Cdk9 cyclin-dependent kinase 9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Cdk9provided by RGD
Official Full Name: cyclin-dependent kinase 9provided by RGD
Primary source: RGD:1359638
See related: AllianceGenome:RGD:1359638
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables chromatin binding activity. Involved in positive regulation of cardiac muscle hypertrophy and response to xenobiotic stimulus. Predicted to be located in PML body and cytoplasmic ribonucleoprotein granule. Predicted to be part of P-TEFb complex. Predicted to be active in nucleus. Orthologous to human CDK9 (cyclin dependent kinase 9). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Spleen (RPKM 124.8), Thymus (RPKM 121.4) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3p11

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (36394168..36399016, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (15996467..16001315, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (11742269..11747117, complement)

Chromosome 3 - NC_086021.1 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: 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Long noncoding RNA small nucleolar RNA host gene 5 facilitates neuropathic pain in spinal nerve injury by promoting SCN9A expression via CDK9.
Title: Long noncoding RNA small nucleolar RNA host gene 5 facilitates neuropathic pain in spinal nerve injury by promoting SCN9A expression via CDK9.
Differential Activation of P-TEFb Complexes in the Development of Cardiomyocyte Hypertrophy following Activation of Distinct G Protein-Coupled Receptors.
Title: Differential Activation of P-TEFb Complexes in the Development of Cardiomyocyte Hypertrophy following Activation of Distinct G Protein-Coupled Receptors.
Cdk9 forms a functional complex with the p300/GATA4 and is required for p300/GATA4- transcriptional pathway during cardiomyocyte hypertrophy
Title: Cyclin-dependent kinase-9 is a component of the p300/GATA4 complex required for phenylephrine-induced hypertrophy in cardiomyocytes.
Results indicate that P-TEFb is recruited in vivo to Myc-target promoters and CDK9 activity is important for Myc-dependent stimulation of responsive genes.
Title: P-TEFb is a crucial co-factor for Myc transactivation.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH129246 (e-PCR)
- UniSTS:212553

Cdk9 (e-PCR), detects polymorphism
- UniSTS:527281

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 7SK snRNA binding	IEA Inferred from Electronic Annotation more info
enables 7SK snRNA binding	ISO Inferred from Sequence Orthology more info
enables 7SK snRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II CTD heptapeptide repeat kinase activity	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II CTD heptapeptide repeat kinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables cyclin-dependent protein serine/threonine kinase activity	IBA Inferred from Biological aspect of Ancestor more info
enables cyclin-dependent protein serine/threonine kinase activity	IEA Inferred from Electronic Annotation more info
enables cyclin-dependent protein serine/threonine kinase activity	ISO Inferred from Sequence Orthology more info
enables kinase activity	ISO Inferred from Sequence Orthology more info
enables protein kinase binding	ISO Inferred from Sequence Orthology more info
enables protein serine kinase activity	IEA Inferred from Electronic Annotation more info
enables protein serine/threonine kinase activity	ISO Inferred from Sequence Orthology more info
enables protein serine/threonine kinase activity	ISS Inferred from Sequence or Structural Similarity more info
enables snRNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator binding	IEA Inferred from Electronic Annotation more info
enables transcription coactivator binding	ISO Inferred from Sequence Orthology more info
enables transcription elongation factor activity	IEA Inferred from Electronic Annotation more info
enables transcription elongation factor activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in cellular response to cytokine stimulus	IEA Inferred from Electronic Annotation more info
involved_in cellular response to cytokine stimulus	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein localization to chromatin	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of protein localization to chromatin	ISO Inferred from Sequence Orthology more info
involved_in nucleus localization	IEA Inferred from Electronic Annotation more info
involved_in nucleus localization	ISO Inferred from Sequence Orthology more info
involved_in positive regulation by host of viral transcription	IEA Inferred from Electronic Annotation more info
involved_in positive regulation by host of viral transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cardiac muscle hypertrophy	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of protein localization to chromatin	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of protein localization to chromatin	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of protein localization to chromatin	ISS Inferred from Sequence or Structural Similarity 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 by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity 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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription elongation by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within protein phosphorylation	ISO Inferred from Sequence Orthology more info
involved_in regulation of DNA repair	IEA Inferred from Electronic Annotation more info
involved_in regulation of DNA repair	ISO Inferred from Sequence Orthology more info
involved_in regulation of cell cycle	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of mRNA 3'-end processing	IEA Inferred from Electronic Annotation more info
involved_in regulation of mRNA 3'-end processing	ISO Inferred from Sequence Orthology more info
NOT involved_in regulation of mitotic cell cycle	ISO Inferred from Sequence Orthology more info
involved_in regulation of muscle cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in replication fork processing	IEA Inferred from Electronic Annotation more info
involved_in replication fork processing	ISO Inferred from Sequence Orthology more info
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in transcription elongation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transcription elongation-coupled chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in transcription elongation-coupled chromatin remodeling	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of P-TEFb complex	IEA Inferred from Electronic Annotation more info
part_of P-TEFb complex	ISO Inferred from Sequence Orthology more info
part_of P-TEFb complex	ISS Inferred from Sequence or Structural Similarity more info
located_in PML body	IEA Inferred from Electronic Annotation more info
located_in PML body	ISO Inferred from Sequence Orthology more info
part_of cyclin/CDK positive transcription elongation factor complex	ISO Inferred from Sequence Orthology more info
part_of cyclin/CDK positive transcription elongation factor complex	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic ribonucleoprotein granule	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic ribonucleoprotein granule	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
part_of transcription elongation factor complex	ISO Inferred from Sequence Orthology more info
part_of transcription elongation factor complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: cyclin-dependent kinase 9

Names: cell division protein kinase 9; cyclin-dependent kinase 9 (CDC2-related kinase)

NP_001007744.1

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.

mRNA and Protein(s)

NM_001007743.1 → NP_001007744.1 cyclin-dependent kinase 9

See identical proteins and their annotated locations for NP_001007744.1

Status: PROVISIONAL

Source sequence(s)

BC082037

UniProtKB/Swiss-Prot

Q641Z4

UniProtKB/TrEMBL

A6JU80

Conserved Domains (1) summary

cd07865
Location:6 → 315

STKc_CDK9; Catalytic domain of the Serine/Threonine Kinase, Cyclin-Dependent protein Kinase 9