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Aliases for RGR Gene

Aliases for RGR Gene

  • Retinal G Protein Coupled Receptor 2 3 5
  • RGR-Opsin 2 3
  • RPE-Retinal G Protein-Coupled Receptor 3
  • RP44 3

External Ids for RGR Gene

Previous GeneCards Identifiers for RGR Gene

  • GC10P084961
  • GC10P085226
  • GC10P086136
  • GC10P085669
  • GC10P085994
  • GC10P079850

Summaries for RGR Gene

Entrez Gene Summary for RGR Gene

  • This gene encodes a putative retinal G-protein coupled receptor. The gene is a member of the opsin subfamily of the 7 transmembrane, G-protein coupled receptor 1 family. Like other opsins which bind retinaldehyde, it contains a conserved lysine residue in the seventh transmembrane domain. The protein acts as a photoisomerase to catalyze the conversion of all-trans-retinal to 11-cis-retinal. The reverse isomerization occurs with rhodopsin in retinal photoreceptor cells. The protein is exclusively expressed in tissue adjacent to retinal photoreceptor cells, the retinal pigment epithelium and Mueller cells. This gene may be associated with autosomal recessive and autosomal dominant retinitis pigmentosa (arRP and adRP, respectively). Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]

GeneCards Summary for RGR Gene

RGR (Retinal G Protein Coupled Receptor) is a Protein Coding gene. Diseases associated with RGR include Retinitis Pigmentosa 44 and Fundus Dystrophy. Among its related pathways are Signaling by GPCR and Opsins. GO annotations related to this gene include G-protein coupled receptor activity and photoreceptor activity.

UniProtKB/Swiss-Prot for RGR Gene

  • Receptor for all-trans- and 11-cis-retinal. Binds preferentially to the former and may catalyze the isomerization of the chromophore by a retinochrome-like mechanism.

Gene Wiki entry for RGR Gene

Additional gene information for RGR Gene

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

Genomics for RGR Gene

Regulatory Elements for RGR Gene

Enhancers for RGR Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH10H084230 0.3 FANTOM5 64.3 -6.5 -6548 0 RGR LRIT2 LRIT1 CDHR1 PIR46157 PIR34083
GH10H084244 0.7 ENCODE 15.7 +7.8 7796 1 SOX13 HLF ARID4B CEBPB CEBPG ZNF644 TEAD3 NFIL3 CEBPA KDM1A RGR LRIT2 LRIT1 GC10M084241
GH10H084269 0.5 ENCODE 16.6 +32.9 32897 0 JUND FOS CEBPG RGR LRIT1 LRIT2 LINC00858 GC10P084249 GC10P084248
GH10H084493 0.9 Ensembl ENCODE 4.5 +257.5 257464 2 SMARCE1 JUN MAFG DPF2 FOSL1 CTBP1 JUND ZNF316 MAFF FOS RGR CACYBPP1 RPS3AP5
GH10H084295 0.8 Ensembl ENCODE 4.9 +59.6 59640 2 POLR2A ZNF366 JUN FOS ETS1 CCSER2 LRIT2 CDHR1 RGR GC10M084258 LINC00858
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RGR on UCSC Golden Path with GeneCards custom track

Genomic Location for RGR Gene

Chromosome:
10
Start:
84,237,083 bp from pter
End:
84,259,960 bp from pter
Size:
22,878 bases
Orientation:
Plus strand

Genomic View for RGR Gene

Genes around RGR on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RGR Gene

Proteins for RGR Gene

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

    Protein Symbol:
    P47804-RGR_HUMAN
    Recommended name:
    RPE-retinal G protein-coupled receptor
    Protein Accession:
    P47804
    Secondary Accessions:
    • A6NKK7
    • Q96FC5

    Protein attributes for RGR Gene

    Size:
    291 amino acids
    Molecular mass:
    31874 Da
    Quaternary structure:
    No Data Available

    Alternative splice isoforms for RGR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RGR Gene

Post-translational modifications for RGR Gene

  • Covalently binds all-trans- and 11-cis-retinal.
  • Glycosylation at isoforms=2, 3172
  • Modification sites at PhosphoSitePlus

Other Protein References for RGR Gene

No data available for DME Specific Peptides for RGR Gene

Domains & Families for RGR Gene

Gene Families for RGR Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • G-protein coupled receptors
  • Potential drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins

Suggested Antigen Peptide Sequences for RGR Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

P47804

UniProtKB/Swiss-Prot:

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

Function for RGR Gene

Molecular function for RGR Gene

GENATLAS Biochemistry:
retinal opsin related,(rhodopsin homolog)expressed in the retinal pigment epithelium,encoding a retinaldehyde,preferentially all-trans retinal,binding protein,G protein coupled receptor superfamily
UniProtKB/Swiss-Prot Function:
Receptor for all-trans- and 11-cis-retinal. Binds preferentially to the former and may catalyze the isomerization of the chromophore by a retinochrome-like mechanism.

Phenotypes From GWAS Catalog for RGR Gene

Gene Ontology (GO) - Molecular Function for RGR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004930 G-protein coupled receptor activity TAS 8641686
GO:0005515 protein binding IPI 16189514
GO:0008020 G-protein coupled photoreceptor activity IBA --
GO:0009881 photoreceptor activity IEA --
genes like me logo Genes that share ontologies with RGR: view
genes like me logo Genes that share phenotypes with RGR: view

Human Phenotype Ontology for RGR Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RGR Gene

MGI Knock Outs for RGR:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for RGR
  • Applied Biological Materials Clones for RGR
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for RGR Gene

Localization for RGR Gene

Subcellular locations from UniProtKB/Swiss-Prot for RGR Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

COMPARTMENTS
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 RGR gene
Compartment Confidence
plasma membrane 5

Gene Ontology (GO) - Cellular Components for RGR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005887 integral component of plasma membrane TAS,IEA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
genes like me logo Genes that share ontologies with RGR: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RGR Gene

Pathways & Interactions for RGR Gene

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

Gene Ontology (GO) - Biological Process for RGR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007165 signal transduction IEA --
GO:0007186 G-protein coupled receptor signaling pathway IEA,TAS --
GO:0007601 visual perception IEA,TAS --
GO:0007602 phototransduction IEA --
GO:0009584 detection of visible light IEA --
genes like me logo Genes that share ontologies with RGR: view

No data available for SIGNOR curated interactions for RGR Gene

Drugs & Compounds for RGR Gene

(1) Drugs for RGR Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(3) Additional Compounds for RGR Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Retinal
  • 3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-Nonatetraenal
  • All-E-Retinal
  • All-epsilon-Retinal
  • All-trans-Retinal
  • All-trans-Retinaldehyde
116-31-4
genes like me logo Genes that share compounds with RGR: view

Transcripts for RGR Gene

Unigene Clusters for RGR Gene

Retinal G protein coupled receptor:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for RGR
  • Applied Biological Materials Clones for RGR
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9a · 9b · 9c · 9d · 9e
SP1: - - - -
SP2: - - -
SP3: - -
SP4: - - - - - - -
SP5: - - - - -
SP6: - -
SP7: -
SP8:

Relevant External Links for RGR Gene

GeneLoc Exon Structure for
RGR
ECgene alternative splicing isoforms for
RGR

Expression for RGR Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RGR Gene

This gene is overexpressed in Brain - Nucleus accumbens (basal ganglia) (x6.6), Brain - Caudate (basal ganglia) (x6.4), Brain - Cortex (x6.0), Brain - Frontal Cortex (BA9) (x5.7), Brain - Amygdala (x5.3), and Brain - Anterior cingulate cortex (BA24) (x4.4).

Protein differential expression in normal tissues from HIPED for RGR Gene

This gene is overexpressed in Retina (69.0).

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



Protein tissue co-expression partners for RGR Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RGR Gene:

RGR

SOURCE GeneReport for Unigene cluster for RGR Gene:

Hs.1544

mRNA Expression by UniProt/SwissProt for RGR Gene:

P47804-RGR_HUMAN
Tissue specificity: Preferentially expressed at high levels in the retinal pigment epithelium (RPE) and Mueller cells of the neural retina.

Evidence on tissue expression from TISSUES for RGR Gene

  • Eye(4.6)
  • Nervous system(4.3)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RGR Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Organs:
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
Pelvis:
  • penis
  • testicle
General:
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with RGR: view

Primer Products

Orthologs for RGR Gene

This gene was present in the common ancestor of chordates.

Orthologs for RGR Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RGR 33 34
  • 98.74 (n)
cow
(Bos Taurus)
Mammalia RGR 33 34
  • 85.57 (n)
dog
(Canis familiaris)
Mammalia RGR 33 34
  • 83.39 (n)
mouse
(Mus musculus)
Mammalia Rgr 33 16 34
  • 81.9 (n)
rat
(Rattus norvegicus)
Mammalia Rgr 33
  • 81.44 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia RGR 34
  • 59 (a)
OneToOne
chicken
(Gallus gallus)
Aves RGR 33 34
  • 67.25 (n)
lizard
(Anolis carolinensis)
Reptilia RGR 34
  • 56 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rgr 33
  • 61.97 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.17609 33
zebrafish
(Danio rerio)
Actinopterygii rgra 34 33
  • 62.12 (n)
OneToOne
Species where no ortholog for RGR was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • 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 RGR Gene

ENSEMBL:
Gene Tree for RGR (if available)
TreeFam:
Gene Tree for RGR (if available)

Paralogs for RGR Gene

(1) SIMAP similar genes for RGR Gene using alignment to 2 proteins:

genes like me logo Genes that share paralogs with RGR: view

No data available for Paralogs for RGR Gene

Variants for RGR Gene

Sequence variations from dbSNP and Humsavar for RGR Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
VAR_017034 Retinitis pigmentosa 44 (RP44) [MIM:613769]
rs104894187 Pathogenic 84,247,707(+) GGATC(A/C)GCCTG reference, missense
rs11200938 Likely benign 84,245,109(+) GTGCC(C/T)TGCCC reference, synonymous-codon
rs11817115 Likely benign 84,259,055(+) CTCCA(A/G)TGTCT utr-variant-3-prime
rs3526 Likely benign 84,258,704(+) GCCTC(A/G)GTGGC utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
esv3624030 CNV loss 21293372
nsv1046749 CNV gain 25217958
nsv1141879 OTHER inversion 24896259
nsv527522 CNV loss 19592680
nsv551745 CNV gain 21841781

Variation tolerance for RGR Gene

Residual Variation Intolerance Score: 45.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.07; 60.80% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RGR Gene

Human Gene Mutation Database (HGMD)
RGR
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RGR

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

Disorders for RGR Gene

MalaCards: The human disease database

(6) MalaCards diseases for RGR Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 44
  • rp44
fundus dystrophy
  • retinal dystrophy
rgr-related retinitis pigmentosa
retinitis pigmentosa
  • retinitis pigmentosa 1
retinitis
- elite association - COSMIC cancer census association via MalaCards
Search RGR in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RGR_HUMAN
  • Retinitis pigmentosa 44 (RP44) [MIM:613769]: A retinal dystrophy belonging to the group of pigmentary retinopathies. Retinitis pigmentosa is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well. {ECO:0000269 PubMed:10581022}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RGR

Genetic Association Database (GAD)
RGR
Human Genome Epidemiology (HuGE) Navigator
RGR
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
RGR
genes like me logo Genes that share disorders with RGR: view

No data available for Genatlas for RGR Gene

Publications for RGR Gene

  1. Mutations in RGR, encoding a light-sensitive opsin homologue, in patients with retinitis pigmentosa. (PMID: 10581022) Morimura H … Dryja TP (Nature genetics 1999) 3 4 22 60
  2. Localization of the human RGR opsin gene to chromosome 10q23. (PMID: 8641686) Chen XN … Fong HK (Human genetics 1996) 2 3 22 60
  3. A human opsin-related gene that encodes a retinaldehyde-binding protein. (PMID: 7947717) Shen D … Fong HK (Biochemistry 1994) 3 4 22 60
  4. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij JC … Florijn RJ (Ophthalmology 2011) 3 45 60
  5. Screening genes of the visual cycle RGR, RBP1 and RBP3 identifies rare sequence variations. (PMID: 21067480) Ksantini M … Hamel CP (Ophthalmic genetics 2010) 3 45 60

Products for RGR Gene

  • Addgene plasmids for RGR

Sources for RGR Gene

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