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Aliases for PRPF3 Gene

Aliases for PRPF3 Gene

  • Pre-MRNA Processing Factor 3 2 3
  • HPRP3 3 4 6
  • Pre-MRNA-Splicing Factor 3 3 4
  • U4/U6 SnRNP 90 KDa Protein 3 4
  • RP18 3 6
  • PRP3 3 4
  • PRP3 Pre-MRNA Processing Factor 3 Homolog (S. Cerevisiae) 2
  • PRP3 Pre-MRNA Processing Factor 3 Homolog (Yeast) 2
  • Retinitis Pigmentosa 18 (Autosomal Dominant) 2
  • U4/U6 Small Nuclear Ribonucleoprotein Prp3 3
  • PRP3 Pre-MRNA Processing Factor 3 Homolog 3
  • U4/U6-Associated RNA Splicing Factor 3
  • SNRNP90 3
  • HPRP3P 3
  • Prp3p 3

External Ids for PRPF3 Gene

Previous HGNC Symbols for PRPF3 Gene

  • RP18

Previous GeneCards Identifiers for PRPF3 Gene

  • GC01P147510
  • GC01P147107
  • GC01P148560
  • GC01P150293
  • GC01P121672

Summaries for PRPF3 Gene

Entrez Gene Summary for PRPF3 Gene

  • The removal of introns from nuclear pre-mRNAs occurs on complexes called spliceosomes, which are made up of 4 small nuclear ribonucleoprotein (snRNP) particles and an undefined number of transiently associated splicing factors. This gene product is one of several proteins that associate with U4 and U6 snRNPs. Mutations in this gene are associated with retinitis pigmentosa-18. [provided by RefSeq, Jul 2008]

GeneCards Summary for PRPF3 Gene

PRPF3 (Pre-MRNA Processing Factor 3) is a Protein Coding gene. Diseases associated with PRPF3 include retinitis pigmentosa 18 and prpf3-related retinitis pigmentosa. Among its related pathways are Spliceosome and mRNA Splicing - Major Pathway. GO annotations related to this gene include identical protein binding.

UniProtKB/Swiss-Prot for PRPF3 Gene

  • Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.

Gene Wiki entry for PRPF3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRPF3 Gene

Genomics for PRPF3 Gene

Regulatory Elements for PRPF3 Gene

Epigenetics Products

  • DNA Methylation CpG Assay Predesigned for Pyrosequencing in human,mouse,rat

Genomic Location for PRPF3 Gene

150,321,476 bp from pter
150,353,228 bp from pter
31,753 bases
Plus strand

Genomic View for PRPF3 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PRPF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRPF3 Gene

Proteins for PRPF3 Gene

  • Protein details for PRPF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    U4/U6 small nuclear ribonucleoprotein Prp3
    Protein Accession:
    Secondary Accessions:
    • B4DSY9
    • O43446
    • Q5VT54

    Protein attributes for PRPF3 Gene

    683 amino acids
    Molecular mass:
    77529 Da
    Quaternary structure:
    • Interacts directly with PRPF4. Part of a heteromeric complex containing PPIH, PRPF3 and PRPF4 that is stable in the absence of RNA. Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, SNRNP40, DDX23, CD2BP2, PPIH, NHP2L1, EFTUD2, SART1 and USP39. Interacts with SART3; the interaction is direct and recruits the deubiquitinase USP4 to PRPF3. Interacts with PRPF19. Interacts (Lys-63-linked polyubiquitinated) with PRPF8 (via the MPN (JAB/Mov34) domain); may stabilize the U4/U6-U5 tri-snRNP complex.

    Three dimensional structures from OCA and Proteopedia for PRPF3 Gene

    Alternative splice isoforms for PRPF3 Gene


neXtProt entry for PRPF3 Gene

Proteomics data for PRPF3 Gene at MOPED

Post-translational modifications for PRPF3 Gene

  • Ubiquitinated. Undergoes Lys-63-linked polyubiquitination by PRPF19 and deubiquitination by USP4. Lys-63-linked ubiquitination increases the affinity for PRPF8 and may regulate the assembly of the U4/U6-U5 tri-snRNP complex.
  • Ubiquitination at Lys52
  • Modification sites at PhosphoSitePlus

Other Protein References for PRPF3 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

No data available for DME Specific Peptides for PRPF3 Gene

Domains for PRPF3 Gene

Protein Domains for PRPF3 Gene

Suggested Antigen Peptide Sequences for PRPF3 Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 PWI domain.
  • Contains 1 PWI domain.
genes like me logo Genes that share domains with PRPF3: view

No data available for Gene Families for PRPF3 Gene

Function for PRPF3 Gene

Molecular function for PRPF3 Gene

UniProtKB/Swiss-Prot Function:
Participates in pre-mRNA splicing. Part of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.

Gene Ontology (GO) - Molecular Function for PRPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 15314151
GO:0042802 identical protein binding IPI 22365833
GO:0044822 poly(A) RNA binding IDA 22681889
genes like me logo Genes that share ontologies with PRPF3: view

Phenotypes for PRPF3 Gene

genes like me logo Genes that share phenotypes with PRPF3: view

Animal Model Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PRPF3

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for PRPF3 Gene

Localization for PRPF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRPF3 Gene

Nucleus speckle. Note=Colocalizes with spliceosomal snRNPs.

Subcellular locations from

Jensen Localization Image for PRPF3 Gene COMPARTMENTS Subcellular localization image for PRPF3 gene
Compartment Confidence
nucleus 5
cytosol 3
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PRPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 20595234
GO:0005654 nucleoplasm IDA --
GO:0005681 spliceosomal complex NAS 9328476
GO:0005737 cytoplasm IDA --
GO:0015030 Cajal body IDA 15257298
genes like me logo Genes that share ontologies with PRPF3: view

Pathways for PRPF3 Gene

SuperPathways for PRPF3 Gene

Superpath Contained pathways
1 Spliceosome
2 mRNA Splicing - Major Pathway
genes like me logo Genes that share pathways with PRPF3: view

Pathways by source for PRPF3 Gene

1 BioSystems pathway for PRPF3 Gene
1 KEGG pathway for PRPF3 Gene

Gene Ontology (GO) - Biological Process for PRPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000244 spliceosomal tri-snRNP complex assembly IDA 20595234
GO:0000375 RNA splicing, via transesterification reactions TAS 9328476
GO:0000398 mRNA splicing, via spliceosome NAS 9328476
GO:0006397 mRNA processing TAS 9328476
GO:0008380 RNA splicing TAS 9328476
genes like me logo Genes that share ontologies with PRPF3: view

Transcripts for PRPF3 Gene

Unigene Clusters for PRPF3 Gene

PRP3 pre-mRNA processing factor 3 homolog (S. cerevisiae):
Representative Sequences:

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PRPF3

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRPF3 Gene

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

Relevant External Links for PRPF3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PRPF3 Gene

mRNA expression in normal human tissues for PRPF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues for PRPF3 Gene

This gene is overexpressed in Cervix (44.8).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for PRPF3 Gene

SOURCE GeneReport for Unigene cluster for PRPF3 Gene Hs.11776

mRNA Expression by UniProt/SwissProt for PRPF3 Gene

Tissue specificity: Highly expressed in retina, liver, kidney and blood. Detected at lower levels in heart and brain.
genes like me logo Genes that share expressions with PRPF3: view

Expression partners for PRPF3 Gene

* - Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA differential expression in normal tissues for PRPF3 Gene

Orthologs for PRPF3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRPF3 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PRPF3 35
  • 94.53 (n)
  • 99.56 (a)
PRPF3 36
  • 100 (a)
(Canis familiaris)
Mammalia PRPF3 35
  • 95.17 (n)
  • 100 (a)
PRPF3 36
  • 100 (a)
(Mus musculus)
Mammalia Prpf3 35
  • 92.19 (n)
  • 99.56 (a)
Prpf3 16
Prpf3 36
  • 100 (a)
(Pan troglodytes)
Mammalia PRPF3 35
  • 99.71 (n)
  • 100 (a)
PRPF3 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Prpf3 35
  • 91.53 (n)
  • 99.35 (a)
(Monodelphis domestica)
Mammalia PRPF3 36
  • 98 (a)
(Ornithorhynchus anatinus)
Mammalia PRPF3 36
  • 66 (a)
(Gallus gallus)
Aves PRPF3 35
  • 80.82 (n)
  • 94.58 (a)
PRPF3 36
  • 95 (a)
(Anolis carolinensis)
Reptilia PRPF3 36
  • 93 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia prpf3 35
  • 77.89 (n)
  • 87.44 (a)
Str.6871 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.5815 35
(Danio rerio)
Actinopterygii Dr.6366 35
prpf3 35
  • 68.24 (n)
  • 72.71 (a)
prpf3 36
  • 73 (a)
prpf3 36
  • 73 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004682 35
  • 56.43 (n)
  • 55.38 (a)
fruit fly
(Drosophila melanogaster)
Insecta Prp3 35
  • 57.29 (n)
  • 56.65 (a)
CG7757 36
  • 51 (a)
(Caenorhabditis elegans)
Secernentea prp-3 35
  • 52.06 (n)
  • 43.43 (a)
prp-3 36
  • 37 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP3 36
  • 25 (a)
PRP3 38
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G28060 35
  • 47.98 (n)
  • 37.81 (a)
(Oryza sativa)
Liliopsida Os09g0249600 35
  • 50.93 (n)
  • 41.85 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3638 35
bread mold
(Neurospora crassa)
Ascomycetes NCU01637 35
  • 46.98 (n)
  • 38.89 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp3 35
  • 48.81 (n)
  • 41.38 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9533 36
  • 54 (a)
Species with no ortholog for PRPF3:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • 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 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PRPF3 Gene

Gene Tree for PRPF3 (if available)
Gene Tree for PRPF3 (if available)

Paralogs for PRPF3 Gene Pseudogenes for PRPF3 Gene

genes like me logo Genes that share paralogs with PRPF3: view

No data available for Paralogs for PRPF3 Gene

Variants for PRPF3 Gene

Sequence variations from dbSNP and Humsavar for PRPF3 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type MAF
rs55973252 -- 150,347,416(+) ATAAA(C/T)TGAAA intron-variant
rs55736278 -- 150,342,647(+) CCTCC(C/T)GAGTA intron-variant
rs41300865 -- 150,352,755(+) ATGTT(A/G)CTAGG intron-variant
rs35415059 -- 150,350,206(+) ATTTC(-/T)TTTTT intron-variant
rs35347210 -- 150,347,501(+) CGAGG(C/T)GAGCA intron-variant

Structural Variations from Database of Genomic Variants (DGV) for PRPF3 Gene

Variant ID Type Subtype PubMed ID
nsv831548 CNV Loss 17160897

Relevant External Links for PRPF3 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRPF3 Gene

Disorders for PRPF3 Gene

(1) OMIM Diseases for PRPF3 Gene (607301)


  • Retinitis pigmentosa 18 (RP18) [MIM:601414]: 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:11773002, ECO:0000269 PubMed:12714658}. Note=The disease is caused by mutations affecting the gene represented in this entry.

(2) University of Copenhagen DISEASES for PRPF3 Gene

(1) Novoseek inferred disease relationships for PRPF3 Gene

Disease -log(P) Hits PubMed IDs
retinitis pigmentosa 80.6 6

Relevant External Links for PRPF3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with PRPF3: view

No data available for Genatlas for PRPF3 Gene

Publications for PRPF3 Gene

  1. Mutations in HPRP3, a third member of pre-mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa. (PMID: 11773002) Chakarova C.F. … Bhattacharya S.S. (Hum. Mol. Genet. 2002) 3 4 23
  2. Mutations in the pre-mRNA splicing-factor genes PRPF3, PRPF8, and PRPF31 in Spanish families with autosomal dominant retinitis pigmentosa. (PMID: 12714658) Martinez-Gimeno M. … Carballo M. (Invest. Ophthalmol. Vis. Sci. 2003) 3 4 23
  3. Mutation in the splicing factor Hprp3p linked to retinitis pigmentosa impairs interactions within the U4/U6 snRNP complex. (PMID: 17932117) Gonzalez-Santos J.M. … Hu J. (Hum. Mol. Genet. 2008) 3 4 23
  4. Identification and characterization of human genes encoding Hprp3p and Hprp4p, interacting components of the spliceosome. (PMID: 9328476) Wang A. … Hu J. (Hum. Mol. Genet. 1997) 3 4 23
  5. Clinical features of a Japanese family with autosomal dominant retinitis pigmentosa associated with a Thr494Met mutation in the HPRP3 gene. (PMID: 15085354) Wada Y. … Tamai M. (Graefes Arch. Clin. Exp. Ophthalmol. 2004) 3 23

Products for PRPF3 Gene

Sources for PRPF3 Gene

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