Human Gene CDK13 (ENST00000181839.10) Description and Page Index
  Description: Homo sapiens cyclin dependent kinase 13 (CDK13), transcript variant 1, mRNA. (from RefSeq NM_003718)
RefSeq Summary (NM_003718): 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].
Gencode Transcript: ENST00000181839.10
Gencode Gene: ENSG00000065883.16
Transcript (Including UTRs)
   Position: hg38 chr7:39,950,256-40,099,580 Size: 149,325 Total Exon Count: 14 Strand: +
Coding Region
   Position: hg38 chr7:39,950,642-40,094,980 Size: 144,339 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesGeneReviewsMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr7:39,950,256-40,099,580)mRNA (may differ from genome)Protein (1512 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Cyclin-dependent kinase 13; EC=; EC=; AltName: Full=CDC2-related protein kinase 5; AltName: Full=Cell division cycle 2-like protein kinase 5; AltName: Full=Cell division protein kinase 13; Short=hCDK13; AltName: Full=Cholinesterase-related cell division controller;
FUNCTION: Cyclin-dependent kinase which displays CTD kinase activity and is required for RNA splicing. Has CTD kinase activity by hyperphosphorylating the C-terminal heptapeptide repeat domain (CTD) of the largest RNA polymerase II subunit RPB1, thereby acting as a key regulator of transcription elongation. Required for RNA splicing, probably by phosphorylating SRSF1/SF2. Required during hematopoiesis. In case of infection by HIV-1 virus, interacts with HIV-1 Tat protein acetylated at 'Lys-50' and 'Lys- 51', thereby increasing HIV-1 mRNA splicing and promoting the production of the doubly spliced HIV-1 protein Nef.
CATALYTIC ACTIVITY: ATP + [DNA-directed RNA polymerase] = ADP + [DNA-directed RNA polymerase] phosphate.
CATALYTIC ACTIVITY: ATP + a protein = ADP + a phosphoprotein.
SUBUNIT: Interacts with CCNL1 and CCNL2 (By similarity). Interacts with C1QBP. Interacts with HIV-1 Tat.
TISSUE SPECIFICITY: Expressed in fetal brain, liver, muscle and in adult brain. Also expressed in neuroblastoma and glioblastoma tumors.
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR.
RNA EDITING: Modified_positions=103; Note=Edited at about 88%.
SIMILARITY: Belongs to the protein kinase superfamily. CMGC Ser/Thr protein kinase family. CDC2/CDKX subfamily.
SIMILARITY: Contains 1 protein kinase domain.
SEQUENCE CAUTION: Sequence=AAA58424.1; Type=Frameshift; Positions=1006; Sequence=AAS07490.1; Type=Erroneous gene model prediction;

-  MalaCards Disease Associations
  MalaCards Gene Search: CDK13
Diseases sorted by gene-association score: congenital heart defects, dysmorphic facial features, and intellectual developmental disorder* (1232), corneal endothelial dystrophy, autosomal recessive (18), neuroblastoma (1), strabismus (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 12.38 RPKM in Ovary
Total median expression: 390.58 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -185.70386-0.481 Picture PostScript Text
3' UTR -1098.804600-0.239 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011009 - Kinase-like_dom
IPR000719 - Prot_kinase_cat_dom
IPR017441 - Protein_kinase_ATP_BS
IPR002290 - Ser/Thr_dual-sp_kinase_dom
IPR008271 - Ser/Thr_kinase_AS

Pfam Domains:
PF00069 - Protein kinase domain

ModBase Predicted Comparative 3D Structure on Q14004
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
Protein SequenceProtein Sequence    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003723 RNA binding
GO:0004672 protein kinase activity
GO:0004674 protein serine/threonine kinase activity
GO:0004693 cyclin-dependent protein serine/threonine kinase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008134 transcription factor binding
GO:0008353 RNA polymerase II carboxy-terminal domain kinase activity
GO:0016301 kinase activity
GO:0016740 transferase activity
GO:0019901 protein kinase binding
GO:0030332 cyclin binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0000380 alternative mRNA splicing, via spliceosome
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0006397 mRNA processing
GO:0006468 protein phosphorylation
GO:0007088 regulation of mitotic nuclear division
GO:0007275 multicellular organism development
GO:0008284 positive regulation of cell proliferation
GO:0008380 RNA splicing
GO:0016032 viral process
GO:0016310 phosphorylation
GO:0030097 hemopoiesis
GO:0043312 neutrophil degranulation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0070816 phosphorylation of RNA polymerase II C-terminal domain
GO:2000737 negative regulation of stem cell differentiation

Cellular Component:
GO:0002945 cyclin K-CDK13 complex
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005794 Golgi apparatus
GO:0005829 cytosol
GO:0008024 cyclin/CDK positive transcription elongation factor complex
GO:0016607 nuclear speck
GO:0019908 nuclear cyclin-dependent protein kinase holoenzyme complex
GO:1904813 ficolin-1-rich granule lumen

-  Descriptions from all associated GenBank mRNAs
  BC080601 - Homo sapiens cell division cycle 2-like 5 (cholinesterase-related cell division controller), mRNA (cDNA clone IMAGE:4908582).
AK092534 - Homo sapiens cDNA FLJ35215 fis, clone PROST2000079, highly similar to Homo sapiens mRNA for CDC2L5 protein kinase, (CDC2L5 gene), isoform 1.
LF384906 - JP 2014500723-A/192409: Polycomb-Associated Non-Coding RNAs.
MA620483 - JP 2018138019-A/192409: Polycomb-Associated Non-Coding RNAs.
AJ297709 - Homo sapiens mRNA for CDC2L5 protein kinase, (CDC2L5 gene), isoform 1.
AJ297710 - Homo sapiens mRNA for CDC2L5 protein kinase, (CDC2L5 gene), isoform 2.
BC168380 - Synthetic construct Homo sapiens clone IMAGE:100068276, MGC:195893 cell division cycle 2-like 5 (cholinesterase-related cell division controller) (CDC2L5) mRNA, encodes complete protein.
E03060 - DNA sequence of clone 14 including megakaryocytepoietin coding region.
M80629 - Human cdc2-related protein kinase (CHED) mRNA, complete cds.
CU674638 - Synthetic construct Homo sapiens gateway clone IMAGE:100018928 5' read CDC2L5 mRNA.
BC064414 - Homo sapiens cDNA clone IMAGE:5745754, partial cds.
JD520364 - Sequence 501388 from Patent EP1572962.
JD373484 - Sequence 354508 from Patent EP1572962.
JD458469 - Sequence 439493 from Patent EP1572962.
AK025500 - Homo sapiens cDNA: FLJ21847 fis, clone HEP01910.
LF331088 - JP 2014500723-A/138591: Polycomb-Associated Non-Coding RNAs.
MA566665 - JP 2018138019-A/138591: Polycomb-Associated Non-Coding RNAs.
LF331061 - JP 2014500723-A/138564: Polycomb-Associated Non-Coding RNAs.
MA566638 - JP 2018138019-A/138564: Polycomb-Associated Non-Coding RNAs.
BC001274 - Homo sapiens cell division cycle 2-like 5 (cholinesterase-related cell division controller), mRNA (cDNA clone IMAGE:3454160), complete cds.
LF331059 - JP 2014500723-A/138562: Polycomb-Associated Non-Coding RNAs.
MA566636 - JP 2018138019-A/138562: Polycomb-Associated Non-Coding RNAs.
LF331058 - JP 2014500723-A/138561: Polycomb-Associated Non-Coding RNAs.
MA566635 - JP 2018138019-A/138561: Polycomb-Associated Non-Coding RNAs.
KJ901894 - Synthetic construct Homo sapiens clone ccsbBroadEn_11288 CDK13 gene, encodes complete protein.
LF331053 - JP 2014500723-A/138556: Polycomb-Associated Non-Coding RNAs.
MA566630 - JP 2018138019-A/138556: Polycomb-Associated Non-Coding RNAs.
LF331049 - JP 2014500723-A/138552: Polycomb-Associated Non-Coding RNAs.
MA566626 - JP 2018138019-A/138552: Polycomb-Associated Non-Coding RNAs.
AK223053 - Homo sapiens mRNA for cell division cycle 2-like 5 isoform 2 variant, clone: JTH10784.
AB058694 - Homo sapiens mRNA for KIAA1791 protein, partial cds.
BX647326 - Homo sapiens mRNA; cDNA DKFZp779H0415 (from clone DKFZp779H0415).
LF331033 - JP 2014500723-A/138536: Polycomb-Associated Non-Coding RNAs.
MA566610 - JP 2018138019-A/138536: Polycomb-Associated Non-Coding RNAs.
LF331032 - JP 2014500723-A/138535: Polycomb-Associated Non-Coding RNAs.
MA566609 - JP 2018138019-A/138535: Polycomb-Associated Non-Coding RNAs.
LF331031 - JP 2014500723-A/138534: Polycomb-Associated Non-Coding RNAs.
MA566608 - JP 2018138019-A/138534: Polycomb-Associated Non-Coding RNAs.
LF331030 - JP 2014500723-A/138533: Polycomb-Associated Non-Coding RNAs.
MA566607 - JP 2018138019-A/138533: Polycomb-Associated Non-Coding RNAs.
JD355563 - Sequence 336587 from Patent EP1572962.
JD053596 - Sequence 34620 from Patent EP1572962.
JD504307 - Sequence 485331 from Patent EP1572962.
JD368172 - Sequence 349196 from Patent EP1572962.
AK130653 - Homo sapiens cDNA FLJ27143 fis, clone SPL09242.
LF331027 - JP 2014500723-A/138530: Polycomb-Associated Non-Coding RNAs.
MA566604 - JP 2018138019-A/138530: Polycomb-Associated Non-Coding RNAs.
LF331026 - JP 2014500723-A/138529: Polycomb-Associated Non-Coding RNAs.
MA566603 - JP 2018138019-A/138529: Polycomb-Associated Non-Coding RNAs.
LF331025 - JP 2014500723-A/138528: Polycomb-Associated Non-Coding RNAs.
MA566602 - JP 2018138019-A/138528: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q14004 (Reactome details) participates in the following event(s):

R-HSA-6797100 CCNK binds CDK13
R-HSA-6800434 Exocytosis of ficolin-rich granule lumen proteins
R-HSA-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-6798695 Neutrophil degranulation
R-HSA-212436 Generic Transcription Pathway
R-HSA-168249 Innate Immune System
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-168256 Immune System
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: CDC2L, CDC2L5, CDK13_HUMAN, CHED, KIAA1791, NM_003718, Q14004, Q53G78, Q6DKQ9, Q75MH4, Q75MH5, Q96JN4, Q9H4A0, Q9H4A1, Q9UDR4, uc003thh.1, uc003thh.2, uc003thh.3, uc003thh.4, uc003thh.5, uc003thh.6, uc003thh.7
UCSC ID: uc003thh.7
RefSeq Accession: NM_003718
Protein: Q14004 (aka CDK13_HUMAN)
CCDS: CCDS5461.1, CCDS5462.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CDK13:
cdk13-dis (CDK13-Related Disorder)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.