Opn1mw (opsin 1, medium wave sensitive) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Opn1mw (opsin 1, medium wave sensitive) Rattus norvegicus
Analyze
Symbol: Opn1mw
Name: opsin 1, medium wave sensitive
RGD ID: 620978
Description: Predicted to enable G protein-coupled photoreceptor activity and identical protein binding activity. Predicted to be involved in several processes, including cellular response to light stimulus; phototransduction; and positive regulation of cytokinesis. Located in photoreceptor outer segment. Human ortholog(s) of this gene implicated in blue cone monochromacy; red color blindness; and red-green color blindness. Orthologous to several human genes including OPN1LW (opsin 1, long wave sensitive) and OPN1MW (opsin 1, medium wave sensitive); PARTICIPATES IN retinoid cycle metabolic pathway; visual phototransduction pathway; INTERACTS WITH 17alpha-ethynylestradiol; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: green cone photoreceptor pigment; green-sensitive opsin; medium wavelength-sensitive cone opsin; medium-wave-sensitive opsin 1; opsin 1 (cone pigments), medium-wave-sensitive; opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan); opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan), green opsin
RGD Orthologs
Human
Mouse
Pig
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X157,056,355 - 157,076,716 (+)NCBIGRCr8
mRatBN7.2X151,905,056 - 151,925,419 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,905,096 - 151,925,388 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX154,046,219 - 154,066,443 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,609,455 - 157,629,679 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X155,281,257 - 155,301,483 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,569,683 - 156,589,907 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,569,683 - 156,589,907 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,310,261 - 152,330,485 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X160,095,742 - 160,115,966 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X160,171,359 - 160,191,584 (+)NCBI
Celera1135,969,802 - 135,990,029 (-)NCBICelera
Cytogenetic MapXq37NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
membrane  (IEA)
photoreceptor outer segment  (IBA,IDA,IEA,ISO)
plasma membrane  (ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. 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.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. Online Mendelian Inheritance in Man, OMIM (TM). Online Mendelian Inheritance in Man, OMIM (TM).
7. Genetic analyses of the green visual pigments of rabbit (Oryctolagus cuniculus) and rat (Rattus norvegicus). Radlwimmer FB and Yokoyama S, Gene 1998 Sep 18;218(1-2):103-9.
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.
13. The "five-sites" rule and the evolution of red and green color vision in mammals. Yokoyama S and Radlwimmer FB, Mol Biol Evol 1998 May;15(5):560-7.
Additional References at PubMed
PMID:8185948   PMID:10725384   PMID:12651948   PMID:19332056   PMID:20371244   PMID:20579627   PMID:22888021   PMID:23351594   PMID:23386608   PMID:28402104  


Genomics

Comparative Map Data
Opn1mw
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X157,056,355 - 157,076,716 (+)NCBIGRCr8
mRatBN7.2X151,905,056 - 151,925,419 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX151,905,096 - 151,925,388 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX154,046,219 - 154,066,443 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X157,609,455 - 157,629,679 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X155,281,257 - 155,301,483 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X156,569,683 - 156,589,907 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX156,569,683 - 156,589,907 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01152,310,261 - 152,330,485 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X160,095,742 - 160,115,966 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1X160,171,359 - 160,191,584 (+)NCBI
Celera1135,969,802 - 135,990,029 (-)NCBICelera
Cytogenetic MapXq37NCBI
OPN1MW
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X154,182,596 - 154,196,861 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX154,182,596 - 154,196,861 (+)EnsemblGRCh38hg38GRCh38
GRCh37X153,448,085 - 153,462,352 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X153,101,361 - 153,114,725 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X153,006,131 - 153,019,496NCBI
CeleraX153,643,424 - 153,658,069 (+)NCBICelera
Cytogenetic MapXq28NCBI
CHM1_1X153,322,583 - 153,336,848 (+)NCBICHM1_1
T2T-CHM13v2.0X152,456,258 - 152,470,523 (+)NCBIT2T-CHM13v2.0
Opn1mw
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X73,171,072 - 73,194,362 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX73,171,070 - 73,194,366 (+)EnsemblGRCm39 Ensembl
GRCm38X74,127,466 - 74,150,756 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX74,127,464 - 74,150,760 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X71,372,805 - 71,396,095 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X70,380,186 - 70,403,476 (+)NCBIMGSCv36mm8
CeleraX65,379,870 - 65,403,149 (+)NCBICelera
Cytogenetic MapXA7.3NCBI
LOC494564
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X124,816,014 - 124,828,225 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1

Variants

.
Variants in Opn1mw
32 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:41
Interacting mature miRNAs:44
Transcripts:ENSRNOT00000056325
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

Markers in Region
stSG603914  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X151,913,543 - 151,914,670 (-)MAPPERmRatBN7.2
Rnor_6.0X156,580,333 - 156,581,459NCBIRnor6.0
Rnor_5.01152,320,911 - 152,322,037UniSTSRnor5.0
RGSC_v3.4X160,104,190 - 160,105,316UniSTSRGSC3.4
Celera1135,980,455 - 135,981,581UniSTS
Cytogenetic MapXq37UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

endocrine system exocrine system hepatobiliary system nervous system reproductive system
High
Medium
Low
Below cutoff 1 1 1 4 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000083147   ⟹   ENSRNOP00000072867
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,905,096 - 151,925,322 (+)Ensembl
Rnor_6.0 EnsemblX156,569,683 - 156,589,907 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109312   ⟹   ENSRNOP00000089832
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX151,905,096 - 151,925,388 (+)Ensembl
RefSeq Acc Id: NM_053548   ⟹   NP_446000
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X157,056,355 - 157,076,716 (+)NCBI
mRatBN7.2X151,905,056 - 151,925,419 (+)NCBI
Rnor_6.0X156,569,683 - 156,589,907 (-)NCBI
Rnor_5.01152,310,261 - 152,330,485 (-)NCBI
RGSC_v3.4X160,095,742 - 160,115,966 (+)RGD
Celera1135,969,802 - 135,990,029 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446000 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB86946 (Get FASTA)   NCBI Sequence Viewer  
  AAC64920 (Get FASTA)   NCBI Sequence Viewer  
  EDL84994 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000072867
  ENSRNOP00000072867.1
  ENSRNOP00000089832.1
  ENSRNOP00055035275
  ENSRNOP00060008163
  ENSRNOP00065019224
GenBank Protein O35476 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_446000   ⟸   NM_053548
- UniProtKB: O35476 (UniProtKB/Swiss-Prot),   A6KRS8 (UniProtKB/TrEMBL),   A0A8I6ACH6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000072867   ⟸   ENSRNOT00000083147
RefSeq Acc Id: ENSRNOP00000089832   ⟸   ENSRNOT00000109312
Protein Domains
G-protein coupled receptors family 1 profile

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O35476-F1-model_v2 AlphaFold O35476 1-359 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620978 AgrOrtholog
BioCyc Gene G2FUF-641 BioCyc
Ensembl Genes ENSRNOG00000051529 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00055025092 UniProtKB/Swiss-Prot
  ENSRNOG00060006687 UniProtKB/Swiss-Prot
  ENSRNOG00065014896 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000083147 ENTREZGENE
  ENSRNOT00000083147.2 UniProtKB/Swiss-Prot
  ENSRNOT00000109312.1 UniProtKB/TrEMBL
  ENSRNOT00055043244 UniProtKB/Swiss-Prot
  ENSRNOT00060010959 UniProtKB/Swiss-Prot
  ENSRNOT00065024634 UniProtKB/Swiss-Prot
Gene3D-CATH Rhodopsin 7-helix transmembrane proteins UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro GPCR_Rhodpsn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GPCR_Rhodpsn_7TM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Opsin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Opsin_red/grn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Retinal_BS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:89810 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 89810 ENTREZGENE
PANTHER MEDIUM-WAVE-SENSITIVE OPSIN 1-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OPSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam 7tm_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Opn1mw PhenoGen
PRINTS GPCRRHODOPSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OPSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OPSINREDGRN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE G_PROTEIN_RECEP_F1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  G_PROTEIN_RECEP_F1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  OPSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000051529 RatGTEx
  ENSRNOG00055025092 RatGTEx
  ENSRNOG00060006687 RatGTEx
  ENSRNOG00065014896 RatGTEx
SMART 7TM_GPCR_Srsx UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Family A G protein-coupled receptor-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6ACH6 ENTREZGENE, UniProtKB/TrEMBL
  A6KRS8 ENTREZGENE, UniProtKB/TrEMBL
  O35476 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-02-12 Opn1mw  opsin 1, medium wave sensitive  Opn1mw  opsin 1 (cone pigments), medium-wave-sensitive  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Opn1mw  opsin 1 (cone pigments), medium-wave-sensitive  Opn1mw  opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Opn1mw  opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan)    opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan), green opsin  Name updated 1299863 APPROVED
2002-08-07 Opn1mw  opsin 1 (cone pigments), medium-wave-sensitive (color blindness, deutan), green opsin      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_other has a wavelength of maximal absorption (lambdamax) of 509nm 729211