Six1 (SIX homeobox 1) - Rat Genome Database

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Gene: Six1 (SIX homeobox 1) Rattus norvegicus
Analyze
Symbol: Six1
Name: SIX homeobox 1
RGD ID: 620906
Description: Enables transcription coactivator binding activity. Involved in cellular response to 3,3',5-triiodo-L-thyronine. Predicted to be located in cytoplasm; nucleolus; and nucleoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. 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 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 3,4-methylenedioxymethamphetamine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homeobox protein SIX1; sine oculis homeobox (Drosophila) homolog 1; sine oculis homeobox homolog 1; sine oculis homeobox homolog 1 (Drosophila); sine oculis-related homeobox 1 homolog; sine oculis-related homeobox 1 homolog (Drosophila)
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8697,482,617 - 97,487,853 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl697,482,617 - 97,487,853 (-)EnsemblGRCr8
mRatBN7.2691,746,739 - 91,751,975 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl691,746,739 - 91,751,975 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx692,137,046 - 92,142,281 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0692,436,544 - 92,441,778 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0691,864,445 - 91,869,679 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0695,929,060 - 95,934,296 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl695,929,060 - 95,934,296 (-)Ensemblrn6Rnor6.0
Rnor_5.06105,364,372 - 105,369,608 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4695,470,153 - 95,475,389 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera690,209,553 - 90,214,789 (-)NCBICelera
RGSC_v3.1695,475,346 - 95,478,212 (-)NCBI
Cytogenetic Map6q24NCBI
JBrowse:




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

Gene Ontology Annotations     Click to see Annotation Detail View

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

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

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. 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.
8. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
9. 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.
10. 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.
11. 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.
12. Thymus, kidney and craniofacial abnormalities in Six 1 deficient mice. Laclef C, etal., Mech Dev. 2003 Jun;120(6):669-79.
13. Transcription coactivator Eya2 is a critical regulator of physiological hypertrophy. Lee SH, etal., J Mol Cell Cardiol. 2012 Mar;52(3):718-26. doi: 10.1016/j.yjmcc.2011.12.002. Epub 2011 Dec 14.
14. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
15. 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.
16. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
17. 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.
18. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
19. 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.
20. GOA pipeline RGD automated data pipeline
21. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
22. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
23. Information Derived from GenBank Report RGD, Sept. 2003
24. 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.
25. 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.
26. 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.
27. 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.
28. Eya4 Induces Hypertrophy via Regulation of p27kip1. Williams T, etal., Circ Cardiovasc Genet. 2015 Dec;8(6):752-64. doi: 10.1161/CIRCGENETICS.115.001134. Epub 2015 Oct 23.
Additional References at PubMed
PMID:9826681   PMID:12783782   PMID:12874121   PMID:14628042   PMID:15496442   PMID:15788460   PMID:15955062   PMID:16018995   PMID:16530750   PMID:16916509   PMID:16934795   PMID:16938278  
PMID:17098221   PMID:17300925   PMID:17592144   PMID:19008232   PMID:19027001   PMID:19497856   PMID:19962975   PMID:20110314   PMID:20515681   PMID:20696153   PMID:21281623   PMID:21884692  
PMID:21978088   PMID:22513373   PMID:27923061   PMID:35180623   PMID:37479098  


Genomics

Comparative Map Data
Six1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8697,482,617 - 97,487,853 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl697,482,617 - 97,487,853 (-)EnsemblGRCr8
mRatBN7.2691,746,739 - 91,751,975 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl691,746,739 - 91,751,975 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx692,137,046 - 92,142,281 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0692,436,544 - 92,441,778 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0691,864,445 - 91,869,679 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0695,929,060 - 95,934,296 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl695,929,060 - 95,934,296 (-)Ensemblrn6Rnor6.0
Rnor_5.06105,364,372 - 105,369,608 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4695,470,153 - 95,475,389 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera690,209,553 - 90,214,789 (-)NCBICelera
RGSC_v3.1695,475,346 - 95,478,212 (-)NCBI
Cytogenetic Map6q24NCBI
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 (-)Ensemblhg38GRCh38
GRCh371461,110,139 - 61,116,195 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361460,182,506 - 60,185,933 (-)NCBIBuild 36Build 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
(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 EnsemblGRCm39
GRCm381273,041,827 - 73,046,712 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1273,040,015 - 73,053,887 (-)Ensemblmm10GRCm38
MGSCv371274,142,814 - 74,147,699 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361273,960,668 - 73,965,302 (-)NCBIMGSCv36mm8
Celera1274,158,405 - 74,163,290 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1230.34NCBI
Six1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554668,961,597 - 8,966,069 (+)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha835,430,686 - 35,433,517 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0835,909,922 - 35,912,747 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (-)EnsemblSpeTri2.0 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 (-)EnsemblsusScr11Sscrofa11.1
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 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473440,453,445 - 40,457,551 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Six1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1787,317,308 - 87,322,413 (-)NCBIRrattus_CSIRO_v1

Variants

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

Predicted Target Of
Summary Value
Count of predictions:222
Count of miRNA genes:152
Interacting mature miRNAs:188
Transcripts:ENSRNOT00000034338
Prediction methods:Microtar, Miranda, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
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)671278722116278722Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)664367996109367996Rat
2293088Iddm28Insulin dependent diabetes mellitus QTL 285.21blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)668767270135411972Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)688019181136741135Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)690871046135871046Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)693560258136550638Rat
4889933Bss88Bone structure and strength QTL 883.8tibia size trait (VT:0100001)tibia total bone volume (CMO:0001724)65368492198684921Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)679198463144254945Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)646050607116278722Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)693778632138778632Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)620859430113082285Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)686867923110125012Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)684490437129490437Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)686867923110125012Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)690871046135871046Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)693560258136550638Rat
5684963Bss99Bone structure and strength QTL 993.1tibia area (VT:1000281)tibia area measurement (CMO:0001382)65368492198684921Rat
5684992Bmd83Bone mineral density QTL 824.8tibia mineral mass (VT:1000283)bone mineral content (CMO:0001554)65368492198684921Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)678204640123204640Rat
1581550Pur8Proteinuria QTL 8urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)693560258136550638Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)676937178121937178Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)686494122112380234Rat

Markers in Region
RH139816  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2691,747,144 - 91,747,340 (+)MAPPERmRatBN7.2
Rnor_6.0695,929,466 - 95,929,661NCBIRnor6.0
Rnor_5.06105,364,778 - 105,364,973UniSTSRnor5.0
RGSC_v3.4695,470,559 - 95,470,754UniSTSRGSC3.4
Celera690,209,959 - 90,210,154UniSTS
RH 3.4 Map6658.5UniSTS
Cytogenetic Map6q24UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
7 12 62 131 58 57 26 42 26 6 231 137 11 106 53 82 31 4 4

Sequence


Ensembl Acc Id: ENSRNOT00000034338   ⟹   ENSRNOP00000037345
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl697,482,617 - 97,487,853 (-)Ensembl
mRatBN7.2 Ensembl691,746,739 - 91,751,975 (-)Ensembl
Rnor_6.0 Ensembl695,929,060 - 95,934,296 (-)Ensembl
RefSeq Acc Id: NM_053759   ⟹   NP_446211
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8697,482,617 - 97,487,853 (-)NCBI
mRatBN7.2691,746,739 - 91,751,975 (-)NCBI
Rnor_6.0695,929,060 - 95,934,296 (-)NCBI
Rnor_5.06105,364,372 - 105,369,608 (-)NCBI
RGSC_v3.4695,470,153 - 95,475,389 (-)RGD
Celera690,209,553 - 90,214,789 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446211 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAK11607 (Get FASTA)   NCBI Sequence Viewer  
  EDM03607 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000037345
  ENSRNOP00000037345.4
RefSeq Acc Id: NP_446211   ⟸   NM_053759
- UniProtKB: G3V970 (UniProtKB/TrEMBL),   A6HC52 (UniProtKB/TrEMBL),   Q99P83 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000037345   ⟸   ENSRNOT00000034338
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-G3V970-F1-model_v2 AlphaFold G3V970 1-284 view protein structure

Transcriptome

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

Promoters
RGD ID:13694662
Promoter ID:EPDNEW_R5186
Type:multiple initiation site
Name:Six1_1
Description:SIX homeobox 1
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_6.0695,933,965 - 95,934,025EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620906 AgrOrtholog
BioCyc Gene G2FUF-37120 BioCyc
Ensembl Genes ENSRNOG00000022777 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000034338 ENTREZGENE
  ENSRNOT00000034338.6 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_KN_domain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
KEGG Report rno:114634 UniProtKB/TrEMBL
NCBI Gene 114634 ENTREZGENE
PANTHER HOMEOBOX PROTEIN SIX UniProtKB/TrEMBL
  PTHR10390:SF13 UniProtKB/TrEMBL
Pfam Homeobox_KN UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
PhenoGen Six1 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000022777 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A6HC52 ENTREZGENE, UniProtKB/TrEMBL
  G3V970 ENTREZGENE, UniProtKB/TrEMBL
  Q99P83 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Six1  SIX homeobox 1  Six1  sine oculis-related homeobox 1 homolog (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-25 Six1  sine oculis-related homeobox 1 homolog (Drosophila)  Six1  sine oculis homeobox homolog 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Six1  sine oculis homeobox homolog 1 (Drosophila)  Six1  sine oculis homeobox (Drosophila) homolog 1  Name updated 1299863 APPROVED
2005-01-20 Six1  sine oculis homeobox homolog 1 (Drosophila)    sine oculis homeobox (Drosophila) homolog 1  Name updated 1299863 APPROVED
2002-08-07 Six1  sine oculis homeobox (Drosophila) homolog 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_regulation expression is upregulated in retinal ganglion cells after optic nerve transection 634611