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

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Gene: Sox9 (SRY-box transcription factor 9) Rattus norvegicus
Analyze
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 several processes, including Sertoli cell development; cAMP-mediated signaling; and positive regulation of macromolecule metabolic process. Part of transcription regulator complex. Human ortholog(s) of this gene implicated in 46,XX sex reversal 2; 46,XY sex reversal 10; and campomelic dysplasia. Orthologous to human SOX9 (SRY-box transcription factor 9); INTERACTS WITH (+)-taxifolin; (S)-nicotine; 17alpha-ethynylestradiol.
Type: protein-coding
RefSeq Status: VALIDATED
Also 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21097,806,485 - 97,811,994 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1097,806,485 - 97,811,994 (+)Ensembl
Rnor_6.010101,288,528 - 101,294,030 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10101,288,489 - 101,293,379 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010100,964,754 - 100,970,581 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410102,392,187 - 102,394,256 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110102,408,236 - 102,408,622 (+)NCBI
Celera1096,424,278 - 96,429,703 (+)NCBICelera
Cytogenetic Map10q32.1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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-hydroxypropanoic acid  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (ISO)
allethrin  (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)
azoxystrobin  (ISO)
benzo[a]pyrene  (ISO)
berberine  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (ISO)
Brusatol  (ISO)
buta-1,3-diene  (ISO)
Butylbenzyl phthalate  (EXP)
caffeine  (EXP)
calcitriol  (ISO)
carbon nanotube  (ISO)
carmustine  (ISO)
CHIR 99021  (ISO)
chlordecone  (ISO)
chlorpyrifos  (EXP)
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)
decabromodiphenyl ether  (EXP)
dexamethasone  (ISO)
dextran sulfate  (ISO)
dibenz[a,h]anthracene  (ISO)
dibutyl phthalate  (EXP,ISO)
dicrotophos  (ISO)
diethyl maleate  (EXP)
diheptyl phthalate  (EXP)
diisobutyl phthalate  (EXP)
Diisodecyl phthalate  (EXP)
dioxygen  (ISO)
dipentyl phthalate  (EXP)
disodium selenite  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
endosulfan  (ISO)
Enterolactone  (ISO)
enzalutamide  (ISO)
erlotinib hydrochloride  (ISO)
ethanol  (EXP,ISO)
fenvalerate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
gallic acid  (EXP)
genistein  (ISO)
geraniol  (ISO)
glycerol 2-phosphate  (ISO)
glycidol  (EXP)
hyaluronic acid  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
iohexol  (ISO)
ionomycin  (ISO)
iopamidol  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
kaempferol  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lead diacetate  (ISO)
leflunomide  (ISO)
Licochalcone B  (ISO)
methapyrilene  (ISO)
methylisothiazolinone  (ISO)
mifepristone  (ISO)
Mofezolac (TN)  (ISO)
Monobutylphthalate  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nickel sulfate  (ISO)
nicotinamide  (ISO)
nicotine  (EXP)
oxybenzone  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (EXP,ISO)
PD 0325901  (ISO)
perfluorododecanoic acid  (EXP)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
PhIP  (EXP)
pirinixic acid  (ISO)
prednisolone  (ISO)
progesterone  (ISO)
prostaglandin E2  (ISO)
prostaglandin F2alpha  (ISO)
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)
sodium arsenite  (ISO)
Soman  (EXP)
sulfamethoxazole  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tacrolimus hydrate  (ISO)
tamoxifen  (ISO)
temozolomide  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
titanium dioxide  (ISO)
torin 1  (ISO)
triacsin C  (ISO)
tributylstannane  (ISO)
trichostatin A  (ISO)
triclosan  (ISO)
triphenyl phosphate  (ISO)
troglitazone  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vitamin E  (ISO)
vorinostat  (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  (ISO)
astrocyte fate commitment  (ISO)
branching involved in ureteric bud morphogenesis  (ISO)
bronchus cartilage development  (ISO)
cAMP-mediated signaling  (IDA,ISO)
cartilage condensation  (ISO,ISS)
cartilage development  (IEP,ISO,ISS,NAS,TAS)
cell differentiation  (ISO)
cell fate commitment  (ISO)
cell fate specification  (ISO,ISS)
cell-cell adhesion  (ISO)
cellular response to epidermal growth factor stimulus  (ISO,ISS)
cellular response to heparin  (ISO,ISS)
cellular response to interleukin-1  (ISO)
cellular response to mechanical stimulus  (ISO,ISS)
cellular response to retinoic acid  (ISO)
cellular response to transforming growth factor beta stimulus  (ISO,ISS)
central nervous system development  (ISO)
chondrocyte development  (ISO)
chondrocyte differentiation  (IBA,ISO,ISS)
chondrocyte differentiation involved in endochondral bone morphogenesis  (ISO,ISS)
chondrocyte hypertrophy  (ISO,ISS)
chromatin remodeling  (ISO,ISS)
cochlea morphogenesis  (ISO,ISS)
cytoskeleton organization  (ISO)
endocardial cushion morphogenesis  (ISO,ISS)
endochondral bone morphogenesis  (ISO)
endocrine pancreas development  (ISO)
epidermal growth factor receptor signaling pathway  (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  (ISO,ISS)
extracellular matrix organization  (ISO)
growth plate cartilage chondrocyte growth  (ISO,ISS)
hair follicle development  (ISO,ISS)
Harderian gland development  (ISO)
heart development  (IBA,ISO)
heart valve development  (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  (ISO)
lung epithelial cell differentiation  (ISO)
lung smooth muscle development  (ISO)
male germ-line sex determination  (ISO,ISS)
male gonad development  (ISO,ISS)
male sex determination  (ISO)
mammary gland development  (ISO)
metanephric nephron tubule formation  (ISO,ISS)
metanephric tubule development  (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  (ISO)
negative regulation of biomineral tissue development  (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 epithelial cell differentiation  (ISO)
negative regulation of epithelial cell proliferation  (ISO,ISS)
negative regulation of fatty acid oxidation  (ISO,ISS)
negative regulation of gene expression  (ISO)
negative regulation of immune system process  (ISO,ISS)
negative regulation of mesenchymal cell apoptotic process  (ISO)
negative regulation of myoblast differentiation  (ISO,ISS)
negative regulation of ossification  (ISO,ISS)
negative regulation of osteoblast differentiation  (ISO,ISS)
negative regulation of photoreceptor cell differentiation  (ISO,ISS)
negative regulation of pri-miRNA transcription by RNA polymerase II  (ISO)
negative regulation of transcription by RNA polymerase II  (IBA,ISO)
negative regulation of transcription, DNA-templated  (ISO,ISS)
neural crest cell development  (ISO)
Notch signaling pathway  (ISO)
notochord development  (ISO)
nucleosome assembly  (ISO,ISS)
oligodendrocyte differentiation  (IBA,ISO)
ossification  (ISO)
otic vesicle development  (ISO)
otic vesicle formation  (ISO,ISS)
positive regulation of branching involved in ureteric bud morphogenesis  (ISO,ISS)
positive regulation of cartilage development  (ISO,ISS)
positive regulation of cell population proliferation  (ISO,ISS)
positive regulation of cell proliferation involved in heart morphogenesis  (ISO)
positive regulation of chondrocyte differentiation  (IBA,ISO,ISS)
positive regulation of chondrocyte proliferation  (ISO)
positive regulation of epithelial cell differentiation  (ISO,ISS)
positive regulation of epithelial cell migration  (ISO,ISS)
positive regulation of epithelial cell proliferation  (ISO,ISS)
positive regulation of extracellular matrix assembly  (ISO)
positive regulation of gene expression  (IDA,ISO)
positive regulation of kidney development  (ISO,ISS)
positive regulation of male gonad development  (ISO,ISS)
positive regulation of mesenchymal cell proliferation  (ISO,ISS)
positive regulation of mesenchymal stem cell differentiation  (ISO,ISS)
positive regulation of phosphatidylinositol 3-kinase signaling  (ISO,ISS)
positive regulation of protein catabolic process  (ISO)
positive regulation of protein phosphorylation  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (IDA,ISO)
positive regulation of transcription, DNA-templated  (ISO)
prostate gland development  (ISO)
prostate gland morphogenesis  (ISO)
protein kinase B signaling  (ISO,ISS)
protein localization to nucleus  (ISO)
protein-containing complex assembly  (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  (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  (IBA,ISO)
renal vesicle induction  (ISO,ISS)
response to fatty acid  (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  (ISO,ISS)
skeletal system development  (ISO,ISS)
somatic stem cell population maintenance  (ISO,ISS)
spermatogenesis  (ISO,ISS)
tissue homeostasis  (ISO,ISS)
trachea cartilage development  (ISO)
ureter development  (ISO)
ureter morphogenesis  (ISO)
ureter smooth muscle cell differentiation  (ISO)
ureter urothelium development  (ISO)

Cellular Component

References

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:33293097   PMID:33441835   PMID:33479807  


Genomics

Comparative Map Data
Sox9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21097,806,485 - 97,811,994 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl1097,806,485 - 97,811,994 (+)Ensembl
Rnor_6.010101,288,528 - 101,294,030 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10101,288,489 - 101,293,379 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010100,964,754 - 100,970,581 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410102,392,187 - 102,394,256 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.110102,408,236 - 102,408,622 (+)NCBI
Celera1096,424,278 - 96,429,703 (+)NCBICelera
Cytogenetic Map10q32.1NCBI
SOX9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1772,121,020 - 72,126,416 (+)EnsemblGRCh38hg38GRCh38
GRCh381772,121,020 - 72,126,416 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371770,117,161 - 70,122,557 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361767,628,756 - 67,634,156 (+)NCBINCBI36hg18NCBI36
Build 341767,628,755 - 67,634,156NCBI
Celera1766,688,499 - 66,693,898 (+)NCBI
Cytogenetic Map17q24.3NCBI
HuRef1765,510,108 - 65,515,656 (+)NCBIHuRef
CHM1_11770,181,222 - 70,186,622 (+)NCBICHM1_1
Sox9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911112,673,036 - 112,678,583 (+)NCBIGRCm39mm39
GRCm39 Ensembl11112,673,050 - 112,678,586 (+)Ensembl
GRCm3811112,782,210 - 112,787,757 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11112,782,224 - 112,787,760 (+)EnsemblGRCm38mm10GRCm38
MGSCv3711112,643,524 - 112,649,071 (+)NCBIGRCm37mm9NCBIm37
MGSCv3611112,598,314 - 112,603,839 (+)NCBImm8
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 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955478941,684 - 945,563 (-)NCBIChiLan1.0ChiLan1.0
SOX9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11771,491,419 - 71,498,911 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01766,028,737 - 66,034,122 (+)NCBIMhudiblu_PPA_v0panPan3
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha99,564,949 - 9,568,092 (+)NCBI
ROS_Cfam_1.098,479,949 - 8,483,108 (-)NCBI
UMICH_Zoey_3.198,522,923 - 8,526,068 (-)NCBI
UNSW_CanFamBas_1.098,777,560 - 8,780,707 (-)NCBI
UU_Cfam_GSD_1.098,722,828 - 8,725,975 (-)NCBI
Sox9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056028,350,254 - 8,354,855 (-)NCBI
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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (-)NCBI
ChlSab1.1 Ensembl1649,518,185 - 49,523,898 (-)Ensembl
Vero_WHO_p1.0NW_02366607720,379,690 - 20,385,117 (-)NCBI
Sox9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248012,296,353 - 2,300,853 (+)NCBI

Position Markers
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
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
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


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
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)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
1357344Bp249Blood pressure QTL 2490.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106674365598003205Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)107877551698279596Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1080515287101325465Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1085565469103884409Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
1558652Bw57Body weight QTL 574.20.0008body mass (VT:0001259)body weight (CMO:0000012)1090910316107211142Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091228102104060283Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1092238497101012337Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096120911104060283Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1096703043107057807Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)1096703043107057807Rat
631539Oia6Oil induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1097010147104670812Rat

miRNA Target Status

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.


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 3 6 62 7 19 1
Low 37 33 23 12 23 7 10 12 28 22 10 7
Below cutoff 24 18 7 18 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003511   ⟹   ENSRNOP00000003511
RefSeq Status:
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
RefSeq Acc Id: NM_080403   ⟹   NP_536328
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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  
  F1LYL9 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_536328   ⟸   NM_080403
- UniProtKB: F1LYL9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003511   ⟸   ENSRNOT00000003511

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

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)
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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)
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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
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)
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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
FXLE18/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
GH/OmrMcwi (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)
GK/FarMcwi (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
GK/Ox (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
HXB10/IpcvMcwi (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
HXB2/IpcvMcwi (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
HXB20/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (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
HXB4/IpcvMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/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
LE/Stm (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
LEW/Crl (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
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (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: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/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
LEXF1A/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
LEXF1C/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
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)
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
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)
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
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)
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
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)
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
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)
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
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)
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
WKY/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
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)
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
WN/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
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:620474 AgrOrtholog
Ensembl Genes ENSRNOG00000002607 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000003511 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000003511 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot
InterPro HMG_box_dom UniProtKB/Swiss-Prot
  HMG_box_dom_sf UniProtKB/Swiss-Prot
  SOX-9 UniProtKB/Swiss-Prot
  Sox_N UniProtKB/Swiss-Prot
KEGG Report rno:140586 UniProtKB/Swiss-Prot
NCBI Gene 140586 ENTREZGENE
PANTHER PTHR45803:SF1 UniProtKB/Swiss-Prot
Pfam HMG_box UniProtKB/Swiss-Prot
  Sox_N UniProtKB/Swiss-Prot
PhenoGen Sox9 PhenoGen
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot
SMART HMG UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot
UniProt 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 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 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