biostudies-literatureCoughlin DJNIGMS NIH HHSCIHR195-202https://www.ebi.ac.uk/biostudies/studies/S-EPMC2783191biostudies-literatureUnknown6(2)<h4>Background</h4>Transfer RNA (tRNA) gene predictions are complicated by challenges such as structural variation, limited sequence conservation and the presence of highly reiterated short interspersed sequences (SINEs) that originally derived from tRNA genes or tRNA-like transcription units. Annotation of "tRNA genes" in sequenced genomes generally have not been accompanied by experimental verification of the expression status of predicted sequences.<h4>Results</h4>To address this for mouse tRNA genes, we have employed two programs, tRNAScan-SE and ARAGORN, to predict the tRNA genes in the nuclear genome, resulting in diverse but overlapping predicted gene sets. From these, we removed known SINE repeats and sorted the genes into predicted families and single-copy genes. In particular, foRNA biologyPrediction and verification of mouse tRNA gene families.PMC2783191R01 GM082875R01 GM034869GM082875MOP-49451T32 GM007767Engelke DRHughes TRBabak TNihranz CCoughlin DJfalsePrediction and verification of mouse tRNA gene families.<h4>Background</h4>Transfer RNA (tRNA) gene predictions are complicated by challenges such as structural variation, limited sequence conservation and the presence of highly reiterated short interspersed sequences (SINEs) that originally derived from tRNA genes or tRNA-like transcription units. Annotation of "tRNA genes" in sequenced genomes generally have not been accompanied by experimental verification of the expression status of predicted sequences.<h4>Results</h4>To address this for mouse tRNA genes, we have employed two programs, tRNAScan-SE and ARAGORN, to predict the tRNA genes in the nuclear genome, resulting in diverse but overlapping predicted gene sets. From these, we removed known SINE repeats and sorted the genes into predicted families and single-copy genes. In particular, fo2009-01-01T00:00:00Z2009 Apr-Jun2026-05-02T23:39:10.853Z2026-04-07T18:37:15.717ZS-EPMC27831911924698910.4161/rna.6.2.8050