Rpgr retinitis pigmentosa GTPase regulator [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rpgrprovided by MGI
Official Full Name: retinitis pigmentosa GTPase regulatorprovided by MGI
Primary source: MGI:MGI:1344037
See related: Ensembl:ENSMUSG00000031174 AllianceGenome:MGI:1344037
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Rd9; Rp3h
Summary: Predicted to enable guanyl-nucleotide exchange factor activity. Involved in intraciliary transport. Acts upstream of or within cellular response to light stimulus; eye morphogenesis; and visual perception. Located in several cellular components, including ciliary basal body; photoreceptor distal connecting cilium; and sperm flagellum. Is expressed in several structures, including genitourinary system; nervous system; and sensory organ. Used to study X-linked cone-rod dystrophy 1 and retinitis pigmentosa 3. Human ortholog(s) of this gene implicated in X-linked atrophic macular degeneration; X-linked cone-rod dystrophy 1; X-linked retinitis pigmentosa and sinorespiratory infections; retinitis pigmentosa; and retinitis pigmentosa 3. Orthologous to human RPGR (retinitis pigmentosa GTPase regulator). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Broad expression in CNS E14 (RPKM 3.9), whole brain E14.5 (RPKM 3.6) and 19 other tissues See more
Orthologs: human all
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Genomic context

Location:: X; X A1.1

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
109	current	GRCm39 (GCF_000001635.27)	X	NC_000086.8 (10024455..10083034, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	X	NC_000086.7 (10158216..10216795, complement)

Chromosome X - NC_000086.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

These studies provide a human-XLRP disease model but also act as a platform to design genome editing technology for retinal degenerative diseases using the currently available endonucleases.
Title: Toward genome editing in X-linked RP-development of a mouse model with specific treatment relevant features.
In induced pluripotent stem cells and mouse knockouts that RPGR mediates actin dynamics in photoreceptors via the actin-severing protein, gelsolin.
Title: Gelsolin dysfunction causes photoreceptor loss in induced pluripotent cell and animal retinitis pigmentosa models.
Together with a physical interaction between RPGR and the C-terminal domain of CEP290, our data suggest that RPGR and CEP290 genetically interact and highlight the involvement of hypomorphic alleles of genes as potential modifiers of heterogeneous retinal ciliopathies.
Title: Ciliopathy-associated protein CEP290 modifies the severity of retinal degeneration due to loss of RPGR.
We also correlated the features observed in patients with those of three Rpgr-mutant (Rpgr-ko, Rd9, and Rpgr-cko) mice. In patients, there was pronounced macular disease
Title: Variegated yet non-random rod and cone photoreceptor disease patterns in RPGR-ORF15-associated retinal degeneration.
The discordant effect of the loss of RPGR on rod-dominant or cone-only rodent retinas is shown.
Title: Loss of human disease protein retinitis pigmentosa GTPase regulator (RPGR) differentially affects rod or cone-enriched retina.
study uncovers the pathogenic mechanism whereby absence of RPGR(ORF15) glutamylation leads to retinal pathology in patients with TTLL5 gene mutations and connects these two genes into a common disease pathway.
Title: Loss of RPGR glutamylation underlies the pathogenic mechanism of retinal dystrophy caused by TTLL5 mutations.
Given a frequent occurrence of RPGR mutations in severe photoreceptor degeneration due to ciliary disorders, our results provide insights into pathways resulting in altered mature cilia function in ciliopathies.
Title: Ablation of retinal ciliopathy protein RPGR results in altered photoreceptor ciliary composition.
Data shsow that Rpgr ORF15 transcripts, but not protein, were detected in retinas from Rd9/Y male mice that exhibited retinal pathology.
Title: Rd9 is a naturally occurring mouse model of a common form of retinitis pigmentosa caused by mutations in RPGR-ORF15.
Misexpression of Rpgr(ex1-19) causes retinal degeneration that is considerably more severe than that caused by Rpgr knockout but photoreceptors tolerate overexpression of Rpgr(ORF15) without evidence of degeneration.
Title: Misexpression of the constitutive Rpgr(ex1-19) variant leads to severe photoreceptor degeneration.
RPGR localizes to the podocytes in the glomerulus as well as to primary cilia in parietal epithelium and tubules
Title: Expression and localization of the ciliary disease protein retinitis pigmentosa GTPase regulator in mammalian kidney.

Submit: New GeneRIF Correction See all GeneRIFs (14)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Spontaneous (1) 1 citation
Targeted (5) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Rpgr (e-PCR), detects polymorphism
- UniSTS:257084

UniSTS:495977 (e-PCR)
- UniSTS:495977

Avpr1b (e-PCR), detects polymorphism
- UniSTS:495977

Homology

Homologs of the Rpgr gene: The Rpgr gene is conserved in human, chimpanzee, dog, rat, zebrafish, and frog.
Orthologs from Annotation Pipeline: 330 organisms have orthologs with human gene Rpgr
Orthologs

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables guanyl-nucleotide exchange factor activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	IBA Inferred from Biological aspect of Ancestor more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell projection organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cellular response to light stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cilium assembly	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within eye photoreceptor cell development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intraciliary transport	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in intraciliary transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within response to stimulus	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within retina morphogenesis in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ubiquitin-dependent protein catabolic process	IBA Inferred from Biological aspect of Ancestor more info	PubMed
involved_in visual perception	IBA Inferred from Biological aspect of Ancestor more info	PubMed
acts_upstream_of_or_within visual perception	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in visual perception	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info
located_in cell projection	ISO Inferred from Sequence Orthology more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in ciliary basal body	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	IDA Inferred from Direct Assay more info	PubMed
located_in cilium	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
located_in motile cilium	IEA Inferred from Electronic Annotation more info
located_in photoreceptor connecting cilium	IDA Inferred from Direct Assay more info	PubMed
located_in photoreceptor distal connecting cilium	IDA Inferred from Direct Assay more info	PubMed
is_active_in photoreceptor outer segment	IBA Inferred from Biological aspect of Ancestor more info	PubMed
located_in photoreceptor outer segment	ISO Inferred from Sequence Orthology more info
located_in sperm flagellum	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: X-linked retinitis pigmentosa GTPase regulator

Names: mRpgr

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001177950.1 → NP_001171421.1 X-linked retinitis pigmentosa GTPase regulator isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AL671042

Consensus CDS

CCDS53001.1

UniProtKB/TrEMBL

A0A067XG46

Related

ENSMUSP00000037358.7, ENSMUST00000044598.13

Conserved Domains (2) summary

pfam00415
Location:246 → 296

RCC1; Regulator of chromosome condensation (RCC1) repeat

pfam13540
Location:180 → 209

RCC1_2; Regulator of chromosome condensation (RCC1) repeat
NM_001177951.1 → NP_001171422.1 X-linked retinitis pigmentosa GTPase regulator isoform 2

See identical proteins and their annotated locations for NP_001171422.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 3' UTR and CDS compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AK029864, AL671042

Consensus CDS

CCDS53002.1

UniProtKB/TrEMBL

Q8CDM3

Related

ENSMUSP00000111194.2, ENSMUST00000115532.2

Conserved Domains (2) summary

pfam00415
Location:246 → 296

RCC1; Regulator of chromosome condensation (RCC1) repeat

pfam13540
Location:180 → 209

RCC1_2; Regulator of chromosome condensation (RCC1) repeat
NM_001177952.1 → NP_001171423.1 X-linked retinitis pigmentosa GTPase regulator isoform 4

See identical proteins and their annotated locations for NP_001171423.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and initiates translation at a downstream start codon, and lacks an alternate in-frame exon in the 3' coding region compared to variant 1. The resulting protein (isoform 4) is shorter and has a distinct N-terminus compared to isoform 1.

Source sequence(s)

AK138977, AL671042

Consensus CDS

CCDS53000.1

UniProtKB/TrEMBL

Q3UTY5

Related

ENSMUSP00000111196.2, ENSMUST00000115534.8

Conserved Domains (2) summary

pfam00415
Location:151 → 201

RCC1; Regulator of chromosome condensation (RCC1) repeat

pfam13540
Location:85 → 114

RCC1_2; Regulator of chromosome condensation (RCC1) repeat
NM_001177953.1 → NP_001171424.1 X-linked retinitis pigmentosa GTPase regulator isoform 5

See identical proteins and their annotated locations for NP_001171424.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks exons in the 3' coding region and differs in the 3' coding region and UTR compared to variant 1. The resulting protein (isoform 5) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AK038652, AL671042

UniProtKB/TrEMBL

Q8CAJ5

Related

ENSMUST00000155734.8

Conserved Domains (2) summary

pfam00415
Location:93 → 139

RCC1; Regulator of chromosome condensation (RCC1) repeat

pfam13540
Location:180 → 209

RCC1_2; Regulator of chromosome condensation (RCC1) repeat
NM_001177954.1 → NP_001171425.1 X-linked retinitis pigmentosa GTPase regulator isoform 6

Status: VALIDATED

Description

Transcript Variant: This variant (6) lacks exons in the 3' coding region and differs in the 3' coding region and UTR compared to variant 1. The resulting protein (isoform 6) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AK081631, AL671042

Related

ENSMUST00000124744.2

Conserved Domains (2) summary

pfam00415
Location:93 → 139

RCC1; Regulator of chromosome condensation (RCC1) repeat

pfam13540
Location:180 → 209

RCC1_2; Regulator of chromosome condensation (RCC1) repeat
NM_011285.2 → NP_035415.1 X-linked retinitis pigmentosa GTPase regulator isoform 3

See identical proteins and their annotated locations for NP_035415.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the 3' coding region compared to variant 1. Isoform 3 is shorter compared to isoform 1.

Source sequence(s)

AF044677, AL671042

Consensus CDS

CCDS30014.1

UniProtKB/Swiss-Prot

Q9R0X5

UniProtKB/TrEMBL

A2ADP2

Related

ENSMUSP00000073106.5, ENSMUST00000073392.11

Conserved Domains (2) summary

pfam00415
Location:246 → 296

RCC1; Regulator of chromosome condensation (RCC1) repeat

pfam13540
Location:180 → 209

RCC1_2; Regulator of chromosome condensation (RCC1) repeat