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 homo... See more...

Aliases for PRPF4B Gene

Aliases for PRPF4B Gene

  • Pre-MRNA Processing Factor 4B 2 3 5
  • Serine/Threonine-Protein Kinase PRP4 Homolog 3 4
  • PRP4 Pre-MRNA-Processing Factor 4 Homolog 3 4
  • PRP4 Kinase 3 4
  • EC 2.7.11.1 4 50
  • KIAA0536 2 4
  • PRP4H 3 4
  • PRP4K 3 4
  • PR4H 2 3
  • PRP4 3 4
  • PRP4 Pre-MRNA Processing Factor 4 Homolog B (Yeast) 2
  • PRP4 Pre-MRNA Processing Factor 4 Homolog B 3
  • DJ1013A10.1 (PRP4 Protein Kinase Homolog) 3
  • Protein-Serine/Threonine Kinase 3
  • DJ1013A10.1 3
  • PRPF4B 5
  • Prp4 2

External Ids for PRPF4B Gene

Previous GeneCards Identifiers for PRPF4B Gene

  • GC06P004006
  • GC06P003966
  • GC06P003898

Summaries for PRPF4B Gene

Entrez Gene Summary for PRPF4B Gene

  • 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]

GeneCards Summary for PRPF4B Gene

PRPF4B (Pre-MRNA Processing Factor 4B) is a Protein Coding gene. Among its related pathways are Translational Control and mRNA Splicing - Major Pathway. Gene Ontology (GO) annotations related to this gene include protein kinase activity. An important paralog of this gene is CDK13.

UniProtKB/Swiss-Prot Summary for PRPF4B Gene

Gene Wiki entry for PRPF4B Gene

No data available for CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PRPF4B Gene

Genomics for PRPF4B Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PRPF4B Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PRPF4B on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PRPF4B

Top Transcription factor binding sites by QIAGEN in the PRPF4B gene promoter:
  • ATF
  • E2F
  • E2F-1
  • FAC1
  • FOXD3
  • GATA-1
  • HSF1 (long)
  • HSF1short
  • Nkx2-5
  • YY1

Genomic Locations for PRPF4B Gene

Latest Assembly
chr6:4,021,267-4,064,983
(GRCh38/hg38)
Size:
43,717 bases
Orientation:
Plus strand

Previous Assembly
chr6:4,021,534-4,065,217
(GRCh37/hg19 by Entrez Gene)
Size:
43,684 bases
Orientation:
Plus strand

chr6:4,021,501-4,065,217
(GRCh37/hg19 by Ensembl)
Size:
43,717 bases
Orientation:
Plus strand

Genomic View for PRPF4B Gene

Genes around PRPF4B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PRPF4B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PRPF4B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PRPF4B Gene

Proteins for PRPF4B Gene

  • Protein details for PRPF4B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q13523-PRP4B_HUMAN
    Recommended name:
    Serine/threonine-protein kinase PRP4 homolog
    Protein Accession:
    Q13523
    Secondary Accessions:
    • A8K5C9
    • Q5D0F6
    • Q5TAY8
    • Q8IVC3
    • Q8TDP2
    • Q96QT7
    • Q9UEE6

    Protein attributes for PRPF4B Gene

    Size:
    1007 amino acids
    Molecular mass:
    116987 Da
    Quaternary structure:
    • Identified in the spliceosome C complex. Interacts with Clk1 C-terminus.
    SequenceCaution:
    • Sequence=AAH09844.1; Type=Frameshift; Evidence={ECO:0000305}; Sequence=BAA25462.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PRPF4B Gene

neXtProt entry for PRPF4B Gene

Selected DME Specific Peptides for PRPF4B Gene

Q13523:
  • SRLRRRSRSRGG
  • DIKPDNI
  • KIIRNNE
  • KHKHKHKHKKHKRKEV
  • RRSRSPL
  • SVPSEPSSPQSSTR
  • GCTLYEL
  • KKRSKSRSKERTRHRSDK
  • RRRSRSKVKEDKFKGSLSEGMKVEQESSSDDNLEDFDVE
  • KSPSKDASSGKENRSPSRRPGRSPKRRSLSPK
  • SPAKRTKLDDLALLEDLEKQRALIKAELDNELMEGKVQS

Post-translational modifications for PRPF4B Gene

Domains & Families for PRPF4B Gene

Gene Families for PRPF4B Gene

IUPHAR :
Human Protein Atlas (HPA):
  • Enzymes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for PRPF4B Gene

Suggested Antigen Peptide Sequences for PRPF4B Gene

GenScript: Design optimal peptide antigens:
  • PRP4 pre-mRNA-processing factor 4 homolog (PRP4B_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q13523

UniProtKB/Swiss-Prot:

PRP4B_HUMAN :
  • Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family.
Family:
  • Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family.
genes like me logo Genes that share domains with PRPF4B: view

Function for PRPF4B Gene

Molecular function for PRPF4B Gene

UniProtKB/Swiss-Prot Function:
Has a role in pre-mRNA splicing. Phosphorylates SF2/ASF.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein]; Xref=Rhea:RHEA:17989, Rhea:RHEA-COMP:9863, Rhea:RHEA-COMP:11604, ChEBI:CHEBI:15378, ChEBI:CHEBI:29999, ChEBI:CHEBI:30616, ChEBI:CHEBI:83421, ChEBI:CHEBI:456216; EC=2.7.11.1;.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=ATP + L-threonyl-[protein] = ADP + H(+) + O-phospho-L-threonyl-[protein]; Xref=Rhea:RHEA:46608, Rhea:RHEA-COMP:11060, Rhea:RHEA-COMP:11605, ChEBI:CHEBI:15378, ChEBI:CHEBI:30013, ChEBI:CHEBI:30616, ChEBI:CHEBI:61977, ChEBI:CHEBI:456216; EC=2.7.11.1;.

Enzyme Numbers (IUBMB) for PRPF4B Gene

Phenotypes From GWAS Catalog for PRPF4B Gene

Gene Ontology (GO) - Molecular Function for PRPF4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding IEA --
GO:0003723 RNA binding HDA 22681889
GO:0004672 protein kinase activity IEA,TAS 9102632
GO:0004674 protein serine/threonine kinase activity IEA --
GO:0005515 protein binding IPI 15452250
genes like me logo Genes that share ontologies with PRPF4B: view
genes like me logo Genes that share phenotypes with PRPF4B: view

Animal Models for research

  • Taconic Biosciences Mouse Models for PRPF4B

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRPF4B

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PRPF4B Gene

Localization for PRPF4B Gene

Subcellular locations from UniProtKB/Swiss-Prot for PRPF4B Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PRPF4B gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear speckles (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PRPF4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
GO:0005681 spliceosomal complex IEA --
GO:0005694 chromosome IEA --
GO:0016607 nuclear speck IDA --
GO:0071013 catalytic step 2 spliceosome IDA 11991638
genes like me logo Genes that share ontologies with PRPF4B: view

Pathways & Interactions for PRPF4B Gene

PathCards logo

SuperPathways for PRPF4B Gene

genes like me logo Genes that share pathways with PRPF4B: view

Pathways by source for PRPF4B Gene

1 BioSystems pathway for PRPF4B Gene
1 Cell Signaling Technology pathway for PRPF4B Gene

SIGNOR curated interactions for PRPF4B Gene

Activates:
Inactivates:

Gene Ontology (GO) - Biological Process for PRPF4B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome IC 11991638
GO:0006397 mRNA processing IEA --
GO:0006468 protein phosphorylation IEA,IBA 21873635
GO:0008380 RNA splicing TAS 9102632
GO:0016310 phosphorylation IEA --
genes like me logo Genes that share ontologies with PRPF4B: view

Drugs & Compounds for PRPF4B Gene

(2) Drugs for PRPF4B Gene - From: DrugBank and HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
fostamatinib Approved, Investigational Pharma Target, inhibitor Kinase Inhibitors 0
ATP Investigational Nutra 0

(1) Additional Compounds for PRPF4B Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • 5'-Adenylphosphoric acid
  • Adenosine 5'-diphosphate
  • ADENOSINE-5'-diphosphATE
  • H3ADP
  • 5'-Adenylphosphate
58-64-0
genes like me logo Genes that share compounds with PRPF4B: view

Transcripts for PRPF4B Gene

mRNA/cDNA for PRPF4B Gene

2 REFSEQ mRNAs :
11 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PRPF4B

Alternative Splicing Database (ASD) splice patterns (SP) for PRPF4B Gene

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15a · 15b · 15c ^ 16a · 16b · 16c ^ 17 ^ 18 ^ 19a · 19b ·
SP1: - - - - - - -
SP2: -
SP3: - - -
SP4:
SP5:
SP6: - -
SP7:
SP8:
SP9:

ExUns: 19c ^ 20a · 20b · 20c ^ 21a · 21b · 21c ^ 22a · 22b
SP1: - - - -
SP2: - - -
SP3: -
SP4: - - - -
SP5:
SP6:
SP7: - -
SP8:
SP9:

Relevant External Links for PRPF4B Gene

GeneLoc Exon Structure for
PRPF4B

Expression for PRPF4B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for PRPF4B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PRPF4B Gene

This gene is overexpressed in Peripheral blood mononuclear cells (20.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PRPF4B Gene



Protein tissue co-expression partners for PRPF4B Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PRPF4B

SOURCE GeneReport for Unigene cluster for PRPF4B Gene:

Hs.159014

mRNA Expression by UniProt/SwissProt for PRPF4B Gene:

Q13523-PRP4B_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for PRPF4B Gene

  • Nervous system(4.8)
  • Liver(4.4)
  • Lung(4.3)
  • Heart(2.7)
  • Skin(2.1)
  • Intestine(2.1)
  • Blood(2.1)
  • Kidney(2.1)
genes like me logo Genes that share expression patterns with PRPF4B: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for PRPF4B Gene

Orthologs for PRPF4B Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PRPF4B Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PRPF4B 29 30
  • 99.8 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PRPF4B 30
  • 97 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia PRPF4B 30
  • 95 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PRPF4B 30
  • 93 (a)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PRPF4B 30
  • 92 (a)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Prpf4b 29
  • 89.1 (n)
Mouse
(Mus musculus)
Mammalia Prpf4b 29 16 30
  • 89.1 (n)
OneToOne
Chicken
(Gallus gallus)
Aves PRPF4B 29 30
  • 82.02 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PRPF4B 30
  • 88 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.10066 29
Zebrafish
(Danio rerio)
Actinopterygii prpf4bb 30
  • 70 (a)
OneToMany
prpf4ba 30
  • 66 (a)
OneToMany
Dr.4891 29
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7851 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG7028 30
  • 45 (a)
OneToOne
Worm
(Caenorhabditis elegans)
Secernentea prpf-4 30
  • 46 (a)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes KNS1 30
  • 18 (a)
OneToMany
Barley
(Hordeum vulgare)
Liliopsida Hv.13166 29
Rice
(Oryza sativa)
Liliopsida Os.17376 29
Corn
(Zea mays)
Liliopsida Zm.16814 29
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 72 (a)
OneToMany
-- 30
  • 64 (a)
OneToMany
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.3457 29
Species where no ortholog for PRPF4B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)

Evolution for PRPF4B Gene

ENSEMBL:
Gene Tree for PRPF4B (if available)
TreeFam:
Gene Tree for PRPF4B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PRPF4B: view image
Alliance of Genome Resources:
Additional Orthologs for PRPF4B

Paralogs for PRPF4B Gene

(13) SIMAP similar genes for PRPF4B Gene using alignment to 3 proteins:

  • PRP4B_HUMAN
  • F5H2U2_HUMAN
  • H0YDJ3_HUMAN

Pseudogenes.org Pseudogenes for PRPF4B Gene

genes like me logo Genes that share paralogs with PRPF4B: view

Variants for PRPF4B Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PRPF4B Gene

SNP ID Clinical significance and condition Chr 06 pos Variation AA Info Type
rs123049140 A breast cancer sample p.Phe658Leu
rs147022134 Benign: not provided 4,031,721(+) A/G
NM_003913.5(PRPF4B):c.204A>G (p.Lys68=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs55652448 Benign: not provided 4,052,813(+) A/G
NM_003913.5(PRPF4B):c.2406A>G (p.Ala802=)
NON_CODING_TRANSCRIPT_VARIANT,SYNONYMOUS
rs56267049 -- p.Ile584Val
rs9503893 -- p.Ile83Val

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PRPF4B Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for PRPF4B Gene

Variant ID Type Subtype PubMed ID
dgv3258n106 CNV deletion 24896259
esv1454617 CNV deletion 17803354
esv2201190 CNV deletion 18987734
esv2527172 CNV deletion 19546169
esv2731501 CNV deletion 23290073
esv3567187 CNV deletion 23714750
esv4480 CNV loss 18987735
esv9631 CNV loss 19470904
esv993339 CNV deletion 20482838
nsv1034223 CNV gain 25217958
nsv1072593 CNV deletion 25765185
nsv1150431 CNV deletion 26484159
nsv349483 CNV deletion 16902084
nsv349965 CNV deletion 16902084
nsv600860 CNV loss 21841781
nsv956525 CNV deletion 24416366

Variation tolerance for PRPF4B Gene

Residual Variation Intolerance Score: 12.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.71; 32.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PRPF4B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PRPF4B
Leiden Open Variation Database (LOVD)
PRPF4B

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PRPF4B Gene

Disorders for PRPF4B Gene

Additional Disease Information for PRPF4B

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform

No disorders were found for PRPF4B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PRPF4B Gene

Publications for PRPF4B Gene

  1. Cloning of human PRP4 reveals interaction with Clk1. (PMID: 11418604) Kojima T … Hagiwara M (The Journal of biological chemistry 2001) 2 3 4 22
  2. Prediction of the coding sequences of unidentified human genes. IX. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9628581) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1998) 2 3 4
  3. Functional analysis of the fission yeast Prp4 protein kinase involved in pre-mRNA splicing and isolation of a putative mammalian homologue. (PMID: 9102632) Gross T … Käufer NF (Nucleic acids research 1997) 3 4 22
  4. Human PRP4 kinase is required for stable tri-snRNP association during spliceosomal B complex formation. (PMID: 20118938) Schneider M … Lührmann R (Nature structural & molecular biology 2010) 3 22
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4

Products for PRPF4B Gene

Sources for PRPF4B Gene