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

Gene ID: 8621, updated on 11-Sep-2019

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
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
109.20190905 current GRCh38.p13 (GCF_000001405.39) 7 NC_000007.14 (39949664..40099580)
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 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 Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What'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_003718.5NP_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)
    AC006023, AC072061, AJ297709, AK092534, AK223053, BC001274, BC080601, BM699295, BM727913, BU686489, CR748837
    Consensus CDS
    CCDS5461.1
    UniProtKB/Swiss-Prot
    Q14004
    UniProtKB/TrEMBL
    A0A024RA85, Q9BVE2
    Related
    ENSP00000181839.4, ENST00000181839.10
    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, ENST00000340829.10
    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.p13 Primary Assembly

Genomic

  1. NC_000007.14 Reference GRCh38.p13 Primary Assembly

    Range
    39949664..40099580
    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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