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Aliases for PRPF6 Gene

Aliases for PRPF6 Gene

  • Pre-MRNA Processing Factor 6 2 3 5
  • U5 SnRNP-Associated 102 KDa Protein 3 4
  • U5-102 KDa Protein 3 4
  • PRP6 Homolog 3 4
  • C20orf14 3 4
  • ANT-1 3 4
  • P102 U5 Small Nuclear Ribonucleoprotein Particle-Binding Protein 3
  • Androgen Receptor N-Terminal Domain Transactivating Protein-1 3
  • Putative Mitochondrial Outer Membrane Protein Import Receptor 3
  • Androgen Receptor N-Terminal Domain-Transactivating Protein 1 4
  • PRP6 Pre-MRNA Processing Factor 6 Homolog (S. Cerevisiae) 2
  • PRP6 Pre-MRNA Processing Factor 6 Homolog (Yeast) 2
  • PRP6 Pre-MRNA Processing Factor 6 Homolog 3
  • Chromosome 20 Open Reading Frame 14 2
  • Pre-MRNA-Processing Factor 6 3
  • SNRNP102 3
  • U5-102K 3
  • HPrp6 3
  • ANT1 3
  • Prp6 3
  • RP60 3
  • TOM 3

External Ids for PRPF6 Gene

Previous HGNC Symbols for PRPF6 Gene

  • C20orf14

Previous GeneCards Identifiers for PRPF6 Gene

  • GC20P062083
  • GC20P062612
  • GC20P059347

Summaries for PRPF6 Gene

Entrez Gene Summary for PRPF6 Gene

  • The protein encoded by this gene appears to be involved in pre-mRNA splicing, possibly acting as a bridging factor between U5 and U4/U6 snRNPs in formation of the spliceosome. The encoded protein also can bind androgen receptor, providing a link between transcriptional activation and splicing. [provided by RefSeq, Jul 2008]

GeneCards Summary for PRPF6 Gene

PRPF6 (Pre-MRNA Processing Factor 6) is a Protein Coding gene. Diseases associated with PRPF6 include Retinitis Pigmentosa 60 and Retinitis Pigmentosa. Among its related pathways are mRNA Splicing - Major Pathway and mRNA Splicing - Minor Pathway. Gene Ontology (GO) annotations related to this gene include transcription coactivator activity.

UniProtKB/Swiss-Prot for PRPF6 Gene

  • Involved in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex, one of the building blocks of the spliceosome. Enhances dihydrotestosterone-induced transactivation activity of AR, as well as dexamethasone-induced transactivation activity of NR3C1, but does not affect estrogen-induced transactivation.

Gene Wiki entry for PRPF6 Gene

Additional gene information for PRPF6 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRPF6 Gene

Genomics for PRPF6 Gene

GeneHancer (GH) Regulatory Elements for PRPF6 Gene

Promoters and enhancers for PRPF6 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
GH20J063977 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 674.2 -1.3 -1265 4.8 MLX ZFP64 YBX1 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 PRPF6 SAMD10 C20orf204 GMEB2 CICP4 RTEL1 ZNF512B
GH20J063863 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 48.2 -116.2 -116197 3.6 MLX ZFP64 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 DNAJC5 ENSG00000268858 TPD52L2 DIDO1 GMEB2 PRPF6 CICP4 RTEL1 MIR647 ARFRP1
GH20J063519 Promoter/Enhancer 2.4 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 26.7 -459.6 -459613 4 HDGF PKNOX1 FOXA2 NEUROD1 SIN3A ZBTB7B YY1 POLR2B ZNF143 ZNF207 PPDPF GC20M063514 DIDO1 CICP4 GMEB2 PRPF6 RTEL1 MIR647 ARFRP1 UCKL1
GH20J064254 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 25.4 +274.9 274910 2.2 FOXA2 ZFP64 ARID4B SIN3A DMAP1 ZBTB7B YY1 SLC30A9 ZNF207 ZNF143 PCMTD2 GMEB2 PRPF6 RTEL1 CICP4 ARFRP1 TNFRSF6B UCKL1 SAMD10 GC20P064253
GH20J064038 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 25.6 +59.4 59396 4.7 ZFP64 ARID4B SIN3A DMAP1 ZNF2 SLC30A9 ZNF207 ZNF143 DEK PAF1 TCEA2 GMEB2 PRPF6 ENSG00000237371 C20orf204 RTEL1 ARFRP1 TNFRSF6B YTHDF1 CICP4
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRPF6 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRPF6 gene promoter:
  • Nkx2-5
  • HFH-1
  • Lmo2
  • c-Myb
  • HNF-4alpha2
  • HNF-4alpha1
  • STAT1beta
  • STAT1
  • STAT1alpha
  • LUN-1

Genomic Locations for PRPF6 Gene

Genomic Locations for PRPF6 Gene
52,032 bases
Plus strand
52,023 bases
Plus strand

Genomic View for PRPF6 Gene

Genes around PRPF6 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRPF6 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRPF6 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRPF6 Gene

Proteins for PRPF6 Gene

  • Protein details for PRPF6 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Pre-mRNA-processing factor 6
    Protein Accession:
    Secondary Accessions:
    • B2RAR5
    • B3KMC6
    • O95109
    • Q5VXS5
    • Q9H3Z1
    • Q9H4T9
    • Q9H4U8
    • Q9NTE6

    Protein attributes for PRPF6 Gene

    941 amino acids
    Molecular mass:
    106925 Da
    Quaternary structure:
    • Associates with the U5 snRNP particle. 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, LSm proteins LSm2-8 and Sm proteins. Interacts with ARAF1. Identified in the spliceosome C complex. Interacts with AR and NR3C1, but not ESR1, independently of the presence of hormones.

    Three dimensional structures from OCA and Proteopedia for PRPF6 Gene

    Alternative splice isoforms for PRPF6 Gene


neXtProt entry for PRPF6 Gene

Post-translational modifications for PRPF6 Gene

  • Ubiquitination at posLast=775775 and posLast=618618
  • Modification sites at PhosphoSitePlus

Other Protein References for PRPF6 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PRPF6 Gene

Domains & Families for PRPF6 Gene

Gene Families for PRPF6 Gene

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

Suggested Antigen Peptide Sequences for PRPF6 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PRPF6: view

No data available for UniProtKB/Swiss-Prot for PRPF6 Gene

Function for PRPF6 Gene

Molecular function for PRPF6 Gene

UniProtKB/Swiss-Prot Function:
Involved in pre-mRNA splicing as component of the U4/U6-U5 tri-snRNP complex, one of the building blocks of the spliceosome. Enhances dihydrotestosterone-induced transactivation activity of AR, as well as dexamethasone-induced transactivation activity of NR3C1, but does not affect estrogen-induced transactivation.

Phenotypes From GWAS Catalog for PRPF6 Gene

Gene Ontology (GO) - Molecular Function for PRPF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IGI 16414017
GO:0003723 RNA binding IDA 20797886
GO:0005515 protein binding IPI 12620389
GO:0043021 ribonucleoprotein complex binding IDA 10788320
GO:0050681 androgen receptor binding IPI 16414017
genes like me logo Genes that share ontologies with PRPF6: view
genes like me logo Genes that share phenotypes with PRPF6: view

Human Phenotype Ontology for PRPF6 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PRPF6 Gene

MGI Knock Outs for PRPF6:
  • Prpf6 Prpf6<tm1.1(KOMP)Vlcg>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRPF6

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PRPF6 Gene

Localization for PRPF6 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRPF6 Gene

Nucleus, nucleoplasm. Nucleus speckle. Note=Localized in splicing speckles.

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 PRPF6 gene
Compartment Confidence
nucleus 5
cytosol 3
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRPF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 16414017
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex NAS 10788320
GO:0005682 U5 snRNP IDA 10788320
GO:0016020 membrane HDA 19946888
genes like me logo Genes that share ontologies with PRPF6: view

Pathways & Interactions for PRPF6 Gene

genes like me logo Genes that share pathways with PRPF6: view

Pathways by source for PRPF6 Gene

1 KEGG pathway for PRPF6 Gene

Gene Ontology (GO) - Biological Process for PRPF6 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000244 spliceosomal tri-snRNP complex assembly IMP 15257298
GO:0000245 spliceosomal complex assembly NAS 10788320
GO:0000375 RNA splicing, via transesterification reactions NAS 10788320
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006396 RNA processing IEA --
genes like me logo Genes that share ontologies with PRPF6: view

No data available for SIGNOR curated interactions for PRPF6 Gene

Drugs & Compounds for PRPF6 Gene

(3) Drugs for PRPF6 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with PRPF6: view

Transcripts for PRPF6 Gene

mRNA/cDNA for PRPF6 Gene

(2) REFSEQ mRNAs :
(8) Additional mRNA sequences :
(544) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PRPF6 Gene

PRP6 pre-mRNA processing factor 6 homolog (S. cerevisiae):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRPF6

Alternative Splicing Database (ASD) splice patterns (SP) for PRPF6 Gene

No ASD Table

Relevant External Links for PRPF6 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PRPF6 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PRPF6 Gene

Protein differential expression in normal tissues from HIPED for PRPF6 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (22.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PRPF6 Gene

Protein tissue co-expression partners for PRPF6 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PRPF6 Gene:


SOURCE GeneReport for Unigene cluster for PRPF6 Gene:


mRNA Expression by UniProt/SwissProt for PRPF6 Gene:

Tissue specificity: Widely expressed.

Evidence on tissue expression from TISSUES for PRPF6 Gene

  • Intestine(4.5)
  • Liver(4.3)
  • Nervous system(4)
  • Pancreas(3.9)
  • Lung(3.2)
  • Skin(3)
  • Eye(2.7)
  • Blood(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PRPF6 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 PRPF6: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PRPF6 Gene

Orthologs for PRPF6 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRPF6 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PRPF6 34 33
  • 99.57 (n)
(Monodelphis domestica)
Mammalia PRPF6 34
  • 97 (a)
(Ornithorhynchus anatinus)
Mammalia PRPF6 34
  • 97 (a)
(Canis familiaris)
Mammalia PRPF6 34 33
  • 91.64 (n)
(Bos Taurus)
Mammalia PRPF6 34 33
  • 89.66 (n)
(Mus musculus)
Mammalia Prpf6 16 34 33
  • 88.63 (n)
(Rattus norvegicus)
Mammalia Prpf6 33
  • 88.59 (n)
(Gallus gallus)
Aves PRPF6 34 33
  • 82.39 (n)
(Anolis carolinensis)
Reptilia PRPF6 34
  • 92 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia prpf6 33
  • 80.92 (n)
Str.1900 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.3510 33
(Danio rerio)
Actinopterygii PRPF6 (1 of 2) 34
  • 80 (a)
prpf6 34 33
  • 79.34 (n)
wufa05f07 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP005640 33
  • 67.47 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG6841 34 33
  • 66.41 (n)
(Caenorhabditis elegans)
Secernentea prp-6 34 33
  • 55.76 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP6 36 34
  • 28 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons EMB2770 33
  • 57.99 (n)
(Oryza sativa)
Liliopsida Os10g0498600 33
  • 57.34 (n)
Os.21457 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2072 34
  • 56 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU04606 33
  • 53.89 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes prp1 33
  • 51.01 (n)
Species where no ortholog for PRPF6 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 PRPF6 Gene

Gene Tree for PRPF6 (if available)
Gene Tree for PRPF6 (if available)
Evolutionary constrained regions (ECRs) for PRPF6: view image

Paralogs for PRPF6 Gene

No data available for Paralogs for PRPF6 Gene

Variants for PRPF6 Gene

Sequence variations from dbSNP and Humsavar for PRPF6 Gene

SNP ID Clin Chr 20 pos Variation AA Info Type
rs111366685 likely-benign, Retinitis Pigmentosa, Dominant 64,011,428(+) G/A coding_sequence_variant, intron_variant, synonymous_variant
rs113298469 likely-benign, Retinitis Pigmentosa, Dominant 64,028,467(+) T/C intron_variant
rs114227570 likely-benign, Retinitis Pigmentosa, Dominant 63,981,167(+) C/T 5_prime_UTR_variant
rs114637353 likely-benign, Retinitis Pigmentosa, Dominant 64,033,000(+) G/A/T 3_prime_UTR_variant
rs115265032 likely-benign, Retinitis Pigmentosa, Dominant 63,981,127(+) G/A 5_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for PRPF6 Gene

Variant ID Type Subtype PubMed ID
esv1033490 CNV deletion 17803354
esv2378872 CNV deletion 18987734
esv24865 CNV loss 19812545
esv2677716 CNV deletion 23128226
esv2758807 CNV gain+loss 17122850
esv989902 CNV deletion 20482838
nsv1073088 CNV deletion 25765185
nsv1147933 CNV deletion 26484159
nsv1160691 CNV deletion 26073780
nsv428381 CNV gain+loss 18775914
nsv469773 CNV gain 16826518
nsv470564 CNV gain 18288195
nsv509784 CNV insertion 20534489
nsv509785 CNV insertion 20534489
nsv586703 CNV loss 21841781
nsv820696 CNV deletion 20802225
nsv953310 CNV deletion 24416366
nsv9830 CNV gain 18304495
nsv9831 CNV gain+loss 18304495

Variation tolerance for PRPF6 Gene

Residual Variation Intolerance Score: 1.28% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.77; 16.24% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRPF6 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 PRPF6 Gene

Disorders for PRPF6 Gene

MalaCards: The human disease database

(4) MalaCards diseases for PRPF6 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
retinitis pigmentosa 60
  • rp60
retinitis pigmentosa
  • retinitis pigmentosa 1
punctate epithelial keratoconjunctivitis
  • punctate keratitis
superficial keratitis
- elite association - COSMIC cancer census association via MalaCards
Search PRPF6 in MalaCards View complete list of genes associated with diseases


  • Retinitis pigmentosa 60 (RP60) [MIM:613983]: 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:21549338}. Note=The disease may be caused by mutations affecting the gene represented in this entry. Cells from RP60 patients show intron retention for pre-mRNA bearing specific splicing signals.

Additional Disease Information for PRPF6

genes like me logo Genes that share disorders with PRPF6: view

No data available for Genatlas for PRPF6 Gene

Publications for PRPF6 Gene

  1. Activation function-1 domain of androgen receptor contributes to the interaction between subnuclear splicing factor compartment and nuclear receptor compartment. Identification of the p102 U5 small nuclear ribonucleoprotein particle-binding protein as a coactivator for the receptor. (PMID: 12039962) Zhao Y … Nawata H (The Journal of biological chemistry 2002) 3 4 22 58
  2. The human homologue of the yeast splicing factor prp6p contains multiple TPR elements and is stably associated with the U5 snRNP via protein-protein interactions. (PMID: 10788320) Makarov EM … Lührmann R (Journal of molecular biology 2000) 2 3 4 58
  3. Isoform-specific localization of A-RAF in mitochondria. (PMID: 10848612) Yuryev A … Wennogle LP (Molecular and cellular biology 2000) 3 4 22 58
  4. A novel mammalian nuclear protein similar to Schizosaccharomyces pombe Prp1p/Zer1p and Saccharomyces cerevisiae Prp6p pre-mRNA splicing factors. (PMID: 10561546) Nishikimi A … Yamada M (Biochimica et biophysica acta 1999) 2 3 4 58
  5. A missense mutation in PRPF6 causes impairment of pre-mRNA splicing and autosomal-dominant retinitis pigmentosa. (PMID: 21549338) Tanackovic G … Rivolta C (American journal of human genetics 2011) 3 4 58

Products for PRPF6 Gene

Sources for PRPF6 Gene

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