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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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See Cdk13 in Genome Data Viewer
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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