Pseudouridylate synthase that catalyzes pseudouridylation of tRNAs and mRNAs (PubMed:10094309, PubMed:15327771, PubMed:27197761). Acts on positions 27/28 in the anticodon stem and also positions 34 and 36 in the anticodon of an intron containing tRNA (PubMed:10094309). Also catalyzes pseudouridylation of mRNAs: mediates pseudouridylation of mRNAs with the consensus sequence 5'-UGUAG-3' (By similarity). Acts as a regulator of pre-mRNA splicing by mediating pseudouridylation of pre-mRNAs at locations associated with alternatively spliced regions (By similarity). Pseudouridylation of pre-mRNAs near splice sites directly regulates mRNA splicing and mRNA 3'-end processing (By similarity). Involved in regulation of nuclear receptor activity through pseudouridylation of SRA1 mRNA (PubMed:15327771). Does not form pseudouridine when expressed in vitro. Does not form pseudouridine when expressed in vitro. a uridine in tRNA = a pseudouridine in tRNA uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA a uridine in mRNA = a pseudouridine in mRNA Monomer (By similarity). Forms a complex with RARG and the SRA1 RNA in the nucleus (PubMed:15327771). Impaired muscle morphology and physiology leading to impaired exercise capacity (PubMed:27197761). Mice were born at the expected Mendelian frequency (PubMed:27197761). At 14 weeks, mice display reduced exercise capacity, probably caused by alterations in muscle metabolism related to mitochondrial content and oxidative capacity (PubMed:27197761). Cells show reduced pseudouridylation of cytoplasmic and mitochondrial tRNAs (PubMed:27197761). Belongs to the tRNA pseudouridine synthase TruA family.