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
Also 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 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2117,536,929 - 117,539,338 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
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)
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)
all-trans-retinoic acid  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
antirheumatic drug  (ISO)
apigenin  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (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)
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)
crystal violet  (ISO)
Cuprizon  (EXP)
curcumin  (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)
fluoxetine  (ISO)
flurbiprofen  (ISO)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
gemcitabine  (ISO)
genistein  (ISO)
glycerol 2-phosphate  (ISO)
hexachlorophene  (ISO)
hydroquinone  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (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)
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)
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)
Tanshinone I  (EXP,ISO)
taurocholic acid  (ISO)
temozolomide  (ISO)
terbufos  (ISO)
Tetrachlorobisphenol A  (ISO)
titanium dioxide  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
Triptolide  (ISO)
Tungsten carbide  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vanadyl sulfate  (ISO)
vinclozolin  (EXP)
vorinostat  (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)
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 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)
neuron fate commitment  (ISO)
neuronal stem cell population maintenance  (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 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)
positive regulation of transcription, DNA-templated  (ISO)
regulation of cell cycle  (ISO)
regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
regulation of gene expression  (ISO)
regulation of neurogenesis  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
regulation of transcription, DNA-templated  (IBA,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)

Cellular Component

References

References - curated
1. Aktug H, etal., Adv Clin Exp Med. 2013 May-Jun;22(3):327-35.
2. Brustmann H and Brunner A, Int J Gynecol Pathol. 2013 May;32(3):323-8. doi: 10.1097/PGP.0b013e31825d820e.
3. Du L, etal., Oral Oncol. 2011 Aug;47(8):709-13. doi: 10.1016/j.oraloncology.2011.05.017.
4. Fantes J, etal., Nat Genet. 2003 Apr;33(4):461-3. Epub 2003 Mar 3.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Huang YH, etal., Histopathology. 2014 Mar;64(4):494-503. doi: 10.1111/his.12257. Epub 2013 Nov 28.
7. Kitamura H, etal., Mod Pathol. 2013 Jan;26(1):117-24. doi: 10.1038/modpathol.2012.139. Epub 2012 Aug 17.
8. Laga AC, etal., Exp Dermatol. 2011 Apr;20(4):339-45. doi: 10.1111/j.1600-0625.2011.01247.x.
9. Lee HJ, etal., J Neurosci Res. 2013 Feb;91(2):196-210. doi: 10.1002/jnr.23151. Epub 2012 Nov 21.
10. Leis O, etal., Oncogene. 2012 Mar 15;31(11):1354-65. doi: 10.1038/onc.2011.338. Epub 2011 Aug 8.
11. Mihelec M, etal., Eur J Hum Genet. 2009 Nov;17(11):1417-22. doi: 10.1038/ejhg.2009.79. Epub 2009 May 27.
12. 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.
13. OMIM Disease Annotation Pipeline
14. Parrinello S, etal., Cell. 2010 Oct 1;143(1):145-55. doi: 10.1016/j.cell.2010.08.039.
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. RGD comprehensive gene curation
18. Schneider A, etal., Am J Med Genet A. 2009 Dec;149A(12):2706-15. doi: 10.1002/ajmg.a.33098.
19. Schrock A, etal., PLoS One. 2013;8(3):e59201. doi: 10.1371/journal.pone.0059201. Epub 2013 Mar 27.
20. Song N, etal., Cell Prolif. 2010 Feb;43(1):49-55. doi: 10.1111/j.1365-2184.2009.00653.x. Epub 2009 Oct 21.
21. Stolzenburg S, etal., Nucleic Acids Res. 2012 Aug;40(14):6725-40. Epub 2012 May 4.
22. 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.
23. Wiebe MS, etal., J Biol Chem. 2003 May 16;278(20):17901-11. Epub 2003 Mar 10.
24. 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  


Genomics

Comparative Map Data
Sox2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22117,536,929 - 117,539,338 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl2117,536,929 - 117,539,338 (+)Ensembl
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 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2112,569,723 - 112,572,132 (+)NCBICelera
Cytogenetic Map2q24NCBI
SOX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3181,711,925 - 181,714,436 (+)EnsemblGRCh38hg38GRCh38
GRCh383181,711,925 - 181,714,436 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh373181,429,713 - 181,432,224 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363182,912,416 - 182,914,918 (+)NCBINCBI36hg18NCBI36
Build 343182,912,423 - 182,914,923NCBI
Celera3179,863,407 - 179,865,909 (+)NCBI
Cytogenetic Map3q26.33NCBI
HuRef3178,834,536 - 178,837,048 (+)NCBIHuRef
CHM1_13181,392,587 - 181,395,099 (+)NCBICHM1_1
Sox2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39334,704,144 - 34,706,610 (+)NCBIGRCm39mm39
GRCm39 Ensembl334,704,554 - 34,706,610 (+)Ensembl
GRCm38334,649,995 - 34,652,461 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl334,650,405 - 34,652,461 (+)EnsemblGRCm38mm10GRCm38
MGSCv37334,548,927 - 34,551,383 (+)NCBIGRCm37mm9NCBIm37
MGSCv36334,841,604 - 34,844,008 (+)NCBImm8
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_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 (+)NCBI
ROS_Cfam_1.03414,755,806 - 14,757,946 (+)NCBI
UMICH_Zoey_3.13414,797,347 - 14,799,478 (+)NCBI
UNSW_CanFamBas_1.03414,782,119 - 14,784,242 (+)NCBI
UU_Cfam_GSD_1.03415,026,650 - 15,028,779 (+)NCBI
Sox2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602111,588,129 - 111,590,044 (+)NCBI
SpeTri2.0NW_0049365661,630,698 - 1,632,607 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)NCBI
ChlSab1.1 Ensembl157,674,867 - 7,675,826 (-)Ensembl
Vero_WHO_p1.0NW_02366606316,496,978 - 16,500,141 (-)NCBI
Sox2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473059,570,879 - 59,573,001 (+)NCBI

Position Markers
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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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
61438Cia7Collagen induced arthritis QTL 74.60.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)259324377141596857Rat
631198Cm22Cardiac mass QTL 224.30.0008heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)276539322150540526Rat
631266Bp132Blood pressure QTL 1320.0005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)246123260202447032Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)243154682202446871Rat
61467Bp14Blood pressure QTL 142.2arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)243154682202446871Rat
724534Uae6Urinary albumin excretion QTL 610urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)278665619249053267Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)256043031202447032Rat
1298074Bp164Blood pressure QTL 1640.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
1298080Bp163Blood pressure QTL 1630.02arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118275202447032Rat
1298085Bp165Blood pressure QTL 1650.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)242804607202447032Rat
631566Bp90Blood pressure QTL 900.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2102803808147803808Rat
1581552Pur12Proteinuria QTL 125.190.0009total urine 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
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1581569Uae32Urinary albumin excretion QTL 320.0001urine protein amount (VT:0005160)urine albumin excretion rate (CMO:0000757)278665619219826953Rat
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
1598865Bp296Blood pressure QTL 2962.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)281018907126018907Rat
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
2293671Bss44Bone structure and strength QTL 4410.970.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)243162366148478373Rat
634308Sach6Saccharin preference QTL 64.9taste sensitivity trait (VT:0001986)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)2112456140212696837Rat
1578772Stresp14Stress response QTL 1450.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)282345893130923501Rat
1578648Bss11Bone structure and strength QTL 114.7femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)2114837527211674221Rat
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
1354601Slep1Serum leptin concentration QTL 15.39blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)243171017184114403Rat
1354603Bp243Blood pressure QTL 2433.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)226917817127469484Rat
1354605Rf48Renal function QTL 482.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)274786664206665859Rat
1354622Kidm16Kidney mass QTL 163kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)281754530222436696Rat
1354648Bp239Blood pressure QTL 2390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)266118463226797303Rat
1354649Kidm17Kidney mass QTL 172.9kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)281754530227146641Rat
2299162Iddm32Insulin dependent diabetes mellitus QTL 322.36blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)278665616143657569Rat
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
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
1554319Bmd2Bone mineral density QTL 213.40.0001lumbar vertebra area (VT:0010570)lumbar vertebra cross-sectional area (CMO:0001689)2114837675212549332Rat
2290453Scl55Serum cholesterol level QTL 552.83blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)226917817136917119Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
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
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
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
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527185876470Rat
1359030Bp277Blood pressure QTL 277arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527185876470Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)2114837527143657569Rat
1359035Bp276Blood pressure QTL 276arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2114837527143657569Rat
61374Edpm2Estrogen-dependent pituitary mass QTL 24.420.86pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)276539322202447032Rat
61392Bp6Blood pressure QTL 67arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)280270434125270434Rat
7207808Bmd89Bone mineral density QTL 894.1femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)288862519133862519Rat
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
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

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.


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

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565646 AgrOrtholog
Ensembl Genes ENSRNOG00000012199 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000016236 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000016236 ENTREZGENE, 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