A splicing-competent intron has been found to affect the expression of a gene at almost every step between transcription and translation. In this investigation, we performed a comprehensive analysis of the role of an intron from two yeast genes, ASC1 and APE2, on cellular fitness and at different steps of gene expression. Mutants containing intronless versions of either gene grew 30-60% slower than their intron-containing counterparts, and their growth was compromised on ethanol and glycerol medium. Furthermore, there was an enhanced R-loop signal in the coding region of both genes in the absence of the intron. Steady-state RNA levels of ASC1 and APE2 decreased by about 30-fold and 5-fold, respectively, in the absence of the intron. Nascent transcription analysis revealed a drop in transcription of both ASC1 and APE2 by 4-10 fold and 2-5 fold, respectively, in the intronless state. The half-life of mRNA of both genes registered a 2- to 3-fold decline in the absence of an intron. A fluorescence in situ hybridization approach detected an increase in nuclear retention of mRNA in the absence of the intron for both genes. Measurement of protein level by western blot found no detectable signal for either protein in the absence of an intron. These results suggest that the introns of both genes affect the expression of their genes at the level of transcription, mRNA stability, and nucleocytoplasmic transport of mRNA. Furthermore, both ASC1 and APE2 introns affect the fitness of cells in terms of growth rate and the ability to grow on different carbon sources.