Cdk9 (cyclin-dependent kinase 9) - Rat Genome Database

Name: Cdk9
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

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Gene: Cdk9 (cyclin-dependent kinase 9) Rattus norvegicus

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Symbol:

Cdk9

Name:

cyclin-dependent kinase 9

RGD ID:

1359638

Description:

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); PARTICIPATES IN RNA polymerase II transcription elongation pathway; RNA polymerase II transcription pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Previously known as:

cell division protein kinase 9; cyclin-dependent kinase 9 (CDC2-related kinase); MGC95175

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	CDK9 (cyclin dependent kinase 9)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Cdk9 (cyclin dependent kinase 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Cdk9 (cyclin dependent kinase 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CDK9 (cyclin dependent kinase 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CDK9 (cyclin dependent kinase 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cdk9 (cyclin dependent kinase 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CDK9 (cyclin dependent kinase 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	CDK9 (cyclin dependent kinase 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cdk9 (cyclin dependent kinase 9)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	SFMBT2 (Scm like with four mbt domains 2)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	CDK9 (cyclin dependent kinase 9)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Cdk9 (cyclin dependent kinase 9)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	cdk9 (cyclin-dependent kinase 9 (CDC2-related kinase))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	CTK1	Alliance	DIOPT (InParanoid\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	Cdk9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	SGV1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|OrthoFinder)
Caenorhabditis elegans (roundworm):	cdk-9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	cdk9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	36,394,168 - 36,399,016 (-)	NCBI		GRCr8
mRatBN7.2	3	15,996,467 - 16,001,315 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	15,996,468 - 16,002,410 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	19,065,041 - 19,069,877 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	27,650,044 - 27,654,880 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	25,901,304 - 25,906,154 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	11,742,269 - 11,747,117 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	11,742,266 - 11,747,113 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	17,081,164 - 17,086,012 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	11,672,861 - 11,677,709 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	11,569,232 - 11,574,081 (-)	NCBI
Celera	3	10,737,357 - 10,742,205 (-)	NCBI		Celera
Cytogenetic Map	3	p11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

congenital disorder of glycosylation Iu (ISO)

congestive heart failure (ISO)

developmental and epileptic encephalopathy (ISO)

developmental and epileptic encephalopathy 31A (ISO)

dystonia (ISO)

early infantile epileptic encephalopathy (ISO)

Experimental Diabetes Mellitus (IEP)

medulloblastoma (ISO)

primary coenzyme Q10 deficiency 7 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane (EXP,ISO)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4,6-tribromophenol (ISO)

2,4-dinitrotoluene (EXP)

3,3',5,5'-tetrabromobisphenol A (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

4-hydroxynon-2-enal (ISO)

afimoxifene (ISO)

aflatoxin B1 (ISO)

Aflatoxin B2 alpha (ISO)

aldehydo-D-glucose (ISO)

all-trans-retinoic acid (ISO)

alvocidib (ISO)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (EXP,ISO)

benzo[a]pyrene diol epoxide I (ISO)

berberine (EXP)

bisphenol A (EXP)

bisphenol F (ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

Cinobufagin (ISO)

clofibrate (ISO)

curcumin (ISO)

cyclosporin A (ISO)

cypermethrin (EXP)

D-glucose (ISO)

decabromodiphenyl ether (ISO)

deferasirox (ISO)

dexamethasone (ISO)

diazinon (EXP)

dimethylarsinic acid (EXP)

dinaciclib (ISO)

disodium selenite (ISO)

divanadium pentaoxide (ISO)

doxorubicin (ISO)

enzyme inhibitor (ISO)

fenofibrate (EXP)

fenvalerate (EXP)

folic acid (ISO)

formaldehyde (ISO)

FR900359 (ISO)

glucose (ISO)

hydrogen peroxide (ISO)

indometacin (ISO)

ivermectin (ISO)

lipopolysaccharide (ISO)

lycopene (ISO)

methamphetamine (ISO)

nickel dichloride (EXP)

ozone (ISO)

paracetamol (ISO)

perfluorooctanoic acid (ISO)

PhIP (ISO)

progesterone (ISO)

quercetin (ISO)

rucaparib (ISO)

sodium arsenate (ISO)

sodium arsenite (ISO)

sorafenib (ISO)

streptozocin (EXP,ISO)

sunitinib (ISO)

thioacetamide (EXP)

thiram (ISO)

titanium dioxide (ISO)

triphenyl phosphate (ISO)

triptonide (ISO)

urethane (ISO)

valproic acid (ISO)

wogonin (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to cytokine stimulus (IEA,ISO)

DNA repair (IEA)

negative regulation of protein localization to chromatin (IEA,ISO)

nucleus localization (IEA,ISO)

positive regulation by host of viral transcription (IEA,ISO)

positive regulation of cardiac muscle hypertrophy (IMP)

positive regulation of protein localization to chromatin (IEA,ISO,ISS)

positive regulation of transcription by RNA polymerase II (ISO,ISS)

positive regulation of transcription elongation by RNA polymerase II (IBA,IEA,ISO,ISS)

protein phosphorylation (ISO)

regulation of cell cycle (IEA,ISO)

regulation of DNA repair (IEA,ISO)

regulation of mitotic cell cycle (ISO)

regulation of mRNA 3'-end processing (IEA,ISO)

regulation of muscle cell differentiation (IEA,ISO)

replication fork processing (IEA,ISO)

response to xenobiotic stimulus (IEP)

transcription by RNA polymerase II (ISO,ISS)

transcription elongation by RNA polymerase II (ISO)

transcription elongation-coupled chromatin remodeling (IEA,ISO)

Cellular Component

cyclin/CDK positive transcription elongation factor complex (ISO,ISS)

cytoplasm (IEA)

cytoplasmic ribonucleoprotein granule (IEA,ISO)

nucleoplasm (ISO)

nucleus (IBA,ISO)

P-TEFb complex (IEA,ISO,ISS)

PML body (IEA,ISO)

transcription elongation factor complex (ISO,ISS)

Molecular Function

7SK snRNA binding (IEA,ISO,ISS)

ATP binding (IEA)

chromatin binding (IDA,ISO)

cyclin-dependent protein serine/threonine kinase activity (IBA,IEA,ISO)

DNA binding (IEA,ISO)

kinase activity (ISO)

protein binding (ISO)

protein kinase binding (ISO)

protein serine kinase activity (IEA)

protein serine/threonine kinase activity (ISO,ISS)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (ISO)

RNA polymerase II CTD heptapeptide repeat kinase activity (IBA,IEA,ISO,ISS)

RNA polymerase II CTD heptapeptide repeat S2 kinase activity (IEA)

RNA polymerase II CTD heptapeptide repeat S5 kinase activity (IEA)

RNA polymerase II CTD heptapeptide repeat S7 kinase activity (IEA)

RNA polymerase II CTD heptapeptide repeat T4 kinase activity (IEA)

RNA polymerase II CTD heptapeptide repeat Y1 kinase activity (IEA)

snRNA binding (ISO)

transcription cis-regulatory region binding (ISO)

transcription coactivator binding (IEA,ISO)

transcription elongation factor activity (IEA,ISO)

transcription factor binding (IPI)

Molecular Pathway Annotations Click to see Annotation Detail View

RNA polymerase II transcription elongation pathway (ISO)

RNA polymerase II transcription pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Updating the RNA polymerase CTD code: adding gene-specific layers.	Egloff S, etal., Trends Genet. 2012 Jul;28(7):333-41. doi: 10.1016/j.tig.2012.03.007. Epub 2012 May 21.
2.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3.	The writers, readers, and functions of the RNA polymerase II C-terminal domain code.	Jeronimo C, etal., Chem Rev. 2013 Nov 13;113(11):8491-522. doi: 10.1021/cr4001397. Epub 2013 Jul 10.
4.	Control of transcriptional elongation.	Kwak H and Lis JT, Annu Rev Genet. 2013;47:483-508. doi: 10.1146/annurev-genet-110711-155440. Epub 2013 Sep 11.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	GOA pipeline	RGD automated data pipeline
7.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
8.	Activation of cardiac Cdk9 represses PGC-1 and confers a predisposition to heart failure.	Sano M, etal., EMBO J 2004 Sep 1;23(17):3559-69. Epub 2004 Aug 5.
9.	Activation of MyoD-dependent transcription by cdk9/cyclin T2.	Simone C, etal., Oncogene 2002 Jun 13;21(26):4137-48.
10.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
11.	Cyclin-dependent kinase-9 is a component of the p300/GATA4 complex required for phenylephrine-induced hypertrophy in cardiomyocytes.	Sunagawa Y, etal., J Biol Chem. 2010 Mar 26;285(13):9556-68. doi: 10.1074/jbc.M109.070458. Epub 2010 Jan 17.
12.	Protective effect of berberine on antioxidant enzymes and positive transcription elongation factor b expression in diabetic rat liver.	Zhou JY and Zhou SW, Fitoterapia. 2011 Mar;82(2):184-9. doi: 10.1016/j.fitote.2010.08.019. Epub 2010 Sep 7.

Additional References at PubMed

PMID:9499409	PMID:11713533	PMID:12037672	PMID:12721286	PMID:15489334	PMID:15905409	PMID:16109376	PMID:16245309	PMID:17700062	PMID:17956865	PMID:18250157	PMID:19575011
PMID:19844166	PMID:19946888	PMID:20493174	PMID:20570862	PMID:20930849	PMID:21245044	PMID:22195968	PMID:22509028	PMID:22547058	PMID:22767893	PMID:23154982	PMID:23752591
PMID:28426094	PMID:32341082	PMID:38167752

Genomics

Comparative Map Data

Cdk9
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	3	36,394,168 - 36,399,016 (-)	NCBI		GRCr8
mRatBN7.2	3	15,996,467 - 16,001,315 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	3	15,996,468 - 16,002,410 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	3	19,065,041 - 19,069,877 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	3	27,650,044 - 27,654,880 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	3	25,901,304 - 25,906,154 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	3	11,742,269 - 11,747,117 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	3	11,742,266 - 11,747,113 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	3	17,081,164 - 17,086,012 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	3	11,672,861 - 11,677,709 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	3	11,569,232 - 11,574,081 (-)	NCBI
Celera	3	10,737,357 - 10,742,205 (-)	NCBI		Celera
Cytogenetic Map	3	p11	NCBI

CDK9
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	9	127,786,034 - 127,790,792 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	9	127,785,679 - 127,790,792 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	9	130,548,313 - 130,553,071 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	9	129,588,152 - 129,592,184 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	9	127,627,890 - 127,631,917	NCBI
Celera	9	101,199,168 - 101,203,915 (+)	NCBI		Celera
Cytogenetic Map	9	q34.11	NCBI
HuRef	9	100,164,574 - 100,169,598 (+)	NCBI		HuRef
CHM1_1	9	130,699,854 - 130,704,602 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	9	139,993,485 - 139,998,243 (+)	NCBI		T2T-CHM13v2.0

Cdk9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	2	32,595,794 - 32,608,098 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	2	32,595,796 - 32,603,088 (-)	Ensembl		GRCm39 Ensembl
GRCm38	2	32,705,782 - 32,712,784 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	2	32,705,784 - 32,713,076 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	2	32,561,302 - 32,568,304 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	2	32,529,447 - 32,534,794 (-)	NCBI		MGSCv36	mm8
Celera	2	32,412,389 - 32,419,391 (-)	NCBI		Celera
Cytogenetic Map	2	B	NCBI
cM Map	2	22.09	NCBI

Cdk9
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955419	873,289 - 883,160 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955419	874,959 - 883,160 (-)	NCBI	ChiLan1.0	ChiLan1.0

CDK9
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	11	11,558,761 - 11,569,295 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	9	11,561,106 - 11,571,580 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	9	98,905,468 - 98,909,923 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	9	127,580,862 - 127,584,936 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	9	127,580,862 - 127,584,935 (+)	Ensembl	panpan1.1		panPan2

CDK9
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	55,615,271 - 55,619,493 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	55,615,827 - 55,620,236 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	54,808,829 - 54,812,940 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	56,536,951 - 56,541,065 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	9	56,536,954 - 56,541,348 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	9	55,296,987 - 55,301,098 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	55,611,719 - 55,615,827 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	55,703,144 - 55,707,256 (-)	NCBI		UU_Cfam_GSD_1.0

Cdk9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404947	195,678,357 - 195,682,223 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936487	15,446,858 - 15,452,796 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936487	15,446,864 - 15,450,750 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CDK9
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	1	268,276,841 - 268,281,052 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	1	268,277,083 - 268,280,493 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	1	302,142,973 - 302,146,162 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CDK9
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	12	10,342,240 - 10,346,792 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	12	10,342,801 - 10,346,502 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666079	5,874,123 - 5,879,334 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Cdk9
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624760	7,760,474 - 7,765,711 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Cdk9
18 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	376
Count of miRNA genes:	220
Interacting mature miRNAs:	258
Transcripts:	ENSRNOT00000032893
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1358357	Srcrtb1	Stress Responsive Cort Basal QTL 1	6.36	0.002	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	3	8658162	27494778	Rat
6893355	Bw101	Body weight QTL 101	0.4	0.38	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
10401810	Kidm53	Kidney mass QTL 53			kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	3	8227194	47233430	Rat
1298526	Arunc3	Aerobic running capacity QTL 3	2.2		exercise endurance trait (VT:0002332)	maximum distance run on treadmill (CMO:0001406)	3	8227194	33703538	Rat
8693641	Alc30	Alcohol consumption QTL 30	2	0.739	drinking behavior trait (VT:0001422)	calculated ethanol drink intake rate (CMO:0001615)	3	10434306	24512004	Rat
2298542	Neuinf11	Neuroinflammation QTL 11	3.9		nervous system integrity trait (VT:0010566)	spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)	3	15005422	76927699	Rat
1558657	Cm43	Cardiac mass QTL 43	6.6	3e-08	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	Rat
631568	Bp92	Blood pressure QTL 92	2.2	0.005	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	39874793	Rat
6893363	Bw105	Body weight QTL 105	2.6	0.0036	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
61468	Bp15	Blood pressure QTL 15	4.4		blood pressure trait (VT:0000183)	pulse pressure (CMO:0000292)	3	1	33278763	Rat
631831	Alc8	Alcohol consumption QTL 8	2.7		consumption behavior trait (VT:0002069)	calculated ethanol drink intake rate (CMO:0001615)	3	1	33230976	Rat
1558647	Cm46	Cardiac mass QTL 46	5.4	0.0000055	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	3	10778823	30356773	Rat
4889966	Bss95	Bone structure and strength QTL 95	4.4		tibia area (VT:1000281)	tibia-fibula cross-sectional area (CMO:0001718)	3	1	36847613	Rat
1558654	Bw56	Body weight QTL 56	4.5	0.0000171	body mass (VT:0001259)	body weight (CMO:0000012)	3	10778704	30357018	Rat
1558650	Cm48	Cardiac mass QTL 48	4	0.0001	heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	3	10778823	30356773	Rat
1358905	Hrtrt17	Heart rate QTL 17	5.9	0.000014	heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	3	10861912	89878372	Rat
70191	BpQTLcluster4	Blood pressure QTL cluster 4	3		arterial blood pressure trait (VT:2000000)	absolute change in systolic blood pressure (CMO:0000607)	3	10778704	50302886	Rat
631545	Bp85	Blood pressure QTL 85	3.1		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	3	1	33278763	Rat
1358885	Bp251	Blood pressure QTL 251	3.8		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat
631679	Cm10	Cardiac mass QTL 10	7.34	0.0001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	3	1	31158234	Rat
2290452	Scl56	Serum cholesterol level QTL 56	2.26		blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	3	1	91609953	Rat
70203	Gcr2	Gastric cancer resistance QTL 2	2.6		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	3	8658162	27494778	Rat
70202	Alc19	Alcohol consumption QTL 19	2.5		drinking behavior trait (VT:0001422)	ethanol intake volume to total fluid intake volume ratio (CMO:0001591)	3	1	27494778	Rat
2312664	Scl62	Serum cholesterol level QTL 62		0.05	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	3	1	38710544	Rat
1358888	Bp264	Blood pressure QTL 264	4.43		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	3	14489145	121056321	Rat

Markers in Region

RH129246

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	15,996,557 - 15,996,773 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	11,742,360 - 11,742,575	NCBI	Rnor6.0
Rnor_5.0	3	17,081,255 - 17,081,470	UniSTS	Rnor5.0
RGSC_v3.4	3	11,672,952 - 11,673,167	UniSTS	RGSC3.4
Celera	3	10,737,448 - 10,737,663	UniSTS
RH 3.4 Map	3	70.3	UniSTS
Cytogenetic Map	3	p11	UniSTS

Cdk9

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	3	15,996,503 - 15,998,178 (+)	MAPPER	mRatBN7.2
Rnor_6.0	3	11,742,306 - 11,743,980	NCBI	Rnor6.0
Rnor_5.0	3	17,081,201 - 17,082,875	UniSTS	Rnor5.0
RGSC_v3.4	3	11,672,898 - 11,674,572	UniSTS	RGSC3.4
Celera	3	10,737,394 - 10,739,068	UniSTS
Cytogenetic Map	3	p11	UniSTS

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	nervous system	renal system	reproductive system	respiratory system
9	11	49	113	91	90	59	25	59	6	218	97	93	45	60	31

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001007743	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC142126	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC082037	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000003	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000032893 ⟹ ENSRNOP00000037778

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	3	15,996,468 - 16,002,410 (-)	Ensembl
Rnor_6.0 Ensembl	3	11,742,266 - 11,747,113 (-)	Ensembl

RefSeq Acc Id:

NM_001007743 ⟹ NP_001007744

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	3	36,394,168 - 36,399,016 (-)	NCBI
mRatBN7.2	3	15,996,467 - 16,001,315 (-)	NCBI
Rnor_6.0	3	11,742,269 - 11,747,117 (-)	NCBI
Rnor_5.0	3	17,081,164 - 17,086,012 (-)	NCBI
RGSC_v3.4	3	11,672,861 - 11,677,709 (-)	RGD
Celera	3	10,737,357 - 10,742,205 (-)	RGD

Sequence:

show sequence

GCGGCGGCGGCGGCGGCGGCGGCGGCGGCGCGCTGGAGGCGGCCATGGCCAAGCAGTACGACTC
AGTGGAATGCCCGTTTTGCGATGAGGTCACCAAGTACGAGAAACTTGCCAAGATCGGCCAAGGC
ACATTCGGGGAAGTATTTAAAGCCAAGCACCGTCAGACCGGCCAGAAGGTGGCTCTGAAGAAAG
TGTTGATGGAGAATGAGAAGGAGGGGTTCCCCATCACAGCCTTGCGGGAAATCAAGATTCTACA
GCTCCTAAAGCACGAGAATGTGGTCAACCTGATTGAGATTTGTCGAACCAAAGCTTCACCCTAT
AACCGCTGCAAAGGCAGCATCTATCTGGTGTTCGACTTCTGTGAGCATGACCTCGCTGGGCTGC
TGAGCAATGTCTTAGTGAAGTTCACGTTGTCTGAGATCAAGAGAGTAATGCAGATGCTGCTGAA
TGGCCTCTACTACATCCACAGGAACAAGATCCTGCACAGGGACATGAAGGCTGCCAACGTGCTC
ATTACCCGAGATGGGGTCCTAAAGCTGGCAGATTTTGGGCTGGCTCGCGCCTTCAGCCTAGCTA
AGAATAGCCAGCCCAACCGATACACCAACCGTGTGGTGACATTGTGGTACCGACCTCCGGAGCT
CCTGCTCGGAGAGCGGGACTACGGCCCGCCCATTGACCTGTGGGGTGCTGGGTGCATCATGGCA
GAGATGTGGACCCGCAGCCCCATCATGCAGGGCAACACAGAGCAGCACCAGCTTGCCCTCATCA
GCCAGCTCTGTGGCTCCATCACTCCAGAGGTGTGGCCAAACGTGGACAAGTATGAGCTGTTCGA
AAAGCTGGAACTGGTCAAGGGCCAGAAGCGGAAGGTGAAGGACCGTCTGAAGGCCTACGTCCGG
GACCCCTATGCTCTGGACCTCATTGACAAGCTGCTGGTGCTGGACCCTGCACAGCGGATTGACA
GTGATGATGCCCTCAACCATGACTTCTTCTGGTCGGACCCCATGCCCTCGGACCTCAAGGGCAT
GCTGTCTACTCACTTGACGTCTATGTTTGAGTACCTGGCCCCACCACGACGGAAGGGTAGCCAG
ATCACCCAGCAGTCCACCAACCAGAGCCGAAATCCCGCCACTACCAACCAGACGGAATTTGAAC
GTGTCTTCTGAGGCTGTCGCTGGCCGGTGTTCTTAGGTTAGGGGTGGATTGCTTCTGCTCTGAC
TTGCATGAACATGTGACATGATGGGACGTTTGAGATTTTCTCCTCCAGTACATATCAACTCCAC
CCTGGCGCTGGGAACAGCTGCCTGAGTGGACTGGGGCAGAGCATTGGCTGCAAGCCCTGAGGGT
CCTGGGGCTGTCCTGCCTGCCTCTCTCTGGAGGTCTCAGCATGGATACGAAGTGGGGTGGGAGA
AGCTCACCCACTGTGACTTTTAAGAACTCCTGTGTGATGGGAGGAAGGTACAGGTTCCTCACCA
TCCCCAGCCCTTCCTCTGGATGAGGATGTGAAGGACAGAGGCATCTCCAAAATGGGCTACTTTT
GGTATAGACCTTAGGAGTGTGGGGCTGGTGTAAGCTCTTGGTTCCTTTAAAAGGAGAATTTTAT
TTTGTTTTGTTCAGTTTAGACATTCCTGGATGCAGTTTGATTGGTTAAATTAAAAGTTGATTTT
TTTTTCCAGTAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001007744	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH82037	(Get FASTA)	NCBI Sequence Viewer
	EDL93216	(Get FASTA)	NCBI Sequence Viewer
	EDL93217	(Get FASTA)	NCBI Sequence Viewer
	EDL93218	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000037778.4
GenBank Protein	Q641Z4	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_001007744 ⟸ NM_001007743

- UniProtKB:

Q641Z4 (UniProtKB/Swiss-Prot), A6JU80 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MAKQYDSVECPFCDEVTKYEKLAKIGQGTFGEVFKAKHRQTGQKVALKKVLMENEKEGFPITAL
REIKILQLLKHENVVNLIEICRTKASPYNRCKGSIYLVFDFCEHDLAGLLSNVLVKFTLSEIKR
VMQMLLNGLYYIHRNKILHRDMKAANVLITRDGVLKLADFGLARAFSLAKNSQPNRYTNRVVTL
WYRPPELLLGERDYGPPIDLWGAGCIMAEMWTRSPIMQGNTEQHQLALISQLCGSITPEVWPNV
DKYELFEKLELVKGQKRKVKDRLKAYVRDPYALDLIDKLLVLDPAQRIDSDDALNHDFFWSDPM
PSDLKGMLSTHLTSMFEYLAPPRRKGSQITQQSTNQSRNPATTNQTEFERVF

hide sequence

Ensembl Acc Id:

ENSRNOP00000037778 ⟸ ENSRNOT00000032893

Protein Domains

Protein kinase

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q641Z4-F1-model_v2	AlphaFold	Q641Z4	1-372	view protein structure

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13691991

Promoter ID:

EPDNEW_R2516

Type:

initiation region

Name:

Cdk9_1

Description:

cyclin-dependent kinase 9

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	3	11,747,183 - 11,747,243	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1359638	AgrOrtholog
BioCyc Gene	G2FUF-50126	BioCyc
Ensembl Genes	ENSRNOG00000022586	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000032893.5	UniProtKB/TrEMBL
Gene3D-CATH	Transferase(Phosphotransferase) domain 1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7130973	IMAGE-MGC_LOAD
InterPro	CDK	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Kinase-like_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Prot_kinase_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Protein_kinase_ATP_BS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ser/Thr_kinase_AS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:362110	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:95175	IMAGE-MGC_LOAD
NCBI Gene	362110	ENTREZGENE
PANTHER	CELL DIVISION PROTEIN KINASE	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	CYCLIN-DEPENDENT KINASE 9	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Pkinase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Cdk9	PhenoGen
PROSITE	PROTEIN_KINASE_ATP	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PROTEIN_KINASE_DOM	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PROTEIN_KINASE_ST	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000022586	RatGTEx
SMART	S_TKc	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF56112	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A8L2QJI9_RAT	UniProtKB/TrEMBL
	A6JU79_RAT	UniProtKB/TrEMBL
	A6JU80	ENTREZGENE, UniProtKB/TrEMBL
	A6JU81_RAT	UniProtKB/TrEMBL
	CDK9_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-09	Cdk9	cyclin-dependent kinase 9	Cdk9	cyclin-dependent kinase 9 (CDC2-related kinase)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-03-30	Cdk9	cyclin-dependent kinase 9 (CDC2-related kinase)		cyclin-dependent kinase 9	Name updated	1299863	APPROVED
2005-07-29	Cdk9	cyclin-dependent kinase 9			Symbol and Name status set to provisional	70820	PROVISIONAL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - CTD

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Imported Disease Annotations - ClinVar

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