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Catalyzes uridine to pseudouridine isomerization (pseudouridylation) of different mitochondrial RNA substrates . Acts on position 1397 in 16S mitochondrial ribosomal RNA (16S mt-rRNA) . This modification is required for the assembly of 16S mt-rRNA into a functional mitochondrial ribosome . As a component of a functional protein-RNA module, consisting of RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2 and 16S mt-rRNA, controls 16S mt-rRNA abundance and is required for intra-mitochondrial translation . Acts on position 39 in mitochondrial tRNA(Phe) . Also catalyzes pseudouridylation of mRNAs in nucleus: acts as a regulator of pre-mRNA splicing by mediating pseudouridylation of pre-mRNAs at locations associated with alternatively spliced regions . Pseudouridylation of pre-mRNAs near splice sites directly regulates mRNA splicing and mRNA 3'-end processing .