PRP4K pre-mRNA processing factor kinase PRP4K [Homo sapiens (human)] - Gene

Summary

Official Symbol: PRP4Kprovided by HGNC
Official Full Name: pre-mRNA processing factor kinase PRP4Kprovided by HGNC
Primary source: HGNC:HGNC:17346
See related: Ensembl:ENSG00000112739 MIM:602338; AllianceGenome:HGNC:17346
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: PR4H; PRP4; PRP4H; Prp4B; PRPF4B; dJ1013A10.1
Summary: Pre-mRNA splicing occurs in two sequential transesterification steps, and the protein encoded by this gene is thought to be involved in pre-mRNA splicing and in signal transduction. This protein belongs to a kinase family that includes serine/arginine-rich protein-specific kinases and cyclin-dependent kinases (CDKs). This protein is regarded as a CDK-like kinase (Clk) with homology to mitogen-activated protein kinases (MAPKs). [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in bone marrow (RPKM 15.0), lymph node (RPKM 13.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p25.2

Exon count:: 21

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (4021300..4064983)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (3890936..3934285)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (4021534..4065217)

Chromosome 6 - NC_000006.12 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
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?

PRP4 Induces Epithelial-Mesenchymal Transition and Drug Resistance in Colon Cancer Cells via Activation of p53.
Title: PRP4 Induces Epithelial-Mesenchymal Transition and Drug Resistance in Colon Cancer Cells via Activation of p53.
Haploinsufficient tumor suppressor PRP4K is negatively regulated during epithelial-to-mesenchymal transition.
Title: Haploinsufficient tumor suppressor PRP4K is negatively regulated during epithelial-to-mesenchymal transition.
PRP4 Kinase Domain Loss Nullifies Drug Resistance and Epithelial-Mesenchymal Transition in Human Colorectal Carcinoma Cells.
Title: PRP4 Kinase Domain Loss Nullifies Drug Resistance and Epithelial-Mesenchymal Transition in Human Colorectal Carcinoma Cells.
PRPF4B is essential for triple-negative breast cancer metastasis formation in vivo, making PRPF4B a candidate for further drug development.
Title: Uncovering the signaling landscape controlling breast cancer cell migration identifies novel metastasis driver genes.
a SNP in PRPF4B was associated with anhedonia
Title: Genes associated with anhedonia: a new analysis in a large clinical trial (GENDEP).
PRP4K inhibits proliferation and invasiveness of cultured breast cancer cells and its high expression correlates with good prognosis in breast cancer patients.
Title: Regulation of Yki/Yap subcellular localization and Hpo signaling by a nuclear kinase PRP4K.
Study identifies a novel role for PRP4K in regulating the endosomal trafficking of EGFR leading to altered anoikis sensitivity in epithelial cancer cells.
Title: Loss of PRP4K drives anoikis resistance in part by dysregulation of epidermal growth factor receptor endosomal trafficking.
Results from a study on gene expression variability markers in early-stage human embryos shows that PRPF4B is a putative expression variability marker for the 3-day, 8-cell embryo stage.
Title: Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development.
Low PRP4K expression correlates with significantly worse overall survival in high-grade serous ovarian cancer, and its depletion increased metastasis in the mouse ID8 ovarian carcinoma model and promoted both sustained growth factor signalling in detached conditions and anoikis resistance in human cervical, breast and ovarian cancer cells.
Title: Loss of PRP4K drives anoikis resistance in part by dysregulation of epidermal growth factor receptor endosomal trafficking.
PRP4K is novel estrogen regulated kinase, and its levels can be reduced by 4-OHT in ER+ breast cancer cells altering their response to taxanes
Title: Estrogen receptor alpha (ESR1)-signaling regulates the expression of the taxane-response biomarker PRP4K.

Submit: New GeneRIF Correction See all GeneRIFs (19)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Rev	rev	HIV-1 Rev interacting protein, pre-mRNA processing factor 4 homolog B (PRPF4B), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with PRPF4B is increased by RRE	PubMed
retropepsin	gag-pol	Positional proteomics analysis identifies the cleavage of human PRP4 pre-mRNA processing factor 4 homolog B (yeast) (PRPF4B) at amino acid residues 105-106 by the HIV-1 protease	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S1932 (e-PCR)
- UniSTS:57909

PRP4 (e-PCR)
- UniSTS:266141

SHGC-102104 (e-PCR)
- UniSTS:168896

STS-N39448 (e-PCR)
- UniSTS:56830

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3-phosphoinositide-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables AMP-activated protein kinase activity	IEA Inferred from Electronic Annotation more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA-dependent protein kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables Rho-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables eukaryotic translation initiation factor 2alpha kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS1 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AS121 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AT120 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2AXS139 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS14 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H2BS36 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S10 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S28 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3S57 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T11 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T3 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T45 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3T6 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H4S1 kinase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein serine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein serine/threonine kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables ribosomal protein S6 kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in mRNA cis splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IC Inferred by Curator more info	PubMed
involved_in positive regulation of hippo signaling	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of mitotic cell cycle spindle assembly checkpoint	IDA Inferred from Direct Assay more info	PubMed
involved_in spliceosomal snRNP assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in spliceosomal tri-snRNP complex assembly	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of catalytic step 2 spliceosome	IDA Inferred from Direct Assay more info	PubMed
located_in kinetochore	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear speck	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: serine/threonine-protein kinase PRP4 homolog

Names: PRP4 kinase; PRP4 pre-mRNA processing factor 4 homolog B; PRP4 pre-mRNA-processing factor 4 homolog; dJ1013A10.1 (PRP4 protein kinase homolog); pre-mRNA processing factor 4B; protein-serine/threonine kinase

NP_003904.3

EC 2.7.11.1

XP_011513272.1

EC 2.7.11.1

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.

mRNA and Protein(s)

NM_003913.5 → NP_003904.3 serine/threonine-protein kinase PRP4 homolog

See identical proteins and their annotated locations for NP_003904.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the protein-coding transcript.

Source sequence(s)

AL033383, AL138831, AY029347, CN314758, CN314761

Consensus CDS

CCDS4488.1

UniProtKB/Swiss-Prot

A8K5C9, Q13523, Q5D0F6, Q5TAY8, Q8IVC3, Q8TDP2, Q96QT7, Q9UEE6

UniProtKB/TrEMBL

B4DZQ5

Related

ENSP00000337194.6, ENST00000337659.11

Conserved Domains (3) summary

PHA03307
Location:283 → 427

PHA03307; transcriptional regulator ICP4; Provisional

PTZ00108
Location:170 → 381

PTZ00108; DNA topoisomerase 2-like protein; Provisional

cd14135
Location:686 → 1003

STKc_PRP4; Catalytic domain of the Serine/Threonine Kinase, Pre-mRNA-Processing factor 4

RNA

NR_146783.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL033383, AL138831
NR_146784.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL033383, AL138831
NR_146785.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL033383, AL138831

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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

4021300..4064983

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011514970.4 → XP_011513272.1 serine/threonine-protein kinase PRP4 homolog isoform X1

UniProtKB/TrEMBL

B4DZQ5

Conserved Domains (1) summary

cl21453
Location:686 → 822

PKc_like; Protein Kinases, catalytic domain

RNA

XR_007059353.1 RNA Sequence
XR_007059354.1 RNA Sequence
XR_007059355.1 RNA Sequence
XR_007059356.1 RNA Sequence
XR_007059363.1 RNA Sequence
XR_007059365.1 RNA Sequence
XR_007059357.1 RNA Sequence
XR_007059361.1 RNA Sequence
XR_007059358.1 RNA Sequence
XR_007059362.1 RNA Sequence
XR_007059360.1 RNA Sequence
XR_007059367.1 RNA Sequence
XR_007059366.1 RNA Sequence
XR_007059364.1 RNA Sequence
XR_007059359.1 RNA Sequence
XR_007059370.1 RNA Sequence
XR_007059368.1 RNA Sequence
XR_007059373.1 RNA Sequence
XR_007059369.1 RNA Sequence
XR_007059371.1 RNA Sequence
XR_007059376.1 RNA Sequence
XR_007059375.1 RNA Sequence
XR_007059372.1 RNA Sequence
XR_007059377.1 RNA Sequence
XR_007059381.1 RNA Sequence
XR_007059374.1 RNA Sequence
XR_007059379.1 RNA Sequence
XR_007059378.1 RNA Sequence
XR_007059380.1 RNA Sequence
XR_007059382.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

3890936..3934285

Download

GenBank, FASTA, Sequence Viewer (Graphics)

RNA

XR_008487457.1 RNA Sequence
XR_008487458.1 RNA Sequence
XR_008487459.1 RNA Sequence
XR_008487460.1 RNA Sequence
XR_008487461.1 RNA Sequence
XR_008487462.1 RNA Sequence
XR_008487465.1 RNA Sequence
XR_008487476.1 RNA Sequence
XR_008487479.1 RNA Sequence
XR_008487463.1 RNA Sequence
XR_008487464.1 RNA Sequence
XR_008487468.1 RNA Sequence
XR_008487466.1 RNA Sequence
XR_008487475.1 RNA Sequence
XR_008487473.1 RNA Sequence
XR_008487469.1 RNA Sequence
XR_008487474.1 RNA Sequence
XR_008487472.1 RNA Sequence
XR_008487481.1 RNA Sequence
XR_008487480.1 RNA Sequence
XR_008487467.1 RNA Sequence
XR_008487477.1 RNA Sequence
XR_008487478.1 RNA Sequence
XR_008487470.1 RNA Sequence
XR_008487471.1 RNA Sequence
XR_008487485.1 RNA Sequence
XR_008487486.1 RNA Sequence
XR_008487484.1 RNA Sequence
XR_008487482.1 RNA Sequence
XR_008487488.1 RNA Sequence
XR_008487490.1 RNA Sequence
XR_008487483.1 RNA Sequence
XR_008487487.1 RNA Sequence
XR_008487495.1 RNA Sequence
XR_008487491.1 RNA Sequence
XR_008487492.1 RNA Sequence
XR_008487494.1 RNA Sequence
XR_008487489.1 RNA Sequence
XR_008487499.1 RNA Sequence
XR_008487496.1 RNA Sequence
XR_008487501.1 RNA Sequence
XR_008487493.1 RNA Sequence
XR_008487498.1 RNA Sequence
XR_008487497.1 RNA Sequence
XR_008487500.1 RNA Sequence
XR_008487502.1 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_176800.2: Suppressed sequence

Description

NM_176800.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.