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CLK2 CDC like kinase 2 [ Homo sapiens (human) ]

Gene ID: 1196, updated on 2-Nov-2024

Summary

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Official Symbol
CLK2provided by HGNC
Official Full Name
CDC like kinase 2provided by HGNC
Primary source
HGNC:HGNC:2069
See related
Ensembl:ENSG00000176444 MIM:602989; AllianceGenome:HGNC:2069
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
Summary
This gene encodes a dual specificity protein kinase that phosphorylates serine/threonine and tyrosine-containing substrates. Activity of this protein regulates serine- and arginine-rich (SR) proteins of the spliceosomal complex, thereby influencing alternative transcript splicing. Chromosomal translocations have been characterized between this locus and the PAFAH1B3 (platelet-activating factor acetylhydrolase 1b, catalytic subunit 3 (29kDa)) gene on chromosome 19, resulting in the production of a fusion protein. Note that this gene is distinct from the TELO2 gene (GeneID:9894), which shares the CLK2 alias, but encodes a protein that is involved in telomere length regulation. There is a pseudogene for this gene on chromosome 7. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
Expression
Ubiquitous expression in spleen (RPKM 18.0), lymph node (RPKM 16.4) and 25 other tissues See more
Orthologs
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Genomic context

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See CLK2 in Genome Data Viewer
Location:
1q22
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (155262868..155273504, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (154401428..154412064, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (155232659..155243295, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:155219706-155220308 Neighboring gene endosomal transmembrane epsin interactor 3 Neighboring gene secretory carrier membrane protein 3 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:155243888-155244388 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:155254443-155254943 Neighboring gene hyperpolarization activated cyclic nucleotide gated potassium channel 3 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:155263898-155264430 Neighboring gene pyruvate kinase L/R Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:155275791-155276290 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1812 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1813 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1814 Neighboring gene farnesyl diphosphate synthase Neighboring gene RUSC1 antisense RNA 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Cdc2-like kinase 2 is a key regulator of the cell cycle via FOXO3a/p27 in glioblastoma. Park SY, et al. Oncotarget, 2016 May 3. PMID 27050366, Free PMC Article
  2. CLK2 Is an Oncogenic Kinase and Splicing Regulator in Breast Cancer. Yoshida T, et al. Cancer Res, 2015 Apr 1. PMID 25670169
  3. Homozygosity mapping of a gene responsible for gelatinous drop-like corneal dystrophy to chromosome 1p. Tsujikawa M, et al. Am J Hum Genet, 1998 Oct. PMID 9758629, Free PMC Article
  4. CDC Like Kinase 2 plays an oncogenic role in colorectal cancer via modulating the Wnt/β-catenin signaling. Zhou HB, et al. Neoplasma, 2022 May. PMID 35293765
  5. CLK2 promotes occurrence and development of non-small cell lung cancer. Liu B, et al. J BUON, 2021 Jan-Feb. PMID 33721432

See all (71) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. CDC Like Kinase 2 plays an oncogenic role in colorectal cancer via modulating the Wnt/beta-catenin signaling.
    Title: CDC Like Kinase 2 plays an oncogenic role in colorectal cancer via modulating the Wnt/β-catenin signaling.
  2. CLK2 promotes occurrence and development of non-small cell lung cancer.
    Title: CLK2 promotes occurrence and development of non-small cell lung cancer.
  3. These findings suggest that CLK2 plays a critical role in controlling the cell cycle and survival of glioblastoma
    Title: Cdc2-like kinase 2 is a key regulator of the cell cycle via FOXO3a/p27 in glioblastoma.
  4. Clk1, Clk2 and Clk4 prevent chromatin breakage by regulating the Aurora B-dependent abscission checkpoint.
    Title: Clks 1, 2 and 4 prevent chromatin breakage by regulating the Aurora B-dependent abscission checkpoint.
  5. Loss of CLK2 in luminal breast cancer cells leads to the upregulation of epithelial-to-mesenchymal transition (EMT)-related genes and a switch to mesenchymal splice variants of several genes.
    Title: CLK2 Is an Oncogenic Kinase and Splicing Regulator in Breast Cancer.
  6. LAMMER/Cdc2-like kinase, represented by Doa and its mammalian homolog CLK2, is a critical and conserved component in the regulatory program of the mitosis-to-meiosis switch
    Title: The highly conserved LAMMER/CLK2 protein kinases prevent germ cell overproliferation in Drosophila.
  7. CLK1 Increases While CLK2 Decreases HIV-1 Gene Expression.
    Title: Differential effect of CLK SR Kinases on HIV-1 gene expression: potential novel targets for therapy.
  8. AKT activation controls cell survival to ionizing radiation by phosphorylating CLK2, revealing an important regulatory mechanism required for promoting cell survival.
    Title: Phosphorylation of CLK2 at serine 34 and threonine 127 by AKT controls cell survival after ionizing radiation.
  9. Cdc2-like kinases and DNA topoisomerase I regulate alternative splicing of tissue factor in human endothelial cells.
    Title: Cdc2-like kinases and DNA topoisomerase I regulate alternative splicing of tissue factor in human endothelial cells.
Submit: New GeneRIF Correction

Phenotypes

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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)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC61500

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
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 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
  
Process Evidence Code Pubs
involved_in negative regulation of gluconeogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein autophosphorylation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in protein phosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of RNA splicing IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of RNA splicing IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in response to ionizing radiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in nuclear body IDA
Inferred from Direct Assay
more info
  
located_in nuclear speck IEA
Inferred from Electronic Annotation
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 IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
dual specificity protein kinase CLK2
Names
CLK kinase
NP_001281267.1
NP_001281268.1
NP_001350633.1
NP_003984.2
XP_011507445.1
XP_047300365.1
XP_047300370.1
XP_047300373.1
XP_047300378.1
XP_054185445.1
XP_054185446.1
XP_054185447.1
XP_054185448.1
XP_054185449.1
XP_054190193.1
XP_054190194.1
XP_054190195.1
XP_054190196.1
XP_054190197.1

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)

  1. NM_001294338.2 → NP_001281267.1  dual specificity protein kinase CLK2 isoform 1

    See identical proteins and their annotated locations for NP_001281267.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AL713999, BC014067, BC053603, HY049688
    Consensus CDS
    CCDS72939.1
    UniProtKB/Swiss-Prot
    B1AVS9, B5MBX6, P49760, Q96CQ0
    UniProtKB/TrEMBL
    A8K7I0
    Related
    ENSP00000357345.4, ENST00000368361.9
    Conserved Domains (1) summary
    cd14215
    Location:150 → 479
    PKc_CLK2; Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 2

  2. NM_001294339.2 → NP_001281268.1  dual specificity protein kinase CLK2 isoform 3

    See identical proteins and their annotated locations for NP_001281268.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AU136826, BC014067, HY049688, L29216
    UniProtKB/TrEMBL
    B7Z8N6, E7EQU3, Q9BRG8
    Related
    ENST00000476983.5
    Conserved Domains (1) summary
    cl21453
    Location:1 → 251
    PKc_like; Protein Kinases, catalytic domain

  3. NM_001363704.2 → NP_001350633.1  dual specificity protein kinase CLK2 isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) uses multiple alternate in-frame splice sites, compared to variant 1. The encoded isoform (4) is shorter than isoform 1.
    Source sequence(s)
    AL713999
    Consensus CDS
    CCDS86020.1
    UniProtKB/TrEMBL
    B1AVT0
    Related
    ENSP00000347759.4, ENST00000355560.4
    Conserved Domains (1) summary
    cd14215
    Location:148 → 477
    PKc_CLK2; Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 2

  4. NM_003993.4 → NP_003984.2  dual specificity protein kinase CLK2 isoform 2

    See identical proteins and their annotated locations for NP_003984.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AU136826, BC014067, HY049688
    Consensus CDS
    CCDS1107.1
    UniProtKB/Swiss-Prot
    P49760
    Related
    ENSP00000354856.5, ENST00000361168.9
    Conserved Domains (1) summary
    cd14215
    Location:149 → 478
    PKc_CLK2; Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 2

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

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    155262868..155273504 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011509143.2 → XP_011507445.1  dual specificity protein kinase CLK2 isoform X1

    See identical proteins and their annotated locations for XP_011507445.1

    Conserved Domains (1) summary
    cd14215
    Location:149 → 478
    PKc_CLK2; Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 2

  2. XM_047444422.1 → XP_047300378.1  dual specificity protein kinase CLK2 isoform X5

  3. XM_047444414.1 → XP_047300370.1  dual specificity protein kinase CLK2 isoform X3

  4. XM_047444409.1 → XP_047300365.1  dual specificity protein kinase CLK2 isoform X2

  5. XM_047444417.1 → XP_047300373.1  dual specificity protein kinase CLK2 isoform X4

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003315906.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    67891..78527 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329470.1 → XP_054185445.1  dual specificity protein kinase CLK2 isoform X1

  2. XM_054329474.1 → XP_054185449.1  dual specificity protein kinase CLK2 isoform X5

  3. XM_054329472.1 → XP_054185447.1  dual specificity protein kinase CLK2 isoform X3

  4. XM_054329471.1 → XP_054185446.1  dual specificity protein kinase CLK2 isoform X2

  5. XM_054329473.1 → XP_054185448.1  dual specificity protein kinase CLK2 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    154401428..154412064 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054334218.1 → XP_054190193.1  dual specificity protein kinase CLK2 isoform X1

  2. XM_054334222.1 → XP_054190197.1  dual specificity protein kinase CLK2 isoform X5

  3. XM_054334220.1 → XP_054190195.1  dual specificity protein kinase CLK2 isoform X3

  4. XM_054334219.1 → XP_054190194.1  dual specificity protein kinase CLK2 isoform X2

  5. XM_054334221.1 → XP_054190196.1  dual specificity protein kinase CLK2 isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001291.2: Suppressed sequence

    Description
    NM_001291.2: 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
P49760.1 GenPept UniProtKB/Swiss-Prot:P49760

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