SOX3_DANRE
ID SOX3_DANRE Reviewed; 300 AA.
AC Q6EJB7; Q762C1;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 16-AUG-2004, sequence version 1.
DT 03-AUG-2022, entry version 125.
DE RecName: Full=Transcription factor Sox-3;
GN Name=sox3 {ECO:0000312|ZFIN:ZDB-GENE-980526-333}; ORFNames=zgc:110279;
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] {ECO:0000305, ECO:0000312|EMBL:AAP79985.1}
RP NUCLEOTIDE SEQUENCE [MRNA], AND DEVELOPMENTAL STAGE.
RX PubMed=15262889; DOI=10.1242/dev.01227;
RA Kudoh T., Concha M.L., Houart C., Dawid I.B., Wilson S.W.;
RT "Combinatorial Fgf and Bmp signalling patterns the gastrula ectoderm into
RT prospective neural and epidermal domains.";
RL Development 131:3581-3592(2004).
RN [2] {ECO:0000305, ECO:0000312|EMBL:BAE48584.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, AND DEVELOPMENTAL STAGE.
RC TISSUE=Embryo {ECO:0000269|PubMed:16408288};
RX PubMed=16408288; DOI=10.1002/dvdy.20678;
RA Okuda Y., Yoda H., Uchikawa M., Furutani-Seiki M., Takeda H., Kondoh H.,
RA Kamachi Y.;
RT "Comparative genomic and expression analysis of group B1 sox genes in
RT zebrafish indicates their diversification during vertebrate evolution.";
RL Dev. Dyn. 235:811-825(2006).
RN [3] {ECO:0000312|EMBL:BAD11369.2}
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Shimizu T., Hibi M.;
RT "Danio rerio Sox3 mRNA.";
RL Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.
RN [4]
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 [5] {ECO:0000312|EMBL:BAD11369.2}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC TISSUE=Olfactory epithelium {ECO:0000312|EMBL:AAH92845.1};
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP DEVELOPMENTAL STAGE.
RX PubMed=15532058; DOI=10.1002/dvdy.20244;
RA Rentzsch F., Bakkers J., Kramer C., Hammerschmidt M.;
RT "Fgf signaling induces posterior neuroectoderm independently of Bmp
RT signaling inhibition.";
RL Dev. Dyn. 231:750-757(2004).
RN [7]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-235, AND IDENTIFICATION BY
RP MASS SPECTROMETRY.
RC TISSUE=Embryo;
RX PubMed=18307296; DOI=10.1021/pr700667w;
RA Lemeer S., Pinkse M.W.H., Mohammed S., van Breukelen B., den Hertog J.,
RA Slijper M., Heck A.J.R.;
RT "Online automated in vivo zebrafish phosphoproteomics: from large-scale
RT analysis down to a single embryo.";
RL J. Proteome Res. 7:1555-1564(2008).
CC -!- FUNCTION: Transcriptional activator. {ECO:0000269|PubMed:16408288}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000305}.
CC -!- DEVELOPMENTAL STAGE: Expressed both maternally and zygotically.
CC Maternal expression is weak and zygotic expression is strong by the 30%
CC epiboly stage. At the gastrula stage, expressed in all prospective
CC neural tissue with the exception of a band of cells in the prospective
CC midbrain and hindbrain. At the tail bud to 3-somite stage, expressed in
CC distinct regions of the future brain, the anterior margin of the neural
CC plate and the primordia of the epibranchial placodes. At the 12-somite
CC stage, broad expression in the central nervous system (CNS), with
CC weakest expression at the forebrain-midbrain and midbrain-hindbrain
CC boundaries and in the posterior CNS. At the 21- to 25-somite stage,
CC broad expression in the CNS and the lens. {ECO:0000269|PubMed:15262889,
CC ECO:0000269|PubMed:15532058, ECO:0000269|PubMed:16408288}.
CC -!- DOMAIN: The 9aaTAD motif is a transactivation domain present in a large
CC number of yeast and animal transcription factors.
CC {ECO:0000250|UniProtKB:P41225}.
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DR EMBL; AY316135; AAP79985.1; -; mRNA.
DR EMBL; AB242330; BAE48584.1; -; mRNA.
DR EMBL; AB117960; BAD11369.2; -; mRNA.
DR EMBL; BX088596; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC092845; AAH92845.1; -; mRNA.
DR RefSeq; NP_001001811.2; NM_001001811.2.
DR AlphaFoldDB; Q6EJB7; -.
DR SMR; Q6EJB7; -.
DR STRING; 7955.ENSDARP00000070099; -.
DR iPTMnet; Q6EJB7; -.
DR PaxDb; Q6EJB7; -.
DR PRIDE; Q6EJB7; -.
DR Ensembl; ENSDART00000075617; ENSDARP00000070099; ENSDARG00000053569.
DR GeneID; 30529; -.
DR KEGG; dre:30529; -.
DR CTD; 6658; -.
DR ZFIN; ZDB-GENE-980526-333; sox3.
DR eggNOG; KOG0527; Eukaryota.
DR GeneTree; ENSGT00940000162359; -.
DR HOGENOM; CLU_021123_0_0_1; -.
DR InParanoid; Q6EJB7; -.
DR OMA; AYPQHHG; -.
DR OrthoDB; 1161594at2759; -.
DR PhylomeDB; Q6EJB7; -.
DR TreeFam; TF351735; -.
DR Reactome; R-DRE-3769402; Deactivation of the beta-catenin transactivating complex.
DR PRO; PR:Q6EJB7; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 14.
DR Bgee; ENSDARG00000053569; Expressed in midbrain and 77 other tissues.
DR ExpressionAtlas; Q6EJB7; baseline and differential.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0001228; F:DNA-binding transcription activator activity, RNA polymerase II-specific; IDA:ZFIN.
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:0009653; P:anatomical structure morphogenesis; IBA:GO_Central.
DR GO; GO:0030154; P:cell differentiation; IBA:GO_Central.
DR GO; GO:0007417; P:central nervous system development; IMP:ZFIN.
DR GO; GO:0030182; P:neuron differentiation; IMP:ZFIN.
DR GO; GO:1905040; P:otic placode development; IMP:ZFIN.
DR GO; GO:0043049; P:otic placode formation; IMP:ZFIN.
DR GO; GO:0007422; P:peripheral nervous system development; IMP:ZFIN.
DR GO; GO:0051091; P:positive regulation of DNA-binding transcription factor activity; IDA:ZFIN.
DR GO; GO:0006357; P:regulation of transcription by RNA polymerase II; IDA:ZFIN.
DR GO; GO:0006355; P:regulation of transcription, DNA-templated; IBA:GO_Central.
DR Gene3D; 1.10.30.10; -; 1.
DR InterPro; IPR009071; HMG_box_dom.
DR InterPro; IPR036910; HMG_box_dom_sf.
DR InterPro; IPR029550; SOX-3.
DR InterPro; IPR022097; SOX_fam.
DR PANTHER; PTHR10270:SF111; PTHR10270:SF111; 1.
DR Pfam; PF00505; HMG_box; 1.
DR Pfam; PF12336; SOXp; 1.
DR SMART; SM00398; HMG; 1.
DR SUPFAM; SSF47095; SSF47095; 1.
DR PROSITE; PS50118; HMG_BOX_2; 1.
PE 1: Evidence at protein level;
KW Activator; Developmental protein; DNA-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Transcription; Transcription regulation.
FT CHAIN 1..300
FT /note="Transcription factor Sox-3"
FT /id="PRO_0000238912"
FT DNA_BIND 35..103
FT /note="HMG box"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00267"
FT REGION 1..35
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 251..262
FT /note="9aaTAD"
FT /evidence="ECO:0000250|UniProtKB:P41225"
FT COMPBIAS 9..29
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 235
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:18307296"
FT CONFLICT 218
FT /note="S -> G (in Ref. 3; BAD11369)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 300 AA; 33417 MW; FF01F5CBE8DED535 CRC64;
MYNMMETEIK SPIPQSNTGS VTGGKNNSAN DQDRVKRPMN AFMVWSRGQR RKMAQENPKM
HNSEISKRLG ADWKLLTDAE KRPFIDEAKR LRAMHMKEHP DYKYRPRRKT KTLLKKDKYS
LPGGLLAPGA NAVNNAVSVG QRMDYTHMNG WTNSAYSLMQ DQLAYPQHPS MNSPQIQQMH
RYDMAGLQYP MMSTAQTYMN AASTYSSMSP AYTQQTSSAM GLGSMASVCK TEPSSPPPAI
TSHSQRACLG DLRDMISMYL PPGGDSADHS SLQTSRLHSV HPHYQSAGTG VNGTLPLTHI
