Sox2 (SRY-box transcription factor 2) - Rat Genome Database

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Gene: Sox2 (SRY-box transcription factor 2) Rattus norvegicus
Analyze
Symbol: Sox2
Name: SRY-box transcription factor 2
RGD ID: 1565646
Description: 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); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol 3-benzoate; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100912162; LOC499593; RGD1565646; similar to SOX2 protein; SRY (sex determining region Y)-box 2; SRY box 2; SRY-box containing gene 2; transcription factor SOX-2; uncharacterized LOC100912162
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22117,536,929 - 117,539,338 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2117,536,929 - 117,539,338 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2124,123,587 - 124,125,999 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02122,236,249 - 122,238,661 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02116,863,148 - 116,865,560 (+)NCBIRnor_WKY
Rnor_6.02121,165,137 - 121,167,545 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2121,165,137 - 121,167,545 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02140,810,593 - 140,813,001 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42120,969,021 - 120,971,430 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2112,569,723 - 112,572,132 (+)NCBICelera
Cytogenetic Map2q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(20S)-ginsenoside Rg3  (ISO)
(R)-pantothenic acid  (ISO)
(S)-naringenin  (ISO)
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (EXP)
3-methyladenine  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (EXP)
5-fluorouracil  (ISO)
acrylamide  (ISO)
aflatoxin B1  (ISO)
aflatoxin M1  (ISO)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
Aroclor 1254  (EXP)
arotinoid acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
aspartame  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bromochloroacetic acid  (ISO)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium dichloride  (ISO)
cadmium sulfate  (ISO)
carbofuran  (EXP)
carbon atom  (ISO)
carbon nanotube  (ISO)
carboplatin  (ISO)
carvedilol  (EXP,ISO)
celecoxib  (ISO)
CGP 52608  (ISO)
CHIR 99021  (ISO)
chlordecone  (ISO)
chloroprene  (ISO)
chlorpromazine  (ISO)
chromium(6+)  (ISO)
chrysene  (ISO)
ciprofloxacin  (ISO)
cisplatin  (ISO)
Citreoviridin  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (ISO)
colforsin daropate hydrochloride  (ISO)
cortisol  (ISO)
crystal violet  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP,ISO)
deoxycholic acid  (ISO)
dexamethasone  (EXP,ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
eckol  (ISO)
elemental carbon  (ISO)
ethanol  (EXP)
etodolac  (ISO)
etoposide  (ISO)
fluoxetine  (ISO)
flurbiprofen  (ISO)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
genistein  (ISO)
glucose  (ISO)
glycerol 2-phosphate  (ISO)
GS-441524  (ISO)
hexachlorophene  (ISO)
hydroquinone  (ISO)
isoorientin  (ISO)
ivermectin  (ISO)
kaempferol  (ISO)
L-ascorbic acid  (ISO)
L-ascorbic acid 2-phosphate  (ISO)
lapatinib  (ISO)
lead diacetate  (ISO)
lupeol  (ISO)
LY294002  (ISO)
mercury dibromide  (ISO)
methylmercury chloride  (ISO)
methylparaben  (ISO)
miconazole  (ISO)
naphthalene  (ISO)
nickel dichloride  (ISO)
Nonylphenol  (ISO)
ochratoxin A  (EXP)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
paclitaxel  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
parathion  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenylephrine  (EXP)
phenylmercury acetate  (ISO)
poly(I:C)  (ISO)
prostaglandin E2  (ISO)
quercetin  (ISO)
remdesivir  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sterigmatocystin  (EXP)
Tanshinone I  (EXP,ISO)
taurocholic acid  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
Tetrachlorobisphenol A  (ISO)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (ISO)
Triptolide  (ISO)
Tungsten carbide  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vanadyl sulfate  (ISO)
verapamil  (ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
XAV939  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adenohypophysis development  (IEP,ISO)
anatomical structure formation involved in morphogenesis  (ISO)
anatomical structure morphogenesis  (IBA)
cell differentiation  (IBA)
cell fate commitment  (IBA,ISO)
cell fate specification  (ISO)
cellular response to cadmium ion  (ISO)
cerebral cortex development  (ISO)
detection of mechanical stimulus involved in equilibrioception  (ISO)
detection of mechanical stimulus involved in sensory perception of sound  (ISO)
diencephalon morphogenesis  (ISO)
embryonic organ development  (ISO)
endodermal cell fate specification  (ISO)
epithelial tube branching involved in lung morphogenesis  (ISO)
eye development  (ISO)
forebrain development  (IBA,ISO)
forebrain neuron differentiation  (ISO)
gene expression  (ISO)
inner ear development  (IBA,ISO)
inner ear morphogenesis  (ISO)
lens induction in camera-type eye  (ISO)
lung alveolus development  (ISO)
male genitalia development  (ISO)
negative regulation of canonical Wnt signaling pathway  (ISO)
negative regulation of cell cycle G1/S phase transition  (ISO)
negative regulation of cell differentiation  (ISO)
negative regulation of epithelial cell proliferation  (ISO)
negative regulation of neuron differentiation  (ISO)
negative regulation of osteoblast differentiation  (ISO)
negative regulation of transcription by RNA polymerase II  (IBA,ISO)
negative regulation of Wnt signaling pathway  (ISO)
neuroblast proliferation  (ISO)
neuron differentiation  (ISO)
neuron fate commitment  (ISO)
neuronal stem cell population maintenance  (ISO)
Notch signaling pathway  (ISO)
olfactory placode formation  (ISO)
osteoblast differentiation  (ISO)
pigment biosynthetic process  (ISO)
pituitary gland development  (ISO)
positive regulation of cell differentiation  (IMP)
positive regulation of cell-cell adhesion  (IMP)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of epithelial cell differentiation  (ISO)
positive regulation of MAPK cascade  (ISO)
positive regulation of neuroblast proliferation  (ISO)
positive regulation of neuron differentiation  (ISO)
positive regulation of Notch signaling pathway  (ISO)
positive regulation of transcription by RNA polymerase II  (IBA,IDA,ISO)
regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
regulation of DNA-templated transcription  (IBA,ISO)
regulation of gene expression  (ISO)
regulation of neurogenesis  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
response to growth factor  (ISO)
response to organic substance  (ISO)
response to retinoic acid  (ISO)
response to wounding  (ISO)
retina morphogenesis in camera-type eye  (ISO)
sensory perception of sound  (ISO)
somatic stem cell population maintenance  (ISO)
stem cell differentiation  (ISO)
stem cell population maintenance  (ISO)
tissue regeneration  (IEP)
tongue development  (ISO)
trophectodermal cell differentiation  (ISO)
Wnt signaling pathway  (ISO)

Cellular Component

References

References - curated
# Reference Title Reference Citation
1. The detrimental effects of diabetes on pluripotency determined by KLF4, SOX2, C-MYC and OCT4 immunoreactivity in rat testes. Aktug H, etal., Adv Clin Exp Med. 2013 May-Jun;22(3):327-35.
2. Immunohistochemical expression of SOX2 in vulvar intraepithelial neoplasia and squamous cell carcinoma. Brustmann H and Brunner A, Int J Gynecol Pathol. 2013 May;32(3):323-8. doi: 10.1097/PGP.0b013e31825d820e.
3. Sox2 nuclear expression is closely associated with poor prognosis in patients with histologically node-negative oral tongue squamous cell carcinoma. Du L, etal., Oral Oncol. 2011 Aug;47(8):709-13. doi: 10.1016/j.oraloncology.2011.05.017.
4. Mutations in SOX2 cause anophthalmia. Fantes J, etal., Nat Genet. 2003 Apr;33(4):461-3. Epub 2003 Mar 3.
5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Increased SOX2 expression in less differentiated breast carcinomas and their lymph node metastases. Huang YH, etal., Histopathology. 2014 Mar;64(4):494-503. doi: 10.1111/his.12257. Epub 2013 Nov 28.
7. Prognostic impact of the expression of ALDH1 and SOX2 in urothelial cancer of the upper urinary tract. Kitamura H, etal., Mod Pathol. 2013 Jan;26(1):117-24. doi: 10.1038/modpathol.2012.139. Epub 2012 Aug 17.
8. SOX2 and nestin expression in human melanoma: an immunohistochemical and experimental study. Laga AC, etal., Exp Dermatol. 2011 Apr;20(4):339-45. doi: 10.1111/j.1600-0625.2011.01247.x.
9. SOX2 expression is upregulated in adult spinal cord after contusion injury in both oligodendrocyte lineage and ependymal cells. Lee HJ, etal., J Neurosci Res. 2013 Feb;91(2):196-210. doi: 10.1002/jnr.23151. Epub 2012 Nov 21.
10. Sox2 expression in breast tumours and activation in breast cancer stem cells. Leis O, etal., Oncogene. 2012 Mar 15;31(11):1354-65. doi: 10.1038/onc.2011.338. Epub 2011 Aug 8.
11. Identification of key genes and pathways associated with cholangiocarcinoma development based on weighted gene correlation network analysis. Liu J, etal., PeerJ. 2019 Oct 31;7:e7968. doi: 10.7717/peerj.7968. eCollection 2019.
12. Novel SOX2 partner-factor domain mutation in a four-generation family. Mihelec M, etal., Eur J Hum Genet. 2009 Nov;17(11):1417-22. doi: 10.1038/ejhg.2009.79. Epub 2009 May 27.
13. A role for SOX2 in the generation of microtubule-associated protein 2-positive cells from microglia. Nonaka H, etal., Biochem Biophys Res Commun. 2009 Feb 27;380(1):60-4. doi: 10.1016/j.bbrc.2009.01.027. Epub 2009 Jan 20.
14. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
15. EphB signaling directs peripheral nerve regeneration through Sox2-dependent Schwann cell sorting. Parrinello S, etal., Cell. 2010 Oct 1;143(1):145-55. doi: 10.1016/j.cell.2010.08.039.
16. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
18. Comprehensive gene review and curation RGD comprehensive gene curation
19. Novel SOX2 mutations and genotype-phenotype correlation in anophthalmia and microphthalmia. Schneider A, etal., Am J Med Genet A. 2009 Dec;149A(12):2706-15. doi: 10.1002/ajmg.a.33098.
20. Sex determining region Y-box 2 (SOX2) amplification is an independent indicator of disease recurrence in sinonasal cancer. Schrock A, etal., PLoS One. 2013;8(3):e59201. doi: 10.1371/journal.pone.0059201. Epub 2013 Mar 27.
21. Expression and role of Oct3/4, Nanog and Sox2 in regeneration of rat tracheal epithelium. Song N, etal., Cell Prolif. 2010 Feb;43(1):49-55. doi: 10.1111/j.1365-2184.2009.00653.x. Epub 2009 Oct 21.
22. Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer. Stolzenburg S, etal., Nucleic Acids Res. 2012 Aug;40(14):6725-40. Epub 2012 May 4.
23. SOX2 autoantibodies as noninvasive serum biomarker for breast carcinoma. Sun Y, etal., Cancer Epidemiol Biomarkers Prev. 2012 Nov;21(11):2043-7. doi: 10.1158/1055-9965.EPI-12-0498. Epub 2012 Jul 25.
24. Identification of novel domains within Sox-2 and Sox-11 involved in autoinhibition of DNA binding and partnership specificity. Wiebe MS, etal., J Biol Chem. 2003 May 16;278(20):17901-11. Epub 2003 Mar 10.
25. Significant quantitative and qualitative transition in pituitary stem / progenitor cells occurs during the postnatal development of the rat anterior pituitary. Yoshida S, etal., J Neuroendocrinol. 2011 Oct;23(10):933-43. doi: 10.1111/j.1365-2826.2011.02198.x.
Additional References at PubMed
PMID:7590241   PMID:7628452   PMID:8625802   PMID:9512512   PMID:9649510   PMID:9669521   PMID:9851841   PMID:12036291   PMID:12514105   PMID:12665572   PMID:15082719   PMID:15240551  
PMID:15781477   PMID:15846349   PMID:15863505   PMID:15959507   PMID:15988017   PMID:16153702   PMID:16631155   PMID:16651659   PMID:16767105   PMID:16932809   PMID:17015430   PMID:17097055  
PMID:17140559   PMID:17291498   PMID:17507372   PMID:17522155   PMID:17875931   PMID:17982423   PMID:18000303   PMID:18027866   PMID:18187129   PMID:18268498   PMID:18285410   PMID:18287078  
PMID:18374910   PMID:18388306   PMID:18400104   PMID:18407919   PMID:18448678   PMID:18710938   PMID:19328208   PMID:19409607   PMID:19427902   PMID:19442651   PMID:19490090   PMID:19736317  
PMID:19796622   PMID:19816951   PMID:20123909   PMID:20531390   PMID:20713518   PMID:20720539   PMID:20852734   PMID:21028992   PMID:21076177   PMID:21245162   PMID:21300049   PMID:21928068  
PMID:22194602   PMID:22198669   PMID:22232070   PMID:22344693   PMID:22513373   PMID:22992956   PMID:23056351   PMID:23169531   PMID:23284756   PMID:23447615   PMID:23644741   PMID:24036311  
PMID:24191021   PMID:24268575   PMID:24427323   PMID:24718042   PMID:25335925   PMID:25535395   PMID:25901318   PMID:26116536   PMID:26290228   PMID:26607632   PMID:26640231   PMID:26691508  
PMID:27096226   PMID:27221278   PMID:28623139   PMID:29110214   PMID:29208635   PMID:29253717   PMID:29764313   PMID:30270540   PMID:32029747   PMID:32152663   PMID:33208157   PMID:33603338  
PMID:33843023   PMID:34521353  


Genomics

Comparative Map Data
Sox2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22117,536,929 - 117,539,338 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2117,536,929 - 117,539,338 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2124,123,587 - 124,125,999 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02122,236,249 - 122,238,661 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02116,863,148 - 116,865,560 (+)NCBIRnor_WKY
Rnor_6.02121,165,137 - 121,167,545 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2121,165,137 - 121,167,545 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02140,810,593 - 140,813,001 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42120,969,021 - 120,971,430 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2112,569,723 - 112,572,132 (+)NCBICelera
Cytogenetic Map2q24NCBI
SOX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383181,711,925 - 181,714,436 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl3181,711,925 - 181,714,436 (+)EnsemblGRCh38hg38GRCh38
GRCh373181,429,713 - 181,432,224 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363182,912,416 - 182,914,918 (+)NCBINCBI36Build 36hg18NCBI36
Build 343182,912,423 - 182,914,923NCBI
Celera3179,863,407 - 179,865,909 (+)NCBICelera
Cytogenetic Map3q26.33NCBI
HuRef3178,834,536 - 178,837,048 (+)NCBIHuRef
CHM1_13181,392,587 - 181,395,099 (+)NCBICHM1_1
T2T-CHM13v2.03184,516,501 - 184,519,012 (+)NCBIT2T-CHM13v2.0
Sox2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39334,704,144 - 34,706,610 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl334,704,554 - 34,706,610 (+)EnsemblGRCm39 Ensembl
GRCm38334,649,995 - 34,652,461 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl334,650,405 - 34,652,461 (+)EnsemblGRCm38mm10GRCm38
MGSCv37334,548,927 - 34,551,383 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36334,841,604 - 34,844,008 (+)NCBIMGSCv36mm8
Celera334,551,711 - 34,554,169 (+)NCBICelera
Cytogenetic Map3A3NCBI
cM Map316.93NCBI
Sox2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542010,671,978 - 10,672,934 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542010,671,888 - 10,674,080 (+)NCBIChiLan1.0ChiLan1.0
SOX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13186,922,223 - 186,924,785 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3186,922,705 - 186,923,662 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03178,744,881 - 178,747,392 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SOX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13414,853,000 - 14,855,153 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3418,934,171 - 18,936,303 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03414,755,806 - 14,757,946 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.13414,797,347 - 14,799,478 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03414,782,119 - 14,784,242 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03415,026,650 - 15,028,779 (+)NCBIUU_Cfam_GSD_1.0
Sox2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602111,588,129 - 111,590,044 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365661,631,822 - 1,632,613 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049365661,630,698 - 1,632,607 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13119,668,476 - 119,669,435 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113119,668,476 - 119,669,435 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213128,979,657 - 128,980,616 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap13q23-q41NCBI
SOX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1157,673,581 - 7,676,812 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl157,674,867 - 7,675,826 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606316,496,978 - 16,500,141 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sox2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473059,570,915 - 59,571,871 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473059,570,879 - 59,573,001 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sox2
7 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:260
Count of miRNA genes:184
Interacting mature miRNAs:201
Transcripts:ENSRNOT00000016236
Prediction methods:Microtar, Miranda
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
2293835Kiddil5Kidney dilation QTL 53.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607157142209Rat
2293843Kiddil6Kidney dilation QTL 63.1kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)242804607182042367Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1558648Smcn1Smooth muscle cell number QTL 10.039blood vessel smooth muscle cell quantity (VT:0010525)aorta smooth muscle cell count per unit vessel length (CMO:0001646)259134147127460910Rat
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1558653Prcr1Prostate cancer resistance QTL 15prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)272532993157142209Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)276539322150540526Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)278665616143657569Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)280270434125270434Rat
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)281018907126018907Rat
8662832Vetf7Vascular elastic tissue fragility QTL 73.5aorta elastin amount (VT:0003905)aorta wall extracellular elastin dry weight to aorta wall dry weight ratio (CMO:0002002)281689826221035911Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
1578772Stresp14Stress response QTL 1450.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)282345893130923501Rat
7207808Bmd89Bone mineral density QTL 894.1femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)288862519133862519Rat
2300165Bmd49Bone mineral density QTL 494.80.0001lumbar vertebra mineral mass (VT:0010511)bone mineral density (CMO:0001226)288862519133862519Rat
2300170Bmd45Bone mineral density QTL 4512.10.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
2300185Bmd46Bone mineral density QTL 468.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)288862519133862519Rat
1598862Glom9Glomerulus QTL 93.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)292337601137337601Rat
1598863Cm65Cardiac mass QTL 652.3heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)292337601137337601Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2102803808147803808Rat
8662836Vetf8Vascular elastic tissue fragility QTL 80.66thoracic aorta molecular composition trait (VT:0010568)aorta wall extracellular elastin dry weight to aorta wall extracellular collagen weight ratio (CMO:0002003)2104559726149559726Rat
1581552Pur12Proteinuria QTL 125.190.0009urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)2112103657148076632Rat
631507Bp105Blood pressure QTL 1050.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2112456140212696837Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1354594Despr10Despair related QTL 100.00000249locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)2114654253159654253Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527143657569Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527143657569Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat

Markers in Region
X94127  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22117,538,619 - 117,538,805 (+)MAPPERmRatBN7.2
Rnor_6.02121,166,827 - 121,167,012NCBIRnor6.0
Rnor_5.02140,812,283 - 140,812,468UniSTSRnor5.0
RGSC_v3.42120,970,712 - 120,970,897UniSTSRGSC3.4
Celera2112,571,414 - 112,571,599UniSTS
Cytogenetic Map2q25UniSTS
Sox2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22117,537,291 - 117,538,251 (+)MAPPERmRatBN7.2
Rnor_6.02121,165,500 - 121,166,459NCBIRnor6.0
Rnor_5.02140,810,956 - 140,811,915UniSTSRnor5.0
RGSC_v3.42120,969,384 - 120,970,343UniSTSRGSC3.4
Celera2112,570,086 - 112,571,045UniSTS
Cytogenetic Map2q25UniSTS
UniSTS:471104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22117,537,666 - 117,538,078 (+)MAPPERmRatBN7.2
Rnor_6.02121,165,875 - 121,166,286NCBIRnor6.0
Rnor_5.02140,811,331 - 140,811,742UniSTSRnor5.0
RGSC_v3.42120,969,759 - 120,970,170UniSTSRGSC3.4
Celera2112,570,461 - 112,570,872UniSTS
Cytogenetic Map2q25UniSTS
PMC304100P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22117,537,871 - 117,537,993 (+)MAPPERmRatBN7.2
Rnor_6.02121,166,080 - 121,166,201NCBIRnor6.0
Rnor_5.02140,811,536 - 140,811,657UniSTSRnor5.0
RGSC_v3.42120,969,964 - 120,970,085UniSTSRGSC3.4
Celera2112,570,666 - 112,570,787UniSTS
Cytogenetic Map2q25UniSTS
Sox2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22117,538,991 - 117,539,176 (+)MAPPERmRatBN7.2
Rnor_6.02121,167,199 - 121,167,383NCBIRnor6.0
Rnor_5.02140,812,655 - 140,812,839UniSTSRnor5.0
RGSC_v3.42120,971,084 - 120,971,268UniSTSRGSC3.4
Celera2112,571,786 - 112,571,970UniSTS
Cytogenetic Map2q25UniSTS
Sox2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22117,538,902 - 117,539,232 (+)MAPPERmRatBN7.2
Rnor_6.02121,167,110 - 121,167,439NCBIRnor6.0
Rnor_5.02140,812,566 - 140,812,895UniSTSRnor5.0
RGSC_v3.42120,970,995 - 120,971,324UniSTSRGSC3.4
Celera2112,571,697 - 112,572,026UniSTS
Cytogenetic Map2q25UniSTS
Sox2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22117,537,481 - 117,537,685 (+)MAPPERmRatBN7.2
Rnor_6.02121,165,690 - 121,165,893NCBIRnor6.0
Rnor_5.02140,811,146 - 140,811,349UniSTSRnor5.0
RGSC_v3.42120,969,574 - 120,969,777UniSTSRGSC3.4
Celera2112,570,276 - 112,570,479UniSTS
Cytogenetic Map2q25UniSTS
Sox2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22117,537,801 - 117,537,932 (+)MAPPERmRatBN7.2
Rnor_6.02121,166,010 - 121,166,140NCBIRnor6.0
Rnor_5.02140,811,466 - 140,811,596UniSTSRnor5.0
RGSC_v3.42120,969,894 - 120,970,024UniSTSRGSC3.4
Celera2112,570,596 - 112,570,726UniSTS
Cytogenetic Map2q25UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 74 5
Low 1 4 4 4 4 12 11
Below cutoff 2 23 18 4 13 4 8 9 16 19 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000016236   ⟹   ENSRNOP00000016236
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2117,536,929 - 117,539,338 (+)Ensembl
Rnor_6.0 Ensembl2121,165,137 - 121,167,545 (+)Ensembl
RefSeq Acc Id: NM_001109181   ⟹   NP_001102651
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22117,536,929 - 117,539,338 (+)NCBI
Rnor_6.02121,165,137 - 121,167,545 (+)NCBI
Rnor_5.02140,810,593 - 140,813,001 (+)NCBI
RGSC_v3.42120,969,021 - 120,971,430 (+)RGD
Celera2112,569,723 - 112,572,132 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102651 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM01248 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102651   ⟸   NM_001109181
- UniProtKB: D4A543 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000016236   ⟸   ENSRNOT00000016236
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A543-F1-model_v2 AlphaFold D4A543 1-319 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565646 AgrOrtholog
BioCyc Gene G2FUF-53364 BioCyc
Ensembl Genes ENSRNOG00000012199 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016236 ENTREZGENE
  ENSRNOP00000016236.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016236 ENTREZGENE
  ENSRNOT00000016236.4 UniProtKB/TrEMBL
Gene3D-CATH 1.10.30.10 UniProtKB/TrEMBL
InterPro HMG_box_dom_sf UniProtKB/TrEMBL
  HMG_superfamily UniProtKB/TrEMBL
  SOX-2 UniProtKB/TrEMBL
  TF_SOX UniProtKB/TrEMBL
KEGG Report rno:499593 UniProtKB/TrEMBL
NCBI Gene 499593 ENTREZGENE
PANTHER PTHR10270:SF231 UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/TrEMBL
  SOXp UniProtKB/TrEMBL
PhenoGen Sox2 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/TrEMBL
SMART HMG UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL
UniProt D4A543 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Sox2  SRY-box transcription factor 2  Sox2  SRY box 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Sox2  SRY box 2  Sox2  SRY (sex determining region Y)-box 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-07-29 Sox2  SRY (sex determining region Y)-box 2  LOC100912162  uncharacterized LOC100912162  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100912162  uncharacterized LOC100912162      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-09-18 Sox2  SRY (sex determining region Y)-box 2  Sox2  SRY-box containing gene 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Sox2  SRY-box containing gene 2  RGD1565646_predicted  similar to SOX2 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1565646_predicted  similar to SOX2 protein (predicted)  LOC499593  similar to SOX2 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC499593  similar to SOX2 protein      Symbol and Name status set to provisional 70820 PROVISIONAL