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Aliases for PRPF31 Gene

Aliases for PRPF31 Gene

  • Pre-MRNA Processing Factor 31 2 3 5
  • Serologically Defined Breast Cancer Antigen NY-BR-99 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
  • U4/U6 Small Nuclear Ribonucleoprotein Prp31 3
  • Pre-MRNA-Processing Factor 31 4
  • 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 Retinitis Pigmentosa 11 and Prpf31-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 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

Additional gene information for PRPF31 Gene

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

Genomics for PRPF31 Gene

Regulatory Elements for PRPF31 Gene

Enhancers for PRPF31 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH19H054199 1.9 FANTOM5 ENCODE dbSUPER 70.2 +90.3 90335 12.1 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D PRPF31 CNOT3 LENG8 LENG8-AS1 ZNF525 LILRB5 ZNF845 ZNF765 ENSG00000235681 RPS9
GH19H054186 1.4 ENCODE dbSUPER 48.6 +74.2 74246 6.8 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 PRPF31 ZNF665 LENG8 LENG8-AS1 CNOT3 ZNF845 ZNF525 ZNF677 ENSG00000269001 ENSG00000269288
GH19H053977 1.3 Ensembl ENCODE 51.1 -135.4 -135415 5.8 HDGF PKNOX1 SIN3A FEZF1 ZNF2 ZNF766 ZNF143 SP3 NFYC REST PRPF31 ZNF525 LENG8-AS1 ZNF160 ZNF845 ZNF665 ZNF761 ZNF347 LENG8 ENSG00000235681
GH19H054459 1.9 FANTOM5 Ensembl ENCODE dbSUPER 24.1 +350.5 350479 12.4 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF143 ZNF207 PAF1 SP3 LENG8-AS1 LENG8 CNOT3 PRPF31 ENSG00000267838 ENSG00000235681 LENG9 MYADM TPM3P6 TTYH1
GH19H053517 1.1 ENCODE 34.8 -595.8 -595762 4.8 PKNOX1 ARNT ARID4B SIN3A YY1 ZNF766 ZNF143 SP3 ZHX2 MXD4 ZNF137P LENG8-AS1 PRPF31 ZNF160 ZNF761 ZNF525 ZNF611 LENG8 ZNF665 ZNF677
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PRPF31 on UCSC Golden Path with GeneCards custom track

Promoters for PRPF31 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Locations for PRPF31 Gene

Genomic Locations for PRPF31 Gene
16,344 bases
Plus strand

Genomic View for PRPF31 Gene

Genes around PRPF31 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRPF31 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
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
    • F1T0A5
    • 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, SNU13, EFTUD2, SART1 and USP39. Interacts with a complex formed by SNU13 and U4 snRNA, but not with SNU13 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

Post-translational modifications for PRPF31 Gene

  • Ubiquitination at Lys417, Lys430, and Lys478
  • Modification sites at PhosphoSitePlus

Other Protein References for PRPF31 Gene

No data available for DME Specific Peptides for PRPF31 Gene

Domains & Families for PRPF31 Gene

Gene Families for PRPF31 Gene

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

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.
  • Belongs to the PRP31 family.
genes like me logo Genes that share domains with PRPF31: view

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:0003723 RNA binding IEA,IDA 22658674
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
genes like me logo Genes that share ontologies with PRPF31: view
genes like me logo Genes that share phenotypes with PRPF31: view

Human Phenotype Ontology for PRPF31 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PRPF31 Gene

MGI Knock Outs for PRPF31:

Animal Model Products

CRISPR Products

miRNA for PRPF31 Gene

miRTarBase miRNAs that target PRPF31

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

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 PRPF31 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PRPF31 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005684 U2-type spliceosomal complex IC 17412961
GO:0005687 U4 snRNP IDA 17412961
genes like me logo Genes that share ontologies with PRPF31: view

Pathways & Interactions for PRPF31 Gene

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

Pathways by source 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 TAS,IDA --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA --
GO:0048254 NOT snoRNA localization IMP 17636026
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:

CRISPR Products

Inhibitory RNA Products

Clone 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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for PRPF31 Gene

Protein tissue co-expression partners for PRPF31 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PRPF31 Gene:


SOURCE GeneReport for Unigene cluster for PRPF31 Gene:


mRNA Expression by UniProt/SwissProt for PRPF31 Gene:

Tissue specificity: Ubiquitously expressed.

Evidence on tissue expression from TISSUES for PRPF31 Gene

  • Nervous system(4.8)
  • Kidney(4.4)
  • Liver(4.3)
  • Eye(3.6)
  • Lung(3.3)
  • Intestine(2.4)
  • Skin(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PRPF31 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 PRPF31: view

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
(Pan troglodytes)
Mammalia PRPF31 33 34
  • 99.27 (n)
(Monodelphis domestica)
Mammalia PRPF31 34
  • 94 (a)
(Bos Taurus)
Mammalia PRPF31 33 34
  • 92.92 (n)
(Canis familiaris)
Mammalia PRPF31 33 34
  • 91.38 (n)
(Mus musculus)
Mammalia Prpf31 33 16 34
  • 89.58 (n)
(Rattus norvegicus)
Mammalia Prpf31 33
  • 88.98 (n)
(Ornithorhynchus anatinus)
Mammalia PRPF31 34
  • 75 (a)
(Anolis carolinensis)
Reptilia PRPF31 34
  • 95 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia prpf31 33
  • 75.16 (n)
Str.2964 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.5894 33
(Danio rerio)
Actinopterygii prpf31 33 34
  • 75.67 (n)
zgc66177 33
fruit fly
(Drosophila melanogaster)
Insecta Prp31 33 34
  • 65.03 (n)
CG6876 35
  • 63 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP012142 33
  • 53.9 (n)
(Caenorhabditis elegans)
Secernentea prp-31 33 34
  • 50.33 (n)
Y110A7A.8 35
  • 47 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP31 34 36
  • 24 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons emb1220 33
  • 50.84 (n)
(Oryza sativa)
Liliopsida Os04g0555400 33
  • 51.45 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9354 34
  • 59 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU02716 33
  • 50.04 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp31 33
  • 45.86 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.2747 33
Species where no ortholog for PRPF31 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)
  • 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
rs119475042 Retinitis pigmentosa 11 (RP11) [MIM:600138]
rs119475043 Retinitis pigmentosa 11 (RP11) [MIM:600138]

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

Variant ID Type Subtype PubMed ID
nsv953613 CNV deletion 24416366
nsv833877 CNV loss 17160897
nsv515623 CNV loss 19592680
nsv510773 CNV deletion 20534489
nsv470157 CNV loss 18288195
nsv2545 CNV insertion 18451855
nsv2543 CNV insertion 18451855
esv2718812 CNV deletion 23290073
esv1131677 CNV deletion 17803354

Variation tolerance for PRPF31 Gene

Residual Variation Intolerance Score: 12.3% 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

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

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

Disorders for PRPF31 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
retinitis pigmentosa 11
  • rp11
prpf31-related retinitis pigmentosa
  • retinitis pigmentosa 11
retinitis pigmentosa
  • retinitis pigmentosa 1
retinitis pigmentosa 18
  • rp18
- elite association - COSMIC cancer census association via MalaCards


  • 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:12444105, ECO:0000269 PubMed:12923864, ECO:0000269 PubMed:17412961, 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 EN … Bhattacharya SS (Molecular cell 2001) 2 3 4 22 60
  2. Retinitis pigmentosa: mutation analysis of RHO, PRPF31, RP1, and IMPDH1 genes in patients from India. (PMID: 18552984) Gandra M … Govindasamy K (Molecular vision 2008) 3 22 45 60
  3. Mutations in the gene coding for the pre-mRNA splicing factor, PRPF31, in patients with autosomal dominant retinitis pigmentosa. (PMID: 17325180) Waseem NH … Bhattacharya SS (Investigative ophthalmology & visual science 2007) 3 22 45 60
  4. Protein 61K, encoded by a gene (PRPF31) linked to autosomal dominant retinitis pigmentosa, is required for U4/U6*U5 tri-snRNP formation and pre-mRNA splicing. (PMID: 11867543) Makarova OV … Lührmann R (The EMBO journal 2002) 3 4 22 60
  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 45 60

Products for PRPF31 Gene

Sources for PRPF31 Gene

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