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RPGR retinitis pigmentosa GTPase regulator [ Homo sapiens (human) ]

Gene ID: 6103, updated on 17-Jun-2019

Summary

Official Symbol
RPGRprovided by HGNC
Official Full Name
retinitis pigmentosa GTPase regulatorprovided by HGNC
Primary source
HGNC:HGNC:10295
See related
Ensembl:ENSG00000156313 MIM:312610
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CRD; RP3; COD1; PCDX; RP15; XLRP3; orf15; CORDX1
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 2.6), lung (RPKM 2.3) and 25 other tissues See more
Orthologs

Genomic context

See RPGR in Genome Data Viewer
Location:
Xp11.4
Exon count:
25
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) X NC_000023.11 (38269163..38327509, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (38128423..38186817, complement)

Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene synaptotagmin like 5 Neighboring gene microRNA 548aj-2 Neighboring gene sushi repeat containing protein X-linked Neighboring gene HNF4 motif-containing MPRA enhancer 122 Neighboring gene ornithine carbamoyltransferase Neighboring gene teratocarcinoma-derived growth factor 1 pseudogene 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Replication interactions

Interaction Pubs
Knockdown of retinitis pigmentosa GTPase regulator (RPGR) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
guanyl-nucleotide exchange factor activity IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular protein transport TAS
Traceable Author Statement
more info
PubMed 
intraciliary transport ISS
Inferred from Sequence or Structural Similarity
more info
 
response to stimulus IEA
Inferred from Electronic Annotation
more info
 
visual perception IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
Golgi apparatus IDA
Inferred from Direct Assay
more info
 
Golgi apparatus ISS
Inferred from Sequence or Structural Similarity
more info
 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
ciliary basal body ISS
Inferred from Sequence or Structural Similarity
more info
 
photoreceptor outer segment IDA
Inferred from Direct Assay
more info
PubMed 
sperm flagellum ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
X-linked retinitis pigmentosa GTPase regulator
Names
retinitis pigmentosa 15
retinitis pigmentosa 3 GTPase regulator

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_009553.1 RefSeqGene

    Range
    5001..63366
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_000328.3NP_000319.1  X-linked retinitis pigmentosa GTPase regulator isoform A

    See identical proteins and their annotated locations for NP_000319.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (A) uses an alternate splice site and contains multiple alternative exons in the 3' coding region, compared to variant C. The resulting isoform (A, also referred to as isoform 1) is shorter and has a distinct C-terminus, compared to isoform C.
    Source sequence(s)
    AL606748, BX644678, CA313540, U57629
    Consensus CDS
    CCDS14246.1
    UniProtKB/Swiss-Prot
    Q92834
    Related
    ENSP00000493468.1, ENST00000642395.1
    Conserved Domains (2) summary
    pfam00415
    Location:158205
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    pfam13540
    Location:142171
    RCC1_2; Regulator of chromosome condensation (RCC1) repeat
  2. NM_001034853.2NP_001030025.1  X-linked retinitis pigmentosa GTPase regulator isoform C

    See identical proteins and their annotated locations for NP_001030025.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (C) encodes the longest isoform (C).
    Source sequence(s)
    AL606748, BK005711, BP233620
    Consensus CDS
    CCDS35229.1
    UniProtKB/Swiss-Prot
    Q92834
    Related
    ENSP00000367766.2, ENST00000378505.7
    Conserved Domains (2) summary
    pfam00415
    Location:314360
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38312
    RCC1; Regulator of chromosome condensation (RCC1) repeat
  3. NM_001367245.1NP_001354174.1  X-linked retinitis pigmentosa GTPase regulator isoform D

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Conserved Domains (2) summary
    pfam00415
    Location:313359
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38311
    RCC1; Regulator of chromosome condensation (RCC1) repeat
  4. NM_001367246.1NP_001354175.1  X-linked retinitis pigmentosa GTPase regulator isoform E

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Conserved Domains (2) summary
    pfam00415
    Location:314342
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38312
    RCC1; Regulator of chromosome condensation (RCC1) repeat
  5. NM_001367247.1NP_001354176.1  X-linked retinitis pigmentosa GTPase regulator isoform F

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Conserved Domains (3) summary
    pfam00415
    Location:314360
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl26511
    Location:456688
    Neuromodulin_N; Gap junction protein N-terminal region
    cl27697
    Location:38312
    RCC1; Regulator of chromosome condensation (RCC1) repeat
  6. NM_001367248.1NP_001354177.1  X-linked retinitis pigmentosa GTPase regulator isoform G

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Conserved Domains (2) summary
    pfam00415
    Location:324370
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:48322
    RCC1; Regulator of chromosome condensation (RCC1) repeat
  7. NM_001367249.1NP_001354178.1  X-linked retinitis pigmentosa GTPase regulator isoform H

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Conserved Domains (2) summary
    pfam00415
    Location:313359
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38311
    RCC1; Regulator of chromosome condensation (RCC1) repeat
  8. NM_001367250.1NP_001354179.1  X-linked retinitis pigmentosa GTPase regulator isoform I

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Conserved Domains (3) summary
    pfam00415
    Location:313359
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl26511
    Location:455687
    Neuromodulin_N; Gap junction protein N-terminal region
    cl27697
    Location:38311
    RCC1; Regulator of chromosome condensation (RCC1) repeat
  9. NM_001367251.1NP_001354180.1  X-linked retinitis pigmentosa GTPase regulator isoform J

    Status: REVIEWED

    Source sequence(s)
    AL606748
    Conserved Domains (2) summary
    pfam00415
    Location:314342
    RCC1; Regulator of chromosome condensation (RCC1) repeat
    cl27697
    Location:38312
    RCC1; Regulator of chromosome condensation (RCC1) repeat

RNA

  1. NR_159803.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748
  2. NR_159804.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748
  3. NR_159805.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748
  4. NR_159806.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748
  5. NR_159807.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748, BC031624
  6. NR_159808.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL606748

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000023.11 Reference GRCh38.p13 Primary Assembly

    Range
    38269163..38327509 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001023582.1: Suppressed sequence

    Description
    NM_001023582.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
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