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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

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Associated conditions

Description Tests
Retinitis pigmentosa 18 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
Products Interactant Other Gene Complex Source Pubs Description

Markers

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

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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_001350529.1NP_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:411538
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:173386
    PRP3; pre-mRNA processing factor 3 (PRP3)
  2. NM_004698.4NP_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:373
    PWI; domain in splicing factors
    pfam06544
    Location:546673
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:308521
    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_047434009.1XP_047289965.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X5

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

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

    Conserved Domains (2) summary
    smart00311
    Location:373
    PWI; PWI, domain in splicing factors
    pfam08572
    Location:309398
    PRP3; pre-mRNA processing factor 3 (PRP3)
  4. XM_011510131.4XP_011508433.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X3

    Conserved Domains (2) summary
    smart00311
    Location:373
    PWI; PWI, domain in splicing factors
    pfam08572
    Location:309427
    PRP3; pre-mRNA processing factor 3 (PRP3)
  5. XM_047433995.1XP_047289951.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X1

    UniProtKB/Swiss-Prot
    B4DSY9, O43395, O43446, Q5VT54
    UniProtKB/TrEMBL
    B2R791
  6. XM_011510130.4XP_011508432.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X2

    UniProtKB/TrEMBL
    B4DM28
    Conserved Domains (2) summary
    pfam06544
    Location:402529
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:165377
    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_054339564.1XP_054195539.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X5

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

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

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

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

    UniProtKB/Swiss-Prot
    B4DSY9, O43395, O43446, Q5VT54
    UniProtKB/TrEMBL
    B2R791
  6. XM_054339561.1XP_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