachev,M., Murphy,L.C., Spasic-Boskovic,O., van
            Heyningen,V., Kind,P., Abbott,C.M., Osterweil,E., Raymond,F.L.,
            Roest Crollius,H. and FitzPatrick,D.R.
  TITLE     Identification and functional modelling of plausibly causative
            cis-regulatory variants in a highly-selected cohort with X-linked
            intellectual disability
  JOURNAL   PLoS One 16 (8), e0256181 (2021)
   PUBMED   34388204
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1914)
  AUTHORS   Sidik,A., Dixon,G., Buckley,D.M., Kirby,H.G., Sun,S. and
            Eberhart,J.K.
  TITLE     Exposure to ethanol leads to midfacial hypoplasia in a zebrafish
            model of FASD via indirect interactions with the Shh pathway
  JOURNAL   BMC Biol 19 (1), 134 (2021)
   PUBMED   34210294
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1914)
  AUTHORS   Buono,L., Corbacho,J., Naranjo,S., Almuedo-Castillo,M.,
            Moreno-Marmol,T., de la Cerda,B., Sanabria-Reinoso,E., Polvillo,R.,
            Diaz-Corrales,F.J., Bogdanovic,O., Bovolenta,P. and
            Martinez-Morales,J.R.
  TITLE     Analysis of gene network bifurcation during optic cup morphogenesis
            in zebrafish
  JOURNAL   Nat Commun 12 (1), 3866 (2021)
   PUBMED   34162866
  REMARK    Erratum:[Nat Commun. 2021 Jul 27;12(1):4665. PMID: 34315888]
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 1914)
  AUTHORS   Becker,T., Ostendorff,H.P., Bossenz,M., Schluter,A., Becker,C.G.,
            Peirano,R.I. and Bach,I.
  TITLE     Multiple functions of LIM domain-binding CLIM/NLI/Ldb cofactors
            during zebrafish development
  JOURNAL   Mech Dev 117 (1-2), 75-85 (2002)
   PUBMED   12204249
REFERENCE   7  (bases 1 to 1914)
  AUTHORS   Reim,G. and Brand,M.
  TITLE     Spiel-ohne-grenzen/pou2 mediates regional competence to respond to
            Fgf8 during zebrafish early neural development
  JOURNAL   Development 129 (4), 917-933 (2002)
   PUBMED   11861475
REFERENCE   8  (bases 1 to 1914)
  AUTHORS   Chai,C. and Chan,W.K.
  TITLE     Developmental expression of a novel Ftz-F1 homologue, ff1b (NR5A4),
            in the zebrafish Danio rerio
  JOURNAL   Mech Dev 91 (1-2), 421-426 (2000)
   PUBMED   10704877
REFERENCE   9  (bases 1 to 1914)
  AUTHORS   Thisse,B., Wright,C.V. and Thisse,C.
  TITLE     Activin- and Nodal-related factors control antero-posterior
            patterning of the zebrafish embryo
  JOURNAL   Nature 403 (6768), 425-428 (2000)
   PUBMED   10667793
REFERENCE   10 (bases 1 to 1914)
  AUTHORS   Kobayashi,M., Toyama,R., Takeda,H., Dawid,I.B. and Kawakami,K.
  TITLE     Overexpression of the forebrain-specific homeobox gene six3 induces
            rostral forebrain enlargement in zebrafish
  JOURNAL   Development 125 (15), 2973-2982 (1998)
   PUBMED   9655819
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from AF030280.1.
            
            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 :: AF030280.1, BC059414.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505371, SAMEA3505375
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1914
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="13"
                     /map="13"
     gene            1..1914
                     /gene="six3a"
                     /gene_synonym="six3; six3.1; wu:fc10a08"
                     /note="SIX homeobox 3a"
                     /db_xref="GeneID:30635"
                     /db_xref="ZFIN:ZDB-GENE-990415-127"
     exon            1..808
                     /gene="six3a"
                     /gene_synonym="six3; six3.1; wu:fc10a08"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    48..50
                     /gene="six3a"
                     /gene_synonym="six3; six3.1; wu:fc10a08"
                     /note="upstream in-frame stop codon"
     CDS             117..1001
                     /gene="six3a"
                     /gene_synonym="six3; six3.1; wu:fc10a08"
                     /note="etID309945.13; etID46760.13; sine oculis homeobox
                     homolog 3a"
                     /codon_start=1
                     /product="homeobox protein SIX3a"
                     /protein_id="NP_571437.1"
                     /db_xref="GeneID:30635"
                     /db_xref="ZFIN:ZDB-GENE-990415-127"
                     /translation="

MVFRSPLELYPSHFFLPNFADRPLLLASSAPSTRSPEDLSMFQLPTLNFSPEQVASVCETLEETGDIERLGRFLWSLPVAPGACEAINKHESILRARAVVAFHTGNFRDLYHILENHKFTKDSHGKLQAMWLEAHYQEAEKLRGRPLGPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRSLLREWYLQDPYPNPSKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRLQHQAIGQNGMRSLSESGCAPRSSAESPSTAASPTTSVSSMTERVDTGTSILSVTSSDSECDV"

     misc_feature    261..602
                     /gene="six3a"
                     /gene_synonym="six3; six3.1; wu:fc10a08"
                     /note="Transcriptional regulator, SIX1, N-terminal SD
                     domain; Region: SIX1_SD; pfam16878"
                     /db_xref="CDD:465293"
     misc_feature    624..770
                     /gene="six3a"
                     /gene_synonym="six3; six3.1; wu:fc10a08"
                     /note="Homeodomain; DNA binding domains involved in the
                     transcriptional regulation of key eukaryotic developmental
                     processes; may bind to DNA as monomers or as homo- and/or
                     heterodimers, in a sequence-specific manner; Region:
                     homeodomain; cd00086"
                     /db_xref="CDD:238039"
     misc_feature    order(627..629,636..638,756..758,765..770)
                     /gene="six3a"
                     /gene_synonym="six3; six3.1; wu:fc10a08"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            809..1888
                     /gene="six3a"
                     /gene_synonym="six3; six3.1; wu:fc10a08"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atttagggggagatattatgaggctggtgtcattaggcgatagctattgaatcattcaatctgaattcgtcgttcttttttccttcgcaaatttcactctctctcaggtcatttccatggttttcagatcgcctttagagctttatccctctcatttcttcctgccaaactttgctgatcgccctttgctcttggcgagcagtgcgcccagcaccaggtctcccgaagacttgtcaatgtttcagctaccgaccctaaacttctctccagagcaagtggcgagcgtctgcgagacgctggaggagaccggggacatcgagcggctgggtcgcttcctatggtcgcttccagtggcaccgggtgcttgcgaggcgatcaacaagcatgaatccatcctacgcgcccgggctgttgtcgcctttcacaccggcaattttcgcgatctctaccacattttggagaaccacaagtttaccaaggactcgcatggtaaactacaagcgatgtggctagaggctcactatcaggaggccgagaaactacgcgggcgtcccctaggaccggttgataagtacagggtgcgaaagaagtttcccctgcctagaaccatctgggacggtgagcagaagacgcattgtttcaaggagcgaacgcggagtctgttacgagagtggtaccttcaggacccctacccaaaccccagcaagaaaagggaactggctcaagccactggactcactcctacacaggtcggaaattggtttaaaaacaggagacaacgagacagggcagcggcagcaaaaaacaggctccagcatcaagcaatagggcagaatggcatgcggtccctttcagaatccggctgcgccccacggagttcggcggagtcgccatcaactgcggctagtccaacaaccagtgtctcgagtatgacagaacgagtcgacacgggcacgtcaattctttcagtaacatcaagtgactcggaatgcgacgtatgatacgcacacagagaaatatataaaggagaatggacctgaaaaactttattaattatcggggaagatgaaaaaggaccaattgatattactattataaaaagaaaagcataaaagcacgtcttttttcaagcgctttcaatggaccccacacctttcccccaccccaccacttgcatgatatatatatatctaaatatattttttctcatttttgtatatggggaaatgccccacgttattatgtctaccaggaccaccgtgaagagggaattaccagaaagcggtgtccaacgccttttttctgttttagtccgagtgacgacgagcagccaggatgcaatcctttttttcttttatgttcatcagacaatcatttgagtcgtaagcacctttttactacacttctgtcactgcctgtgtggggtactggtcaaatgtggaactgaatcgttatgactgtatcagatttttatttttatttcgagattttatattgaattatgtatatcttaaataatgcgatcattctcccagtctgtaatatatgtgtagaaatacgtctgtaaataatattgctattcccattctcttttctatccctgttcacttttcttggcttggtgtccctacataaactattcgtcaaaacgtaactattaagtgctaggcgttttgtttctctgttttatgccatgaaaagaacgctagtgactatgaaatatcagtcgagattaatgcaaaagaaaatattggatatcatcatcgactgaccaagtctacttcatgtttccagtccagcgcttataattcaatactactttcttgcgtgtttctgttaatgtatacgtttctaaactgaaaatacagtattcaattttgttataaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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