Sox11 (SRY (sex determining region Y)-box 11) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Sox11 (SRY (sex determining region Y)-box 11) Mus musculus
Analyze
Symbol: Sox11
Name: SRY (sex determining region Y)-box 11
RGD ID: 735735
MGI Page MGI
Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and cis-regulatory region sequence-specific DNA binding activity. Involved in several processes, including camera-type eye development; nervous system development; and regulation of gene expression. Acts upstream of or within skeletal muscle cell differentiation. Located in nucleus. Is expressed in several structures, including alimentary system; brain; genitourinary system; limb; and sensory organ. Used to study Weissenbacher-Zweymuller syndrome. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 9. Orthologous to human SOX11 (SRY-box transcription factor 11).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1110038H03Rik; 6230403H02Rik; AI836553; end; end1; SRY-box containing gene 11; transcription factor SOX-11
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391227,384,267 - 27,392,717 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1227,384,263 - 27,392,573 (-)EnsemblGRCm39 Ensembl
GRCm381227,334,268 - 27,342,718 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1227,334,264 - 27,342,574 (-)EnsemblGRCm38mm10GRCm38
MGSCv371228,019,133 - 28,027,583 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361227,921,484 - 27,928,980 (-)NCBIMGSCv36mm8
Celera1228,811,290 - 28,819,758 (-)NCBICelera
Cytogenetic Map12A2NCBI
cM Map129.95NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (EXP)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP)
2,2',5,5'-tetrachlorobiphenyl  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (ISO)
aflatoxin B1  (ISO)
alachlor  (ISO)
all-trans-retinoic acid  (EXP)
amitriptyline  (ISO)
aristolochic acid A  (ISO)
Aroclor 1254  (ISO)
arsane  (EXP)
arsenic atom  (EXP)
arsenite(3-)  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (EXP)
bisphenol A  (EXP,ISO)
camptothecin  (ISO)
carbon nanotube  (EXP)
CGP 52608  (ISO)
chloroprene  (EXP)
chlorpyrifos  (EXP,ISO)
choline  (EXP)
cisplatin  (ISO)
clobetasol  (EXP)
clofibrate  (EXP)
Cuprizon  (ISO)
dexamethasone  (EXP,ISO)
dibutyl phthalate  (EXP)
dioxygen  (EXP)
dorsomorphin  (ISO)
entinostat  (ISO)
flavonoids  (ISO)
folic acid  (EXP)
genistein  (EXP)
gentamycin  (ISO)
glyphosate  (ISO)
graphite  (ISO)
hydroquinone  (ISO)
ketamine  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (EXP)
linalool  (ISO)
methylphenidate  (EXP)
ozone  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
PCB138  (EXP)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP)
progesterone  (ISO)
Ptaquiloside  (EXP)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (EXP)
Soman  (ISO)
streptozocin  (ISO)
temozolomide  (ISO)
testosterone  (ISO)
titanium dioxide  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
valproic acid  (EXP,ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
brain development  (IBA)
camera-type eye morphogenesis  (IBA)
closure of optic fissure  (IMP)
cornea development in camera-type eye  (IMP)
embryonic digestive tract morphogenesis  (IMP)
embryonic skeletal system morphogenesis  (IMP)
eyelid development in camera-type eye  (IMP)
glial cell development  (IMP)
glial cell proliferation  (IMP)
hard palate development  (IMP)
kidney development  (IEA,ISO)
lens morphogenesis in camera-type eye  (IMP)
lung morphogenesis  (IMP)
negative regulation of gene expression  (IMP,ISO)
negative regulation of glial cell proliferation  (IMP,ISO)
negative regulation of lymphocyte proliferation  (IEA,ISO)
negative regulation of transcription by RNA polymerase II  (IBA,IDA,ISO)
nervous system development  (IMP)
neuroepithelial cell differentiation  (IMP)
neuron differentiation  (IBA)
noradrenergic neuron differentiation  (IMP,ISO)
oligodendrocyte development  (IEA,ISO)
outflow tract morphogenesis  (IMP)
positive regulation of BMP signaling pathway  (IMP)
positive regulation of DNA-templated transcription  (IDA,IMP)
positive regulation of gene expression  (IMP,ISO)
positive regulation of hippo signaling  (IMP)
positive regulation of hormone secretion  (IMP)
positive regulation of lens epithelial cell proliferation  (IMP)
positive regulation of neurogenesis  (IDA)
positive regulation of neuron differentiation  (IDA,IMP,ISO)
positive regulation of ossification  (IMP,ISO)
positive regulation of osteoblast differentiation  (ISO,ISS)
positive regulation of stem cell proliferation  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (IBA,IDA,ISO)
regulation of transforming growth factor beta receptor signaling pathway  (IEA)
skeletal muscle cell differentiation  (IMP)
soft palate development  (IMP)
spinal cord development  (IMP)
sympathetic nervous system development  (IMP)
ventricular septum morphogenesis  (IMP)

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (IBA,IDA,ISO)
plasma membrane  (IEA,ISO)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal axon fasciculation  (IAGP)
abnormal bone mineralization  (IAGP)
abnormal bone ossification  (IAGP)
abnormal bronchus morphology  (IAGP)
abnormal calcaneum morphology  (IAGP)
abnormal caudal vertebrae morphology  (IAGP)
abnormal cell death  (IAGP)
abnormal cerebellum morphology  (IAGP)
abnormal cerebral cortex morphology  (IAGP)
abnormal craniofacial morphology  (IAGP)
abnormal cranium morphology  (IAGP)
abnormal dentate gyrus morphology  (IAGP)
abnormal embryonic/fetal subventricular zone morphology  (IAGP)
abnormal eye development  (IAGP)
abnormal eyelid morphology  (IAGP)
abnormal heart development  (IAGP)
abnormal hippocampus CA2 region morphology  (IAGP)
abnormal hippocampus CA3 region morphology  (IAGP)
abnormal hippocampus morphology  (IAGP)
abnormal innervation pattern to muscle  (IAGP)
abnormal limb mesenchyme morphology  (IAGP)
abnormal lumbar vertebrae morphology  (IAGP)
abnormal lung development  (IAGP)
abnormal mandible morphology  (IAGP)
abnormal Meibomian gland morphology  (IAGP)
abnormal nervous system development  (IAGP)
abnormal neural tube morphology  (IAGP)
abnormal neuron differentiation  (IAGP)
abnormal neuronal precursor proliferation  (IAGP)
abnormal notochord morphology  (IAGP)
abnormal olfactory bulb morphology  (IAGP)
abnormal palatal mesenchymal cell proliferation  (IAGP)
abnormal pancreas morphology  (IAGP)
abnormal phalanx morphology  (IAGP)
abnormal pharyngeal arch development  (IAGP)
abnormal pharyngeal arch mesenchyme morphology  (IAGP)
abnormal pterygoid process morphology  (IAGP)
abnormal retina bipolar cell morphology  (IAGP)
abnormal retina morphology  (IAGP)
abnormal retina outer plexiform layer morphology  (IAGP)
abnormal rib morphology  (IAGP)
abnormal secondary palate development  (IAGP)
abnormal skeleton development  (IAGP)
abnormal stellate ganglion morphology  (IAGP)
abnormal sternebra morphology  (IAGP)
abnormal sternum ossification  (IAGP)
abnormal stomach pyloric region morphology  (IAGP)
abnormal sympathetic ganglion morphology  (IAGP)
abnormal sympathetic neuron innervation pattern  (IAGP)
abnormal talus morphology  (IAGP)
abnormal tongue position  (IAGP)
abnormal truncus arteriosus septation  (IAGP)
abnormal vertebrae morphology  (IAGP)
abnormal xiphoid process morphology  (IAGP)
absent limb buds  (IAGP)
absent optic nerve  (IAGP)
absent retina ganglion cell  (IAGP)
absent retina ganglion layer  (IAGP)
absent retina inner plexiform layer  (IAGP)
absent spleen  (IAGP)
aphakia  (IAGP)
asymmetric sternocostal joints  (IAGP)
barrel chest  (IAGP)
blepharoptosis  (IAGP)
cardia bifida  (IAGP)
cleft palate  (IAGP)
cleft secondary palate  (IAGP)
cleft upper lip  (IAGP)
curly tail  (IAGP)
cyanosis  (IAGP)
decreased amacrine cell number  (IAGP)
decreased birth body size  (IAGP)
decreased birth weight  (IAGP)
decreased brain size  (IAGP)
decreased cell proliferation  (IAGP)
decreased cortical ventricular zone thickness  (IAGP)
decreased embryo size  (IAGP)
decreased palatal shelf size  (IAGP)
decreased pulmonary respiratory rate  (IAGP)
decreased retina ganglion cell number  (IAGP)
delayed palatal shelf elevation  (IAGP)
double outlet right ventricle  (IAGP)
edema  (IAGP)
embryonic growth arrest  (IAGP)
embryonic lethality during organogenesis, complete penetrance  (IAGP)
eyelids open at birth  (IAGP)
failure of heart looping  (IAGP)
impaired somite development  (IAGP)
incomplete embryo turning  (IAGP)
incomplete rostral neuropore closure  (IAGP)
increased neuron apoptosis  (IAGP)
increased retina apoptosis  (IAGP)
increased rib number  (IAGP)
kinked neural tube  (IAGP)
kinked tail  (IAGP)
lethality throughout fetal growth and development, complete penetrance  (IAGP)
mandible hypoplasia  (IAGP)
maxilla hypoplasia  (IAGP)
median cleft palate  (IAGP)
micrognathia  (IAGP)
microphthalmia  (IAGP)
myocardium hypoplasia  (IAGP)
neonatal lethality, complete penetrance  (IAGP)
no abnormal phenotype detected  (IAGP)
omphalocele  (IAGP)
open neural tube  (IAGP)
optic nerve hypoplasia  (IAGP)
palatal shelves fail to meet at midline  (IAGP)
perinatal lethality, complete penetrance  (IAGP)
persistent truncus arteriosus  (IAGP)
postnatal lethality, complete penetrance  (IAGP)
pulmonary hypoplasia  (IAGP)
semilunar valve hypoplasia  (IAGP)
short mandible  (IAGP)
small cerebellum  (IAGP)
small hippocampus  (IAGP)
small lung  (IAGP)
small Meckel's cartilage  (IAGP)
small olfactory bulb  (IAGP)
small spleen  (IAGP)
small stomach  (IAGP)
small superior cervical ganglion  (IAGP)
sternebra fusion  (IAGP)
sternum hypoplasia  (IAGP)
thin cerebral cortex  (IAGP)
thin retina ganglion layer  (IAGP)
thin retina inner nuclear layer  (IAGP)
ventricular septal defect  (IAGP)
wavy neural tube  (IAGP)
wide cranial sutures  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, etal., Science 2004 Dec 24;306(5705):2255-7.
2. Functional annotation of a full-length mouse cDNA collection. Kawai J, etal., Nature. 2001 Feb 8;409(6821):685-90.
3. Cooperative function of POU proteins and SOX proteins in glial cells. Kuhlbrodt K, etal., J Biol Chem 1998 Jun 26;273(26):16050-7.
4. Electronic Transfer of Homolog Data MGD and Homologene mouse data transfer
5. MGDs mouse GO annotations MGD data from the GO Consortium
6. MGD IEA MGD IEA
7. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
8. Mouse MP Annotation Import Pipeline RGD automated import pipeline
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7590241   PMID:7821514   PMID:8441686   PMID:8666406   PMID:8889548   PMID:8921394   PMID:9337129   PMID:10037800   PMID:10349636   PMID:10925158   PMID:11042159   PMID:11071752  
PMID:11076861   PMID:11793228   PMID:12447396   PMID:12477932   PMID:12815626   PMID:12923295   PMID:14573547   PMID:14681479   PMID:15163632   PMID:15172686   PMID:15226823   PMID:15254231  
PMID:15345747   PMID:15456859   PMID:15489334   PMID:15778864   PMID:16107646   PMID:16141072   PMID:16141073   PMID:16306355   PMID:16602821   PMID:16919269   PMID:17055661   PMID:17084361  
PMID:17515609   PMID:17623775   PMID:17697936   PMID:18287559   PMID:18403418   PMID:18423449   PMID:18505825   PMID:18640244   PMID:18725516   PMID:19030180   PMID:19133245   PMID:19272164  
PMID:19303107   PMID:19369396   PMID:19386638   PMID:19490090   PMID:19799774   PMID:19808959   PMID:20147379   PMID:20436479   PMID:20463296   PMID:20596238   PMID:20646169   PMID:20847309  
PMID:21117150   PMID:21267068   PMID:21527504   PMID:21677750   PMID:21731673   PMID:21873192   PMID:21873635   PMID:21880559   PMID:21985610   PMID:22024412   PMID:22085726   PMID:22331573  
PMID:22371338   PMID:22378879   PMID:22465478   PMID:22678282   PMID:22687574   PMID:23060611   PMID:23201825   PMID:23313252   PMID:23318640   PMID:23356643   PMID:23483698   PMID:23516376  
PMID:23559562   PMID:23649630   PMID:23888050   PMID:23933087   PMID:24115909   PMID:24154525   PMID:24310815   PMID:24589730   PMID:24722414   PMID:24859337   PMID:24886874   PMID:24952961  
PMID:25043184   PMID:25234735   PMID:25452386   PMID:25652387   PMID:25698749   PMID:25761772   PMID:25775587   PMID:26203155   PMID:26504244   PMID:26687222   PMID:26826126   PMID:26864488  
PMID:27225767   PMID:27241892   PMID:27600842   PMID:28053041   PMID:28118982   PMID:28215559   PMID:28411269   PMID:28429312   PMID:28641110   PMID:28641113   PMID:29031500   PMID:29180573  
PMID:29459093   PMID:29513653   PMID:29746989   PMID:29749639   PMID:29807017   PMID:29954934   PMID:29973868   PMID:30329130   PMID:30385877   PMID:30619460   PMID:30786278   PMID:30871468  
PMID:30879763   PMID:31082736   PMID:31155355   PMID:31291246   PMID:31351040   PMID:31492871   PMID:31724774   PMID:32080705   PMID:32346881   PMID:32553152   PMID:33236128   PMID:33441400  
PMID:33579706   PMID:33662665   PMID:33674582   PMID:33951080   PMID:33969421   PMID:34158358   PMID:34184026   PMID:34321999   PMID:34374250   PMID:34431536   PMID:35254515   PMID:35301318  
PMID:35302059   PMID:35613274   PMID:35642566   PMID:35830813   PMID:35915179   PMID:35942939   PMID:36343245   PMID:36450980   PMID:36571426   PMID:37365500   PMID:37585469   PMID:37705115  
PMID:38237141   PMID:38324208   PMID:38594232   PMID:39095712  


Genomics

Comparative Map Data
Sox11
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391227,384,267 - 27,392,717 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1227,384,263 - 27,392,573 (-)EnsemblGRCm39 Ensembl
GRCm381227,334,268 - 27,342,718 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1227,334,264 - 27,342,574 (-)EnsemblGRCm38mm10GRCm38
MGSCv371228,019,133 - 28,027,583 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361227,921,484 - 27,928,980 (-)NCBIMGSCv36mm8
Celera1228,811,290 - 28,819,758 (-)NCBICelera
Cytogenetic Map12A2NCBI
cM Map129.95NCBI
SOX11
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3825,692,384 - 5,701,385 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl25,692,384 - 5,701,385 (+)EnsemblGRCh38hg38GRCh38
GRCh3725,832,516 - 5,841,517 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3625,750,250 - 5,758,968 (+)NCBINCBI36Build 36hg18NCBI36
Build 3425,783,396 - 5,792,114NCBI
Celera25,748,512 - 5,756,851 (+)NCBICelera
Cytogenetic Map2p25.2NCBI
HuRef25,676,397 - 5,685,112 (+)NCBIHuRef
CHM1_125,762,093 - 5,770,810 (+)NCBICHM1_1
T2T-CHM13v2.025,713,811 - 5,722,812 (+)NCBIT2T-CHM13v2.0
Sox11
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8649,736,773 - 49,738,794 (-)NCBIGRCr8
mRatBN7.2644,008,333 - 44,010,354 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl644,008,340 - 44,010,354 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx644,315,859 - 44,317,880 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0644,630,739 - 44,632,760 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0644,063,910 - 44,065,931 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0646,629,967 - 46,631,988 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl646,629,974 - 46,631,983 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0655,343,067 - 55,345,088 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4645,141,366 - 45,143,387 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1645,144,498 - 45,146,513 (-)NCBI
Celera643,252,857 - 43,254,878 (-)NCBICelera
Cytogenetic Map6q16NCBI
Sox11
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554872,679,145 - 2,680,521 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554872,678,961 - 2,680,869 (-)NCBIChiLan1.0ChiLan1.0
SOX11
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v212120,808,899 - 120,820,381 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A120,812,876 - 120,824,358 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A5,699,738 - 5,711,210 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A5,840,399 - 5,841,762 (+)NCBIpanpan1.1PanPan1.1panPan2
SOX11
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha173,570,850 - 3,572,822 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0173,680,433 - 3,682,409 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl173,680,517 - 3,682,010 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1173,573,068 - 3,575,034 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0173,576,503 - 3,578,454 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0173,580,950 - 3,582,922 (+)NCBIUU_Cfam_GSD_1.0
Sox11
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244050589,632,081 - 9,635,331 (-)NCBIHiC_Itri_2
SpeTri2.0NW_004937107203,120 - 207,185 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SOX11
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl3129,798,854 - 129,800,197 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.13129,797,438 - 129,800,568 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23138,751,621 - 138,754,531 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SOX11
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.114101,982,551 - 101,991,305 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl14101,989,895 - 101,991,220 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604510,348,860 - 10,357,867 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sox11
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248464,044,893 - 4,046,248 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248464,043,010 - 4,046,660 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Sox11
340 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:195
Count of miRNA genes:141
Interacting mature miRNAs:156
Transcripts:ENSMUST00000079063
Prediction methods:Miranda, Rnahybrid, Targetscan
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
12910983Pifs1_mpeptide-induced fatal syndrome 1 (mouse)12130433078Mouse
4141436Chldq7_mcholesterol and HDL QTL 7 (mouse)Not determined12127920733Mouse
1301207Circp1_mcircadian photosensitivity 1 (mouse)Not determined12133430339Mouse
1301723Fcsa7_mfemoral cross-sectional area 7 (mouse)Not determined12949100443491112Mouse
15039339Nmrs29_mNAFLD-associated magnetic resonance shift 29 (mouse)121782585251825852Mouse
4141296Femwf9_mfemur work to failure 9 (mouse)Not determined127920733Mouse
1302172Skts5_mskin tumor susceptibility 5 (mouse)Not determined122214886656149016Mouse
10043977Obq34_mobesity QTL 34 (mouse)Not determined121514733149147331Mouse
10043848Hdlq90_mHDL QTL 90 (mouse)Not determined121783993951840081Mouse
1558978Cplaq10_mcircadian period of locomotor activity 10 (mouse)Not determined121534102679040364Mouse
1301574Lmblgq5_mlimb length QTL 5 (mouse)Not determined121759644780956883Mouse
1300870Ath18_matherosclerosis 18 (mouse)Not determined121825996652260067Mouse
13207568Tcq14_mtotal cholesterol QTL 14 (mouse)121166000197176774Mouse
27226753Femd7_mfemur midshaft diameter 7, 10 week (mouse)12955000084146774Mouse
26884410Bzwq15_mbi-zygomatic width QTL 15, 16 week (mouse)12365000029749999Mouse
4141660Nbwa1_mNZB and NZW autoimmunity 1 (mouse)Not determined1234013434340302Mouse
4142234Tmc1m3_mTmc1 modifier 3 (mouse)Not determined12541844077031203Mouse
13524843Ppiq8_mprepulse inhibition QTL 8 (mouse)121104319450945796Mouse
26884413Bzwq9_mbi-zygomatic width QTL 9, 10 week (mouse)121615000147746783Mouse
13524839Ppiq10_mprepulse inhibition QTL 10 (mouse)121304319554945798Mouse
13208568Bmiq11_mbody mass index QTL 11 (mouse)12805000040049999Mouse
4141516slwr_mslowlearner (mouse)Not determined1239247546392614Mouse
1301925Ath6_matherosclerosis 6 (mouse)Not determined12132758756Mouse
1301163Eae16_msusceptibility to experimental allergic encephalomyelitis 16 (mouse)Not determined12772315841723301Mouse
12904956Edlmmq10_mextensor digitorum longus muscle mass QTL 10 (mouse)121973983353739833Mouse
14746972Manh72_mmandible shape 72 (mouse)121061528144615281Mouse
1301037Cd4ts5_mCD4 T cell subset 5 (mouse)Not determined12835244442352581Mouse
10401249Bglu15_mblood glucose level 15 (mouse)Not determined121062064244620809Mouse

Markers in Region
AI836553  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381227,334,831 - 27,334,975UniSTSGRCm38
MGSCv371228,019,696 - 28,019,840UniSTSGRCm37
Celera1228,811,854 - 28,811,998UniSTS
Cytogenetic Map12A3UniSTS
Whitehead/MRC_RH12227.28UniSTS
Sox11  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381227,339,910 - 27,340,639UniSTSGRCm38
MGSCv371228,024,775 - 28,025,504UniSTSGRCm37
Celera1228,816,946 - 28,817,679UniSTS
Cytogenetic Map12A3UniSTS
cM MapUN UniSTS
cM Map12 UniSTS
RH140068  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381227,341,164 - 27,341,359UniSTSGRCm38
MGSCv371228,026,029 - 28,026,224UniSTSGRCm37
Celera1228,818,204 - 28,818,399UniSTS
Cytogenetic Map12A3UniSTS
BE117478  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381227,336,039 - 27,336,234UniSTSGRCm38
MGSCv371228,020,904 - 28,021,099UniSTSGRCm37
Celera1228,813,060 - 28,813,255UniSTS
Cytogenetic Map12A3UniSTS
PMC85614P1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381227,341,501 - 27,342,153UniSTSGRCm38
MGSCv371228,026,366 - 28,027,018UniSTSGRCm37
Celera1228,818,541 - 28,819,193UniSTS
Cytogenetic Map12A3UniSTS
Sox11  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381227,342,073 - 27,342,223UniSTSGRCm38
MGSCv371228,026,938 - 28,027,088UniSTSGRCm37
Celera1228,819,113 - 28,819,263UniSTS
Cytogenetic Map12A3UniSTS
cM MapUN UniSTS
cM Map12 UniSTS
Sox11  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12A3UniSTS
Sox11  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12A3UniSTS
Sox11  
Mouse AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map12A3UniSTS


Expression

RNA-SEQ Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_009234 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB108675 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC158383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF009414 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK004158 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK012222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK012306 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK017690 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK018080 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK020994 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK021300 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK086263 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK086326 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK146514 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK165005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK165693 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC053503 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC062095 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC078643 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BK001484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  Z18960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSMUST00000079063   ⟹   ENSMUSP00000078070
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1227,384,263 - 27,392,573 (-)Ensembl
GRCm38.p6 Ensembl1227,334,264 - 27,342,574 (-)Ensembl
RefSeq Acc Id: NM_009234   ⟹   NP_033260
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391227,384,267 - 27,392,717 (-)NCBI
GRCm381227,334,268 - 27,342,718 (-)ENTREZGENE
MGSCv371228,019,133 - 28,027,583 (-)RGD
Celera1228,811,290 - 28,819,758 (-)RGD
cM Map12 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_033260   ⟸   NM_009234
- UniProtKB: Q7M6Y2 (UniProtKB/Swiss-Prot),   Q04889 (UniProtKB/Swiss-Prot),   O89036 (UniProtKB/Swiss-Prot),   O35178 (UniProtKB/Swiss-Prot),   Q80XF0 (UniProtKB/Swiss-Prot),   Q6AZA6 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000078070   ⟸   ENSMUST00000079063
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7M6Y2-F1-model_v2 AlphaFold Q7M6Y2 1-395 view protein structure

Promoters
RGD ID:8678040
Promoter ID:EPDNEW_M17051
Type:initiation region
Name:Sox11_1
Description:Mus musculus SRY -box 11 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381227,342,704 - 27,342,764EPDNEW
RGD ID:6823437
Promoter ID:MM_KWN:11382
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   ES_Cell
Transcripts:NM_009234
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361228,026,416 - 28,027,592 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:98359 AgrOrtholog
Ensembl Genes ENSMUSG00000063632 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000079063 ENTREZGENE
  ENSMUST00000079063.7 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.30.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro HMG_box_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HMG_box_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOX-11/4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SRY-related_HMG-box_TFs UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:20666 UniProtKB/Swiss-Prot
MGD MGI:98359 ENTREZGENE
NCBI Gene 20666 ENTREZGENE
PANTHER PTHR10270:SF113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SOX TRANSCRIPTION FACTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam HMG_box UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sox11 PhenoGen
PIRSF SOX-12/11/4a UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE HMG_BOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47095 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt O35178 ENTREZGENE
  O89036 ENTREZGENE
  Q04889 ENTREZGENE
  Q6AZA6 ENTREZGENE, UniProtKB/TrEMBL
  Q7M6Y2 ENTREZGENE
  Q80XF0 ENTREZGENE
  SOX11_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary O35178 UniProtKB/Swiss-Prot
  O89036 UniProtKB/Swiss-Prot
  Q04889 UniProtKB/Swiss-Prot
  Q80XF0 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-26 Sox11  SRY (sex determining region Y)-box 11    SRY-box containing gene 11  Symbol and/or name change 5135510 APPROVED