LOCUS       NM_001009904            1610 bp    mRNA    linear   VRT 19-OCT-2024
DEFINITION  Danio rerio SIX homeobox 1a (six1a), mRNA.
ACCESSION   NM_001009904
VERSION     NM_001009904.1
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 1610)
  AUTHORS   Megerson,E., Kuehn,M., Leifer,B., Bell,J.M., Snyder,J.L. and
            McGraw,H.F.
  TITLE     Kremen1 regulates the regenerative capacity of support cells and
            mechanosensory hair cells in the zebrafish lateral line
  JOURNAL   iScience 27 (1), 108678 (2023)
   PUBMED   38205258
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1610)
  AUTHORS   Talbot,J.C., Teets,E.M., Ratnayake,D., Duy,P.Q., Currie,P.D. and
            Amacher,S.L.
  TITLE     Muscle precursor cell movements in zebrafish are dynamic and
            require Six family genes
  JOURNAL   Development 146 (10) (2019)
   PUBMED   31023879
  REMARK    Publication Status: Online-Only
REFERENCE   3  (bases 1 to 1610)
  AUTHORS   Pasquier,J., Cabau,C., Nguyen,T., Jouanno,E., Severac,D.,
            Braasch,I., Journot,L., Pontarotti,P., Klopp,C., Postlethwait,J.H.,
            Guiguen,Y. and Bobe,J.
  TITLE     Gene evolution and gene expression after whole genome duplication
            in fish: the PhyloFish database
  JOURNAL   BMC Genomics 17, 368 (2016)
   PUBMED   27189481
  REMARK    Publication Status: Online-Only
REFERENCE   4  (bases 1 to 1610)
  AUTHORS   Elkon,R., Milon,B., Morrison,L., Shah,M., Vijayakumar,S.,
            Racherla,M., Leitch,C.C., Silipino,L., Hadi,S., Weiss-Gayet,M.,
            Barras,E., Schmid,C.D., Ait-Lounis,A., Barnes,A., Song,Y.,
            Eisenman,D.J., Eliyahu,E., Frolenkov,G.I., Strome,S.E., Durand,B.,
            Zaghloul,N.A., Jones,S.M., Reith,W. and Hertzano,R.
  TITLE     RFX transcription factors are essential for hearing in mice
  JOURNAL   Nat Commun 6, 8549 (2015)
   PUBMED   26469318
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 1610)
  AUTHORS   Ogawa,Y., Shiraki,T., Kojima,D. and Fukada,Y.
  TITLE     Homeobox transcription factor Six7 governs expression of green
            opsin genes in zebrafish
  JOURNAL   Proc Biol Sci 282 (1812), 20150659 (2015)
   PUBMED   26180064
REFERENCE   6  (bases 1 to 1610)
  AUTHORS   Bricaud,O. and Collazo,A.
  TITLE     Balancing cell numbers during organogenesis: Six1a differentially
            affects neurons and sensory hair cells in the inner ear
  JOURNAL   Dev Biol 357 (1), 191-201 (2011)
   PUBMED   21745464
  REMARK    GeneRIF: Balancing cell numbers during organogenesis: Six1a
            differentially affects neurons and sensory hair cells in the inner
            ear
REFERENCE   7  (bases 1 to 1610)
  AUTHORS   Diep,C.Q., Ma,D., Deo,R.C., Holm,T.M., Naylor,R.W., Arora,N.,
            Wingert,R.A., Bollig,F., Djordjevic,G., Lichman,B., Zhu,H.,
            Ikenaga,T., Ono,F., Englert,C., Cowan,C.A., Hukriede,N.A.,
            Handin,R.I. and Davidson,A.J.
  TITLE     Identification of adult nephron progenitors capable of kidney
            regeneration in zebrafish
  JOURNAL   Nature 470 (7332), 95-100 (2011)
   PUBMED   21270795
REFERENCE   8  (bases 1 to 1610)
  AUTHORS   Lin,C.Y., Chen,W.T., Lee,H.C., Yang,P.H., Yang,H.J. and Tsai,H.J.
  TITLE     The transcription factor Six1a plays an essential role in the
            craniofacial myogenesis of zebrafish
  JOURNAL   Dev Biol 331 (2), 152-166 (2009)
   PUBMED   19409884
  REMARK    GeneRIF: six1a and pax3 do not function in the same regulatory
            network. We proposed four putative regulatory pathways to
            understand how six1a distinctly interacts with either myf5 or myod
            during zebrafish craniofacial muscle development.
REFERENCE   9  (bases 1 to 1610)
  AUTHORS   Bessarab,D.A., Chong,S.W., Srinivas,B.P. and Korzh,V.
  TITLE     Six1a is required for the onset of fast muscle differentiation in
            zebrafish
  JOURNAL   Dev Biol 323 (2), 216-228 (2008)
   PUBMED   18789916
  REMARK    GeneRIF: Six1a plays an essential role at the onset of fast muscle
            differentiation.
REFERENCE   10 (bases 1 to 1610)
  AUTHORS   Seo,H.C., Curtiss,J., Mlodzik,M. and Fjose,A.
  TITLE     Six class homeobox genes in drosophila belong to three distinct
            families and are involved in head development
  JOURNAL   Mech Dev 83 (1-2), 127-139 (1999)
   PUBMED   10381573
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC076015.1.
            
            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 :: BC076015.1, EH451622.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA3505392, SAMEA4476729
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1610
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="13"
                     /map="13"
     gene            1..1610
                     /gene="six1a"
                     /gene_synonym="six1b; six2; zgc:92332"
                     /note="SIX homeobox 1a"
                     /db_xref="GeneID:494168"
                     /db_xref="ZFIN:ZDB-GENE-040718-155"
     exon            1..796
                     /gene="six1a"
                     /gene_synonym="six1b; six2; zgc:92332"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    135..137
                     /gene="six1a"
                     /gene_synonym="six1b; six2; zgc:92332"
                     /note="upstream in-frame stop codon"
     CDS             237..1088
                     /gene="six1a"
                     /gene_synonym="six1b; six2; zgc:92332"
                     /note="homeodomain transcription factor Six1b; sine oculis
                     homeobox homolog 2; homeobox protein six1b; sine oculis
                     homeobox homolog 1b; sine oculis homeobox homolog 1a"
                     /codon_start=1
                     /product="homeobox protein six1a"
                     /protein_id="NP_001009904.1"
                     /db_xref="GeneID:494168"
                     /db_xref="ZFIN:ZDB-GENE-040718-155"
                     /translation="

MSILPSFGFTQEQVACVCEVLQQGGNLERLGRFLWSLPACDHLHKNESVLKAKAVVAFHRGNFRELYKILESYQFSTHNHPKMQQLWLKAHYVEAEKLRGRPLGAVGKYRVRRKFPLPRTIWDGEETSYCFKEKSRSVLREWYTHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKERENGENNGVGGKQSQRSPLDGVKSLMSSSEDEFSPPQSPEHSSVLLLQGTMNNPGAPAYPMPGLGAPHPLHGMQGHPHQIQDSLLGSLTSSLVDLGS"

     misc_feature    261..590
                     /gene="six1a"
                     /gene_synonym="six1b; six2; zgc:92332"
                     /note="Transcriptional regulator, SIX1, N-terminal SD
                     domain; Region: SIX1_SD; pfam16878"
                     /db_xref="CDD:465293"
     misc_feature    621..776
                     /gene="six1a"
                     /gene_synonym="six1b; six2; zgc:92332"
                     /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(624..626,744..746,753..758,765..767)
                     /gene="six1a"
                     /gene_synonym="six1b; six2; zgc:92332"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     misc_feature    738..1028
                     /gene="six1a"
                     /gene_synonym="six1b; six2; zgc:92332"
                     /note="propagated from UniProtKB/Swiss-Prot (Q6DHF9.2);
                     Region: Disordered. /evidence=ECO:0000256|SAM:MobiDB-lite"
     exon            797..1573
                     /gene="six1a"
                     /gene_synonym="six1b; six2; zgc:92332"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

cgggatgacgctgtgccggctttctctgtcaaatatccatccagaaaaaccacattcgaatctcacgtgtgcaaaccgggagggtgacagggggtgccacacaaccggttatcaaaactggagtgcgccacagataaatccggcacggggacttttgtcctgggataaatttgagaggaatacccacagagccagggattagcagtacattaaagggtggattgcataggggagccatgtcaatcttgccctcgttcggctttacgcaagagcaagtcgcgtgcgtctgcgaggtgctgcagcagggtgggaacctggagaggctcggacggttcctttggtccctgccagcctgcgaccacctccacaagaacgaatccgtgctcaaagcgaaggctgtggttgccttccaccggggaaacttccgtgagctctacaagatcttggagagctaccagttctccacgcacaaccacccgaagatgcagcagctgtggctgaaggcgcactatgttgaggcggaaaagttgcgggggcgcccgctaggcgctgtgggcaaatatcgtgtgcgcaggaaattccctttgccccgtactatctgggacggcgaggaaaccagttattgttttaaggaaaagtctcggagcgtgctgcgtgaatggtacacgcacaacccttatccatctccacgggagaagcgagagctggcagaggcaacaggactgaccactacacaggtcagcaactggtttaaaaacaggagacagagagaccgggcagccgaggcaaaagagagagaaaacggcgagaacaacggcgtcggcggaaagcagagccagcggtctccgctcgacggagtgaagtcgctgatgtcgagctcggaggatgagttttctccgccgcagagccccgagcacagctccgtgcttcttctgcaaggcaccatgaacaatcccggggctcccgcatacccaatgcccggcctgggtgcgccgcacccgctacacggcatgcaagggcatccgcatcagatccaggattcactattaggatctctaacatccagccttgtggatttaggatcgtaggacgccttaagcacggttagacgagaagacttaatacccaatacagcatatacttctgacgcagaggacgtttacatcaagaaaaaagaaaaacgattgttgcatatcattagaaaagcgaggaaaatcaaaagagcttgtggattttgggaactttgggttttctggacaagtgcgtaaattttgttaaaccattaaggccactatttaagaaaattcacagcattgaagtatgcatttaaaacattttaataatttataatgttttacacaaatattaatttatataaactgttctgtactgaacgaggagtagagattttaatgagaaaatcattcaaacgtcaactaaacaccaaagtggaatctaaggttctttgtttttattcagtttacatatataatatgtttacattacaattgtagtttttaaaaatatcagatgaaaagaaaaggaaaaacaccaattaaaagtatctgttgcaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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