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Gene: Opn3 (opsin 3) Rattus norvegicus

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Symbol:

Opn3

Name:

opsin 3

RGD ID:

1594385

Description:

Predicted to enable 11-cis retinal binding activity; G protein-coupled photoreceptor activity; and all-trans retinal binding activity. Predicted to be involved in several processes, including cellular response to UV-A; positive regulation of D-glucose import; and regulation of melanin biosynthetic process. Predicted to be located in cytoplasm. Predicted to be active in photoreceptor outer segment and plasma membrane. Orthologous to human OPN3 (opsin 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; acrylamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

LOC498289; opsin-3; similar to Opsin-3 (Encephalopsin) (Panopsin)

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):	OPN3 (opsin 3)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Opn3 (opsin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Opn3 (opsin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	OPN3 (opsin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	OPN3 (opsin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Opn3 (opsin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	OPN3 (opsin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Opn3 (opsin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus rattus (black rat):	Opn3 (opsin 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	EN1 (engrailed homeobox 1)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	OPN3 (opsin 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Opn3 (opsin 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	opn3 (opsin 3)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	sro-1	Alliance	DIOPT (Ensembl Compara\|InParanoid\|OrthoFinder)
Xenopus tropicalis (tropical clawed frog):	opn3	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	opn3	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|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	13	90,121,560 - 90,152,076 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	13	90,121,560 - 90,152,076 (-)	Ensembl				GRCr8
mRatBN7.2	13	87,589,333 - 87,619,847 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	87,589,333 - 87,619,847 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	13	90,089,224 - 90,119,705 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	91,489,484 - 91,519,964 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	88,668,631 - 88,699,112 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	93,716,481 - 93,746,994 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	93,716,481 - 93,746,994 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	13	98,180,840 - 98,211,263 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	13	91,396,311 - 91,427,005 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	13	87,187,867 - 87,218,156 (-)	NCBI		Celera
Cytogenetic Map	13	q24	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

COVID-19 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

17beta-estradiol (ISO)

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

2-methylcholine (ISO)

4-hydroxyphenyl retinamide (ISO)

acetamide (EXP)

acrylamide (EXP)

aflatoxin B1 (ISO)

arsenous acid (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

beta-lapachone (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

CGP 52608 (ISO)

cisplatin (ISO)

cyclophosphamide (ISO)

cyclosporin A (ISO)

diarsenic trioxide (ISO)

dicrotophos (ISO)

dorsomorphin (ISO)

doxorubicin (ISO)

endosulfan (EXP)

entinostat (ISO)

ethyl methanesulfonate (ISO)

folic acid (ISO)

folpet (ISO)

formaldehyde (ISO)

furan (EXP)

iron atom (ISO)

iron(0) (ISO)

lead diacetate (ISO)

methylmercury chloride (ISO)

niclosamide (ISO)

oxaliplatin (EXP)

paracetamol (EXP,ISO)

pentanal (ISO)

perfluorohexanesulfonic acid (ISO)

progesterone (ISO)

SB 431542 (ISO)

silicon dioxide (ISO)

sodium arsenite (EXP,ISO)

sodium dichromate (EXP)

sulforaphane (ISO)

sunitinib (ISO)

tert-butyl hydroperoxide (ISO)

thioacetamide (EXP)

thiram (ISO)

titanium dioxide (ISO)

topotecan (EXP)

trichostatin A (ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (ISO)

triptonide (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway (IEA,ISO)

cellular response to light stimulus (IBA)

cellular response to UV-A (IEA,ISO)

detection of visible light (IEA)

G protein-coupled receptor signaling pathway (IBA,IEA)

keratinocyte differentiation (IEA,ISO)

melanosome localization (IEA,ISO)

negative regulation of apoptotic process (IEA,ISO)

negative regulation of melanin biosynthetic process (IEA,ISO)

phototransduction (IBA,IEA)

positive regulation of cellular respiration (IEA,ISO)

positive regulation of D-glucose import across plasma membrane (IEA,ISO)

positive regulation of eating behavior (IEA,ISO)

positive regulation of melanin biosynthetic process (IEA,ISO)

positive regulation of metabolic process (IEA)

response to blue light (IEA,ISO)

signal transduction (IEA)

Cellular Component

cytoplasm (IEA,ISO)

cytosol (IEA,ISO)

membrane (IEA)

nucleoplasm (ISO)

photoreceptor outer segment (IBA)

plasma membrane (IBA,IEA,ISO)

Molecular Function

11-cis retinal binding (IEA,ISO)

all-trans retinal binding (IEA,ISO)

G protein-coupled photoreceptor activity (IBA,IEA,ISO)

G protein-coupled receptor activity (IEA,ISO)

photoreceptor activity (IEA)

protein binding (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:38192267

Genomics

Comparative Map Data

Opn3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	13	90,121,560 - 90,152,076 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	13	90,121,560 - 90,152,076 (-)	Ensembl				GRCr8
mRatBN7.2	13	87,589,333 - 87,619,847 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	13	87,589,333 - 87,619,847 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	13	90,089,224 - 90,119,705 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	13	91,489,484 - 91,519,964 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	13	88,668,631 - 88,699,112 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	13	93,716,481 - 93,746,994 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	13	93,716,481 - 93,746,994 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	13	98,180,840 - 98,211,263 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	13	91,396,311 - 91,427,005 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	13	87,187,867 - 87,218,156 (-)	NCBI		Celera
Cytogenetic Map	13	q24	NCBI

OPN3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	1	241,593,124 - 241,640,369 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	1	241,628,851 - 241,640,369 (-)	Ensembl			hg38	GRCh38
GRCh38.p14 Ensembl	1	241,590,102 - 241,677,376 (-)	Ensembl			hg38	GRCh38
GRCh37	1	241,756,426 - 241,803,671 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	1	239,823,075 - 239,870,324 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	1	238,082,955 - 238,129,652	NCBI
Celera	1	215,011,455 - 215,058,805 (-)	NCBI		Celera
Cytogenetic Map	1	q43	NCBI
HuRef	1	212,214,768 - 212,261,760 (-)	NCBI		HuRef
CHM1_1	1	243,029,126 - 243,076,370 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	1	241,004,525 - 241,051,843 (-)	NCBI		T2T-CHM13v2.0

Opn3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	1	175,489,993 - 175,520,198 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	1	175,489,987 - 175,520,342 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	1	175,662,421 - 175,692,901 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	1	175,662,421 - 175,692,776 (-)	Ensembl			mm10	GRCm38
MGSCv37	1	177,592,558 - 177,622,721 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	1	177,499,102 - 177,529,265 (-)	NCBI		MGSCv36	mm8
Celera	1	182,748,089 - 182,778,248 (-)	NCBI		Celera
Cytogenetic Map	1	H3	NCBI
cM Map	1	81.66	NCBI

Opn3
(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_004955406	10,450,768 - 10,493,958 (+)	Ensembl
ChiLan1.0	NW_004955406	10,450,810 - 10,493,958 (+)	NCBI	ChiLan1.0	ChiLan1.0

OPN3
(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	1	7,506,682 - 7,553,372 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	1	7,730,302 - 7,777,306 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	1	217,155,765 - 217,202,577 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	1	222,136,416 - 222,218,839 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	1	222,136,422 - 222,184,598 (-)	Ensembl			panPan2	panpan1.1

OPN3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	7	32,995,047 - 33,040,873 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	7	32,996,938 - 33,040,876 (-)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	7	32,468,970 - 32,518,427 (-)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	7	32,817,978 - 32,867,661 (-)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	7	32,823,417 - 32,867,883 (-)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	7	32,652,968 - 32,702,181 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	7	32,677,092 - 32,726,558 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	7	32,925,094 - 32,974,549 (-)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Opn3
(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_024409344	45,872,261 - 45,913,815 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936526	8,833,455 - 8,876,729 (+)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936526	8,833,495 - 8,876,631 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

OPN3
(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	25	78,671,900 - 78,720,697 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	25	78,671,600 - 78,719,139 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666055	80,804,584 - 80,852,534 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Opn3
(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_004624771	11,943,914 - 11,991,411 (-)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624771	11,943,894 - 11,991,477 (-)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Opn3
(Rattus rattus - black rat)

Black Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Black Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rrattus_CSIRO_v1	10	54,186,586 - 54,216,933 (-)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Opn3
337 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	83
Count of miRNA genes:	66
Interacting mature miRNAs:	79
Transcripts:	ENSRNOT00000005072
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
738027	Lnnr6	Liver neoplastic nodule remodeling QTL 6	3.3		liver integrity trait (VT:0010547)	liver remodeling tumorous lesion number (CMO:0001461)	13	65613454	109350286	Rat
7207885	Glom27	Glomerulus QTL 27	3.9		kidney glomerulus integrity trait (VT:0010546)	kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)	13	21120177	109350286	Rat
7387280	Uae43	Urinary albumin excretion QTL 43	5.69	0.4174	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	13	68983334	109350286	Rat
1298066	Bp159	Blood pressure QTL 159		0.004	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	48639634	93639634	Rat
2293702	Bss34	Bone structure and strength QTL 34	4.61	0.0001	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	13	67635937	109350286	Rat
1576318	Schws5	Schwannoma susceptibility QTL 5		0.0351	nervous system integrity trait (VT:0010566)	post-insult time to trigeminal nerve neurilemmoma formation (CMO:0002019)	13	64497900	109350286	Rat
1354621	Rf47	Renal function QTL 47	3.7		kidney renin amount (VT:0010559)	kidney renin level (CMO:0002166)	13	11081740	103588154	Rat
1354655	Bp241	Blood pressure QTL 241	3.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	38975045	103588154	Rat
8655951	Rf63	Renal function QTL 63	12.2		blood urea nitrogen amount (VT:0005265)	plasma urea nitrogen level (CMO:0000586)	13	71610804	109350286	Rat
4889606	Gluco63	Glucose level QTL 63	2.86	0.003	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	13	83286150	109350286	Rat
8655959	Pur32	Proteinuria QTL 32	8.4		urine total protein amount (VT:0000032)	urine total protein excretion rate (CMO:0000756)	13	72984506	99745408	Rat
1302791	Stl29	Serum triglyceride level QTL 29	3.3	0.0011	blood triglyceride amount (VT:0002644)	plasma triglyceride level (CMO:0000548)	13	89333129	92500981	Rat
2293687	Bss26	Bone structure and strength QTL 26	4.6	0.0001	femur morphology trait (VT:0000559)	femur cross-sectional area (CMO:0001661)	13	67635937	109350286	Rat
12879475	Bp400	Blood pressure QTL 400			arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	13	64375743	109350286	Rat
1354666	Bp244	Blood pressure QTL 244	4.9		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	13	1	103588154	Rat
724564	Uae11	Urinary albumin excretion QTL 11	5.7		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	13	47354258	94285672	Rat
2293341	Glom15	Glomerulus QTL 15	9.1		kidney glomerulus integrity trait (VT:0010546)	kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)	13	67635937	109350286	Rat

Markers in Region

D13Rat86

Rat Assembly	Chr	Position (strand)	Source	JBrowse
GRCr8	13	90,135,822 - 90,136,052 (+)	Marker Load Pipeline
mRatBN7.2	13	87,603,589 - 87,603,819 (+)	MAPPER	mRatBN7.2
Rnor_6.0	13	93,730,745 - 93,730,972	NCBI	Rnor6.0
Rnor_5.0	13	98,195,014 - 98,195,241	UniSTS	Rnor5.0
RGSC_v3.4	13	91,410,706 - 91,411,049	RGD	RGSC3.4
RGSC_v3.4	13	91,410,756 - 91,410,983	UniSTS	RGSC3.4
Celera	13	87,202,018 - 87,202,245	UniSTS
RGSC_v3.1	13	91,599,640 - 91,599,867	RGD
RH 3.4 Map	13	586.0	UniSTS
RH 3.4 Map	13	586.0	RGD
RH 2.0 Map	13	633.9	RGD
SHRSP x BN Map	13	40.7498	RGD
Cytogenetic Map	13	q25	UniSTS

RH128985

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	13	87,609,802 - 87,609,984 (+)	MAPPER	mRatBN7.2
Rnor_6.0	13	93,736,956 - 93,737,137	NCBI	Rnor6.0
Rnor_5.0	13	98,201,225 - 98,201,406	UniSTS	Rnor5.0
RGSC_v3.4	13	91,416,967 - 91,417,148	UniSTS	RGSC3.4
Celera	13	87,208,229 - 87,208,410	UniSTS
RH 3.4 Map	13	585.3	UniSTS
Cytogenetic Map	13	q25	UniSTS

AI136952

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	13	87,589,389 - 87,589,607 (+)	MAPPER	mRatBN7.2
Rnor_6.0	13	93,716,538 - 93,716,755	NCBI	Rnor6.0
Rnor_5.0	13	98,180,897 - 98,181,114	UniSTS	Rnor5.0
RGSC_v3.4	13	91,396,368 - 91,396,585	UniSTS	RGSC3.4
Celera	13	87,187,924 - 87,188,141	UniSTS
RH 3.4 Map	13	573.2	UniSTS
Cytogenetic Map	13	q25	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	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
16	12	67	161	91	90	59	92	59	6	355	192	11	140	80	92	31	17	17

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001191933	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC119639	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473985	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ226107	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000013	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000005072 ⟹ ENSRNOP00000005072

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	13	90,121,560 - 90,152,076 (-)	Ensembl
mRatBN7.2 Ensembl	13	87,589,333 - 87,619,847 (-)	Ensembl
Rnor_6.0 Ensembl	13	93,716,481 - 93,746,994 (-)	Ensembl

RefSeq Acc Id:

NM_001191933 ⟹ NP_001178862

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	13	90,121,560 - 90,152,076 (-)	NCBI
mRatBN7.2	13	87,589,333 - 87,619,847 (-)	NCBI
Rnor_6.0	13	93,716,481 - 93,746,994 (-)	NCBI
Rnor_5.0	13	98,180,840 - 98,211,263 (-)	NCBI
Celera	13	87,187,867 - 87,218,156 (-)	NCBI

Sequence:

show sequence

TGAGCGTGAGCTCCACCCGGTTCGCTGCGTGGCGGGCAGCCGGGCGCACGGAGCCCTCTCCCTC
ACGGCGCGTCGGCGTCGGGCCATGTACTCGGGGAACCGTAGCGGCGGCCAGGGCTACTGGGAGG
ACGGGGCGGGCGCCGAGGGCGCAGCACCGGCCGGCACGCGGAGCCCCGCGCCTCTCTTCAGCCC
CACCGCGTACGAGCGCCTGGCGCTGCTGCTCGGTTGCCTCGCGCTGCTGGGCGTCGGCGGCAAC
CTGCTGGTGCTGCTTCTCTACTCCAAGTTCCCGCGACTGCGCACGCCCACCCACCTCTTCCTGG
TCAACCTCAGTCTGGGCGATCTGCTGGTATCCCTGTTCGGAGTCACCTTCACCTTCGCGTCGTG
CCTGCGGAACGGCTGGGTGTGGGACGCCGTGGGCTGCGCGTGGGACGGGTTTAGCGGCAGCCTC
TTTGGGTTTGTTTCCATTACCACCCTCACTGTGCTGGCTTATGAACGTTATATCCGTGTGGTAC
ATGCCAGAGTGATCAATTTTTCCTGGGCCTGGAGGGCCATTACCTATATCTGGCTCTACTCTTT
GGCATGGGCAGGAGCGCCTCTCCTGGGCTGGAACAGGTACATCCTCGATGTACATGGACTGGGC
TGTACTGTGGACTGGAAATCCAAGGATGCCAACGACTCCTCCTTTGTGCTCTTCCTGTTTCTTG
GCTGTCTGGTGGTGCCCATGGGCATCATAGCCCATTGCTACGGTCATATTCTGTATTCTGTTCG
AATGCTTCGCTGTGTTGAAGATCTTCAGACAATTCAAGTGATCAAGATGTTGCGATACGAAAAG
AAAGTTGCCAAGATGTGCTTTTTGATGGCCTTTGTCTTTCTCACCTGCTGGATGCCTTATGTTG
TAACCCGCTTCTTGGTGGTCAATGGCTATGGACACCTGGTCACCCCAACTGTGTCTATCGTTTC
TTATCTCTTTGCTAAATCGAGCACTGTGTACAACCCAGTTATCTACATCTTCATGATCAGAAAG
TTTCGGAGGTCCCTTCTGCAACTCCTCTGTTTCCGCCTGCTGAGATGCCAGAGGCCTGCTAAAA
ACCTCCCAGCAGCTGAGAGTGAAATGCAGATCAGGCCCATTGTGATGTCACAGAAAGATGGGGA
CAGGCCAAAGAAGAAAGTGACATTTAACTCTTCCTCCATCATCTTCATCATCACCAGTGATGAG
TCCCTGTCAGTCGAGGACAGCGACAGAAGCAGCGCATCTAAGGTCGATGTAATCCAAGTGCGTC
CTTTATGAGAACGGAAGACAGTCTTACCTCAGCTGCGACACAGTGGCCCTGTCAGGAGTGCCCC
CCAGAGTTCCCATTTGGTATAACAGTGACAGAATCTCTGTGGCCCTGCAGGGAATCCGAATGGC
CCATGCGCTGTCTGTCTTCAAGAAGTGACGGAGCAAGACAAATTACTTTAACTCAATGGGTGCT
TTTTAACTTGAGAAACTCCTGGTGGCACAAGATGAGCGTCTGGCACCACCGTCTCCTATGCCAG
GATTTAATATTTGAACGACTGTATTTGCCAAAGCACATAATACATTTTGTCTATCAAATGTGTC
CCACTATAAAACTAACTGTCTCACATACACGTGTACAATGACTGGACATCTGGAGTATGTTGCA
GTATTGGGTCCTATTTTGTGCCATGTTGTGTGTTTGACCAATTCAATCTACTGAGATAATAAAT
CAACCCCCACTTTTATCTGAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001178862	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	EDL94771	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000005072
	ENSRNOP00000005072.3

RefSeq Acc Id:

NP_001178862 ⟸ NM_001191933

- UniProtKB:

D3ZFS1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MYSGNRSGGQGYWEDGAGAEGAAPAGTRSPAPLFSPTAYERLALLLGCLALLGVGGNLLVLLLY
SKFPRLRTPTHLFLVNLSLGDLLVSLFGVTFTFASCLRNGWVWDAVGCAWDGFSGSLFGFVSIT
TLTVLAYERYIRVVHARVINFSWAWRAITYIWLYSLAWAGAPLLGWNRYILDVHGLGCTVDWKS
KDANDSSFVLFLFLGCLVVPMGIIAHCYGHILYSVRMLRCVEDLQTIQVIKMLRYEKKVAKMCF
LMAFVFLTCWMPYVVTRFLVVNGYGHLVTPTVSIVSYLFAKSSTVYNPVIYIFMIRKFRRSLLQ
LLCFRLLRCQRPAKNLPAAESEMQIRPIVMSQKDGDRPKKKVTFNSSSIIFIITSDESLSVEDS
DRSSASKVDVIQVRPL

hide sequence

Ensembl Acc Id:

ENSRNOP00000005072 ⟸ ENSRNOT00000005072

Protein Domains

G-protein coupled receptors family 1 profile

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZFS1-F1-model_v2	AlphaFold	D3ZFS1	1-400	view protein structure

Transcriptome

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

Promoters

RGD ID:

13699042

Promoter ID:

EPDNEW_R9566

Type:

multiple initiation site

Name:

Opn3_1

Description:

opsin 3

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	13	93,747,015 - 93,747,075	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1594385	AgrOrtholog
BioCyc Gene	G2FUF-17231	BioCyc
Ensembl Genes	ENSRNOG00000003778	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000005072	ENTREZGENE
	ENSRNOT00000005072.7	UniProtKB/TrEMBL
Gene3D-CATH	Rhodopsin 7-helix transmembrane proteins	UniProtKB/TrEMBL
InterPro	7TM_GPCR_Rhodpsn	UniProtKB/TrEMBL
	GPCR_opsins	UniProtKB/TrEMBL
	GPCR_Rhodpsn_supfam	UniProtKB/TrEMBL
	Retinal_BS	UniProtKB/TrEMBL
KEGG Report	rno:498289	UniProtKB/TrEMBL
NCBI Gene	498289	ENTREZGENE
PANTHER	OPSIN	UniProtKB/TrEMBL
Pfam	7tm_1	UniProtKB/TrEMBL
PhenoGen	Opn3	PhenoGen
PRINTS	GPCRRHODOPSN	UniProtKB/TrEMBL
PROSITE	G_PROTEIN_RECEP_F1_1	UniProtKB/TrEMBL
	G_PROTEIN_RECEP_F1_2	UniProtKB/TrEMBL
	OPSIN	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000003778	RatGTEx
Superfamily-SCOP	Family A G protein-coupled receptor-like	UniProtKB/TrEMBL
UniProt	D3ZFS1	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-06-27			Opn3	opsin 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-03-05	Opn3	opsin 3	LOC498289	similar to Opsin-3 (Encephalopsin) (Panopsin)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-11-20	LOC498289	similar to Opsin-3 (Encephalopsin) (Panopsin)			Symbol and Name status set to provisional	70820	PROVISIONAL

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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