Cyclin-dependent protein kinase that acts as a regulator of transcription and pre-mRNA splicing (PubMed:12501247, PubMed:32367068, PubMed:36104565, PubMed:40858114). Acts as a key regulator of pre-mRNA splicing by mediating phosphorylation of SF3B1, enabling the association between SF3B1 and U5 and U6 snRNAs in the activated spliceosome, thereby promoting spliceosome assembly (PubMed:36104565, PubMed:38059508). Also acts as a regulator of transcription by phosphorylating 'Ser-2' of the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAP II) POLR2A (PubMed:32367068, PubMed:40858114). Involved in replication-dependent transcription of histone genes: binds to histone genes and phosphorylates POLR2A at 'Ser-2' of the CTD to specifically control transcriptional elongation of histones and recruitment of 3'-end processing factors (PubMed:32367068). Part of a transcription checkpoint upstream of CDK9, which regulates promoter-proximal pausing by RNA polymerase II, a transcription halt following transcription initiation, but prior to elongation (PubMed:40858114). Probably regulates promoter-proximal pausing by mediating phosphorylation of POLR2A at 'Ser-2' of the CTD (PubMed:40858114). {ECO:0000269|PubMed:12501247, ECO:0000269|PubMed:32367068, ECO:0000269|PubMed:36104565, ECO:0000269|PubMed:38059508, ECO:0000269|PubMed:40858114}. [Isoform SV6]: Isoform expressed in a non-cell cycle- dependent manner. . [Isoform 4]: Isoform specifically expressed during the G2-M phases of the cell cycle (PubMed:12082095). Phosphorylates 'Ser-2' of the CTD (C-terminal domain) of the large subunit of RNA polymerase II (RNAP II) POLR2A (PubMed:38019613). Promotes centromeric transcription to maintain centromeric cohesion during mitosis (PubMed:24436071, PubMed:38019613). {ECO:0000269|PubMed:12082095, ECO:0000269|PubMed:24436071, ECO:0000269|PubMed:38019613}. This is the function of CDK11A (cyclin dependent kinase 11A, Ensembl gene identifier ENSG00000008128).