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

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; AllianceGenome:HGNC:1733
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: mouse all
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Genomic context

Location:: 7p14.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (39950256..40099580)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (40107756..40257030)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (39989855..40139179)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CDK13 promotes lipid deposition and prostate cancer progression by stimulating NSUN5-mediated m5C modification of ACC1 mRNA.
Title: CDK13 promotes lipid deposition and prostate cancer progression by stimulating NSUN5-mediated m5C modification of ACC1 mRNA.
CDK13-related disorder: a deep characterization of speech and language abilities and addition of 33 novel cases.
Title: CDK13-related disorder: a deep characterization of speech and language abilities and addition of 33 novel cases.
CDK12/13 promote splicing of proximal introns by enhancing the interaction between RNA polymerase II and the splicing factor SF3B1.
Title: CDK12/13 promote splicing of proximal introns by enhancing the interaction between RNA polymerase II and the splicing factor SF3B1.
Oncogenic CDK13 mutations impede nuclear RNA surveillance.
Title: Oncogenic CDK13 mutations impede nuclear RNA surveillance.
CDK13-related disorder: Report of a series of 18 previously unpublished individuals and description of an epigenetic signature.
Title: CDK13-related disorder: Report of a series of 18 previously unpublished individuals and description of an epigenetic signature.
HIV-1 Nef interacts with the cyclin K/CDK13 complex to antagonize SERINC5 for optimal viral infectivity.
Title: HIV-1 Nef interacts with the cyclin K/CDK13 complex to antagonize SERINC5 for optimal viral infectivity.
An ADAR1-dependent RNA editing event in the cyclin-dependent kinase CDK13 promotes thyroid cancer hallmarks.
Title: An ADAR1-dependent RNA editing event in the cyclin-dependent kinase CDK13 promotes thyroid cancer hallmarks.
Expression of CDK13 Was Associated with Prognosis and Expression of HIF-1alpha and beclin1 in Breast Cancer Patients.
Title: Expression of CDK13 Was Associated with Prognosis and Expression of HIF-1α and beclin1 in Breast Cancer Patients.
Wolfram-like syndrome with bicuspid aortic valve due to a homozygous missense variant in CDK13.
Title: Wolfram-like syndrome with bicuspid aortic valve due to a homozygous missense variant in CDK13.
CDK13 upregulation-induced formation of the positive feedback loop among circCDK13, miR-212-5p/miR-449a and E2F5 contributes to prostate carcinogenesis.
Title: CDK13 upregulation-induced formation of the positive feedback loop among circCDK13, miR-212-5p/miR-449a and E2F5 contributes to prostate carcinogenesis.

Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Congenital heart defects, dysmorphic facial features, and intellectual developmental disorder MedGen: C4479246 OMIM: 617360 GeneReviews: CDK13-Related Disorder	Compare labs

Copy number response

Description
Copy number response Haploinsufficency Some evidence for dosage pathogenicity (Last evaluated 2024-03-27) ClinGen Genome Curation PagePubMed Triplosensitivity No evidence available (Last evaluated 2024-03-27) ClinGen Genome Curation Page

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

CDC2L5 (e-PCR)
- UniSTS:503553

HSC209_(7Gr397mb) (e-PCR)
- UniSTS:255234

RH139622 (e-PCR)
- UniSTS:221706

CDC2L5_3913 (e-PCR)
- UniSTS:462093

RH47846 (e-PCR)
- UniSTS:51482

D7S3089 (e-PCR)
- UniSTS:186658

GDB:1318476 (e-PCR)
- UniSTS:30755

G16022 (e-PCR)
- UniSTS:53283

RH45694 (e-PCR)
- UniSTS:36675

RH93376 (e-PCR)
- UniSTS:84819

RH66471 (e-PCR)
- UniSTS:40555

RH93929 (e-PCR)
- UniSTS:85425

RH119268 (e-PCR)
- UniSTS:133830

RH120012 (e-PCR)
- UniSTS:133336

RH36512 (e-PCR)
- UniSTS:59356

GDB:1318631 (e-PCR)
- UniSTS:77054

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables RNA polymerase II CTD heptapeptide repeat S2 kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S5 kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat S7 kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat T4 kinase activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat Y1 kinase activity	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	IDA Inferred from Direct Assay more info	PubMed
enables cyclin binding	IBA Inferred from Biological aspect of Ancestor more info
enables cyclin binding	IPI Inferred from Physical Interaction more info	PubMed
enables cyclin-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase activity	TAS Traceable Author Statement more info	PubMed
enables protein kinase binding	IEA Inferred from Electronic Annotation more info
enables protein serine kinase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in alternative mRNA splicing, via spliceosome	ISS Inferred from Sequence or Structural Similarity more info
involved_in alternative mRNA splicing, via spliceosome	TAS Traceable Author Statement more info	PubMed
involved_in hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of stem cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of cell cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of signal transduction	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info
part_of cyclin K-CDK13 complex	IPI Inferred from Physical Interaction more info	PubMed
part_of cyclin/CDK positive transcription elongation factor complex	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in extracellular region	TAS Traceable Author Statement more info
located_in extracellular space	HDA more info	PubMed
located_in ficolin-1-rich granule lumen	TAS Traceable Author Statement more info
part_of nuclear cyclin-dependent protein kinase holoenzyme complex	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear speck	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement 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: 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

EC 2.7.11.22

EC 2.7.11.23

NP_112557.2

EC 2.7.11.22

EC 2.7.11.23

XP_011513899.1

EC 2.7.11.22

EC 2.7.11.23

XP_016868239.1

EC 2.7.11.22

EC 2.7.11.23

XP_016868240.1

EC 2.7.11.22

EC 2.7.11.23

XP_054215253.1

EC 2.7.11.22

EC 2.7.11.23

XP_054215254.1

EC 2.7.11.22

EC 2.7.11.23

XP_054215255.1

EC 2.7.11.22

EC 2.7.11.23

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.

Genomic

NG_052965.2 RefSeqGene

Range

5002..154326

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_003718.5 → NP_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, Q53G78, Q6DKQ9, Q75MH4, Q75MH5, Q96JN4, Q9H4A0, Q9H4A1, Q9UDR4

UniProtKB/TrEMBL

A0A2R8Y4Z0

Related

ENSP00000181839.4, ENST00000181839.10

Conserved Domains (2) summary

smart00220
Location:705 → 994

S_TKc; Serine/Threonine protein kinases, catalytic domain

cd07864
Location:697 → 998

STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12
NM_031267.3 → NP_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/TrEMBL

A0A2R8Y4Z0

Related

ENSP00000340557.5, ENST00000340829.10

Conserved Domains (2) summary

smart00220
Location:705 → 994

S_TKc; Serine/Threonine protein kinases, catalytic domain

cd07864
Location:697 → 998

STKc_CDK12; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 12

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000007.14 Reference GRCh38.p14 Primary Assembly

Range

39950256..40099580

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017012750.3 → XP_016868239.1 cyclin-dependent kinase 13 isoform X1

UniProtKB/TrEMBL

A0A2R8Y4Z0
XM_017012751.3 → XP_016868240.1 cyclin-dependent kinase 13 isoform X2

UniProtKB/TrEMBL

A0A2R8Y4Z0
XM_011515597.4 → XP_011513899.1 cyclin-dependent kinase 13 isoform X3

Conserved Domains (2) summary

smart00220
Location:705 → 868

S_TKc; Serine/Threonine protein kinases, catalytic domain

cl21453
Location:697 → 881

PKc_like; Protein Kinases, catalytic domain