Advanced Search (OLGA)

Gene: Otx1 (orthodenticle homeobox 1) Rattus norvegicus

Analyze

Symbol:

Otx1

Name:

orthodenticle homeobox 1

RGD ID:

3237

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 positive regulation of transcription by RNA polymerase II. Predicted to act upstream of or within anterior/posterior pattern specification; brain development; and inner ear morphogenesis. Predicted to be active in nucleus. Orthologous to human OTX1 (orthodenticle homeobox 1); INTERACTS WITH bisphenol A; Cuprizon; ethanol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

homeobox protein OTX1; homeobox protein OTX1-like; LOC100364498; Orthodenticle (Drosophila) homolog 1; orthodenticle homolog 1 (Drosophila); OTX1X

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):	OTX1 (orthodenticle homeobox 1)	HGNC	HomoloGene, NCBI, Panther
Mus musculus (house mouse):	Otx1 (orthodenticle homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Otx1 (orthodenticle homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	OTX1 (orthodenticle homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	OTX1 (orthodenticle homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Otx1 (orthodenticle homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	OTX1 (orthodenticle homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	OTX1 (orthodenticle homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Otx1 (orthodenticle homeobox 1)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	OTX1 (orthodenticle homeobox 1)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Otx1 (orthodenticle homeobox 1)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	ceh-37	Alliance	DIOPT (Hieranoid\|InParanoid\|OrthoInspector\|SonicParanoid)
Drosophila melanogaster (fruit fly):	oc	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoInspector\|PANTHER)
Caenorhabditis elegans (roundworm):	ttx-1	Alliance	DIOPT (Ensembl Compara\|OrthoInspector\|PANTHER)
Danio rerio (zebrafish):	otx1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	otx2a	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB)

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	14	100,283,406 - 100,290,421 (-)	NCBI		GRCr8
mRatBN7.2	14	96,082,146 - 96,089,161 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	96,082,151 - 96,089,086 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	100,434,962 - 100,438,425 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	101,675,306 - 101,678,769 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	98,148,827 - 98,152,290 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	106,861,556 - 106,864,933 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	106,861,676 - 106,864,892 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	106,926,505 - 106,929,875 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	102,721,413 - 102,724,748 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	102,740,623 - 102,743,959 (-)	NCBI
Celera	14	95,081,129 - 95,084,585 (-)	NCBI		Celera
Cytogenetic Map	14	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Bardet-Biedl syndrome (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

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

2,4,4'-trichlorobiphenyl (ISO)

4,4'-sulfonyldiphenol (ISO)

aflatoxin B1 (ISO)

arsane (ISO)

arsenic atom (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (ISO)

choline (ISO)

copper(II) sulfate (ISO)

Cuprizon (EXP)

dicrotophos (ISO)

dorsomorphin (ISO)

enzyme inhibitor (ISO)

ethanol (EXP)

ethylbenzene (ISO)

flusilazole (ISO)

folic acid (ISO)

formaldehyde (ISO)

genistein (ISO)

hexaconazole (ISO)

hydroquinone O-beta-D-glucopyranoside (ISO)

iron dichloride (ISO)

kojic acid (ISO)

L-methionine (ISO)

leflunomide (ISO)

methotrexate (ISO)

paracetamol (EXP,ISO)

PCB138 (ISO)

resveratrol (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sodium fluoride (ISO)

titanium dioxide (ISO)

toluene (ISO)

triadimefon (ISO)

trichostatin A (ISO)

triptonide (ISO)

tris(2-butoxyethyl) phosphate (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

anterior/posterior pattern specification (IEA,ISO)

diencephalon morphogenesis (IEA,ISO)

forebrain development (IEA,ISO)

inner ear morphogenesis (IEA,ISO)

metencephalon development (IEA,ISO)

midbrain development (IEA,ISO)

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

regulation of DNA-templated transcription (IEA)

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

Cellular Component

nucleus (IBA,IEA)

Molecular Function

DNA binding (IEA)

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

DNA-binding transcription factor activity (IEA)

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

protein binding (ISO)

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

sequence-specific double-stranded DNA binding (IEA,ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Otx1 and Otx2 define layers and regions in developing cerebral cortex and cerebellum.	Frantz GD, etal., J Neurosci 1994 Oct;14(10):5725-40.
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 GOA human gene data--August 2006	GOA data from the GO Consortium
4.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
5.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
6.	GOA pipeline	RGD automated data pipeline
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
8.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
9.	Regulated nuclear trafficking of the homeodomain protein otx1 in cortical neurons.	Zhang YA, etal., Mol Cell Neurosci 2002 Mar;19(3):430-46.

Additional References at PubMed

PMID:8613727	PMID:10225993	PMID:15105370	PMID:15201224	PMID:15917450	PMID:18849347	PMID:20816794	PMID:38635011

Genomics

Comparative Map Data

Otx1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	100,283,406 - 100,290,421 (-)	NCBI		GRCr8
mRatBN7.2	14	96,082,146 - 96,089,161 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	96,082,151 - 96,089,086 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	100,434,962 - 100,438,425 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	101,675,306 - 101,678,769 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	98,148,827 - 98,152,290 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	106,861,556 - 106,864,933 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	106,861,676 - 106,864,892 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	106,926,505 - 106,929,875 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	102,721,413 - 102,724,748 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	14	102,740,623 - 102,743,959 (-)	NCBI
Celera	14	95,081,129 - 95,084,585 (-)	NCBI		Celera
Cytogenetic Map	14	q22	NCBI

OTX1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	63,049,735 - 63,057,831 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	63,050,057 - 63,057,836 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	63,276,870 - 63,284,966 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	63,131,469 - 63,137,818 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	63,189,615 - 63,195,961	NCBI
Celera	2	63,122,518 - 63,128,867 (+)	NCBI		Celera
Cytogenetic Map	2	p15	NCBI
HuRef	2	63,016,136 - 63,023,910 (+)	NCBI		HuRef
CHM1_1	2	63,207,478 - 63,215,248 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	63,056,812 - 63,064,908 (+)	NCBI		T2T-CHM13v2.0

Otx1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	21,944,764 - 21,954,044 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	11	21,944,764 - 21,952,897 (-)	Ensembl		GRCm39 Ensembl
GRCm38	11	21,994,764 - 22,001,651 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	21,994,764 - 22,002,897 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	21,894,767 - 21,901,654 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	11	21,894,767 - 21,901,654 (-)	NCBI		MGSCv36	mm8
Celera	11	24,135,716 - 24,142,604 (-)	NCBI		Celera
Cytogenetic Map	11	A3.2	NCBI
cM Map	11	14.1	NCBI

Otx1
(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_004955424	21,140,038 - 21,146,694 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955424	21,140,038 - 21,147,268 (-)	NCBI	ChiLan1.0	ChiLan1.0

OTX1
(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	63,333,760 - 63,340,516 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	63,338,922 - 63,344,466 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	63,125,700 - 63,133,702 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	64,255,217 - 64,262,221 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	64,255,217 - 64,262,221 (+)	Ensembl	panpan1.1		panPan2

OTX1
(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	62,830,515 - 62,836,449 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	10	62,830,187 - 62,837,172 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	62,717,998 - 62,724,904 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	63,837,537 - 63,844,443 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	63,837,583 - 63,844,385 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	63,520,614 - 63,527,516 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	63,823,813 - 63,830,718 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	64,121,011 - 64,127,929 (+)	NCBI		UU_Cfam_GSD_1.0

Otx1
(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	20,382,689 - 20,389,733 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936491	8,181,575 - 8,188,608 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936491	8,181,600 - 8,188,600 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

OTX1
(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	78,896,675 - 78,903,122 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	78,895,142 - 78,903,045 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	82,961,896 - 82,968,756 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

OTX1
(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	43,959,586 - 43,967,194 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	14	43,961,534 - 43,964,879 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	67,875,707 - 67,882,786 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Otx1
(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_004624762	10,379,917 - 10,386,708 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624762	10,379,775 - 10,388,262 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Otx1
13 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	41
Count of miRNA genes:	34
Interacting mature miRNAs:	38
Transcripts:	ENSRNOT00000011668
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 (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
634328	Hc5	Hypercalciuria QTL 5	2.3		urine calcium amount (VT:0002985)	urine calcium excretion rate (CMO:0000763)	14	58184885	103184885	Rat
9590294	Uminl4	Urine mineral level QTL 4	5.66	0.001	urine mineral amount (VT:0015086)	urine electrolyte level (CMO:0000593)	14	55624247	100624247	Rat
2317879	Alcrsp27	Alcohol response QTL 27	3.3	0.63	response to alcohol trait (VT:0010489)	duration of loss of righting reflex (CMO:0002289)	14	56631369	101631369	Rat
1641900	Alcrsp11	Alcohol response QTL 11			alcohol metabolism trait (VT:0015089)	blood ethanol level (CMO:0000535)	14	70053989	104886043	Rat
2300197	Scl59	Serum cholesterol level QTL 59			blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	14	55147478	100147478	Rat
9589034	Epfw11	Epididymal fat weight QTL 11	6	0.001	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	14	55624247	100624247	Rat
631523	Pia13	Pristane induced arthritis QTL 13	3.3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	14	40793460	98037301	Rat
1582259	Gluco23	Glucose level QTL 23	3.1	0.0008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	14	70053989	104886043	Rat

Markers in Region

RH131109

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	96,082,210 - 96,082,430 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	106,860,290 - 106,860,509	NCBI	Rnor6.0
Rnor_5.0	14	106,925,239 - 106,925,458	UniSTS	Rnor5.0
RGSC_v3.4	14	102,720,147 - 102,720,366	UniSTS	RGSC3.4
Celera	14	95,079,863 - 95,080,082	UniSTS
RH 3.4 Map	14	762.2	UniSTS
Cytogenetic Map	14	q22	UniSTS

RH94705

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	96,083,516 - 96,083,616 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	106,861,596 - 106,861,695	NCBI	Rnor6.0
Rnor_5.0	14	106,926,545 - 106,926,644	UniSTS	Rnor5.0
RGSC_v3.4	14	102,721,453 - 102,721,552	UniSTS	RGSC3.4
Celera	14	95,081,169 - 95,081,268	UniSTS
Cytogenetic Map	14	q22	UniSTS

Otx1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	96,085,870 - 96,086,900 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	106,863,863 - 106,864,892	NCBI	Rnor6.0
Rnor_5.0	14	106,928,805 - 106,929,834	UniSTS	Rnor5.0
RGSC_v3.4	14	102,723,678 - 102,724,707	UniSTS	RGSC3.4
Celera	14	95,083,515 - 95,084,544	UniSTS
Cytogenetic Map	14	q22	UniSTS

UniSTS:470671

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Celera	14	95,081,564 - 95,081,657	UniSTS
Cytogenetic Map	14	q22	UniSTS

Otx1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	14	96,085,801 - 96,085,888 (+)	MAPPER	mRatBN7.2
Rnor_6.0	14	106,863,794 - 106,863,880	NCBI	Rnor6.0
Rnor_5.0	14	106,928,736 - 106,928,822	UniSTS	Rnor5.0
RGSC_v3.4	14	102,723,609 - 102,723,695	UniSTS	RGSC3.4
Celera	14	95,083,446 - 95,083,532	UniSTS
Cytogenetic Map	14	q22	UniSTS

Expression

RNA-SEQ Expression

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

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
2	18	100	24	29	9	4	9	6	47	30	89	6	33	20

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_013109	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039091640	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	CH473996	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212299	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	L32602	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000090664 ⟹ ENSRNOP00000072147

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	14	106,861,676 - 106,864,892 (-)	Ensembl

Ensembl Acc Id:

ENSRNOT00000113729 ⟹ ENSRNOP00000088754

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	14	96,082,151 - 96,089,086 (-)	Ensembl

RefSeq Acc Id:

NM_013109 ⟹ NP_037241

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	100,283,406 - 100,290,421 (-)	NCBI
mRatBN7.2	14	96,082,146 - 96,089,161 (-)	NCBI
Rnor_6.0	14	106,861,556 - 106,864,933 (-)	NCBI
Rnor_5.0	14	106,926,505 - 106,929,875 (-)	NCBI
RGSC_v3.4	14	102,721,413 - 102,724,748 (-)	RGD
Celera	14	95,081,129 - 95,084,585 (-)	NCBI

Sequence:

show sequence

GCCCCCTGGATCCGTCGGGGCGCCTCCACCCGGCTGTTAGCATGATGTCTTACCTCAAACAACC
CCCATACGGCATGAACGGGCTGGGCCTAGCTGGCCCTGCCATGGACCTCCTGCACCCTTCCGTG
GGCTACCCTGCCACCCCGCGGAAGCAGCGACGGGAGCGCACCACCTTCACGCGCTCACAGCTGG
ACGTGCTCGAGGCGCTGTTCGCAAAGACTCGCTACCCAGACATCTTCATGCGCGAGGAGGTGGC
TCTCAAGATCAACCTGCCCGAGTCCAGAGTCCAGGTTTGGTTCAAGAACCGCCGAGCCAAGTGC
CGCCAGCAGCAGCAGAGCGGGAATGGAACGAAAAGCCGGCCGGTCAAGAAGAAGTCGTCTCCGG
TGCGCGAGAGCTCGGGTTCCGAGAGCAGCGGCCAGTTCACGCCGCCCGCCGTATCTAGCTCTGC
GTCTTCGTCTAGCTCAGCGTCCAGTGCCTCCGCTAACCCGGCGGCTGCTGCGGCCGCGGGCCTG
GGTGGGAACCCGGTGGCAGCCGCGTCCTCTCTGAGCACGCCTACTGCTTCGTCCATCTGGAGCC
CGGCCTCCATCTCTCCCGGCTCAGCGCCGGCATCCGTATCAGTGCCAGAGCCATTAGGCGCTCC
GAGCAACGCCTCATGCATGCAGCGCTCGGTAGCCGCAGGTGCGGCCACTGCCGCGACCTCCTAC
CCTATGTCCTATGGCCAGGGCAGAAGCTATGGCCAGGGCTACCCCGCGCCTTCCTCTTCTTACT
TTGGCGGTGTAGACTGCAGCTCCTACCTTGCGCCCATGCACTCTCATCACCACCCGCACCAGCT
TAGCCCCATGGCACCCTCCTCCATGGCTGGCCACCACCACCACCACCCGCACGCGCACCACCCA
CTGAGCCAATCTTCAGGCCACCACCACCACCACCATCACCACCACCACCACCAAGGTTATGGAG
GCTCTGGGCTCGCCTTCAACTCTGCCGACTGCTTGGATTACAAGGAGCCCGCCGCCGCCGCTGC
TTCCTCTGCCTGGAAACTCAACTTCAACTCTCCCGACTGTCTGGACTATAAGGACCAAGCCTCA
TGGCGGTTCCAGGTCTTGTGAGCCCAGGAGGGAAAGGAAGTGGAGAAGAAACGCAACTACCTTC
GCCCTCCGTGGTCCCTATCATGTTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTGCTG
CTGCTGCTGCTGC

hide sequence

RefSeq Acc Id:

XM_039091640 ⟹ XP_038947568

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	14	100,283,416 - 100,290,404 (-)	NCBI
mRatBN7.2	14	96,082,151 - 96,089,161 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_037241	(Get FASTA)	NCBI Sequence Viewer
	XP_038947568	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAA53557	(Get FASTA)	NCBI Sequence Viewer
	EDL97962	(Get FASTA)	NCBI Sequence Viewer
	EDL97963	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000088754
GenBank Protein	Q63410	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_037241 ⟸ NM_013109

- UniProtKB:

Q64203 (UniProtKB/Swiss-Prot), Q63410 (UniProtKB/Swiss-Prot), A0A8I6AA41 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MMSYLKQPPYGMNGLGLAGPAMDLLHPSVGYPATPRKQRRERTTFTRSQLDVLEALFAKTRYPD
IFMREEVALKINLPESRVQVWFKNRRAKCRQQQQSGNGTKSRPVKKKSSPVRESSGSESSGQFT
PPAVSSSASSSSSASSASANPAAAAAAGLGGNPVAAASSLSTPTASSIWSPASISPGSAPASVS
VPEPLGAPSNASCMQRSVAAGAATAATSYPMSYGQGRSYGQGYPAPSSSYFGGVDCSSYLAPMH
SHHHPHQLSPMAPSSMAGHHHHHPHAHHPLSQSSGHHHHHHHHHHHQGYGGSGLAFNSADCLDY
KEPAAAAASSAWKLNFNSPDCLDYKDQASWRFQVL

hide sequence

Ensembl Acc Id:

ENSRNOP00000072147 ⟸ ENSRNOT00000090664

RefSeq Acc Id:	XP_038947568 ⟸ XM_039091640
- Peptide Label:	isoform X1
- UniProtKB:	Q64203 (UniProtKB/Swiss-Prot), Q63410 (UniProtKB/Swiss-Prot), A0A8I6AA41 (UniProtKB/TrEMBL)

Ensembl Acc Id:

ENSRNOP00000088754 ⟸ ENSRNOT00000113729

Protein Domains

Homeobox

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q63410-F1-model_v2	AlphaFold	Q63410	1-355	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:3237	AgrOrtholog
BioCyc Gene	G2FUF-14823	BioCyc
Ensembl Genes	ENSRNOG00000059469	Ensembl
	ENSRNOG00000065081	Ensembl, ENTREZGENE
Ensembl Transcript	ENSRNOT00000113729	ENTREZGENE
Gene3D-CATH	Homeodomain-like	UniProtKB/Swiss-Prot
InterPro	Homeobox-like_sf	UniProtKB/Swiss-Prot
	Homeobox_CS	UniProtKB/Swiss-Prot
	Homeobox_dom	UniProtKB/Swiss-Prot
	Otx1_TF	UniProtKB/Swiss-Prot
	Otx_TF	UniProtKB/Swiss-Prot
	Otx_TF_C	UniProtKB/Swiss-Prot
KEGG Report	rno:25646	UniProtKB/Swiss-Prot
NCBI Gene	25646	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN	UniProtKB/Swiss-Prot
	HOMEOBOX PROTEIN OTX1	UniProtKB/Swiss-Prot
Pfam	Homeodomain	UniProtKB/Swiss-Prot
	TF_Otx	UniProtKB/Swiss-Prot
PhenoGen	Otx1	PhenoGen
PRINTS	OTX1HOMEOBOX	UniProtKB/Swiss-Prot
	OTXHOMEOBOX	UniProtKB/Swiss-Prot
PROSITE	HOMEOBOX_1	UniProtKB/Swiss-Prot
	HOMEOBOX_2	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000059469	RatGTEx
	ENSRNOG00000065081	RatGTEx
SMART	HOX	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot
TIGR	TC219556
UniProt	A0A8I6AA41	ENTREZGENE, UniProtKB/TrEMBL
	A6JQ45_RAT	UniProtKB/TrEMBL
	A6JQ46_RAT	UniProtKB/TrEMBL
	OTX1_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
	Q64203	ENTREZGENE
UniProt Secondary	Q64203	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-04-12	Otx1	orthodenticle homeobox 1	LOC100364498	homeobox protein OTX1-like	Data merged from RGD:2320962	737654	PROVISIONAL
2010-05-05	LOC100364498	homeobox protein OTX1-like			Symbol and Name status set to provisional	70820	PROVISIONAL
2008-09-24	Otx1	orthodenticle homeobox 1	Otx1	orthodenticle homolog 1 (Drosophila)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-06-10	Otx1	Orthodenticle (Drosophila) homolog 1			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_cellular_localization	prenatally localized to the cytoplasm but is translocated to the nucleus in first week of postnatal life	727353

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)

Send us a Message

Imported Disease Annotations - ClinVar