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

Gene ID: 9129, updated on 3-Jun-2018
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; Vega:OTTHUMG00000012807
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
See PRPF3 in Genome Data Viewer
Location:
1q21.2
Exon count:
20
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (150321468..150353228)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (150293928..150325704)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371434 Neighboring gene mitochondrial ribosomal protein S21 Neighboring gene regulation of nuclear pre-mRNA domain containing 2 Neighboring gene microRNA 6878 Neighboring gene threonyl-tRNA synthetase 2, mitochondrial

  • 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 Jun 15 11:32:44 2016

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

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

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA 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 
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 
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

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_008245.1 RefSeqGene

    Range
    4990..36777
    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
    Conserved Domains (2) summary
    pfam06544
    Location:411535
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:174386
    PRP3; pre-mRNA processing factor 3 (PRP3)
  2. NM_004698.3NP_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, BQ002848, DC337198, DC407158
    Consensus CDS
    CCDS951.1
    UniProtKB/Swiss-Prot
    O43395
    Related
    ENSP00000315379.6, OTTHUMP00000014935, ENST00000324862.6
    Conserved Domains (3) summary
    smart00311
    Location:373
    PWI; PWI, domain in splicing factors
    pfam06544
    Location:546670
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:309521
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

    Range
    150321468..150353228
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002791.2XP_016858280.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X4

  2. XM_011510132.3XP_011508434.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X3

    Conserved Domains (2) summary
    smart00311
    Location:373
    PWI; PWI, domain in splicing factors
    pfam08572
    Location:309398
    PRP3; pre-mRNA processing factor 3 (PRP3)
  3. XM_011510131.3XP_011508433.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X2

    Conserved Domains (2) summary
    smart00311
    Location:373
    PWI; PWI, domain in splicing factors
    pfam08572
    Location:309427
    PRP3; pre-mRNA processing factor 3 (PRP3)
  4. XM_017002790.1XP_016858279.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X1

    Conserved Domains (2) summary
    pfam06544
    Location:402529
    DUF1115; Protein of unknown function (DUF1115)
    pfam08572
    Location:165377
    PRP3; pre-mRNA processing factor 3 (PRP3)
  5. XM_011510130.3XP_011508432.1  U4/U6 small nuclear ribonucleoprotein Prp3 isoform X1

    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_002958010.1 RNA Sequence

  2. XR_001737536.2 RNA Sequence

  3. XR_921997.3 RNA Sequence

  4. XR_001737537.2 RNA Sequence

  5. XR_241103.3 RNA Sequence

  6. XR_002958012.1 RNA Sequence

  7. XR_921998.3 RNA Sequence

  8. XR_001737541.2 RNA Sequence

  9. XR_002958009.1 RNA Sequence

  10. XR_001737540.2 RNA Sequence

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