Format

Send to:

Choose Destination

PRPF4 pre-mRNA processing factor 4 [ Homo sapiens (human) ]

Gene ID: 9128, updated on 4-Nov-2018

Summary

Official Symbol
PRPF4provided by HGNC
Official Full Name
pre-mRNA processing factor 4provided by HGNC
Primary source
HGNC:HGNC:17349
See related
Ensembl:ENSG00000136875 MIM:607795; Vega:OTTHUMG00000020517
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
PRP4; RP70; HPRP4; Prp4p; HPRP4P; SNRNP60
Summary
The protein encoded by this gene is part of a heteromeric complex that binds U4, U5, and U6 small nuclear RNAs and is involved in pre-mRNA splicing. The encoded protein also is a mitotic checkpoint protein and a regulator of chemoresistance in human ovarian cancer. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2016]
Expression
Ubiquitous expression in appendix (RPKM 8.9), kidney (RPKM 8.4) and 25 other tissues See more
Orthologs

Genomic context

See PRPF4 in Genome Data Viewer
Location:
9q32
Exon count:
14
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (113275634..113292905)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (116037914..116056079)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107987119 Neighboring gene solute carrier family 31 member 1 Neighboring gene cell division cycle 26 Neighboring gene ring finger protein 183 Neighboring gene WD repeat domain 31

Genomic regions, transcripts, and products

Expression

  • 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

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • 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

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
U4 snRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U6 snRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA processing TAS
Traceable Author Statement
more info
PubMed 
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
RNA splicing, via transesterification reactions NAS
Non-traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
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 snRNP 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 
nuclear speck IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
spliceosomal complex IC
Inferred by Curator
more info
PubMed 
spliceosomal complex NAS
Non-traceable Author Statement
more info
PubMed 
spliceosomal snRNP complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
U4/U6 small nuclear ribonucleoprotein Prp4
Names
PRP4 homolog
PRP4 pre-mRNA processing factor 4 homolog
PRP4/STK/WD splicing factor
U4/U6 snRNP 60 kDa protein
WD splicing factor Prp4

NCBI Reference Sequences (RefSeq)

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_034225.1 RefSeqGene

    Range
    5001..22272
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001244926.1NP_001231855.1  U4/U6 small nuclear ribonucleoprotein Prp4 isoform 2

    See identical proteins and their annotated locations for NP_001231855.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is 1 aa shorter compared to isoform 1.
    Source sequence(s)
    AW052006, BC001588, BC007424, CA420073, DA815191
    Consensus CDS
    CCDS59142.1
    UniProtKB/Swiss-Prot
    O43172
    UniProtKB/TrEMBL
    Q5T1M7
    Related
    ENSP00000363315.3, OTTHUMP00000021946, ENST00000374199.8, OTTHUMT00000053707
    Conserved Domains (3) summary
    smart00500
    Location:102140
    SFM; Splicing Factor Motif, present in Prp18 and Pr04
    cd00200
    Location:232518
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:233270
    7WD40; WD40 repeat [structural motif]
  2. NM_001322266.1NP_001309195.1  U4/U6 small nuclear ribonucleoprotein Prp4 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) and variant 4 both encode the same isoform (3).
    Source sequence(s)
    AL449305
    Conserved Domains (3) summary
    COG2319
    Location:10276
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:8276
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:4278
    7WD40; WD40 repeat [structural motif]
  3. NM_001322267.1NP_001309196.1  U4/U6 small nuclear ribonucleoprotein Prp4 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) and variant 3 both encode the same isoform (3).
    Source sequence(s)
    AL449305
    Conserved Domains (3) summary
    COG2319
    Location:10276
    WD40; WD40 repeat [General function prediction only]
    cd00200
    Location:8276
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:4278
    7WD40; WD40 repeat [structural motif]
  4. NM_004697.4NP_004688.2  U4/U6 small nuclear ribonucleoprotein Prp4 isoform 1

    See identical proteins and their annotated locations for NP_004688.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AW052006, BC001588, CA420073, DA815191
    Consensus CDS
    CCDS6791.1
    UniProtKB/Swiss-Prot
    O43172
    Related
    ENSP00000363313.3, OTTHUMP00000021947, ENST00000374198.4, OTTHUMT00000053708
    Conserved Domains (3) summary
    smart00500
    Location:103141
    SFM; Splicing Factor Motif, present in Prp18 and Pr04
    cd00200
    Location:233519
    WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    sd00039
    Location:234271
    7WD40; WD40 repeat [structural motif]

RNA

  1. NR_136265.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL449305
  2. NR_136266.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL449305

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_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    113275634..113292905
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Support Center