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Aliases for RPGR Gene

Aliases for RPGR Gene

  • Retinitis Pigmentosa GTPase Regulator 2 3 5
  • Retinitis Pigmentosa 15 2 3
  • XLRP3 3 4
  • RP3 3 4
  • X-Linked Retinitis Pigmentosa GTPase Regulator 3
  • Retinitis Pigmentosa 3 GTPase Regulator 3
  • Cone Dystrophy 1 (X-Linked) 2
  • CORDX1 3
  • Orf15 3
  • COD1 3
  • PCDX 3
  • RP15 3
  • CRD 3

External Ids for RPGR Gene

Previous HGNC Symbols for RPGR Gene

  • CRD
  • RP3
  • RP15
  • COD1

Previous GeneCards Identifiers for RPGR Gene

  • GC0XM036233
  • GC0XM036416
  • GC0XM036972
  • GC0XM037159
  • GC0XM037884
  • GC0XM038013
  • GC0XM038128
  • GC0XM035873

Summaries for RPGR Gene

Entrez Gene Summary for RPGR Gene

  • This gene encodes a protein with a series of six RCC1-like domains (RLDs), characteristic of the highly conserved guanine nucleotide exchange factors. The encoded protein is found in the Golgi body and interacts with RPGRIP1. This protein localizes to the outer segment of rod photoreceptors and is essential for their viability. Mutations in this gene have been associated with X-linked retinitis pigmentosa (XLRP). Multiple alternatively spliced transcript variants that encode different isoforms of this gene have been reported, but the full-length natures of only some have been determined. [provided by RefSeq, Dec 2008]

GeneCards Summary for RPGR Gene

RPGR (Retinitis Pigmentosa GTPase Regulator) is a Protein Coding gene. Diseases associated with RPGR include Retinitis Pigmentosa, X-Linked, And Sinorespiratory Infections, With Or Without Deafness and Retinitis Pigmentosa 3. GO annotations related to this gene include poly(A) RNA binding and guanyl-nucleotide exchange factor activity. An important paralog of this gene is RCBTB2.

UniProtKB/Swiss-Prot for RPGR Gene

  • Could be a guanine-nucleotide releasing factor. Plays a role in ciliogenesis. Probably regulates cilia formation by regulating actin stress filaments and cell contractility. Plays an important role in photoreceptor integrity. May play a critical role in spermatogenesis and in intraflagellar transport processes (By similarity). May be involved in microtubule organization and regulation of transport in primary cilia.

Gene Wiki entry for RPGR Gene

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

Genomics for RPGR Gene

Regulatory Elements for RPGR Gene

Enhancers for RPGR 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
GH0XF038268 1 FANTOM5 17.4 +59.4 59378 0.3 RPGR ENSG00000226679 SRPX CYBB GC0XM038216 ENSG00000252050
GH0XF038271 0.9 FANTOM5 Ensembl 14.5 +56.0 56030 0.5 TBL1XR1 BMI1 RELA ZNF316 CBX5 NFE2 CREM MAFK MTA2 ZBED1 RPGR SRPX ENSG00000226679 CYBB GC0XM038216 ENSG00000252050
GH0XF038350 0.2 ENCODE 13 -27.3 -27341 8.3 ZNF664 JUND HLF HNF4G ATF2 RPGR OTC SRPX TDGF1P1
GH0XF038181 0.3 FANTOM5 11.5 +145.6 145632 0.0 RPGR SYTL5 SRPX GC0XM038061
GH0XF038231 1 Ensembl ENCODE 11 +94.3 94256 3.3 JUND NFE2 RPGR SRPX GC0XM038216 ENSG00000252050
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around RPGR on UCSC Golden Path with GeneCards custom track

Promoters for RPGR Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000160351 464 2201 ATF1 ARID4B SIN3A GLI4 ZNF48 ZNF2 GLIS2 ELK1 ZNF143 SP3

Genomic Location for RPGR Gene

Chromosome:
X
Start:
38,269,163 bp from pter
End:
38,327,564 bp from pter
Size:
58,402 bases
Orientation:
Minus strand

Genomic View for RPGR Gene

Genes around RPGR on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for RPGR Gene

Proteins for RPGR Gene

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

    Protein Symbol:
    Q92834-RPGR_HUMAN
    Recommended name:
    X-linked retinitis pigmentosa GTPase regulator
    Protein Accession:
    Q92834
    Secondary Accessions:
    • B1ARN3
    • E9PE28
    • O00702
    • O00737
    • Q3KN84
    • Q8N5T6
    • Q93039
    • Q9HD29
    • Q9UMR1

    Protein attributes for RPGR Gene

    Size:
    1020 amino acids
    Molecular mass:
    113387 Da
    Quaternary structure:
    • Interacts with CEP290 (By similarity). Interacts with WHRN (By similarity). Interacts with PDE6D, RPGRIP1 and RPGRIP1L; PDE6D, RPGRIP1 and RPGRIP1L may compete for the same binding sites(PubMed:24981858). Isoform 6 interacts with NPM1 (via C-terminus) (PubMed:15772089). Isoform 6 interacts with SMC1A and SMC3 (PubMed:16043481).

    Three dimensional structures from OCA and Proteopedia for RPGR Gene

    Alternative splice isoforms for RPGR Gene

neXtProt entry for RPGR Gene

Post-translational modifications for RPGR Gene

No data available for DME Specific Peptides for RPGR Gene

Domains & Families for RPGR Gene

Protein Domains for RPGR Gene

Suggested Antigen Peptide Sequences for RPGR Gene

Graphical View of Domain Structure for InterPro Entry

Q92834

UniProtKB/Swiss-Prot:

RPGR_HUMAN :
  • The RCC1 repeat region mediates interactions with RPGRIP1.
  • Contains 6 RCC1 repeats.
Domain:
  • The RCC1 repeat region mediates interactions with RPGRIP1.
Similarity:
  • Contains 6 RCC1 repeats.
genes like me logo Genes that share domains with RPGR: view

No data available for Gene Families for RPGR Gene

Function for RPGR Gene

Molecular function for RPGR Gene

GENATLAS Biochemistry:
retinitis pigmentosa GTPase regulator,ubiquitously expressed,localized in the Golgi apparatus,potentially involved in vesicle transport,exhibiting several alternatively spliced isoforms,including a truncated form,retina specific using exon 15a and lacking exons 16 to 19
UniProtKB/Swiss-Prot Function:
Could be a guanine-nucleotide releasing factor. Plays a role in ciliogenesis. Probably regulates cilia formation by regulating actin stress filaments and cell contractility. Plays an important role in photoreceptor integrity. May play a critical role in spermatogenesis and in intraflagellar transport processes (By similarity). May be involved in microtubule organization and regulation of transport in primary cilia.

Gene Ontology (GO) - Molecular Function for RPGR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005085 guanyl-nucleotide exchange factor activity IEA --
GO:0005515 protein binding IPI 9990021
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with RPGR: view
genes like me logo Genes that share phenotypes with RPGR: view

Human Phenotype Ontology for RPGR Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for RPGR Gene

MGI Knock Outs for RPGR:

Animal Model Products

miRNA for RPGR Gene

miRTarBase miRNAs that target RPGR

Inhibitory RNA Products

Flow Cytometry Products

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

Localization for RPGR Gene

Subcellular locations from UniProtKB/Swiss-Prot for RPGR Gene

Cytoplasm, cytoskeleton, flagellum axoneme. Golgi apparatus.
Isoform 6: Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, cilium axoneme.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for RPGR Gene COMPARTMENTS Subcellular localization image for RPGR gene
Compartment Confidence
cytoskeleton 5
golgi apparatus 4
nucleus 3
cytosol 2
endoplasmic reticulum 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for RPGR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001750 photoreceptor outer segment IDA 12140192
GO:0005737 cytoplasm IEA --
GO:0005794 Golgi apparatus ISS --
GO:0005813 centrosome IDA 15772089
GO:0005815 microtubule organizing center IEA --
genes like me logo Genes that share ontologies with RPGR: view

Pathways & Interactions for RPGR Gene

SuperPathways for RPGR Gene

No Data Available

Gene Ontology (GO) - Biological Process for RPGR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport TAS 9990021
GO:0007601 visual perception IMP 9399904
GO:0030030 cell projection organization IEA --
GO:0042073 intraciliary transport ISS --
GO:0043547 positive regulation of GTPase activity IEA --
genes like me logo Genes that share ontologies with RPGR: view

No data available for Pathways by source and SIGNOR curated interactions for RPGR Gene

Drugs & Compounds for RPGR Gene

(2) Drugs for RPGR Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(1) Additional Compounds for RPGR Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RPGR: view

Transcripts for RPGR Gene

Unigene Clusters for RPGR Gene

Retinitis pigmentosa GTPase regulator:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17 ^ 18 ^ 19
SP1: -
SP2: - -
SP3: - - - - - -
SP4:
SP5:
SP6: - - - -

Relevant External Links for RPGR Gene

GeneLoc Exon Structure for
RPGR
ECgene alternative splicing isoforms for
RPGR

Expression for RPGR Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RPGR Gene

This gene is overexpressed in Breast (21.8), Cerebrospinal fluid (21.2), and Monocytes (11.6).

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



NURSA nuclear receptor signaling pathways regulating expression of RPGR Gene:

RPGR

SOURCE GeneReport for Unigene cluster for RPGR Gene:

Hs.61438

mRNA Expression by UniProt/SwissProt for RPGR Gene:

Q92834-RPGR_HUMAN
Tissue specificity: Heart, brain, placenta, lung, liver, muscle, kidney, retina, pancreas and fetal retinal pigment epithelium. Isoform 3 is found only in the retina. Colocalizes with RPGRIP1 in the outer segment of rod photoreceptors and cone outer segments.
genes like me logo Genes that share expression patterns with RPGR: view

Primer Products

No data available for mRNA differential expression in normal tissues and Protein tissue co-expression partners for RPGR Gene

Orthologs for RPGR Gene

This gene was present in the common ancestor of chordates.

Orthologs for RPGR Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RPGR 34
  • 93.81 (n)
dog
(Canis familiaris)
Mammalia RPGR 34
  • 81.89 (n)
rat
(Rattus norvegicus)
Mammalia Rpgr 34
  • 79.61 (n)
mouse
(Mus musculus)
Mammalia Rpgr 34 16 35
  • 75.75 (n)
cow
(Bos Taurus)
Mammalia RPGR 35
  • 46 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RPGR 35
  • 46 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RPGR 35
  • 41 (a)
OneToOne
chicken
(Gallus gallus)
Aves RPGR 35
  • 48 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia RPGR 35
  • 76 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rpgr 34
  • 64.37 (n)
Str.3813 34
zebrafish
(Danio rerio)
Actinopterygii rpgrb 34 35
  • 60.49 (n)
rpgra 35
  • 23 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 18 (a)
OneToOne
Species where no ortholog for RPGR 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)
  • 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)
  • 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 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 RPGR Gene

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

Paralogs for RPGR Gene

Paralogs for RPGR Gene

Pseudogenes.org Pseudogenes for RPGR Gene

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

Variants for RPGR Gene

Sequence variations from dbSNP and Humsavar for RPGR Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs137852550 Retinitis pigmentosa and sinorespiratory infections with or without deafness (RPDSI) [MIM:300455], Retinitis pigmentosa 3 (RP3) [MIM:300029], Pathogenic 38,317,418(-) AAATT(C/G)GTTTA reference, missense
rs62635004 Retinitis pigmentosa 3 (RP3) [MIM:300029], untested 38,297,391(-) TCTTG(A/G)CCTTT reference, missense
rs62638629 Retinitis pigmentosa 3 (RP3) [MIM:300029], untested 38,323,426(-) CATGT(A/G)GAGAT reference, missense
rs62638630 Retinitis pigmentosa 3 (RP3) [MIM:300029], untested 38,323,425(-) ATGTG(A/G)AGATG reference, missense
rs62638634 Retinitis pigmentosa 3 (RP3) [MIM:300029], Pathogenic 38,322,921(-) GTTTG(G/T)CAGTA reference, missense

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

Variant ID Type Subtype PubMed ID
dgv510n21 CNV gain 19592680
esv3576846 CNV gain 25503493
nsv516365 CNV gain 19592680
nsv522957 CNV gain 19592680

Variation tolerance for RPGR Gene

Residual Variation Intolerance Score: 98.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.90; 87.12% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for RPGR Gene

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

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

Disorders for RPGR Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
retinitis pigmentosa, x-linked, and sinorespiratory infections, with or without deafness
  • primary ciliary dyskinesia-retinitis pigmentosa syndrome
retinitis pigmentosa 3
  • rp3
cone-rod dystrophy, x-linked, 1
  • cone-rod dystrophy x-linked 1
macular degeneration, x-linked atrophic
  • macular degeneration, x-linked, atrophic
retinitis pigmentosa
  • retinitis pigmentosa 1
- elite association - COSMIC cancer census association via MalaCards
Search RPGR in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

RPGR_HUMAN
  • Cone-rod dystrophy, X-linked 1 (CORDX1) [MIM:304020]: An inherited retinal dystrophy characterized by retinal pigment deposits visible on fundus examination, predominantly in the macular region, and initial loss of cone photoreceptors followed by rod degeneration. This leads to decreased visual acuity and sensitivity in the central visual field, followed by loss of peripheral vision. Severe loss of vision occurs earlier than in retinitis pigmentosa. In cone-rod dystrophy X-linked type 1 the degree of rod-photoreceptor involvement can be variable, with degeneration increasing as the disease progresses. Affected individuals (essentially all of whom are males) present with decreased visual acuity, myopia, photophobia, abnormal color vision, full peripheral visual fields, decreased photopic electroretinographic responses, and granularity of the macular retinal pigment epithelium. Although penetrance appears to be nearly 100%, there is variable expressivity with respect to age at onset and severity of symptoms. {ECO:0000269 PubMed:11857109}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Macular degeneration, X-linked, atrophic (MDXLA) [MIM:300834]: An ocular disorder characterized by macular atrophy causing progressive loss of visual acuity with minimal peripheral visual impairment. Some patients manifest extensive macular degeneration plus peripheral loss of retinal pigment epithelium and choriocapillaries. Full-field electroretinograms (ERGs) show normal cone and rod responses in some affected males despite advanced macular degeneration. {ECO:0000269 PubMed:12160730}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa 3 (RP3) [MIM:300029]: A X-linked 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. In RP3, affected males have a severe phenotype, and carrier females show a wide spectrum of clinical features ranging from completely asymptomatic to severe retinitis pigmentosa. Heterozygous women can manifest a form of choroidoretinal degeneration which is distinguished from other types by the absence of visual defects in the presence of a brilliant, scintillating, golden-hued, patchy appearance most striking around the macula, called a tapetal-like retinal reflex. {ECO:0000269 PubMed:10482958, ECO:0000269 PubMed:10737996, ECO:0000269 PubMed:10932196, ECO:0000269 PubMed:10937588, ECO:0000269 PubMed:10970770, ECO:0000269 PubMed:11180598, ECO:0000269 PubMed:11992260, ECO:0000269 PubMed:12657579, ECO:0000269 PubMed:14564670, ECO:0000269 PubMed:8673101, ECO:0000269 PubMed:8817343, ECO:0000269 PubMed:9399904, ECO:0000269 PubMed:9855162}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Retinitis pigmentosa and sinorespiratory infections with or without deafness (RPDSI) [MIM:300455]: A disease characterized by the association primary ciliary dyskinesia features with retinitis pigmentosa. Some patients also manifest deafness. {ECO:0000269 PubMed:12920075, ECO:0000269 PubMed:14627685}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for RPGR

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

No data available for Genatlas for RPGR Gene

Publications for RPGR Gene

  1. RP2 and RPGR mutations and clinical correlations in patients with X- linked retinitis pigmentosa. (PMID: 14564670) Sharon D. … Berson E.L. (Am. J. Hum. Genet. 2003) 3 4 22 46 64
  2. A gene (RPGR) with homology to the RCC1 guanine nucleotide exchange factor is mutated in X-linked retinitis pigmentosa (RP3). (PMID: 8673101) Meindl A. … Wright A.F. (Nat. Genet. 1996) 2 3 4 22 64
  3. Disease course of patients with X-linked retinitis pigmentosa due to RPGR gene mutations. (PMID: 17325176) Sandberg M.A. … Berson E.L. (Invest. Ophthalmol. Vis. Sci. 2007) 3 22 46 64
  4. Comprehensive survey of mutations in RP2 and RPGR in patients affected with distinct retinal dystrophies: genotype-phenotype correlations and impact on genetic counseling. (PMID: 16969763) Pelletier V. … Rozet J.M. (Hum. Mutat. 2007) 3 22 46 64
  5. RPGR-ORF15, which is mutated in retinitis pigmentosa, associates with SMC1, SMC3, and microtubule transport proteins. (PMID: 16043481) Khanna H. … Swaroop A. (J. Biol. Chem. 2005) 3 4 22 64

Products for RPGR Gene

Sources for RPGR Gene

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