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Aliases for CLK3 Gene

Aliases for CLK3 Gene

  • CDC Like Kinase 3 2 3 5
  • CDC-Like Kinase 3 2 4
  • EC 2.7.12.1 4 58
  • Dual Specificity Protein Kinase CLK3 3
  • PHCLK3/152 3
  • PHCLK3 3

External Ids for CLK3 Gene

Previous GeneCards Identifiers for CLK3 Gene

  • GC15U990010
  • GC15P068014
  • GC15P072476
  • GC15P072616
  • GC15P072687
  • GC15P074900
  • GC15P051698

Summaries for CLK3 Gene

Entrez Gene Summary for CLK3 Gene

  • This gene encodes a protein belonging to the serine/threonine type protein kinase family. This protein is a nuclear dual-specificity kinase that regulates the intranuclear distribution of the serine/arginine-rich (SR) family of splicing factors. Two transcript variants encoding different isoforms have been found for this gene. Related pseudogenes are located on chromosomes 1 and 9. [provided by RefSeq, Jul 2008]

GeneCards Summary for CLK3 Gene

CLK3 (CDC Like Kinase 3) is a Protein Coding gene. Among its related pathways are Translational Control and mRNA Splicing - Major Pathway. GO annotations related to this gene include poly(A) RNA binding and protein kinase activity. An important paralog of this gene is CLK2.

UniProtKB/Swiss-Prot for CLK3 Gene

  • Dual specificity kinase acting on both serine/threonine and tyrosine-containing substrates. Phosphorylates serine- and arginine-rich (SR) proteins of the spliceosomal complex. May be a constituent of a network of regulatory mechanisms that enable SR proteins to control RNA splicing and can cause redistribution of SR proteins from speckles to a diffuse nucleoplasmic distribution. Phosphorylates SRSF1 and SRSF3. Regulates the alternative splicing of tissue factor (F3) pre-mRNA in endothelial cells.

Tocris Summary for CLK3 Gene

  • CLKs (Cdc2-like kinase) are dual specificity protein kinases which are involved in gene splicing regulation. The CLK family has four family members: CLK1/STY, CLK2, CLK3 and CLK4. CLKs are useful targets for studying diseases attributed to gene mis-splicing events.

Gene Wiki entry for CLK3 Gene

Additional gene information for CLK3 Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLK3 Gene

Genomics for CLK3 Gene

Regulatory Elements for CLK3 Gene

Enhancers for CLK3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH15H074412 2 FANTOM5 Ensembl ENCODE dbSUPER 36.8 -174.3 -174293 22 HDGF PKNOX1 FOXA2 ARID4B SIN3A ZNF2 ZNF143 ZNF207 FOS SP3 ENSG00000260274 MAN2C1 EDC3 CLK3 LOC101929333 PML COMMD4 ENSG00000212279 UBL7-AS1 ISLR
GH15H074614 1.4 ENCODE dbSUPER 25.6 +17.8 17838 4 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SIN3A EDC3 MAN2C1 ENSG00000260274 CLK3 PML UBL7-AS1 PTPN9 FAM219B LOC101929333
GH15H074759 1 ENCODE 35.2 +161.8 161829 0 HNRNPUL1 PKNOX1 FOXA2 ATF1 ARNT ARID4B ETS1 ZNF143 SP5 GTF2B SIN3A CLK3 PML ENSG00000260274 LOC101929333 MAN2C1 ULK3 EDC3 RPP25 DNM1P34
GH15H074768 1.2 Ensembl ENCODE 26.1 +170.5 170526 0 PKNOX1 ATF1 SIN3A GLIS2 ZNF143 REST ZNF518A ZNF292 ZNF610 GLIS1 MAN2C1 SIN3A ENSG00000260274 EDC3 ENSG00000203392 CLK3 PML DNM1P35 COMMD4 SNX33
GH15H074775 2.1 FANTOM5 Ensembl ENCODE dbSUPER 13 +189.7 189698 25 HDGF PKNOX1 FOXA2 ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 SIN3A EDC3 ENSG00000260274 LOC441728 ULK3 C15orf39 DNM1P35 ENSG00000203392 CSK RPP25
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CLK3 on UCSC Golden Path with GeneCards custom track

Promoters for CLK3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000079272 324 801 HDGF PKNOX1 MLX ARNT ZFP64 SIN3A ARID4B DMAP1 YY1 SLC30A9

Genomic Location for CLK3 Gene

Chromosome:
15
Start:
74,598,476 bp from pter
End:
74,645,418 bp from pter
Size:
46,943 bases
Orientation:
Plus strand

Genomic View for CLK3 Gene

Genes around CLK3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLK3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLK3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLK3 Gene

Proteins for CLK3 Gene

  • Protein details for CLK3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P49761-CLK3_HUMAN
    Recommended name:
    Dual specificity protein kinase CLK3
    Protein Accession:
    P49761
    Secondary Accessions:
    • D3DW59
    • Q53Y48
    • Q9BRS3
    • Q9BUJ7

    Protein attributes for CLK3 Gene

    Size:
    638 amino acids
    Molecular mass:
    73515 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAH02555.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAH19881.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for CLK3 Gene

    Alternative splice isoforms for CLK3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CLK3 Gene

Selected DME Specific Peptides for CLK3 Gene

P49761:
  • DFGSATFDHEHH
  • PYRTRKHAHHCHKRRTRSCSSASSRSQQSSKRSSRSVEDD
  • MMEKILGP
  • GFTLFQTH
  • EAARLEINVL
  • LTHTDLKPENILFV
  • VALKIIRN
  • HRRRSRER
  • VRHMAYQLC
  • GDWLQERYEIV
  • TRKQKYFY

Post-translational modifications for CLK3 Gene

Domains & Families for CLK3 Gene

Gene Families for CLK3 Gene

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

Protein Domains for CLK3 Gene

Graphical View of Domain Structure for InterPro Entry

P49761

UniProtKB/Swiss-Prot:

CLK3_HUMAN :
  • Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. Lammer subfamily.
Family:
  • Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. Lammer subfamily.
genes like me logo Genes that share domains with CLK3: view

Function for CLK3 Gene

Molecular function for CLK3 Gene

GENATLAS Biochemistry:
CDC-like kinase 3,with two alternatively spliced forms,one catalytically active and one inactive isoforms,interacting with and inducing the nuclear redistribution of SR proteins SFRS* (see symbols),widely expressed
UniProtKB/Swiss-Prot CatalyticActivity:
ATP + a protein = ADP + a phosphoprotein.
UniProtKB/Swiss-Prot EnzymeRegulation:
Leucettine L41 inhibits its kinase activity and affects the regulation of alternative splicing mediated by phosphorylation of SR proteins.
UniProtKB/Swiss-Prot Function:
Dual specificity kinase acting on both serine/threonine and tyrosine-containing substrates. Phosphorylates serine- and arginine-rich (SR) proteins of the spliceosomal complex. May be a constituent of a network of regulatory mechanisms that enable SR proteins to control RNA splicing and can cause redistribution of SR proteins from speckles to a diffuse nucleoplasmic distribution. Phosphorylates SRSF1 and SRSF3. Regulates the alternative splicing of tissue factor (F3) pre-mRNA in endothelial cells.

Enzyme Numbers (IUBMB) for CLK3 Gene

Phenotypes From GWAS Catalog for CLK3 Gene

Gene Ontology (GO) - Molecular Function for CLK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IDA 22658674
GO:0004672 protein kinase activity IEA --
GO:0004674 protein serine/threonine kinase activity TAS,ISS --
GO:0004712 protein serine/threonine/tyrosine kinase activity IEA --
GO:0004713 protein tyrosine kinase activity IEA --
genes like me logo Genes that share ontologies with CLK3: view
genes like me logo Genes that share phenotypes with CLK3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for CLK3

CRISPR Products

miRNA for CLK3 Gene

miRTarBase miRNAs that target CLK3

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CLK3
  • Applied Biological Materials Clones for CLK3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for CLK3 Gene

Localization for CLK3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLK3 Gene

Isoform 1: Nucleus. Cytoplasm. Cytoplasmic vesicle, secretory vesicle, acrosome.
Isoform 2: Nucleus speckle. Note=Co-localizes with serine- and arginine-rich (SR) proteins in the nuclear speckles.

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 CLK3 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Intermediate filaments (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001669 acrosomal vesicle IEA --
GO:0005634 nucleus IEA,IDA 9637771
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IEA --
GO:0016020 membrane IDA 19946888
genes like me logo Genes that share ontologies with CLK3: view

Pathways & Interactions for CLK3 Gene

genes like me logo Genes that share pathways with CLK3: view

Pathways by source for CLK3 Gene

1 Cell Signaling Technology pathway for CLK3 Gene
1 BioSystems pathway for CLK3 Gene

Gene Ontology (GO) - Biological Process for CLK3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006468 protein phosphorylation IDA,IEA 9637771
GO:0016310 phosphorylation IEA --
GO:0018108 peptidyl-tyrosine phosphorylation IEA --
GO:0043484 regulation of RNA splicing IDA 9637771
GO:0046777 protein autophosphorylation IEA --
genes like me logo Genes that share ontologies with CLK3: view

No data available for SIGNOR curated interactions for CLK3 Gene

Drugs & Compounds for CLK3 Gene

(2) Drugs for CLK3 Gene - From: DrugBank

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE Experimental Pharma Target 0
ethyl 3-[(E)-2-amino-1-cyanoethenyl]-6,7-dichloro-1-methyl-1H-indole-2-carboxylate Experimental Pharma Target 0
genes like me logo Genes that share compounds with CLK3: view

Transcripts for CLK3 Gene

Unigene Clusters for CLK3 Gene

CDC-like kinase 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CLK3
  • Applied Biological Materials Clones for CLK3
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for CLK3 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c · 4d ^ 5a · 5b ^ 6 ^ 7a · 7b · 7c · 7d ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c ^ 12 ^ 13 ^
SP1: -
SP2:
SP3: - - -
SP4: - - - - -
SP5: - -
SP6: -
SP7: - - - -
SP8: - - -
SP9: - -
SP10: - - - - - -
SP11:
SP12: -
SP13: - - - - -
SP14: -

ExUns: 14a · 14b · 14c ^ 15a · 15b
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:
SP12:
SP13:
SP14:

Relevant External Links for CLK3 Gene

GeneLoc Exon Structure for
CLK3
ECgene alternative splicing isoforms for
CLK3

Expression for CLK3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLK3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLK3 Gene

This gene is overexpressed in Whole Blood (x4.2).

Protein differential expression in normal tissues from HIPED for CLK3 Gene

This gene is overexpressed in Plasma (36.5), Liver (16.1), and Heart (10.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CLK3 Gene



NURSA nuclear receptor signaling pathways regulating expression of CLK3 Gene:

CLK3

SOURCE GeneReport for Unigene cluster for CLK3 Gene:

Hs.584748

mRNA Expression by UniProt/SwissProt for CLK3 Gene:

P49761-CLK3_HUMAN
Tissue specificity: Endothelial cells.

Evidence on tissue expression from TISSUES for CLK3 Gene

  • Liver(4.3)
  • Nervous system(3.9)
  • Intestine(2.4)
  • Bone marrow(2)
genes like me logo Genes that share expression patterns with CLK3: view

Primer Products

No data available for Protein tissue co-expression partners and Phenotype-based relationships between genes and organs from Gene ORGANizer for CLK3 Gene

Orthologs for CLK3 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for CLK3 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CLK3 33 34
  • 99.73 (n)
cow
(Bos Taurus)
Mammalia CLK3 33 34
  • 95.58 (n)
dog
(Canis familiaris)
Mammalia CLK3 33 34
  • 94.35 (n)
rat
(Rattus norvegicus)
Mammalia Clk3 33
  • 92.93 (n)
mouse
(Mus musculus)
Mammalia Clk3 33 16 34
  • 86.94 (n)
oppossum
(Monodelphis domestica)
Mammalia CLK3 34
  • 78 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CLK3 34
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves CLK3 33 34
  • 76.39 (n)
lizard
(Anolis carolinensis)
Reptilia CLK3 34
  • 87 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia clk3 33
  • 72.68 (n)
fruit fly
(Drosophila melanogaster)
Insecta Doa 34
  • 13 (a)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea tag-172 34
  • 25 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes KNS1 34
  • 21 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea CSA.719 34
  • 50 (a)
OneToMany
Species where no ortholog for CLK3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • 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)
  • wheat (Triticum aestivum)
  • zebrafish (Danio rerio)

Evolution for CLK3 Gene

ENSEMBL:
Gene Tree for CLK3 (if available)
TreeFam:
Gene Tree for CLK3 (if available)

Paralogs for CLK3 Gene

Paralogs for CLK3 Gene

Pseudogenes.org Pseudogenes for CLK3 Gene

genes like me logo Genes that share paralogs with CLK3: view

Variants for CLK3 Gene

Sequence variations from dbSNP and Humsavar for CLK3 Gene

SNP ID Clin Chr 15 pos Sequence Context AA Info Type
rs1000030976 -- 74,626,447(+) AGAAA(A/G)GCTCC intron-variant
rs1000051165 -- 74,619,052(+) AGTTC(G/T)TCTTC intron-variant
rs1000093008 -- 74,609,836(+) AGACC(A/G)TTGAT intron-variant, nc-transcript-variant, utr-variant-5-prime
rs1000181948 -- 74,598,274(+) ACGCC(G/T)TCTTC downstream-variant-500B, upstream-variant-2KB
rs1000198387 -- 74,645,344(+) ACACT(G/T)AATTT intron-variant, nc-transcript-variant

Structural Variations from Database of Genomic Variants (DGV) for CLK3 Gene

Variant ID Type Subtype PubMed ID
esv28499 CNV gain 19812545
nsv1121512 CNV deletion 24896259
nsv457204 CNV loss 19166990
nsv527730 CNV loss 19592680
nsv569991 CNV loss 21841781
nsv817698 CNV gain 17921354
nsv951994 CNV deletion 24416366

Variation tolerance for CLK3 Gene

Residual Variation Intolerance Score: 13.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 8.84; 86.95% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CLK3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
CLK3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLK3 Gene

Disorders for CLK3 Gene

Relevant External Links for CLK3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
CLK3

No disorders were found for CLK3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for CLK3 Gene

Publications for CLK3 Gene

  1. The Clk2 and Clk3 dual-specificity protein kinases regulate the intranuclear distribution of SR proteins and influence pre-mRNA splicing. (PMID: 9637771) Duncan PI … Bell JC (Experimental cell research 1998) 3 4 22 60
  2. Characterization by cDNA cloning of two new human protein kinases. Evidence by sequence comparison of a new family of mammalian protein kinases. (PMID: 7990150) Hanes J … Scheit KH (Journal of molecular biology 1994) 2 3 4 60
  3. Cdc2-like kinases and DNA topoisomerase I regulate alternative splicing of tissue factor in human endothelial cells. (PMID: 19168442) Eisenreich A … Rauch U (Circulation research 2009) 3 4 60
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 60
  5. An unappreciated role for RNA surveillance. (PMID: 14759258) Hillman RT … Brenner SE (Genome biology 2004) 3 4 60

Products for CLK3 Gene

  • Addgene plasmids for CLK3

Sources for CLK3 Gene

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