Six3 (SIX homeobox 3) - Rat Genome Database

Name: Six3
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Six3 (SIX homeobox 3) Ictidomys tridecemlineatus

Analyze

Symbol:

Six3

Name:

SIX homeobox 3

RGD ID:

12726797

Description:

ENCODES a protein that exhibits DNA-binding transcription activator activity, RNA polymerase II-specific (ortholog); histone deacetylase binding (ortholog); sequence-specific DNA binding (ortholog); INVOLVED IN apoptotic process involved in development (ortholog); brain development (ortholog); camera-type eye development (ortholog); ASSOCIATED WITH genetic disease (ortholog); holoprosencephaly (ortholog); holoprosencephaly 2 (ortholog); FOUND IN nucleus (inferred); transcription regulator complex (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

homeobox protein SIX3

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):	SIX3 (SIX homeobox 3)	NCBI	Ortholog
Mus musculus (house mouse):	Six3 (sine oculis-related homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Six3 (SIX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Six3 (SIX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SIX3 (SIX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SIX3 (SIX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SIX3 (SIX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SIX3 (SIX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Six3 (SIX homeobox 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024406292	35,674,153 - 35,677,974 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936508	7,104,066 - 7,107,597 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936508	7,103,578 - 7,106,588 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

holoprosencephaly (ISO)

holoprosencephaly 2 (ISO)

Liver Neoplasms (ISO)

Lynch syndrome (ISO)

pre-malignant neoplasm (ISO)

Schizencephaly (ISO)

solitary median maxillary central incisor (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

apoptotic process involved in development (ISO)

brain development (IEA,ISO)

camera-type eye development (ISO)

cell proliferation in forebrain (ISO)

circadian behavior (ISO)

diencephalon development (ISO)

epithelial cell maturation (ISO)

eye development (IEA,ISO)

forebrain anterior/posterior pattern specification (ISO)

forebrain dorsal/ventral pattern formation (IEA)

gonad development (ISO)

lens development in camera-type eye (ISO)

lens fiber cell apoptotic process (ISO)

lens fiber cell differentiation (ISO)

lens induction in camera-type eye (ISO)

multicellular organism growth (ISO)

negative regulation of DNA-templated transcription (IEA,ISO)

negative regulation of neuron differentiation (ISO)

negative regulation of Wnt signaling pathway (ISO)

neuroblast differentiation (ISO)

neuroblast migration (ISO)

optic vesicle morphogenesis (ISO)

pituitary gland development (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

protein import into nucleus (ISO)

proximal/distal axis specification (ISO)

regulation of cell cycle phase transition (ISO)

regulation of cell population proliferation (ISO)

regulation of neural precursor cell proliferation (ISO)

regulation of neural retina development (ISO)

regulation of neuroblast proliferation (ISO)

regulation of transcription by RNA polymerase II (IEA)

telencephalon development (ISO)

telencephalon regionalization (ISO)

thyroid gland development (ISO)

Cellular Component

nucleus (IEA)

transcription regulator complex (IEA)

Molecular Function

DNA binding (IEA)

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

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

histone deacetylase binding (ISO)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IEA)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (IEA)

signaling receptor binding (ISO)

transcription corepressor binding (IEA)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Six3
(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	35,674,153 - 35,677,974 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936508	7,104,066 - 7,107,597 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936508	7,103,578 - 7,106,588 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SIX3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	44,941,702 - 44,946,071 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	44,941,702 - 44,946,071 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	45,168,841 - 45,173,210 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	45,022,541 - 45,025,894 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	45,080,511 - 45,084,092	NCBI
Celera	2	45,007,709 - 45,011,888 (+)	NCBI		Celera
Cytogenetic Map	2	p21	NCBI
HuRef	2	44,885,400 - 44,910,885 (+)	NCBI		HuRef
CHM1_1	2	45,098,943 - 45,103,122 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	44,946,967 - 44,951,332 (+)	NCBI		T2T-CHM13v2.0

Six3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	85,921,036 - 85,933,619 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	85,921,036 - 85,936,730 (+)	Ensembl		GRCm39 Ensembl
GRCm38	17	85,613,608 - 85,626,191 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	85,613,608 - 85,629,302 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	86,020,174 - 86,025,531 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	17	85,529,160 - 85,532,488 (+)	NCBI		MGSCv36	mm8
Celera	17	89,974,811 - 89,987,580 (+)	NCBI		Celera
Cytogenetic Map	17	E4	NCBI
cM Map	17	55.42	NCBI

Six3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	14,791,937 - 14,796,365 (-)	NCBI		GRCr8
mRatBN7.2	6	9,039,017 - 9,043,336 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	9,036,434 - 9,053,301 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	9,326,170 - 9,330,489 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	9,635,567 - 9,639,890 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	9,156,148 - 9,160,452 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	8,886,730 - 8,891,094 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	8,886,591 - 8,889,925 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	8,778,756 - 8,815,903 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	8,981,995 - 9,019,365 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	9,015,373 - 9,019,374 (+)	NCBI
Celera	6	8,770,011 - 8,793,533 (-)	NCBI		Celera
Cytogenetic Map	6	q12	NCBI

Six3
(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	11,966,389 - 11,979,466 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955441	11,966,389 - 11,978,545 (+)	NCBI	ChiLan1.0	ChiLan1.0

SIX3
(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	81,436,292 - 81,469,922 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	81,440,269 - 81,466,464 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	45,038,634 - 45,072,867 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	45,978,828 - 45,988,078 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

SIX3
(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	47,332,875 - 47,369,359 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	47,332,888 - 47,343,635 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	47,190,442 - 47,227,035 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	48,209,368 - 48,245,952 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	48,209,335 - 48,244,622 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	47,917,957 - 47,954,541 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	48,207,086 - 48,217,927 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	48,389,961 - 48,426,595 (+)	NCBI		UU_Cfam_GSD_1.0

SIX3
(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	95,521,334 - 95,525,436 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	95,521,330 - 95,527,004 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

SIX3
(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	62,278,124 - 62,292,942 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	14	62,278,461 - 62,281,127 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	49,599,060 - 49,626,248 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Six3
(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	26,380,088 - 26,394,252 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624738	26,379,172 - 26,391,669 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_021725892	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010001352	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSTOT00000023795 ⟹ ENSSTOP00000020304

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936508	7,104,066 - 7,107,597 (-)	Ensembl

RefSeq Acc Id:

XM_021725892 ⟹ XP_021581567

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024406292	35,674,153 - 35,677,974 (-)	NCBI
SpeTri2.0	NW_004936508	7,103,578 - 7,106,588 (-)	NCBI

Sequence:

show sequence

GTGGCCAGCGTCTGCGAGACGCTGGAGGAGACGGGCGACATTGAGCGGCTGGGCCGCTTCCTCT
GGTCGCTGCCTGTGGCCCCCGGGGCGTGCGAGGCCATCAACAAACACGAGTCGATCCTGCGCGC
GCGCGCCGTGGTCGCCTTCCACACGGGCAACTTCCGCGACCTGTACCACATCCTGGAGAACCAC
AAGTTCACCAAGGAGTCTCACGGCAAGCTGCAGGCCATGTGGCTCGAGGCTCACTACCAGGAGG
CCGAGAAGCTGCGCGGCCGCCCACTCGGCCCGGTGGACAAGTACCGCGTGCGCAAGAAGTTCCC
GCTGCCGCGCACCATCTGGGACGGCGAGCAGAAGACGCATTGCTTCAAGGAGCGGACTCGGAGC
CTGCTGCGGGAGTGGTACCTGCAGGACCCCTACCCCAACCCCAGCAAGAAACGCGAACTGGCGC
AGGCCACCGGCCTCACTCCCACACAAGTAGGCAACTGGTTTAAGAACCGGCGGCAGCGCGACCG
CGCCGCAGCGGCCAAGAACAGGGATCGTCGTCCTTTGCTGCGTGCCCAGGCCACCCCAGGCGGC
CGGCCTCTGGTTCTACCTCTCCTGAGTCCGGTCCCTATCTGGGAAGCTTTGGGAAGCTTCCCTG
GGGAAGGGAGCCAAGAGCCAAGACTCGGGCTGGGGAGTCTCTTCAGCGCCCAAGGAGTAGCTGG
GCTCCAGCACCAGGCCATCGGACCCAGCGGCATGCGCTCGCTGGCCGAACCCGGCTGCCCCACG
CACGGCTCGGCAGAGTCGCCGTCCACGGCGGCCAGCCCCACCACCAGTGTGTCCAGCCTGACGG
AGCGCGCGGACACCGGCACCTCCATCCTCTCGGTAACCTCCAGCGACTCGGAATGTGATGTATG
ATAGCCAAGGCTGCCCTCCTCCTCCCACCCCCTCCTTCCCCTCCTCTTTCCCCTCCTCCTCCTA
GCCCTCCTCCTCTTCCTCCTCTTCCTCCTCCATCCCCAGAACAAACCGAAATCAGGATACACAA
CCATACACACACATAAGTCCACACACACTCCCGCCCCAGCCAAAAATATATAAAAATCAAGAAA
AATAGCAAATTAACCGCAAACCATCAACAATCCCAAACCACCATCTACCACCACGGCCAACCCA
AAGGACCTCGACGCCAACAGACAGTCACAAACGCTGATGTTGCGGGCAGAAAACATAAAAGAGG
TGACAATTGTATACTTTCTAGGACAAGCACGGCTTCTCCTTTTGGTTCCCACGGACCCGGCACC
CCACCTGCATGACGATTTATTTGTATCTGGGAAAATATTCTCTCTAGTTTAAAATGATTTAAAG
AGTCGACTATACAAAAACCACCACCACCACCACGACGACAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_021581567	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000020304.2
GenBank Protein	KAG3267381	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_021581567 ⟸ XM_021725892

- Sequence:

show sequence

VASVCETLEETGDIERLGRFLWSLPVAPGACEAINKHESILRARAVVAFHTGNFRDLYHILENH
KFTKESHGKLQAMWLEAHYQEAEKLRGRPLGPVDKYRVRKKFPLPRTIWDGEQKTHCFKERTRS
LLREWYLQDPYPNPSKKRELAQATGLTPTQVGNWFKNRRQRDRAAAAKNRDRRPLLRAQATPGG
RPLVLPLLSPVPIWEALGSFPGEGSQEPRLGLGSLFSAQGVAGLQHQAIGPSGMRSLAEPGCPT
HGSAESPSTAASPTTSVSSLTERADTGTSILSVTSSDSECDV

hide sequence

RefSeq Acc Id:

ENSSTOP00000020304 ⟸ ENSSTOT00000023795

Protein Domains

Homeobox

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000028280	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000023795.2	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	SIX1_SD	UniProtKB/TrEMBL
NCBI Gene	Six3	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN SIX	UniProtKB/TrEMBL
	PTHR10390:SF31	UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/TrEMBL
	SIX1_SD	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	I3N7F8_ICTTR	UniProtKB/TrEMBL

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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