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

    Gene ID: 9129, updated on 10-Dec-2024

    Summary

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    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
    mouse all
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    Genomic context

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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

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. A ninth locus (RP18) for autosomal dominant retinitis pigmentosa maps in the pericentromeric region of chromosome 1. Xu SY, et al. Hum Mol Genet, 1996 Aug. PMID 8842740
    2. 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
    3. Contribution of the individual subunits of protein kinase CK2 and of hPrp3p to the splicing process. Dörr J, et al. Mol Cell Biochem, 2008 Sep. PMID 18553058
    4. 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
    5. Mutations in splicing factor PRPF3, causing retinal degeneration, form detrimental aggregates in photoreceptor cells. Comitato A, et al. Hum Mol Genet, 2007 Jul 15. PMID 17517693

    See all (179) 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)

    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

    EBI GWAS Catalog

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

    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 PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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 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 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 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 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear speck IDA
    Inferred from Direct Assay
    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 
    part_of 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

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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