SIX1B_DANRE
ID SIX1B_DANRE Reviewed; 284 AA.
AC Q6NZ04; Q05FF5;
DT 26-JUN-2013, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=Homeobox protein six1b;
DE AltName: Full=Homeobox protein six1a;
DE AltName: Full=Sine oculis homeobox homolog 1a;
DE AltName: Full=Sine oculis homeobox homolog 1b;
GN Name=six1b; Synonyms=six1, six1a;
OS Danio rerio (Zebrafish) (Brachydanio rerio).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
OC Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes;
OC Danionidae; Danioninae; Danio.
OX NCBI_TaxID=7955;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
RX PubMed=15254912; DOI=10.1002/dvdy.20093;
RA Bessarab D.A., Chong S.W., Korzh V.;
RT "Expression of zebrafish six1 during sensory organ development and
RT myogenesis.";
RL Dev. Dyn. 230:781-786(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DISRUPTION PHENOTYPE, AND
RP DEVELOPMENTAL STAGE.
RX PubMed=17035528; DOI=10.1523/jneurosci.1025-06.2006;
RA Bricaud O., Collazo A.;
RT "The transcription factor six1 inhibits neuronal and promotes hair cell
RT fate in the developing zebrafish (Danio rerio) inner ear.";
RL J. Neurosci. 26:10438-10451(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Tuebingen;
RX PubMed=23594743; DOI=10.1038/nature12111;
RA Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M.,
RA Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I.,
RA Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.,
RA White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y.,
RA Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B.,
RA Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S.,
RA Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M.,
RA Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J.,
RA Clee C., Oliver K., Clark R., Riddle C., Elliot D., Threadgold G.,
RA Harden G., Ware D., Begum S., Mortimore B., Kerry G., Heath P.,
RA Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S.,
RA Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N.,
RA Lloyd C., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J.,
RA Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J.,
RA Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D.,
RA McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S.,
RA Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E.,
RA Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A.,
RA Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P.,
RA Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J.,
RA Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E.,
RA Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C.,
RA Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C.,
RA Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M.,
RA Oberlander M., Rudolph-Geiger S., Teucke M., Lanz C., Raddatz G.,
RA Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F.,
RA Schuster S.C., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M.,
RA Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M.,
RA de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C.,
RA Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.;
RT "The zebrafish reference genome sequence and its relationship to the human
RT genome.";
RL Nature 496:498-503(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Embryo;
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (FEB-2004) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP FUNCTION, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=18789916; DOI=10.1016/j.ydbio.2008.08.015;
RA Bessarab D.A., Chong S.W., Srinivas B.P., Korzh V.;
RT "Six1a is required for the onset of fast muscle differentiation in
RT zebrafish.";
RL Dev. Biol. 323:216-228(2008).
RN [6]
RP FUNCTION, DEVELOPMENTAL STAGE, AND DISRUPTION PHENOTYPE.
RX PubMed=19409884; DOI=10.1016/j.ydbio.2009.04.029;
RA Lin C.Y., Chen W.T., Lee H.C., Yang P.H., Yang H.J., Tsai H.J.;
RT "The transcription factor Six1a plays an essential role in the craniofacial
RT myogenesis of zebrafish.";
RL Dev. Biol. 331:152-166(2009).
RN [7]
RP FUNCTION, DNA-BINDING, INTERACTION WITH EYA1, AND MUTAGENESIS OF ARG-110;
RP TYR-129 AND GLU-133.
RX PubMed=21745464; DOI=10.1016/j.ydbio.2011.06.035;
RA Bricaud O., Collazo A.;
RT "Balancing cell numbers during organogenesis: Six1a differentially affects
RT neurons and sensory hair cells in the inner ear.";
RL Dev. Biol. 357:191-201(2011).
RN [8]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RX PubMed=23444384; DOI=10.1242/jcs.119917;
RA Nord H., Skalman L.N., von Hofsten J.;
RT "Six1 regulates proliferation of Pax7+ muscle progenitors in zebrafish.";
RL J. Cell Sci. 126:1868-1880(2013).
CC -!- FUNCTION: Transcription factor that is involved in the regulation of
CC cell proliferation, apoptosis and embryonic development. Depending on
CC context, functions as transcriptional repressor or activator.
CC Transcriptional activation is enhanced by eya1 (in vitro). Plays an
CC important role in the development of the inner ear, where it promotes
CC hair cell proliferation and inhibits proliferation of neural progenitor
CC cells. Required for normal myogenesis. Plays a role in the development
CC of fast muscle fibers throughout the body, as well as the development
CC of craniofacial muscles. Required for normal expression of myod1 and
CC myog during myogenesis. {ECO:0000269|PubMed:17035528,
CC ECO:0000269|PubMed:18789916, ECO:0000269|PubMed:19409884,
CC ECO:0000269|PubMed:21745464, ECO:0000269|PubMed:23444384}.
CC -!- SUBUNIT: Interacts with eya1. {ECO:0000305|PubMed:21745464}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:Q15475}. Cytoplasm
CC {ECO:0000250|UniProtKB:Q15475}.
CC -!- DEVELOPMENTAL STAGE: First detected at mid-gastrulation. After the
CC onset of segmentation, detected in cranial placode. At later stages of
CC development, detected in the olfactory, otic, and lateral line
CC placodes, in the developing inner ear and in neuromasts. After 48 hpf,
CC no longer detected in the inner ear, but continues to be expressed in
CC lateral line neuromasts. In addition, detected in the pituitary,
CC branchial arches, somites, pectoral fin, ventral abdomen muscle, and
CC the cranial muscles of the eye and lower jaw. Detected in developing
CC fast muscle. {ECO:0000269|PubMed:15254912, ECO:0000269|PubMed:17035528,
CC ECO:0000269|PubMed:18789916, ECO:0000269|PubMed:19409884}.
CC -!- DISRUPTION PHENOTYPE: Morpholino knockdown of the protein increases
CC both cell proliferation and apoptosis in the otocyst. Increases
CC proliferation of neuronal cells and decreases the number of cells
CC destined to form hair cells. Disrupts myogenesis by interfering with
CC the proliferation of dermomyotomal cells expressing pax7 and loss of
CC myog expression. {ECO:0000269|PubMed:17035528,
CC ECO:0000269|PubMed:18789916, ECO:0000269|PubMed:19409884,
CC ECO:0000269|PubMed:23444384}.
CC -!- SIMILARITY: Belongs to the SIX/Sine oculis homeobox family.
CC {ECO:0000305}.
CC -!- CAUTION: Zebrafish has two genes coding for six1 orthologs. This gene
CC is called six1b by ZFIN and in PubMed:23444384, but has also been
CC described as six1 (PubMed:17035528) and as six1a (PubMed:15254912,
CC PubMed:18789916, PubMed:19409884). {ECO:0000305|PubMed:15254912,
CC ECO:0000305|PubMed:17035528, ECO:0000305|PubMed:18789916,
CC ECO:0000305|PubMed:19409884}.
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DR EMBL; AY466110; AAS46283.1; -; mRNA.
DR EMBL; AY254196; AAO83592.1; -; mRNA.
DR EMBL; BX649231; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC066396; AAH66396.1; -; mRNA.
DR RefSeq; NP_996978.1; NM_207095.1.
DR AlphaFoldDB; Q6NZ04; -.
DR SMR; Q6NZ04; -.
DR STRING; 7955.ENSDARP00000028379; -.
DR PaxDb; Q6NZ04; -.
DR Ensembl; ENSDART00000036124; ENSDARP00000028379; ENSDARG00000026473.
DR GeneID; 404627; -.
DR KEGG; dre:404627; -.
DR CTD; 404627; -.
DR ZFIN; ZDB-GENE-040426-2308; six1b.
DR eggNOG; KOG0775; Eukaryota.
DR GeneTree; ENSGT00940000156487; -.
DR HOGENOM; CLU_046914_2_0_1; -.
DR InParanoid; Q6NZ04; -.
DR OMA; NSGANKQ; -.
DR OrthoDB; 1061244at2759; -.
DR PhylomeDB; Q6NZ04; -.
DR TreeFam; TF315545; -.
DR PRO; PR:Q6NZ04; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 20.
DR Bgee; ENSDARG00000026473; Expressed in muscle tissue and 52 other tissues.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005634; C:nucleus; IBA:GO_Central.
DR GO; GO:0005667; C:transcription regulator complex; IBA:GO_Central.
DR GO; GO:0000981; F:DNA-binding transcription factor activity, RNA polymerase II-specific; IBA:GO_Central.
DR GO; GO:0000978; F:RNA polymerase II cis-regulatory region sequence-specific DNA binding; IBA:GO_Central.
DR GO; GO:0021984; P:adenohypophysis development; IGI:ZFIN.
DR GO; GO:0006915; P:apoptotic process; IEA:UniProtKB-KW.
DR GO; GO:0002074; P:extraocular skeletal muscle development; IMP:ZFIN.
DR GO; GO:0048839; P:inner ear development; IMP:ZFIN.
DR GO; GO:0045892; P:negative regulation of transcription, DNA-templated; IEA:InterPro.
DR GO; GO:0048935; P:peripheral nervous system neuron development; IMP:ZFIN.
DR GO; GO:0043282; P:pharyngeal muscle development; IMP:ZFIN.
DR GO; GO:0014857; P:regulation of skeletal muscle cell proliferation; IMP:ZFIN.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IBA:GO_Central.
DR GO; GO:0048741; P:skeletal muscle fiber development; IGI:ZFIN.
DR GO; GO:0051146; P:striated muscle cell differentiation; IMP:ZFIN.
DR CDD; cd00086; homeodomain; 1.
DR InterPro; IPR009057; Homeobox-like_sf.
DR InterPro; IPR017970; Homeobox_CS.
DR InterPro; IPR001356; Homeobox_dom.
DR InterPro; IPR031278; SIX1.
DR InterPro; IPR031701; SIX1_SD.
DR PANTHER; PTHR10390:SF13; PTHR10390:SF13; 1.
DR Pfam; PF00046; Homeodomain; 1.
DR Pfam; PF16878; SIX1_SD; 1.
DR SMART; SM00389; HOX; 1.
DR SUPFAM; SSF46689; SSF46689; 1.
DR PROSITE; PS00027; HOMEOBOX_1; 1.
DR PROSITE; PS50071; HOMEOBOX_2; 1.
PE 1: Evidence at protein level;
KW Activator; Apoptosis; Cytoplasm; Developmental protein; DNA-binding;
KW Homeobox; Nucleus; Reference proteome; Repressor; Transcription;
KW Transcription regulation.
FT CHAIN 1..284
FT /note="Homeobox protein six1b"
FT /id="PRO_0000422774"
FT DNA_BIND 124..183
FT /note="Homeobox"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00108"
FT REGION 167..238
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 173..192
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 193..238
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 110
FT /note="R->W: Abolishes regulation of hair cell
FT proliferation. No effect on regulation of neuron
FT proliferation."
FT /evidence="ECO:0000269|PubMed:21745464"
FT MUTAGEN 129
FT /note="Y->C: Impairs transcription factor activity."
FT /evidence="ECO:0000269|PubMed:21745464"
FT MUTAGEN 133
FT /note="Missing: Impairs transcription factor activity."
FT /evidence="ECO:0000269|PubMed:21745464"
FT CONFLICT 107
FT /note="G -> V (in Ref. 2; AAO83592)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 284 AA; 31975 MW; 8953F2AC44CFBE9A CRC64;
MSMLPSFGFT QEQVACVCEV LQQGGNLERL GRFLWSLPAC DHLHKNESVL KAKAVVAFHR
GNFRELYKIL ESHQFSPHNH PKLQQLWLKA HYIEAEKLRG RPLGAVGKYR VRRKFPLPRT
IWDGEETSYC FKEKSRGVLR EWYTHNPYPS PREKRELAEA TGLTTTQVSN WFKNRRQRDR
AAEAKERENS ENNNTGANKQ NQLSPLDGGK SLMSSSEDEF SPPQSPDQNS VLLLQGNMSH
PGASAYSMTG LGAAQSVHGM QGHPHQLQDS LLGPLTSSLV DLGS
