Sox9 (SRY-box transcription factor 9) - Rat Genome Database

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Gene: Sox9 (SRY-box transcription factor 9) Rattus norvegicus
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Symbol: Sox9
Name: SRY-box transcription factor 9
RGD ID: 620474
Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific; bHLH transcription factor binding activity; and cis-regulatory region sequence-specific DNA binding activity. Involved in Sertoli cell development; cartilage development; and positive regulation of macromolecule biosynthetic process. Part of transcription regulator complex. Human ortholog(s) of this gene implicated in 46,XX sex reversal 2; 46,XY sex reversal 10; campomelic dysplasia; lung cancer; and lung carcinoma. Orthologous to human SOX9 (SRY-box transcription factor 9); INTERACTS WITH (+)-taxifolin; (S)-nicotine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC100361122; LOC363699; SRY; SRY (sex determining region Y)-box 9; SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal); SRY box 9; SRY-box containing gene 9; transcription factor SOX-9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81098,305,744 - 98,311,250 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1098,305,744 - 98,311,250 (+)EnsemblGRCr8
mRatBN7.21097,806,485 - 97,811,994 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1097,806,485 - 97,811,994 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx10102,866,804 - 102,872,316 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010102,329,807 - 102,335,320 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01097,726,102 - 97,731,622 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.010101,288,528 - 101,294,030 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10101,288,489 - 101,293,379 (+)Ensemblrn6Rnor6.0
Rnor_5.010100,964,754 - 100,970,581 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.410102,392,187 - 102,394,256 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1096,424,278 - 96,429,703 (+)NCBICelera
RGSC_v3.110102,408,236 - 102,408,622 (+)NCBI
Cytogenetic Map10q32.1NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-taxifolin  (EXP)
(S)-nicotine  (EXP)
1,1-dichloroethene  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dibromophenyl 2,4,5-tribromophenyl ether  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,3',5-triiodo-L-thyronine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
3-Nitrobenzanthrone  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetamide  (EXP)
acrylamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (ISO)
alendronic acid  (ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (ISO)
allethrin  (EXP)
alpha-Zearalanol  (EXP)
amitrole  (EXP)
ammonium chloride  (EXP)
androgen antagonist  (EXP)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
arachidonic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
atrazine  (ISO)
avobenzone  (ISO)
Azoxymethane  (ISO)
azoxystrobin  (ISO)
bellidifolin  (ISO)
benzo[a]pyrene  (ISO)
Benzo[ghi]perylene  (ISO)
berberine  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
Bisphenol B  (EXP)
bisphenol F  (EXP)
Brusatol  (ISO)
buta-1,3-diene  (ISO)
Butylbenzyl phthalate  (EXP,ISO)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
caffeine  (EXP,ISO)
calcitriol  (ISO)
cannabidiol  (ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
CGP 52608  (ISO)
CHIR 99021  (ISO)
chlordecone  (ISO)
chlorpyrifos  (EXP,ISO)
choline  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
crotonaldehyde  (ISO)
Cuprizon  (EXP)
curcumin  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
cypermethrin  (EXP)
D-glucose  (ISO)
DDE  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
diethyl maleate  (EXP)
diethyl phthalate  (ISO)
diheptyl phthalate  (EXP)
diisobutyl phthalate  (EXP,ISO)
Diisodecyl phthalate  (EXP)
diisononyl phthalate  (ISO)
dimethyl sulfoxide  (ISO)
dimethylarsinous acid  (ISO)
dioxygen  (ISO)
dipentyl phthalate  (EXP)
diquat  (ISO)
disodium selenite  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (ISO)
Enterolactone  (ISO)
enzalutamide  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (EXP,ISO)
Ethylenethiourea  (EXP,ISO)
fenvalerate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
FR900359  (ISO)
fructose  (ISO)
furan  (EXP)
gallic acid  (EXP)
genistein  (ISO)
geraniol  (ISO)
glucose  (ISO)
glycerol 2-phosphate  (ISO)
glycidol  (EXP)
glyphosate  (ISO)
hyaluronic acid  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
inulin  (ISO)
iohexol  (ISO)
ionomycin  (ISO)
iopamidol  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
isoprenaline  (ISO)
kaempferol  (ISO)
ketoconazole  (EXP)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
leptomycin B  (ISO)
Licochalcone B  (ISO)
methapyrilene  (ISO)
methimazole  (EXP)
methylisothiazolinone  (ISO)
mifepristone  (ISO)
Mofezolac (TN)  (ISO)
mono(2-ethylhexyl) phthalate  (ISO)
monobenzyl phthalate  (ISO)
Monobutylphthalate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel sulfate  (ISO)
nicotinamide  (ISO)
nicotine  (EXP)
NMN zwitterion  (ISO)
okadaic acid  (ISO)
oxybenzone  (EXP)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
PD 0325901  (ISO)
perfluorododecanoic acid  (EXP)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (EXP)
PhIP  (EXP)
pirinixic acid  (ISO)
prednisolone  (ISO)
prednisone  (ISO)
progesterone  (ISO)
prostaglandin E2  (ISO)
prostaglandin F2alpha  (ISO)
pyrethrins  (EXP)
rac-lactic acid  (ISO)
resmethrin  (ISO)
resveratrol  (ISO)
rotenone  (ISO)
SB 203580  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sirolimus  (ISO)
sodium acetate trihydrate  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
Soman  (EXP)
sulfamethoxazole  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
Theaflavin 3,3'-digallate  (EXP)
thimerosal  (ISO)
thioacetamide  (EXP)
thiram  (ISO)
titanium dioxide  (ISO)
torin 1  (ISO)
triacsin C  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (ISO)
triphenylstannane  (EXP)
triticonazole  (EXP)
troglitazone  (ISO)
uranium atom  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vitamin E  (ISO)
vorinostat  (ISO)
warfarin  (ISO)
XL147  (ISO)
zearalenone  (ISO)
zileuton  (ISO)
ziram  (EXP)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anterior head development  (ISO)
aortic valve morphogenesis  (IEA,ISO)
astrocyte fate commitment  (ISO)
branching involved in ureteric bud morphogenesis  (IEA,ISO)
bronchus cartilage development  (ISO)
cartilage condensation  (ISO,ISS)
cartilage development  (IEA,IEP,ISO,ISS,NAS,TAS)
cell differentiation  (IEA,ISO)
cell fate commitment  (ISO)
cell fate specification  (ISO,ISS)
cell-cell adhesion  (ISO)
cellular response to epidermal growth factor stimulus  (IEA,ISO,ISS)
cellular response to heparin  (IEA,ISO,ISS)
cellular response to interleukin-1  (IEA,ISO)
cellular response to mechanical stimulus  (IEA,ISO,ISS)
cellular response to retinoic acid  (IEA,ISO)
cellular response to transforming growth factor beta stimulus  (IEA,ISO,ISS)
central nervous system development  (IEA,ISO)
chondrocyte development  (ISO)
chondrocyte differentiation  (IBA,IEA,ISO,ISS)
chondrocyte differentiation involved in endochondral bone morphogenesis  (IEA,ISO,ISS)
chondrocyte hypertrophy  (IEA,ISO,ISS)
chromatin remodeling  (IEA,ISO,ISS)
cochlea morphogenesis  (ISO,ISS)
cytoskeleton organization  (ISO)
DNA-templated transcription  (IEA)
endocardial cushion morphogenesis  (ISO,ISS)
endochondral bone morphogenesis  (ISO)
endocrine pancreas development  (ISO)
epidermal growth factor receptor signaling pathway  (IEA,ISO,ISS)
epithelial cell proliferation involved in prostatic bud elongation  (ISO,ISS)
epithelial to mesenchymal transition  (ISO,ISS)
epithelial tube branching involved in lung morphogenesis  (ISO)
ERK1 and ERK2 cascade  (IEA,ISO,ISS)
extracellular matrix organization  (ISO)
gene expression  (IEA,ISO)
growth plate cartilage chondrocyte growth  (IEA,ISO,ISS)
hair follicle development  (ISO,ISS)
Harderian gland development  (ISO)
heart development  (IBA,ISO)
heart valve development  (IEA,ISO,ISS)
heart valve formation  (ISO)
heart valve morphogenesis  (ISO,ISS)
homeostasis of number of cells within a tissue  (ISO)
intestinal epithelial structure maintenance  (ISO,ISS)
intrahepatic bile duct development  (ISO)
lacrimal gland development  (ISO)
limb bud formation  (IEA,ISO)
lung epithelial cell differentiation  (ISO)
lung smooth muscle development  (ISO)
male germ-line sex determination  (ISO,ISS)
male gonad development  (IEA,ISO,ISS)
male sex determination  (ISO)
mammary gland development  (IEA,ISO)
metanephric nephron tubule formation  (ISO,ISS)
metanephric tubule development  (IEA,ISO)
morphogenesis of a branching epithelium  (ISO,ISS)
morphogenesis of an epithelium  (IBA)
negative regulation of apoptotic process  (ISO,ISS)
negative regulation of beta-catenin-TCF complex assembly  (IEA,ISO)
negative regulation of biomineral tissue development  (IEA,ISO,ISS)
negative regulation of bone mineralization  (ISO)
negative regulation of canonical Wnt signaling pathway  (ISO,ISS)
negative regulation of cell population proliferation  (ISO)
negative regulation of chondrocyte differentiation  (ISO,ISS)
negative regulation of DNA-templated transcription  (IEA,ISO,ISS)
negative regulation of epithelial cell differentiation  (ISO)
negative regulation of epithelial cell proliferation  (ISO,ISS)
negative regulation of fatty acid oxidation  (IEA,ISO,ISS)
negative regulation of gene expression  (ISO)
negative regulation of immune system process  (IEA,ISO,ISS)
negative regulation of mesenchymal cell apoptotic process  (ISO)
negative regulation of miRNA transcription  (IEA,ISO)
negative regulation of myoblast differentiation  (ISO,ISS)
negative regulation of ossification  (IEA,ISO,ISS)
negative regulation of osteoblast differentiation  (IEA,ISO,ISS)
negative regulation of photoreceptor cell differentiation  (ISO,ISS)
negative regulation of transcription by RNA polymerase II  (IBA,IEA,ISO)
neural crest cell development  (ISO)
Notch signaling pathway  (ISO)
notochord development  (IEA,ISO)
nucleosome assembly  (IEA,ISO,ISS)
oligodendrocyte differentiation  (IBA,ISO)
ossification  (IEA,ISO)
otic vesicle development  (IEA,ISO)
otic vesicle formation  (ISO,ISS)
positive regulation of branching involved in ureteric bud morphogenesis  (IEA,ISO,ISS)
positive regulation of cartilage development  (IEA,ISO,ISS)
positive regulation of cell population proliferation  (IEA,ISO,ISS)
positive regulation of cell proliferation involved in heart morphogenesis  (ISO)
positive regulation of chondrocyte differentiation  (IBA,IEA,ISO,ISS)
positive regulation of chondrocyte proliferation  (IEA,ISO)
positive regulation of DNA-templated transcription  (IEA,ISO)
positive regulation of epithelial cell differentiation  (ISO,ISS)
positive regulation of epithelial cell migration  (IEA,ISO,ISS)
positive regulation of epithelial cell proliferation  (IEA,ISO,ISS)
positive regulation of extracellular matrix assembly  (ISO)
positive regulation of gene expression  (IDA,IEA,ISO)
positive regulation of kidney development  (IEA,ISO,ISS)
positive regulation of male gonad development  (IEA,ISO,ISS)
positive regulation of mesenchymal cell proliferation  (ISO,ISS)
positive regulation of mesenchymal stem cell differentiation  (IEA,ISO,ISS)
positive regulation of protein catabolic process  (ISO)
positive regulation of protein phosphorylation  (ISO)
positive regulation of transcription by RNA polymerase II  (IDA,IEA,ISO)
prostate gland development  (IEA,ISO)
prostate gland morphogenesis  (ISO)
protein localization to nucleus  (ISO)
protein-containing complex assembly  (IEA,ISO,ISS)
regulation of apoptotic process  (ISS)
regulation of branching involved in lung morphogenesis  (ISO)
regulation of cell adhesion  (ISO)
regulation of cell cycle process  (IEA,ISO,ISS)
regulation of cell differentiation  (ISO)
regulation of cell population proliferation  (ISO,ISS)
regulation of cell proliferation involved in tissue homeostasis  (ISO,ISS)
regulation of epithelial cell proliferation involved in lung morphogenesis  (ISO)
regulation of gene expression  (ISO)
regulation of transcription by RNA polymerase II  (ISO)
renal vesicle induction  (IEA,ISO,ISS)
response to fatty acid  (IEA,ISO,ISS)
retina development in camera-type eye  (ISO,ISS)
retinal rod cell differentiation  (ISO,ISS)
Sertoli cell development  (IEP,ISO)
Sertoli cell differentiation  (ISO,ISS)
signal transduction  (IEA,ISO,ISS)
skeletal system development  (IEA,ISO,ISS)
somatic stem cell population maintenance  (ISO,ISS)
spermatogenesis  (ISO,ISS)
tissue homeostasis  (IEA,ISO,ISS)
trachea cartilage development  (ISO)
ureter development  (ISO)
ureter morphogenesis  (ISO)
ureter smooth muscle cell differentiation  (ISO)
ureter urothelium development  (IEA,ISO)

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IEA,ISO,ISS)
protein-containing complex  (IEA,ISO,ISS)
transcription regulator complex  (IDA,IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene. Foster JW, etal., Nature. 1994 Dec 8;372(6506):525-30.
2. Scleraxis and E47 cooperatively regulate the Sox9-dependent transcription. Furumatsu T, etal., Int J Biochem Cell Biol. 2010 Jan;42(1):148-56. doi: 10.1016/j.biocel.2009.10.003. Epub 2009 Oct 12.
3. 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.
4. Alterations in growth plate and articular cartilage morphology are associated with reduced SOX9 localization in the magnesium-deficient rat. Gruber HE, etal., Biotech Histochem. 2004 Feb;79(1):45-52.
5. Phosphorylation of SOX9 by cyclic AMP-dependent protein kinase A enhances SOX9's ability to transactivate a Col2a1 chondrocyte-specific enhancer. Huang W, etal., Mol Cell Biol. 2000 Jun;20(11):4149-58.
6. The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis. Liu CF and Lefebvre V, Nucleic Acids Res. 2015 Sep 30;43(17):8183-203. doi: 10.1093/nar/gkv688. Epub 2015 Jul 6.
7. Expression of transcription factor Sox9 in rat L6 myoblastic cells. Matsushita T, etal., Connect Tissue Res. 2004;45(3):164-73.
8. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
9. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
10. The transcription factor SOX9 regulates cell cycle and differentiation genes in chondrocytic CFK2 cells. Panda DK, etal., J Biol Chem 2001 Nov 2;276(44):41229-36.
11. GOA pipeline RGD automated data pipeline
12. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
13. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
14. The UV filter benzophenone 3, alters early follicular assembly in rat whole ovary cultures. Santamaría CG, etal., Toxicol Lett. 2019 Mar 15;303:48-54. doi: 10.1016/j.toxlet.2018.12.016. Epub 2018 Dec 30.
15. Regulation of the orphan nuclear receptor steroidogenic factor 1 by Sox proteins. Shen JH and Ingraham HA, Mol Endocrinol 2002 Mar;16(3):529-40.
16. Sox9 expression during fracture repair. Shintaku Y, etal., Cells Tissues Organs. 2011;194(1):38-48. doi: 10.1159/000322557. Epub 2011 Jan 22.
17. SOX9 dependent FOXA1 expression promotes tumorigenesis in lung carcinoma. Wang X, etal., Biochem Biophys Res Commun. 2019 Aug 13;516(1):236-244. doi: 10.1016/j.bbrc.2019.05.169. Epub 2019 Jun 17.
18. Bcl-2 positively regulates Sox9-dependent chondrocyte gene expression by suppressing the MEK-ERK1/2 signaling pathway. Yagi R, etal., J Biol Chem. 2005 Aug 26;280(34):30517-25. Epub 2005 Jun 23.
Additional References at PubMed
PMID:8640233   PMID:8787755   PMID:9119111   PMID:9171829   PMID:9755172   PMID:10319868   PMID:11371614   PMID:11431689   PMID:11951052   PMID:12133909   PMID:12381733   PMID:12414734  
PMID:12420222   PMID:12732652   PMID:12782625   PMID:12842915   PMID:12915303   PMID:15056615   PMID:15096597   PMID:15229180   PMID:15585950   PMID:15590666   PMID:15691760   PMID:15694126  
PMID:15722556   PMID:15778499   PMID:15800003   PMID:15893981   PMID:15944199   PMID:16085486   PMID:16109717   PMID:16207837   PMID:16554309   PMID:16700629   PMID:17084361   PMID:17267606  
PMID:17350610   PMID:17467696   PMID:17525254   PMID:17644814   PMID:17681175   PMID:17698607   PMID:17848411   PMID:17875931   PMID:17968906   PMID:18182117   PMID:18287078   PMID:18325490  
PMID:18377888   PMID:18403418   PMID:18415932   PMID:18512230   PMID:18685078   PMID:18723011   PMID:18794798   PMID:19047045   PMID:19124014   PMID:19269367   PMID:19389355   PMID:19403103  
PMID:19490914   PMID:19725955   PMID:19796622   PMID:20056916   PMID:20079164   PMID:20103652   PMID:20346939   PMID:20404928   PMID:20484372   PMID:20492757   PMID:20530484   PMID:20592578  
PMID:20651055   PMID:20676705   PMID:20871603   PMID:20881014   PMID:20937378   PMID:20940257   PMID:21073445   PMID:21212101   PMID:21346191   PMID:21367821   PMID:21401405   PMID:21412441  
PMID:21427722   PMID:21464233   PMID:21512138   PMID:21757499   PMID:21991325   PMID:22110751   PMID:22344693   PMID:22500632   PMID:22984422   PMID:23606745   PMID:23711496   PMID:23786676  
PMID:23840004   PMID:23946534   PMID:24058167   PMID:24120428   PMID:24191021   PMID:24218621   PMID:24681825   PMID:24854956   PMID:24924191   PMID:24971829   PMID:25446530   PMID:25632159  
PMID:26234751   PMID:26599103   PMID:26634652   PMID:26687115   PMID:26950443   PMID:27325675   PMID:27881681   PMID:28263186   PMID:29503843   PMID:30334860   PMID:30430007   PMID:31194875  
PMID:32020624   PMID:32313200   PMID:32747445   PMID:32750029   PMID:32901875   PMID:33161310   PMID:33208157   PMID:33293097   PMID:33441835   PMID:33479807   PMID:33811247   PMID:35634668  
PMID:36192639   PMID:36642539   PMID:38901791  


Genomics

Comparative Map Data
Sox9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81098,305,744 - 98,311,250 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1098,305,744 - 98,311,250 (+)EnsemblGRCr8
mRatBN7.21097,806,485 - 97,811,994 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1097,806,485 - 97,811,994 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx10102,866,804 - 102,872,316 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010102,329,807 - 102,335,320 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01097,726,102 - 97,731,622 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.010101,288,528 - 101,294,030 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10101,288,489 - 101,293,379 (+)Ensemblrn6Rnor6.0
Rnor_5.010100,964,754 - 100,970,581 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.410102,392,187 - 102,394,256 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1096,424,278 - 96,429,703 (+)NCBICelera
RGSC_v3.110102,408,236 - 102,408,622 (+)NCBI
Cytogenetic Map10q32.1NCBI
SOX9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381772,121,020 - 72,126,416 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1772,121,020 - 72,126,416 (+)Ensemblhg38GRCh38
GRCh371770,117,161 - 70,122,557 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361767,628,756 - 67,634,156 (+)NCBIBuild 36Build 36hg18NCBI36
Build 341767,628,755 - 67,634,156NCBI
Celera1766,688,499 - 66,693,898 (+)NCBICelera
Cytogenetic Map17q24.3NCBI
HuRef1765,510,108 - 65,515,656 (+)NCBIHuRef
CHM1_11770,181,222 - 70,186,622 (+)NCBICHM1_1
T2T-CHM13v2.01772,994,224 - 72,999,619 (+)NCBIT2T-CHM13v2.0
Sox9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911112,673,036 - 112,678,583 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11112,673,050 - 112,678,586 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm3811112,782,210 - 112,787,757 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11112,782,224 - 112,787,760 (+)Ensemblmm10GRCm38
MGSCv3711112,643,524 - 112,649,071 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3611112,598,314 - 112,603,839 (+)NCBIMGSCv36mm8
Celera11124,540,008 - 124,545,554 (+)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1177.27NCBI
Sox9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955478940,177 - 945,563 (-)Ensembl
ChiLan1.0NW_004955478941,684 - 945,563 (-)NCBIChiLan1.0ChiLan1.0
SOX9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21988,118,202 - 88,123,589 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11792,942,486 - 92,947,874 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01766,028,737 - 66,034,122 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11771,491,419 - 71,498,911 (+)NCBIPanPan1.1PanPan1.1panPan2
SOX9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.198,275,049 - 8,278,172 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl98,275,049 - 8,278,172 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha99,564,949 - 9,568,092 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.098,479,949 - 8,483,108 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl98,479,863 - 8,483,490 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.198,522,923 - 8,526,068 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.098,777,560 - 8,780,707 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.098,722,828 - 8,725,975 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sox9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056028,350,254 - 8,354,855 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366551,847,272 - 1,852,705 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366551,849,044 - 1,852,648 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl128,642,158 - 8,647,315 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1128,642,154 - 8,647,315 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2129,029,449 - 9,032,820 (-)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap12p13-p11NCBI
SOX9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11649,519,749 - 49,523,967 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1649,518,185 - 49,523,898 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607720,379,690 - 20,385,117 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sox9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248012,296,168 - 2,301,596 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248012,296,353 - 2,300,853 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Sox9
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1976,531,235 - 76,535,398 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sox9
17 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:8
Count of miRNA genes:8
Interacting mature miRNAs:8
Transcripts:ENSRNOT00000003511
Prediction methods:Miranda, Rnahybrid
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093723381107556066Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102702353598502431Rat
8657410Bp374Blood pressure QTL 374heart left ventricle size trait (VT:0002753)heart left ventricle end-diastolic diameter (CMO:0000982)1067476608107713808Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063719161107713808Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1058073360103073360Rat
12903252Cm113Cardiac mass QTL 1130.047heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105429633699451733Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1064939013107713808Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076951790107713808Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1079272424102982300Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1073599825107713808Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1054296227107713808Rat
12903269Am15Aortic mass QTL 150.042aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
12903266Cm114Cardiac mass QTL 1140.02heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1066817119107713808Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)1097202388107556066Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062556066107556066Rat
12880372Am12Aortic mass QTL 120.003aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062556066107556066Rat
12880375Kidm66Kidney mass QTL 660.009kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087807758107713808Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106724133498502431Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
12880370Cm105Cardiac mass QTL 1050.008heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
12880371Cm106Cardiac mass QTL 1060.007heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106184349698710773Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1091127270107556066Rat
11565453Kidm58Kidney mass QTL 580.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1097202388107556066Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1065390777107713808Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1081012077101828297Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1052269185107713808Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068920187107713808Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)1065307813107713808Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1089039175107713808Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1061843496106843496Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070698731107713808Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1061843496100198886Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040535708107713808Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1066108888107555881Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1061843496100198886Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1076128947107713808Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)1061997479106997479Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091727883107713808Rat
2301405Cm69Cardiac mass QTL 690.031heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat

Markers in Region
AV220920  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21097,810,235 - 97,810,355 (+)MAPPERmRatBN7.2
Rnor_6.010101,292,274 - 101,292,393NCBIRnor6.0
Rnor_5.010100,968,825 - 100,968,944UniSTSRnor5.0
RGSC_v3.410102,389,658 - 102,389,777UniSTSRGSC3.4
Celera1096,427,947 - 96,428,066UniSTS
Cytogenetic Map10q32.1UniSTS
RH134713  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21097,811,740 - 97,811,941 (+)MAPPERmRatBN7.2
Rnor_6.010101,293,777 - 101,293,977NCBIRnor6.0
Rnor_5.010100,970,328 - 100,970,528UniSTSRnor5.0
RGSC_v3.410102,391,161 - 102,391,361UniSTSRGSC3.4
Celera1096,429,450 - 96,429,650UniSTS
RH 3.4 Map101105.8UniSTS
Cytogenetic Map10q32.1UniSTS
PMC34415P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21097,806,798 - 97,807,095 (+)MAPPERmRatBN7.2
Rnor_6.010101,288,842 - 101,289,138NCBIRnor6.0
Rnor_5.010100,965,138 - 100,965,434UniSTSRnor5.0
RGSC_v3.410102,393,823 - 102,394,119UniSTSRGSC3.4
Celera1096,424,592 - 96,424,888UniSTS
Cytogenetic Map10q32.1UniSTS
Sox9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21097,809,268 - 97,809,475 (+)MAPPERmRatBN7.2
Rnor_6.010101,291,307 - 101,291,513NCBIRnor6.0
Rnor_5.010100,967,858 - 100,968,064UniSTSRnor5.0
RGSC_v3.410102,388,691 - 102,388,897UniSTSRGSC3.4
Celera1096,426,980 - 96,427,186UniSTS
Cytogenetic Map10q32.1UniSTS
GDB:580585  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.010101,289,212 - 101,290,136NCBIRnor6.0
Rnor_5.010100,965,508 - 100,966,687UniSTSRnor5.0
Celera1096,424,962 - 96,425,812UniSTS
Cytogenetic Map10q32.1UniSTS
Sox9  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81098,306,416 - 98,307,341 (+)Marker Load Pipeline
Rnor_6.010101,289,201 - 101,290,121NCBIRnor6.0
Rnor_5.010100,965,497 - 100,966,672UniSTSRnor5.0
Celera1096,424,951 - 96,425,797UniSTS
Cytogenetic Map10q32.1UniSTS
Sox9  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81098,306,432 - 98,307,398 (+)Marker Load Pipeline
Rnor_6.010101,289,217 - 101,290,178NCBIRnor6.0
Rnor_5.010100,965,513 - 100,966,729UniSTSRnor5.0
Celera1096,424,967 - 96,425,854UniSTS
Cytogenetic Map10q32.1UniSTS
Sox9  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21097,808,225 - 97,809,532 (+)MAPPERmRatBN7.2
Rnor_6.010101,290,265 - 101,291,570NCBIRnor6.0
Rnor_5.010100,966,816 - 100,968,121UniSTSRnor5.0
RGSC_v3.410102,387,649 - 102,388,954UniSTSRGSC3.4
Celera1096,425,941 - 96,427,243UniSTS
Cytogenetic Map10q32.1UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 66 163 91 90 59 26 59 6 289 125 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000003511   ⟹   ENSRNOP00000003511
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1097,806,485 - 97,811,994 (+)Ensembl
Rnor_6.0 Ensembl10101,288,489 - 101,293,379 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000133949   ⟹   ENSRNOP00000107327
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1098,305,744 - 98,311,250 (+)Ensembl
RefSeq Acc Id: NM_080403   ⟹   NP_536328
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81098,305,744 - 98,311,250 (+)NCBI
mRatBN7.21097,806,485 - 97,811,994 (+)NCBI
Rnor_6.010101,288,528 - 101,294,030 (+)NCBI
Celera1096,424,278 - 96,429,703 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_536328 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AJK26762 (Get FASTA)   NCBI Sequence Viewer  
  BAB71726 (Get FASTA)   NCBI Sequence Viewer  
  EDM06505 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000003511.5
  ENSRNOP00000107327
GenBank Protein F1LYL9 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_536328   ⟸   NM_080403
- UniProtKB: F1LYL9 (UniProtKB/TrEMBL),   A0A0C5AMK0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000003511   ⟸   ENSRNOT00000003511
Ensembl Acc Id: ENSRNOP00000107327   ⟸   ENSRNOT00000133949
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-F1LYL9-F1-model_v2 AlphaFold F1LYL9 1-507 view protein structure

Transcriptome

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

Promoters
RGD ID:13697873
Promoter ID:EPDNEW_R8392
Type:single initiation site
Name:Sox9_1
Description:SRY box 9
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.010101,288,478 - 101,288,538EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620474 AgrOrtholog
BioCyc Gene G2FUF-22781 BioCyc
Ensembl Genes ENSRNOG00000002607 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000080699 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000003511.7 UniProtKB/Swiss-Prot
  ENSRNOT00000133949 ENTREZGENE
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot
InterPro HMG_box_dom UniProtKB/Swiss-Prot
  HMG_box_dom_sf UniProtKB/Swiss-Prot
  Sox_N UniProtKB/Swiss-Prot
  SOX_TF UniProtKB/Swiss-Prot
KEGG Report rno:140586 UniProtKB/Swiss-Prot
NCBI Gene 140586 ENTREZGENE
PANTHER PTHR45803:SF1 UniProtKB/Swiss-Prot
  SOX100B UniProtKB/Swiss-Prot
Pfam HMG_box UniProtKB/Swiss-Prot
  Sox_N UniProtKB/Swiss-Prot
PhenoGen Sox9 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000002607 RatGTEx
  ENSRNOG00000080699 RatGTEx
SMART HMG UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot
UniProt A0A0C5AMK0 ENTREZGENE, UniProtKB/TrEMBL
  F1LYL9 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Sox9  SRY-box transcription factor 9  Sox9  SRY box 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-12 Sox9  SRY box 9  Sox9  SRY (sex determining region Y)-box 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-04-17 Sox9  SRY (sex determining region Y)-box 9  LOC100361122  SRY-box containing gene 9  Data merged from RGD:2320738 737654 PROVISIONAL
2013-04-01 Sox9  SRY (sex determining region Y)-box 9  Sox9  SRY-box containing gene 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 LOC100361122  SRY-box containing gene 9      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-04-27 Sox9  SRY-box containing gene 9  Sox9_predicted  SRY-box containing gene 9 (predicted)  Data merged from RGD:1311187 737654 APPROVED
2005-07-08 Sox9  SRY-box containing gene 9    SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal)  Name updated 1299863 APPROVED
2005-01-12 Sox9_predicted  SRY-box containing gene 9 (predicted)      Symbol and Name status set to approved 70820 APPROVED
2002-08-07 Sox9  SRY (sex determining region Y)-box 9 (campomelic dysplasia, autosomal sex-reversal)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in testis, brain and heart 70568
gene_function transcription factor with HMG DNA-binding domain 70568
gene_function high-affinity binding to and activation of the Sox-BS1 element 1299273
gene_other related to mammalian Y-linked sex-determining gene SRY 70568
gene_process induces certain MAP kinases and N-cadherin 70568
gene_process may regulate p53 and p21-cip expression 70568
gene_process essential for chondrocyte differentiation and cartilage formation 70568
gene_process plays critical role in cell fate decisions in a few cell types 70568