CDK9

General Information

Gene Name       : CDK9
Gene ID             : ENSG00000136807.13
Essential Gene : Yes

Functions

Localization

Domains (AlphaFold: CDK9)


Antibody Validation

 View validation images for all CDK9 antibodies

Expression Level in Cell lines

Cell Line Gene Name Ensembl ID Rep1 TPM Rep2 TPM Average TPM Experiment ID
Gm12878CDK9ENSG00000136807.1326.3038.7932.55ENCSR000AEF
HepG2CDK9ENSG00000136807.1323.3922.4822.94ENCSR985KAT
K562CDK9ENSG00000136807.1343.7236.4040.06ENCSR000AEO

Assays

2 Released experiments are available on ENCORE database.

Assay TypeExp_NameENCODE IDTarget labelBiosampleStatusLinked AntibodyControlsMethodNote
knockdown followed by RNA-seq CDK9-BGKcLV28-K562ENCSR049YEZCDK9K562ReleasedENCSR220DTX   CRISPRKD% = 57.5,61.3
knockdown followed by RNA-seq CDK9-BGHcLV29-HepG2ENCSR470SBKCDK9HepG2ReleasedENCSR462MFN   CRISPRKD% = 70.4,83.8






  eCLIP  

No eCLIP experiment available



  Antibody Validation  
  GeneName    Antibody_DCC_ID    Product_ID    Lot_ID    Phosphate    HepG2 Primary Validation    K562 Primary Validation    HepG2 Secondary Validation    K562 Secondary Validation  
CDK9ENCAB348XNDA303-493A1Released, ENCODE4BGHcLV29-13, Released, ENCODE4BGKcLV28-13, Released, ENCODE4
CDK92316S9Submitted, ENCORE2BGHcLV29-13, Submitted, ENCORE2


  KD RNA-Seq  
  GeneName    Cell_Line    Method    Exp_ID    Control_ID    Sample_reps    Control_reps    KD%    Status    Project    Note  
CDK9K562CRISPRENCSR049YEZENCSR220DTXCDK9-BGKcLV28-13,CDK9-BGKcLV28-14NT-BGKcLV28-1,NT-BGKcLV28-257.5,61.3ReleasedENCODE4
CDK9HepG2CRISPRENCSR470SBKENCSR462MFNCDK9-BGHcLV29-13,CDK9-BGHcLV29-14NT-BGHcLV29-1,NT-BGHcLV29-270.4,83.8ReleasedENCODE4


  RNA Bind-n-Seqn  

No RBNS experiment available



  Localization Image in HepG2  

No Localization Information available













RBP Antibody InfoPrimary-HepG2Secondary-HepG2Primary-K562Secondary-K562Primary-UBERONPrimary-Hela
CDK9Product_ID: A303-493A
Lot_ID: 1
Source: Bethyl Labs
Target Name: CDK9-human		 CDK9-HEPG2-CRISPR-A303-493A.png<br>Caption: Western blot following CRISPR against CDK9 in HepG2 whole cell lysate using CDK9 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against CDK9. CDK9 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 Bethyl_A303-493A_1_CDK9.png<br>Caption: IP-WB analysis of K562 whole cell lysate using the CDK9 specific antibody, A303-493A. Lanes 1 and 2 are 2.5% of five million whole cell lysate input and 50% of IP enrichment, respectively, using a normal IgG antibody. Lane 3 is 50% of IP enrichment from five million whole cell lysate using the CDK9-specific antibody, A303-493A. The same antibody was used to detect protein levels via Western blot. This antibody passes preliminary validation and will be further pursued for secondary validation. *NOTE* Protein sizes are taken from Genecards.org and are only estimates based on sequence. Actual protein size may differ based on protein characteristics and electrophoresis method used.
 CDK9-K562-CRISPR-A303-493A.png<br>Caption: Western blot following CRISPR against CDK9 in K562 whole cell lysate using CDK9 specific antibody. Lane 1 is a ladder, lane 2 is K562 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against CDK9. CDK9 protein appears as the green arrow, GAPDH serves as a control and appears in red arrow.
CDK9Product_ID: 2316S
Lot_ID: 9
Source: Cell Signaling Technology
Target Name: CDK9-human		 CDK9-HEPG2-CRISPR-2316S.png<br>Caption: Western blot following CRISPR against CDK9 in HepG2 whole cell lysate using CDK9 specific antibody. Lane 1 is a ladder, lane 2 is HepG2 non-targeting control knockdown, lane 3 and 4 are two different CRISPR against CDK9. CDK9 protein appears as the green arrow, Beta-actin serves as a control and appears in red arrow.
 CST_2316S_9_CDK9.png<br>Caption: IP-WB analysis of 2316S whole cell lysate using the CDK9 specific antibody, 2316S. Lanes 1 and 2 are 2.5% of five million whole cell lysate input and 50% of IP enrichment, respectively, using a normal IgG antibody. Lane 3 is 50% of IP enrichment from five million whole cell lysate using the CDK9-specific antibody, 2316S. The same antibody was used to detect protein levels via Western blot. This antibody passes preliminary validation and will be further pursued for secondary validation. *NOTE* Protein sizes are taken from Genecards.org and are only estimates based on sequence. Actual protein size may differ based on protein characteristics and electrophoresis method used.








RNA Targets

  • eCLIP assay for CDK9 is not avaliable on ENCORE database.



Proteins bound to RNA
  • CDK9 RNA is bound by 21 proteins.  







eCLIP assay for CDK9 is not avaliable on ENCORE database.





21 proteins are bound to CDK9 RNA:

Chr Start End Strand Matched Area log2(fold change) -log(p-value) Cell Line Binding Protein Name
chr9130551811130551843+3'-UTR,CDS3.589563.77784K562RBM15
chr9130551926130551975+3'-UTR3.097873.33955HepG2RBM15
chr9130552376130552427+3'-UTR4.174648.14668K562RBM15
chr9130551860130551908+3'-UTR4.3108412.20960K562RBM15
chr9130552060130552140+3'-UTR4.198714.40113HepG2AKAP1
chr9130552031130552099+3'-UTR3.767776.58465HepG2RBM15
chr9130552088130552147+3'-UTR4.6903712.38910K562RBM15
chr9130551862130551913+3'-UTR3.967645.86270K562TIA1
chr9130551978130552012+3'-UTR5.3525910.23340K562RBM15
chr9130552099130552140+3'-UTR3.274733.70236HepG2RBM15
chr9130551927130551978+3'-UTR3.7477211.89781K562RBM15
chr9130552035130552063+3'-UTR4.549229.71739K562TROVE2
chr9130552057130552119+3'-UTR3.745226.40324K562UPF1
chr9130552063130552104+3'-UTR3.462218.78998K562TROVE2
chr9130551922130551978+3'-UTR3.336283.20756HepG2UPF1
chr9130552785130552872+3'-UTR4.439178.85840K562UPF1
chr9130552031130552088+3'-UTR4.0887311.53861K562RBM15
chr9130548344130548480+5'-UTR,CDS3.854216.35230K562DDX3X
chr9130548405130548460+5'-UTR,CDS4.623444.01285K562GEMIN5
chr9130548378130548451+5'-UTR,CDS4.488613.71613K562UCHL5
chr9130550968130551018+CDS,intron-Proximal5.354479.96618HepG2AQR
chr9130549796130549938+CDS,intron-Proximal3.810628.55049K562DDX24
chr9130550936130550972+CDS,intron-Proximal3.357195.58370HepG2PPIG
chr9130550660130550708+CDS,intron-Proximal4.267145.93840HepG2PRPF8
chr9130550203130550252+CDS,intron-Proximal4.9304310.52912K562SF3B4
chr9130550844130550902+CDS4.284148.85903K562RBM15
chr9130549798130549883+CDS3.368207.58911K562UCHL5
chr9130548518130548548+CDS,intron-Proximal4.1433911.27315K562AQR
chr9130549050130549087+CDS,intron-Proximal4.922565.32906HepG2AQR
chr9130548887130549008+CDS,intron-Proximal3.9352715.56018K562SF3B4
chr9130551380130551482+CDS,intron-Proximal3.142805.68089HepG2BUD13
chr9130551377130551472+CDS,intron-Proximal3.443474.20336HepG2AQR
chr9130550208130550256+CDS,intron-Proximal3.728725.52332K562SMNDC1
chr9130551418130551465+CDS,intron-Proximal3.873079.84724K562PRPF8
chr9130549865130549922+CDS,intron-Proximal3.962654.39974K562GPKOW
chr9130549885130549899+CDS,intron-Proximal4.7925614.01838K562AQR
chr9130549845130549931+CDS,intron-Proximal4.165698.46423K562PRPF8
chr9130549798130549862+CDS4.045375.80295HepG2PPIG
chr9130551420130551473+CDS,intron-Proximal5.2290818.60307K562AQR
chr9130551484130551544+CDS3.286104.39623HepG2PPIG
chr9130550964130551021+CDS,intron-Proximal3.323236.93851K562BUD13
chr9130551452130551469+CDS,intron-Proximal3.695874.96634HepG2PPIG
chr9130551716130551755+CDS3.950305.71420K562RBM15
chr9130549803130549828+CDS5.210816.22530K562AQR
chr9130550213130550278+CDS,intron-Proximal3.603316.02419K562AQR
chr9130550962130550982+CDS,intron-Proximal4.119068.17589HepG2PRPF8
chr9130548508130548559+CDS,intron-Proximal3.978665.90528HepG2AQR
chr9130549060130549107+CDS,intron-Proximal5.327998.38577HepG2PRPF8
chr9130548492130548569+CDS,intron-Proximal4.1293210.32997HepG2PRPF8
chr9130548962130549025+CDS,intron-Proximal3.305326.47255K562BUD13
chr9130550207130550261+CDS,intron-Proximal3.680537.53629K562BUD13
chr9130551425130551492+CDS,intron-Proximal3.106757.14163K562BUD13
chr9130550549130550600+CDS4.043143.38114HepG2GRWD1
chr9130548730130548763+intron-Distal4.100584.36481K562EFTUD2
chr9130550025130550078+intron-Distal3.270424.24009K562U2AF1
chr9130550105130550160+intron-Distal,intron-Proximal3.979803.53067K562SRSF1
chr9130550018130550078+intron-Distal3.651576.77200HepG2U2AF2
chr9130551039130551085+intron-Distal,intron-Proximal3.808435.28701K562PRPF8
chr9130549173130549212+intron-Distal3.618125.24705K562BUD13
chr9130549991130550059+intron-Distal5.2450414.00496K562SF3B4
chr9130548829130548896+intron-Distal,intron-Proximal5.308094.24111K562EFTUD2
chr9130550016130550078+intron-Distal3.336483.23253K562SMNDC1
chr9130551085130551158+intron-Distal3.530827.41728K562PRPF8
chr9130551022130551066+intron-Proximal5.5608615.34985K562AQR
chr9130549899130549928+intron-Proximal5.5305216.18931K562AQR
chr9130549069130549110+intron-Proximal6.1996315.31585K562AQR
chr9130551015130551018+intron-Proximal5.544285.69951K562AQR
chr9130548898130548962+intron-Proximal3.546524.10684HepG2AQR
chr9130549087130549097+intron-Proximal4.654204.62947HepG2AQR
chr9130550982130551017+intron-Proximal4.111517.56654HepG2PRPF8
chr9130550971130550976+intron-Proximal5.8283244.21082K562AQR
chr9130550976130551013+intron-Proximal6.0950551.22554K562AQR
chr9130550435130550487+intron-Proximal6.0631613.56104K562SF3B4
chr9130549061130549067+intron-Proximal4.8957911.12698K562AQR
chr9130549894130549932+intron-Proximal4.159485.68247K562SF3B4
chr9130548548130548569+intron-Proximal5.2642714.19592K562AQR
ChrStartEndStrandMatched Arealog2(fold change)-log(p-value)Cell LineBinding Protein Name




eCLIP assay for CDK9 is not avaliable on ENCORE database.



Diffrential Expression

  • The Knockdown/knockout assay for CDK9 is not available on ENCORE database.

  • 93 RBPs can affect the levels of CDK9.  








The Knockdown/knockout RNA-Seq assay for CDK9 is not available on ENCORE database.





93 RBPs can affect the gene expression of CDK9 :

Gene NameGene IDKDMeanCNMeanlog2(fold change) *-log(pval) **-log(padj) **Cell LineAffected by RBPBound by RBP
CDK9ENSG00000136807.71494.30980692.318601.1099014.4531013.33540HepG2AKAP1
CDK9ENSG00000136807.7916.74440626.712800.548603.863202.63690HepG2AKAP8
CDK9ENSG00000136807.7797.07110616.376600.370803.558902.70210HepG2AKAP8L
CDK9ENSG00000136807.7817.25510572.799100.512702.629901.86490HepG2ASCC1
CDK9ENSG00000136807.7781.12550470.352500.731705.206503.91430HepG2BCCIP
CDK9ENSG00000136807.71088.75190526.420901.0483016.7034015.41350HepG2BOP1
CDK9ENSG00000136807.71123.03740451.418901.3148013.1549011.54000HepG2CNOT7
CDK9ENSG00000136807.7321.99420483.28600-0.585803.725302.94010HepG2CPSF6
CDK9ENSG00000136807.7775.19940591.880700.389203.816803.08360HepG2CELF1
CDK9ENSG00000136807.7672.94360462.471200.541002.938302.14470HepG2DDX55
CDK9ENSG00000136807.7989.43700569.809800.796007.451106.48210HepG2DDX6
CDK9ENSG00000136807.7522.26020360.263200.535604.725403.82780HepG2DNAJC21
CDK9ENSG00000136807.7522.11840357.050600.548105.899605.00040HepG2DNAJC2
CDK9ENSG00000136807.7544.37640354.267400.619703.936702.86750HepG2EIF3D
CDK9ENSG00000136807.7848.38790589.281700.525702.912302.20700HepG2EIF4B
CDK9ENSG00000136807.7403.36840601.43590-0.576303.775302.83320HepG2EIF4G2
CDK9ENSG00000136807.71357.566901083.369700.325403.662902.98690HepG2ETF1
CDK9ENSG00000136807.7437.17860316.683000.465103.059601.81970HepG2FAM120A
CDK9ENSG00000136807.7973.55810733.255400.408902.160401.47640HepG2FIP1L1
CDK9ENSG00000136807.7906.63920610.749800.569804.548803.67720HepG2FXR1
CDK9ENSG00000136807.71141.39220566.419401.0108012.7644011.38880HepG2G3BP1
CDK9ENSG00000136807.7449.75730315.420900.511802.751201.85540HepG2GEMIN5
CDK9ENSG00000136807.7823.31260547.850600.587604.394703.59970HepG2GPKOW
CDK9ENSG00000136807.7803.42210585.716300.455905.260003.95940HepG2HDGF
CDK9ENSG00000136807.7778.51650573.879200.439902.988302.26340HepG2HNRNPK
CDK9ENSG00000136807.7715.23390579.647200.303102.737802.06730HepG2HNRNPL
CDK9ENSG00000136807.7516.51920401.880600.362002.769802.16180HepG2HNRNPU
CDK9ENSG00000136807.7931.53260575.702900.694206.606705.60450HepG2IGF2BP2
CDK9ENSG00000136807.7527.63660410.509500.362003.152202.37430HepG2ILF2
CDK9ENSG00000136807.7680.47920560.814300.278902.318801.38410HepG2KIF1C
CDK9ENSG00000136807.7644.06420458.206700.491103.626702.23380HepG2LIN28B
CDK9ENSG00000136807.71103.18790614.340200.844508.546707.48830HepG2MATR3
CDK9ENSG00000136807.7646.00790370.752700.801003.772602.55100HepG2METAP2
CDK9ENSG00000136807.7755.87770593.230300.349502.091601.38390HepG2MSI2
CDK9ENSG00000136807.7916.30630628.776000.543204.004303.24720HepG2NCBP2
CDK9ENSG00000136807.7961.81780631.008000.608008.154406.86720HepG2NOL12
CDK9ENSG00000136807.7665.00490424.754600.646602.641301.57450HepG2NONO
CDK9ENSG00000136807.7769.17090559.803700.458302.963502.21880HepG2PABPC4
CDK9ENSG00000136807.7532.29500397.806000.420103.340002.41730HepG2PARN
CDK9ENSG00000136807.7500.10640292.975400.771407.597305.64040HepG2PKM
CDK9ENSG00000136807.7487.86070358.447200.444603.363802.55760HepG2PPIL4
CDK9ENSG00000136807.7425.91850579.62120-0.444503.927703.02120HepG2PRPF4
CDK9ENSG00000136807.7839.41010604.821000.472805.651504.92560HepG2PTBP1
CDK9ENSG00000136807.7815.97650639.464400.351604.081703.39120HepG2PUM1
CDK9ENSG00000136807.71150.44390638.984000.8482014.7526013.28230HepG2PUM2
CDK9ENSG00000136807.7765.24260624.902400.292202.533201.93660HepG2PUS1
CDK9ENSG00000136807.71008.77410654.996000.622908.138707.15460HepG2QKI
CDK9ENSG00000136807.7877.42460704.540000.316502.414801.60730HepG2RBM15
CDK9ENSG00000136807.7806.25370594.466100.439503.667802.89800HepG2RBM25
CDK9ENSG00000136807.7897.50260673.092100.415004.227703.58440HepG2NELFE
CDK9ENSG00000136807.7667.57600344.746700.9533011.5506010.40020HepG2RPS19
CDK9ENSG00000136807.7700.54220485.258300.529603.997403.04440HepG2RPS2
CDK9ENSG00000136807.7688.83540495.330300.475703.251302.08020HepG2RPS5
CDK9ENSG00000136807.7488.03430357.898600.447303.693502.96840HepG2SAFB2
CDK9ENSG00000136807.7355.96040517.49650-0.539803.448202.66880HepG2SF3B1
CDK9ENSG00000136807.7606.50140417.380500.539006.094105.19800HepG2SMN1
CDK9ENSG00000136807.7680.276901022.72780-0.588209.775708.99050HepG2SRFBP1
CDK9ENSG00000136807.7971.22970594.778900.7074012.3674011.17200HepG2SRSF5
CDK9ENSG00000136807.7815.30300676.318500.269502.128501.50870HepG2SRSF7
CDK9ENSG00000136807.7641.39660534.716200.262301.920401.44450HepG2SRSF9
CDK9ENSG00000136807.7726.62100887.97270-0.289302.631502.12680HepG2SSB
CDK9ENSG00000136807.71298.72990676.405500.9410026.6140025.00930HepG2SUCLG1
CDK9ENSG00000136807.7418.78680590.79620-0.496404.258403.58560HepG2TAF15
CDK9ENSG00000136807.7353.19050509.56890-0.528803.359802.57020HepG2TARDBP
CDK9ENSG00000136807.7703.40730542.820700.373802.780801.94310HepG2TIA1
CDK9ENSG00000136807.7496.73680390.541100.346902.053301.60930HepG2TIAL1
CDK9ENSG00000136807.7520.61990393.990400.402003.343702.73660HepG2TRIM56
CDK9ENSG00000136807.71060.72640588.525500.849806.976105.48520HepG2TUFM
CDK9ENSG00000136807.7177.21620271.92880-0.617703.274102.45000HepG2UCHL5
CDK9ENSG00000136807.7740.61030594.215300.317602.557001.54400HepG2UTP18
CDK9ENSG00000136807.7867.97250558.129600.636909.555208.55090HepG2UTP3
CDK9ENSG00000136807.7345.08520572.02720-0.729109.557308.43510HepG2ZC3H8
CDK9ENSG00000136807.71047.67700635.795000.7205015.5478014.51450HepG2ZNF622
CDK9ENSG00000136807.71065.52510803.342000.407404.573003.87520K562AGGF1
CDK9ENSG00000136807.71271.10190835.898000.604606.785105.72570K562AKAP8L
CDK9ENSG00000136807.71093.15790877.028200.317702.772801.85830K562ATP5C1
CDK9ENSG00000136807.71407.883801836.15670-0.383204.640403.36620K562CELF1
CDK9ENSG00000136807.71456.464801109.571800.392405.396804.53070K562DDX47
CDK9ENSG00000136807.7747.45230568.828600.393903.427301.93010K562DDX6
CDK9ENSG00000136807.71124.69470927.156600.278502.479501.79200K562EIF2S2
CDK9ENSG00000136807.7600.01750385.571800.637906.364405.17440K562EIF3G
CDK9ENSG00000136807.71226.340901493.16380-0.284003.009302.03020K562EIF4G2
CDK9ENSG00000136807.7337.02580539.63620-0.679102.996901.81460K562FKBP4
CDK9ENSG00000136807.7176.37620327.85470-0.894405.399104.33500K562G3BP2
CDK9ENSG00000136807.7432.83940620.73310-0.520103.331502.68440K562HNRNPC
CDK9ENSG00000136807.7772.25620523.195800.561603.787802.51630K562IGF2BP2
CDK9ENSG00000136807.7329.51850459.10710-0.478502.167901.35290K562KRR1
CDK9ENSG00000136807.7784.79250516.284900.604004.637902.83760K562NONO
CDK9ENSG00000136807.7760.50830556.609900.450203.364502.35340K562PSIP1
CDK9ENSG00000136807.7724.74210533.934600.440703.741102.97990K562PTBP1
CDK9ENSG00000136807.71010.193401629.12810-0.689509.318807.80030K562PUF60
CDK9ENSG00000136807.71221.26870807.734000.596308.331407.32910K562RBM15
CDK9ENSG00000136807.7706.60520518.996700.445102.440401.67450K562RPS19
CDK9ENSG00000136807.7965.55690736.397800.390803.102701.95410K562SAFB
CDK9ENSG00000136807.7355.57910511.33130-0.524102.368101.47350K562SF3B1
CDK9ENSG00000136807.71157.11610671.267300.785503.537401.99790K562SFPQ
CDK9ENSG00000136807.7715.14410508.984900.490503.447401.58900K562SRP68
CDK9ENSG00000136807.7857.320101109.17470-0.371604.440803.28520K562SRPK2
CDK9ENSG00000136807.7697.13170948.11280-0.443603.387401.86030K562SSRP1
CDK9ENSG00000136807.7726.78340529.708300.456202.204701.56850K562TARDBP
CDK9ENSG00000136807.7673.46880510.983800.398202.580601.79330K562TIA1
CDK9ENSG00000136807.7658.34680501.610400.392202.524401.49040K562TRA2A
CDK9ENSG00000136807.7815.69040569.030700.519404.353703.10580K562TRIM56
CDK9ENSG00000136807.7192.72900317.71910-0.721204.059302.68160K562U2AF1
CDK9ENSG00000136807.7235.84930328.16040-0.476502.711201.91560K562U2AF2
CDK9ENSG00000136807.7733.35310531.785500.463603.054601.76380K562XRN2
Gene NameGene IDKDMeanCNMeanlog2(fold change)-log(pval)-log(padj)Cell LineAffected by RBPBound by RBP

*: "Inf" was shown as "99999.99999" and "-Inf" was shown as "-99999.99999".
**: "-log(0)" was displayed as "99999.99999".






The Knockdown/knockout RNA-Seq assay for CDK9 is not available on ENCORE database.





2 RBPs can affect the splicing of CDK9 :

Event TypeGene NameGene IDchrStrandExonStartExonEnd2ndExonStart2ndExonEndupstreamESupstreamEEdownstreamESdownstreamEEdPSIp-valueFDRis_includedCell LineAffected by RBPBound by RBP
SECDK9ENSG00000136807.7chr9+1305500311305501341305497961305498871305502251305503920.167000.000000.00007includedHepG2PCBP2
A5SSCDK9ENSG00000136807.7chr9+1305489791305491491305489791305490611305497961305498870.051000.000000.00010longerK562AQR

*: "Inf" was shown as "99999.99999" and "-Inf" was shown as "-99999.99999".
**: "-log(0)" was displayed as "99999.99999".





The Knockdown/knockout RNA-Seq assay for CDK9 is not avaliable on ENCORE database.