Six2 (SIX homeobox 2) - Rat Genome Database

Name: Six2
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	SIX2 (SIX homeobox 2)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther
Mus musculus (house mouse):	Six2 (sine oculis-related homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Six2 (SIX homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SIX2 (SIX homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SIX2 (SIX homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Six2 (SIX homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SIX2 (SIX homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SIX2 (SIX homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Six2 (SIX homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	SIX2 (SIX homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Six2 (sine oculis-related homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	six2a (SIX homeobox 2a)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	six2b (SIX homeobox 2b)	Alliance	DIOPT (Ensembl Compara\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	ceh-32	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ceh-33	Alliance	DIOPT (InParanoid\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	so	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ceh-34	Alliance	DIOPT (Hieranoid\|OMA\|PANTHER\|PhylomeDB)
Xenopus tropicalis (tropical clawed frog):	six2	Alliance	DIOPT (OrthoFinder\|PANTHER)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	14,727,756 - 14,734,219 (+)	NCBI		GRCr8
mRatBN7.2	6	8,974,859 - 8,981,345 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	8,967,157 - 8,981,193 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	9,252,089 - 9,255,407 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	9,561,498 - 9,564,816 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	9,089,205 - 9,092,512 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	8,952,572 - 8,955,893 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	8,952,572 - 8,956,276 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	8,875,432 - 8,878,685 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	9,094,655 - 9,097,973 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	9,095,089 - 9,098,000 (-)	NCBI
Celera	6	8,702,767 - 8,705,759 (+)	NCBI		Celera
Cytogenetic Map	6	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

amyotrophic lateral sclerosis type 1 (ISO)

CAKUT (ISO)

chronic kidney disease (ISO)

cleft palate (ISS)

frontonasal dysplasia (ISO)

genetic disease (ISO)

holoprosencephaly 2 (ISO)

kidney disease (ISO)

Kidney Reperfusion Injury (ISO)

Lynch syndrome (ISO)

nephroblastoma (ISO)

renal Wilms' tumor (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dichloroethane (ISO)

17beta-estradiol (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

4,4'-diaminodiphenylmethane (ISO)

4,4'-sulfonyldiphenol (ISO)

5-azacytidine (ISO)

6-propyl-2-thiouracil (ISO)

all-trans-retinoic acid (ISO)

antirheumatic drug (ISO)

arsenous acid (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium atom (ISO)

cadmium dichloride (ISO)

chlorpyrifos (ISO)

cisplatin (ISO)

copper atom (ISO)

copper(0) (ISO)

diarsenic trioxide (ISO)

diiodine (ISO)

epoxiconazole (ISO)

folic acid (ISO)

formaldehyde (ISO)

lead(0) (ISO)

mono(2-ethylhexyl) phthalate (ISO)

Monobutylphthalate (ISO)

N,N-diethyl-m-toluamide (EXP)

N-methyl-4-phenylpyridinium (ISO)

pentanal (ISO)

permethrin (EXP)

propanal (ISO)

silicon dioxide (ISO)

testosterone (ISO)

vanadyl sulfate (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior axis specification (ISO)

cell migration (ISO)

cell population proliferation (ISO)

chondrocyte differentiation (ISO)

condensed mesenchymal cell proliferation (ISO)

embryonic cranial skeleton morphogenesis (ISO)

embryonic digestive tract morphogenesis (ISO)

embryonic skeletal system morphogenesis (ISO)

epithelial cell differentiation (ISO)

kidney development (IBA,ISO)

mesenchymal cell differentiation involved in kidney development (ISO)

mesenchymal stem cell maintenance involved in nephron morphogenesis (ISO)

mesenchymal stem cell proliferation (ISO)

mesenchymal to epithelial transition involved in metanephros morphogenesis (ISO)

mesodermal cell fate specification (ISO)

metanephros development (ISO)

middle ear morphogenesis (ISO)

negative regulation of epithelial cell differentiation (ISO)

nephron development (ISO)

nephron morphogenesis (ISO)

positive regulation of chondrocyte proliferation (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

protein import into nucleus (ISO)

regulation of branching involved in ureteric bud morphogenesis (ISO)

regulation of chondrocyte differentiation (ISO)

regulation of ossification (ISO)

regulation of transcription by RNA polymerase II (IBA)

Cellular Component

nucleus (IBA,ISO)

transcription regulator complex (IBA)

Molecular Function

DNA-binding transcription activator activity, RNA polymerase II-specific (ISO)

DNA-binding transcription factor activity (ISO)

DNA-binding transcription factor activity, RNA polymerase II-specific (IBA)

protein binding (ISO)

protein-containing complex binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IBA,ISO)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (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 Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	14,727,756 - 14,734,219 (+)	NCBI		GRCr8
mRatBN7.2	6	8,974,859 - 8,981,345 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	8,967,157 - 8,981,193 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	9,252,089 - 9,255,407 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	9,561,498 - 9,564,816 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	9,089,205 - 9,092,512 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	8,952,572 - 8,955,893 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	8,952,572 - 8,956,276 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	8,875,432 - 8,878,685 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	9,094,655 - 9,097,973 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	9,095,089 - 9,098,000 (-)	NCBI
Celera	6	8,702,767 - 8,705,759 (+)	NCBI		Celera
Cytogenetic Map	6	q12	NCBI

SIX2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	45,005,182 - 45,009,452 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	45,005,182 - 45,009,452 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	45,232,321 - 45,236,591 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	45,085,847 - 45,090,026 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	45,143,994 - 45,148,173	NCBI
Celera	2	45,070,945 - 45,075,163 (-)	NCBI		Celera
Cytogenetic Map	2	p21	NCBI
HuRef	2	44,969,941 - 44,974,159 (-)	NCBI		HuRef
CHM1_1	2	45,162,931 - 45,167,149 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	2	45,010,408 - 45,014,884 (-)	NCBI		T2T-CHM13v2.0

Six2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	85,970,276 - 85,995,682 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	85,991,705 - 85,995,702 (-)	Ensembl		GRCm39 Ensembl
GRCm38	17	85,662,736 - 85,688,254 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	85,684,277 - 85,688,274 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	86,083,608 - 86,087,594 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	17	85,592,594 - 85,596,573 (-)	NCBI		MGSCv36	mm8
MGSCv36	17	84,980,193 - 84,984,172 (-)	NCBI		MGSCv36	mm8
Celera	17	90,046,891 - 90,050,640 (-)	NCBI		Celera
Cytogenetic Map	17	E4	NCBI
cM Map	17	55.72	NCBI

Six2
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955441	12,029,480 - 12,033,214 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955441	12,029,530 - 12,033,214 (-)	NCBI	ChiLan1.0	ChiLan1.0

SIX2
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	12	81,393,947 - 81,398,443 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	81,397,915 - 81,402,411 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	45,109,414 - 45,113,887 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	46,040,067 - 46,044,029 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	46,039,582 - 46,044,035 (-)	Ensembl	panpan1.1		panPan2

SIX2
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	10	47,399,152 - 47,403,503 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	47,400,034 - 47,403,509 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	47,259,008 - 47,263,037 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	48,278,170 - 48,282,199 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	48,279,055 - 48,282,792 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	47,986,666 - 47,990,695 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	48,275,743 - 48,279,772 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	48,458,612 - 48,462,641 (-)	NCBI		UU_Cfam_GSD_1.0

Six2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024406292	35,619,153 - 35,623,120 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936508	7,047,304 - 7,051,732 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936508	7,047,563 - 7,051,129 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SIX2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	95,459,945 - 95,463,251 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	95,460,046 - 95,463,428 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	101,507,697 - 101,511,756 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SIX2
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	14	62,212,920 - 62,219,976 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	14	62,213,115 - 62,220,069 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	49,662,672 - 49,667,207 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Six2
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624738	26,442,965 - 26,446,942 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624738	26,442,935 - 26,447,100 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Six2
27 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.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
738023	Alc17	Alcohol consumption QTL 17	3.1	0.003	consumption behavior trait (VT:0002069)	ethanol drink intake rate to body weight ratio (CMO:0001616)	6	1	27574569	Rat
1354616	Despr12	Despair related QTL 12		0.0012	locomotor behavior trait (VT:0001392)	amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)	6	1	27574569	Rat
1549905	Stresp10	Stress response QTL 10	6.83	0.0066	stress-related behavior trait (VT:0010451)	number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)	6	1	27574569	Rat
2300176	Bmd51	Bone mineral density QTL 51	11.7	0.0001	femur mineral mass (VT:0010011)	bone mineral density (CMO:0001226)	6	1	27574569	Rat
2300190	Bmd52	Bone mineral density QTL 52	11.2	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	6	1	27574569	Rat
1331743	Uae28	Urinary albumin excretion QTL 28	4.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	1	34235784	Rat
1578758	Tcas9	Tongue tumor susceptibility QTL 9	3.29		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	6	1	37618905	Rat
1598843	Cm63	Cardiac mass QTL 63	2.6		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	6	1	39036266	Rat
7411603	Foco13	Food consumption QTL 13	5.5	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	41223769	Rat
8552962	Pigfal16	Plasma insulin-like growth factor 1 level QTL 16	9.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	6	1	41223769	Rat
7411542	Bw127	Body weight QTL 127	5.5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	6	1	41223769	Rat
9589129	Insul24	Insulin level QTL 24	19.06	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	6	1	41223769	Rat
9589048	Scfw3	Subcutaneous fat weight QTL 3	4.57	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	6	1	41223769	Rat
2293709	Bss23	Bone structure and strength QTL 23	5.18	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	6	1	42487980	Rat
2293650	Bss31	Bone structure and strength QTL 31	5.05	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	6	1	42487980	Rat
2293656	Bss28	Bone structure and strength QTL 28	6.79	0.0001	femur morphology trait (VT:0000559)	femur midshaft cortical cross-sectional area (CMO:0001663)	6	1	42487980	Rat
7411584	Foco4	Food consumption QTL 4	4.3	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	6	1	42838846	Rat
738024	Sach5	Saccharine consumption QTL 5	3.9	0.00039	consumption behavior trait (VT:0002069)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	6	1	43394190	Rat
2301972	Bp325	Blood pressure QTL 325	4.8		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	1	72227641	Rat
2293706	Bmd20	Bone mineral density QTL 20	4.3	0.0002	femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	6	5074497	19988050	Rat
1300128	Rf16	Renal function QTL 16	3.89		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	5074497	34434305	Rat
1300164	Rf15	Renal function QTL 15	3.12		renal blood flow trait (VT:2000006)	absolute change in renal blood flow rate (CMO:0001168)	6	5074497	54641141	Rat

Markers in Region

Six2

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	6	8,977,959 - 8,978,854 (-)	MAPPER	mRatBN7.2
Rnor_6.0	6	8,952,174 - 8,953,066	NCBI	Rnor6.0
Rnor_5.0	6	8,875,034 - 8,875,926	UniSTS	Rnor5.0
Celera	6	8,705,265 - 8,705,891	UniSTS
Cytogenetic Map	6	q12	UniSTS

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

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001191908	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039112616	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039112617	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000079027 ⟹ ENSRNOP00000069414

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	6	8,952,572 - 8,956,276 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000103686 ⟹ ENSRNOP00000091206

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	8,967,157 - 8,981,193 (+)	Ensembl

RefSeq Acc Id:

NM_001191908 ⟹ NP_001178837

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	14,728,058 - 14,731,376 (+)	NCBI
mRatBN7.2	6	8,975,136 - 8,978,454 (+)	NCBI
Rnor_6.0	6	8,952,572 - 8,955,893 (-)	NCBI
Rnor_5.0	6	8,875,432 - 8,878,685 (-)	NCBI
Celera	6	8,702,767 - 8,705,759 (+)	NCBI

Sequence:

show sequence

ATGTCCATGCTGCCCACCTTCGGCTTCACGCAGGAGCAAGTGGCGTGCGTGTGCGAGGTGCTGC
AGCAGGGCGGCAACATCGAGCGGCTAGGTCGCTTCCTGTGGTCGCTGCCTGCCTGCGAGCACCT
CCACAAGAATGAAAGCGTGCTCAAGGCCAAGGCCGTGGTGGCCTTTCACCGGGGCAACTTCCGC
GAGCTCTACAAAATCCTGGAGAGCCACCAGTTCTCGCCGCACAACCACGCCAAGCTGCAGCAGC
TGTGGCTCAAGGCGCACTACATCGAGGCGGAGAAGCTGCGCGGCCGGCCCCTGGGCGCCGTGGG
CAAGTACCGCGTGCGGCGCAAGTTCCCGCTGCCCCGCTCCATCTGGGACGGCGAGGAGACCAGC
TACTGCTTCAAGGAGAAGAGCCGCAGCGTGCTGCGCGAGTGGTATGCGCACAACCCTTACCCGT
CGCCGCGGGAGAAGCGCGAGCTGGCCGAGGCCACCGGCCTCACCACCACGCAGGTCAGCAACTG
GTTCAAAAACCGGCGGCAGCGCGACAGGGCGGCGGAGGCCAAGGAAAGGGAGAACAGCGAGAAC
TCCAATTCCAGTAGCCACAACCCGCTGGCTTCCTCGCTCAATGGCAGCGGCAAGTCGGTGCTAG
GCAGTTCCGAGGACGAGAAGACGCCGTCGGGGACTCCAGACCACTCGTCATCCAGTCCCGCACT
GTTGCTCAGCCCGCCGCCGCCCCCTGGGTTGCCTTCCCTACACAGCCTGGGCCACCCTCCGGGC
CCGAGCGCAGTGCCCGTGCCAGTGCCCGGTGGAGGCGGCGCGGATCCACTGCAGCATCACCACA
GCCTGCAGGACTCCATACTCAACCCCATGTCGGCCAACCTTGTGGACCTAGGCTCCTAGAGCTC
TGCTCGCCTCCCGGCGCTTGCTTTCCGTGCTTGGTGCGGGGACTTGAGAGGCGGTGTGGGAGGG
CGGTAGATTGGAGTCTGGACCGGGTACTGGAAGACTGCCCTGCCACGCTGGAGCGGCAGAACCG
GCGGCGGGACAAAGTGGACAATGGTCTGCTCGGGGTCCTTTGCGGGATTCATTCTCAAGTTGCT
TTTGAGATCCTTTGGAGGCCAGGGACCTAGTCTTGAACTGGGCAAGGGAATAAATTATAAACGA
CCACCACCCCTTTTAAAATCTCTTCCCTTTCTCTTGCTCTTTTCTTTCCTCCATTTTCCCTTCG
GGTTTCTTATGTCTCCTCTTTTCATTTTTTTCTCTCTGCCTCTTTTTGCTTTTCTTTTTCCCCT
TTATACATTTCTGGATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTC

hide sequence

RefSeq Acc Id:

XM_039112616 ⟹ XP_038968544

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	14,727,762 - 14,731,846 (+)	NCBI
mRatBN7.2	6	8,974,859 - 8,978,926 (+)	NCBI

RefSeq Acc Id:

XM_039112617 ⟹ XP_038968545

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	14,727,756 - 14,734,219 (+)	NCBI
mRatBN7.2	6	8,974,859 - 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:

show sequence

MSMLPTFGFTQEQVACVCEVLQQGGNIERLGRFLWSLPACEHLHKNESVLKAKAVVAFHRGNFR
ELYKILESHQFSPHNHAKLQQLWLKAHYIEAEKLRGRPLGAVGKYRVRRKFPLPRSIWDGEETS
YCFKEKSRSVLREWYAHNPYPSPREKRELAEATGLTTTQVSNWFKNRRQRDRAAEAKERENSEN
SNSSSHNPLASSLNGSGKSVLGSSEDEKTPSGTPDHSSSSPALLLSPPPPPGLPSLHSLGHPPG
PSAVPVPVPGGGGADPLQHHHSLQDSILNPMSANLVDLGS

hide 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

External Database Links

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	ENSRNOT00000103686.1	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

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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