Opn1sw opsin 1, short wave sensitive [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Opn1swprovided by RGD
Official Full Name: opsin 1, short wave sensitiveprovided by RGD
Primary source: RGD:621033
See related: EnsemblRapid:ENSRNOG00000006874 AllianceGenome:RGD:621033
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: 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 phototransduction. 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). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 2.3), Uterus (RPKM 2.2) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q22

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (58942685..58945825, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (57977317..57980457, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (56653840..56656980, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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General gene information

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Markers

Opn1sw (e-PCR), detects polymorphism
- UniSTS:141171

Opn1sw (e-PCR), detects polymorphism
- UniSTS:536457

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables G protein-coupled photoreceptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables G protein-coupled receptor activity	IEA Inferred from Electronic Annotation more info
enables photoreceptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in G protein-coupled receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
involved_in cellular response to UV-A	IEA Inferred from Electronic Annotation more info
involved_in cellular response to UV-A	ISO Inferred from Sequence Orthology more info
involved_in cellular response to UV-A	ISS Inferred from Sequence or Structural Similarity more info
involved_in cellular response to light stimulus	IBA Inferred from Biological aspect of Ancestor more info
involved_in detection of visible light	IEA Inferred from Electronic Annotation more info
involved_in phototransduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in phototransduction	IEA Inferred from Electronic Annotation more info
involved_in visual perception	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell body	IDA Inferred from Direct Assay more info	PubMed
located_in cone photoreceptor outer segment	IEA Inferred from Electronic Annotation more info
located_in cone photoreceptor outer segment	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in intercellular bridge	IEA Inferred from Electronic Annotation more info
located_in intercellular bridge	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IEA Inferred from Electronic Annotation more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in photoreceptor inner segment	IEA Inferred from Electronic Annotation more info
is_active_in photoreceptor outer segment	IBA Inferred from Biological aspect of Ancestor more info
located_in photoreceptor outer segment	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor outer segment	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in terminal bouton	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: short-wave-sensitive opsin 1

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

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_031015.2 → NP_112277.2 short-wave-sensitive opsin 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

O70363, Q63652

UniProtKB/TrEMBL

A6IEC9, G3V6V4

Related

ENSRNOP00000009278.1, ENSRNOT00000009278.5

Conserved Domains (1) summary

cd15076
Location:33 → 312

7tmA_SWS1_opsin; short wave-sensitive 1 opsins, member of the class A family of seven-transmembrane G protein-coupled receptors