LOCUS       NM_201105               1317 bp    mRNA    linear   VRT 14-MAR-2021
DEFINITION  Danio rerio SIX homeobox 6a (six6a), mRNA.
ACCESSION   NM_201105
VERSION     NM_201105.1
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 1317)
  AUTHORS   Covello G, Rossello FJ, Filosi M, Gajardo F, Duchemin AL, Tremonti
            BF, Eichenlaub M, Polo JM, Powell D, Ngai J, Allende ML, Domenici
            E, Ramialison M and Poggi L.
  TITLE     Transcriptome analysis of the zebrafish atoh7-/- Mutant, lakritz,
            highlights Atoh7-dependent genetic networks with potential
            implications for human eye diseases
  JOURNAL   FASEB Bioadv 2 (7), 434-448 (2020)
   PUBMED   32676583
  REMARK    Publication Status: Online-Only
REFERENCE   2  (bases 1 to 1317)
  AUTHORS   Seifinejad A, Li S, Mikhail C, Vassalli A, Pradervand S, Arribat Y,
            Pezeshgi Modarres H, Allen B, John RM, Amati F and Tafti M.
  TITLE     Molecular codes and in vitro generation of hypocretin and melanin
            concentrating hormone neurons
  JOURNAL   Proc Natl Acad Sci U S A 116 (34), 17061-17070 (2019)
   PUBMED   31375626
REFERENCE   3  (bases 1 to 1317)
  AUTHORS   Ogawa Y, Shiraki T, Asano Y, Muto A, Kawakami K, Suzuki Y, Kojima D
            and Fukada Y.
  TITLE     Six6 and Six7 coordinately regulate expression of middle-wavelength
            opsins in zebrafish
  JOURNAL   Proc Natl Acad Sci U S A 116 (10), 4651-4660 (2019)
   PUBMED   30765521
  REMARK    GeneRIF: Six6b and six7 govern expression of the SWS2 and RH2
            opsins responsible for middle-wavelength sensitivity.
REFERENCE   4  (bases 1 to 1317)
  AUTHORS   Taylor SM, Alvarez-Delfin K, Saade CJ, Thomas JL, Thummel R, Fadool
            JM and Hitchcock PF.
  TITLE     The bHLH Transcription Factor NeuroD Governs Photoreceptor Genesis
            and Regeneration Through Delta-Notch Signaling
  JOURNAL   Invest Ophthalmol Vis Sci 56 (12), 7496-7515 (2015)
   PUBMED   26580854
REFERENCE   5  (bases 1 to 1317)
  AUTHORS   Elkon R, Milon B, Morrison L, Shah M, Vijayakumar S, Racherla M,
            Leitch CC, Silipino L, Hadi S, Weiss-Gayet M, Barras E, Schmid CD,
            Ait-Lounis A, Barnes A, Song Y, Eisenman DJ, Eliyahu E, Frolenkov
            GI, Strome SE, Durand B, Zaghloul NA, Jones SM, 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   6  (bases 1 to 1317)
  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   7  (bases 1 to 1317)
  AUTHORS   Gomez-Marin C, Tena JJ, Acemel RD, Lopez-Mayorga M, Naranjo S, de
            la Calle-Mustienes E, Maeso I, Beccari L, Aneas I, Vielmas E,
            Bovolenta P, Nobrega MA, Carvajal J and Gomez-Skarmeta JL.
  TITLE     Evolutionary comparison reveals that diverging CTCF sites are
            signatures of ancestral topological associating domains borders
  JOURNAL   Proc Natl Acad Sci U S A 112 (24), 7542-7547 (2015)
   PUBMED   26034287
REFERENCE   8  (bases 1 to 1317)
  AUTHORS   Diotel N, Rodriguez Viales R, Armant O, Marz M, Ferg M, Rastegar S
            and Strahle U.
  TITLE     Comprehensive expression map of transcription regulators in the
            adult zebrafish telencephalon reveals distinct neurogenic niches
  JOURNAL   J Comp Neurol 523 (8), 1202-1221 (2015)
   PUBMED   25556858
REFERENCE   9  (bases 1 to 1317)
  AUTHORS   Carnes MU, Liu YP, Allingham RR, Whigham BT, Havens S, Garrett ME,
            Qiao C, Katsanis N, Wiggs JL, Pasquale LR, Ashley-Koch A, Oh EC and
            Hauser MA.
  CONSRTM   NEIGHBORHOOD Consortium Investigators
  TITLE     Discovery and functional annotation of SIX6 variants in primary
            open-angle glaucoma
  JOURNAL   PLoS Genet 10 (5), e1004372 (2014)
   PUBMED   24875647
  REMARK    Publication Status: Online-Only
REFERENCE   10 (bases 1 to 1317)
  AUTHORS   Iglesias AI, Springelkamp H, van der Linde H, Severijnen LA, Amin
            N, Oostra B, Kockx CE, van den Hout MC, van Ijcken WF, Hofman A,
            Uitterlinden AG, Verdijk RM, Klaver CC, Willemsen R and van Duijn
            CM.
  TITLE     Exome sequencing and functional analyses suggest that SIX6 is a
            gene involved in an altered proliferation-differentiation balance
            early in life and optic nerve degeneration at old age
  JOURNAL   Hum Mol Genet 23 (5), 1320-1332 (2014)
   PUBMED   24150847
COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
            NCBI review. The reference sequence was derived from BC053123.1.
            
            ##Evidence-Data-START##
            Transcript exon combination :: BC053123.1, CA470126.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA2168446, SAMEA2168447
                                           [ECO:0000348]
            ##Evidence-Data-END##
FEATURES             Location/Qualifiers
     source          1..1317
                     /organism="Danio rerio"
                     /mol_type="mRNA"
                     /db_xref="taxon:7955"
                     /chromosome="13"
                     /map="13"
     gene            1..1317
                     /gene="six6a"
                     /gene_synonym="Six6; zgc:63871"
                     /note="SIX homeobox 6a"
                     /db_xref="GeneID:394080"
                     /db_xref="ZFIN:ZDB-GENE-040426-1282"
     exon            1..760
                     /gene="six6a"
                     /gene_synonym="Six6; zgc:63871"
                     /inference="alignment:Splign:2.1.0"
     misc_feature    33..35
                     /gene="six6a"
                     /gene_synonym="Six6; zgc:63871"
                     /note="upstream in-frame stop codon"
     CDS             189..926
                     /gene="six6a"
                     /gene_synonym="Six6; zgc:63871"
                     /note="sine oculis homeobox homolog 6; sine oculis-related
                     homeobox 6a"
                     /codon_start=1
                     /product="homeobox protein SIX6a"
                     /protein_id="NP_957399.1"
                     /db_xref="GeneID:394080"
                     /db_xref="ZFIN:ZDB-GENE-040426-1282"
                     /translation="

MFQLPILNFSPQQVAGVCETLEESGDVERLGRFLWSLPVAPSACDVLGKNESVLRARAVVAFHAGNFRELYHILENHKFTKDSHAKLQALWLEAHYQEAEKLRGRPLGPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRHLLREWYLQDPYPNPSKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRLQQQVLSGGSVRSLGDDDTTVDRLGPASSPEVSLSSKAATSAISITSSDSECDI"

     misc_feature    213..554
                     /gene="six6a"
                     /gene_synonym="Six6; zgc:63871"
                     /note="Transcriptional regulator, SIX1, N-terminal SD
                     domain; Region: SIX1_SD; pfam16878"
                     /db_xref="CDD:465293"
     misc_feature    576..722
                     /gene="six6a"
                     /gene_synonym="Six6; zgc:63871"
                     /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(579..581,588..590,708..710,717..722)
                     /gene="six6a"
                     /gene_synonym="Six6; zgc:63871"
                     /note="specific DNA base contacts [nucleotide binding];
                     other site"
                     /db_xref="CDD:238039"
     exon            761..1257
                     /gene="six6a"
                     /gene_synonym="Six6; zgc:63871"
                     /inference="alignment:Splign:2.1.0"
ORIGIN      

atcaaagaagagattttgccgttcaggctgcttgagcctgccgcacggcaccgctcctcggcgcgttttgtgacacggctgttaacttttgccgttttctgacagacaggcttaacaaaaagaggggcgagacagacgaggaacagcaccagacaggaggaccaaaggagagagacattacagtctccatgttccagctgcccattttgaatttcagccctcagcaggtcgcgggggtctgtgagacgctcgaggagagtggagacgtggagaggctcggccgctttctctggtcactcccggtggcgccgtccgcctgcgatgtgctcggaaagaacgagtctgtcctgcgcgcgcgcgcggtcgtggcctttcacgcgggcaacttccgcgagctctaccacatactagagaaccacaaattcaccaaagactcacacgcaaaactgcaggcgctctggctcgaggcgcattaccaggaggctgagaaactccgtgggcgtccgttaggacccgtggacaagtaccgcgtccgaaagaagtttccactgcccaggacgatatgggacggggaacagaaaacgcactgctttaaggaaagaacgcggcatctgctgagagagtggtacctgcaggacccttacccaaatcccagcaaaaaaagagaactggcgcaggcgactggactcacacccacgcaagtgggcaactggtttaaaaaccggaggcaaagggaccgagcggcagcggccaagaacaggctacagcagcaagttctgtccggtggctcggtccgatcgctgggggacgatgacaccacagtagaccgcctgggtcccgcctcaagcccagaagtcagtctctcgagcaaggccgccacctccgccatctccatcacctccagcgacagtgaatgtgacatctaacgtgacaggcttcaaaagagcaaaccgaagaactgtaagagacaatctcacaaaaaaaaaaaaaaactttagtgcctgcaaccggcccaaagataggctaaaatgaaagatggaagaaaaccattacacactttcatttcccattcgttgatttgatcgaaatgggcagtgcttctcacgaagacagaaaaagggagtatttgggggaaaagcatctgagggtcgagcttattattgtatgtgtgcatactttatcacgaaaagactgaataatgttttaatgtttgtcttttttaatatataaatgatgtttatttgcttatttataataaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa

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