Post-transcriptional modifications are very common to tRNAs. Some of the modifications at the first position of the anticodon allows "wobble" base pairing with codons in mRNAs that eliminates the need of one tRNA gene per codon. For example, most eukaryotic genomes do not tRNAs with "G" at the first position of anticodon with the exception of tRNAGly(GCC) while archaeal and bacterial genomes do not tRNAs with "A" at the first position of anticodon with the exception of bacterial tRNAArg(ACG). To understand this in more details, we suggest reviewing the following article: Grojean H, de Crécy-Lagard V, and Marck C. Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes. FEBS Lett. 2010 584:252-64.
tRNA-derived repetitive elements, whose primary sequences are very similar to real tRNA genes, have been commonly found in a lot of vertebrates, some worms, and some plants. To address this problem, we applied a multi-step post-filtering process to the predictions in large eukaryotes by using EukHighConfidenceFilter from tRNAscan-SE 2.0. The tool assesses the predictions with a combination of domain-specific, isotype-specific, and secondary structure scores in two filtering stages on top of the pseudogene classification, and determines the "high confidence" set of genes that are most likely to be functioned in the translation process. A small number of the predictions that have high scores but atypical features such as unexpected anticodons are separately marked for further investigation.
Some vertebrates such as zebra fish have a much larger number of high-scoring identical tRNA genes than other genomes such as mammals. Since further studies will be needed to understand the sources of the high copy number, we categorize these genes as "high scoring" tRNA set.
You can use tRNA Sifter under the Search menu to find the tRNAs in our database and download the search results that include gene annotations and sequences. For more information, please check out the User Guide.
Our lab provides a web server version and a standalone unix/linux version of tRNAscan-SE for gene prediction. You can access it at http://trna.soe.ucsc.edu/tRNAscan-SE. If you would like the gene predictions of your interested genome to be included in GtRNAdb, please email us at firstname.lastname@example.org.