Human Gene OPN3 (ENST00000366554.3) from GENCODE V44
  Description: Homo sapiens opsin 3 (OPN3), transcript variant 1, mRNA. (from RefSeq NM_014322)
RefSeq Summary (NM_014322): 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].
Gencode Transcript: ENST00000366554.3
Gencode Gene: ENSG00000054277.14
Transcript (Including UTRs)
   Position: hg38 chr1:241,593,124-241,640,369 Size: 47,246 Total Exon Count: 4 Strand: -
Coding Region
   Position: hg38 chr1:241,594,428-241,640,254 Size: 45,827 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:241,593,124-241,640,369)mRNA (may differ from genome)Protein (402 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: OPN3_HUMAN
DESCRIPTION: RecName: Full=Opsin-3; AltName: Full=Encephalopsin; AltName: Full=Panopsin;
FUNCTION: May play a role in encephalic photoreception.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
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.
SIMILARITY: Belongs to the G-protein coupled receptor 1 family. Opsin subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.47 RPKM in Cells - Cultured fibroblasts
Total median expression: 86.46 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -48.90115-0.425 Picture PostScript Text
3' UTR -287.771304-0.221 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000276 - 7TM_GPCR_Rhodpsn
IPR017452 - GPCR_Rhodpsn_supfam
IPR001760 - Opsin

Pfam Domains:
PF00001 - 7 transmembrane receptor (rhodopsin family)

ModBase Predicted Comparative 3D Structure on Q9H1Y3
FrontTopSide
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGDEnsembl   
Protein SequenceProtein SequenceProtein Sequence   
AlignmentAlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004871 signal transducer activity
GO:0004930 G-protein coupled receptor activity
GO:0008020 G-protein coupled photoreceptor activity
GO:0009881 photoreceptor activity

Biological Process:
GO:0007165 signal transduction
GO:0007186 G-protein coupled receptor signaling pathway
GO:0007602 phototransduction
GO:0009583 detection of light stimulus
GO:0009584 detection of visible light
GO:0018298 protein-chromophore linkage
GO:0042752 regulation of circadian rhythm
GO:0050896 response to stimulus

Cellular Component:
GO:0001750 photoreceptor outer segment
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane


-  Descriptions from all associated GenBank mRNAs
  AF303588 - Homo sapiens panopsin (OPN3) mRNA, complete cds.
BC073872 - Homo sapiens opsin 3, mRNA (cDNA clone IMAGE:4452104), complete cds.
BC026242 - Homo sapiens mRNA similar to opsin 3 (encephalopsin, panopsin) (cDNA clone IMAGE:4669517).
AF140242 - Homo sapiens encephalopsin mRNA, complete cds.
BC062622 - Homo sapiens opsin 3, mRNA (cDNA clone IMAGE:5200803), complete cds.
BC036773 - Homo sapiens opsin 3, mRNA (cDNA clone MGC:46103 IMAGE:5723543), complete cds.
BC051900 - Homo sapiens opsin 3, mRNA (cDNA clone IMAGE:5181517).
JD173402 - Sequence 154426 from Patent EP1572962.
JD108507 - Sequence 89531 from Patent EP1572962.
JD540179 - Sequence 521203 from Patent EP1572962.
JD546704 - Sequence 527728 from Patent EP1572962.
JD042203 - Sequence 23227 from Patent EP1572962.
JD296329 - Sequence 277353 from Patent EP1572962.
JD381876 - Sequence 362900 from Patent EP1572962.
JD315859 - Sequence 296883 from Patent EP1572962.
AK310307 - Homo sapiens cDNA, FLJ17349.
KJ893412 - Synthetic construct Homo sapiens clone ccsbBroadEn_02806 OPN3 gene, encodes complete protein.
JD450233 - Sequence 431257 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9H1Y3 (Reactome details) participates in the following event(s):

R-HSA-419841 Light stimulates opsin receptors
R-HSA-8982637 Opsins binds G alpha-t
R-HSA-8982640 G-alpha(t):G-beta-gamma:Opsins complex dissociates to active G-alpha(t)
R-HSA-420883 Opsins act as GEFs for G alpha-t
R-HSA-419771 Opsins
R-HSA-418594 G alpha (i) signalling events
R-HSA-373076 Class A/1 (Rhodopsin-like receptors)
R-HSA-388396 GPCR downstream signalling
R-HSA-500792 GPCR ligand binding
R-HSA-372790 Signaling by GPCR
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ECPN, ENST00000366554.1, ENST00000366554.2, NM_014322, OPN3_HUMAN, Q8IX08, Q9H1Y3, Q9Y344, uc001hza.1, uc001hza.2, uc001hza.3, uc001hza.4, uc001hza.5
UCSC ID: ENST00000366554.3
RefSeq Accession: NM_014322
Protein: Q9H1Y3 (aka OPN3_HUMAN)
CCDS: CCDS31072.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.