Polynucleotide 5'-kinase involved in rRNA processing. Required for the efficient termination by RNA polymerase I and the processing of the IST2 pre-rRNA internal transcribed spacer localized between the 5.8S and 25S rRNAs. May act by maintaining the phosphorylated status of the downstream RNT1 cleavage product, which in turn allows the torpedo activity of RAT1 to efficiently terminate Pol I transcription. In vitro, displays polynucleotide kinase activity on both single- and double-stranded RNA and on single-stranded DNA alone, but not double-stranded DNA alone. Associates with rDNA. Cell cycle-regulated with a peak of transcription at the G1/S boundary. Belongs to the Clp1 family. NOL9/GRC3 subfamily.