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Aliases for PRPF4B Gene

Aliases for PRPF4B Gene

  • Pre-MRNA Processing Factor 4B 2 3 5
  • PRP4 Pre-MRNA-Processing Factor 4 Homolog 3 4
  • PRP4 Kinase 3 4
  • EC 2.7.11.1 4 56
  • PRP4H 3 4
  • PRP4K 3 4
  • PRP4 3 4
  • PRP4 Pre-MRNA Processing Factor 4 Homolog B (Yeast) 2
  • Serine/Threonine-Protein Kinase PRP4 Homolog 3
  • PRP4 Pre-MRNA Processing Factor 4 Homolog B 3
  • DJ1013A10.1 (PRP4 Protein Kinase Homolog) 3
  • Protein-Serine/Threonine Kinase 3
  • DJ1013A10.1 3
  • KIAA0536 4
  • PR4H 3

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 mRNA Splicing - Major Pathway and Translational Control. Gene Ontology (GO) annotations related to this gene include protein kinase activity. An important paralog of this gene is CLK1.

UniProtKB/Swiss-Prot for PRPF4B Gene

  • Has a role in pre-mRNA splicing. Phosphorylates SF2/ASF.

Gene Wiki entry for PRPF4B Gene

Additional gene information for PRPF4B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PRPF4B Gene

Genomics for PRPF4B Gene

GeneHancer (GH) Regulatory Elements for PRPF4B Gene

Promoters and enhancers for PRPF4B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06I004017 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 688.6 -0.7 -741 7 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF416 ZNF143 ZNF548 PRPF4B ENSG00000230648 ENSG00000272248 RIPK1 PSMG4 ENSG00000228170 C6orf201 ENSG00000272320 CDYL FAM50B
GH06I004774 Promoter/Enhancer 2.3 EPDnew FANTOM5 Ensembl ENCODE 51.2 +755.3 755262 4 ATF1 ZNF133 SIN3A ZBTB7B ZNF48 GLIS2 ZNF207 ZNF143 ATF7 RUNX3 CDYL LOC101927913 PRPF4B LYRM4 GC06P004847
GH06I003156 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 25.6 -859.2 -859159 11.6 DMAP1 YY1 SLC30A9 ZNF213 E2F8 ZNF143 SP3 NFYC SSRP1 ZNF610 TUBB2A TUBB2B TUBB2BP1 PSMG4 PRPF4B C6orf201 RIPK1 BPHL LOC105374889 GC06P003150
GH06I004316 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 41.3 +298.8 298775 7.6 PKNOX1 SMAD1 FOXA2 ARNT SIN3A FEZF1 ZNF2 ZNF766 ZNF213 E2F8 PRPF4B CDYL C6orf201 LYRM4-AS1 ENSG00000270504 PIR45023 GC06P004318 LOC101927888
GH06I003021 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 33 -996.5 -996463 5.8 HDGF HNRNPUL1 PKNOX1 SMAD1 ARNT ARID4B SIN3A IRF4 SLC30A9 POLR2B HTATSF1P2 LOC101927759 NQO2 PRPF4B RIPK1 LINC01011 BPHL ENSG00000272277 GC06P002980
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PRPF4B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PRPF4B gene promoter:

Genomic Locations for PRPF4B Gene

Genomic Locations for PRPF4B Gene
chr6:4,021,267-4,064,983
(GRCh38/hg38)
Size:
43,717 bases
Orientation:
Plus strand
chr6:4,021,501-4,065,217
(GRCh37/hg19)

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; Positions=432; Evidence={ECO:0000305}; Sequence=BAA25462.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; 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:

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 CatalyticActivity:
ATP + a protein = ADP + a phosphoprotein.
UniProtKB/Swiss-Prot Function:
Has a role in pre-mRNA splicing. Phosphorylates SF2/ASF.

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:0003723 RNA binding IDA,HDA 22681889
GO:0004672 protein kinase activity IEA,TAS 9102632
GO:0004674 protein serine/threonine kinase activity IEA --
GO:0004693 NOT cyclin-dependent protein serine/threonine kinase activity IBA --
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 Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

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

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 IEA --
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

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

Pathways by source for PRPF4B Gene

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

(1) Drugs for PRPF4B Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
ATP Investigational Nutra Agonist 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
ADP
  • Adenosindiphosphorsaeure
  • Adenosine 5'-pyrophosphate
  • Adenosine diphosphate
  • Adenosine pyrophosphate
  • Adenosine-5'-diphosphate
Full agonist, Agonist 58-64-0
genes like me logo Genes that share compounds with PRPF4B: view

Transcripts for PRPF4B Gene

Unigene Clusters for PRPF4B Gene

PRP4 pre-mRNA processing factor 4 homolog B (yeast):
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

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
ECgene alternative splicing isoforms for
PRPF4B

Expression for PRPF4B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP 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, PaxDb, MaxQB, and MOPED for PRPF4B Gene



Protein tissue co-expression partners for PRPF4B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PRPF4B Gene:

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(4.7)
  • Liver(4.3)
  • Lung(4.3)
  • Heart(2.3)
genes like me logo Genes that share expression patterns with PRPF4B: view

Primer Products

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 33 34
  • 99.8 (n)
cow
(Bos Taurus)
Mammalia PRPF4B 34
  • 97 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PRPF4B 34
  • 95 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PRPF4B 34
  • 93 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PRPF4B 34
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Prpf4b 33 16 34
  • 89.1 (n)
rat
(Rattus norvegicus)
Mammalia Prpf4b 33
  • 89.1 (n)
chicken
(Gallus gallus)
Aves PRPF4B 33 34
  • 82.02 (n)
lizard
(Anolis carolinensis)
Reptilia PRPF4B 34
  • 88 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.10066 33
zebrafish
(Danio rerio)
Actinopterygii prpf4bb 34
  • 70 (a)
OneToMany
prpf4ba 34
  • 66 (a)
OneToMany
Dr.4891 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.7851 33
fruit fly
(Drosophila melanogaster)
Insecta CG7028 34
  • 45 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea prpf-4 34
  • 46 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes KNS1 34
  • 18 (a)
OneToMany
barley
(Hordeum vulgare)
Liliopsida Hv.13166 33
rice
(Oryza sativa)
Liliopsida Os.17376 33
corn
(Zea mays)
Liliopsida Zm.16814 33
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 72 (a)
OneToMany
-- 34
  • 64 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3457 33
Species where no ortholog for PRPF4B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)

Paralogs for PRPF4B Gene

Paralogs for PRPF4B Gene

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

Pseudogenes.org Pseudogenes for PRPF4B Gene

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

Variants for PRPF4B Gene

Sequence variations from dbSNP and Humsavar for PRPF4B Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
VAR_035633 A breast cancer sample p.Phe658Leu
rs1000057393 -- 4,034,574(+) C/T intron_variant
rs1000105102 -- 4,059,583(+) A/C genic_downstream_transcript_variant, intron_variant
rs1000116888 -- 4,059,864(+) C/T genic_downstream_transcript_variant, intron_variant
rs1000151394 -- 4,018,374(+) G/A upstream_transcript_variant

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

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

Disorders for PRPF4B Gene

Additional Disease Information for PRPF4B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

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 58
  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 58
  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 58
  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 58
  5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58

Products for PRPF4B Gene

Sources for PRPF4B Gene

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