Opn1sw (opsin 1, short wave sensitive)

Gene: Opn1sw (opsin 1, short wave sensitive) Chinchilla lanigera

Analyze

Symbol:

Opn1sw

Name:

opsin 1, short wave sensitive

RGD ID:

8700190

Description:

INVOLVED IN cellular response to UV-A (ortholog); PARTICIPATES IN retinoid cycle metabolic pathway; visual phototransduction pathway; ASSOCIATED WITH atrial fibrillation (ortholog); blue color blindness (ortholog); genetic disease (ortholog); FOUND IN cell body (ortholog); cone photoreceptor outer segment (ortholog); cytosol (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

opsin 1 (cone pigments), short-wave-sensitive; short-wave-sensitive opsin 1

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

Position:

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

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

atrial fibrillation (ISO)

blue color blindness (ISO)

genetic disease (ISO)

pleomorphic xanthoastrocytoma (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to UV-A (ISO)

Cellular Component

cell body (ISO)

cone photoreceptor outer segment (ISO)

cytosol (ISO)

intercellular bridge (ISO)

nucleoplasm (ISO)

perinuclear region of cytoplasm (ISO)

photoreceptor outer segment (ISO)

plasma membrane (ISO)

terminal bouton (ISO)

Molecular Function

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.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species
2.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

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

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	GRCh38		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	NCBI36	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
GRCm38	6	29,376,671 - 29,380,513 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	29,376,671 - 29,388,468 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	29,326,671 - 29,330,513 (-)	NCBI	GRCm37	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
(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
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 Ensembl
UTH_Rnor_SHR_Utx	4	62,960,385 - 62,963,525 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	58,876,538 - 58,879,678 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	57,278,435 - 57,281,575 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	56,653,840 - 56,656,980 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	56,653,844 - 56,656,980 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	56,421,001 - 56,424,141 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	56,256,846 - 56,259,986 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	56,512,971 - 56,516,112 (-)	NCBI
Celera	4	53,085,329 - 53,088,469 (-)	NCBI		Celera
Cytogenetic Map	4	q22	NCBI

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	panpan1.1		panPan2

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	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	14	7,552,256 - 7,555,713 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	14	7,631,370 - 7,634,827 (+)	NCBI		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

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	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	Sscrofa11.1		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	ChlSab1.1 Ensembl	chlSab2
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	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624783	7,412,825 - 7,416,209 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005402383	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01056482	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDF01236722	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCLAT00000009154 ⟹ ENSCLAP00000009026

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955479	9,573,594 - 9,576,668 (-)	Ensembl

RefSeq Acc Id:

XM_005402383 ⟹ XP_005402440

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955479	9,573,594 - 9,576,668 (-)	NCBI

Sequence:

show sequence

TCTAATCCCAGACTGTGTCCTTGGGAGACTTAGGATCATTCACAGAGCCCAAACGTGTCTTTAC
AGGAGGGATTTTTGTGGGGAGGGGGACATGGTAGAAGGATAATCTATAAGAGAGACTGGAGGGA
TGCAGGGGGACAGCCATAAACAAGATGTCGAGGGAAGAGGACTTTTATCTGTTCAAGAACACCT
CCTCGGTGGGGCCATGGGATGGGCCTCAGTACCACATTGCCCCTGCCTGGGCCTTCCACCTCCA
AGCAGCCTTCATGGGCTTTGTCTTCTTTGTAGGGACACCACTCAATGCCGTAGTGCTGGTGGCC
ACGCTGCAATACAAAAAGTTGCGGCAGCCACTCAACTATGTTCTGGTCAACGTGTCCCTGGGGG
GCTTCCTCTTCTGCATATTCTCTGTCTTCACTGTCTTCATTGCCAGCTGTCATGGATACTTCCT
CTTTGGCCGCCATGTCTGTGCTCTAGAGGCCTTCCTGGGCTCCGTGGCAGGTCTGGTGACAGGC
TGGTCACTGGCCTTTCTGGCCTTTGAGCGCTACCTTGTCATCTGTAAGCCCTTTGGCAACTTCC
GCTTCAGCTCCAAACATGCACTGGTGGTGGTCGTGGCTACCTGGGTCATCGGTATTGGCGTCTC
CATCCCACCCTTCTTCGGCTGGAGCCGGTTCATCCCCGAGGGCCTGCAGTGCTCCTGCGGCCCC
GACTGGTACACCGTGGGCACCAAGTACCGCAGCGAGTACTACACCTGGTTCCTCTTCATCTTTT
GCTTCATTGTGCCTCTCTCCCTCATCTGCTTCTCCTACTCTCAGCTGTTGAGGACCCTCAGGGC
TGTGGCAGCTCAGCAGCAGGAGTCAGCTACAACCCAGAAGGCTGAGCGGGAGGTGAGCCGCATG
GTGGTGGTGATGGTGGGATCCTTCTGCGTCTGCTATGTGCCCTACGCTGCCCTGGCCATGTACA
TAGTCAACAATCGTAACCACGGGCTGGACTTACGCCTTGTCACCATTCCTGCTTTCTTTTCCAA
GAGTTCCTGTGTATACAATCCCATCATCTACTGCTTCATGAACAAGCAGTTCCGAGCTTGTATC
ATGGAATTGGTGTGTAGGAAGCCCATGGCAGATGAATCTGATATGTCCAGCTCCCAGAAAACTG
AAGTTTCTGCTGTCTCTTCTAGCAAAGTTGGCCCCAACTAAGGACCC

hide sequence

Protein Sequences


Protein RefSeqs	XP_005402440	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000009026
	ENSCLAP00000009026.1

RefSeq Acc Id:

XP_005402440 ⟸ XM_005402383

- UniProtKB:

A0A8C2V2K1 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MSREEDFYLFKNTSSVGPWDGPQYHIAPAWAFHLQAAFMGFVFFVGTPLNAVVLVATLQYKKLR
QPLNYVLVNVSLGGFLFCIFSVFTVFIASCHGYFLFGRHVCALEAFLGSVAGLVTGWSLAFLAF
ERYLVICKPFGNFRFSSKHALVVVVATWVIGIGVSIPPFFGWSRFIPEGLQCSCGPDWYTVGTK
YRSEYYTWFLFIFCFIVPLSLICFSYSQLLRTLRAVAAQQQESATTQKAEREVSRMVVVMVGSF
CVCYVPYAALAMYIVNNRNHGLDLRLVTIPAFFSKSSCVYNPIIYCFMNKQFRACIMELVCRKP
MADESDMSSSQKTEVSAVSSSKVGPN

hide sequence

RefSeq Acc Id:

ENSCLAP00000009026 ⟸ ENSCLAT00000009154

Protein Domains

G-protein coupled receptors family 1 profile

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000006304	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000009154	ENTREZGENE
	ENSCLAT00000009154.1	UniProtKB/TrEMBL
Gene3D-CATH	Rhodopsin 7-helix transmembrane proteins	UniProtKB/TrEMBL
InterPro	GPCR_Rhodpsn	UniProtKB/TrEMBL
	GPCR_Rhodpsn_7TM	UniProtKB/TrEMBL
	Opsin	UniProtKB/TrEMBL
	Opsin_blue	UniProtKB/TrEMBL
	Retinal_BS	UniProtKB/TrEMBL
NCBI Gene	Opn1sw	ENTREZGENE
PANTHER	OPSIN	UniProtKB/TrEMBL
	SHORT-WAVE-SENSITIVE OPSIN 1	UniProtKB/TrEMBL
Pfam	7tm_1	UniProtKB/TrEMBL
PRINTS	GPCRRHODOPSN	UniProtKB/TrEMBL
	OPSIN	UniProtKB/TrEMBL
	OPSINBLUE	UniProtKB/TrEMBL
PROSITE	G_PROTEIN_RECEP_F1_1	UniProtKB/TrEMBL
	G_PROTEIN_RECEP_F1_2	UniProtKB/TrEMBL
	OPSIN	UniProtKB/TrEMBL
Superfamily-SCOP	Family A G protein-coupled receptor-like	UniProtKB/TrEMBL
UniProt	A0A8C2V2K1	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2017-01-24	Opn1sw	opsin 1, short wave sensitive		opsin 1 (cone pigments), short-wave-sensitive	Symbol and/or name change	5135510	APPROVED

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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations