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

    Gene ID: 1198, updated on 10-Dec-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (74608372..74630201)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72478273..72500102)
    RS_2024_09 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: 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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    Related articles in PubMed

    1. CLK3 positively promoted colorectal cancer proliferation by activating IL-6/STAT3 signaling. Ma Y, et al. Exp Cell Res, 2024 Jul 1. PMID 38885806
    2. 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
    3. 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
    4. 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
    5. 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

    See all (78) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CLK3 positively promoted colorectal cancer proliferation by activating IL-6/STAT3 signaling.
      Title: CLK3 positively promoted colorectal cancer proliferation by activating IL-6/STAT3 signaling.
    2. Targeting CLK3 inhibits the progression of cholangiocarcinoma by reprogramming nucleotide metabolism.
      Title: Targeting CLK3 inhibits the progression of cholangiocarcinoma by reprogramming nucleotide metabolism.
    3. The novel circCLK3/miR-320a/FoxM1 axis promotes cervical cancer progression.
      Title: The novel circCLK3/miR-320a/FoxM1 axis promotes cervical cancer progression.
    4. 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.
    5. 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].
    6. 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)

    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 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 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 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 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 
    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
    		  
    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 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/Swiss-Prot
      D3DW59, P49761, Q53Y48, Q9BRS3, Q9BUJ7
      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/Swiss-Prot
      D3DW59, P49761, Q53Y48, Q9BRS3, Q9BUJ7
      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_2024_08

    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
    P49761.4 GenPept UniProtKB/Swiss-Prot:P49761

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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