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CLK3 CDC like kinase 3 [ Homo sapiens (human) ]

Gene ID: 1198, updated on 5-Mar-2024

Summary

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Official Symbol
CLK3provided by HGNC
Official Full Name
CDC like kinase 3provided by HGNC
Primary source
HGNC:HGNC:2071
See related
Ensembl:ENSG00000179335 MIM:602990; AllianceGenome:HGNC:2071
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
PHCLK3; PHCLK3/152
Summary
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]
Expression
Ubiquitous expression in bone marrow (RPKM 16.0), testis (RPKM 5.8) and 25 other tissues See more
Orthologs
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Genomic context

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See CLK3 in Genome Data Viewer
Location:
15q24.1
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (74608372..74630201)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72478273..72500102)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74900713..74922542)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903528 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74832881-74833422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6652 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74834323-74834507 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9783 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:74838363-74838905 Neighboring gene AT-rich interaction domain 3B Neighboring gene VISTA enhancer hs1510 Neighboring gene uncharacterized LOC124903527 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74880397-74881182 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74881183-74881968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74886857-74887357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74889350-74889850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74890466-74891354 Neighboring gene uncharacterized LOC102723750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6654 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74908320-74908931 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74908932-74909542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74921666-74922166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9786 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9787 Neighboring gene enhancer of mRNA decapping 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9788 Neighboring gene CYP1A1 5' regulatory region Neighboring gene cytochrome P450 family 1 subfamily A member 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
  • 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. A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development. Cesana M, et al. Cell Stem Cell, 2018 Apr 5. PMID 29625070, Free PMC Article
  2. Genome-wide association study identified SNP on 15q24 associated with bladder cancer risk in Japanese population. Matsuda K, et al. Hum Mol Genet, 2015 Feb 15. PMID 25281661, Free PMC Article
  3. Targeting CLK3 inhibits the progression of cholangiocarcinoma by reprogramming nucleotide metabolism. Zhou Q, et al. J Exp Med, 2020 Aug 3. PMID 32453420, Free PMC Article
  4. The novel circCLK3/miR-320a/FoxM1 axis promotes cervical cancer progression. Hong H, et al. Cell Death Dis, 2019 Dec 12. PMID 31831728, Free PMC Article
  5. Chromosomal mapping of three human LAMMER protein-kinase-encoding genes. Talmadge CB, et al. Hum Genet, 1998 Oct. PMID 9856501

See all (70) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Targeting CLK3 inhibits the progression of cholangiocarcinoma by reprogramming nucleotide metabolism.
    Title: Targeting CLK3 inhibits the progression of cholangiocarcinoma by reprogramming nucleotide metabolism.
  2. The novel circCLK3/miR-320a/FoxM1 axis promotes cervical cancer progression.
    Title: The novel circCLK3/miR-320a/FoxM1 axis promotes cervical cancer progression.
  3. The identified the splicing kinase CLK3 that, by regulating HMGA2 splicing, preserves HMGA2 function in the setting of an increase in let-7 miRNA levels, delineating how CLK3 and HMGA2 form a functional axis that influences HSC properties during development.
    Title: A CLK3-HMGA2 Alternative Splicing Axis Impacts Human Hematopoietic Stem Cell Molecular Identity throughout Development.
  4. regulated but the expression of CDK9, CDC20 and CLK3 was down- regulated in azoospermic testes.
    Title: [Expression of cell cycle molecules in human azoospermic testes].
  5. 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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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome wide association study identified SNP on 15q24 associated with bladder cancer risk in Japanese population.
EBI GWAS Catalog

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

  • FLJ22858

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA binding HDA PubMed 
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 ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein serine/threonine/tyrosine kinase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein tyrosine kinase activity IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in protein phosphorylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of RNA splicing IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in acrosomal vesicle IEA
Inferred from Electronic Annotation
more info
  
located_in intermediate filament cytoskeleton IDA
Inferred from Direct Assay
more info
  
located_in membrane HDA PubMed 
located_in nuclear speck IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
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 CLK3
NP_001123500.2
NP_003983.2

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_001130028.2 → NP_001123500.2  dual specificity protein kinase CLK3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AC100835
    Consensus CDS
    CCDS10265.1
    UniProtKB/TrEMBL
    A8K7G8
    Related
    ENSP00000378505.4, ENST00000395066.9
    Conserved Domains (1) summary
    cd14214
    Location:142 → 472
    PKc_CLK3; Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 3

  2. NM_003992.5 → NP_003983.2  dual specificity protein kinase CLK3

    See identical proteins and their annotated locations for NP_003983.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and coding region compared to variant 1. The resulting isoform (b) has a shorter and distinct N-terminus compared to isoform a.
    Source sequence(s)
    BC002555, BQ183959, L29217
    Consensus CDS
    CCDS10265.1
    UniProtKB/TrEMBL
    A8K7G8
    Related
    ENSP00000344112.4, ENST00000345005.8
    Conserved Domains (1) summary
    cd14214
    Location:142 → 472
    PKc_CLK3; Catalytic domain of the Dual-specificity protein kinase, CDC-like kinase 3

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    74608372..74630201
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    72478273..72500102
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001292.1: Suppressed sequence

    Description
    NM_001292.1: 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
P49761.3 GenPept UniProtKB/Swiss-Prot:P49761

Gene LinkOut

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