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Protein

Transcription factor Sox-3

Gene

sox3

Organism
Danio rerio (Zebrafish) (Brachydanio rerio)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Transcriptional activator.1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi35 – 10369HMG boxPROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • central nervous system development Source: ZFIN
  • neuron development Source: InterPro
  • neuron differentiation Source: ZFIN
  • otic placode formation Source: ZFIN
  • peripheral nervous system development Source: ZFIN
  • positive regulation of sequence-specific DNA binding transcription factor activity Source: ZFIN
  • sex determination Source: InterPro
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Activator, Developmental protein

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

ReactomeiR-DRE-3769402. Deactivation of the beta-catenin transactivating complex.

Names & Taxonomyi

Protein namesi
Recommended name:
Transcription factor Sox-3
Gene namesi
Name:sox3Imported
ORF Names:zgc:110279
OrganismiDanio rerio (Zebrafish) (Brachydanio rerio)
Taxonomic identifieri7955 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiActinopterygiiNeopterygiiTeleosteiOstariophysiCypriniformesCyprinidaeDanio
Proteomesi
  • UP000000437 Componenti: Chromosome 14

Organism-specific databases

ZFINiZDB-GENE-980526-333. sox3.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 300300Transcription factor Sox-3PRO_0000238912Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei235 – 2351Phosphoserine1 Publication

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ6EJB7.

PTM databases

iPTMnetiQ6EJB7.

Expressioni

Developmental stagei

Expressed both maternally and zygotically. Maternal expression is weak and zygotic expression is strong by the 30% epiboly stage. At the gastrula stage, expressed in all prospective neural tissue with the exception of a band of cells in the prospective midbrain and hindbrain. At the tail bud to 3-somite stage, expressed in distinct regions of the future brain, the anterior margin of the neural plate and the primordia of the epibranchial placodes. At the 12-somite stage, broad expression in the central nervous system (CNS), with weakest expression at the forebrain-midbrain and midbrain-hindbrain boundaries and in the posterior CNS. At the 21- to 25-somite stage, broad expression in the CNS and the lens.3 Publications

Gene expression databases

BgeeiQ6EJB7.
ExpressionAtlasiQ6EJB7. differential.

Interactioni

Protein-protein interaction databases

STRINGi7955.ENSDARP00000070099.

Structurei

3D structure databases

ProteinModelPortaliQ6EJB7.
SMRiQ6EJB7. Positions 33-111.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Contains 1 HMG box DNA-binding domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiENOG410IPZ0. Eukaryota.
ENOG41102MY. LUCA.
GeneTreeiENSGT00760000118988.
HOGENOMiHOG000231647.
HOVERGENiHBG105663.
InParanoidiQ6EJB7.
KOiK09267.
OMAiSANDQDR.
OrthoDBiEOG7TMZVP.
PhylomeDBiQ6EJB7.
TreeFamiTF351735.

Family and domain databases

Gene3Di1.10.30.10. 1 hit.
InterProiIPR009071. HMG_box_dom.
IPR029550. SOX-3.
IPR022097. SOX_fam.
[Graphical view]
PANTHERiPTHR10270:SF111. PTHR10270:SF111. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF12336. SOXp. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 1 hit.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 1 hit.
PROSITEiPS50118. HMG_BOX_2. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6EJB7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MYNMMETEIK SPIPQSNTGS VTGGKNNSAN DQDRVKRPMN AFMVWSRGQR
60 70 80 90 100
RKMAQENPKM HNSEISKRLG ADWKLLTDAE KRPFIDEAKR LRAMHMKEHP
110 120 130 140 150
DYKYRPRRKT KTLLKKDKYS LPGGLLAPGA NAVNNAVSVG QRMDYTHMNG
160 170 180 190 200
WTNSAYSLMQ DQLAYPQHPS MNSPQIQQMH RYDMAGLQYP MMSTAQTYMN
210 220 230 240 250
AASTYSSMSP AYTQQTSSAM GLGSMASVCK TEPSSPPPAI TSHSQRACLG
260 270 280 290 300
DLRDMISMYL PPGGDSADHS SLQTSRLHSV HPHYQSAGTG VNGTLPLTHI
Length:300
Mass (Da):33,417
Last modified:August 16, 2004 - v1
Checksum:iFF01F5CBE8DED535
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti218 – 2181S → G in BAD11369 (Ref. 3) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY316135 mRNA. Translation: AAP79985.1.
AB242330 mRNA. Translation: BAE48584.1.
AB117960 mRNA. Translation: BAD11369.2.
BX088596 Genomic DNA. No translation available.
BC092845 mRNA. Translation: AAH92845.1.
RefSeqiNP_001001811.2. NM_001001811.2.
UniGeneiDr.104569.

Genome annotation databases

EnsembliENSDART00000075617; ENSDARP00000070099; ENSDARG00000053569.
GeneIDi30529.
KEGGidre:30529.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY316135 mRNA. Translation: AAP79985.1.
AB242330 mRNA. Translation: BAE48584.1.
AB117960 mRNA. Translation: BAD11369.2.
BX088596 Genomic DNA. No translation available.
BC092845 mRNA. Translation: AAH92845.1.
RefSeqiNP_001001811.2. NM_001001811.2.
UniGeneiDr.104569.

3D structure databases

ProteinModelPortaliQ6EJB7.
SMRiQ6EJB7. Positions 33-111.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi7955.ENSDARP00000070099.

PTM databases

iPTMnetiQ6EJB7.

Proteomic databases

PaxDbiQ6EJB7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSDART00000075617; ENSDARP00000070099; ENSDARG00000053569.
GeneIDi30529.
KEGGidre:30529.

Organism-specific databases

CTDi6658.
ZFINiZDB-GENE-980526-333. sox3.

Phylogenomic databases

eggNOGiENOG410IPZ0. Eukaryota.
ENOG41102MY. LUCA.
GeneTreeiENSGT00760000118988.
HOGENOMiHOG000231647.
HOVERGENiHBG105663.
InParanoidiQ6EJB7.
KOiK09267.
OMAiSANDQDR.
OrthoDBiEOG7TMZVP.
PhylomeDBiQ6EJB7.
TreeFamiTF351735.

Enzyme and pathway databases

ReactomeiR-DRE-3769402. Deactivation of the beta-catenin transactivating complex.

Miscellaneous databases

NextBioi20806912.
PROiQ6EJB7.

Gene expression databases

BgeeiQ6EJB7.
ExpressionAtlasiQ6EJB7. differential.

Family and domain databases

Gene3Di1.10.30.10. 1 hit.
InterProiIPR009071. HMG_box_dom.
IPR029550. SOX-3.
IPR022097. SOX_fam.
[Graphical view]
PANTHERiPTHR10270:SF111. PTHR10270:SF111. 1 hit.
PfamiPF00505. HMG_box. 1 hit.
PF12336. SOXp. 1 hit.
[Graphical view]
SMARTiSM00398. HMG. 1 hit.
[Graphical view]
SUPFAMiSSF47095. SSF47095. 1 hit.
PROSITEiPS50118. HMG_BOX_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Combinatorial Fgf and Bmp signalling patterns the gastrula ectoderm into prospective neural and epidermal domains."
    Kudoh T., Concha M.L., Houart C., Dawid I.B., Wilson S.W.
    Development 131:3581-3592(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], DEVELOPMENTAL STAGE.
  2. "Comparative genomic and expression analysis of group B1 sox genes in zebrafish indicates their diversification during vertebrate evolution."
    Okuda Y., Yoda H., Uchikawa M., Furutani-Seiki M., Takeda H., Kondoh H., Kamachi Y.
    Dev. Dyn. 235:811-825(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DEVELOPMENTAL STAGE.
    Tissue: Embryo1 Publication.
  3. "Danio rerio Sox3 mRNA."
    Shimizu T., Hibi M.
    Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  4. "The zebrafish reference genome sequence and its relationship to the human genome."
    Howe K., Clark M.D., Torroja C.F., Torrance J., Berthelot C., Muffato M., Collins J.E., Humphray S., McLaren K., Matthews L., McLaren S., Sealy I., Caccamo M., Churcher C., Scott C., Barrett J.C., Koch R., Rauch G.J.
    , White S., Chow W., Kilian B., Quintais L.T., Guerra-Assuncao J.A., Zhou Y., Gu Y., Yen J., Vogel J.H., Eyre T., Redmond S., Banerjee R., Chi J., Fu B., Langley E., Maguire S.F., Laird G.K., Lloyd D., Kenyon E., Donaldson S., Sehra H., Almeida-King J., Loveland J., Trevanion S., Jones M., Quail M., Willey D., Hunt A., Burton J., Sims S., McLay K., Plumb B., Davis J., Clee C., Oliver K., Clark R., Riddle C., Eliott D., Threadgold G., Harden G., Ware D., Mortimer B., Kerry G., Heath P., Phillimore B., Tracey A., Corby N., Dunn M., Johnson C., Wood J., Clark S., Pelan S., Griffiths G., Smith M., Glithero R., Howden P., Barker N., Stevens C., Harley J., Holt K., Panagiotidis G., Lovell J., Beasley H., Henderson C., Gordon D., Auger K., Wright D., Collins J., Raisen C., Dyer L., Leung K., Robertson L., Ambridge K., Leongamornlert D., McGuire S., Gilderthorp R., Griffiths C., Manthravadi D., Nichol S., Barker G., Whitehead S., Kay M., Brown J., Murnane C., Gray E., Humphries M., Sycamore N., Barker D., Saunders D., Wallis J., Babbage A., Hammond S., Mashreghi-Mohammadi M., Barr L., Martin S., Wray P., Ellington A., Matthews N., Ellwood M., Woodmansey R., Clark G., Cooper J., Tromans A., Grafham D., Skuce C., Pandian R., Andrews R., Harrison E., Kimberley A., Garnett J., Fosker N., Hall R., Garner P., Kelly D., Bird C., Palmer S., Gehring I., Berger A., Dooley C.M., Ersan-Urun Z., Eser C., Geiger H., Geisler M., Karotki L., Kirn A., Konantz J., Konantz M., Oberlander M., Rudolph-Geiger S., Teucke M., Osoegawa K., Zhu B., Rapp A., Widaa S., Langford C., Yang F., Carter N.P., Harrow J., Ning Z., Herrero J., Searle S.M., Enright A., Geisler R., Plasterk R.H., Lee C., Westerfield M., de Jong P.J., Zon L.I., Postlethwait J.H., Nusslein-Volhard C., Hubbard T.J., Roest Crollius H., Rogers J., Stemple D.L.
    Nature 496:498-503(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Tuebingen.
  5. NIH - Zebrafish Gene Collection (ZGC) project
    Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Tissue: Olfactory epitheliumImported.
  6. "Fgf signaling induces posterior neuroectoderm independently of Bmp signaling inhibition."
    Rentzsch F., Bakkers J., Kramer C., Hammerschmidt M.
    Dev. Dyn. 231:750-757(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: DEVELOPMENTAL STAGE.
  7. "Online automated in vivo zebrafish phosphoproteomics: from large-scale analysis down to a single embryo."
    Lemeer S., Pinkse M.W.H., Mohammed S., van Breukelen B., den Hertog J., Slijper M., Heck A.J.R.
    J. Proteome Res. 7:1555-1564(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-235, IDENTIFICATION BY MASS SPECTROMETRY.
    Tissue: Embryo.

Entry informationi

Entry nameiSOX3_DANRE
AccessioniPrimary (citable) accession number: Q6EJB7
Secondary accession number(s): Q762C1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2006
Last sequence update: August 16, 2004
Last modified: January 20, 2016
This is version 95 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.