Six1 (SIX homeobox 1) - Rat Genome Database

Name: Six1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Six1 (SIX homeobox 1) Heterocephalus glaber

Analyze

Symbol:

Six1

Name:

SIX homeobox 1

RGD ID:

18906429

Description:

ENCODES a protein that exhibits transcription coactivator binding (ortholog); INVOLVED IN aorta morphogenesis (ortholog); branching involved in ureteric bud morphogenesis (ortholog); cellular response to 3,3',5-triiodo-L-thyronine (ortholog); ASSOCIATED WITH 22q11 Deletion Syndrome (ortholog); autosomal dominant nonsyndromic deafness (ortholog); autosomal dominant nonsyndromic deafness 23 (ortholog); FOUND IN cytoplasm (inferred); nucleolus (inferred); nucleoplasm (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

Homeobox protein SIX1

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):	SIX1 (SIX homeobox 1)	NCBI	Ortholog
Mus musculus (house mouse):	Six1 (sine oculis-related homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Six1 (SIX homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Six1 (SIX homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	SIX1 (SIX homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	SIX1 (SIX homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Six1 (SIX homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	SIX1 (SIX homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	SIX1 (SIX homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly

Position:

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_004624734	40,453,420 - 40,459,671 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624734	40,453,445 - 40,457,551 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

22q11 Deletion Syndrome (ISO)

autosomal dominant nonsyndromic deafness (ISO)

autosomal dominant nonsyndromic deafness 23 (ISO)

Branchiootic Syndrome 1 (ISO)

Branchiootic Syndrome 3 (ISO)

branchiootorenal syndrome (ISO)

branchiootorenal syndrome 1 (ISO)

breast cancer (ISO)

Congenital Abnormalities (ISO)

Craniofacial Abnormalities (ISO)

Endometrial Neoplasms (ISO)

genetic disease (ISO)

Hearing Loss (ISO)

hepatocellular carcinoma (ISO)

Lung Agenesis (ISO)

Neoplasm Metastasis (ISO)

nephroblastoma (ISO)

neurilemmoma (ISO)

Nonsyndromic Sensorineural Hearing Loss (ISO)

ovarian carcinoma (ISO)

Unilateral Hearing Loss (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

aorta morphogenesis (IEA,ISO)

apoptotic process (IEA)

branching involved in ureteric bud morphogenesis (IEA,ISO)

cellular response to 3,3',5-triiodo-L-thyronine (ISO)

cochlea morphogenesis (IEA,ISO)

embryonic cranial skeleton morphogenesis (IEA,ISO)

embryonic skeletal system morphogenesis (IEA,ISO)

endothelin receptor signaling pathway (IEA)

epithelial cell differentiation (IEA,ISO)

facial nerve morphogenesis (IEA,ISO)

fungiform papilla morphogenesis (IEA)

gene expression (IEA)

generation of neurons (IEA)

inner ear development (IEA)

inner ear morphogenesis (IEA,ISO)

kidney development (IEA)

mesenchymal cell proliferation involved in ureter development (IEA,ISO)

mesonephric tubule formation (IEA)

metanephric mesenchyme development (IEA)

middle ear morphogenesis (IEA,ISO)

myoblast migration (IEA,ISO)

myoblast proliferation (IEA,ISO)

myotome development (IEA)

negative regulation of apoptotic process (IEA)

negative regulation of neuron apoptotic process (IEA)

negative regulation of transcription by RNA polymerase II (IEA,ISO)

neural crest cell differentiation (IEA)

neurogenesis (IEA)

neuron fate specification (IEA,ISO)

Notch signaling pathway (IEA)

olfactory placode formation (IEA)

organ induction (IEA,ISO)

otic vesicle development (IEA,ISO)

outflow tract morphogenesis (IEA,ISO)

pattern specification process (IEA,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)

positive regulation of DNA-templated transcription (IEA)

positive regulation of mesenchymal cell proliferation involved in ureter development (IEA,ISO)

positive regulation of myoblast proliferation (IEA,ISO)

positive regulation of secondary heart field cardioblast proliferation (IEA,ISO)

positive regulation of transcription by RNA polymerase II (IEA,ISO)

positive regulation of ureteric bud formation (IEA)

protein localization to nucleus (IEA)

regulation of branch elongation involved in ureteric bud branching (IEA)

regulation of DNA-templated transcription (IEA,ISO)

regulation of epithelial cell proliferation (IEA)

regulation of gene expression (IEA,ISO)

regulation of neuron differentiation (IEA,ISO)

regulation of protein localization (IEA,ISO)

regulation of skeletal muscle cell differentiation (IEA)

regulation of skeletal muscle cell proliferation (IEA)

regulation of skeletal muscle satellite cell proliferation (IEA)

regulation of synaptic assembly at neuromuscular junction (IEA,ISO)

sensory perception of sound (IEA,ISO)

skeletal muscle fiber development (IEA)

skeletal muscle tissue development (IEA,ISO)

skeletal system morphogenesis (IEA,ISO)

thymus development (IEA,ISO)

thyroid gland development (IEA,ISO)

tongue development (IEA)

trigeminal ganglion development (IEA)

ureter smooth muscle cell differentiation (IEA,ISO)

ureteric bud development (IEA,ISO)

Cellular Component

cytoplasm (IEA)

nucleolus (IEA)

nucleoplasm (IEA)

nucleus (IEA)

transcription regulator complex (IEA)

Molecular Function

chromatin binding (IEA)

DNA binding (IEA)

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

DNA-binding transcription factor activity (IEA)

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

protein binding (ISO)

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

sequence-specific DNA binding (IEA)

sequence-specific double-stranded DNA binding (IEA)

transcription cis-regulatory region binding (IEA)

transcription coactivator binding (ISO)

References

Additional References at PubMed

PMID:21993625	PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Six1
(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_004624734	40,453,420 - 40,459,671 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624734	40,453,445 - 40,457,551 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

SIX1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	14	60,643,421 - 60,649,477 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	14	60,643,421 - 60,658,259 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	14	61,110,139 - 61,116,195 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	60,182,506 - 60,185,933 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	14	60,182,505 - 60,185,933	NCBI
Celera	14	41,161,682 - 41,166,417 (-)	NCBI		Celera
Cytogenetic Map	14	q23.1	NCBI
HuRef	14	41,274,621 - 41,279,356 (-)	NCBI		HuRef
CHM1_1	14	61,050,553 - 61,055,290 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	14	54,849,879 - 54,855,949 (-)	NCBI		T2T-CHM13v2.0

Six1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	73,088,601 - 73,093,486 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	73,086,789 - 73,100,661 (-)	Ensembl		GRCm39 Ensembl
GRCm38	12	73,041,827 - 73,046,712 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	73,040,015 - 73,053,887 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	74,142,814 - 74,147,699 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	12	73,960,668 - 73,965,302 (-)	NCBI		MGSCv36	mm8
Celera	12	74,158,405 - 74,163,290 (-)	NCBI		Celera
Cytogenetic Map	12	C3	NCBI
cM Map	12	30.34	NCBI

Six1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	97,482,617 - 97,487,853 (-)	NCBI		GRCr8
mRatBN7.2	6	91,746,739 - 91,751,975 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	91,746,739 - 91,751,975 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	92,137,046 - 92,142,281 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	92,436,544 - 92,441,778 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	91,864,445 - 91,869,679 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	95,929,060 - 95,934,296 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	95,929,060 - 95,934,296 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	105,364,372 - 105,369,608 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	95,470,153 - 95,475,389 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	95,475,346 - 95,478,212 (-)	NCBI
Celera	6	90,209,553 - 90,214,789 (-)	NCBI		Celera
Cytogenetic Map	6	q24	NCBI

Six1
(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_004955466	8,961,597 - 8,966,069 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955466	8,961,597 - 8,966,069 (+)	NCBI	ChiLan1.0	ChiLan1.0

SIX1
(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	15	61,782,374 - 61,786,732 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	14	60,997,057 - 61,003,141 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	14	41,250,512 - 41,256,567 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	14	59,515,324 - 59,518,740 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	14	59,515,324 - 59,527,494 (-)	Ensembl	panpan1.1		panPan2

SIX1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	8	35,676,705 - 35,679,534 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	8	35,676,479 - 35,679,534 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	35,430,686 - 35,433,517 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	8	35,909,922 - 35,912,747 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	8	35,909,922 - 35,913,208 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	8	35,522,041 - 35,524,863 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	8	35,599,806 - 35,602,627 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	8	35,960,733 - 35,963,565 (-)	NCBI		UU_Cfam_GSD_1.0

Six1
(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_024408640	69,348,816 - 69,353,683 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936495	4,838,051 - 4,842,994 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936495	4,839,496 - 4,842,906 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SIX1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	189,619,855 - 189,624,651 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	189,620,430 - 189,624,652 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	210,729,818 - 210,734,041 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SIX1
(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	24	37,840,399 - 37,855,801 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	24	37,840,309 - 37,845,192 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666053	26,090,242 - 26,095,370 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_004837443	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AHKG01010282	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GEBF01000339	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JH173437	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSHGLT00000020324 ⟹ ENSHGLP00000020123

Type:

CODING

Position:

Naked Mole-Rat Assembly	Chr	Position (strand)	Source
HetGla_female_1.0 Ensembl	NW_004624734	40,453,420 - 40,459,671 (+)	Ensembl

RefSeq Acc Id:

XM_004837443 ⟹ XP_004837500

Type:

CODING

Position:

Naked Mole-Rat Assembly	Chr	Position (strand)	Source
HetGla 1.0	NW_004624734	40,453,445 - 40,457,551 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_004837500	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EHB16789	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSHGLP00000020123
	ENSHGLP00000035073
	ENSHGLP00100040564
GenBank Protein	JAO03294	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	XP_004837500 ⟸ XM_004837443
- UniProtKB:	G5C5H8 (UniProtKB/TrEMBL)

RefSeq Acc Id:

ENSHGLP00000020123 ⟸ ENSHGLT00000020324

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSHGLG00000014403	Ensembl, ENTREZGENE
	ENSHGLG00000042472	UniProtKB/TrEMBL
	ENSHGLG00100045872	UniProtKB/TrEMBL
Ensembl Transcript	ENSHGLT00000020324	ENTREZGENE
	ENSHGLT00000050076	UniProtKB/TrEMBL
	ENSHGLT00100088174	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
	Homeobox_KN_domain	UniProtKB/TrEMBL
	SIX1_SD	UniProtKB/TrEMBL
KEGG Report	hgl:101720008	UniProtKB/TrEMBL
NCBI Gene	Six1	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN SIX	UniProtKB/TrEMBL
	PTHR10390:SF13	UniProtKB/TrEMBL
Pfam	Homeobox_KN	UniProtKB/TrEMBL
	SIX1_SD	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	G5C5H8	ENTREZGENE, 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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