CDK12
cyclin dependent kinase 12 | CRK7, CRKR, KIAA0904, CRKRS

Enables RNA polymerase II CTD heptapeptide repeat kinase activity and cyclin binding activity. Involved in several processes, including positive regulation of transcription elongation by RNA polymerase II; protein autophosphorylation; and regulation of MAP kinase activity. Located in nuclear speck. Part of cyclin K-CDK12 complex. Biomarker of gastric adenocarcinoma; hepatocellular carcinoma; and stomach cancer. [provided by Alliance of Genome Resources, Apr 2025]

Member of: DE-2
Biological processes 34 terms
ATP binding (GO:0005524)RNA polymerase II CTD heptapeptide repeat kinase activity (GO:0008353)RNA polymerase II CTD heptapeptide repeat kinase activity (GO:0008353)RNA polymerase II CTD heptapeptide repeat kinase activity (GO:0008353)RNA polymerase II CTD heptapeptide repeat kinase activity (GO:0008353)RNA splicing (GO:0008380)cellular response to estrogen stimulus (GO:0071391)cyclin K-CDK12 complex (GO:0002944)cyclin binding (GO:0030332)cyclin binding (GO:0030332)cyclin-dependent protein kinase holoenzyme complex (GO:0000307)cyclin-dependent protein serine/threonine kinase activity (GO:0004693)cyclin/CDK positive transcription elongation factor complex (GO:0008024)negative regulation of MAPK cascade (GO:0043409)negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)nuclear speck (GO:0016607)nuclear speck (GO:0016607)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)positive regulation of transcription by RNA polymerase II (GO:0045944)positive regulation of transcription elongation by RNA polymerase II (GO:0032968)positive regulation of transcription elongation by RNA polymerase II (GO:0032968)positive regulation of transcription elongation by RNA polymerase II (GO:0032968)protein binding (GO:0005515)protein kinase activity (GO:0004672)protein kinase activity (GO:0004672)protein kinase binding (GO:0019901)protein serine kinase activity (GO:0106310)regulation of MAP kinase activity (GO:0043405)regulation of cell cycle (GO:0051726)transcription by RNA polymerase II (GO:0006366)
Expression (TPM)
CDK12 — as a Regulated Gene

TFs regulating CDK12 0 TFs

Transcription factors with Perturb-seq knockdown data for CDK12. 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 = CDK12 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to CDK12

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of CDK12, 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
chr17:39,164,617–39,165,311 296.6 kb Distal (>10kb) Multiome 371
chr17:39,197,170–39,198,193 263.8 kb Distal (>10kb) Multiome 515
chr17:39,199,726–39,200,760 261.4 kb Distal (>10kb) Multiome 947
chr17:39,209,452–39,209,995 251.7 kb Distal (>10kb) Multiome 268
chr17:39,225,532–39,226,262 235.5 kb Distal (>10kb) Multiome 235
chr17:39,244,638–39,245,241 216.6 kb Distal (>10kb) Multiome 348
chr17:39,400,997–39,402,766 58.9 kb Distal (>10kb) Multiome 898
chr17:39,450,919–39,451,504 10.2 kb Distal (>10kb) Multiome 722
chr17:39,461,043–39,462,217 11 bp At TSS Multiome 1026
chr17:39,573,453–39,574,243 112.3 kb Distal (>10kb) Multiome 520
chr17:39,636,769–39,637,600 175.6 kb Distal (>10kb) Multiome 853
chr17:39,652,588–39,653,348 191.5 kb Distal (>10kb) Multiome 263
chr17:39,668,234–39,668,690 207.0 kb Distal (>10kb) Multiome 706
chr17:39,687,710–39,688,437 226.5 kb Distal (>10kb) Multiome 800
chr17:39,695,905–39,696,636 234.8 kb Distal (>10kb) Multiome 499
chr17:39,699,516–39,700,527 238.4 kb Distal (>10kb) Multiome 528
chr17:39,730,039–39,730,906 269.0 kb Distal (>10kb) Multiome 886
chr17:39,739,067–39,739,915 278.0 kb Distal (>10kb) Multiome 648
chr17:39,740,384–39,740,910 279.2 kb Distal (>10kb) Multiome 513
chr17:39,753,811–39,754,996 292.9 kb Distal (>10kb) Multiome 1000

Genome Browser

Genomic view of the CDK12 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.

chr17:39,154,617 – 39,764,996
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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