Gene
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.
6010
Gene name Gene Name - the full gene name approved by the HGNC.
Rhodopsin
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.
RHO
Synonyms (NCBI Gene) Gene synonyms aliases
CSNBAD1, OPN2, RP4
Chromosome Chromosome number
3
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.
3q22.1
Summary Summary of gene provided in NCBI Entrez Gene.
The protein encoded by this gene is found in rod cells in the back of the eye and is essential for vision in low-light conditions. The encoded protein binds to 11-cis retinal and is activated when light hits the retinal molecule. Defects in this gene are
SNPs SNP information provided by dbSNP.
SNP ID Visualize variation Clinical significance Consequence
rs28933394 C>G,T Pathogenic Missense variant, coding sequence variant
rs28933395 C>G Pathogenic, likely-pathogenic Missense variant, coding sequence variant
rs28933993 A>C Pathogenic Missense variant, coding sequence variant
rs29001566 C>A,G,T Pathogenic, likely-pathogenic Missense variant, coding sequence variant
rs29001637 C>T Pathogenic Missense variant, coding sequence variant
miRNA miRNA information provided by mirtarbase database.
miRTarBase ID miRNA Experiments Reference
MIRT438893 hsa-miR-21-5p qRT-PCR, Western blot 23446999
MIRT438893 hsa-miR-21-5p qRT-PCR, Western blot 23446999
MIRT736088 hsa-let-7a-3p RNA-seq 31579443
MIRT1305084 hsa-miR-1228 CLIP-seq
MIRT1305085 hsa-miR-1302 CLIP-seq
Transcription factors
Transcription factor Regulation Reference
CRX Repression 15277472
KLF15 Repression 15277472
KLF15 Unknown 15963234
NR2E3 Activation 19898638
NRL Repression 15277472
Gene ontology (GO) Gene ontology information of associated ontologies with gene provided by GO database.
GO ID Ontology Definition Evidence Reference
GO:0000139 Component Golgi membrane TAS
GO:0000226 Process Microtubule cytoskeleton organization IEA
GO:0001750 Component Photoreceptor outer segment IBA
GO:0001750 Component Photoreceptor outer segment IDA 11767049, 23704327
GO:0001750 Component Photoreceptor outer segment IEA
Other IDs Other ids provides unique ids of gene in databases such as OMIM, HGNC, ENSEMBLE.
MIM HGNC e!Ensembl
180380 10012 ENSG00000163914
Protein
UniProt ID P08100
Protein name Rhodopsin (Opsin-2)
Protein function Photoreceptor required for image-forming vision at low light intensity (PubMed:7846071, PubMed:8107847). Required for photoreceptor cell viability after birth (PubMed:12566452, PubMed:2215617). Light-induced isomerization of the chromophore 11-c
PDB 4ZWJ , 5DGY , 5W0P , 6CMO
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF10413 Rhodopsin_N 2 37 Amino terminal of the G-protein receptor rhodopsin Domain
PF00001 7tm_1 54 306 7 transmembrane receptor (rhodopsin family) Family
Tissue specificity TISSUE SPECIFICITY: Rod shaped photoreceptor cells which mediate vision in dim light.
Sequence
Sequence length 348
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG   Reactome
  Phototransduction   The canonical retinoid cycle in rods (twilight vision)
Activation of the phototransduction cascade
Inactivation, recovery and regulation of the phototransduction cascade
G alpha (i) signalling events
Opsins
VxPx cargo-targeting to cilium
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Associated diseases Disease associations categorized as Causal (pathogenic variants), Unknown (uncertain genetic evidence), or Text Mining (literature-based associations)
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Disease merge term Disease name dbSNP ID References
Congenital stationary night blindness Congenital stationary night blindness autosomal dominant 1 rs104893796, rs1578278438, rs104893789, rs104893790, rs984572250, rs104893793 N/A
retinal dystrophy Retinal dystrophy rs104893772, rs527236101, rs2084801700, rs2084757329, rs1560046837, rs2084786704, rs104893791, rs28933993, rs1415160298, rs28933394, rs104893780, rs1402468701, rs104893773, rs527236100, rs104893793
View all (33 more)
N/A
Retinal Dystrophy Pigmentary retinal dystrophy rs1402468701, rs104893771, rs104893790, rs104893772, rs142285818 N/A
Retinitis Pigmentosa retinitis pigmentosa, retinitis pigmentosa 4, Autosomal recessive retinitis pigmentosa rs1578280588, rs104893779, rs104893791, rs28933993, rs104893793, rs104893795, rs104893780, rs28933394, rs104893773, rs527236100, rs779169631, rs1578278088, rs1578280614, rs104893786, rs1415160298
View all (49 more)
N/A
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Disease merge term Disease name Evidence References Source
Cone Dystrophy Cone dystrophy 3 N/A N/A ClinVar
Fundus Albipunctatus fundus albipunctatus N/A N/A GenCC
Associations from Text Mining Disease associations identified through Pubtator
Disease Name Relationship Type References
Abnormalities Drug Induced Associate 2215617
Asthma Associate 39868576
Attention Deficit Disorder with Hyperactivity Associate 32724127
Blindness Associate 11058128
Color Vision Defects Associate 15208011, 19934058
Cone Rod Dystrophies Associate 20164459
Death Associate 19206210
Disease Associate 8317502
Emphysema Associate 16504044
Eye Diseases Associate 1882937