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Aliases for PRPF3 Gene

Aliases for PRPF3 Gene

  • Pre-MRNA Processing Factor 3 2 3 5
  • Pre-MRNA-Splicing Factor 3 3 4
  • U4/U6 SnRNP 90 KDa Protein 3 4
  • HPRP3 3 4
  • 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
  • RP18 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 Retinitis Pigmentosa. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. Gene Ontology (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

Additional gene information for PRPF3 Gene

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

Genomics for PRPF3 Gene

GeneHancer (GH) Regulatory Elements for PRPF3 Gene

Promoters and enhancers for PRPF3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01I149883 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 137.4 -434.8 -434773 5.9 CLOCK MLX ZFP64 FEZF1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 HIST2H2AB BOLA1 GC01M149896 HIST2H2AC HIST2H2BE PRPF3 SF3B4 UBE2D3P3 ARNT GOLPH3L
GH01I150232 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 110.1 -86.3 -86340 4.8 CLOCK MLX DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 ANP32E GC01P150237 RNU2-17P SETDB1 PRPF3 PIP5K1A GABPB2 SF3B4 ARNT UBE2D3P3
GH01I151068 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 90.3 +749.0 749010 3.3 CLOCK FEZF1 IRF4 YY1 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 SP3 GABPB2 CDC42SE1 PRPF3 SETDB1 PI4KB PIP5K1A MRPL9 UBE2D3P3 ARNT CTSK
GH01I150969 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 67.1 +653.5 653481 10.6 CLOCK MLX ZFP64 DMAP1 YY1 E2F8 ZNF143 SP3 SSRP1 GLIS1 CERS2 ENSG00000231073 PRPF3 SETDB1 ZNF687 HORMAD1 PIP5K1A ARNT GOLPH3L PI4KB
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PRPF3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRPF3 gene promoter:

Genomic Locations for PRPF3 Gene

Genomic Locations for PRPF3 Gene
31,753 bases
Plus strand

Genomic View for PRPF3 Gene

Genes around PRPF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRPF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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, SNU13, 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

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

No data available for DME Specific Peptides for PRPF3 Gene

Domains & Families for PRPF3 Gene

Gene Families for PRPF3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PRPF3 Gene

Suggested Antigen Peptide Sequences for PRPF3 Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for PRPF3 Gene

Gene Ontology (GO) - Molecular Function for PRPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA,HDA 22681889
GO:0005515 protein binding IPI 15314151
GO:0042802 identical protein binding IPI 22365833
genes like me logo Genes that share ontologies with PRPF3: view
genes like me logo Genes that share phenotypes with PRPF3: view

Human Phenotype Ontology for PRPF3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA 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

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PRPF3 gene
Compartment Confidence
nucleus 5
cytosol 5
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PRPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus TAS,IDA 20595234
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex NAS 9328476
GO:0005829 cytosol IDA --
GO:0015030 Cajal body IDA 15257298
genes like me logo Genes that share ontologies with PRPF3: view

Pathways & Interactions for PRPF3 Gene

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

Pathways by source for PRPF3 Gene

1 KEGG pathway for PRPF3 Gene

SIGNOR curated interactions for PRPF3 Gene

Is activated by:

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 TAS --
GO:0006397 mRNA processing TAS 9328476
GO:0008380 RNA splicing TAS 9328476
genes like me logo Genes that share ontologies with PRPF3: view

Drugs & Compounds for PRPF3 Gene

No Compound Related Data Available

Transcripts for PRPF3 Gene

Unigene Clusters for PRPF3 Gene

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

CRISPR Products

Inhibitory RNA 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 from GTEx, Illumina, BioGPS, and CGAP SAGE for PRPF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PRPF3 Gene

This gene is overexpressed in Cervix (44.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PRPF3 Gene

Protein tissue co-expression partners for PRPF3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PRPF3 Gene:


SOURCE GeneReport for Unigene cluster for PRPF3 Gene:


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.

Evidence on tissue expression from TISSUES for PRPF3 Gene

  • Eye(4.5)
  • Liver(4.3)
  • Skin(4.3)
  • Nervous system(3.7)
  • Saliva(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PRPF3 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • immune
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • head
  • middle ear
  • nose
  • outer ear
  • skull
  • penis
  • testicle
  • blood
  • blood vessel
  • peripheral nervous system
  • red blood cell
  • skin
genes like me logo Genes that share expression patterns with PRPF3: view

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
(Pan troglodytes)
Mammalia PRPF3 33 34
  • 99.71 (n)
(Monodelphis domestica)
Mammalia PRPF3 34
  • 98 (a)
(Canis familiaris)
Mammalia PRPF3 33 34
  • 95.17 (n)
(Bos Taurus)
Mammalia PRPF3 33 34
  • 94.53 (n)
(Mus musculus)
Mammalia Prpf3 33 16 34
  • 92.19 (n)
(Rattus norvegicus)
Mammalia Prpf3 33
  • 91.53 (n)
(Ornithorhynchus anatinus)
Mammalia PRPF3 34
  • 66 (a)
(Gallus gallus)
Aves PRPF3 33 34
  • 80.82 (n)
(Anolis carolinensis)
Reptilia PRPF3 34
  • 93 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia prpf3 33
  • 77.89 (n)
Str.6871 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.5815 33
(Danio rerio)
Actinopterygii prpf3 33 34 34
  • 68.24 (n)
Dr.6366 33
fruit fly
(Drosophila melanogaster)
Insecta Prp3 33
  • 57.29 (n)
CG7757 34
  • 51 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004682 33
  • 56.43 (n)
(Caenorhabditis elegans)
Secernentea prp-3 33 34
  • 52.06 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP3 34 36
  • 25 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT1G28060 33
  • 47.98 (n)
(Oryza sativa)
Liliopsida Os09g0249600 33
  • 50.93 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9533 34
  • 54 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp3 33
  • 48.81 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01637 33
  • 46.98 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3638 33
Species where no ortholog for PRPF3 was found in the sources mined by GeneCards:
  • 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 Variation AA Info Type
rs116427288 likely-benign, Retinitis Pigmentosa, Dominant 150,346,396(+) C/T genic_downstream_transcript_variant, intron_variant
rs121434241 pathogenic, Retinitis pigmentosa 18, Retinitis pigmentosa 18 (RP18) [MIM:601414] 150,344,216(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs121434242 pathogenic, Retinitis pigmentosa 18, Retinitis pigmentosa 18 (RP18) [MIM:601414] 150,344,212(+) C/T coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs121434243 pathogenic, Retinitis pigmentosa 18 150,344,201(+) C/A coding_sequence_variant, genic_downstream_transcript_variant, missense_variant, non_coding_transcript_variant
rs368160043 likely-benign, Retinitis Pigmentosa, Dominant 150,353,133(+) G/A 3_prime_UTR_variant, genic_downstream_transcript_variant, non_coding_transcript_variant

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

Variant ID Type Subtype PubMed ID
nsv479267 CNV novel sequence insertion 20440878
nsv831548 CNV loss 17160897

Variation tolerance for PRPF3 Gene

Residual Variation Intolerance Score: 15.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.59; 12.61% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRPF3 Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for PRPF3 Gene

MalaCards: The human disease database

(5) MalaCards diseases for PRPF3 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search PRPF3 in MalaCards View complete list of genes associated with diseases


  • 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, ECO:0000269 PubMed:17932117}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PRPF3

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PRPF3: view

No data available for Genatlas for PRPF3 Gene

Publications for PRPF3 Gene

  1. Mutation in the splicing factor Hprp3p linked to retinitis pigmentosa impairs interactions within the U4/U6 snRNP complex. (PMID: 17932117) Gonzalez-Santos JM … Hu J (Human molecular genetics 2008) 3 4 22 58
  2. Mutations in the pre-mRNA splicing-factor genes PRPF3, PRPF8, and PRPF31 in Spanish families with autosomal dominant retinitis pigmentosa. (PMID: 12714658) Martínez-Gimeno M … Carballo M (Investigative ophthalmology & visual science 2003) 3 4 22 58
  3. Mutations in HPRP3, a third member of pre-mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa. (PMID: 11773002) Chakarova CF … Bhattacharya SS (Human molecular genetics 2002) 3 4 22 58
  4. Identification and characterization of human genes encoding Hprp3p and Hprp4p, interacting components of the spliceosome. (PMID: 9328476) Wang A … Hu J (Human molecular genetics 1997) 3 4 22 58
  5. Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip. (PMID: 20801516) Booij JC … Florijn RJ (Ophthalmology 2011) 3 44 58

Products for PRPF3 Gene

Sources for PRPF3 Gene

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