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 condensed mesenchymal cell proliferation; embryonic organ morphogenesis; and protein import into nucleus. 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; N,N-diethyl-m-toluamide; permethrin.
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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.268,974,859 - 8,981,345 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl68,967,157 - 8,981,193 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx69,252,089 - 9,255,407 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.069,561,498 - 9,564,816 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.069,089,205 - 9,092,512 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.068,952,572 - 8,955,893 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl68,952,572 - 8,956,276 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.068,875,432 - 8,878,685 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.469,094,655 - 9,097,973 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.169,095,089 - 9,098,000 (-)NCBI
Celera68,702,767 - 8,705,759 (+)NCBICelera
Cytogenetic Map6q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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
mRatBN7.268,974,859 - 8,981,345 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl68,967,157 - 8,981,193 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx69,252,089 - 9,255,407 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.069,561,498 - 9,564,816 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.069,089,205 - 9,092,512 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.068,952,572 - 8,955,893 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl68,952,572 - 8,956,276 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.068,875,432 - 8,878,685 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.469,094,655 - 9,097,973 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.169,095,089 - 9,098,000 (-)NCBI
Celera68,702,767 - 8,705,759 (+)NCBICelera
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 (-)EnsemblGRCh38hg38GRCh38
GRCh37245,232,321 - 45,236,591 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36245,085,847 - 45,090,026 (-)NCBINCBI36Build 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 Ensembl
GRCm381785,662,736 - 85,688,254 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1785,684,277 - 85,688,274 (-)EnsemblGRCm38mm10GRCm38
MGSCv371786,083,608 - 86,087,594 (-)NCBIGRCm37MGSCv37mm9NCBIm37
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 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544112,029,530 - 12,033,214 (-)NCBIChiLan1.0ChiLan1.0
SIX2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
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 (-)Ensemblpanpan1.1panPan2
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 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1047,259,008 - 47,263,037 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01048,278,170 - 48,282,199 (-)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473826,442,935 - 26,447,100 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Six2
17 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
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)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6507449719988050Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat

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
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 2 6 14 5
Low 24 15 6 8 6 8 9 46 2 11 3 8
Below cutoff 2 16 12 6 6 6 21 6 14 7

Sequence


RefSeq Acc Id: ENSRNOT00000079027   ⟹   ENSRNOP00000069414
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl68,952,572 - 8,956,276 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000103686   ⟹   ENSRNOP00000091206
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl68,967,157 - 8,981,193 (+)Ensembl
RefSeq Acc Id: NM_001191908   ⟹   NP_001178837
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
mRatBN7.268,974,859 - 8,978,926 (+)NCBI
RefSeq Acc Id: XM_039112617   ⟹   XP_038968545
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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 ENSRNOP00000091206
  ENSRNOP00000091206.1
RefSeq Acc Id: NP_001178837   ⟸   NM_001191908
- Sequence:
RefSeq 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)
RefSeq Acc Id: ENSRNOP00000091206   ⟸   ENSRNOT00000103686
Protein Domains
Homeobox

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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000103686 ENTREZGENE
  ENSRNOT00000103686.1 UniProtKB/TrEMBL
Gene3D-CATH Homeodomain-like UniProtKB/TrEMBL
InterPro Homeobox-like_sf UniProtKB/TrEMBL
  Homeobox_CS UniProtKB/TrEMBL
  Homeobox_dom UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
NCBI Gene 366542 ENTREZGENE
PANTHER HOMEOBOX PROTEIN SIX UniProtKB/TrEMBL
  HOMEOBOX PROTEIN SIX2 UniProtKB/TrEMBL
Pfam Homeodomain UniProtKB/TrEMBL
  SIX1_SD UniProtKB/TrEMBL
PhenoGen Six2 PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000058827 RatGTEx
  ENSRNOG00000068029 RatGTEx
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP SSF46689 UniProtKB/TrEMBL
UniProt A0A8I6ADX8 ENTREZGENE, 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