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

Summary

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: mouse all
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Genomic context

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
CLK2 promotes occurrence and development of non-small cell lung cancer.
Title: CLK2 promotes occurrence and development of non-small cell lung cancer.
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.
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.
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.
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.
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.
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.
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.

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Phenotypes

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

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH69036 (e-PCR)
- UniSTS:85517

Clk2 (e-PCR), detects polymorphism
- UniSTS:527289

D7S2838 (e-PCR)
- UniSTS:63207

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables histone H2AXY142 kinase activity	IEA Inferred from Electronic Annotation more info
enables histone H3Y41 kinase activity	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 chromatin remodeling	IEA Inferred from Electronic Annotation more info
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

EC 2.7.12.1

NP_001281268.1

EC 2.7.12.1

NP_001350633.1

EC 2.7.12.1

NP_003984.2

EC 2.7.12.1

XP_011507445.1

EC 2.7.12.1

XP_047300365.1

EC 2.7.12.1

XP_047300370.1

EC 2.7.12.1

XP_047300373.1

EC 2.7.12.1

XP_047300378.1

EC 2.7.12.1

XP_054185445.1

EC 2.7.12.1

XP_054185446.1

EC 2.7.12.1

XP_054185447.1

EC 2.7.12.1

XP_054185448.1

EC 2.7.12.1

XP_054185449.1

EC 2.7.12.1

XP_054190193.1

EC 2.7.12.1

XP_054190194.1

EC 2.7.12.1

XP_054190195.1

EC 2.7.12.1

XP_054190196.1

EC 2.7.12.1

XP_054190197.1

EC 2.7.12.1

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)

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
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
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
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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

155262868..155273504 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_047444422.1 → XP_047300378.1 dual specificity protein kinase CLK2 isoform X5
XM_047444414.1 → XP_047300370.1 dual specificity protein kinase CLK2 isoform X3
XM_047444409.1 → XP_047300365.1 dual specificity protein kinase CLK2 isoform X2
XM_047444417.1 → XP_047300373.1 dual specificity protein kinase CLK2 isoform X4

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NW_003315906.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

67891..78527 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329470.1 → XP_054185445.1 dual specificity protein kinase CLK2 isoform X1
XM_054329474.1 → XP_054185449.1 dual specificity protein kinase CLK2 isoform X5
XM_054329472.1 → XP_054185447.1 dual specificity protein kinase CLK2 isoform X3
XM_054329471.1 → XP_054185446.1 dual specificity protein kinase CLK2 isoform X2
XM_054329473.1 → XP_054185448.1 dual specificity protein kinase CLK2 isoform X4

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

154401428..154412064 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054334218.1 → XP_054190193.1 dual specificity protein kinase CLK2 isoform X1
XM_054334222.1 → XP_054190197.1 dual specificity protein kinase CLK2 isoform X5
XM_054334220.1 → XP_054190195.1 dual specificity protein kinase CLK2 isoform X3
XM_054334219.1 → XP_054190194.1 dual specificity protein kinase CLK2 isoform X2
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

NM_001291.2: Suppressed sequence

Description

NM_001291.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.