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

Summary

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
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: mouse all

Genomic context

Location:: 1q21.2

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
109.20190905	current	GRCh38.p13 (GCF_000001405.39)	1	NC_000001.11 (150321468..150353233)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (150293928..150325704)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
splicing activity is significantly influenced by the CK2-hPrp3p interaction
Title: Protein kinase CK2 interacts with the splicing factor hPrp3p.
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.
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)

Phenotypes

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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	Compare labs

NHGRI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from BioSystems

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Gene Expression, organism-specific biosystem (from REACTOME)
Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
Spliceosome, organism-specific biosystem (from KEGG)
Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
Spliceosome, conserved biosystem (from KEGG)
Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystem (from KEGG)
Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystem (from KEGG)
Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
mRNA Processing, organism-specific biosystem (from WikiPathways)
mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
mRNA Splicing, organism-specific biosystem (from REACTOME)
mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S2345 (e-PCR), detects polymorphism
- UniSTS:23133

D1S498 (e-PCR), detects polymorphism
- UniSTS:80001

D1S2858 (e-PCR), detects polymorphism
- UniSTS:12962

G32330 (e-PCR)
- UniSTS:116923

A006E14 (e-PCR)
- UniSTS:12746

D1S422 (e-PCR), detects polymorphism
- UniSTS:28371

D10S1692 (e-PCR)
- UniSTS:50170

Homology

Homologs of the PRPF3 gene: The PRPF3 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, zebrafish, fruit fly, mosquito, C.elegans, S.pombe, M.oryzae, N.crassa, A.thaliana, rice, and frog.
Orthologs from Annotation Pipeline: 285 organisms have orthologs with human gene PRPF3
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
RNA binding	HDA more info	PubMed
identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
RNA splicing	TAS Traceable Author Statement more info	PubMed
RNA splicing, via transesterification reactions	TAS Traceable Author Statement more info	PubMed
mRNA processing	TAS Traceable Author Statement more info	PubMed
mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info	PubMed
mRNA splicing, via spliceosome	IDA Inferred from Direct Assay more info	PubMed
mRNA splicing, via spliceosome	NAS Non-traceable Author Statement more info	PubMed
mRNA splicing, via spliceosome	TAS Traceable Author Statement more info
spliceosomal tri-snRNP complex assembly	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
Cajal body	IDA Inferred from Direct Assay more info	PubMed
U2-type precatalytic spliceosome	IDA Inferred from Direct Assay more info	PubMed
U4/U6 x U5 tri-snRNP complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
U4/U6 x U5 tri-snRNP complex	IDA Inferred from Direct Assay more info	PubMed
cytosol	IDA Inferred from Direct Assay more info
nuclear speck	IDA Inferred from Direct Assay more info
nucleoplasm	IDA Inferred from Direct Assay more info
nucleoplasm	TAS Traceable Author Statement more info
nucleus	IDA Inferred from Direct Assay more info	PubMed
spliceosomal complex	NAS Non-traceable Author Statement more info	PubMed

General protein information

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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

NCBI Reference Sequences (RefSeq)

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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

NG_008245.1 RefSeqGene

Range

5055..36782

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

Status: REVIEWED

Source sequence(s)

AF016370, BQ002848, DA920350, DC337198

Conserved Domains (2) summary

pfam06544
Location:411 → 538

DUF1115; Protein of unknown function (DUF1115)

pfam08572
Location:174 → 386

PRP3; pre-mRNA processing factor 3 (PRP3)
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

O43395

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:309 → 521

PRP3; pre-mRNA processing factor 3 (PRP3)

RNA

NR_146766.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AF016370, BG740159, BQ002848, DC337198, DC407158
NR_146767.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AF016370, BG740159, BQ002848, BQ932459, DC337198
NR_146768.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AA806093, AF016370, BM799783, BQ002848, CX871870, DC337198
NR_146769.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AA806093, AF016370, BG740159, BM799783, BQ002848, CX871870, DC337198

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p13 Primary Assembly

Range

150321468..150353233

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017002791.2 → XP_016858280.1 U4/U6 small nuclear ribonucleoprotein Prp3 isoform X4
XM_011510132.3 → XP_011508434.1 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 → 398

PRP3; pre-mRNA processing factor 3 (PRP3)
XM_011510131.3 → XP_011508433.1 U4/U6 small nuclear ribonucleoprotein Prp3 isoform X2

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)
XM_017002790.1 → XP_016858279.1 U4/U6 small nuclear ribonucleoprotein Prp3 isoform X1

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)
XM_011510130.3 → XP_011508432.1 U4/U6 small nuclear ribonucleoprotein Prp3 isoform X1

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)