SOX1B_DANRE
ID SOX1B_DANRE Reviewed; 340 AA.
AC Q2Z1R2; A8WFX7;
DT 30-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Transcription factor Sox-1b;
GN Name=sox1b {ECO:0000312|EMBL:BAE48582.1}; ORFNames=si:ch211-138g9.1;
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:BAE48582.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY, AND DEVELOPMENTAL
RP 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 [2]
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RG NIH - Zebrafish Gene Collection (ZGC) project;
RL Submitted (NOV-2007) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Transcriptional activator. {ECO:0000269|PubMed:16408288}.
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00267}.
CC -!- TISSUE SPECIFICITY: At the 3-somite stage, expressed in the forebrain.
CC At the 12-somite stage, strongly expressed in the forebrain and weakly
CC expressed throughout the central nervous system. At the 25-somite
CC stage, also expressed in the lens. {ECO:0000269|PubMed:16408288}.
CC -!- DEVELOPMENTAL STAGE: Expressed zygotically. First detected at the tail
CC bud stage and continues to be expressed for at least the first 48 hours
CC of development. {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; AB242328; BAE48582.1; -; mRNA.
DR EMBL; AL929216; CAX13546.1; -; Genomic_DNA.
DR EMBL; BC154495; AAI54496.1; -; mRNA.
DR RefSeq; NP_001032751.1; NM_001037662.1.
DR AlphaFoldDB; Q2Z1R2; -.
DR SMR; Q2Z1R2; -.
DR STRING; 7955.ENSDARP00000026510; -.
DR PaxDb; Q2Z1R2; -.
DR Ensembl; ENSDART00000010894; ENSDARP00000026510; ENSDARG00000008131.
DR GeneID; 562710; -.
DR KEGG; dre:562710; -.
DR CTD; 562710; -.
DR ZFIN; ZDB-GENE-060322-5; sox1b.
DR eggNOG; KOG0527; Eukaryota.
DR GeneTree; ENSGT00940000162479; -.
DR HOGENOM; CLU_021123_0_0_1; -.
DR InParanoid; Q2Z1R2; -.
DR OMA; HAVPQHY; -.
DR OrthoDB; 1161594at2759; -.
DR PhylomeDB; Q2Z1R2; -.
DR TreeFam; TF351735; -.
DR PRO; PR:Q2Z1R2; -.
DR Proteomes; UP000000437; Genome assembly.
DR Proteomes; UP000814640; Chromosome 1.
DR Bgee; ENSDARG00000008131; Expressed in interneuron and 16 other tissues.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005667; C:transcription regulator complex; IC: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:0007399; P:nervous system development; IEA:InterPro.
DR GO; GO:0051091; P:positive regulation of DNA-binding transcription factor activity; IDA:ZFIN.
DR GO; GO:0045944; P:positive regulation of transcription by RNA polymerase II; IBA:GO_Central.
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; IPR031268; SOX-1.
DR InterPro; IPR022097; SOX_fam.
DR PANTHER; PTHR10270:SF40; PTHR10270:SF40; 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 2: Evidence at transcript level;
KW Activator; Developmental protein; DNA-binding; Nucleus; Reference proteome;
KW Transcription; Transcription regulation.
FT CHAIN 1..340
FT /note="Transcription factor Sox-1b"
FT /id="PRO_0000238910"
FT DNA_BIND 37..105
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 REGION 198..219
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 297..305
FT /note="9aaTAD"
FT /evidence="ECO:0000250|UniProtKB:P41225"
FT COMPBIAS 10..35
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 203..217
FT /note="Basic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 340 AA; 36438 MW; 815F7C66B2165E8B CRC64;
MYSMMMETDL HSPGAQTNTN TGHTGPNSGS KVNQDRVKRP MNAFMVWSRG QRRKMAQENP
KMHNSEISKR LGAEWKLMSE AEKRPFIDEA KRLRAMHMKE HPDYKYRPRR KTKTLLKKDK
YSLAGGLLAG SGGGGGVGLG MGAAGVGQRL ESPVGHGGST AASYAHMNGW TNGAYSGQVA
AAAAAAAMMQ EAQLAYGQHP GSGAHHHHGH HHHPHNPQPM HRYEMTALQY SPLSNSQSYM
SASPSGYGGI SYTQHQNSSV ASSGAIGALG SLVKSEPSVS PPVNAHSRAP CSGDLREMIS
MYLPTAEAGD PSVQSRLHAV PQHYQSSTTS VNGTVPLTHI
