Opn3 (opsin 3) - Rat Genome Database

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Gene: Opn3 (opsin 3) Rattus norvegicus
Analyze
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
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81390,121,560 - 90,152,076 (-)NCBIGRCr8
mRatBN7.21387,589,333 - 87,619,847 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1387,589,333 - 87,619,847 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1390,089,224 - 90,119,705 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01391,489,484 - 91,519,964 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01388,668,631 - 88,699,112 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01393,716,481 - 93,746,994 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1393,716,481 - 93,746,994 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01398,180,840 - 98,211,263 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41391,396,311 - 91,427,005 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1387,187,867 - 87,218,156 (-)NCBICelera
Cytogenetic Map13q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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 AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81390,121,560 - 90,152,076 (-)NCBIGRCr8
mRatBN7.21387,589,333 - 87,619,847 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1387,589,333 - 87,619,847 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1390,089,224 - 90,119,705 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01391,489,484 - 91,519,964 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01388,668,631 - 88,699,112 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01393,716,481 - 93,746,994 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1393,716,481 - 93,746,994 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01398,180,840 - 98,211,263 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41391,396,311 - 91,427,005 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1387,187,867 - 87,218,156 (-)NCBICelera
Cytogenetic Map13q24NCBI
OPN3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381241,593,124 - 241,640,369 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1241,628,851 - 241,640,369 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl1241,590,102 - 241,677,376 (-)EnsemblGRCh38hg38GRCh38
GRCh371241,756,426 - 241,803,671 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361239,823,075 - 239,870,324 (-)NCBINCBI36Build 36hg18NCBI36
Build 341238,082,955 - 238,129,652NCBI
Celera1215,011,455 - 215,058,805 (-)NCBICelera
Cytogenetic Map1q43NCBI
HuRef1212,214,768 - 212,261,760 (-)NCBIHuRef
CHM1_11243,029,126 - 243,076,370 (-)NCBICHM1_1
T2T-CHM13v2.01241,004,525 - 241,051,843 (-)NCBIT2T-CHM13v2.0
Opn3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391175,489,993 - 175,520,198 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1175,489,987 - 175,520,342 (-)EnsemblGRCm39 Ensembl
GRCm381175,662,421 - 175,692,901 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1175,662,421 - 175,692,776 (-)EnsemblGRCm38mm10GRCm38
MGSCv371177,592,558 - 177,622,721 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361177,499,102 - 177,529,265 (-)NCBIMGSCv36mm8
Celera1182,748,089 - 182,778,248 (-)NCBICelera
Cytogenetic Map1H3NCBI
cM Map181.66NCBI
Opn3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540610,450,768 - 10,493,958 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540610,450,810 - 10,493,958 (+)NCBIChiLan1.0ChiLan1.0
OPN3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v217,506,682 - 7,553,372 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan117,730,302 - 7,777,306 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01217,155,765 - 217,202,577 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11222,136,416 - 222,218,839 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1222,136,422 - 222,184,598 (-)Ensemblpanpan1.1panPan2
OPN3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1732,995,047 - 33,040,873 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl732,996,938 - 33,040,876 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha732,468,970 - 32,518,427 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0732,817,978 - 32,867,661 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl732,823,417 - 32,867,883 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1732,652,968 - 32,702,181 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0732,677,092 - 32,726,558 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0732,925,094 - 32,974,549 (-)NCBIUU_Cfam_GSD_1.0
Opn3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934445,872,261 - 45,913,815 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365268,833,455 - 8,876,729 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365268,833,495 - 8,876,631 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OPN3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12578,671,900 - 78,720,697 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2578,671,600 - 78,719,139 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605580,804,584 - 80,852,534 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Opn3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477111,943,914 - 11,991,411 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477111,943,894 - 11,991,477 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Opn3
152 total Variants
miRNA Target Status

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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1366451204106807694Rat
1298066Bp159Blood pressure QTL 1590.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134608804691088046Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133124133193395974Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat
8655959Pur32Proteinuria QTL 328.4urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)137402391897213863Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)135236217197362171Rat
12879441Bp396Blood pressure QTL 396arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)134569998390699983Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat

Markers in Region
D13Rat86  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81390,135,822 - 90,136,052 (+)Marker Load Pipeline
mRatBN7.21387,603,589 - 87,603,819 (+)MAPPERmRatBN7.2
Rnor_6.01393,730,745 - 93,730,972NCBIRnor6.0
Rnor_5.01398,195,014 - 98,195,241UniSTSRnor5.0
RGSC_v3.41391,410,706 - 91,411,049RGDRGSC3.4
RGSC_v3.41391,410,756 - 91,410,983UniSTSRGSC3.4
RGSC_v3.11391,599,640 - 91,599,867RGD
Celera1387,202,018 - 87,202,245UniSTS
RH 3.4 Map13586.0UniSTS
RH 3.4 Map13586.0RGD
RH 2.0 Map13633.9RGD
SHRSP x BN Map1340.7498RGD
Cytogenetic Map13q25UniSTS
RH128985  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21387,609,802 - 87,609,984 (+)MAPPERmRatBN7.2
Rnor_6.01393,736,956 - 93,737,137NCBIRnor6.0
Rnor_5.01398,201,225 - 98,201,406UniSTSRnor5.0
RGSC_v3.41391,416,967 - 91,417,148UniSTSRGSC3.4
Celera1387,208,229 - 87,208,410UniSTS
RH 3.4 Map13585.3UniSTS
Cytogenetic Map13q25UniSTS
AI136952  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21387,589,389 - 87,589,607 (+)MAPPERmRatBN7.2
Rnor_6.01393,716,538 - 93,716,755NCBIRnor6.0
Rnor_5.01398,180,897 - 98,181,114UniSTSRnor5.0
RGSC_v3.41391,396,368 - 91,396,585UniSTSRGSC3.4
Celera1387,187,924 - 87,188,141UniSTS
RH 3.4 Map13573.2UniSTS
Cytogenetic Map13q25UniSTS


Expression

RNA-SEQ Expression

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
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000005072   ⟹   ENSRNOP00000005072
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1387,589,333 - 87,619,847 (-)Ensembl
Rnor_6.0 Ensembl1393,716,481 - 93,746,994 (-)Ensembl
RefSeq Acc Id: NM_001191933   ⟹   NP_001178862
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81390,121,560 - 90,152,076 (-)NCBI
mRatBN7.21387,589,333 - 87,619,847 (-)NCBI
Rnor_6.01393,716,481 - 93,746,994 (-)NCBI
Rnor_5.01398,180,840 - 98,211,263 (-)NCBI
Celera1387,187,867 - 87,218,156 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001178862 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94771 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000005072.3
RefSeq Acc Id: NP_001178862   ⟸   NM_001191933
- UniProtKB: D3ZFS1 (UniProtKB/TrEMBL)
- 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 AssemblyChrPosition (strand)Source
Rnor_6.01393,747,015 - 93,747,075EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1594385 AgrOrtholog
BioCyc Gene G2FUF-17231 BioCyc
Ensembl Genes ENSRNOG00000003778 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005072.6 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