Six1 (sine oculis-related homeobox 1) - Rat Genome Database

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Gene: Six1 (sine oculis-related homeobox 1) Mus musculus
Analyze
Symbol: Six1
Name: sine oculis-related homeobox 1
RGD ID: 1550080
MGI Page MGI
Description: Enables DNA-binding transcription factor activity; chromatin binding activity; and sequence-specific DNA binding activity. Involved in several processes, including kidney development; nervous system development; and positive regulation of morphogenesis of an epithelium. Acts upstream of or within several processes, including embryonic organ morphogenesis; positive regulation of cell population proliferation; and regulation of transcription by RNA polymerase II. Located in nucleus. Part of transcription regulator complex. Is expressed in several structures, including alimentary system; embryo mesenchyme; genitourinary system; limb; and sensory organ. Used to study branchiootorenal syndrome. Human ortholog(s) of this gene implicated in autosomal dominant nonsyndromic deafness 23; branchiootorenal syndrome; and nephroblastoma. Orthologous to human SIX1 (SIX homeobox 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BB138287; homeobox protein SIX1; sine oculis homeobox homolog 1; sine oculis-related homeobox 1 homolog
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
GRCm391273,088,601 - 73,093,486 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1273,086,789 - 73,100,661 (-)EnsemblGRCm39 Ensembl
GRCm381273,041,827 - 73,046,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,040,015 - 73,053,887 (-)EnsemblGRCm38mm10GRCm38
MGSCv371274,142,814 - 74,147,699 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361273,960,668 - 73,965,302 (-)NCBIMGSCv36mm8
Celera1274,158,405 - 74,163,290 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1230.34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-demecolcine  (ISO)
1,2-dichloroethane  (EXP)
15-acetyldeoxynivalenol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (EXP)
4-hydroxyphenyl retinamide  (EXP)
6-propyl-2-thiouracil  (ISO)
acrolein  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
alpha-Zearalanol  (ISO)
amiodarone  (ISO)
ammonium chloride  (ISO)
antimycin A  (ISO)
antirheumatic drug  (ISO)
arsenite(3-)  (ISO)
benzo[a]pyrene  (EXP,ISO)
benzo[b]fluoranthene  (EXP)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP,ISO)
C60 fullerene  (ISO)
carbamazepine  (ISO)
carbon nanotube  (EXP)
chlordecone  (EXP)
choline  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
dexamethasone  (ISO)
diallyl trisulfide  (ISO)
dibenz[a,h]anthracene  (EXP)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
dorsomorphin  (ISO)
folic acid  (EXP)
fulvestrant  (EXP)
genistein  (EXP)
gentamycin  (ISO)
indometacin  (ISO)
L-methionine  (EXP)
lithium chloride  (ISO)
mercury dibromide  (ISO)
methimazole  (ISO)
methylmercury chloride  (ISO)
oxaliplatin  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (ISO)
perfluorooctanoic acid  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (EXP,ISO)
rotenone  (ISO)
SB 431542  (ISO)
sodium arsenite  (ISO)
temozolomide  (ISO)
testosterone  (EXP)
tetrachloromethane  (ISO)
titanium dioxide  (EXP)
topotecan  (ISO)
triazines  (EXP)
trichloroethene  (ISO)
trichostatin A  (ISO)
troglitazone  (EXP)
trovafloxacin  (EXP)
urethane  (ISO)
valproic acid  (EXP,ISO)
vanadyl sulfate  (ISO)
vincristine  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aorta morphogenesis  (IGI)
apoptotic process  (IEA)
branching involved in ureteric bud morphogenesis  (IGI)
cellular response to 3,3',5-triiodo-L-thyronine  (IEA,ISO)
cochlea morphogenesis  (IMP)
embryonic cranial skeleton morphogenesis  (IGI)
embryonic skeletal system morphogenesis  (IGI)
endothelin receptor signaling pathway  (IMP)
epithelial cell differentiation  (IMP)
facial nerve morphogenesis  (IMP)
fungiform papilla morphogenesis  (IMP)
gene expression  (IMP)
generation of neurons  (IMP)
inner ear development  (IMP)
inner ear morphogenesis  (IGI)
kidney development  (IMP)
mesenchymal cell proliferation involved in ureter development  (IGI)
mesonephric tubule formation  (IMP)
metanephric mesenchyme development  (IMP)
middle ear morphogenesis  (IMP)
myoblast migration  (IGI)
myoblast proliferation  (IGI)
myotome development  (IMP)
negative regulation of apoptotic process  (IMP)
negative regulation of neuron apoptotic process  (IMP)
negative regulation of transcription by RNA polymerase II  (IDA)
neural crest cell differentiation  (IGI)
neurogenesis  (IMP)
neuron fate specification  (IGI)
Notch signaling pathway  (IMP)
olfactory placode formation  (IMP)
organ induction  (IMP)
otic vesicle development  (IGI,IMP)
outflow tract morphogenesis  (IGI)
pattern specification process  (IGI,IMP)
pharyngeal system development  (IGI,IMP)
positive regulation of branching involved in ureteric bud morphogenesis  (IGI,IMP)
positive regulation of brown fat cell differentiation  (IMP)
positive regulation of DNA-templated transcription  (IDA,IMP,ISO)
positive regulation of mesenchymal cell proliferation involved in ureter development  (IGI)
positive regulation of myoblast proliferation  (IGI)
positive regulation of secondary heart field cardioblast proliferation  (IGI)
positive regulation of transcription by RNA polymerase II  (IDA,IGI,ISO)
positive regulation of ureteric bud formation  (IMP)
protein localization to nucleus  (IEA,ISO)
regulation of branch elongation involved in ureteric bud branching  (IMP)
regulation of DNA-templated transcription  (IDA)
regulation of epithelial cell proliferation  (IMP)
regulation of gene expression  (IGI)
regulation of neuron differentiation  (IGI,IMP)
regulation of protein localization  (IGI)
regulation of skeletal muscle cell differentiation  (IDA)
regulation of skeletal muscle cell proliferation  (IBA)
regulation of skeletal muscle satellite cell proliferation  (IDA)
regulation of synaptic assembly at neuromuscular junction  (IGI)
regulation of transcription by RNA polymerase II  (IBA)
sensory perception of sound  (IMP)
skeletal muscle fiber development  (IBA)
skeletal muscle tissue development  (IGI,IMP)
skeletal system morphogenesis  (IMP)
thymus development  (IGI,IMP)
thyroid gland development  (IMP)
tongue development  (IMP)
trigeminal ganglion development  (IMP)
ureter smooth muscle cell differentiation  (IMP)
ureteric bud development  (IGI,IMP)

Cellular Component
cytoplasm  (IEA)
nucleolus  (IEA,ISO)
nucleoplasm  (ISO,TAS)
nucleus  (IBA,IDA,ISO)
transcription regulator complex  (IBA,IDA,IPI)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
abnormal blood vessel morphology  (IEA)
abnormal cardiac outflow tract development  (IAGP)
abnormal cardiovascular development  (IAGP)
abnormal cochlea morphology  (IAGP)
abnormal cochlear hair cell morphology  (IAGP)
abnormal common carotid artery morphology  (IAGP)
abnormal common crus morphology  (IAGP)
abnormal cranial neural crest cell morphology  (IAGP)
abnormal craniofacial bone morphology  (IAGP)
abnormal craniofacial development  (IAGP)
abnormal craniofacial morphology  (IEA)
abnormal crista ampullaris morphology  (IAGP)
abnormal dorsal root ganglion morphology  (IAGP)
abnormal endolymphatic duct morphology  (IAGP)
abnormal epaxial muscle morphology  (IAGP)
abnormal external nares morphology  (IAGP)
abnormal extraocular muscle morphology  (IAGP)
abnormal face development  (IAGP)
abnormal facial nerve morphology  (IAGP)
abnormal forelimb morphology  (IAGP)
abnormal frontal bone morphology  (IAGP)
abnormal genioglossus muscle morphology  (IAGP)
abnormal hindlimb morphology  (IAGP)
abnormal hyoid bone greater horn morphology  (IAGP)
abnormal hypaxial muscle morphology  (IAGP)
abnormal incus morphology  (IAGP)
abnormal inner ear canal morphology  (IAGP)
abnormal inner ear morphology  (IAGP)
abnormal inner ear vestibule morphology  (IAGP)
abnormal intercostal muscle morphology  (IAGP)
abnormal intrinsic tongue muscle morphology  (IAGP)
abnormal kidney development  (IAGP)
abnormal kidney morphology  (IAGP)
abnormal lacrimal gland development  (IAGP)
abnormal malleus morphology  (IAGP)
abnormal Meckel's cartilage morphology  (IAGP)
abnormal middle ear morphology  (IAGP)
abnormal midface morphology  (IAGP)
abnormal muscle development  (IAGP)
abnormal muscle fiber morphology  (IAGP)
abnormal muscle physiology  (IAGP)
abnormal muscle precursor cell migration  (IAGP)
abnormal muscle regeneration  (IAGP)
abnormal myogenesis  (IAGP)
abnormal nasal bone morphology  (IAGP)
abnormal nasal cavity morphology  (IAGP)
abnormal nervous system physiology  (IAGP)
abnormal nose morphology  (IAGP)
abnormal olfactory epithelium morphology  (IAGP)
abnormal olfactory system morphology  (IAGP)
abnormal otic vesicle development  (IAGP)
abnormal placenta morphology  (IEA)
abnormal placenta vasculature  (IEA)
abnormal posterior semicircular canal morphology  (IAGP)
abnormal pulmonary artery morphology  (IAGP)
abnormal retina morphology  (IEA)
abnormal rib morphology  (IAGP)
abnormal semicircular canal ampulla morphology  (IAGP)
abnormal semicircular canal morphology  (IAGP)
abnormal skeletal muscle morphology  (IAGP)
abnormal skin morphology  (IEA)
abnormal spleen morphology  (IEA)
abnormal stapes morphology  (IAGP)
abnormal sternocostal joint morphology  (IAGP)
abnormal sternum ossification  (IAGP)
abnormal styloid process morphology  (IAGP)
abnormal submandibular gland development  (IAGP)
abnormal submandibular gland physiology  (IAGP)
abnormal superior semicircular canal morphology  (IAGP)
abnormal thoracic cage morphology  (IAGP)
abnormal trigeminal ganglion morphology  (IAGP)
abnormal tympanic membrane morphology  (IAGP)
abnormal ureteric bud morphology  (IAGP)
abnormal uterus morphology  (IEA)
abnormal vestibular saccule morphology  (IAGP)
abnormal xiphoid process morphology  (IAGP)
absent cochlea  (IAGP)
absent diaphragm  (IAGP)
absent eye muscles  (IAGP)
absent hypaxial muscle  (IAGP)
absent incus  (IAGP)
absent inner ear  (IAGP)
absent inner ear vestibule  (IAGP)
absent kidney  (IAGP)
absent lateral semicircular canal  (IAGP)
absent maxillary shelf  (IAGP)
absent Meckel's cartilage  (IAGP)
absent metanephros  (IAGP)
absent nasal bone  (IAGP)
absent olfactory epithelium  (IAGP)
absent parotid gland  (IAGP)
absent pinna reflex  (IAGP)
absent premaxilla  (IAGP)
absent scala media  (IAGP)
absent semicircular canals  (IAGP)
absent stapedial artery  (IAGP)
absent stapes  (IAGP)
absent tongue muscles  (IAGP)
absent turbinates  (IAGP)
absent tympanic ring  (IAGP)
absent vestibulocochlear ganglion  (IAGP)
absent vomeronasal organ  (IAGP)
absent zygomatic bone  (IAGP)
anotia  (IAGP)
apnea  (IAGP)
athymia  (IAGP)
bradykinesia  (IAGP)
cervical aortic arch  (IAGP)
cervical vertebral fusion  (IAGP)
circling  (IAGP)
conductive hearing loss  (IAGP)
decreased body size  (IAGP)
decreased body weight  (IAGP)
decreased cell proliferation  (IAGP)
decreased circulating calcium level  (IEA)
decreased cochlea coiling  (IAGP)
decreased cochlear inner hair cell number  (IAGP)
decreased embryo size  (IAGP)
decreased heart rate  (IEA)
decreased lateral semicircular canal size  (IAGP)
decreased leukocyte cell number  (IEA)
decreased otic epithelial cell proliferation  (IAGP)
decreased posterior semicircular canal size  (IAGP)
decreased prepulse inhibition  (IEA)
decreased skeletal muscle mass  (IAGP)
decreased submandibular gland size  (IAGP)
decreased superior semicircular canal size  (IAGP)
decreased tongue size  (IAGP)
dilated endolymphatic duct  (IAGP)
distended abdomen  (IAGP)
double outlet right ventricle  (IAGP)
edema  (IEA)
embryonic growth retardation  (IEA)
enlarged cecum  (IEA)
enlarged heart  (IEA)
enlarged kidney  (IEA)
enlarged spleen  (IEA)
epistaxis  (IAGP)
exophthalmos  (IAGP)
eyelids open at birth  (IAGP)
facial muscle hypoplasia  (IAGP)
head bobbing  (IAGP)
head shaking  (IAGP)
impaired branching involved in ureteric bud morphogenesis  (IAGP)
impaired righting response  (IAGP)
increased apoptosis  (IAGP)
increased cochlear inner hair cell number  (IAGP)
increased neuron apoptosis  (IAGP)
increased or absent threshold for auditory brainstem response  (IAGP)
inner ear hypoplasia  (IAGP)
interrupted aortic arch  (IAGP)
interrupted aortic arch, type b  (IAGP)
limb grasping  (IAGP)
micrognathia  (IAGP)
muscle hypoplasia  (IAGP)
neonatal lethality, complete penetrance  (IAGP)
perinatal lethality, complete penetrance  (IAGP)
persistent truncus arteriosus  (IAGP)
pituitary gland hypoplasia  (IAGP)
preweaning lethality, complete penetrance  (IEA)
prolonged RR interval  (IEA)
renal hypoplasia  (IAGP)
retroesophageal right subclavian artery  (IAGP)
rib bifurcation  (IAGP)
rib fusion  (IAGP)
right aortic arch  (IAGP)
short endolymphatic duct  (IAGP)
short mandible  (IAGP)
short maxilla  (IAGP)
short ribs  (IAGP)
short temporal bone squamous part  (IAGP)
short ureter  (IAGP)
short zygomatic bone  (IAGP)
single kidney  (IAGP)
skeletal muscle fibrosis  (IAGP)
small adenohypophysis  (IAGP)
small kidney  (IAGP)
small orbits  (IAGP)
small otic capsule  (IAGP)
small pituitary gland  (IAGP)
small spleen  (IEA)
small temporal bone  (IAGP)
small utricle  (IAGP)
small vestibular saccule  (IAGP)
thin diaphragm muscle  (IAGP)
tongue muscle hypoplasia  (IAGP)
trunk curl  (IAGP)
unilateral deafness  (IAGP)
vascular ring  (IAGP)
References

References - curated
# Reference Title Reference Citation
1. Six1 overexpression in ovarian carcinoma causes resistance to TRAIL-mediated apoptosis and is associated with poor survival. Behbakht K, etal., Cancer Res. 2007 Apr 1;67(7):3036-42.
2. Catweasel mice: a novel role for Six1 in sensory patch development and a model for branchio-oto-renal syndrome. Bosman EA, etal., Dev Biol. 2009 Apr 15;328(2):285-96. doi: 10.1016/j.ydbio.2009.01.030. Epub 2009 Feb 2.
3. Transcriptional activation of the SALL1 by the human SIX1 homeodomain during kidney development. Chai L, etal., J Biol Chem. 2006 Jul 14;281(28):18918-26. Epub 2006 May 2.
4. Six1 transcription factor is critical for coordination of epithelial, mesenchymal and vascular morphogenesis in the mammalian lung. El-Hashash AH, etal., Dev Biol. 2011 May 15;353(2):242-58. doi: 10.1016/j.ydbio.2011.02.031. Epub 2011 Mar 6.
5. Abrogation of the G2 cell cycle checkpoint associated with overexpression of HSIX1: a possible mechanism of breast carcinogenesis. Ford HL, etal., Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12608-13.
6. Expression of Eya1 and Six1 is decreased in distal airways of rats with experimental pulmonary hypoplasia. Friedmacher F, etal., J Pediatr Surg. 2014 Feb;49(2):301-4. doi: 10.1016/j.jpedsurg.2013.11.043. Epub 2013 Nov 18.
7. A Tbx1-Six1/Eya1-Fgf8 genetic pathway controls mammalian cardiovascular and craniofacial morphogenesis. Guo C, etal., J Clin Invest. 2011 Apr;121(4):1585-95. doi: 10.1172/JCI44630.
8. SIX1 mutation screening in 247 branchio-oto-renal syndrome families: a recurrent missense mutation associated with BOR. Kochhar A, etal., Hum Mutat. 2008 Apr;29(4):565. doi: 10.1002/humu.20714.
9. Mutation screening of the EYA1, SIX1, and SIX5 genes in a large cohort of patients harboring branchio-oto-renal syndrome calls into question the pathogenic role of SIX5 mutations. Krug P, etal., Hum Mutat. 2011 Feb;32(2):183-90. doi: 10.1002/humu.21402.
10. Thymus, kidney and craniofacial abnormalities in Six 1 deficient mice. Laclef C, etal., Mech Dev. 2003 Jun;120(6):669-79.
11. MGDs mouse GO annotations MGD data from the GO Consortium
12. MGD IEA MGD IEA
13. Inhibition of Eyes Absent Homolog 4 expression induces malignant peripheral nerve sheath tumor necrosis. Miller SJ, etal., Oncogene. 2010 Jan 21;29(3):368-79. doi: 10.1038/onc.2009.360. Epub 2009 Nov 9.
14. Clinicopathological significance of homeoprotein Six1 in hepatocellular carcinoma. Ng KT, etal., Br J Cancer. 2006 Oct 23;95(8):1050-5. Epub 2006 Sep 26.
15. 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.
16. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
17. Structure-function analyses of the human SIX1-EYA2 complex reveal insights into metastasis and BOR syndrome. Patrick AN, etal., Nat Struct Mol Biol. 2013 Apr;20(4):447-53. doi: 10.1038/nsmb.2505. Epub 2013 Feb 24.
18. Mouse MP Annotation Import Pipeline RGD automated import pipeline
19. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
21. SIX1 mutations cause branchio-oto-renal syndrome by disruption of EYA1-SIX1-DNA complexes. Ruf RG, etal., Proc Natl Acad Sci U S A. 2004 May 25;101(21):8090-5. Epub 2004 May 12.
22. Branchio-oto-renal syndrome: detection of EYA1 and SIX1 mutations in five out of six Danish families by combining linkage, MLPA and sequencing analyses. Sanggaard KM, etal., Eur J Hum Genet. 2007 Nov;15(11):1121-31. Epub 2007 Jul 18.
23. SIX1 protein expression selectively identifies blastemal elements in Wilms tumor. Sehic D, etal., Pediatr Blood Cancer. 2012 Jul 15;59(1):62-8. doi: 10.1002/pbc.24025. Epub 2011 Dec 16.
24. Mutations in the SIX1/2 pathway and the DROSHA/DGCR8 miRNA microprocessor complex underlie high-risk blastemal type Wilms tumors. Wegert J, etal., Cancer Cell. 2015 Feb 9;27(2):298-311. doi: 10.1016/j.ccell.2015.01.002.
Additional References at PubMed
PMID:7720577   PMID:8617500   PMID:8814301   PMID:9551859   PMID:9826681   PMID:10349636   PMID:10471511   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11313460   PMID:11734542  
PMID:11950062   PMID:11978764   PMID:12070080   PMID:12215533   PMID:12477932   PMID:12668636   PMID:12783782   PMID:12837285   PMID:12874121   PMID:12913075   PMID:14610273   PMID:14628042  
PMID:14660441   PMID:14695375   PMID:14704789   PMID:15123840   PMID:15183306   PMID:15226428   PMID:15489334   PMID:15492887   PMID:15496442   PMID:15499560   PMID:15618518   PMID:15634706  
PMID:15652707   PMID:15735644   PMID:15788460   PMID:15804569   PMID:15955062   PMID:16018995   PMID:16141072   PMID:16141073   PMID:16442091   PMID:16530750   PMID:16602821   PMID:16806848  
PMID:16916509   PMID:16934795   PMID:16938278   PMID:17036046   PMID:17098221   PMID:17300925   PMID:17592144   PMID:17880938   PMID:18023262   PMID:18219393   PMID:18287559   PMID:18787044  
PMID:18799693   PMID:19008232   PMID:19027001   PMID:19102749   PMID:19363478   PMID:19371398   PMID:19460349   PMID:19715689   PMID:19898483   PMID:19900183   PMID:19962975   PMID:20059953  
PMID:20074369   PMID:20110314   PMID:20143239   PMID:20211142   PMID:20412779   PMID:20471971   PMID:20503367   PMID:20515681   PMID:20589882   PMID:20601407   PMID:20668922   PMID:20696153  
PMID:20843830   PMID:20869363   PMID:20932939   PMID:21041981   PMID:21267068   PMID:21281623   PMID:21302255   PMID:21309073   PMID:21533152   PMID:21852201   PMID:21873635   PMID:21884692  
PMID:21968101   PMID:21978088   PMID:22158708   PMID:22182523   PMID:22267199   PMID:22340499   PMID:22466647   PMID:22513373   PMID:22659139   PMID:22700049   PMID:22730291   PMID:22945933  
PMID:22987639   PMID:22987640   PMID:22988430   PMID:23060611   PMID:23201021   PMID:23384562   PMID:23390542   PMID:23613228   PMID:23643939   PMID:23840772   PMID:23895934   PMID:23987514  
PMID:24086166   PMID:24102895   PMID:24146773   PMID:24301466   PMID:24479159   PMID:24852826   PMID:24885223   PMID:24952961   PMID:24970368   PMID:25587709   PMID:25654255   PMID:25903664  
PMID:25989023   PMID:26034287   PMID:26295701   PMID:26313368   PMID:26550799   PMID:26831464   PMID:26864490   PMID:26884396   PMID:26940739   PMID:26988119   PMID:27241908   PMID:27259717  
PMID:27302134   PMID:27597886   PMID:27677711   PMID:27923061   PMID:28160066   PMID:28199476   PMID:28280206   PMID:28455376   PMID:28892484   PMID:29106072   PMID:29140246   PMID:29229773  
PMID:29273440   PMID:29455928   PMID:29543863   PMID:29768404   PMID:29771971   PMID:29897331   PMID:29979676   PMID:30188892   PMID:30237319   PMID:30367465   PMID:30723235   PMID:30771307  
PMID:30894749   PMID:30905259   PMID:30959515   PMID:31488567   PMID:31597742   PMID:31956913   PMID:31988190   PMID:32047912   PMID:32243674   PMID:32554463   PMID:32572167   PMID:32591430  
PMID:32826305   PMID:32857879   PMID:33436522   PMID:33631753   PMID:33722956   PMID:33723076   PMID:33795231   PMID:34070742   PMID:34193412   PMID:34266958   PMID:34321664   PMID:35084365  
PMID:35108532   PMID:35178390   PMID:35287543   PMID:35320729   PMID:35420997   PMID:35713404   PMID:35815410   PMID:36521641   PMID:36627077   PMID:36845386   PMID:37017267   PMID:37088973  
PMID:37181748   PMID:37183792   PMID:37267426   PMID:37670778   PMID:37815464   PMID:38167468   PMID:38355793   PMID:38422767   PMID:39798644  


Genomics

Comparative Map Data
Six1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391273,088,601 - 73,093,486 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1273,086,789 - 73,100,661 (-)EnsemblGRCm39 Ensembl
GRCm381273,041,827 - 73,046,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,040,015 - 73,053,887 (-)EnsemblGRCm38mm10GRCm38
MGSCv371274,142,814 - 74,147,699 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361273,960,668 - 73,965,302 (-)NCBIMGSCv36mm8
Celera1274,158,405 - 74,163,290 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1230.34NCBI
SIX1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381460,643,421 - 60,649,477 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1460,643,421 - 60,658,259 (-)EnsemblGRCh38hg38GRCh38
GRCh371461,110,139 - 61,116,195 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361460,182,506 - 60,185,933 (-)NCBINCBI36Build 36hg18NCBI36
Build 341460,182,505 - 60,185,933NCBI
Celera1441,161,682 - 41,166,417 (-)NCBICelera
Cytogenetic Map14q23.1NCBI
HuRef1441,274,621 - 41,279,356 (-)NCBIHuRef
CHM1_11461,050,553 - 61,055,290 (-)NCBICHM1_1
T2T-CHM13v2.01454,849,879 - 54,855,934 (-)NCBIT2T-CHM13v2.0
Six1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8697,482,617 - 97,487,853 (-)NCBIGRCr8
mRatBN7.2691,746,739 - 91,751,975 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl691,746,739 - 91,751,975 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx692,137,046 - 92,142,281 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0692,436,544 - 92,441,778 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0691,864,445 - 91,869,679 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0695,929,060 - 95,934,296 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl695,929,060 - 95,934,296 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06105,364,372 - 105,369,608 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,470,153 - 95,475,389 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1695,475,346 - 95,478,212 (-)NCBI
Celera690,209,553 - 90,214,789 (-)NCBICelera
Cytogenetic Map6q24NCBI
Six1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554668,961,597 - 8,966,069 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554668,961,597 - 8,966,069 (+)NCBIChiLan1.0ChiLan1.0
SIX1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21561,782,374 - 61,786,732 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11460,997,057 - 61,003,141 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01441,250,512 - 41,256,567 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11459,515,324 - 59,518,740 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1459,515,324 - 59,527,494 (-)Ensemblpanpan1.1panPan2
SIX1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1835,676,705 - 35,679,534 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl835,676,479 - 35,679,534 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha835,430,686 - 35,433,517 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0835,909,922 - 35,912,747 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl835,909,922 - 35,913,208 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1835,522,041 - 35,524,863 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0835,599,806 - 35,602,627 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0835,960,733 - 35,963,565 (-)NCBIUU_Cfam_GSD_1.0
Six1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864069,348,816 - 69,353,683 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364954,838,051 - 4,842,994 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364954,839,496 - 4,842,906 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIX1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1189,619,855 - 189,624,651 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11189,620,430 - 189,624,652 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21210,729,818 - 210,734,041 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SIX1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12437,840,399 - 37,855,801 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2437,840,309 - 37,845,192 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605326,090,242 - 26,095,370 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Six1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473440,453,420 - 40,459,671 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473440,453,445 - 40,457,551 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Six1
216 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:2169
Count of miRNA genes:752
Interacting mature miRNAs:1165
Transcripts:ENSMUST00000050029, ENSMUST00000175677, ENSMUST00000176091, ENSMUST00000176310
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
1357749Vtbt13_mvertebral trabecular bone trait 13 (mouse)Not determined125313200287132145Mouse
14746976Manh73_mmandible shape 73 (mouse)126585713199857131Mouse
4142234Tmc1m3_mTmc1 modifier 3 (mouse)Not determined12541844077031203Mouse
1301046Par3_mpulmonary adenoma resistance 3 (mouse)Not determined126395670897956883Mouse
27226776Tibl6_mtibia length 6, 5 week (mouse)126064678692666774Mouse
1357757Lnopy2_mlens opacity 2 (mouse)Not determined125284662686846796Mouse
1301337Cdcs8_mcytokine deficiency colitis susceptibility 8 (mouse)Not determined126468908398689229Mouse
1300633Cdcs7_mcytokine deficiency colitis susceptibility 7 (mouse)Not determined126468908398689229Mouse
27226771Tibl14_mtibia length 14, 10 week (mouse)126834677498766259Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235285496109936243Mouse
13504832Bacszq2_mbaculum size QTL 2 (mouse)125694579875345787Mouse
10043895Bw20_mbody weight QTL 20 (mouse)Not determined126230825296308252Mouse
27226797Scvln19_msacral vertebrae length 2, 16 week (mouse)126214678699466259Mouse
1357479Splwt1_mspleen weight 1 (mouse)Not determined124169317590887526Mouse
12832727Ahrq1_mairway hyperresponsiveness QTL 1 (mouse)125469591082665939Mouse
1558978Cplaq10_mcircadian period of locomotor activity 10 (mouse)Not determined121534102679040364Mouse
1301574Lmblgq5_mlimb length QTL 5 (mouse)Not determined121759644780956883Mouse
10043948Pbft6_mpercent body fat 6 (mouse)Not determined126120542795205427Mouse
4141738Tgq23_mtriglyceride QTL 23 (mouse)Not determined72112877106112877Mouse
27226793Feml10_mfemur length 10, 5 week (mouse)1268346774113363620Mouse
27226728Tibl20_mtibia length 20, 16 week (mouse)125914678693866774Mouse
1301476Pbwg12_mpostnatal body weight growth 12 (mouse)Not determined126204016496040364Mouse
13207568Tcq14_mtotal cholesterol QTL 14 (mouse)121166000197176774Mouse
27226753Femd7_mfemur midshaft diameter 7, 10 week (mouse)12955000084146774Mouse

Markers in Region
BB138287  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381273,042,387 - 73,042,469UniSTSGRCm38
MGSCv371274,143,374 - 74,143,456UniSTSGRCm37
Celera1274,158,965 - 74,159,047UniSTS
Cytogenetic Map12C3UniSTS
cM Map1231.0UniSTS
Whitehead/MRC_RH12678.0UniSTS
X80339  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381273,043,189 - 73,043,371UniSTSGRCm38
MGSCv371274,144,176 - 74,144,358UniSTSGRCm37
Celera1274,159,767 - 74,159,949UniSTS
Cytogenetic Map12C3UniSTS
cM Map1231.0UniSTS
Whitehead/MRC_RH12682.97UniSTS
Whitehead_YAC12 UniSTS
Six1  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381273,042,844 - 73,042,906UniSTSGRCm38
MGSCv371274,143,831 - 74,143,893UniSTSGRCm37
Celera1274,159,422 - 74,159,484UniSTS
Cytogenetic Map12C3UniSTS
cM Map1231.0UniSTS
X80339  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381273,043,230 - 73,043,309UniSTSGRCm38
MGSCv371274,144,217 - 74,144,296UniSTSGRCm37
Celera1274,159,808 - 74,159,887UniSTS
Cytogenetic Map12C3UniSTS
Whitehead/MRC_RH12682.97UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000050029   ⟹   ENSMUSP00000059026
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1273,088,601 - 73,093,953 (-)Ensembl
GRCm38.p6 Ensembl1273,041,827 - 73,047,179 (-)Ensembl
Ensembl Acc Id: ENSMUST00000175677
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1273,090,548 - 73,092,065 (-)Ensembl
GRCm38.p6 Ensembl1273,043,774 - 73,045,291 (-)Ensembl
Ensembl Acc Id: ENSMUST00000176091
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1273,090,305 - 73,100,661 (-)Ensembl
GRCm38.p6 Ensembl1273,043,531 - 73,053,887 (-)Ensembl
Ensembl Acc Id: ENSMUST00000176310
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1273,086,789 - 73,089,589 (-)Ensembl
GRCm38.p6 Ensembl1273,040,015 - 73,042,815 (-)Ensembl
RefSeq Acc Id: NM_009189   ⟹   NP_033215
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391273,088,601 - 73,093,486 (-)NCBI
GRCm381273,041,827 - 73,046,712 (-)ENTREZGENE
MGSCv371274,142,814 - 74,147,699 (-)RGD
Celera1274,158,405 - 74,163,290 (-)RGD
cM Map12 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_033215 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH23304 (Get FASTA)   NCBI Sequence Viewer  
  BAC27265 (Get FASTA)   NCBI Sequence Viewer  
  BAE20875 (Get FASTA)   NCBI Sequence Viewer  
  CAA56585 (Get FASTA)   NCBI Sequence Viewer  
  EDL36515 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000059026
  ENSMUSP00000059026.7
GenBank Protein Q62231 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_033215   ⟸   NM_009189
- UniProtKB: Q8CIL7 (UniProtKB/Swiss-Prot),   Q62231 (UniProtKB/Swiss-Prot),   Q3V2C3 (UniProtKB/TrEMBL),   Q8BSP4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000059026   ⟸   ENSMUST00000050029
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q62231-F1-model_v2 AlphaFold Q62231 1-284 view protein structure

Promoters
RGD ID:8678508
Promoter ID:EPDNEW_M17285
Type:multiple initiation site
Name:Six1_1
Description:Mus musculus sine oculis-related homeobox 1 , 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
GRCm381273,046,711 - 73,046,771EPDNEW
RGD ID:6847009
Promoter ID:MM_ACW:11043
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   Lung,   MEF_B4
Transcripts:SIX1.CSEP07-UNSPLICED
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361274,140,599 - 74,141,099 (-)MPROMDB
RGD ID:6823412
Promoter ID:MM_KWN:11906
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day6,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_009189
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361274,146,886 - 74,147,712 (-)MPROMDB
RGD ID:6847010
Promoter ID:MM_ACW:11044
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   ES_Cell,   Kidney,   MEF_B4,   MEF_B6
Transcripts:SIX1.DSEP07
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361274,154,746 - 74,155,246 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:102780 AgrOrtholog
Ensembl Genes ENSMUSG00000051367 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000050029 ENTREZGENE
  ENSMUST00000050029.8 UniProtKB/Swiss-Prot
Gene3D-CATH Homeodomain-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_KN_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SIX1_SD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:20471 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:102780 ENTREZGENE
NCBI Gene 20471 ENTREZGENE
PANTHER HOMEOBOX PROTEIN SIX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10390:SF13 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeobox_KN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SIX1_SD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Six1 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt Q3V2C3 ENTREZGENE, UniProtKB/TrEMBL
  Q62231 ENTREZGENE
  Q8BSP4 ENTREZGENE, UniProtKB/TrEMBL
  Q8CIL7 ENTREZGENE
  SIX1_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q8CIL7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-07-17 Six1  sine oculis-related homeobox 1  Six1  sine oculis-related homeobox 1 homolog (Drosophila)  Symbol and/or name change 5135510 APPROVED