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Gene: Vsx2 (visual system homeobox 2) Rattus norvegicus

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Symbol:

Vsx2

Name:

visual system homeobox 2

RGD ID:

621215

Description:

Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including negative regulation of neuroblast proliferation; positive regulation of transcription by RNA polymerase II; and retinal bipolar neuron differentiation. Predicted to be located in cytoplasm. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in blindness and isolated microphthalmia 2. Orthologous to human VSX2 (visual system homeobox 2); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

C. elegans ceh-10 homeo domain containing homolog; ceh-10 homeo domain containing homolog; ceh-10 homeo domain containing homolog (C. elegans); Chx10

RGD Orthologs

Alliance Orthologs

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):	VSX2 (visual system homeobox 2)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Vsx2 (visual system homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Vsx2 (visual system homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	VSX2 (visual system homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	VSX2 (visual system homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Vsx2 (visual system homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	VSX2 (visual system homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	VSX2 (visual system homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Vsx2 (visual system homeobox 2)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	VSX2 (visual system homeobox 2)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Mus musculus (house mouse):	Vsx2 (visual system homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	vsx2 (visual system homeobox 2)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ceh-10	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|SonicParanoid)
Drosophila melanogaster (fruit fly):	Vsx2	Alliance	DIOPT (OrthoFinder\|OrthoInspector\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	vsx2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	109,932,943 - 109,972,005 (+)	NCBI		GRCr8
mRatBN7.2	6	104,214,842 - 104,240,264 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	104,217,230 - 104,240,018 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	104,379,571 - 104,402,356 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	104,678,655 - 104,701,440 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	104,048,242 - 104,071,028 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	108,285,031 - 108,308,588 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	108,285,822 - 108,308,587 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	117,237,657 - 117,260,423 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	108,638,063 - 108,660,830 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	108,647,664 - 108,647,779 (+)	NCBI
Celera	6	102,045,137 - 102,067,982 (+)	NCBI		Celera
Cytogenetic Map	6	q31	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Vsx2	Rat	blindness	susceptibility	ISO	VSX2 (Homo sapiens)	734779	microphthalmia more ...	RGD

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Vsx2	Rat	Anophthalmia		ISO	VSX2 (Homo sapiens)	8554872	ClinVar Annotator: match by term: Anophthalmia	ClinVar	PMID:15257456 more ...
Vsx2	Rat	genetic disease		ISO	VSX2 (Homo sapiens)	8554872	ClinVar Annotator: match by term: Inborn genetic diseases	ClinVar	PMID:28492532
Vsx2	Rat	intellectual disability		ISO	VSX2 (Homo sapiens)	8554872	ClinVar Annotator: match by term: Intellectual disability and mild	ClinVar
Vsx2	Rat	isolated microphthalmia 2		ISO	VSX2 (Homo sapiens)	8554872	ClinVar more ...	ClinVar	PMID:10932181 more ...
Vsx2	Rat	isolated microphthalmia 6		ISO	VSX2 (Homo sapiens)	8554872	ClinVar Annotator: match by term: MICROPHTHALMIA and POSTERIOR NONSYNDROMIC	ClinVar	PMID:25741868
Vsx2	Rat	Isolated Microphthalmia with Coloboma 3		ISO	VSX2 (Homo sapiens)	8554872	ClinVar Annotator: match by term: Microphthalmia more ...	ClinVar	PMID:10932181 more ...
Vsx2	Rat	microphthalmia		ISO	VSX2 (Homo sapiens)	8554872	ClinVar more ...	ClinVar	PMID:15257456 more ...
Vsx2	Rat	Microphthalmia, Cataracts, and Iris Abnormalities		ISO	VSX2 (Homo sapiens)	8554872	ClinVar Annotator: match by term: Microphthalmia more ...	ClinVar	PMID:10932181 more ...
Vsx2	Rat	primary ciliary dyskinesia 16		ISO	VSX2 (Homo sapiens)	8554872	ClinVar Annotator: match by term: Primary ciliary dyskinesia 16	ClinVar	PMID:28492532
Vsx2	Rat	retinitis pigmentosa		ISO	VSX2 (Homo sapiens)	8554872	ClinVar Annotator: match by term: Retinitis pigmentosa	ClinVar
Vsx2	Rat	syndromic microphthalmia 5		ISO	VSX2 (Homo sapiens)	8554872	ClinVar Annotator: match by term: Anophthalmia-microphthalmia syndrome	ClinVar	PMID:20414678 more ...

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Vsx2	Rat	isolated microphthalmia 2		ISO	VSX2 (Homo sapiens)	11554173	CTD Direct Evidence: marker/mechanism	CTD
Vsx2	Rat	Isolated Microphthalmia with Coloboma 3		ISO	VSX2 (Homo sapiens)	11554173	CTD Direct Evidence: marker/mechanism	CTD

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Vsx2	Rat	isolated microphthalmia 2		ISO	VSX2 (Homo sapiens)	7240710		OMIM
Vsx2	Rat	Isolated Microphthalmia with Coloboma 3		ISO	VSX2 (Homo sapiens)	7240710		OMIM

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Vsx2	Rat	17beta-estradiol	multiple interactions	EXP		6480464	bisphenol A inhibits the reaction [[Estradiol co-treated with Progesterone] results in increased expression of VSX2 mRNA] and Diethylstilbestrol inhibits the reaction [[Estradiol co-treated with Progesterone] results in increased expression of VSX2 mRNA]	CTD	PMID:18653720
Vsx2	Rat	2,3,7,8-tetrachlorodibenzodioxine	affects expression	ISO	Vsx2 (Mus musculus)	6480464	Tetrachlorodibenzodioxin affects the expression of VSX2 mRNA	CTD	PMID:24058054
Vsx2	Rat	2,3,7,8-tetrachlorodibenzodioxine	decreases expression	EXP		6480464	Tetrachlorodibenzodioxin results in decreased expression of VSX2 mRNA	CTD	PMID:32109520
Vsx2	Rat	4,4'-sulfonyldiphenol	affects methylation	ISO	Vsx2 (Mus musculus)	6480464	bisphenol S affects the methylation of VSX2 exon and bisphenol S affects the methylation of VSX2 gene	CTD	PMID:31683443 and PMID:33297965
Vsx2	Rat	acetamide	increases expression	EXP		6480464	acetamide results in increased expression of VSX2 mRNA	CTD	PMID:31881176
Vsx2	Rat	ammonium chloride	affects expression	EXP		6480464	Ammonium Chloride affects the expression of VSX2 mRNA	CTD	PMID:16483693
Vsx2	Rat	amosite asbestos	decreases methylation	ISO	VSX2 (Homo sapiens)	6480464	Asbestos and Amosite results in decreased methylation of VSX2 promoter	CTD	PMID:29626692
Vsx2	Rat	arsenite(3-)	increases methylation	ISO	VSX2 (Homo sapiens)	6480464	arsenite results in increased methylation of VSX2 promoter	CTD	PMID:23974009
Vsx2	Rat	atrazine	increases expression	ISO	VSX2 (Homo sapiens)	6480464	Atrazine results in increased expression of VSX2 mRNA	CTD	PMID:22378314
Vsx2	Rat	atrazine	affects methylation	EXP		6480464	Atrazine affects the methylation of VSX2 gene	CTD	PMID:35440735
Vsx2	Rat	benzo[a]pyrene	decreases methylation	ISO	VSX2 (Homo sapiens)	6480464	Benzo(a)pyrene results in decreased methylation of VSX2 5' UTR and Benzo(a)pyrene results in decreased methylation of VSX2 exon	CTD	PMID:27901495
Vsx2	Rat	benzo[a]pyrene	affects methylation	ISO	VSX2 (Homo sapiens)	6480464	Benzo(a)pyrene affects the methylation of VSX2 promoter	CTD	PMID:27901495
Vsx2	Rat	bis(2-chloroethyl) sulfide	increases expression	ISO	Vsx2 (Mus musculus)	6480464	Mustard Gas results in increased expression of VSX2 mRNA	CTD	PMID:15674843
Vsx2	Rat	bisphenol A	multiple interactions	EXP		6480464	bisphenol A inhibits the reaction [[Estradiol co-treated with Progesterone] results in increased expression of VSX2 mRNA]	CTD	PMID:18653720
Vsx2	Rat	bisphenol A	increases expression	ISO	VSX2 (Homo sapiens)	6480464	bisphenol A results in increased expression of VSX2 mRNA	CTD	PMID:36126549
Vsx2	Rat	bisphenol A	decreases expression	ISO	Vsx2 (Mus musculus)	6480464	bisphenol A results in decreased expression of VSX2 mRNA	CTD	PMID:35479511
Vsx2	Rat	bisphenol A	increases expression	EXP		6480464	bisphenol A results in increased expression of VSX2 mRNA	CTD	PMID:30816183 and PMID:32528016
Vsx2	Rat	bisphenol A	increases methylation	EXP		6480464	bisphenol A results in increased methylation of VSX2 gene	CTD	PMID:28505145
Vsx2	Rat	bisphenol A	decreases expression	EXP		6480464	bisphenol A results in decreased expression of VSX2 mRNA	CTD	PMID:25181051 and PMID:34947998
Vsx2	Rat	cadmium dichloride	decreases methylation	EXP		6480464	Cadmium Chloride results in decreased methylation of VSX2 promoter	CTD	PMID:22457795
Vsx2	Rat	CGP 52608	multiple interactions	ISO	VSX2 (Homo sapiens)	6480464	CGP 52608 promotes the reaction [RORA protein binds to VSX2 gene]	CTD	PMID:28238834
Vsx2	Rat	crocidolite asbestos	decreases methylation	ISO	VSX2 (Homo sapiens)	6480464	Asbestos and Crocidolite results in decreased methylation of VSX2 promoter	CTD	PMID:29626692
Vsx2	Rat	diazinon	increases methylation	ISO	VSX2 (Homo sapiens)	6480464	Diazinon results in increased methylation of VSX2 gene	CTD	PMID:22964155
Vsx2	Rat	diethylstilbestrol	multiple interactions	EXP		6480464	Diethylstilbestrol inhibits the reaction [[Estradiol co-treated with Progesterone] results in increased expression of VSX2 mRNA]	CTD	PMID:18653720
Vsx2	Rat	endosulfan	increases expression	EXP		6480464	Endosulfan results in increased expression of VSX2 mRNA	CTD	PMID:29391264
Vsx2	Rat	epoxiconazole	increases expression	ISO	Vsx2 (Mus musculus)	6480464	epoxiconazole results in increased expression of VSX2 mRNA	CTD	PMID:35436446
Vsx2	Rat	gentamycin	decreases expression	EXP		6480464	Gentamicins results in decreased expression of VSX2 mRNA	CTD	PMID:33387578
Vsx2	Rat	lead diacetate	multiple interactions	ISO	Vsx2 (Mus musculus)	6480464	[lead acetate results in increased abundance of Lead] which affects the expression of VSX2 protein and [lead acetate results in increased abundance of Lead] which results in increased expression of VSX2 mRNA	CTD	PMID:28050121
Vsx2	Rat	lead(0)	multiple interactions	ISO	Vsx2 (Mus musculus)	6480464	[lead acetate results in increased abundance of Lead] which affects the expression of VSX2 protein and [lead acetate results in increased abundance of Lead] which results in increased expression of VSX2 mRNA	CTD	PMID:28050121
Vsx2	Rat	mono(2-ethylhexyl) phthalate	decreases expression	ISO	VSX2 (Homo sapiens)	6480464	mono-(2-ethylhexyl)phthalate results in decreased expression of VSX2 mRNA	CTD	PMID:36314267
Vsx2	Rat	paracetamol	increases expression	EXP		6480464	Acetaminophen results in increased expression of VSX2 mRNA	CTD	PMID:33387578
Vsx2	Rat	progesterone	multiple interactions	EXP		6480464	bisphenol A inhibits the reaction [[Estradiol co-treated with Progesterone] results in increased expression of VSX2 mRNA] and Diethylstilbestrol inhibits the reaction [[Estradiol co-treated with Progesterone] results in increased expression of VSX2 mRNA]	CTD	PMID:18653720
Vsx2	Rat	Ptaquiloside	decreases expression	ISO	Vsx2 (Mus musculus)	6480464	ptaquiloside results in decreased expression of VSX2 mRNA	CTD	PMID:23274088
Vsx2	Rat	sodium arsenite	increases expression	ISO	VSX2 (Homo sapiens)	6480464	sodium arsenite results in increased expression of VSX2 mRNA	CTD	PMID:34032870
Vsx2	Rat	Theaflavin 3,3'-digallate	affects expression	ISO	VSX2 (Homo sapiens)	6480464	theaflavin-3 and 3'-digallate affects the expression of VSX2 mRNA	CTD	PMID:34925699
Vsx2	Rat	titanium dioxide	decreases methylation	ISO	Vsx2 (Mus musculus)	6480464	titanium dioxide results in decreased methylation of VSX2 gene	CTD	PMID:35295148
Vsx2	Rat	trichloroethene	decreases expression	EXP		6480464	Trichloroethylene results in decreased expression of VSX2 mRNA	CTD	PMID:33387578
Vsx2	Rat	triptonide	increases expression	ISO	Vsx2 (Mus musculus)	6480464	triptonide results in increased expression of VSX2 mRNA	CTD	PMID:33045310
Vsx2	Rat	vinclozolin	decreases methylation	EXP		6480464	vinclozolin results in decreased methylation of VSX2 gene	CTD	PMID:31682807

Biological Process

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Vsx2	Rat	biological_process		ND		1598407	03/2007: no relevant rat data	RGD
Vsx2	Rat	camera-type eye development	acts_upstream_of_or_within	ISO	Vsx2 (Mus musculus)	1624291	MGI:104554 PMID:15576400	RGD	PMID:15576400
Vsx2	Rat	camera-type eye development	acts_upstream_of_or_within	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	cell fate commitment	acts_upstream_of_or_within	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	cell fate commitment	acts_upstream_of_or_within	ISO	Vsx2 (Mus musculus)	1624291	MGI:1856112 PMID:15576400	RGD	PMID:15576400
Vsx2	Rat	cell population proliferation	acts_upstream_of	ISO	Vsx2 (Mus musculus)	1624291	MGI:1856112 PMID:16384989 and PMID:8630490	RGD	PMID:16384989 and PMID:8630490
Vsx2	Rat	cell population proliferation	acts_upstream_of	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	central nervous system neuron differentiation	acts_upstream_of_or_within	ISO	Vsx2 (Mus musculus)	1624291	MGI:1856112 PMID:8630490	RGD	PMID:8630490
Vsx2	Rat	central nervous system neuron differentiation	acts_upstream_of_or_within	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	negative regulation of neuroblast proliferation	acts_upstream_of_or_within	ISO	Vsx2 (Mus musculus)	1624291	MGI:1856112 PMID:16384989	RGD	PMID:16384989
Vsx2	Rat	negative regulation of neuroblast proliferation	acts_upstream_of_or_within	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	negative regulation of transcription by RNA polymerase II	involved_in	ISO	VSX2 (Homo sapiens)	1624291	PMID:15647262	RGD	PMID:15647262
Vsx2	Rat	negative regulation of transcription by RNA polymerase II	involved_in	IEA	UniProtKB:P58304 and ensembl:ENSP00000261980	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	neuroblast proliferation	acts_upstream_of	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	neuroblast proliferation	acts_upstream_of	ISO	Vsx2 (Mus musculus)	1624291	MGI:1856112 PMID:16384989	RGD	PMID:16384989
Vsx2	Rat	positive regulation of cell population proliferation	acts_upstream_of_or_within	ISO	Vsx2 (Mus musculus)	1624291	MGI:1856112 PMID:8630490	RGD	PMID:8630490
Vsx2	Rat	positive regulation of cell population proliferation	acts_upstream_of_or_within	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	positive regulation of transcription by RNA polymerase II	acts_upstream_of_or_within	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	positive regulation of transcription by RNA polymerase II	acts_upstream_of_or_within	ISO	Vsx2 (Mus musculus)	1624291	PMID:15767664	RGD	PMID:15767664
Vsx2	Rat	regulation of DNA-templated transcription	involved_in	IEA	InterPro:IPR017970	1600115	GO_REF:0000002	InterPro	GO_REF:0000002
Vsx2	Rat	regulation of transcription by RNA polymerase II	involved_in	IBA	MGI:88401 more ...	1600115	GO_REF:0000033	GO_Central	GO_REF:0000033
Vsx2	Rat	retina morphogenesis in camera-type eye	acts_upstream_of_or_within	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	retina morphogenesis in camera-type eye	acts_upstream_of_or_within	ISO	Vsx2 (Mus musculus)	1624291	MGI:1856112 PMID:16854970 and PMID:8630490	RGD	PMID:16854970 and PMID:8630490
Vsx2	Rat	retinal bipolar neuron differentiation	acts_upstream_of_or_within	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	retinal bipolar neuron differentiation	acts_upstream_of_or_within	ISO	Vsx2 (Mus musculus)	1624291	MGI:1856112 PMID:8630490	RGD	PMID:8630490
Vsx2	Rat	visual perception	involved_in	IEA	UniProtKB-KW:KW-0844	1600115	GO_REF:0000043	UniProt	GO_REF:0000043

Cellular Component

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Vsx2	Rat	cytoplasm	located_in	ISO	Vsx2 (Mus musculus)	1624291	PMID:15767664 and PMID:19389377	RGD	PMID:15767664 and PMID:19389377
Vsx2	Rat	cytoplasm	located_in	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	nucleus	located_in	IEA	UniProtKB-KW:KW-0539	1600115	GO_REF:0000043	UniProt	GO_REF:0000043
Vsx2	Rat	nucleus	located_in	IEA	UniRule:UR000401037	1600115	GO_REF:0000104	UniProt	GO_REF:0000104
Vsx2	Rat	nucleus	located_in	ISO	Vsx2 (Mus musculus)	1624291	PMID:15767664 and PMID:19389377	RGD	PMID:15767664 and PMID:19389377
Vsx2	Rat	nucleus	is_active_in	IBA	FB:FBgn0263511 more ...	1600115	GO_REF:0000033	GO_Central	GO_REF:0000033
Vsx2	Rat	nucleus	located_in	IEA	UniProtKB-SubCell:SL-0191	1600115	GO_REF:0000044	UniProt	GO_REF:0000044
Vsx2	Rat	nucleus	located_in	IEA	UniProtKB:Q61412 and ensembl:ENSMUSP00000021665	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107

Molecular Function

Only show annotations with direct experimental evidence (0 objects hidden)

Object Symbol	Species	Term	Qualifier	Evidence	With	Reference	Notes	Source	Original Reference(s)
Vsx2	Rat	DNA binding	enables	IEA	InterPro:IPR001356	1600115	GO_REF:0000002	InterPro	GO_REF:0000002
Vsx2	Rat	DNA binding	enables	IEA	UniRule:UR000401037	1600115	GO_REF:0000104	UniProt	GO_REF:0000104
Vsx2	Rat	DNA binding	enables	IEA	UniProtKB-KW:KW-0238 and UniProtKB-KW:KW-0371	1600115	GO_REF:0000043	UniProt	GO_REF:0000043
Vsx2	Rat	DNA-binding transcription factor activity, RNA polymerase II-specific	enables	IEA	InterPro:IPR017970	1600115	GO_REF:0000002	InterPro	GO_REF:0000002
Vsx2	Rat	DNA-binding transcription repressor activity, RNA polymerase II-specific	enables	ISO	VSX2 (Homo sapiens)	1624291	PMID:15647262	RGD	PMID:15647262
Vsx2	Rat	DNA-binding transcription repressor activity, RNA polymerase II-specific	enables	IEA	UniProtKB:P58304 and ensembl:ENSP00000261980	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	protein binding	enables	ISO	VSX2 (Homo sapiens)	1624291	UniProtKB:A0A6Q8PF08 more ...	RGD	PMID:32814053
Vsx2	Rat	protein binding	enables	ISO	Vsx2 (Mus musculus)	1624291	PR:Q6P5F9 more ...	RGD	PMID:15767664 and PMID:9464541
Vsx2	Rat	RNA polymerase II transcription regulatory region sequence-specific DNA binding	enables	ISO	VSX2 (Homo sapiens)	1624291	PMID:15647262	RGD	PMID:15647262
Vsx2	Rat	RNA polymerase II transcription regulatory region sequence-specific DNA binding	enables	IEA	UniProtKB:P58304 and ensembl:ENSP00000261980	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	sequence-specific double-stranded DNA binding	enables	ISO	VSX2 (Homo sapiens)	1624291	PMID:28473536	RGD	PMID:28473536
Vsx2	Rat	sequence-specific double-stranded DNA binding	enables	IEA	UniProtKB:P58304 and ensembl:ENSP00000261980	1600115	GO_REF:0000107	Ensembl	GO_REF:0000107
Vsx2	Rat	sequence-specific double-stranded DNA binding	enables	IBA	PANTHER:PTN000676430 and UniProtKB:P58304	1600115	GO_REF:0000033	GO_Central	GO_REF:0000033

#	Reference Title	Reference Citation
1.	Human microphthalmia associated with mutations in the retinal homeobox gene CHX10.	Ferda Percin E, etal., Nat Genet 2000 Aug;25(4):397-401.
2.	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.
3.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
4.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	GOA pipeline	RGD automated data pipeline
6.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
8.	Comprehensive gene review and curation	RGD comprehensive gene curation

PMID:8630490	PMID:10482234	PMID:15576400	PMID:15767664	PMID:16236706	PMID:16384989	PMID:16547132	PMID:16854970	PMID:19389377

Vsx2
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	109,932,943 - 109,972,005 (+)	NCBI		GRCr8
mRatBN7.2	6	104,214,842 - 104,240,264 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	104,217,230 - 104,240,018 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	104,379,571 - 104,402,356 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	104,678,655 - 104,701,440 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	104,048,242 - 104,071,028 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	108,285,031 - 108,308,588 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	108,285,822 - 108,308,587 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	117,237,657 - 117,260,423 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	108,638,063 - 108,660,830 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	108,647,664 - 108,647,779 (+)	NCBI
Celera	6	102,045,137 - 102,067,982 (+)	NCBI		Celera
Cytogenetic Map	6	q31	NCBI

VSX2
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	14	74,239,449 - 74,262,738 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	14	74,239,449 - 74,262,738 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	14	74,706,152 - 74,729,441 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	14	73,775,928 - 73,799,194 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	14	73,775,927 - 73,799,193	NCBI
Celera	14	54,743,463 - 54,766,749 (+)	NCBI		Celera
Cytogenetic Map	14	q24.3	NCBI
HuRef	14	54,873,146 - 54,896,407 (+)	NCBI		HuRef
CHM1_1	14	74,645,738 - 74,668,970 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	14	68,447,256 - 68,470,582 (+)	NCBI		T2T-CHM13v2.0

Vsx2
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	84,616,602 - 84,642,231 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	84,616,536 - 84,642,231 (+)	Ensembl		GRCm39 Ensembl
GRCm38	12	84,569,828 - 84,595,457 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	84,569,762 - 84,595,457 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	85,910,802 - 85,936,407 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	12	85,459,600 - 85,485,205 (+)	NCBI		MGSCv36	mm8
Celera	12	86,025,411 - 86,051,063 (+)	NCBI		Celera
Cytogenetic Map	12	D1	NCBI
cM Map	12	39.28	NCBI

Vsx2
(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_004955523	1,193,686 - 1,210,641 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955523	1,192,035 - 1,207,949 (-)	NCBI	ChiLan1.0	ChiLan1.0

VSX2
(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	75,328,455 - 75,349,803 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	14	74,544,961 - 74,566,309 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	14	54,797,734 - 54,821,081 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	14	73,651,133 - 73,672,666 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

VSX2
(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	47,455,337 - 47,473,786 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	8	47,455,340 - 47,473,684 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	8	47,140,385 - 47,158,661 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	8	47,682,709 - 47,700,996 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	8	47,682,709 - 47,700,979 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	8	47,351,896 - 47,370,154 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	8	47,373,742 - 47,392,004 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	8	47,760,454 - 47,778,742 (+)	NCBI		UU_Cfam_GSD_1.0

Vsx2
(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	28,561,166 - 28,581,265 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936488	3,487,702 - 3,508,191 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936488	3,487,718 - 3,507,802 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

VSX2
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	97,531,860 - 97,552,033 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	97,532,021 - 97,551,072 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	103,375,425 - 103,394,310 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

VSX2
(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	51,446,781 - 51,471,156 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	24	51,447,714 - 51,469,345 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666053	39,680,858 - 39,704,250 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Vsx2
(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	27,344,221 - 27,363,372 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624734	27,342,668 - 27,363,372 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants in Vsx2
165 total Variants

Predicted Target Of

	Summary Value
Count of predictions:	625
Count of miRNA genes:	271
Interacting mature miRNAs:	335
Transcripts:	ENSRNOT00000015889
Prediction methods:	Microtar, 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.

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
12801411	Schws8	Schwannoma susceptibility QTL 8			nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	94968928	139968928	Rat
1331797	Bp213	Blood pressure QTL 213	3.291		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	104085867	128713626	Rat
1331799	Bp211	Blood pressure QTL 211	3.66407		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	72202632	130919985	Rat
1358355	Srcrt4	Stress Responsive Cort QTL 4	6.39		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	100364669	140994061	Rat
2313399	Anxrr28	Anxiety related response QTL 28			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	6	100671796	132340886	Rat
1331789	Rf37	Renal function QTL 37	3.224		kidney blood vessel physiology trait (VT:0100012)	absolute change in renal vascular resistance (CMO:0001900)	6	72202632	115200186	Rat
1331725	Bp212	Blood pressure QTL 212	3.52475		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	6	93701310	128713626	Rat
1331722	Thshl1	Thyroid stimulating hormone level QTL 1	11.7	0.0001	blood thyroid-stimulating hormone amount (VT:0005119)	serum thyroid stimulating hormone level (CMO:0001248)	6	89762877	106752806	Rat
8552796	Vie3	Viral induced encephalitis QTL 3	2.6		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	6	96833997	140994061	Rat
4145119	Mcs25	Mammary carcinoma susceptibility QTL 25		0.0001	mammary gland integrity trait (VT:0010552)	ratio of deaths to total study population during a period of time (CMO:0001023)	6	10894415	110548006	Rat
1581563	Uae33	Urinary albumin excretion QTL 33			urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	72227641	130729205	Rat
10054138	Gmadr3	Adrenal mass QTL 3	3.68	0.00045	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	6	85140138	130140138	Rat
61414	Pia3	Pristane induced arthritis QTL 3	4.5		joint integrity trait (VT:0010548)	post-insult time to onset of experimental arthritis (CMO:0001450)	6	94968928	137848904	Rat
724524	Uae2	Urinary albumin excretion QTL 2	2.7	0.0005	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	73463459	109394713	Rat
737827	Hcar11	Hepatocarcinoma resistance QTL 11	4.4		liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	6	82523650	110548006	Rat
1641904	Alcrsp4	Alcohol response QTL 4			response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	6	67262953	112262953	Rat
724513	Uae14	Urinary albumin excretion QTL 14	6.5		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	85311061	133478515	Rat
2303624	Vencon5	Ventilatory control QTL 5	4.45		respiration trait (VT:0001943)	minute ventilation (CMO:0000132)	6	88047916	133047916	Rat
1576309	Emca7	Estrogen-induced mammary cancer QTL 7	4		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	6	15107216	107351382	Rat
731173	Uae22	Urinary albumin excretion QTL 22	10.1		urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	65531555	140994061	Rat
2293837	Kiddil1	Kidney dilation QTL 1	3.7		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	81132889	104393926	Rat
2293842	Kiddil3	Kidney dilation QTL 3	4.3		kidney pelvis morphology trait (VT:0004194)	hydronephrosis severity score (CMO:0001208)	6	81132889	104393926	Rat
10054123	Srcrt6	Stress Responsive Cort QTL 6	2.5	0.0043	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	6	85140138	130140138	Rat
724536	Uae7	Urinary albumin excretion QTL 7	3.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	6	72202632	130729475	Rat
70196	BpQTLcluster7	Blood pressure QTL cluster 7	6.82		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	6	72202632	117202632	Rat
1581550	Pur8	Proteinuria QTL 8			urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	6	72227641	130729205	Rat
1576302	Schws4	Schwannoma susceptibility QTL 4		0.0078	nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	83190345	106747639	Rat
1300075	Glom7	Glomerulus QTL 7	5.6	0.0000002	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	6	71201409	116201409	Rat
738034	Anxrr5	Anxiety related response QTL 5	5.9		exploratory behavior trait (VT:0010471)	percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)	6	84130881	129130881	Rat
2290393	Uae37	Urinary albumin excretion QTL 37		0.0001	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	6	65531555	140994061	Rat
12801471	Schws9	Schwannoma susceptibility QTL 9			nervous system integrity trait (VT:0010566)	percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)	6	61747639	106747639	Rat
1300076	Glom8	Glomerulus QTL 8	7	9e-09	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)	6	86894788	131894788	Rat

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	47	113	77	76	45	25	45	6	202	95	93	45	55	31


RefSeq Transcripts	NM_001169128	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017594026	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC114437	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF390079	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473982	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000006	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000015889 ⟹ ENSRNOP00000015889

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	6	104,217,230 - 104,240,018 (+)	Ensembl
Rnor_6.0 Ensembl	6	108,285,822 - 108,308,587 (+)	Ensembl

RefSeq Acc Id:

NM_001169128 ⟹ NP_001162599

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	109,948,313 - 109,971,100 (+)	NCBI
mRatBN7.2	6	104,217,230 - 104,240,018 (+)	NCBI
Rnor_6.0	6	108,285,798 - 108,308,585 (+)	NCBI
Rnor_5.0	6	117,237,657 - 117,260,423 (-)	NCBI
RGSC_v3.4	6	108,638,063 - 108,660,830 (+)	RGD
Celera	6	102,045,137 - 102,067,982 (+)	NCBI

Sequence:

show sequence

GAGCATTAGACACCGGAGGGGGCACCTGGGACCAACTTCACGAAGCGGGGAGCCCGGCGGGGGGGGCTTGGGGGAGCAAAAGACCCGCGGCCTCAGCCCCTCCAAAGAACCGGGAGATGACGGGGAAA
GCGGGGGAAGCGCTGAGCAAGCCTAAATCCGAGACAGTGGCCAAGAGTACCTCGGGGGGTGCCCCGGCCAGGTGCACAGGGTTCGGCATCCAGGAGATCCTAGGCTTGAACAAGGAGCCTCCCAGCTC
CCACCCGCGGGCTGCCCTGGACGGCCTGGCCCCCGGGCATTTGTTAGCTGCGCGCTCTGTTCTCAGCCCCGCAGGAGTGGGCAGCATGGGGCTGCTGGGGCCCGGAGGGCTTCCCGGCTTCTACGCAC
AGCCCACCTTCCTGGAAGTGCTGTCCGATCCGCAGAGCGTCCACTTGCAGCCACTAGGCAGAGCGTCGGGGCCGCTGGACACCAGCCAGACGGCCAGCTCCGATTCCGAAGATGTTTCCTCCAGTGAC
CGAAAAATGTCCAAATCGGCTTTAAACCAGACCAAGAAACGTAAGAAGCGGCGACACAGGACAATCTTTACTTCCTACCAGCTAGAGGAGCTGGAGAAGGCATTCAATGAAGCCCACTACCCAGATGT
CTACGCCCGGGAGATGCTGGCCATGAAAACGGAGCTACCAGAAGACAGGATACAGGTGTGGTTCCAGAACCGCAGAGCCAAATGGAGGAAGAGGGAGAAGTGCTGGGGCCGGAGCAGCGTCATGGCTG
AGTACGGCCTCTATGGAGCCATGGTGAGGCACTCCATCCCCCTGCCAGAGTCCATCCTCAAGTCGGCCAAGGACGGCATCATGGATTCCTGCGCCCCTTGGCTACTGGGGATGCACAAAAAGTCGCTG
GAGGCAGCAGCCGAGTCCGGAAGGAAGCCCGAGGTGGAACGCCAGGTCCTGCCCAAACTCGACAAGATGGAGCAGGAGGAAAGGGCCCCGGATGCTCAGGCAGCCATCTCCCAGGAAGAACTGAGGGA
GAACAGCATTGCGGCCCTCCGAGCCAAAGCTCAGGAGCACAGCACCAAGGTTCTGGGGACTGTATCCGGGCCTGACGGCCTAGCCAGGAATGCTGAGAAGCCAGAAGAGGAGGAAGCCATGGACGAAG
ACAGGCCAGCAGAGAAGCTCAGCCCACCGCAGCTGGAGGACATGGCTTAGGTTAAGGGCTGCAGGCCTTAAGACTGCTCTTCTCGGGTCCTGTGGTGTGGGGAGTTCTCTCTGAGGCAGGGCCATGTC
TGGCTTCTGCTGCACCTCCCCACACCTCAGGCCCTCGACTACCCCACCACTCTAGGCACAGGCCAGTTCTGGCGTAGCTTTGGACCATGCTGAGATATCCTGGACCTACTCCTGATCCAGCATCCTCA
TCCTCAGCCCAGCTCCCCTGCCTCCAAAGCCTTCTTGCTACTCCAACATCGAGGTCCTGCCATTTCATCCCTGAGAGACTCTTGTCCAAGCCTAACCCTTATTCTCTGCTCTCTAAGCCTCCTTCTCA
GCTCAGCCCCACTCGTGCACTCCAGCTCACAGCCTGGCAGAGCTGTGATTGGATTGAGGACATGCACACCAGCTCCGGTGTCCTGAGCACCCCAGTACTGGGCAGACAGGCCTTTCCCTCGTCACCTG
TTCCTTCTCACAGACCTGCGTCCTGCTGTGTGAATGCATTGCTCCACGTGTGACCGCTGCATTCTCTGCCCTACCTAAAGACTAACAGGGCAAGTCTGTCTGAGTCCTTCTGCAAACCTGTCTCATGC
TACGCTGTGGGTCATCCTCAAGCCTTTTCTGTACCCAGCCTGCCCTATAGGTTCCTCCTTTGCAGAGGTGGGCTCACCACATTGCCAGTGTCTAGGCCCTGCACCCTGAGGGTGGGGGCCCTTCTCAG
CAATGCTGTGTCTTGCTGTGCTGCTGGTGAGCCTTCGCCCAGAGCTTTTGCAGGCCAGGGCCTGTGTTCCTGAAGCGTTTTGACCTTTCTGCCTATGATGTTGACTTGCTGGTTAAAGCTTCCTTTCT
CTAGAGCTTCTTGTAGCCCAGTGGTTCTCAAGCTTCCTAATGCTGTGACCCTTTAATACCGTTCCTCATGCTGTGGTGACCACTCCCACCCCCTAACCTCAAATTTATTTCCTTGCTACTTCATAACT
GTAATTTTACTACTGTTGTGAATCACAATGTAAATATCTGATATGCAGAATATCTGACTATGTGACTCCCGCAAAGGGTCATGACCCACAGGTTGAGAATTGCTGTTGTAGCCAATTGGTTCACATGT
GCCTGCTTTGGAGAAAACCAGTGCAGCTCGAAAGCCACAGACATGGCCTCACGCTGACCTAGGCAGTCCTAAAAGGCTAATCTATCTAAATCAGACCTGCACTGTCTACACACACACACACACACACA
CACACACACACACACACACACACACACGATGAATAACAAGAAAGGTACAGGGAAAGCTCAAAGGACGACAAGGCAGGTAGCTAATGAAAAACCCAGACTAAGCTCCAGACACTCCTAGCTCCATGACA
GTTGTATGCCCAGAAACATGGAGCATGTCCAGAGAAGGAGCCATGTTGGACTGAAAGACTTCTGCCTGCAAAGGAGTGGAGCTGTCCATCCTGGTGGCCCATCTGCAGATGTCCCTTCCACCTGACTT
TACACTTGTACTGGGGGGGCGGGGTACCCGGCCTTATGGAATCCTCTGCTTCCAGATCCCCAGGCCAACCACAAGAATCCCTTCATTCTGTGAAACTAGGCACTCCACCCACCATTTTAGGGGCCGCC
TCACAAGAGAGGCGTGAGGCAGTGAGTGGTGGTTTTAAATCTGTTTTGACAGTTGAGTTCTTCTTTCGTTCTGTTCATAGAATTCTCCACTTCCCAGTTCTTGTCTTCTTCGGGTTGAGATGTTAGAC
CGTAGTTCTGCTGTGTAAATAGTGTATATAACGTGAGAAGGAAGAGACTGGATATCGAGGTGTTTGAAACACTGAAGTGTCAGAACTTTTAGGTATCTGAAGCATAATTTCTGTGCTGTTTTCTGTAA
AGACACAAGCAAGAATAAAATTCATGCAAAGACTGCT

hide sequence

RefSeq Acc Id:

XM_017594026 ⟹ XP_017449515

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	6	109,932,943 - 109,972,005 (+)	NCBI
mRatBN7.2	6	104,214,842 - 104,240,264 (+)	NCBI
Rnor_6.0	6	108,285,031 - 108,308,588 (+)	NCBI

Sequence:

show sequence

TGTCAAGTTGGCCCCCAGATGAAATCCCAGCCCTCAGGAGGAGAATATTGAATTTGGGAACAGC
TCGAACTGTATAGAGGTCCTGTCTTAAAACACCAGGAAGAAAGAGGGGGGTGGGAGTAAGGAGGATTAGATAAGGAGGGAAGGAAGACCCCATATTTGTTATCAAACAAAACCCTCACCTTTTCTCTT
TCCCACGAGGGCTTGATCCTAACCCTGATCCCTTTAACGCAGGCCAGTATTTATTGAACAGCTCTTCTGAACTGAACACAATGTCCCATGCTGGAGAGACAAGCCCTACCCACACATCTAAGGCCCTT
GCTGTGTTCTCATTCCCACCACTCAGTTCAGGGCCCTCCAGCCTTCCTTGTCCCGTGTCTGTCTATTTGAGGCTGCTGAGTTAAGAGAGGGGAGAGGTCTCCTAGTTTTGCAGACCATCCCCATCCCC
CTAACCCTACCCCAGGGATCTGTCCCAGCTAACCTTGGCACTGGTCCCAGTCAGGTTATACAACTCAGAGCCCCTATCCACTGTGTCCCCTGGAACAACTCCAAACCTGGCTGTTTCACCTTTGTCCC
TGCAAGAGCACCCTGCAGAGCCCACCACACTTGGGCCTGCAGCGCCCTGGCCCCTCGGTACCGGTGGCGGCGGGAGCTGCCAGCTTTTTGGAATTCCTAATCGCTCCTGGCCCCGGTGATTGGCTGTT
CAGCTCTGACCCCACTTGGGCTGCCGCCTGGTTGGATAAAAAGGGAATCTCCTTGGGGCTCCAGAGCATTAGACACCGGAGGGGGCACCTGGGACCAACTTCACGAAGCGGGGAGCCCGGCGGGGGGG
GCTTGGGGGAGCAAAAGACCCGCGGCCTCAGCCCCTCCAAAGAACCGGGAGATGACGGGGAAAGCGGGGGAAGCGCTGAGCAAGCCTAAATCCGAGACAGTGGCCAAGAGTACCTCGGGGGGTGCCCC
GGCCAGGTGCACAGGGTTCGGCATCCAGGAGATCCTAGGCTTGAACAAGGAGCCTCCCAGCTCCCACCCGCGGGCTGCCCTGGACGGCCTGGCCCCCGGGCATTTGTTAGCTGCGCGCTCTGTTCTCA
GCCCCGCAGGAGTGGGCAGCATGGGGCTGCTGGGGCCCGGAGGGCTTCCCGGCTTCTACGCACAGCCCACCTTCCTGGAAGTGCTGTCCGATCCGCAGAGCGTCCACTTGCAGCCACTAGGCAGAGCG
TCGGGGCCGCTGGACACCAGCCAGACGGCCAGCTCCGATTCCGAAGATGTTTCCTCCAGTGACCGAAAAATGTCCAAATCGGCTTTAAACCAGACCAAGAAACGTAAGAAGCGGCGACACAGGACAAT
CTTTACTTCCTACCAGCTAGAGGAGCTGGAGAAGGCATTCAATGAAGCCCACTACCCAGATGTCTACGCCCGGGAGATGCTGGCCATGAAAACGGAGCTACCAGAAGACAGGATACAGGTGTGGTTCC
AGAACCGCAGAGCCAAATGGAGGAAGAGGGAGAAGTGCTGGGGCCGGAGCAGCGTCATGGCTGAGTACGGCCTCTATGGAGCCATGGTGAGGCACTCCATCCCCCTGCCAGAGTCCATCCTCAAGTCG
GCCAAGGACGGCATCATGGATTCCTGCGCCCCTTGGCTACTGGTTCAAGATGGCTTTCCCAGGCGCTTTTCTAAACCCGAATACCAACAATTCTTTTTAGGGATGCACAAAAAGTCGCTGGAGGCAGC
AGCCGAGTCCGGAAGGAAGCCCGAGGTGGAACGCCAGGTCCTGCCCAAACTCGACAAGATGGAGCAGGAGGAAAGGGCCCCGGATGCTCAGGCAGCCATCTCCCAGGAAGAACTGAGGGAGAACAGCA
TTGCGGCCCTCCGAGCCAAAGCTCAGGAGCACAGCACCAAGGTTCTGGGGACTGTATCCGGGCCTGACGGCCTAGCCAGGAATGCTGAGAAGCCAGAAGAGGAGGAAGCCATGGACGAAGACAGGCCA
GCAGAGAAGCTCAGCCCACCGCAGCTGGAGGACATGGCTTAGGTTAAGGGCTGCAGGCCTTAAGACTGCTCTTCTCGGGTCCTGTGGTGTGGGGAGTTCTCTCTGAGGCAGGGCCATGTCTGGCTTCT
GCTGCACCTCCCCACACCTCAGGCCCTCGACTACCCCACCACTCTAGGCACAGGCCAGTTCTGGCGTAGCTTTGGACCATGCTGAGATATCCTGGACCTACTCCTGATCCAGCATCCTCATCCTCAGC
CCAGCTCCCCTGCCTCCAAAGCCTTCTTGCTACTCCAACATCGAGGTCCTGCCATTTCATCCCTGAGAGACTCTTGTCCAAGCCTAACCCTTATTCTCTGCTCTCTAAGCCTCCTTCTCAGCTCAGCC
CCACTCGTGCACTCCAGCTCACAGCCTGGCAGAGCTGTGATTGGATTGAGGACATGCACACCAGCTCCGGTGTCCTGAGCACCCCAGTACTGGGCAGACAGGCCTTTCCCTCGTCACCTGTTCCTTCT
CACAGACCTGCGTCCTGCTGTGTGAATGCATTGCTCCACGTGTGACCGCTGCATTCTCTGCCCTACCTAAAGACTAACAGGGCAAGTCTGTCTGAGTCCTTCTGCAAACCTGTCTCATGCTACGCTGT
GGGTCATCCTCAAGCCTTTTCTGTACCCAGCCTGCCCTATAGGTTCCTCCTTTGCAGAGGTGGGCTCACCACATTGCCAGTGTCTAGGCCCTGCACCCTGAGGGTGGGGGCCCTTCTCAGCAATGCTG
TGTCTTGCTGTGCTGCTGGTGAGCCTTCGCCCAGAGCTTTTGCAGGCCAGGGCCTGTGTTCCTGAAGCGTTTTGACCTTTCTGCCTATGATGTTGACTTGCTGGTTAAAGCTTCCTTTCTCTAGAGCT
TCTTGTAGCCCAGTGGTTCTCAAGCTTCCTAATGCTGTGACCCTTTAATACCGTTCCTCATGCTGTGGTGACCACTCCCACCCCCTAACCTCAAATTTATTTCCTTGCTACTTCATAACTGTAATTTT
ACTACTGTTGTGAATCACAATGTAAATATCTGATATGCAGAATATCTGACTATGTGACTCCCGCAAAGGGTCATGACCCACAGGTTGAGAATTGCTGTTGTAGCCAATTGGTTCACATGTGCCTGCTT
TGGAGAAAACCAGTGCAGCTCGAAAGCCACAGACATGGCCTCACGCTGACCTAGGCAGTCCTAAAAGGCTAATCTATCTAAATCAGACCTGCACTGTCTACACACACACACACACACACACACACACA
CACACACACACACACACACGATGAATAACAAGAAAGGTACAGGGAAAGCTCAAAGGACGACAAGGCAGGTAGCTAATGAAAAACCCAGACTAAGCTCCAGACACTCCTAGCTCCATGACAGTTGTATG
CCCAGAAACATGGAGCATGTCCAGAGAAGGAGCCATGTTGGACTGAAAGACTTCTGCCTGCAAAGGAGTGGAGCTGTCCATCCTGGTGGCCCATCTGCAGATGTCCCTTCCACCTGACTTTACACTTG
TACTGGGGGGGCGGGGTACCCGGCCTTATGGAATCCTCTGCTTCCAGATCCCCAGGCCAACCACAAGAATCCCTTCATTCTGTGAAACTAGGCACTCCACCCACCATTTTAGGGGCCGCCTCACAAGA
GAGGCGTGAGGCAGTGAGTGGTGGTTTTAAATCTGTTTTGACAGTTGAGTTCTTCTTTCGTTCTGTTCATAGAATTCTCCACTTCCCAGTTCTTGTCTTCTTCGGGTTGAGATGTTAGACCGTAGTTC
TGCTGTGTAAATAGTGTATATAACGTGAGAAGGAAGAGACTGGATATCGAGGTGTTTGAAACACTGAAGTGTCAGAACTTTTAGGTATCTGAAGCATAATTTCTGTGCTGTTTTCTGTAAAGACACAA
GCAAGAATAAAATTCATGCAAAGACTGCTGGA

hide sequence


Protein RefSeqs	NP_001162599	(Get FASTA)	NCBI Sequence Viewer
	XP_017449515	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAK70506	(Get FASTA)	NCBI Sequence Viewer
	EDL81517	(Get FASTA)	NCBI Sequence Viewer
	EDL81518	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000015889
	ENSRNOP00000015889.6

RefSeq Acc Id:

NP_001162599 ⟸ NM_001169128

- UniProtKB:

G3V7K0 (UniProtKB/TrEMBL), A6JDX4 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MTGKAGEALSKPKSETVAKSTSGGAPARCTGFGIQEILGLNKEPPSSHPRAALDGLAPGHLLAARSVLSPAGVGSMGLLGPGGLPGFYAQPTFLEVLSDPQSVHLQPLGRASGPLDTSQTASSDSEDV
SSSDRKMSKSALNQTKKRKKRRHRTIFTSYQLEELEKAFNEAHYPDVYAREMLAMKTELPEDRIQVWFQNRRAKWRKREKCWGRSSVMAEYGLYGAMVRHSIPLPESILKSAKDGIMDSCAPWLLGMH
KKSLEAAAESGRKPEVERQVLPKLDKMEQEERAPDAQAAISQEELRENSIAALRAKAQEHSTKVLGTVSGPDGLARNAEKPEEEEAMDEDRPAEKLSPPQLEDMA

hide sequence

RefSeq Acc Id:	XP_017449515 ⟸ XM_017594026
- Peptide Label:	isoform X1
- UniProtKB:	A6JDX3 (UniProtKB/TrEMBL)
- Sequence:	show sequence MTGKAGEALSKPKSETVAKSTSGGAPARCTGFGIQEILGLNKEPPSSHPRAALDGLAPGHLLAARSVLSPAGVGSMGLLGPGGLPGFYAQPTFLEVLSDPQSVHLQPLGRASGPLDTSQTASSDSEDV SSSDRKMSKSALNQTKKRKKRRHRTIFTSYQLEELEKAFNEAHYPDVYAREMLAMKTELPEDRIQVWFQNRRAKWRKREKCWGRSSVMAEYGLYGAMVRHSIPLPESILKSAKDGIMDSCAPWLLVQD GFPRRFSKPEYQQFFLGMHKKSLEAAAESGRKPEVERQVLPKLDKMEQEERAPDAQAAISQEELRENSIAALRAKAQEHSTKVLGTVSGPDGLARNAEKPEEEEAMDEDRPAEKLSPPQLEDMA hide sequence

Ensembl Acc Id:

ENSRNOP00000015889 ⟸ ENSRNOT00000015889

Protein Domains

CVC Homeobox OAR

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-G3V7K0-F1-model_v2	AlphaFold	G3V7K0	1-361	view protein structure

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

Database	Acc Id	Source(s)
BioCyc Gene	G2FUF-36816	BioCyc
Ensembl Genes	ENSRNOG00000011918	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000015889	ENTREZGENE
	ENSRNOT00000015889.7	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	CVC	UniProtKB/TrEMBL
	Homeobox	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeodomain-like	UniProtKB/TrEMBL
	OAR_dom	UniProtKB/TrEMBL
	VSX_homeobox_regulators	UniProtKB/TrEMBL
KEGG Report	rno:171360	UniProtKB/TrEMBL
NCBI Gene	171360	ENTREZGENE
PANTHER	VISUAL SYSTEM HOMEOBOX 2	UniProtKB/TrEMBL
	VISUAL SYSTEM HOMEOBOX 2	UniProtKB/TrEMBL
Pfam	Homeobox	UniProtKB/TrEMBL
	OAR	UniProtKB/TrEMBL
PhenoGen	Vsx2	PhenoGen
PROSITE	CVC	UniProtKB/TrEMBL
	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
	OAR	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000011918	RatGTEx
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	Homeodomain_like	UniProtKB/TrEMBL
UniProt	A6JDX3	ENTREZGENE, UniProtKB/TrEMBL
	A6JDX4	ENTREZGENE, UniProtKB/TrEMBL
	G3V7K0	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-02-19	Vsx2	visual system homeobox 2	Chx10	ceh-10 homeo domain containing homolog (C. elegans)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	Chx10	ceh-10 homeo domain containing homolog (C. elegans)		C. elegans ceh-10 homeo domain containing homolog	Name updated	1299863	APPROVED
2002-08-07	Chx10	C. elegans ceh-10 homeo domain containing homolog			Symbol and Name status set to provisional	70820	PROVISIONAL

Note Type	Note	Reference
gene_other	mouse homolog is mutated in the ocular retardationJ mutant	634855

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


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


Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
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MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable

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