PRPF4 pre-mRNA splicing tri-snRNP complex factor PRPF4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PRPF4provided by HGNC
Official Full Name: pre-mRNA splicing tri-snRNP complex factor PRPF4provided by HGNC
Primary source: HGNC:HGNC:17349
See related: Ensembl:ENSG00000136875 MIM:607795; AllianceGenome:HGNC:17349
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: mouse all
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Genomic context

Location:: 9q32

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (113275658..113292905)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (125474498..125491706)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (116037938..116055185)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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 confirmed that the PRPF4 gene was overexpressed in various breast cancer cell lines. Its knockdown slows down breast cancer progression via suppression of p38 MAPK phosphorylation. In conclusion, the PRPF4 gene plays an important role in the growth of breast cancer cells.
Title: PRPF4 is a novel therapeutic target for the treatment of breast cancer by influencing growth, migration, invasion, and apoptosis of breast cancer cells via p38 MAPK signaling pathway.
Possible molecular mechanism of PRP4-induced actin cytoskeleton remodeling and epithelial-mesenchymal transition, makes PRP4 an important target in colon cancer.
Title: PRP4 kinase induces actin rearrangement and epithelial-mesenchymal transition through modulation of the actin-binding protein cofilin.
The p.R192H variant of PRPF4 represents a functional null allele which compromises the function of the tri-snRNP, reinforcing the notion that this spliceosomal particle is of crucial importance in the physiology of the retina.
Title: Identification of a PRPF4 loss-of-function variant that abrogates U4/U6.U5 tri-snRNP integration and is associated with retinitis pigmentosa.
PRPF4 missense mutations is associated with autosomal dominant retinitis pigmentosa.
Title: PRPF4 mutations cause autosomal dominant retinitis pigmentosa.
the requirement of enzymatic activity of PRP4 in regulating cancer cell growth and identified an array of potential novel substrates through orthogonal proteomics approaches
Title: Evaluation of cancer dependence and druggability of PRP4 kinase using cellular, biochemical, and structural approaches.
PRP-4 belongs to the serine/threonine protein kinase family, plays a role in pre-mRNA splicing and cell mitosis, and interacts with CLK1
Title: Lentiviral short hairpin RNA screen of genes associated with multidrug resistance identifies PRP-4 as a new regulator of chemoresistance in human ovarian cancer.
PRP4 is a spindle assembly checkpoint protein required for MPS1, MAD1, and MAD2 localization to the kinetochores.
Title: PRP4 is a spindle assembly checkpoint protein required for MPS1, MAD1, and MAD2 localization to the kinetochores.
interaction between Hprp3p and Hprp4p
Title: Central region of the human splicing factor Hprp3p interacts with Hprp4p.

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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 70 MedGen: C4014681 OMIM: 615922 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D9S1962 (e-PCR)
- UniSTS:39277

D1S3697 (e-PCR)
- UniSTS:474275

D9S1962 (e-PCR)
- UniSTS:69869

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables U4 snRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables U6 snRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA processing	TAS Traceable Author Statement more info	PubMed
involved_in RNA splicing	TAS Traceable Author Statement more info	PubMed
involved_in RNA splicing, via transesterification reactions	NAS Non-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	IC Inferred by Curator more info	PubMed
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

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 snRNP	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	IPI Inferred from Physical Interaction more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	NAS Non-traceable Author Statement more info	PubMed
part_of spliceosomal complex	IC Inferred by Curator more info	PubMed
part_of spliceosomal complex	NAS Non-traceable Author Statement more info	PubMed
part_of spliceosomal snRNP complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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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; pre-mRNA processing factor 4

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_034225.1 RefSeqGene

Range

5025..22272

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001244926.2 → NP_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/TrEMBL

B2R7V4, Q5T1M7, Q6IAP9

Related

ENSP00000363313.4, ENST00000374198.5

Conserved Domains (3) summary

smart00500
Location:102 → 140

SFM; Splicing Factor Motif, present in Prp18 and Pr04

cd00200
Location:232 → 518

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:233 → 270

7WD40; WD40 repeat [structural motif]
NM_001322266.2 → NP_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 (2) summary

cd00200
Location:8 → 276

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:42 → 78

7WD40; WD40 repeat [structural motif]
NM_001322267.2 → NP_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 (2) summary

cd00200
Location:8 → 276

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:42 → 78

7WD40; WD40 repeat [structural motif]
NM_004697.5 → NP_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, O43445, O43864, Q5T1M8, Q96DG2, Q96IK4

UniProtKB/TrEMBL

B2R7V4

Related

ENSP00000363315.4, ENST00000374199.9

Conserved Domains (3) summary

smart00500
Location:103 → 141

SFM; Splicing Factor Motif, present in Prp18 and Pr04

cd00200
Location:233 → 519

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:234 → 271

7WD40; WD40 repeat [structural motif]