The protein encoded by this gene is a member of the cyclin-dependent protein kinase (CDK) family. CDK family members are highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2, and known as important cell cycle regulators. This kinase was found to be a component of the multiprotein complex TAK/P-TEFb, which is an elongation factor for RNA polymerase II-directed transcription and functions by phosphorylating the C-terminal domain of the largest subunit of RNA polymerase II. This protein forms a complex with and is regulated by its regulatory subunit cyclin T or cyclin K. HIV-1 Tat protein was found to interact with this protein and cyclin T, which suggested a possible involvement of this protein in AIDS. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for CDK9. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = CDK9 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CDK9, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr9:127,567,936–127,569,972 | 216.8 kb | Distal (>10kb) Multiome | 660 | |
| chr9:127,608,129–127,608,913 | 177.5 kb | Distal (>10kb) Multiome | 700 | |
| chr9:127,611,734–127,612,761 | 173.8 kb | Distal (>10kb) Multiome | 566 | |
| chr9:127,699,155–127,699,632 | 86.6 kb | Distal (>10kb) Multiome | 440 | |
| chr9:127,715,013–127,716,345 | 70.2 kb | Distal (>10kb) Multiome | 735 | |
| chr9:127,734,444–127,735,606 | 50.8 kb | Distal (>10kb) Multiome | 836 | |
| chr9:127,741,739–127,743,092 | 43.2 kb | Distal (>10kb) Multiome | 367 | |
| chr9:127,754,123–127,755,506 | 30.7 kb | Distal (>10kb) Multiome | 279 | |
| chr9:127,770,807–127,771,925 | 14.6 kb | Distal (>10kb) Multiome | 550 | |
| chr9:127,784,682–127,787,009 | 541 bp | At TSS Multiome | 858 | |
| chr9:127,802,385–127,803,632 | 16.9 kb | Distal (>10kb) Multiome | 867 | |
| chr9:127,809,338–127,810,272 | 23.8 kb | Distal (>10kb) Multiome | 276 | |
| chr9:127,825,222–127,826,046 | 39.6 kb | Distal (>10kb) Multiome | 451 | |
| chr9:127,828,234–127,829,024 | 42.5 kb | Distal (>10kb) Multiome | 521 | |
| chr9:127,877,282–127,878,202 | 91.7 kb | Distal (>10kb) Multiome | 531 | |
| chr9:127,897,316–127,897,796 | 111.4 kb | Distal (>10kb) Multiome | 437 | |
| chr9:127,898,861–127,900,094 | 113.6 kb | Distal (>10kb) Multiome | 630 | |
| chr9:127,916,386–127,917,505 | 131.1 kb | Distal (>10kb) Multiome HiCAR | 474 | |
| chr9:127,926,756–127,928,574 | 141.5 kb | Distal (>10kb) Multiome HiCAR | 411 | |
| chr9:127,930,321–127,931,068 | 144.7 kb | Distal (>10kb) Multiome | 537 | |
| chr9:127,937,578–127,938,244 | 151.9 kb | Distal (>10kb) Multiome | 674 | |
| chr9:127,955,445–127,955,915 | 169.6 kb | Distal (>10kb) Multiome | 540 | |
| chr9:127,980,172–127,981,966 | 195.1 kb | Distal (>10kb) Multiome | 691 | |
| chr9:128,033,544–128,034,106 | 247.8 kb | Distal (>10kb) Multiome | 69 | |
| chr9:128,034,940–128,035,527 | 249.3 kb | Distal (>10kb) Multiome | 480 | |
| chr9:128,066,577–128,068,774 | 281.3 kb | Distal (>10kb) Multiome | 874 |
Genomic view of the CDK9 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.