Six2 (SIX homeobox 2) - Rat Genome Database

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Gene: Six2 (SIX homeobox 2) Rattus norvegicus
Analyze
Symbol: Six2
Name: SIX homeobox 2
RGD ID: 1310792
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in several processes, including embryonic morphogenesis; kidney development; and positive regulation of chondrocyte proliferation. Predicted to act upstream of or within several processes, including chondrocyte differentiation; condensed mesenchymal cell proliferation; and embryonic organ morphogenesis. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in renal Wilms' tumor. Orthologous to human SIX2 (SIX homeobox 2); INTERACTS WITH bisphenol A; dimethylarsinic acid; N,N-diethyl-m-toluamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: homeobox protein SIX2; LOC366542; sine oculis-related homeobox 2 homolog; sine oculis-related homeobox 2 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
GRCr8614,727,756 - 14,734,219 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl614,727,859 - 14,731,941 (+)EnsemblGRCr8
mRatBN7.268,974,859 - 8,981,345 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl68,967,157 - 8,981,193 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx69,252,089 - 9,255,407 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.069,561,498 - 9,564,816 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.069,089,205 - 9,092,512 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.068,952,572 - 8,955,893 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl68,952,572 - 8,956,276 (-)Ensemblrn6Rnor6.0
Rnor_5.068,875,432 - 8,878,685 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.469,094,655 - 9,097,973 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera68,702,767 - 8,705,759 (+)NCBICelera
RGSC_v3.169,095,089 - 9,098,000 (-)NCBI
Cytogenetic Map6q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleoplasm  (ISO)
nucleus  (IEA,ISO)

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Accumulation of malignant renal stem cells is associated with epigenetic changes in normal renal progenitor genes. Metsuyanim S, etal., Stem Cells. 2008 Jul;26(7):1808-17. doi: 10.1634/stemcells.2007-0322. Epub 2008 May 8.
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Therapeutic potential of human induced pluripotent stem cells and renal progenitor cells in experimental chronic kidney disease. Ribeiro PC, etal., Stem Cell Res Ther. 2020 Dec 9;11(1):530. doi: 10.1186/s13287-020-02060-4.
Additional References at PubMed
PMID:8814301   PMID:10322633   PMID:15327782   PMID:15634706   PMID:16024294   PMID:17036046   PMID:17785448   PMID:18305125   PMID:18321982   PMID:18682239   PMID:19660448   PMID:20515681  
PMID:21350016   PMID:22902740   PMID:22995329   PMID:24598167   PMID:26116661  


Genomics

Comparative Map Data
Six2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8614,727,756 - 14,734,219 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl614,727,859 - 14,731,941 (+)EnsemblGRCr8
mRatBN7.268,974,859 - 8,981,345 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl68,967,157 - 8,981,193 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx69,252,089 - 9,255,407 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.069,561,498 - 9,564,816 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.069,089,205 - 9,092,512 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.068,952,572 - 8,955,893 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl68,952,572 - 8,956,276 (-)Ensemblrn6Rnor6.0
Rnor_5.068,875,432 - 8,878,685 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.469,094,655 - 9,097,973 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera68,702,767 - 8,705,759 (+)NCBICelera
RGSC_v3.169,095,089 - 9,098,000 (-)NCBI
Cytogenetic Map6q12NCBI
SIX2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38245,005,182 - 45,009,452 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl245,005,182 - 45,009,452 (-)Ensemblhg38GRCh38
GRCh37245,232,321 - 45,236,591 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36245,085,847 - 45,090,026 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34245,143,994 - 45,148,173NCBI
Celera245,070,945 - 45,075,163 (-)NCBICelera
Cytogenetic Map2p21NCBI
HuRef244,969,941 - 44,974,159 (-)NCBIHuRef
CHM1_1245,162,931 - 45,167,149 (-)NCBICHM1_1
T2T-CHM13v2.0245,010,408 - 45,014,884 (-)NCBIT2T-CHM13v2.0
Six2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391785,970,276 - 85,995,682 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1785,991,705 - 85,995,702 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381785,662,736 - 85,688,254 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1785,684,277 - 85,688,274 (-)Ensemblmm10GRCm38
MGSCv371786,083,608 - 86,087,594 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361785,592,594 - 85,596,573 (-)NCBIMGSCv36mm8
MGSCv361784,980,193 - 84,984,172 (-)NCBIMGSCv36mm8
Celera1790,046,891 - 90,050,640 (-)NCBICelera
Cytogenetic Map17E4NCBI
cM Map1755.72NCBI
Six2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544112,029,480 - 12,033,214 (-)Ensembl
ChiLan1.0NW_00495544112,029,530 - 12,033,214 (-)NCBIChiLan1.0ChiLan1.0
SIX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21281,393,947 - 81,398,443 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12A81,397,915 - 81,402,411 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02A45,109,414 - 45,113,887 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12A46,040,067 - 46,044,029 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A46,039,582 - 46,044,035 (-)EnsemblpanPan2panpan1.1
SIX2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11047,399,152 - 47,403,503 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1047,400,034 - 47,403,509 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1047,259,008 - 47,263,037 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01048,278,170 - 48,282,199 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1048,279,055 - 48,282,792 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11047,986,666 - 47,990,695 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01048,275,743 - 48,279,772 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01048,458,612 - 48,462,641 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Six2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629235,619,153 - 35,623,120 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365087,047,304 - 7,051,732 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365087,047,563 - 7,051,129 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SIX2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl395,459,945 - 95,463,251 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1395,460,046 - 95,463,428 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.23101,507,697 - 101,511,756 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SIX2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11462,212,920 - 62,219,976 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1462,213,115 - 62,220,069 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604549,662,672 - 49,667,207 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Six2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473826,442,965 - 26,446,942 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473826,442,935 - 26,447,100 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Six2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v177,310,659 - 7,313,982 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Six2
46 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:63
Count of miRNA genes:49
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000035406
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6197587946975879Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6197587946975879Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6144788383Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6197587946975879Rat
8693699Alc37Alcohol consumption QTL 372.60.224drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)61371716927053860Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6125740059Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6197587946975879Rat
2301964Bp323Blood pressure QTL 3234.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6186868070Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6323998948239989Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6323998948239989Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6140163351Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6120510098Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)61459947363457687Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6323998948239989Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6144788383Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6323998948239989Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6197587946975879Rat
8693690Alc35Alcohol consumption QTL 352.20.606drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)61371716927053860Rat

Markers in Region
Six2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.268,977,959 - 8,978,854 (-)MAPPERmRatBN7.2
Rnor_6.068,952,174 - 8,953,066NCBIRnor6.0
Rnor_5.068,875,034 - 8,875,926UniSTSRnor5.0
Celera68,705,265 - 8,705,891UniSTS
Cytogenetic Map6q12UniSTS


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
12 12 64 129 55 54 24 24 24 6 199 119 10 104 36 64 30 3 3

Sequence


Ensembl Acc Id: ENSRNOT00000079027   ⟹   ENSRNOP00000069414
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl68,952,572 - 8,956,276 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000103686   ⟹   ENSRNOP00000091206
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl68,967,157 - 8,981,193 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000141758   ⟹   ENSRNOP00000102713
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl614,727,859 - 14,731,941 (+)Ensembl
RefSeq Acc Id: NM_001191908   ⟹   NP_001178837
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8614,728,058 - 14,731,376 (+)NCBI
mRatBN7.268,975,136 - 8,978,454 (+)NCBI
Rnor_6.068,952,572 - 8,955,893 (-)NCBI
Rnor_5.068,875,432 - 8,878,685 (-)NCBI
Celera68,702,767 - 8,705,759 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039112616   ⟹   XP_038968544
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8614,727,762 - 14,731,846 (+)NCBI
mRatBN7.268,974,859 - 8,978,926 (+)NCBI
RefSeq Acc Id: XM_039112617   ⟹   XP_038968545
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8614,727,756 - 14,734,219 (+)NCBI
mRatBN7.268,974,859 - 8,981,345 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001178837 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968544 (Get FASTA)   NCBI Sequence Viewer  
  XP_038968545 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000102713
  ENSRNOP00000102713.1
RefSeq Acc Id: NP_001178837   ⟸   NM_001191908
- Sequence:
Ensembl Acc Id: ENSRNOP00000069414   ⟸   ENSRNOT00000079027
RefSeq Acc Id: XP_038968545   ⟸   XM_039112617
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038968544   ⟸   XM_039112616
- Peptide Label: isoform X1
- UniProtKB: A0A8I6ADX8 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000091206   ⟸   ENSRNOT00000103686
Ensembl Acc Id: ENSRNOP00000102713   ⟸   ENSRNOT00000141758

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JVB1-F1-model_v2 AlphaFold A0A0G2JVB1 1-296 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310792 AgrOrtholog
BioCyc Gene G2FUF-38675 BioCyc
Ensembl Genes ENSRNOG00000058827 Ensembl
  ENSRNOG00000068029 Ensembl
  ENSRNOG00000085124 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000141758 ENTREZGENE
  ENSRNOT00000141758.1 UniProtKB/TrEMBL
NCBI Gene 366542 ENTREZGENE
PhenoGen Six2 PhenoGen
RatGTEx ENSRNOG00000058827 RatGTEx
  ENSRNOG00000068029 RatGTEx
  ENSRNOG00000085124 RatGTEx
UniProt A0A8I6ADX8 ENTREZGENE
  A0ABK0LM21_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Six2  SIX homeobox 2  Six2  sine oculis-related homeobox 2 homolog (Drosophila)   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Six2  sine oculis-related homeobox 2 homolog (Drosophila)   Six2_predicted  sine oculis-related homeobox 2 homolog (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Six2_predicted  sine oculis-related homeobox 2 homolog (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED