sox2 SRY-box transcription factor 2 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: sox2provided by ZNC
Official Full Name: SRY-box transcription factor 2provided by ZNC
Primary source: ZFIN:ZDB-GENE-030909-1
See related: Ensembl:ENSDARG00000070913 AllianceGenome:ZFIN:ZDB-GENE-030909-1
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: soxp; cb236; zgc:65860; zgc:77389; wu:fb83g04; wu:fc14d07
Summary: Enables chromatin binding activity and sequence-specific DNA binding activity. Contributes to DNA-binding transcription factor activity. Acts upstream of or within several processes, including animal organ development; fin regeneration; and otic placode development. Predicted to be located in cytoplasm and nucleus. Predicted to be part of transcription regulator complex. Is expressed in several structures, including immature eye; nervous system; neural keel; neural rod; and presumptive structure. Human ortholog(s) of this gene implicated in breast cancer; nasal cavity cancer; and syndromic microphthalmia 3. Orthologous to human SOX2 (SRY-box transcription factor 2). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 22

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	22	NC_007133.7 (37347893..37349978, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	22	NC_007133.6 (37412975..37415060, complement)

Chromosome 22 - NC_007133.7 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?

Specific Activation of Yamanaka Factors via HSF1 Signaling in the Early Stage of Zebrafish Optic Nerve Regeneration.
Title: Specific Activation of Yamanaka Factors via HSF1 Signaling in the Early Stage of Zebrafish Optic Nerve Regeneration.
Zebrafish sox2 Is Required for the Swim Bladder Inflation by Controlling the Swim-Up Behavior.
Title: Zebrafish sox2 Is Required for the Swim Bladder Inflation by Controlling the Swim-Up Behavior.
Sox2 expression in the visual system of two teleost species.
Title: Sox2 expression in the visual system of two teleost species.
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.
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.
Findings indicate a pivotal role for ZNF32 function in SOX2 expression and regeneration regulation.
Title: Loss of ZNF32 augments the regeneration of nervous lateral line system through negative regulation of SOX2 transcription.
Both sox2 and p27kip are regulated by the retinoic acid signal pathway and are essential for hair cell regeneration.
Title: Retinoic Acid Signaling Mediates Hair Cell Regeneration by Repressing p27kip and sox2 in Supporting Cells.
a role of Sox2 as one of the proliferation initiators in ependymal cells after spinal cord injury
Title: Function of Sox2 in ependymal cells of lesioned spinal cords in adult zebrafish.
Sox2 is identified as the unknown factor responsible for pineal photoreceptor prepatterning and performs this function independently of the BMP signaling.
Title: Pleiotropic effects of Sox2 during the development of the zebrafish epithalamus.
By western blot three protein bands of 28 kDa, 34 kDa (main band), and 38 kDa were detected in the brain of animals 180 days post-fertilizaton.
Title: Developmental changes in the expression of Sox2 in the zebrafish brain.

Submit: New GeneRIF Correction See all GeneRIFs (16)

General gene information

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Markers

fc14d07.x1 (e-PCR)
- UniSTS:203810

AI584301 (e-PCR)
- UniSTS:206250

fb83g04.x1 (e-PCR)
- UniSTS:187646

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
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
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epithalamus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within eye morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within fin regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in forebrain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in inner ear development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within inner ear receptor cell development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within inner ear receptor cell 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 otic placode development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otic vesicle development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pineal gland 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 regeneration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of motor neuron axon guidance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within spinal cord motor neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of transcription regulator complex	IC Inferred by Curator more info	PubMed

General protein information

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Preferred Names: transcription factor Sox-2

Names: SRY (sex determining region Y)-box 2; SRY-box containing gene 2; transcription factor SOX2

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_213118.1 → NP_998283.1 transcription factor Sox-2

See identical proteins and their annotated locations for NP_998283.1

Status: PROVISIONAL

Source sequence(s)

BC065656

UniProtKB/Swiss-Prot

Q6P0E1

Related

ENSDARP00000095266.3, ENSDART00000104493.5

Conserved Domains (2) summary

cd01388
Location:37 → 108

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:107 → 197

SOXp; SOX transcription factor