Homo sapiens gene RGR, encoding retinal G protein coupled receptor.
SUMMARY back to top
RefSeq summary
[RGR] 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].

RefSeq annotates 3 representative transcripts (NM included in AceView variants .a, .b and .d), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 10 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is well expressed, 0.6 times the average gene in this release. The sequence of this gene is defined by 67 GenBank accessions from 49 cDNA clones, some from brain (seen 15 times), eye (14), anaplastic oligodendroglioma with 1p/19qloss (11), retina (7), RPE and choroid (6), human skeletal muscle (5), brain, anaplastic oligodendroglioma with1p/19q loss (4) and 13 other tissues. We annotate structural defects or features in 13 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 14 distinct gt-ag introns. Transcription produces 12 different mRNAs, 10 alternatively spliced variants and 2 unspliced forms. There are 2 probable alternative promotors, 4 non overlapping alternative last exons and 7 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 3 cassette exons, overlapping exons with different boundaries, splicing versus retention of 3 introns.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant cAug10).
Function: There are 15 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (Alzheimer Disease; retinitis pigmentosa; Retinitis pigmentosa, autosomal dominant; Retinitis pigmentosa, autosomal recessive; Retinitis pigmentosa-44) and proposed to participate in processes (phototransduction, protein-chromophore linkage, response to stimulus, visual perception). Proteins are expected to have molecular functions (G-protein coupled receptor activity, photoreceptor activity) and to localize in membrane. Putative protein interactors have been described (BLOC1S1ANDRDH5, KIAA1279).
Protein coding potential: 9 spliced mRNAs putatively encode good proteins, altogether 9 different isoforms (6 complete, 2 COOH complete, 1 partial), some containing 7 transmembrane receptor (rhodopsin family) domain [Pfam], some transmembrane domains, a N-myristoylation domain [Psort2]. The remaining 3 mRNA variants (1 spliced, 2 unspliced; 1 partial) appear not to encode good proteins.
2 isoforms are annotated using as Met a Kozak-compatible non-AUG start, thereby gaining a minimum of 163 amino acids N-terminal to the first AUG.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 10, links to other databases and other names
Map: This gene RGR maps on chromosome 10, at 10q23 according to Entrez Gene. In AceView, it covers 14.91 kb, from 86004804 to 86019715 (NCBI 37, August 2010), on the direct strand.
Links to: , manual annotations from GAD, the SNP view, gene overviews from Entrez Gene 5995, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as RGR or RP44, LOC5995. It has been described as RPE-retinal G protein-coupled receptor, RGR-opsin, RPE retinal G-protein coupled receptor.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Rgr (e=4 10-99).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene tyra-2 (e=0.035), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the Flash version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
Downstream sequence
aAug10 2246 bp 295 aa 38 bp 1320 bp 2kb probably including promoter 14907 bp 1kb
bAug10 1463 bp 291 aa 38 bp 549 bp 2kb probably including promoter 14136 bp 1kb
cAug10 2588 bp 274 aa 1263 bp 500 bp 285 bp 2kb probably including promoter 14087 bp 1kb
dAug10 1354 bp 253 aa 43 bp 549 bp 2kb probably including promoter 14141 bp 1kb
eAug10 2390 bp 236 aa 1179 bp 500 bp 2kb probably including promoter 14053 bp 1kb
fAug10 696 bp 232 aa 2kb probably including promoter 13526 bp 1kb
gAug10 697 bp 231 aa 2kb 10448 bp 1kb
hAug10 798 bp 169 aa 286 bp 2kb 7736 bp 1kb
iAug10 852 bp 120 aa 6 bp 483 bp 2kb probably including promoter 5826 bp 1kb
jAug10-unspliced 861 bp 80 aa 39 bp 579 bp 2kb probably including promoter 861 bp 1kb
kAug10 746 bp 44 aa 336 bp 275 bp 2kb 3745 bp 1kb
lAug10-unspliced 508 bp 71 aa 291 bp 2kb 508 bp 1kb

Gene neighbors and Navigator on chromosome 10q23 back to top
ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications        
Annotated mRNA diagrams back to top
Bibliography:               15 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g, .h, .i, .j-u, .k, .l-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !