OBJECTIVE To explore the effect of nudix hydrolase 21 (NUDT 21) on alternative splicing of transcripts in leukemia K562 cells. METHODS The K562 cell line was used as the research objects. The NUDT 21 was knocked-down by lentivirus vector, then the expression of transcripts before and after interference was determined by transcriptome sequencing (RNA seq). The bioinformatics methods including GO analysis and KEGG pathway analysis were used to analyze the changes of differentially expressed genes and 3' alternative splicing, then these changes were confirmed by qPCR. RESULTS After the NUDT 21 in K562 cells was knoced-down, the differentially expressed genes showed that 5 196 were up-regulated, 3 917 were down-regulated. GO analysis and KEGG pathway analysis showed that the very differentially expressed transcripts mainly related with cell adhesion and differentiation, hematopoietic cell lines and autoimmunity. There were 436 significant alternative splicing, which mainly involved in the regulation of some biological processes such as cell proliferation and metabolism. The ERBB2, MAPK kinase MKNK2, G protein-coupled receptor GRK6, eukaryotic translation elongation factor EEF1B2, cyclin L2 CCNL2, mitotic checkpoint protein BUB3 were changed by 3' alternative splicing. Among them the expression of variant 1 of ERBB2 mRNA decreased and variant 4 increased. CONCLUSIONS NUDT21 influences the cell biological function at a higher level by variously regulating ways, including 3' end APA.