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CLK1 CDC like kinase 1 [ Homo sapiens (human) ]

Gene ID: 1195, updated on 25-Nov-2025
Official Symbol
CLK1provided by HGNC
Official Full Name
CDC like kinase 1provided by HGNC
Primary source
HGNC:HGNC:2068
See related
Ensembl:ENSG00000013441 MIM:601951; AllianceGenome:HGNC:2068
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
CLK; STY; CLK/STY
Summary
This gene encodes a member of the CDC2-like (or LAMMER) family of dual specificity protein kinases. In the nucleus, the encoded protein phosphorylates serine/arginine-rich proteins involved in pre-mRNA processing, releasing them into the nucleoplasm. The choice of splice sites during pre-mRNA processing may be regulated by the concentration of transacting factors, including serine/arginine rich proteins. Therefore, the encoded protein may play an indirect role in governing splice site selection. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]
Expression
Ubiquitous expression in bone marrow (RPKM 96.5), lymph node (RPKM 51.9) and 25 other tissues See more
Orthologs
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See CLK1 in Genome Data Viewer
Location:
2q33.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2025_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (200853009..200864658, complement)
RS_2025_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (201336455..201348106, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (201717732..201729381, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene BICD cargo adaptor 1 pseudogene 1 Neighboring gene Sharpr-MPRA regulatory region 5577 Neighboring gene RNA, 5S ribosomal pseudogene 115 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16964 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16965 Neighboring gene peptidylprolyl isomerase like 3 Neighboring gene RNA, U6 small nuclear 312, pseudogene Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr2:201753436-201754635 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16968 Neighboring gene NGG1 interacting factor 3 like 1 Neighboring gene RNA, U6 small nuclear 762, pseudogene

Go to nucleotide: Graphics FASTA GenBank

  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Related articles in PubMed

  1. Molecular cloning of a novel human cdc2/CDC28-like protein kinase. Johnson KW, et al. J Biol Chem, 1991 Feb 25. PMID 1704889
  2. Regulation and substrate specificity of the SR protein kinase Clk/Sty. Prasad J, et al. Mol Cell Biol, 2003 Jun. PMID 12773558, Free PMC Article
  3. Manipulation of alternative splicing by a newly developed inhibitor of Clks. Muraki M, et al. J Biol Chem, 2004 Jun 4. PMID 15010457
  4. Nuclear protein kinase CLK1 uses a non-traditional docking mechanism to select physiological substrates. Keshwani MM, et al. Biochem J, 2015 Dec 15. PMID 26443864, Free PMC Article
  5. An extensive program of periodic alternative splicing linked to cell cycle progression. Dominguez D, et al. Elife, 2016 Mar 25. PMID 27015110, Free PMC Article

See all (74) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Functions of SRPK, CLK and DYRK kinases in stem cells, development, and human developmental disorders.
    Title: Functions of SRPK, CLK and DYRK kinases in stem cells, development, and human developmental disorders.
  2. CLK1 reorganizes the splicing factor U1-70K for early spliceosomal protein assembly.
    Title: CLK1 reorganizes the splicing factor U1-70K for early spliceosomal protein assembly.
  3. Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer.
    Title: Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer.
  4. A conserved sequence motif bridges two protein kinases for enhanced phosphorylation and nuclear function of a splicing factor.
    Title: A conserved sequence motif bridges two protein kinases for enhanced phosphorylation and nuclear function of a splicing factor.
  5. LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation.
    Title: LncRNA-dependent nuclear stress bodies promote intron retention through SR protein phosphorylation.
  6. found that CLK1 amplifies its presence in the nucleus by forming a stable complex with the Ser-Arg protein substrate
    Title: Disordered protein interactions for an ordered cellular transition: Cdc2-like kinase 1 is transported to the nucleus via its Ser-Arg protein substrate.
  7. We now show that the ability of SRPK1 to mobilize SRSF1 from speckles to the nucleoplasm is dependent on active CLK1. Diffusion from speckles is promoted by the formation of an SRPK1-CLK1 complex that facilitates dissociation of SRSF1 from CLK1 and enhances the phosphorylation of several serine-proline dipeptides in this SR protein
    Title: Mobilization of a splicing factor through a nuclear kinase-kinase complex.
  8. Data suggest that CLK1 activity in both transformed and normal cells is carefully regulated via CLK1 alternative splicing through both exon 4 skipping and intron 4 retention. CLK1 autoregulates by favoring the expression of truncated isoforms, CLK1T1 and CLKT2 in environmental stress.
    Title: Autoregulation of the human splice factor kinase CLK1 through exon skipping and intron retention.
  9. These results thus reveal a large program of CLK1-regulated periodic alternative splicing intimately associated with cell cycle control.
    Title: An extensive program of periodic alternative splicing linked to cell cycle progression.
  10. Global CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor has been described.
    Title: CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor.
Submit: New GeneRIF Correction See all GeneRIFs (23)

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables non-membrane spanning protein tyrosine kinase activity TAS
Traceable Author Statement
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase activity IEA
Inferred from Electronic Annotation
more info
  
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 protein serine/threonine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein serine/threonine kinase activity TAS
Traceable Author Statement
more info
  
enables protein serine/threonine/tyrosine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein tyrosine kinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein tyrosine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables transferase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in regulation of RNA splicing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of RNA splicing IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of RNA splicing IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in nuclear membrane IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
Preferred Names
dual specificity protein kinase CLK1
Names
CDC28/CDC2-like kinase
protein tyrosine kinase STY
NP_001155879.1
NP_004062.2

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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)

  1. NM_001162407.1 → NP_001155879.1  dual specificity protein kinase CLK1 isoform 2

    See identical proteins and their annotated locations for NP_001155879.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site and upstream start codon, compared to variant 1. The resulting isoform (2) has a longer N-terminus, compared to isoform 1.
    Source sequence(s)
    AI251890, AK294295
    Consensus CDS
    CCDS54427.1
    UniProtKB/TrEMBL
    B7ZA12
    Related
    ENSP00000394734.2, ENST00000434813.3
    Conserved Domains (2) summary
    smart00220
    Location:203 → 519
    S_TKc; Serine/Threonine protein kinases, catalytic domain
    cd14213
    Location:190 → 519
    PKc_CLK1_4; Catalytic domain of the Dual-specificity protein kinases, CDC-like kinases 1 and 4

  2. NM_004071.4 → NP_004062.2  dual specificity protein kinase CLK1 isoform 1

    See identical proteins and their annotated locations for NP_004062.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the shorter isoform (1).
    Source sequence(s)
    AI251890, BC031549, DA225472
    Consensus CDS
    CCDS2331.1
    UniProtKB/Swiss-Prot
    B4DFW7, P49759, Q0P694, Q8N5V8
    UniProtKB/TrEMBL
    B7ZA12
    Related
    ENSP00000326830.4, ENST00000321356.9
    Conserved Domains (1) summary
    cd14213
    Location:148 → 477
    PKc_CLK1_4; Catalytic domain of the Dual-specificity protein kinases, CDC-like kinases 1 and 4

RNA

  1. NR_027855.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI251890, BC028149, DA225472
    Related
    ENST00000432425.5

  2. NR_027856.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) retains several introns, compared to variant 1. The transcript is sufficiently abundant to represent as a RefSeq record; however, the variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AI251890, BC028573, DA225472, DB164846
    Related
    ENST00000473565.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    200853009..200864658 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    201336455..201348106 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001024646.1: Suppressed sequence

    Description
    NM_001024646.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P49759.2 GenPept UniProtKB/Swiss-Prot:P49759

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