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

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Gene: Six1 (sine oculis-related homeobox 1) Mus musculus
Symbol: Six1
Name: sine oculis-related homeobox 1
RGD ID: 1550080
Description: Enables DNA-binding transcription factor activity; chromatin binding activity; and sequence-specific DNA binding activity. Involved in several processes, including animal organ development; myotome development; and positive regulation of morphogenesis of an epithelium. Acts upstream of or within several processes, including animal organ development; 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); INTERACTS WITH 1,2-dichloroethane; 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: BB138287; homeobox protein SIX1; sine oculis homeobox homolog 1; sine oculis-related homeobox 1 homolog
RGD Orthologs
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391273,088,601 - 73,093,486 (-)NCBIGRCm39mm39
GRCm39 Ensembl1273,086,789 - 73,100,661 (-)Ensembl
GRCm381273,041,827 - 73,046,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,040,015 - 73,053,887 (-)EnsemblGRCm38mm10GRCm38
MGSCv371274,142,814 - 74,147,699 (-)NCBIGRCm37mm9NCBIm37
MGSCv361273,960,668 - 73,965,302 (-)NCBImm8
Celera1274,158,405 - 74,163,290 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1230.34NCBI
JBrowse: View Region in Genome Browser (JBrowse)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anatomical structure development  (IGI)
aorta morphogenesis  (IGI)
apoptotic process  (IEA)
branching involved in ureteric bud morphogenesis  (IGI)
cellular response to 3,3',5-triiodo-L-thyronine  (ISO)
cochlea morphogenesis  (IMP)
embryonic cranial skeleton morphogenesis  (IGI)
embryonic skeletal system morphogenesis  (IGI)
epithelial cell differentiation  (IMP)
facial nerve morphogenesis  (IMP)
fungiform papilla morphogenesis  (IMP)
generation of neurons  (IMP)
inner ear development  (IMP)
inner ear morphogenesis  (IGI)
kidney development  (IMP)
mesonephric tubule formation  (IMP)
metanephric mesenchyme development  (IMP)
middle ear morphogenesis  (IMP)
myoblast migration  (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)
negative regulation of transcription, DNA-templated  (IEA)
neurogenesis  (IMP)
neuron fate specification  (IGI)
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 mesenchymal cell proliferation involved in ureter development  (IGI)
positive regulation of secondary heart field cardioblast proliferation  (IGI)
positive regulation of transcription by RNA polymerase II  (IDA,IGI,ISO)
positive regulation of transcription, DNA-templated  (IDA,IMP,ISO)
positive regulation of ureteric bud formation  (IMP)
protein localization to nucleus  (ISO)
regulation of branch elongation involved in ureteric bud branching  (IMP)
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)
regulation of transcription, DNA-templated  (IDA)
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  (ISO)
nucleoplasm  (ISO)
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 heart morphology  (IEA)
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 rib morphology  (IAGP)
abnormal semicircular canal ampulla morphology  (IAGP)
abnormal semicircular canal morphology  (IAGP)
abnormal skeletal muscle morphology  (IAGP)
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 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 alkaline phosphatase level  (IEA)
decreased cochlear 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 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 heart  (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 exploration in new environment  (IEA)
increased neuron apoptosis  (IAGP)
increased or absent threshold for auditory brainstem response  (IAGP)
increased thigmotaxis  (IEA)
inner ear hypoplasia  (IAGP)
interrupted aortic arch  (IAGP)
limb grasping  (IAGP)
micrognathia  (IAGP)
muscle hypoplasia  (IAGP)
neonatal lethality, complete penetrance  (IAGP)
perinatal lethality, complete penetrance  (IAGP)
persistent truncus arteriosis  (IAGP)
pituitary gland hypoplasia  (IAGP)
preweaning lethality, complete penetrance  (IEA)
prolonged RR interval  (IEA)
rectal prolapse  (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 - curated
1. Behbakht K, etal., Cancer Res. 2007 Apr 1;67(7):3036-42.
2. 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. Chai L, etal., J Biol Chem. 2006 Jul 14;281(28):18918-26. Epub 2006 May 2.
4. 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. Ford HL, etal., Proc Natl Acad Sci U S A. 1998 Oct 13;95(21):12608-13.
6. 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. Guo C, etal., J Clin Invest. 2011 Apr;121(4):1585-95. doi: 10.1172/JCI44630.
8. Kochhar A, etal., Hum Mutat. 2008 Apr;29(4):565. doi: 10.1002/humu.20714.
9. Krug P, etal., Hum Mutat. 2011 Feb;32(2):183-90. doi: 10.1002/humu.21402.
10. Laclef C, etal., Mech Dev. 2003 Jun;120(6):669-79.
11. MGD data from the GO Consortium
13. Miller SJ, etal., Oncogene. 2010 Jan 21;29(3):368-79. doi: 10.1038/onc.2009.360. Epub 2009 Nov 9.
14. Ng KT, etal., Br J Cancer. 2006 Oct 23;95(8):1050-5. Epub 2006 Sep 26.
15. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
16. OMIM Disease Annotation Pipeline
17. Patrick AN, etal., Nat Struct Mol Biol. 2013 Apr;20(4):447-53. doi: 10.1038/nsmb.2505. Epub 2013 Feb 24.
18. RGD automated import pipeline
19. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. RGD automated import pipeline for gene-chemical interactions
21. Ruf RG, etal., Proc Natl Acad Sci U S A. 2004 May 25;101(21):8090-5. Epub 2004 May 12.
22. Sanggaard KM, etal., Eur J Hum Genet. 2007 Nov;15(11):1121-31. Epub 2007 Jul 18.
23. Sehic D, etal., Pediatr Blood Cancer. 2012 Jul 15;59(1):62-8. doi: 10.1002/pbc.24025. Epub 2011 Dec 16.
24. 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: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:25654255   PMID:25903664   PMID:25989023   PMID:26034287  
PMID:26295701   PMID:26313368   PMID:26550799   PMID:26884396   PMID:26940739   PMID:26988119   PMID:27241908   PMID:27259717   PMID:27302134   PMID:27597886   PMID:27677711   PMID:27847210  
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:30723235   PMID:30771307   PMID:30894749   PMID:30905259   PMID:30959515   PMID:31597742  
PMID:31956913   PMID:31988190   PMID:32243674   PMID:32554463   PMID:32591430   PMID:33722956   PMID:33723076   PMID:33795231  


Comparative Map Data
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
GRCm391273,088,601 - 73,093,486 (-)NCBIGRCm39mm39
GRCm39 Ensembl1273,086,789 - 73,100,661 (-)Ensembl
GRCm381273,041,827 - 73,046,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,040,015 - 73,053,887 (-)EnsemblGRCm38mm10GRCm38
MGSCv371274,142,814 - 74,147,699 (-)NCBIGRCm37mm9NCBIm37
MGSCv361273,960,668 - 73,965,302 (-)NCBImm8
Celera1274,158,405 - 74,163,290 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1230.34NCBI
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
GRCh38.p13 Ensembl1460,643,421 - 60,658,259 (-)EnsemblGRCh38hg38GRCh38
GRCh381460,643,421 - 60,649,489 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371461,110,139 - 61,116,195 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361460,182,506 - 60,185,933 (-)NCBINCBI36hg18NCBI36
Build 341460,182,505 - 60,185,933NCBI
Celera1441,161,682 - 41,166,417 (-)NCBI
Cytogenetic Map14q23.1NCBI
HuRef1441,274,621 - 41,279,356 (-)NCBIHuRef
CHM1_11461,050,553 - 61,055,290 (-)NCBICHM1_1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
mRatBN7.2691,746,739 - 91,751,975 (-)NCBI
Rnor_6.0 Ensembl695,929,060 - 95,934,296 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0695,929,060 - 95,934,296 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06105,364,372 - 105,369,608 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4695,470,153 - 95,475,389 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1695,475,346 - 95,478,212 (-)NCBI
Celera690,209,553 - 90,214,789 (-)NCBICelera
Cytogenetic Map6q24NCBI
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
ChiLan1.0 EnsemblNW_0049554668,961,597 - 8,966,069 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554668,961,597 - 8,966,069 (+)NCBIChiLan1.0ChiLan1.0
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
PanPan1.11459,515,324 - 59,518,740 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1459,515,324 - 59,527,494 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01441,250,512 - 41,256,567 (-)NCBIMhudiblu_PPA_v0panPan3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
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 (-)NCBI
ROS_Cfam_1.0835,909,922 - 35,912,747 (-)NCBI
UMICH_Zoey_3.1835,522,041 - 35,524,863 (-)NCBI
UNSW_CanFamBas_1.0835,599,806 - 35,602,627 (-)NCBI
UU_Cfam_GSD_1.0835,960,733 - 35,963,565 (-)NCBI
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
HiC_Itri_2NW_02440864069,348,816 - 69,353,683 (+)NCBI
SpeTri2.0NW_0049364954,839,496 - 4,842,906 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
Sscrofa11.1 Ensembl1189,619,853 - 189,628,187 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11189,620,430 - 189,624,652 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21210,729,818 - 210,734,041 (-)NCBISscrofa10.2Sscrofa10.2susScr3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
ChlSab1.12437,840,399 - 37,855,801 (-)NCBI
ChlSab1.1 Ensembl2437,840,309 - 37,845,192 (-)Ensembl
Vero_WHO_p1.0NW_02366605326,090,242 - 26,095,370 (-)NCBI
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
HetGla 1.0NW_00462473440,453,445 - 40,457,551 (+)NCBI

Position Markers
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
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_YAC12 UniSTS
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
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381273,043,230 - 73,043,309UniSTSGRCm38
MGSCv371274,144,217 - 74,144,296UniSTSGRCm37
Celera1274,159,808 - 74,159,887UniSTS
Cytogenetic Map12C3UniSTS

QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142234Tmc1m3_mTmc1 modifier 3 (mouse)Not determined12536844076984429Mouse
27226753Femd7_mfemur midshaft diameter 7, 10 week (mouse)12950000084100000Mouse
13207568Tcq14_mtotal cholesterol QTL 14 (mouse)121161000097210000Mouse
1558978Cplaq10_mcircadian period of locomotor activity 10 (mouse)Not determined121529102578993590Mouse
1301574Lmblgq5_mlimb length QTL 5 (mouse)Not determined121754644680910109Mouse
4142002Tbqt3_mtibia bone quality traits 3 (mouse)Not determined1235235497109969809Mouse
1357479Splwt1_mspleen weight 1 (mouse)Not determined124164639290920752Mouse
1357757Lnopy2_mlens opacity 2 (mouse)Not determined125279985286800022Mouse
1357749Vtbt13_mvertebral trabecular bone trait 13 (mouse)Not determined125308522887085371Mouse
12832727Ahrq1_mairway hyperresponsiveness QTL 1 (mouse)125464912582619165Mouse
4140993Tglq2b_mtriglyceride QTL 2b (mouse)Not determined125529146189291675Mouse
9850127Tglq6_mtriglyceride QTL6 (mouse)Not determined125529146189291675Mouse
27226728Tibl20_mtibia length 20, 16 week (mouse)125910000093900000Mouse
27226776Tibl6_mtibia length 6, 5 week (mouse)126060000092700000Mouse
10043948Pbft6_mpercent body fat 6 (mouse)Not determined126115865395158653Mouse
1301476Pbwg12_mpostnatal body weight growth 12 (mouse)Not determined126199339095993590Mouse
27226797Scvln19_msacral vertebrae length 2, 16 week (mouse)126210000099500000Mouse
10043895Bw20_mbody weight QTL 20 (mouse)Not determined126226147896261478Mouse
1301046Par3_mpulmonary adenoma resistance 3 (mouse)Not determined126390993497910109Mouse
1301337Cdcs8_mcytokine deficiency colitis susceptibility 8 (mouse)Not determined126464230998642455Mouse
1300633Cdcs7_mcytokine deficiency colitis susceptibility 7 (mouse)Not determined126464230998642455Mouse
14746976Manh73_mmandible shape 73 (mouse)126581035799810357Mouse
27226771Tibl14_mtibia length 14, 10 week (mouse)126830000098800000Mouse
27226793Feml10_mfemur length 10, 5 week (mouse)1268300000113400000Mouse
4141738Tgq23_mtriglyceride QTL 23 (mouse)Not determined72146107106146107Mouse

miRNA Target Status

Confirmed Target Of
miRNA GeneMature miRNAMethod NameResult TypeData TypeSupport TypePMID

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 (
For more information about miRGate, see PMID:25858286 or access the full paper here.



Reference Sequences
RefSeq Acc Id: ENSMUST00000050029   ⟹   ENSMUSP00000059026
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1273,041,827 - 73,047,179 (-)Ensembl
RefSeq Acc Id: ENSMUST00000175677
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1273,043,774 - 73,045,291 (-)Ensembl
RefSeq Acc Id: ENSMUST00000176091
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1273,043,531 - 73,053,887 (-)Ensembl
RefSeq Acc Id: ENSMUST00000176310
RefSeq Status:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl1273,040,015 - 73,042,815 (-)Ensembl
RefSeq Acc Id: NM_009189   ⟹   NP_033215
RefSeq Status: VALIDATED
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
Reference Sequences
RefSeq Acc Id: NP_033215   ⟸   NM_009189
- UniProtKB: Q62231 (UniProtKB/Swiss-Prot),   Q3V2C3 (UniProtKB/TrEMBL),   Q8BSP4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSMUSP00000059026   ⟸   ENSMUST00000050029
Protein Domains

RGD ID:8678508
Promoter ID:EPDNEW_M17285
Type:multiple initiation site
Description:Mus musculus sine oculis-related homeobox 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database,
Experiment Methods:Single-end sequencing.
Mouse AssemblyChrPosition (strand)Source
GRCm381273,046,711 - 73,046,771EPDNEW
RGD ID:6847009
Promoter ID:MM_ACW:11043
SO ACC ID:SO:0000170
Tissues & Cell Lines:Brain,   Lung,   MEF_B4
Mouse AssemblyChrPosition (strand)Source
MGSCv361274,140,599 - 74,141,099 (-)MPROMDB
RGD ID:6823412
Promoter ID:MM_KWN:11906
SO ACC ID:SO:0000170
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day6,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6,   Spleen
Mouse AssemblyChrPosition (strand)Source
MGSCv361274,146,886 - 74,147,712 (-)MPROMDB
RGD ID:6847010
Promoter ID:MM_ACW:11044
SO ACC ID:SO:0000170
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   ES_Cell,   Kidney,   MEF_B4,   MEF_B6
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 Protein ENSMUSP00000059026 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000050029 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Homeobox-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SIX1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SIX1_SD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:20471 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PANTHER PTHR10390:SF13 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SIX1_SD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Six1 PhenoGen
  HOMEOBOX_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART HOX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  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