Free for academic non-profit institutions. Other users need a Commercial license

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
  • 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 Prpf3-Related Retinitis Pigmentosa. Among its related pathways are mRNA Splicing - Major Pathway and Gene Expression. GO annotations related to this gene include poly(A) RNA binding and 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

Enhancers for PRPF3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around PRPF3 on UCSC Golden Path with GeneCards custom track

Promoters for PRPF3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PRPF3 on UCSC Golden Path with GeneCards custom track

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

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

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 Lys 52
  • Modification sites at PhosphoSitePlus

Other Protein References for PRPF3 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PRPF3 Gene

Domains & Families 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.
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

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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 4
cytosol 3
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for PRPF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
GO:0016607 nuclear speck IEA --
GO:0043234 protein complex IEA --
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:0000375 RNA splicing, via transesterification reactions 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:

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 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, 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 expression patterns with PRPF3: view

Protein tissue co-expression partners for PRPF3 Gene

- Elite partner

Primer 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
VAR_016877 Retinitis pigmentosa 18 (RP18)
VAR_046735 Retinitis pigmentosa 18 (RP18)
rs12736964 - 150,324,978(+) CTGAA(A/C)CCATG nc-transcript-variant, reference, missense, utr-variant-5-prime
rs14654 -- 150,353,076(+) GTGAT(A/C)TCAGA nc-transcript-variant, utr-variant-3-prime
rs698914 -- 150,326,292(+) GTAGA(A/G)GTTTC intron-variant

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

Variant ID Type Subtype PubMed ID
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)

Relevant External Links for PRPF3 Gene

Human Gene Mutation Database (HGMD)

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: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 18
  • rp 18
prpf3-related retinitis pigmentosa
  • retinitis pigmentosa 18
retinitis pigmentosa
  • retinitis pigmentosa 1
  • blind spot area scotoma
- 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}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PRPF3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) 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. 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 67
  2. 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 23
  3. Splicing factor SPF30 bridges an interaction between the prespliceosome protein U2AF35 and tri-small nuclear ribonucleoprotein protein hPrp3. (PMID: 18211889) Little J.T. … Jurica M.S. (J. Biol. Chem. 2008) 3 23
  4. 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
  5. 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 23

Products for PRPF3 Gene

Sources for PRPF3 Gene