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Aliases for OPN3 Gene

Aliases for OPN3 Gene

  • Opsin 3 2 3 5
  • Encephalopsin 2 3 4
  • Protein Phosphatase 1, Regulatory Subunit 116 2 3
  • Panopsin 2 4
  • ECPN 3 4
  • Opsin 3 (Encephalopsin, Panopsin) 3
  • PPP1R116 3
  • Opsin-3 3

External Ids for OPN3 Gene

Previous HGNC Symbols for OPN3 Gene

  • ECPN

Previous GeneCards Identifiers for OPN3 Gene

  • GC01M239842
  • GC01M237209
  • GC01M238053
  • GC01M238797
  • GC01M238798
  • GC01M238082
  • GC01M241753
  • GC01M212214

Summaries for OPN3 Gene

Entrez Gene Summary for OPN3 Gene

  • Opsins are members of the guanine nucleotide-binding protein (G protein)-coupled receptor superfamily. In addition to the visual opsins, mammals possess several photoreceptive non-visual opsins that are expressed in extraocular tissues. This gene, opsin 3, is strongly expressed in brain and testis and weakly expressed in liver, placenta, heart, lung, skeletal muscle, kidney, and pancreas. The gene may also be expressed in the retina. The protein has the canonical features of a photoreceptive opsin protein. [provided by RefSeq, Jul 2008]

GeneCards Summary for OPN3 Gene

OPN3 (Opsin 3) is a Protein Coding gene. Among its related pathways are Peptide ligand-binding receptors and Signaling by GPCR. Gene Ontology (GO) annotations related to this gene include G-protein coupled receptor activity and G-protein coupled photoreceptor activity. An important paralog of this gene is RHO.

UniProtKB/Swiss-Prot for OPN3 Gene

  • May play a role in encephalic photoreception.

Gene Wiki entry for OPN3 Gene

Additional gene information for OPN3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for OPN3 Gene

Genomics for OPN3 Gene

GeneHancer (GH) Regulatory Elements for OPN3 Gene

Promoters and enhancers for OPN3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J241637 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 661.4 +37.4 37412 6 HDGF PKNOX1 CLOCK FOXA2 ARNT ARID4B SIN3A ZNF2 YY1 CBX5 CHML OPN3 RPL23AP20 BECN2 RFKP1 GC01M241629
GH01J241677 Enhancer 0.5 Ensembl ENCODE 650.7 -0.3 -292 1 RUNX3 OPN3 GC01P241686 GC01P241649 WDR64
GH01J241603 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 5.9 +68.9 68880 10.5 ATF1 PKNOX1 FOXA2 ARNT ZFP64 SIN3A YBX1 YY1 TCF12 ARID2 KMO CHML WDR64 PLD5 OPN3 GC01M241589 LOC105373233
GH01J241653 Enhancer 0.6 ENCODE 4.7 +23.1 23109 0.9 HDAC1 LEF1 TAL1 CBFA2T3 DPF2 TCF12 NCOR1 HDAC2 CBFA2T2 EHMT2 WDR64 OPN3 GC01P241649
GH01J242459 Enhancer 0.5 ENCODE 4.8 -782.6 -782617 1.1 ZNF217 SMARCE1 CTBP1 GATA3 OPN3 GC01M242468 PLD5 LOC100421344
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around OPN3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the OPN3 gene promoter:
  • E47
  • CUTL1
  • AML1a
  • C/EBPalpha
  • POU3F1
  • AREB6
  • MIF-1
  • Evi-1
  • POU2F1a
  • POU2F1

Genomic Locations for OPN3 Gene

Genomic Locations for OPN3 Gene
87,275 bases
Minus strand
87,275 bases
Minus strand

Genomic View for OPN3 Gene

Genes around OPN3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
OPN3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for OPN3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for OPN3 Gene

Proteins for OPN3 Gene

  • Protein details for OPN3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • Q8IX08
    • Q9Y344

    Protein attributes for OPN3 Gene

    402 amino acids
    Molecular mass:
    44873 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for OPN3 Gene


neXtProt entry for OPN3 Gene

Post-translational modifications for OPN3 Gene

  • Glycosylation at Asn198 and Asn5
  • Modification sites at PhosphoSitePlus

Other Protein References for OPN3 Gene

No data available for DME Specific Peptides for OPN3 Gene

Domains & Families for OPN3 Gene

Gene Families for OPN3 Gene

Protein Domains for OPN3 Gene


Suggested Antigen Peptide Sequences for OPN3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the G-protein coupled receptor 1 family. Opsin subfamily.
  • Belongs to the G-protein coupled receptor 1 family. Opsin subfamily.
genes like me logo Genes that share domains with OPN3: view

Function for OPN3 Gene

Molecular function for OPN3 Gene

UniProtKB/Swiss-Prot Function:
May play a role in encephalic photoreception.

Phenotypes From GWAS Catalog for OPN3 Gene

Gene Ontology (GO) - Molecular Function for OPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004871 obsolete signal transducer activity IEA --
GO:0004930 G-protein coupled receptor activity IEA,TAS 10234000
GO:0008020 G-protein coupled photoreceptor activity NAS 10234000
GO:0009881 photoreceptor activity NAS 10234000
genes like me logo Genes that share ontologies with OPN3: view
genes like me logo Genes that share phenotypes with OPN3: view

Animal Models for OPN3 Gene

MGI Knock Outs for OPN3:
  • Opn3 Opn3<tm2b(EUCOMM)Wtsi>

Animal Model Products

miRNA for OPN3 Gene

miRTarBase miRNAs that target OPN3

Clone Products

  • Addgene plasmids for OPN3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for OPN3 Gene

Localization for OPN3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for OPN3 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for OPN3 gene
Compartment Confidence
plasma membrane 5

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for OPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment IBA --
GO:0005887 integral component of plasma membrane TAS 10234000
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA,NAS 10234000
genes like me logo Genes that share ontologies with OPN3: view

Pathways & Interactions for OPN3 Gene

genes like me logo Genes that share pathways with OPN3: view

Gene Ontology (GO) - Biological Process for OPN3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007186 G-protein coupled receptor signaling pathway IEA --
GO:0007602 phototransduction NAS 10234000
GO:0009583 detection of light stimulus NAS 10234000
GO:0009584 detection of visible light IEA --
genes like me logo Genes that share ontologies with OPN3: view

No data available for SIGNOR curated interactions for OPN3 Gene

Drugs & Compounds for OPN3 Gene

(1) Drugs for OPN3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with OPN3: view

Transcripts for OPN3 Gene

mRNA/cDNA for OPN3 Gene

Unigene Clusters for OPN3 Gene

Opsin 3:
Representative Sequences:

Clone Products

  • Addgene plasmids for OPN3

Alternative Splicing Database (ASD) splice patterns (SP) for OPN3 Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c
SP1: - - - -
SP2: - - - - -
SP4: - - - - - -

Relevant External Links for OPN3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for OPN3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for OPN3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for OPN3 Gene

Protein tissue co-expression partners for OPN3 Gene

NURSA nuclear receptor signaling pathways regulating expression of OPN3 Gene:


SOURCE GeneReport for Unigene cluster for OPN3 Gene:


mRNA Expression by UniProt/SwissProt for OPN3 Gene:

Tissue specificity: Strongly expressed in brain. Highly expressed in the preoptic area and paraventricular nucleus of the hypothalamus. Shows highly patterned expression in other regions of the brain, being enriched in selected regions of the cerebral cortex, cerebellar Purkinje cells, a subset of striatal neurons, selected thalamic nuclei, and a subset of interneurons in the ventral horn of the spinal cord.

Evidence on tissue expression from TISSUES for OPN3 Gene

  • Nervous system(2)
genes like me logo Genes that share expression patterns with OPN3: view

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for OPN3 Gene

Orthologs for OPN3 Gene

This gene was present in the common ancestor of animals.

Orthologs for OPN3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia OPN3 34 33
  • 99.59 (n)
(Canis familiaris)
Mammalia OPN3 34 33
  • 90.75 (n)
(Rattus norvegicus)
Mammalia Opn3 33
  • 85.5 (n)
(Mus musculus)
Mammalia Opn3 16 34 33
  • 84.75 (n)
(Bos Taurus)
Mammalia OPN3 33
  • 73.22 (n)
(Monodelphis domestica)
Mammalia OPN3 34
  • 57 (a)
(Gallus gallus)
Aves OPN3 34 33
  • 76.69 (n)
(Anolis carolinensis)
Reptilia OPN3 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100494279 33
  • 56.2 (n)
(Danio rerio)
Actinopterygii opn3 34 33
  • 64.22 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rh6 34
  • 22 (a)
ninaE 34
  • 21 (a)
Rh2 34
  • 21 (a)
Rh4 34
  • 19 (a)
Rh3 34
  • 19 (a)
Rh7 34
  • 18 (a)
Rh5 34
  • 18 (a)
Species where no ortholog for OPN3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for OPN3 Gene

Gene Tree for OPN3 (if available)
Gene Tree for OPN3 (if available)
Evolutionary constrained regions (ECRs) for OPN3: view image

Paralogs for OPN3 Gene

Paralogs for OPN3 Gene

(4) SIMAP similar genes for OPN3 Gene using alignment to 4 proteins:

  • L8E9L4_HUMAN
  • Q6P5W7_HUMAN
genes like me logo Genes that share paralogs with OPN3: view

Variants for OPN3 Gene

Sequence variations from dbSNP and Humsavar for OPN3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000283356 -- 241,636,743(-) G/A intron_variant
rs1000378858 -- 241,626,775(-) A/T intron_variant
rs1000467306 -- 241,630,269(-) C/T intron_variant
rs1000493510 -- 241,632,826(-) G/A intron_variant
rs1000499225 -- 241,602,244(-) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for OPN3 Gene

Variant ID Type Subtype PubMed ID
esv1007397 CNV insertion 20482838
esv1555339 CNV insertion 17803354
esv2726229 CNV deletion 23290073
esv3589345 CNV loss 21293372
esv3589346 CNV loss 21293372
esv3589348 CNV loss 21293372
esv7009 CNV gain 19470904
nsv1002214 CNV gain 25217958
nsv1078175 CNV insertion 25765185
nsv1152156 CNV insertion 26484159
nsv159993 CNV deletion 16902084
nsv549460 CNV gain 21841781

Variation tolerance for OPN3 Gene

Residual Variation Intolerance Score: 64.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.80; 66.91% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for OPN3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for OPN3 Gene

Disorders for OPN3 Gene

Additional Disease Information for OPN3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for OPN3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for OPN3 Gene

Publications for OPN3 Gene

  1. Characterization of a novel human opsin gene with wide tissue expression and identification of embedded and flanking genes on chromosome 1q43. (PMID: 11401433) Halford S … Hunt DM (Genomics 2001) 2 3 4 22 58
  2. Encephalopsin: a novel mammalian extraretinal opsin discretely localized in the brain. (PMID: 10234000) Blackshaw S … Snyder SH (The Journal of neuroscience : the official journal of the Society for Neuroscience 1999) 2 3 4 22 58
  3. Identification of a novel asthma susceptibility gene on chromosome 1qter and its functional evaluation. (PMID: 18344558) White JH … Pillai SG (Human molecular genetics 2008) 3 22 44 58
  4. Different structural organization of the encephalopsin gene in man and mouse. (PMID: 12242008) Kasper G … Rump A (Gene 2002) 3 4 22 58
  5. Follow-up examination of linkage and association to chromosome 1q43 in multiple sclerosis. (PMID: 19626040) McCauley JL … Haines JL (Genes and immunity 2009) 3 44 58

Products for OPN3 Gene

Sources for OPN3 Gene

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