Sox11 (SRY-box transcription factor 11) - Rat Genome Database

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Gene: Sox11 (SRY-box transcription factor 11) Rattus norvegicus
Analyze
Symbol: Sox11
Name: SRY-box transcription factor 11
RGD ID: 69351
Description: Enables DNA-binding transcription activator activity, RNA polymerase II-specific and transcription cis-regulatory region binding activity. Involved in kidney development; neurogenesis; and positive regulation of transcription by RNA polymerase II. Located in nucleus. Human ortholog(s) of this gene implicated in Coffin-Siris syndrome 9. Orthologous to human SOX11 (SRY-box transcription factor 11); INTERACTS WITH 6-propyl-2-thiouracil; alachlor; amitriptyline.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: SRY (sex determining region Y)-box 11; SRY box 11; SRY-box 11; SRY-box containing gene 11; transcription factor SOX-11
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
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dichloroethane  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',5,5'-tetrachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-methylcholine  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
alachlor  (EXP)
all-trans-retinoic acid  (ISO)
amitriptyline  (EXP)
aristolochic acid A  (ISO)
Aroclor 1254  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
camptothecin  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloroprene  (ISO)
chlorpyrifos  (EXP,ISO)
choline  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
clofibrate  (ISO)
Cuprizon  (EXP)
dexamethasone  (EXP,ISO)
dibutyl phthalate  (ISO)
dioxygen  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
flavonoids  (EXP)
folic acid  (ISO)
genistein  (ISO)
gentamycin  (EXP)
graphite  (EXP)
hydroquinone  (ISO)
ketamine  (EXP)
L-ascorbic acid  (EXP)
L-methionine  (ISO)
linalool  (EXP)
methylphenidate  (ISO)
ozone  (ISO)
panobinostat  (ISO)
paracetamol  (EXP)
PCB138  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
Ptaquiloside  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
Soman  (EXP)
streptozocin  (EXP)
temozolomide  (ISO)
testosterone  (EXP)
titanium dioxide  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
valproic acid  (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  (ISO,ISS)
cornea development in camera-type eye  (ISO,ISS)
embryonic digestive tract morphogenesis  (ISO,ISS)
embryonic skeletal system morphogenesis  (ISO,ISS)
eyelid development in camera-type eye  (ISO,ISS)
glial cell development  (ISO)
glial cell proliferation  (ISO,ISS)
hard palate development  (ISO,ISS)
kidney development  (IEP)
lens morphogenesis in camera-type eye  (ISO,ISS)
lung morphogenesis  (ISO,ISS)
negative regulation of gene expression  (ISO,ISS)
negative regulation of glial cell proliferation  (ISO,ISS)
negative regulation of lymphocyte proliferation  (ISO)
negative regulation of transcription by RNA polymerase II  (IBA,ISO,ISS)
nervous system development  (ISO,ISS)
neuroepithelial cell differentiation  (ISO,ISS)
neuron differentiation  (IBA,ISO)
noradrenergic neuron differentiation  (IMP,ISO)
oligodendrocyte development  (IEP)
outflow tract morphogenesis  (ISO,ISS)
positive regulation of BMP signaling pathway  (ISO,ISS)
positive regulation of DNA-templated transcription  (ISO)
positive regulation of gene expression  (ISO,ISS)
positive regulation of hippo signaling  (ISO,ISS)
positive regulation of hormone secretion  (ISO,ISS)
positive regulation of lens epithelial cell proliferation  (ISO,ISS)
positive regulation of neurogenesis  (ISO,ISS)
positive regulation of neuron differentiation  (ISO,ISS)
positive regulation of ossification  (ISO,ISS)
positive regulation of osteoblast differentiation  (ISO,ISS)
positive regulation of stem cell proliferation  (ISO,ISS)
positive regulation of transcription by RNA polymerase II  (IBA,IMP,ISO,ISS)
regulation of transforming growth factor beta receptor signaling pathway  (ISO)
skeletal muscle cell differentiation  (ISO)
soft palate development  (ISO,ISS)
spinal cord development  (ISO,ISS)
sympathetic nervous system development  (ISO,ISS)
ventricular septum morphogenesis  (ISO,ISS)

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

References

References - curated
# Reference Title Reference Citation
1. The helix-loop-helix inhibitor of differentiation (ID) proteins induce post-mitotic terminally differentiated Sertoli cells to re-enter the cell cycle and proliferate. Chaudhary J, etal., Biol Reprod. 2005 May;72(5):1205-17. Epub 2005 Jan 12.
2. The three SoxC proteins--Sox4, Sox11 and Sox12--exhibit overlapping expression patterns and molecular properties. Dy P, etal., Nucleic Acids Res. 2008 May;36(9):3101-17. doi: 10.1093/nar/gkn162. Epub 2008 Apr 10.
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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. The Optimedin gene is a downstream target of Pax6. Grinchuk O, etal., J Biol Chem. 2005 Oct 21;280(42):35228-37. Epub 2005 Aug 22.
6. Cooperative function of POU proteins and SOX proteins in glial cells. Kuhlbrodt K, etal., J Biol Chem 1998 Jun 26;273(26):16050-7.
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. Mesenchymal-epithelial transition in the developing metanephric kidney: gene expression study by differential display. Plisov SY, etal., Genesis. 2000 May;27(1):22-31.
9. Sequential requirement of Sox4 and Sox11 during development of the sympathetic nervous system. Potzner MR, etal., Development. 2010 Mar;137(5):775-84. doi: 10.1242/dev.042101.
10. GOA pipeline RGD automated data pipeline
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Fibroblast growth factor-inducible-14 is induced in axotomized neurons and promotes neurite outgrowth. Tanabe K, etal., J Neurosci. 2003 Oct 22;23(29):9675-86.
13. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
14. Identification of novel domains within Sox-2 and Sox-11 involved in autoinhibition of DNA binding and partnership specificity. Wiebe MS, etal., J Biol Chem. 2003 May 16;278(20):17901-11. Epub 2003 Mar 10.
Additional References at PubMed
PMID:10574465   PMID:10606637   PMID:15254231   PMID:15456859   PMID:17934069   PMID:18261853   PMID:18423449   PMID:18505825   PMID:19490090   PMID:19808959   PMID:20596238   PMID:20624318  
PMID:20626275   PMID:20646169   PMID:20847309   PMID:21124928   PMID:21527504   PMID:25466891   PMID:31916393   PMID:32935389   PMID:38407972  


Genomics

Comparative Map Data
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
(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
(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
(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
6 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:263
Count of miRNA genes:172
Interacting mature miRNAs:196
Transcripts:ENSRNOT00000045963
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63207442872227641Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63330954957730294Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63509870971636405Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63569161857730540Rat
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat

Markers in Region
RH140068  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2644,008,807 - 44,009,003 (+)MAPPERmRatBN7.2
Rnor_6.0646,630,442 - 46,630,637NCBIRnor6.0
Rnor_5.0655,343,542 - 55,343,737UniSTSRnor5.0
RGSC_v3.4645,141,841 - 45,142,036UniSTSRGSC3.4
Celera643,253,332 - 43,253,527UniSTS
RH 3.4 Map6263.2UniSTS
Cytogenetic Map6q16UniSTS
Sox11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2644,007,548 - 44,008,282 (+)MAPPERmRatBN7.2
Rnor_6.0646,629,183 - 46,629,916NCBIRnor6.0
Rnor_5.0655,342,283 - 55,343,016UniSTSRnor5.0
RGSC_v3.4645,140,582 - 45,141,315UniSTSRGSC3.4
Celera643,252,073 - 43,252,806UniSTS
Cytogenetic Map6q16UniSTS
PMC85614P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2644,009,144 - 44,009,797 (+)MAPPERmRatBN7.2
Rnor_6.0646,630,779 - 46,631,431NCBIRnor6.0
Rnor_5.0655,343,879 - 55,344,531UniSTSRnor5.0
RGSC_v3.4645,142,178 - 45,142,830UniSTSRGSC3.4
Celera643,253,669 - 43,254,321UniSTS
Cytogenetic Map6q16UniSTS
Sox11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2644,009,716 - 44,009,867 (+)MAPPERmRatBN7.2
Rnor_6.0646,631,351 - 46,631,501NCBIRnor6.0
Rnor_5.0655,344,451 - 55,344,601UniSTSRnor5.0
RGSC_v3.4645,142,750 - 45,142,900UniSTSRGSC3.4
Celera643,254,241 - 43,254,391UniSTS
Cytogenetic Map6q16UniSTS
UniSTS:547149  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2644,008,873 - 44,008,933 (+)MAPPERmRatBN7.2
Rnor_6.0646,630,508 - 46,630,567NCBIRnor6.0
Rnor_5.0655,343,608 - 55,343,667UniSTSRnor5.0
Celera643,253,398 - 43,253,457UniSTS
Cytogenetic Map6q16UniSTS


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 12 4 4 4 54 14 21
Low 15 13 6 17 6 2 2 18 19 12 6 2
Below cutoff 2 12 22 15 2 15 6 9 2 2 8 4 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000045963   ⟹   ENSRNOP00000040127
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl644,008,340 - 44,010,354 (-)Ensembl
Rnor_6.0 Ensembl646,629,974 - 46,631,983 (-)Ensembl
RefSeq Acc Id: NM_053349   ⟹   NP_445801
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8649,736,773 - 49,738,794 (-)NCBI
mRatBN7.2644,008,333 - 44,010,354 (-)NCBI
Rnor_6.0646,629,967 - 46,631,988 (-)NCBI
Rnor_5.0655,343,067 - 55,345,088 (-)NCBI
RGSC_v3.4645,141,366 - 45,143,387 (-)RGD
Celera643,252,857 - 43,254,878 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_445801 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein CAA06166 (Get FASTA)   NCBI Sequence Viewer  
  EDM03208 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000040127
  ENSRNOP00000040127.3
  ENSRNOP00055007474
  ENSRNOP00060012573
  ENSRNOP00065013751
GenBank Protein P0C1G9 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_445801   ⟸   NM_053349
- UniProtKB: P0C1G9 (UniProtKB/Swiss-Prot),   A6HB03 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000040127   ⟸   ENSRNOT00000045963
Protein Domains
HMG box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P0C1G9-F1-model_v2 AlphaFold P0C1G9 1-395 view protein structure

Transcriptome

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

Promoters
RGD ID:13694529
Promoter ID:EPDNEW_R5052
Type:single initiation site
Name:Sox11_1
Description:SRY box 11
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_6.0646,631,983 - 46,632,043EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69351 AgrOrtholog
BioCyc Gene G2FUF-37986 BioCyc
Ensembl Genes ENSRNOG00000030034 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055005963 UniProtKB/Swiss-Prot
  ENSRNOG00060009512 UniProtKB/Swiss-Prot
  ENSRNOG00065011137 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000045963 ENTREZGENE
  ENSRNOT00000045963.5 UniProtKB/Swiss-Prot
  ENSRNOT00055009669 UniProtKB/Swiss-Prot
  ENSRNOT00060016064 UniProtKB/Swiss-Prot
  ENSRNOT00065018027 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
KEGG Report rno:84046 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 84046 ENTREZGENE
PANTHER PTHR10270:SF113 UniProtKB/Swiss-Prot
  SOX TRANSCRIPTION FACTOR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TRANSCRIPTION FACTOR SOX-11 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
RatGTEx ENSRNOG00000030034 RatGTEx
  ENSRNOG00055005963 RatGTEx
  ENSRNOG00060009512 RatGTEx
  ENSRNOG00065011137 RatGTEx
SMART HMG UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP HMG-box UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
TIGR TC221702
UniProt A6HB03 ENTREZGENE, UniProtKB/TrEMBL
  P0C1G9 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary O35178 UniProtKB/Swiss-Prot
  O89036 UniProtKB/Swiss-Prot
  Q04889 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-05 Sox11  SRY-box transcription factor 11  Sox11  SRY box 11  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-13 Sox11  SRY box 11  Sox11  SRY (sex determining region Y)-box 11  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-18 Sox11  SRY (sex determining region Y)-box 11  Sox11  SRY-box containing gene 11  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Sox11  SRY-box containing gene 11      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference