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    CLK4 CDC like kinase 4 [ Homo sapiens (human) ]

    Gene ID: 57396, updated on 27-Nov-2024

    Summary

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    Official Symbol
    CLK4provided by HGNC
    Official Full Name
    CDC like kinase 4provided by HGNC
    Primary source
    HGNC:HGNC:13659
    See related
    Ensembl:ENSG00000113240 MIM:607969; AllianceGenome:HGNC:13659
    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
    The protein encoded by this gene belongs to the CDC2-like protein kinase (CLK) family. This protein kinase can interact with and phosphorylate the serine- and arginine-rich (SR) proteins, which are known to play an important role in the formation of spliceosomes, and thus may be involved in the regulation of alternative splicing. Studies in the Israeli sand rat Psammomys obesus suggested that the ubiquitin-like 5 (UBL5/BEACON), a highly conserved ubiquitin-like protein, may interact with and regulate the activity of this kinase. Multiple alternatively spliced transcript variants have been observed, but the full-length natures of which have not yet been determined. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in lymph node (RPKM 15.9), bone marrow (RPKM 13.8) and 25 other tissues See more
    Orthologs
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    Genomic context

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    See CLK4 in Genome Data Viewer
    Location:
    5q35.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (178602664..178627050, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (179154636..179179025, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (178029665..178054051, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene collagen type XXIII alpha 1 chain Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177807438-177808244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177809466-177810284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177810285-177811102 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177811103-177811920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177811921-177812737 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177813862-177814680 Neighboring gene RNA, 7SL, cytoplasmic 646, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177845119-177846008 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:177864141-177864644 Neighboring gene uncharacterized LOC124901148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177890827-177891326 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177892321-177893201 Neighboring gene ReSE screen-validated silencer GRCh37_chr5:177896312-177896463 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177929402-177929902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177929903-177930403 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:177951804-177953003 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177953380-177954128 Neighboring gene Sharpr-MPRA regulatory region 11707 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:177981034-177981592 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177988600-177989128 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177989129-177989656 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:177989809-177990318 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:178009527-178010026 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:178015840-178016740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16721 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:178052997-178053677 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:178057087-178058286 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:178070356-178071555 Neighboring gene RN7SK pseudogene 70 Neighboring gene vomeronasal 2 receptor 2 pseudogene Neighboring gene Myb/SANT DNA binding domain containing 5

    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. Molecular characterization of a cDNA encoding functional human CLK4 kinase and localization to chromosome 5q35 [correction of 4q35]. Schultz J, et al. Genomics, 2001 Feb 1. PMID 11170754
    2. Methionine oxidation of CLK4 promotes the metabolic switch and redox homeostasis in esophageal carcinoma via inhibiting MITF selective autophagy. Shen Y, et al. Clin Transl Med, 2022 Jan. PMID 35092699, Free PMC Article
    3. Structural analysis of UBL5, a novel ubiquitin-like modifier. McNally T, et al. Protein Sci, 2003 Jul. PMID 12824502, Free PMC Article
    4. Clks 1, 2 and 4 prevent chromatin breakage by regulating the Aurora B-dependent abscission checkpoint. Petsalaki E, et al. Nat Commun, 2016 Apr 29. PMID 27126587, Free PMC Article
    5. Novel SR-rich-related protein clasp specifically interacts with inactivated Clk4 and induces the exon EB inclusion of Clk. Katsu R, et al. J Biol Chem, 2002 Nov 15. PMID 12169693

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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

    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

    • DKFZp686A20267

    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 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 regulation of RNA splicing IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of RNA splicing IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    dual specificity protein kinase CLK4
    Names
    protein serine threonine kinase Clk4
    NP_065717.1

    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_020666.3 → NP_065717.1  dual specificity protein kinase CLK4

      See identical proteins and their annotated locations for NP_065717.1

      Status: REVIEWED

      Source sequence(s)
      BC015942, BC063116, CB127989
      Consensus CDS
      CCDS4437.1
      UniProtKB/Swiss-Prot
      Q9HAZ1
      UniProtKB/TrEMBL
      B9EG64
      Related
      ENSP00000316948.4, ENST00000316308.9
      Conserved Domains (1) summary
      cd14213
      Location:146 → 475
      PKc_CLK1_4; Catalytic domain of the Dual-specificity protein kinases, CDC-like kinases 1 and 4

    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_000005.10 Reference GRCh38.p14 Primary Assembly

      Range
      178602664..178627050 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060929.1 Alternate T2T-CHM13v2.0

      Range
      179154636..179179025 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HAZ1.1 GenPept UniProtKB/Swiss-Prot:Q9HAZ1

    Gene LinkOut

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

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