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    Cdk13 cyclin-dependent kinase 13 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 306998, updated on 13-Apr-2024

    Summary

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    Official Symbol
    Cdk13provided by RGD
    Official Full Name
    cyclin-dependent kinase 13provided by RGD
    Primary source
    RGD:1311226
    See related
    Ensembl:ENSRNOG00000013620 AllianceGenome:RGD:1311226
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Cdc2l5
    Summary
    Predicted to enable cyclin binding activity; protein kinase binding activity; and protein serine/threonine kinase activity. Predicted to be involved in RNA metabolic process; hemopoiesis; and regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of stem cell differentiation. Predicted to be located in Golgi apparatus; cytosol; and nuclear speck. Predicted to be part of cyclin K-CDK13 complex and cyclin/CDK positive transcription elongation factor complex. Predicted to be active in nucleus. Human ortholog(s) of this gene implicated in congenital heart defects, dysmorphic facial features, and intellectual developmental disorder. Orthologous to human CDK13 (cyclin dependent kinase 13). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Thymus (RPKM 250.0), Spleen (RPKM 226.6) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    17q11
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 17 NC_086035.1 (51945975..52040218)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 17 NC_051352.1 (47251145..47344675)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 17 NC_005116.4 (49833194..49922932)

    Chromosome 17 - NC_086035.1Genomic Context describing neighboring genes Neighboring gene RAS like proto-oncogene A Neighboring gene phosphoglycerate mutase 1, pseudogene 5 Neighboring gene M-phase specific PLK1 interacting protein Neighboring gene succinylCoA:glutarate-CoA transferase

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. De novo variants in CDK13 associated with syndromic ID/DD: Molecular and clinical delineation of 15 individuals and a further review. van den Akker WMR, et al. Clin Genet, 2018 May. PMID 29393965
    2. Redefining the phenotypic spectrum of de novo heterozygous CDK13 variants: Three patients without cardiac defects. Uehara T, et al. Eur J Med Genet, 2018 May. PMID 29222009
    3. Heterozygous mutations affecting the protein kinase domain of CDK13 cause a syndromic form of developmental delay and intellectual disability. Hamilton MJ, et al. J Med Genet, 2018 Jan. PMID 29021403, Free PMC Article
    4. Phenotypic and molecular characterisation of CDK13-related congenital heart defects, dysmorphic facial features and intellectual developmental disorders. Bostwick BL, et al. Genome Med, 2017 Aug 14. PMID 28807008, Free PMC Article
    5. Cloning and antisense oligodeoxynucleotide inhibition of a human homolog of cdc2 required in hematopoiesis. Lapidot-Lifson Y, et al. Proc Natl Acad Sci U S A, 1992 Jan 15. PMID 1731328, Free PMC Article

    See all (18) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II CTD heptapeptide repeat kinase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables cyclin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables cyclin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables protein kinase binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in alternative mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in hemopoiesis ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of stem cell differentiation ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription elongation by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of transcription elongation by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein phosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of signal transduction ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi apparatus ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of cyclin K-CDK13 complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of cyclin/CDK positive transcription elongation factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of nuclear cyclin-dependent protein kinase holoenzyme complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    cyclin-dependent kinase 13
    Names
    cell division cycle 2-like 5 (cholinesterase-related cell division controller)
    cell division protein kinase 13
    NP_001258224.2
    NP_001258225.2
    XP_038951649.1
    XP_038951650.1
    XP_038951651.1
    XP_038951652.1
    XP_038951653.1
    XP_063132528.1

    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_001271295.2 → NP_001258224.2  cyclin-dependent kinase 13 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      JAXUCZ010000017
      UniProtKB/TrEMBL
      F1M1X9
      Related
      ENSRNOP00000018431.8, ENSRNOT00000018431.8
      Conserved Domains (1) summary
      cd07864
      Location:697 → 998
      STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12

    2. NM_001271296.2 → NP_001258225.2  cyclin-dependent kinase 13 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      JAXUCZ010000017
      Conserved Domains (1) summary
      cd07864
      Location:697 → 998
      STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086035.1 Reference GRCr8

      Range
      51945975..52040218
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039095721.2 → XP_038951649.1  cyclin-dependent kinase 13 isoform X1

      UniProtKB/TrEMBL
      A0A8I6AEX0
      Related
      ENSRNOP00000091047.1
      Conserved Domains (1) summary
      cd07864
      Location:697 → 998
      STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12

    2. XM_039095722.2 → XP_038951650.1  cyclin-dependent kinase 13 isoform X2

      Conserved Domains (1) summary
      cd07864
      Location:697 → 998
      STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12

    3. XM_039095724.2 → XP_038951652.1  cyclin-dependent kinase 13 isoform X5

      Conserved Domains (1) summary
      cl21453
      Location:697 → 867
      PKc_like; Protein Kinases, catalytic domain

    4. XM_039095723.2 → XP_038951651.1  cyclin-dependent kinase 13 isoform X4

      Conserved Domains (1) summary
      cl21453
      Location:697 → 862
      PKc_like; Protein Kinases, catalytic domain

    5. XM_039095725.2 → XP_038951653.1  cyclin-dependent kinase 13 isoform X6

      Conserved Domains (1) summary
      cl21453
      Location:697 → 784
      PKc_like; Protein Kinases, catalytic domain

    6. XM_063276458.1 → XP_063132528.1  cyclin-dependent kinase 13 isoform X3

    Nucleotide Protein Strain
    Heading Accession and Version

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