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Gene: Opn1sw (opsin 1, short wave sensitive) Rattus norvegicus

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Symbol:

Opn1sw

Name:

opsin 1, short wave sensitive

RGD ID:

621033

Description:

Predicted to enable G protein-coupled photoreceptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway; cellular response to UV-A; and detection of light stimulus. Located in cell body; photoreceptor outer segment; and terminal bouton. Human ortholog(s) of this gene implicated in blue color blindness. Orthologous to human OPN1SW (opsin 1, short wave sensitive); PARTICIPATES IN retinoid cycle metabolic pathway; visual phototransduction pathway; INTERACTS WITH ammonium chloride; bisphenol A; fenvalerate.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

blue cone opsin-like pigment; blue cone photoreceptor pigment; blue-sensitive opsin; BOP; opsin 1 (cone pigments), short-wave-sensitive; opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan); s opsin; short wavelength-sensitive cone opsin; short-wave-sensitive opsin 1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

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	4	58,942,685 - 58,945,825 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	58,942,681 - 58,945,825 (-)	Ensembl				GRCr8
mRatBN7.2	4	57,977,317 - 57,980,457 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	57,977,313 - 57,980,457 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	62,960,385 - 62,963,525 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	58,876,538 - 58,879,678 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	57,278,435 - 57,281,575 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	56,653,840 - 56,656,980 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	56,653,844 - 56,656,980 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	56,421,001 - 56,424,141 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	56,256,846 - 56,259,986 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	53,085,329 - 53,088,469 (-)	NCBI		Celera
RGSC_v3.1	4	56,512,971 - 56,516,112 (-)	NCBI
Cytogenetic Map	4	q22	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

atrial fibrillation (ISO)

blue color blindness (ISO)

retinitis pigmentosa 1 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

ammonium chloride (EXP)

aristolochic acid A (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

disodium selenite (ISO)

ethylparaben (ISO)

fenvalerate (EXP)

resveratrol (ISO)

rotenone (EXP)

sodium arsenite (ISO)

Theaflavin 3,3'-digallate (ISO)

titanium dioxide (ISO)

trichostatin A (ISO)

urethane (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

absorption of visible light (IBA,IEA,ISO,ISS)

biological_process (ND)

cellular response to light stimulus (IBA)

cellular response to UV-A (IEA,ISO,ISS)

detection of visible light (IEA)

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

phototransduction (IBA,IEA)

signal transduction (IEA)

visual perception (IEA,ISO)

Cellular Component

cell body (IDA)

membrane (IEA)

perinuclear region of cytoplasm (IEA,ISO,ISS)

photoreceptor inner segment (IEA)

photoreceptor outer segment (IBA,IDA,IEA,ISO)

plasma membrane (IBA,IEA,ISO,ISS)

terminal bouton (IDA)

Molecular Function

G protein-coupled photoreceptor activity (IBA)

G protein-coupled receptor activity (IEA)

photoreceptor activity (IEA)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

retinoid cycle metabolic pathway (ISO)

visual phototransduction pathway (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.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
3.	CNTF induces regeneration of cone outer segments in a rat model of retinal degeneration.	Li Y, etal., PLoS One. 2010 Mar 2;5(3):e9495.
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.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
7.	Online Mendelian Inheritance in Man, OMIM (TM).	Online Mendelian Inheritance in Man, OMIM (TM).
8.	GOA pipeline	RGD automated data pipeline
9.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
11.	Comprehensive gene review and curation	RGD comprehensive gene curation
12.	Membrane receptors and transporters involved in the function and transport of vitamin A and its derivatives.	Sun H Biochim Biophys Acta. 2012 Jan;1821(1):99-112. Epub 2011 Jun 17.

Additional References at PubMed

PMID:9147475	PMID:10725384	PMID:10813773	PMID:12651948	PMID:19332056	PMID:22183407	PMID:23351594	PMID:23386608

Genomics

Comparative Map Data

Opn1sw
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	58,942,685 - 58,945,825 (-)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	4	58,942,681 - 58,945,825 (-)	Ensembl				GRCr8
mRatBN7.2	4	57,977,317 - 57,980,457 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	57,977,313 - 57,980,457 (-)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	4	62,960,385 - 62,963,525 (-)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	58,876,538 - 58,879,678 (-)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	57,278,435 - 57,281,575 (-)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	56,653,840 - 56,656,980 (-)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	56,653,844 - 56,656,980 (-)	Ensembl			rn6	Rnor6.0
Rnor_5.0	4	56,421,001 - 56,424,141 (-)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	4	56,256,846 - 56,259,986 (-)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	4	53,085,329 - 53,088,469 (-)	NCBI		Celera
RGSC_v3.1	4	56,512,971 - 56,516,112 (-)	NCBI
Cytogenetic Map	4	q22	NCBI

OPN1SW
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	7	128,772,485 - 128,775,794 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	7	128,772,485 - 128,775,794 (-)	Ensembl			hg38	GRCh38
GRCh37	7	128,412,539 - 128,415,848 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	7	128,199,783 - 128,203,087 (-)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	7	128,006,497 - 128,009,802	NCBI
Celera	7	123,208,297 - 123,211,598 (-)	NCBI		Celera
Cytogenetic Map	7	q32.1	NCBI
HuRef	7	122,773,527 - 122,776,828 (-)	NCBI		HuRef
CHM1_1	7	128,345,783 - 128,349,084 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	7	130,084,638 - 130,087,947 (-)	NCBI		T2T-CHM13v2.0
CRA_TCAGchr7v2	7	127,795,527 - 127,798,828 (-)	NCBI

Opn1sw
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	29,376,670 - 29,380,512 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	29,376,670 - 29,388,467 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	6	29,376,671 - 29,380,513 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	29,376,671 - 29,388,468 (-)	Ensembl			mm10	GRCm38
MGSCv37	6	29,326,671 - 29,330,513 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	6	29,326,680 - 29,330,490 (-)	NCBI		MGSCv36	mm8
Celera	6	29,383,859 - 29,387,702 (-)	NCBI		Celera
Cytogenetic Map	6	A3.3	NCBI
cM Map	6	12.36	NCBI

Opn1sw
(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_004955479	9,573,594 - 9,576,668 (-)	Ensembl
ChiLan1.0	NW_004955479	9,573,594 - 9,576,668 (-)	NCBI	ChiLan1.0	ChiLan1.0

OPN1SW
(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	6	165,576,694 - 165,584,445 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	7	17,586,802 - 17,590,192 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	7	120,724,363 - 120,727,649 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	7	133,246,131 - 133,251,464 (-)	NCBI	PanPan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	7	133,246,131 - 133,251,464 (-)	Ensembl			panPan2	panpan1.1

OPN1SW
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	14	7,865,370 - 7,869,516 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	14	7,865,561 - 7,868,745 (+)	Ensembl			canFam3	CanFam3.1
Dog10K_Boxer_Tasha	14	7,552,256 - 7,555,713 (+)	NCBI	Dog10K_Boxer_Tasha	Dog10K_Boxer_Tasha
ROS_Cfam_1.0	14	7,631,370 - 7,634,827 (+)	NCBI	ROS_Cfam_1.0	ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	14	7,630,992 - 7,634,662 (+)	Ensembl				ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	14	7,836,320 - 7,839,777 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	14	7,578,515 - 7,581,972 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	14	7,723,749 - 7,727,206 (+)	NCBI	UU_Cfam_GSD_1.0	UU_Cfam_GSD_1.0

Opn1sw
(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_024405118	54,572,299 - 54,578,533 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936479	15,699,604 - 15,702,352 (-)	Ensembl		SpeTri2.0 Ensembl
SpeTri2.0	NW_004936479	15,696,063 - 15,702,311 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

OPN1SW
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	18	19,836,453 - 19,839,425 (+)	Ensembl			susScr11	Sscrofa11.1
Sscrofa11.1	18	19,836,453 - 19,839,425 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	18	20,905,871 - 20,908,843 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

OPN1SW
(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	21	97,370,824 - 97,377,433 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	21	97,372,863 - 97,376,406 (-)	Ensembl		ChlSab1.1 Ensembl	chlSab2	Vervet-AGM
Vero_WHO_p1.0	NW_023666042	6,028,013 - 6,032,554 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Opn1sw
(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_004624783	7,412,825 - 7,416,095 (+)	Ensembl		HetGla_female_1.0 Ensembl	hetGla2	HetGla_female_1.0 Ensembl
HetGla 1.0	NW_004624783	7,412,825 - 7,416,209 (+)	NCBI	HetGla 1.0	HetGla 1.0	hetGla2

Opn1sw
(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	6	110,185,066 - 110,188,237 (+)	NCBI		Rrattus_CSIRO_v1

Variants

Variants in Opn1sw
19 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	97
Count of miRNA genes:	72
Interacting mature miRNAs:	87
Transcripts:	ENSRNOT00000009278
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
2303585	Bw86	Body weight QTL 86	4		body mass (VT:0001259)	body weight (CMO:0000012)	4	15644309	60644309	Rat
5685012	Bmd87	Bone mineral density QTL 87	5.1		tibia mineral mass (VT:1000283)	bone mineral content (CMO:0001554)	4	35113290	80113290	Rat
1358352	Srcrt3	Stress Responsive Cort QTL 3	2.29		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	39431983	123203361	Rat
61445	Strs3	Sensitivity to stroke QTL 3	3		cerebrum integrity trait (VT:0010549)	post-insult time to onset of cerebrovascular lesion (CMO:0002343)	4	41400577	86400577	Rat
5685009	Bmd86	Bone mineral density QTL 86	3.7		tibia mineral mass (VT:1000283)	bone mineral density (CMO:0001226)	4	57613242	102613242	Rat
6893678	Bw108	Body weight QTL 108	2.6	0.006	body mass (VT:0001259)	body weight (CMO:0000012)	4	44425024	89425024	Rat
10755501	Bp390	Blood pressure QTL 390	2.5		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	4	27730518	170099664	Rat
1331807	Rf31	Renal function QTL 31	2.988		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	4	40490442	75726188	Rat
634311	Sach7	Saccharin preference QTL 7			taste sensitivity trait (VT:0001986)	saccharin intake volume to total fluid intake volume ratio (CMO:0001601)	4	58079875	82597589	Rat
1358363	Sradr3	Stress Responsive Adrenal Weight QTL 3	6.19		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	4	58817672	103817672	Rat
61330	Eau1	Experimental allergic uveoretinitis QTL 1		0.0003	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	4	26234499	134199155	Rat
631261	Tcas3	Tongue tumor susceptibility QTL 3	6.88		tongue integrity trait (VT:0010553)	number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)	4	11706604	92690519	Rat
61336	Bp21	Blood pressure QTL 21	4.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	58080146	80212111	Rat
2313401	Anxrr27	Anxiety related response QTL 27			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	4	18900697	63900697	Rat
8655961	Kidm43	Kidney mass QTL 43	18		kidney mass (VT:0002707)	both kidneys wet weight (CMO:0000085)	4	37269577	82269577	Rat
1354612	Foco1	Food consumption QTL 1	8.87		eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	4	45429897	149763204	Rat
6909128	Pancm4	Pancreatic morphology QTL 4	11.35		pancreas mass (VT:0010144)	pancreas wet weight (CMO:0000626)	4	27862204	126119996	Rat
2303168	Bp330	Blood pressure QTL 330	4.25	0.017	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	4	5889999	148002343	Rat
61475	Aia2	Adjuvant induced arthritis QTL 2	5.8		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	4	40471453	75939996	Rat
8694439	Bw168	Body weight QTL 168	9.57	0.001	retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	4	41400603	86400603	Rat
61412	Pia2	Pristane induced arthritis QTL 2	3.9		joint integrity trait (VT:0010548)	post-insult time to onset of experimental arthritis (CMO:0001450)	4	22288453	63245191	Rat
8552807	Vie4	Viral induced encephalitis QTL 4	7.3		brain integrity trait (VT:0010579)	encephalitis incidence/prevalence measurement (CMO:0002361)	4	18900697	63900697	Rat
8655906	Rf60	Renal function QTL 60	3.8		blood creatinine amount (VT:0005328)	creatinine clearance (CMO:0000765)	4	30448961	82336920	Rat
1576305	Emca6	Estrogen-induced mammary cancer QTL 6	5.8		mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	4	45429709	157555683	Rat
7387227	Uae40	Urinary albumin excretion QTL 40	2.9	0.0052	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	4	18913151	63913151	Rat
6909122	Insul22	Insulin level QTL 22	4.63		blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	4	27862204	62997402	Rat
1558651	Swd3	Spike wave discharge measurement QTL 3	4.62	0.000024	brain electrophysiology trait (VT:0010557)	brain spike-and-wave discharge frequency (CMO:0001742)	4	41400577	86400577	Rat
1358203	Stl19	Serum triglyceride level QTL 19	2.8	0.002	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	4	21925151	66925151	Rat
1641833	Alc21	Alcohol consumption QTL 21	8.6	0.0001	drinking behavior trait (VT:0001422)	ethanol drink intake rate (CMO:0001407)	4	57664252	127749483	Rat
1354660	Salc1	Saline consumption QTL 1	11.26		drinking behavior trait (VT:0001422)	saline drink intake rate (CMO:0001627)	4	45429897	149763204	Rat
70192	BpQTLcluster5	Blood pressure QTL cluster 5	4.183		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	4	1	63900697	Rat
1298082	Stresp4	Stress response QTL 4			blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	4	51085655	113588029	Rat
631546	Bp86	Blood pressure QTL 86	3.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	4	58079875	92690793	Rat
1300139	Hrtrt6	Heart rate QTL 6	2.85		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	4	40490442	117737312	Rat
70200	Alc18	Alcohol consumption QTL 18	9.2		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	4	57613339	151163960	Rat
4889969	Bss96	Bone structure and strength QTL 96	4.9		tibia size trait (VT:0100001)	tibia cortical bone volume (CMO:0001725)	4	57613242	102613242	Rat
12798520	Anxrr55	Anxiety related response QTL 55	4.45	0.01	locomotor behavior trait (VT:0001392)	number of rearing movements with lid-pushing in an experimental apparatus (CMO:0002715)	4	33538597	116185060	Rat
2316958	Gluco58	Glucose level QTL 58	10		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	4	12212457	182430611	Rat
4889972	Bss97	Bone structure and strength QTL 97	5.6		tibia size trait (VT:0100001)	tibia total bone volume (CMO:0001724)	4	57613242	102613242	Rat

Markers in Region

Opn1sw

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	57,977,914 - 57,978,799 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	56,654,438 - 56,655,322	NCBI	Rnor6.0
Rnor_5.0	4	56,421,599 - 56,422,483	UniSTS	Rnor5.0
RGSC_v3.4	4	56,257,444 - 56,258,328	UniSTS	RGSC3.4
Celera	4	53,085,927 - 53,086,811	UniSTS
Cytogenetic Map	4	q22	UniSTS

Opn1sw

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	4	57,979,803 - 57,980,313 (+)	MAPPER	mRatBN7.2
Rnor_6.0	4	56,656,327 - 56,656,836	NCBI	Rnor6.0
Rnor_5.0	4	56,423,488 - 56,423,997	UniSTS	Rnor5.0
Celera	4	53,087,816 - 53,088,325	UniSTS
Cytogenetic Map	4	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	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	sensory system	visual system
2	7	11	62	28	31	6	24	6	2	82	44	58	23	28	25	13	13

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_031015	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC095491	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF051163	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473959	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000004	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	U63972	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000009278 ⟹ ENSRNOP00000009278

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	4	58,942,681 - 58,945,825 (-)	Ensembl
mRatBN7.2 Ensembl	4	57,977,313 - 57,980,457 (-)	Ensembl
Rnor_6.0 Ensembl	4	56,653,844 - 56,656,980 (-)	Ensembl

RefSeq Acc Id:

NM_031015 ⟹ NP_112277

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	4	58,942,685 - 58,945,825 (-)	NCBI
mRatBN7.2	4	57,977,317 - 57,980,457 (-)	NCBI
Rnor_6.0	4	56,653,840 - 56,656,980 (-)	NCBI
Rnor_5.0	4	56,421,001 - 56,424,141 (-)	NCBI
RGSC_v3.4	4	56,256,846 - 56,259,986 (-)	RGD
Celera	4	53,085,329 - 53,088,469 (-)	RGD

Sequence:

show sequence

GAATTCGGCACGAGACCAGAGGTGGTGGTGAGGCATCCCAAGCGCAAGATGTCGGGAGAGGWCG
AGTTTTACCTGTTTCAGAATATCTCCTCAGTGGGGCCCTGGGATGGGCCTCAGTACCACATTGC
TCCCGTCTGGGCCTTCCACCTCCAGGCAGCCTTCATGGGATTTGTCTTCTTTGCAGGGACCCCA
CTCAATGCCACAGTGTTGGTGGCCACACTGCACTACAAAAAGTTGCGGCAGCCCCTCAACTACA
TTCTGGTCAATGTATCCCTCGGAGGCTTCCTCTTCTGCATCTTCTCTGTCTTCACAGTCTTCAT
CGCCAGCTGTCATGGATACTTCCTCTTTGGTCGCCACGTTTGTGCTCTGGAGGCCTTCTTGGGC
TCTGTAGCAGGTCTAGTGACAGGATGGTCCTTGGCTTTCCTGGCCTTTGAGCGCTACCTTGTCA
TCTGTAAACCCTTTGGCAACATCCGCTTCAACTCCAAGCACGCACTGACGGTGGTTCTGATTAC
TTGGACCATTGGCATCGGGGTGTCCATCCCGCCCTTCTTTGGCTGGAGCAGGTTCATCCCTGAG
GGCCTGCAGTGCTCCTGTGGCCCGGACTGGTACACCGTGGGCACCAAGTATCGAAGCGAGCACT
ATACCTGGTTTCTGTTCATCTTCTGTTTCATCATTCCTCTTTCCCTCATCTGTTTCTCCTACTT
CCAGTTGCTGAGGACTCTCAGAGCTGTGGCGGCCCAGCAGCAAGAGTCAGCTACAACTCAAAAG
GCTGAACGGGAGGTGAGCCATATGGTGGTGGTGATGGTGGGATCCTTCTGTCTCTGCTACGTGC
CCTATGCTGCCCTGGCCATGTACATGGTCAACAATCGTAACCACGGGCTGTACTTACGGCTTGT
CACCATCCCCGCCTTCTTTTCCAAGAGTTCATGTGTCTACAACCCCATCATCTACTGCTTCATG
AATAAGCAGTTCCGGGCCTGCATCCTGGAGATGGTGTGCAGGAAGCCCATGACAGACGAATCTG
ACATGTCTGGCTCTCAGAAAACAGAAGTTTCTACTGTTTCTTCCAGCAAAGTTGGCCCTCACTA
AGGACCCTCAGTTGGCCTGCTGGCAGCAACCATGGGGCCACATTGAATTATCTACATCTCCATT
AGAATTCAAACCATTAACAATGTAGGGAACAGACAGGAGCAGTGGCATCTGGCCGGTCAGTTTC
ATTTTCCTGTTACTCTCTCCCTGTCAGCAGGGCCACACGGGCCATTTCAACAGTCACAGTTTCT
AAGTGATACCTTCATCTCTGGAGAACTGTGAGAGAAGGGCCGTGCCTCTGGTGTATGGGTAACA
CCTGGTTGTTCTTTTATTCCGTGCTGGGATCTGAGTTGATATATCCTGTTAGAATAAGCTTGGC
ATGGGGCAGTGTGAAGAAAAAGCAGCAGACACCAAACACCTGCAGTGAGCTGAAGCTTTCCTAT
GCGGCCTCTCCCAGTTGCTGCCGTCTGGGCTATGGCTGCCCTGCCCAGAACTGCCCCWCCTCAC
TCATCTGACAGTTATTCTAAGTCTTCTCCCCTCCATTTGGCTAAATGTATCCATTTAAAGCTGT
GTGTTGATTAAAGTTAGTGTCTTAATCTCTTGACGACCTCAAAAAAAAAAAAAAAAAACTC

hide sequence

Protein Sequences


Protein RefSeqs	NP_112277	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAB05931	(Get FASTA)	NCBI Sequence Viewer
	AAC05294	(Get FASTA)	NCBI Sequence Viewer
	EDM15215	(Get FASTA)	NCBI Sequence Viewer
	EDM15216	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000009278
GenBank Protein	Q63652	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_112277 ⟸ NM_031015

- UniProtKB:

Q63652 (UniProtKB/Swiss-Prot), O70363 (UniProtKB/Swiss-Prot), G3V6V4 (UniProtKB/TrEMBL), A6IEC9 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSGEXEFYLFQNISSVGPWDGPQYHIAPVWAFHLQAAFMGFVFFAGTPLNATVLVATLHYKKLR
QPLNYILVNVSLGGFLFCIFSVFTVFIASCHGYFLFGRHVCALEAFLGSVAGLVTGWSLAFLAF
ERYLVICKPFGNIRFNSKHALTVVLITWTIGIGVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTK
YRSEHYTWFLFIFCFIIPLSLICFSYFQLLRTLRAVAAQQQESATTQKAEREVSHMVVVMVGSF
CLCYVPYAALAMYMVNNRNHGLYLRLVTIPAFFSKSSCVYNPIIYCFMNKQFRACILEMVCRKP
MTDESDMSGSQKTEVSTVSSSKVGPH

hide sequence

Ensembl Acc Id:

ENSRNOP00000009278 ⟸ ENSRNOT00000009278

Protein Domains

G-protein coupled receptors family 1 profile

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q63652-F1-model_v2	AlphaFold	Q63652	1-346	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:621033	AgrOrtholog
BioCyc Gene	G2FUF-45397	BioCyc
Ensembl Genes	ENSRNOG00000006874	Ensembl, ENTREZGENE
Ensembl Transcript	ENSRNOT00000009278	ENTREZGENE
Gene3D-CATH	Rhodopsin 7-helix transmembrane proteins	UniProtKB/Swiss-Prot
InterPro	GPCR_opsins	UniProtKB/Swiss-Prot
	GPCR_Rhodpsn	UniProtKB/Swiss-Prot
	GPCR_Rhodpsn_7TM	UniProtKB/Swiss-Prot
	Opsin	UniProtKB/Swiss-Prot
	Opsin_blue	UniProtKB/Swiss-Prot
	Retinal_BS	UniProtKB/Swiss-Prot
KEGG Report	rno:81644	UniProtKB/Swiss-Prot
NCBI Gene	81644	ENTREZGENE
PANTHER	OPSIN	UniProtKB/Swiss-Prot
Pfam	7tm_1	UniProtKB/Swiss-Prot
PhenoGen	Opn1sw	PhenoGen
PRINTS	GPCRRHODOPSN	UniProtKB/Swiss-Prot
	OPSIN	UniProtKB/Swiss-Prot
	OPSINBLUE	UniProtKB/Swiss-Prot
PROSITE	G_PROTEIN_RECEP_F1_1	UniProtKB/Swiss-Prot
	G_PROTEIN_RECEP_F1_2	UniProtKB/Swiss-Prot
	OPSIN	UniProtKB/Swiss-Prot
RatGTEx	ENSRNOG00000006874	RatGTEx
Superfamily-SCOP	Family A G protein-coupled receptor-like	UniProtKB/Swiss-Prot
UniProt	A6IEC8_RAT	UniProtKB/TrEMBL
	A6IEC9	ENTREZGENE, UniProtKB/TrEMBL
	G3V6V4	ENTREZGENE, UniProtKB/TrEMBL
	O70363	ENTREZGENE
	OPSB_RAT	UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary	O70363	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-02-01	Opn1sw	opsin 1, short wave sensitive	Opn1sw	opsin 1 (cone pigments), short-wave-sensitive	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-25	Opn1sw	opsin 1 (cone pigments), short-wave-sensitive	Opn1sw	opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-02-26	Opn1sw	opsin 1 (cone pigments), short-wave-sensitive (color blindness, tritan)			Symbol and Name status set to approved	625702	APPROVED
2002-08-07	Opn1sw				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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Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

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