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Aliases for PRPF31 Gene

Aliases for PRPF31 Gene

  • Pre-MRNA Processing Factor 31 2 3
  • Serologically Defined Breast Cancer Antigen NY-BR-99 3 4
  • Pre-MRNA-Processing Factor 31 3 4
  • U4/U6 SnRNP 61 KDa Protein 3 4
  • Protein 61K 3 4
  • HPrp31 3 4
  • PRP31 3 4
  • PRP31 Pre-MRNA Processing Factor 31 Homolog (S. Cerevisiae) 2
  • PRP31 Pre-MRNA Processing Factor 31 Homolog (Yeast) 2
  • PRP31 Pre-MRNA Processing Factor 31 Homolog 3
  • NY-BR-99 3
  • SNRNP61 3
  • RP11 3

External Ids for PRPF31 Gene

Previous HGNC Symbols for PRPF31 Gene

  • RP11

Previous GeneCards Identifiers for PRPF31 Gene

  • GC19P055264
  • GC19P055043
  • GC19P059294
  • GC19P059310
  • GC19P054618
  • GC19P050934

Summaries for PRPF31 Gene

Entrez Gene Summary for PRPF31 Gene

  • This gene encodes a component of the spliceosome complex and is one of several retinitis pigmentosa-causing genes. When the gene product is added to the spliceosome complex, activation occurs.[provided by RefSeq, Jan 2009]

GeneCards Summary for PRPF31 Gene

PRPF31 (Pre-MRNA Processing Factor 31) is a Protein Coding gene. Diseases associated with PRPF31 include prpf31-related retinitis pigmentosa and retinitis pigmentosa 11. Among its related pathways are mRNA Splicing - Major Pathway. GO annotations related to this gene include poly(A) RNA binding and snRNP binding.

UniProtKB/Swiss-Prot for PRPF31 Gene

  • Involved in pre-mRNA splicing. Required for the assembly of the U4/U5/U6 tri-snRNP complex, one of the building blocks of the spliceosome.

Gene Wiki entry for PRPF31 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRPF31 Gene

Genomics for PRPF31 Gene

Regulatory Elements for PRPF31 Gene

Epigenetics Products

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

Genomic Location for PRPF31 Gene

54,115,376 bp from pter
54,131,719 bp from pter
16,344 bases
Plus strand

Genomic View for PRPF31 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for PRPF31 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRPF31 Gene

Proteins for PRPF31 Gene

  • Protein details for PRPF31 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    U4/U6 small nuclear ribonucleoprotein Prp31
    Protein Accession:
    Secondary Accessions:
    • E7ESA8
    • F1T0A4
    • Q17RB4
    • Q8N7F9
    • Q9H271
    • Q9Y439

    Protein attributes for PRPF31 Gene

    499 amino acids
    Molecular mass:
    55456 Da
    Quaternary structure:
    • 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 a complex formed by NHP2L1 and U4 snRNA, but not with NHP2L1 or U4 snRNA alone. Interacts with PRPF6/U5 snRNP-associated 102 kDa protein. Component of some MLL1/MLL complex, at least composed of the core components KMT2A/MLL1, ASH2L, HCFC1/HCF1, WDR5 and RBBP5, as well as the facultative components BAP18, CHD8, E2F6, HSP70, INO80C, KANSL1, LAS1L, MAX, MCRS1, MGA, KAT8/MOF, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9 and TEX10. Interacts (via its NLS) with CTNNBL1.

    Three dimensional structures from OCA and Proteopedia for PRPF31 Gene

    Alternative splice isoforms for PRPF31 Gene


neXtProt entry for PRPF31 Gene

Proteomics data for PRPF31 Gene at MOPED

Post-translational modifications for PRPF31 Gene

  • Ubiquitination at Lys 417, Lys 430, and Lys 478
  • Modification sites at PhosphoSitePlus

Other Protein References for PRPF31 Gene

Antibody Products

No data available for DME Specific Peptides for PRPF31 Gene

Domains & Families for PRPF31 Gene

Protein Domains for PRPF31 Gene

Graphical View of Domain Structure for InterPro Entry



  • Interacts with the snRNP via the Nop domain
  • Belongs to the PRP31 family.
  • Interacts with the snRNP via the Nop domain
  • The coiled coil domain is formed by two non-contiguous helices
  • Contains 1 Nop domain.
  • Belongs to the PRP31 family.
genes like me logo Genes that share domains with PRPF31: view

No data available for Gene Families for PRPF31 Gene

Function for PRPF31 Gene

Molecular function for PRPF31 Gene

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

Gene Ontology (GO) - Molecular Function for PRPF31 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21385873
GO:0030621 U4 snRNA binding IDA 16857676
GO:0030622 U4atac snRNA binding IDA 16857676
GO:0043021 ribonucleoprotein complex binding IDA 11867543
GO:0044822 poly(A) RNA binding IDA 22658674
genes like me logo Genes that share ontologies with PRPF31: view
genes like me logo Genes that share phenotypes with PRPF31: view

Animal Models for PRPF31 Gene

MGI Knock Outs for PRPF31:

Animal Model Products

miRNA for PRPF31 Gene

miRTarBase miRNAs that target PRPF31

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PRPF31

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PRPF31 Gene

Localization for PRPF31 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRPF31 Gene

Nucleus speckle. Nucleus, Cajal body. Note=Predominantly found in speckles and in Cajal bodies.

Subcellular locations from

Jensen Localization Image for PRPF31 Gene COMPARTMENTS Subcellular localization image for PRPF31 gene
Compartment Confidence
nucleus 1

Gene Ontology (GO) - Cellular Components for PRPF31 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005684 U2-type spliceosomal complex IC 17412961
GO:0005687 U4 snRNP IDA 17412961
GO:0005690 U4atac snRNP TAS 17412961
GO:0015030 Cajal body IDA 11867543
genes like me logo Genes that share ontologies with PRPF31: view

Pathways & Interactions for PRPF31 Gene

SuperPathways for PRPF31 Gene

Superpath Contained pathways
1 mRNA Splicing - Major Pathway
genes like me logo Genes that share pathways with PRPF31: view

Pathways by source for PRPF31 Gene

1 KEGG pathway for PRPF31 Gene

Gene Ontology (GO) - Biological Process for PRPF31 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000244 spliceosomal tri-snRNP complex assembly IMP 15257298
GO:0000398 mRNA splicing, via spliceosome IDA 11867543
genes like me logo Genes that share ontologies with PRPF31: view

No data available for SIGNOR curated interactions for PRPF31 Gene

Drugs & Compounds for PRPF31 Gene

No Compound Related Data Available

Transcripts for PRPF31 Gene

Unigene Clusters for PRPF31 Gene

PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae):
Representative Sequences:

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for PRPF31

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for PRPF31 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5 ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b
SP1: -
SP3: -

Relevant External Links for PRPF31 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PRPF31 Gene

mRNA expression in normal human tissues for PRPF31 Gene

Protein differential expression in normal tissues from HIPED for PRPF31 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (9.3) and Blymphocyte (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PRPF31 Gene

SOURCE GeneReport for Unigene cluster for PRPF31 Gene Hs.515598

mRNA Expression by UniProt/SwissProt for PRPF31 Gene

Tissue specificity: Ubiquitously expressed.
genes like me logo Genes that share expression patterns with PRPF31: view

Protein tissue co-expression partners for PRPF31 Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PRPF31 Gene

Orthologs for PRPF31 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRPF31 Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PRPF31 35
  • 92.92 (n)
  • 99.4 (a)
PRPF31 36
  • 99 (a)
(Canis familiaris)
Mammalia PRPF31 35
  • 91.38 (n)
  • 99.6 (a)
PRPF31 36
  • 100 (a)
(Mus musculus)
Mammalia Prpf31 35
  • 89.58 (n)
  • 99 (a)
Prpf31 16
Prpf31 36
  • 99 (a)
(Pan troglodytes)
Mammalia PRPF31 35
  • 99.27 (n)
  • 100 (a)
PRPF31 36
  • 100 (a)
(Rattus norvegicus)
Mammalia Prpf31 35
  • 88.98 (n)
  • 99.4 (a)
(Monodelphis domestica)
Mammalia PRPF31 36
  • 94 (a)
(Ornithorhynchus anatinus)
Mammalia PRPF31 36
  • 75 (a)
(Anolis carolinensis)
Reptilia PRPF31 36
  • 95 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia prpf31 35
  • 75.16 (n)
  • 92.29 (a)
Str.2964 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.5894 35
(Danio rerio)
Actinopterygii prpf31 35
  • 75.67 (n)
  • 85.53 (a)
zgc66177 35
prpf31 36
  • 82 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG6876 37
  • 63 (a)
Prp31 35
  • 65.03 (n)
  • 63.39 (a)
Prp31 36
  • 60 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012142 35
  • 53.9 (n)
  • 48.27 (a)
(Caenorhabditis elegans)
Secernentea Y110A7A.8 37
  • 47 (a)
prp-31 35
  • 50.33 (n)
  • 47.48 (a)
prp-31 36
  • 45 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP31 36
  • 24 (a)
PRP31 38
thale cress
(Arabidopsis thaliana)
eudicotyledons emb1220 35
  • 50.84 (n)
  • 47.95 (a)
(Oryza sativa)
Liliopsida Os04g0555400 35
  • 51.45 (n)
  • 49.31 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2747 35
bread mold
(Neurospora crassa)
Ascomycetes NCU02716 35
  • 50.04 (n)
  • 42.03 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp31 35
  • 45.86 (n)
  • 42.79 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9354 36
  • 59 (a)
Species with no ortholog for PRPF31:
  • 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)
  • chicken (Gallus gallus)
  • 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 PRPF31 Gene

Gene Tree for PRPF31 (if available)
Gene Tree for PRPF31 (if available)

Paralogs for PRPF31 Gene

(1) SIMAP similar genes for PRPF31 Gene using alignment to 10 proteins:

genes like me logo Genes that share paralogs with PRPF31: view

No data available for Paralogs for PRPF31 Gene

Variants for PRPF31 Gene

Sequence variations from dbSNP and Humsavar for PRPF31 Gene

SNP ID Clin Chr 19 pos Sequence Context AA Info Type MAF
rs71195728 -- 54,128,505(+) GGGGG(-/A/T)GGAGG intron-variant
rs119475042 Pathogenic 54,123,867(+) TCATC(A/C/G)CACCC missense, reference, nc-transcript-variant
rs119475043 Pathogenic 54,123,802(+) CATGG(A/C)GCTGG missense, reference, nc-transcript-variant
rs144738703 Pathogenic 54,123,836(+) ATCTA(A/C/G/T)GAGTA reference, synonymous-codon, nc-transcript-variant
rs373578680 Uncertain significance 54,118,427(+) CAAGA(C/T)CATCG reference, missense, nc-transcript-variant

Structural Variations from Database of Genomic Variants (DGV) for PRPF31 Gene

Variant ID Type Subtype PubMed ID
esv2718812 CNV Deletion 23290073
nsv833877 CNV Loss 17160897
nsv510773 CNV Loss 20534489
nsv470157 CNV Loss 18288195
dgv4001n71 CNV Loss 21882294
nsv515623 CNV Loss 19592680
nsv2543 CNV Insertion 18451855
dgv4002n71 CNV Loss 21882294
nsv2545 CNV Insertion 18451855
esv1131677 CNV Deletion 17803354

Variation tolerance for PRPF31 Gene

Residual Variation Intolerance Score: 12.29% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.42; 9.19% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PRPF31 Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRPF31 Gene

Disorders for PRPF31 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PRPF31 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, NovoSeek, and GeneCards

Disorder Aliases PubMed IDs
prpf31-related retinitis pigmentosa
  • rp11
retinitis pigmentosa 11
  • rp 11
retinitis pigmentosa
  • retinitis pigmentosa 1
retinitis pigmentosa autosomal recessive
  • retinitis pigmentosa
- elite association


  • Retinitis pigmentosa 11 (RP11) [MIM:600138]: 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:11545739, ECO:0000269 PubMed:12923864, ECO:0000269 PubMed:8808602}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PRPF31

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 PRPF31: view

No data available for Genatlas for PRPF31 Gene

Publications for PRPF31 Gene

  1. A human homolog of yeast pre-mRNA splicing gene, PRP31, underlies autosomal dominant retinitis pigmentosa on chromosome 19q13.4 (RP11). (PMID: 11545739) Vithana E.N. … Bhattacharya S.S. (Mol. Cell 2001) 2 23 67
  2. Risk of ovarian cancer and inherited variants in relapse-associated genes. (PMID: 20111712) Peedicayil A. … Goode E.L. (PLoS ONE 2010) 23 67
  3. Study of gene-targeted mouse models of splicing factor gene Prpf31 implicated in human autosomal dominant retinitis pigmentosa (RP). (PMID: 19578015) Bujakowska K. … Bhattacharya S.S. (Invest. Ophthalmol. Vis. Sci. 2009) 23 67
  4. Breakpoint characterization of a novel approximately 59 kb genomic deletion on 19q13.42 in autosomal-dominant retinitis pigmentosa with incomplete penetrance. (PMID: 19050727) KAPhn L. … Golovleva I. (Eur. J. Hum. Genet. 2009) 23 67
  5. Identification and functional characterization of a novel splicing mutation in RP gene PRPF31. (PMID: 18177735) Liu J.Y. … Wang Q.K. (Biochem. Biophys. Res. Commun. 2008) 23 67

Products for PRPF31 Gene

Sources for PRPF31 Gene

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