Sox2 SRY-box transcription factor 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Sox2provided by RGD
Official Full Name: SRY-box transcription factor 2provided by RGD
Primary source: RGD:1565646
See related: Ensembl:ENSRNOG00000012199 AllianceGenome:RGD:1565646
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: RGD1565646
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and transcription cis-regulatory region binding activity. Involved in several processes, including adenohypophysis development; positive regulation of transcription by RNA polymerase II; and tissue regeneration. Located in nucleus. 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]
Expression: Biased expression in Brain (RPKM 93.0) and Lung (RPKM 9.9) See more
Orthologs: human mouse all
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Genomic context

Location:: 2q24

Exon count:: 1

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	2	NC_086020.1 (119465131..119467542)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	2	NC_051337.1 (117536929..117539340)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	2	NC_005101.4 (121165137..121167545)

Chromosome 2 - NC_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Fluctuation of CD9/SOX2-positive cell populations during the turnover of GH- and TSH-producing cells in the adult anterior pituitary gland.
Title: Fluctuation of CD9/SOX2-positive cell populations during the turnover of GH- and TSH-producing cells in the adult anterior pituitary gland.
Silencing of long non-coding RNA SOX2-overlapping transcript relieves myocardial ischemia/reperfusion injury through up-regulating miRNA-146a-5p.
Title: Silencing of long non-coding RNA SOX2-overlapping transcript relieves myocardial ischemia/reperfusion injury through up-regulating miRNA-146a-5p.
Depleting SOX2 improves ischemic stroke via lncRNA PVT1/microRNA-24-3p/STAT3 axis.
Title: Depleting SOX2 improves ischemic stroke via lncRNA PVT1/microRNA-24-3p/STAT3 axis.
Chlorpromazine affects the numbers of Sox-2, Musashi1 and DCX-expressing cells in the rat brain subventricular zone.
Title: Chlorpromazine affects the numbers of Sox-2, Musashi1 and DCX-expressing cells in the rat brain subventricular zone.
Long Noncoding RNA SOX2-OT Aggravates Doxorubicin-Induced Apoptosis of Cardiomyocyte by Targeting miR-942-5p/DP5.
Title: Long Noncoding RNA SOX2-OT Aggravates Doxorubicin-Induced Apoptosis of Cardiomyocyte by Targeting miR-942-5p/DP5.
ROBO2 signaling in lung development regulates SOX2/SOX9 balance, branching morphogenesis and is dysregulated in nitrofen-induced congenital diaphragmatic hernia.
Title: ROBO2 signaling in lung development regulates SOX2/SOX9 balance, branching morphogenesis and is dysregulated in nitrofen-induced congenital diaphragmatic hernia.
CX3CL1/CX3CR1-signalling in the CD9/S100beta/SOX2-positive adult pituitary stem/progenitor cells modulates differentiation into endothelial cells.
Title: CX3CL1/CX3CR1-signalling in the CD9/S100β/SOX2-positive adult pituitary stem/progenitor cells modulates differentiation into endothelial cells.
Sox2 controls Schwann cell self-organization through fibronectin fibrillogenesis.
Title: Sox2 controls Schwann cell self-organization through fibronectin fibrillogenesis.
AKT pathway was activated by SOX2 overexpression. Mitochondrial oxidative stress and energy production were increased by SOX2 overexpression. SOX2 activation promotes wound healing and regeneration in CECs.
Title: SOX2 Activation Using CRISPR/dCas9 Promotes Wound Healing in Corneal Endothelial Cells.
Studied effect of 2,5-Hexanedione on hippocampal Sox2+ cells; found 2,5-Hexanedione increases the percentage of proliferative Sox2+ cells in the hippocampal granule cell layer and subgranular zone.
Title: 2,5-Hexanedione increases the percentage of proliferative Sox2(+) cells in rat hippocampus.

Submit: New GeneRIF Correction See all GeneRIFs (29)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Sox2 (e-PCR), detects polymorphism
- UniSTS:516866

UniSTS:471104 (e-PCR)
- UniSTS:471104

Sox2 (e-PCR), detects polymorphism
- UniSTS:471104

Sox2 (e-PCR), detects polymorphism
- UniSTS:547912

Sox2 (e-PCR), detects polymorphism
- UniSTS:474706

Sox2 (e-PCR), detects polymorphism
- UniSTS:144487

Sox2 (e-PCR), detects polymorphism
- UniSTS:508019

PMC304100P2 (e-PCR)
- UniSTS:272527

Sox2 (e-PCR), detects polymorphism
- UniSTS:499114

X94127 (e-PCR)
- UniSTS:125893

Sox2 (e-PCR), detects polymorphism
- UniSTS:548082

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA binding	ISO Inferred from Sequence Orthology 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 factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables miRNA binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of Notch signaling pathway	ISO Inferred from Sequence Orthology more info
acts_upstream_of Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in adenohypophysis development	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within adenohypophysis development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within anatomical structure formation involved in morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell fate commitment	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell fate specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to cadmium ion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cerebral cortex development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within detection of mechanical stimulus involved in equilibrioception	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within detection of mechanical stimulus involved in sensory perception of sound	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within diencephalon morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic organ development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within endodermal cell fate specification	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epithelial tube branching involved in lung morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in eye development	ISO Inferred from Sequence Orthology more info
involved_in forebrain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in forebrain development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within forebrain neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in gene expression	ISO Inferred from Sequence Orthology more info
involved_in inner ear development	IBA Inferred from Biological aspect of Ancestor more info
involved_in inner ear development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lens induction in camera-type eye	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within lung alveolus development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within male genitalia development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell cycle G1/S phase transition	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of epithelial cell proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within negative regulation of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of neuroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of neuron differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron fate commitment	ISO Inferred from Sequence Orthology more info
involved_in neuronal stem cell population maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within olfactory placode formation	ISO Inferred from Sequence Orthology more info
acts_upstream_of osteoblast differentiation	ISO Inferred from Sequence Orthology more info
involved_in osteoblast differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pigment biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in pituitary gland development	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of MAPK cascade	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of Notch signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell-cell adhesion	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of epithelial cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of neuroblast proliferation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in regulation of myofibroblast cell apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in response to growth factor	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to organic substance	ISO Inferred from Sequence Orthology more info
involved_in response to oxygen-glucose deprivation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to retinoic acid	ISO Inferred from Sequence Orthology more info
involved_in response to wounding	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within retina morphogenesis in camera-type eye	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sensory perception of sound	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within somatic stem cell population maintenance	ISO Inferred from Sequence Orthology more info
involved_in somatic stem cell population maintenance	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within stem cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in stem cell population maintenance	ISO Inferred from Sequence Orthology more info
involved_in tissue regeneration	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within tongue development	ISO Inferred from Sequence Orthology more info
acts_upstream_of trophectodermal cell differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of chromatin	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription regulator complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: transcription factor SOX-2

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

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_001109181.2 → NP_001102651.1 transcription factor SOX-2

See identical proteins and their annotated locations for NP_001102651.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000002

UniProtKB/TrEMBL

A6IHU9, D4A543

Related

ENSRNOP00000016236.2, ENSRNOT00000016236.4

Conserved Domains (2) summary

cd01388
Location:42 → 113

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 vertebrates, and ...

pfam12336
Location:112 → 202

SOXp; SOX transcription factor