sox3 SRY-box transcription factor 3 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sox3provided by ZNC
Official Full Name: SRY-box transcription factor 3provided by ZNC
Primary source: ZFIN:ZDB-GENE-980526-333
See related: Ensembl:ENSDARG00000053569 AllianceGenome:ZFIN:ZDB-GENE-980526-333
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: sb:cb493; id:ibd2036; wu:fd02a08; zgc:110279
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific. Contributes to DNA-binding transcription factor activity. Involved in regulation of transcription by RNA polymerase II. Acts upstream of or within several processes, including nervous system development; otic placode development; and otic placode formation. Predicted to be active in nucleus. Is expressed in several structures, including ectoderm; nervous system; neural keel; neural tube; and presumptive structure. Human ortholog(s) of this gene implicated in X-linked panhypopituitarism. Orthologous to human SOX3 (SRY-box transcription factor 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: chromosome: 14

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	14	NC_007125.7 (32742701..32744464, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	14	NC_007125.6 (32402387..32404150, complement)

Chromosome 14 - NC_007125.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The authors showed Sox3 functions as a regulator of Cyp19a1a expression, via 17beta-E2 linking apoptosis suppression, which is implicated in improving female fecundity.
Title: Loss-of-function of sox3 causes follicle development retardation and reduces fecundity in zebrafish.
these data show that sox2 and sox3 exhibit intrinsic differences in promoting sensory vs. neural competence, but at high levels these factors can mimic each other to enhance both states. Regional cofactors like pax2a and fgf8 also modify sox2/3 functions.
Title: sox2 and sox3 Play unique roles in development of hair cells and neurons in the zebrafish inner ear.
these findings show that sox2 and sox3 are together required for proper otic induction, but the level of expression must be tightly regulated to avoid suppression of differentiation and maintenance of pluripotency.
Title: sox2 and sox3 cooperate to regulate otic/epibranchial placode induction in zebrafish.
significant decreases in sox3 (up to 3-fold) expression following chilling. Significant increases in expression of sox3 (up to 33-fold) during warming of chilled zebrafish embyos.
Title: Effect of chilling on sox2, sox3 and sox19a gene expression in zebrafish (Danio rerio) embryos.
Knockdown of fgf24 or sox3 causes severe epibranchial deficiencies but has little effect on otic development
Title: Pax2/8 proteins coordinate sequential induction of otic and epibranchial placodes through differential regulation of foxi1, sox3 and fgf24.
Knockdown of the four B1 sox genes sox2/3/19a/19b resulted in severe developmental abnormalities.
Title: B1 SOX coordinate cell specification with patterning and morphogenesis in the early zebrafish embryo.
The pro-neural effects of Sox3 can compensate for inhibition of fibroblast growth factor (Fgf) signalling in inducing neural tissue but it is not sufficient to maintain neural fate, suggesting the presence of Sox3-independent roles of Fgf at later stages.
Title: Sox3 regulates both neural fate and differentiation in the zebrafish ectoderm.

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General gene information

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Markers

fd02a08.x1 (e-PCR)
- UniSTS:194859

PMC304098P3 (e-PCR)
- UniSTS:272522

fb98e04.x1 (e-PCR)
- UniSTS:191971

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IPI Inferred from Physical Interaction more info	PubMed
contributes_to DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within central nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic placode development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic placode formation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within otic placode formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of ovarian follicle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peripheral nervous system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within peripheral nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: transcription factor Sox-3

Names: SRY (sex determining region Y)-box 3; SRY-box containing gene 3; transcription factor SOX3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001001811.2 → NP_001001811.2 transcription factor Sox-3

See identical proteins and their annotated locations for NP_001001811.2

Status: PROVISIONAL

Source sequence(s)

BC092845

UniProtKB/Swiss-Prot

Q6EJB7, Q762C1

UniProtKB/TrEMBL

A9JSZ3

Related

ENSDARP00000070099.3, ENSDART00000075617.5

Conserved Domains (2) summary

cd01388
Location:34 → 105

SOX-TCF_HMG-box; SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and ...

pfam12336
Location:104 → 182

SOXp; SOX transcription factor