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PRPF3 pre-mRNA processing factor 3 [ Homo sapiens (human) ]

Gene ID: 9129, updated on 6-Jul-2025
Official Symbol
PRPF3provided by HGNC
Official Full Name
pre-mRNA processing factor 3provided by HGNC
Primary source
HGNC:HGNC:17348
See related
Ensembl:ENSG00000117360 MIM:607301; AllianceGenome:HGNC:17348
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PRP3; RP18; HPRP3; Prp3p; HPRP3P; SNRNP90
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 15.4), endometrium (RPKM 11.5) and 25 other tissues See more
Orthologs
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See PRPF3 in Genome Data Viewer
Location:
1q21.2
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (150321468..150353233)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (149446460..149478314)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150293917..150325709)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371434 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1681 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:150269465-150270023 Neighboring gene mitochondrial ribosomal protein S21 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:150293095-150293660 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:150334918-150335860 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1685 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1686 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1687 Neighboring gene regulation of nuclear pre-mRNA domain containing 2 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:150383836-150384059 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:150444960-150445472 Neighboring gene uncharacterized LOC124904416

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. SUMO conjugation to spliceosomal proteins is required for efficient pre-mRNA splicing. Pozzi B, et al. Nucleic Acids Res, 2017 Jun 20. PMID 28379520, Free PMC Article
  2. Clinical features of a Japanese family with autosomal dominant retinitis pigmentosa associated with a Thr494Met mutation in the HPRP3 gene. Wada Y, et al. Graefes Arch Clin Exp Ophthalmol, 2004 Nov. PMID 15085354
  3. Variable phenotypic expressivity in a Swiss family with autosomal dominant retinitis pigmentosa due to a T494M mutation in the PRPF3 gene. Vaclavik V, et al. Mol Vis, 2010 Mar 19. PMID 20309403, Free PMC Article
  4. Two novel mutations in PRPF3 causing autosomal dominant retinitis pigmentosa. Zhong Z, et al. Sci Rep, 2016 Nov 25. PMID 27886254, Free PMC Article
  5. Mutation in the splicing factor Hprp3p linked to retinitis pigmentosa impairs interactions within the U4/U6 snRNP complex. Gonzalez-Santos JM, et al. Hum Mol Genet, 2008 Jan 15. PMID 17932117, Free PMC Article

See all (182) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Results from whole-exome sequencing identified 2 variants c.1345C > G (p.R449G) and c.1532A > C (p.H511P) in PRPF3 which co-segregate with retinitis pigmentosa in two families respectively.
    Title: Two novel mutations in PRPF3 causing autosomal dominant retinitis pigmentosa.
  2. SUMO conjugation plays a role during mRNA splicing processes including a role for Prp3 SUMOylation in U4/U6*U5 tri-snRNP formation and/or recruitment.
    Title: SUMO conjugation to spliceosomal proteins is required for efficient pre-mRNA splicing.
  3. RP-PRPF defects affect the stoichiometry of spliceosomal small nuclear RNAs. Mutant PRPF3 proteins stably associated with tri-snRNPs.
    Title: PRPF mutations are associated with generalized defects in spliceosome formation and pre-mRNA splicing in patients with retinitis pigmentosa.
  4. Observational study of genetic testing. (HuGE Navigator)
    Title: Simultaneous mutation detection in 90 retinal disease genes in multiple patients using a custom-designed 300-kb retinal resequencing chip.
  5. A mutation in the PRPF3 gene is rare compared to other genes causing autosomal dominant retinitis pigmentosa.
    Title: Variable phenotypic expressivity in a Swiss family with autosomal dominant retinitis pigmentosa due to a T494M mutation in the PRPF3 gene.
  6. These data support the notion about individual roles for CK2alpha and CK2alpha' in the splicing process.
    Title: Contribution of the individual subunits of protein kinase CK2 and of hPrp3p to the splicing process.
  7. U2AF35 and hPrp3 interactions with SPF30 can occur simultaneously, thereby potentially linking 3' splice site recognition with tri-small nuclear ribonucleoprotein addition
    Title: Splicing factor SPF30 bridges an interaction between the prespliceosome protein U2AF35 and tri-small nuclear ribonucleoprotein protein hPrp3.
  8. splicing activity is significantly influenced by the CK2-hPrp3p interaction
    Title: Protein kinase CK2 interacts with the splicing factor hPrp3p.
  9. TASP1, EPS15R, and PRPF3 expression were significantly induced in HCCs of transgenic EGF2B mice as was P2 promoter-driven HNF4alpha
    Title: EPS15R, TASP1, and PRPF3 are novel disease candidate genes targeted by HNF4alpha splice variants in hepatocellular carcinomas.
  10. Findings suggest that the loss of Hprp3p phosphorylation at Thr494 is a key step for initiating Thr494Met aberrant interactions within U4/U6 snRNP complex and these are likely linked to the retinitis pigmentosa type 18 phenotype.
    Title: Mutation in the splicing factor Hprp3p linked to retinitis pigmentosa impairs interactions within the U4/U6 snRNP complex.
Submit: New GeneRIF Correction See all GeneRIFs (18)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Retinitis pigmentosa 18
MedGen: C1832378 OMIM: 601414 GeneReviews: Nonsyndromic Retinitis Pigmentosa Overview
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EBI GWAS Catalog

Description
Identification of risk loci with shared effects on five major psychiatric disorders: a genome-wide analysis.
EBI GWAS Catalog

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in RNA splicing TAS
Traceable Author Statement
more info
 PubMed 
involved_in RNA splicing, via transesterification reactions TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA processing IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA processing TAS
Traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IEA
Inferred from Electronic Annotation
more info
  
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in spliceosomal tri-snRNP complex assembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in Cajal body IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IEA
Inferred from Electronic Annotation
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
  
located_in nuclear speck IDA
Inferred from Direct Assay
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 
part_of protein-containing complex IEA
Inferred from Electronic Annotation
more info
  
part_of spliceosomal complex IEA
Inferred from Electronic Annotation
more info
  
part_of spliceosomal complex NAS
Non-traceable Author Statement
more info
 PubMed 
Preferred Names
U4/U6 small nuclear ribonucleoprotein Prp3
Names
PRP3 pre-mRNA processing factor 3 homolog
U4/U6 snRNP 90 kDa protein
U4/U6-associated RNA splicing factor
pre-mRNA-splicing factor 3

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008245.2 RefSeqGene

    Range
    5067..36767
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001350529.1 → NP_001337458.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AF016370, BQ002848, DA920350, DC337198
    UniProtKB/TrEMBL
    B4DM28
    Conserved Domains (2) summary
    pfam06544
    Location:411 → 538
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:173 → 386
    PRP3; pre-mRNA processing factor 3 (PRP3)

  2. NM_004698.4 → NP_004689.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform 1

    See identical proteins and their annotated locations for NP_004689.1

    Status: REVIEWED

    Source sequence(s)
    AF016370, AL611942, BQ002848, DC407158
    Consensus CDS
    CCDS951.1
    UniProtKB/Swiss-Prot
    B4DSY9, O43395, O43446, Q5VT54
    UniProtKB/TrEMBL
    B2R791
    Related
    ENSP00000315379.6, ENST00000324862.7
    Conserved Domains (3) summary
    smart00311
    Location:3 → 73
    PWI; domain in splicing factors
    pfam06544
    Location:546 → 673
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:308 → 521
    PRP3; pre-mRNA processing factor 3 (PRP3)

RNA

  1. NR_146766.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AF016370, BG740159, BQ002848, DC337198, DC407158

  2. NR_146767.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AF016370, BG740159, BQ002848, BQ932459, DC337198

  3. NR_146768.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AA806093, AF016370, BM799783, BQ002848, CX871870, DC337198

  4. NR_146769.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AA806093, AF016370, BG740159, BM799783, BQ002848, CX871870, DC337198

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    150321468..150353233
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047434009.1 → XP_047289965.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X5

  2. XM_017002791.3 → XP_016858280.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X5

  3. XM_011510132.4 → XP_011508434.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X4

    Conserved Domains (2) summary
    smart00311
    Location:3 → 73
    PWI; PWI, domain in splicing factors
    pfam08572
    Location:309 → 398
    PRP3; pre-mRNA processing factor 3 (PRP3)

  4. XM_011510131.4 → XP_011508433.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X3

    Conserved Domains (2) summary
    smart00311
    Location:3 → 73
    PWI; PWI, domain in splicing factors
    pfam08572
    Location:309 → 427
    PRP3; pre-mRNA processing factor 3 (PRP3)

  5. XM_047433995.1 → XP_047289951.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X1

    UniProtKB/Swiss-Prot
    B4DSY9, O43395, O43446, Q5VT54
    UniProtKB/TrEMBL
    B2R791

  6. XM_011510130.4 → XP_011508432.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X2

    UniProtKB/TrEMBL
    B4DM28
    Conserved Domains (2) summary
    pfam06544
    Location:402 → 529
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:165 → 377
    PRP3; pre-mRNA processing factor 3 (PRP3)

RNA

  1. XR_007064872.1 RNA Sequence

  2. XR_007064873.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    149446460..149478314
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054339564.1 → XP_054195539.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X5

  2. XM_054339565.1 → XP_054195540.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X5

  3. XM_054339563.1 → XP_054195538.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X4

  4. XM_054339562.1 → XP_054195537.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X3

  5. XM_054339560.1 → XP_054195535.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X1

    UniProtKB/Swiss-Prot
    B4DSY9, O43395, O43446, Q5VT54
    UniProtKB/TrEMBL
    B2R791

  6. XM_054339561.1 → XP_054195536.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X2

    UniProtKB/TrEMBL
    B4DM28

RNA

  1. XR_008486204.1 RNA Sequence

  2. XR_008486205.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O43395.2 GenPept UniProtKB/Swiss-Prot:O43395

Gene LinkOut

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