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    CDK13 cyclin dependent kinase 13 [ Homo sapiens (human) ]

    Gene ID: 8621, updated on 9-Sep-2018

    Summary

    Official Symbol
    CDK13provided by HGNC
    Official Full Name
    cyclin dependent kinase 13provided by HGNC
    Primary source
    HGNC:HGNC:1733
    See related
    Ensembl:ENSG00000065883 MIM:603309; Vega:OTTHUMG00000023726
    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
    CHED; CDC2L; CDC2L5; hCDK13; CHDFIDD
    Summary
    The protein encoded by this gene is a member of the cyclin-dependent serine/threonine protein kinase family. Members of this family are well known for their essential roles as master switches in cell cycle control. The exact function of this protein has not yet been determined, but it may play a role in mRNA processing and may be involved in regulation of hematopoiesis. Alternatively spliced transcript variants have been described.[provided by RefSeq, Dec 2009]
    Expression
    Ubiquitous expression in testis (RPKM 7.7), lymph node (RPKM 7.0) and 25 other tissues See more
    Orthologs

    Genomic context

    See CDK13 in Genome Data Viewer
    Location:
    7p14.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 7 NC_000007.14 (39949664..40097134)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (39989959..40136733)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928688 Neighboring gene RWD domain containing 4 pseudogene 2 Neighboring gene RNA, 7SL, cytoplasmic 496, pseudogene Neighboring gene uncharacterized LOC112267983 Neighboring gene HIG1 hypoxia inducible domain family member 1A pseudogene 7 Neighboring gene M-phase specific PLK1 interacting protein

    Genomic regions, transcripts, and products

    Expression

    • 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 Jun 15 11:32:44 2016

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp160, precursor env Overexpression of cyclin-dependent kinase 13 (CDK13) decreases the production of the viral proteins Gag and Env and subsequently suppresses virus production PubMed
    Nef nef Cyclin-dependent kinase 13 (CDK13) upregulates HIV-1 mRNA splicing and favors the production of the doubly spliced protein Nef PubMed
    Pr55(Gag) gag Overexpression of cyclin-dependent kinase 13 (CDK13) decreases the production of the viral proteins Gag and Env and subsequently suppresses virus production PubMed
    Tat tat HIV-1 Tat interacts with cyclin-dependent kinase 13 (CDK13) PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
      Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • Innate Immune System, organism-specific biosystem (from REACTOME)
      Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
    • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
      Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
    • TP53 Regulates Transcription of DNA Repair Genes, organism-specific biosystem (from REACTOME)
      TP53 Regulates Transcription of DNA Repair Genes, organism-specific biosystemSeveral DNA repair genes contain p53 response elements and their transcription is positively regulated by TP53 (p53). TP53-mediated regulation probably ensures increased protein level of DNA repair g...
    • Transcriptional Regulation by TP53, organism-specific biosystem (from REACTOME)
      Transcriptional Regulation by TP53, organism-specific biosystemThe tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many gen...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ35215, KIAA1791

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    RNA binding HDA PubMed 
    RNA polymerase II CTD heptapeptide repeat kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    RNA polymerase II CTD heptapeptide repeat kinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cyclin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cyclin binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    cyclin-dependent protein serine/threonine kinase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein kinase activity TAS
    Traceable Author Statement
    more info
    PubMed 
    protein kinase binding IEA
    Inferred from Electronic Annotation
    more info
     
    transcription factor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    transcription regulatory region DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    Process Evidence Code Pubs
    alternative mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    alternative mRNA splicing, via spliceosome TAS
    Traceable Author Statement
    more info
    PubMed 
    hemopoiesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    multicellular organism development TAS
    Traceable Author Statement
    more info
    PubMed 
    negative regulation of stem cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    neutrophil degranulation TAS
    Traceable Author Statement
    more info
     
    phosphorylation of RNA polymerase II C-terminal domain IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    phosphorylation of RNA polymerase II C-terminal domain IDA
    Inferred from Direct Assay
    more info
    PubMed 
    positive regulation of cell proliferation TAS
    Traceable Author Statement
    more info
    PubMed 
    positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    positive regulation of transcription elongation from RNA polymerase II promoter IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    protein phosphorylation IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    regulation of mitotic nuclear division TAS
    Traceable Author Statement
    more info
    PubMed 
    transcription elongation from RNA polymerase II promoter IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    viral process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    Golgi apparatus IDA
    Inferred from Direct Assay
    more info
     
    chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cyclin K-CDK13 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    cyclin-dependent protein kinase holoenzyme complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cyclin/CDK positive transcription elongation factor complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    extracellular region TAS
    Traceable Author Statement
    more info
     
    extracellular space HDA PubMed 
    ficolin-1-rich granule lumen TAS
    Traceable Author Statement
    more info
     
    nuclear chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nuclear cyclin-dependent protein kinase holoenzyme complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    nuclear speck IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    cyclin-dependent kinase 13
    Names
    CDC2-related protein kinase 5
    cell division cycle 2-like protein kinase 5
    cell division protein kinase 13
    cholinesterase-related cell division controller
    NP_003709.3
    NP_112557.2
    XP_011513899.1
    XP_016868239.1
    XP_016868240.1

    NCBI Reference Sequences (RefSeq)

    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.

    Genomic

    1. NG_052965.1 RefSeqGene

      Range
      5001..151775
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003718.4NP_003709.3  cyclin-dependent kinase 13 isoform 1

      See identical proteins and their annotated locations for NP_003709.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AJ297709, AK092534, AK223053, BC001274, BC080601, BM699295, BM727913, BU686489, CR748837
      Consensus CDS
      CCDS5461.1
      UniProtKB/Swiss-Prot
      Q14004
      UniProtKB/TrEMBL
      A0A024RA85, Q9BVE2
      Related
      ENSP00000181839.4, OTTHUMP00000159007, ENST00000181839.9, OTTHUMT00000250726
      Conserved Domains (2) summary
      smart00220
      Location:705994
      S_TKc; Serine/Threonine protein kinases, catalytic domain
      cd07864
      Location:697998
      STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12
    2. NM_031267.3NP_112557.2  cyclin-dependent kinase 13 isoform 2

      See identical proteins and their annotated locations for NP_112557.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AJ297709, AJ297710, AK092534, AK223053, BC001274, BC080601, BM699295, BM727913, BU686489, CR748837
      Consensus CDS
      CCDS5462.1
      UniProtKB/Swiss-Prot
      Q14004
      UniProtKB/TrEMBL
      A0A024RA66, Q9BVE2
      Related
      ENSP00000340557.5, OTTHUMP00000159008, ENST00000340829.10, OTTHUMT00000250727
      Conserved Domains (2) summary
      smart00220
      Location:705994
      S_TKc; Serine/Threonine protein kinases, catalytic domain
      cd07864
      Location:697998
      STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

    Reference GRCh38.p12 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p12 Primary Assembly

      Range
      39949664..40097134
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017012750.2XP_016868239.1  cyclin-dependent kinase 13 isoform X1

    2. XM_017012751.2XP_016868240.1  cyclin-dependent kinase 13 isoform X2

    3. XM_011515597.3XP_011513899.1  cyclin-dependent kinase 13 isoform X3

      Conserved Domains (2) summary
      smart00220
      Location:705868
      S_TKc; Serine/Threonine protein kinases, catalytic domain
      cl21453
      Location:697881
      PKc_like; Protein Kinases, catalytic domain
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