The attached file proposes a logical and systematic nomenclature for the ~300 D. melanogaster (Dmel) genes coding for cytoplasmic tRNAs, based on the tRNAscan-SE analysis of release 6 of the genome, as provided at the GtRNAdb (http://gtrnadb.ucsc.edu/genomes/eukaryota/Dmela6/).
Note that the current GtRNAdb (January 2016) contains a total of 295 Dmel tRNA genes, of which 288 encode tRNAs decoding the 20 standard 20 amino acids; 1 encodes a selenocysteine tRNA; 2 encode tRNAs with undetermined or unknown isotypes (CR30253 and CR31905); and 4 are predicted pseudogenes (CR30449, CR32761, CR32518 and CR32034).  The current analysis includes the following differences: CR30253 is identified as a His-GTG pseudogene (see FBrf0041470); CR31905 is identified as a Tyr-GTA tRNA gene; CR31485 is added as a Lys-CTT pseudogene (and was included in previous releases of the GtRNAdb); CR32123 is added as a tRNA pseudogene of unclear isotype (and was included in a previous release of the GtRNAdb). Together, these revisions result in the current analysis containing a total of 297 Dmel tRNA genes, of which 289 encode tRNAs decoding the 20 standard 20 amino acids; 1 encodes a selenocysteine tRNA; and 7 are predicted pseudogenes (CR30449, CR32761, CR32518, CR32034, CR30253, CR31485 and CR32123).
Some notes on nomenclature:
(i) Through to FB2016_01, <50% of Dmel tRNA genes were named, and those that were named used the single letter amino acid code, didn’t specify the anticodon, and used (Dmel-specific) cytological or arbitrary additional identifiers.
(ii) The new nomenclature proposed herein assigns informative names to all 297 cytoplasmic tRNA genes, uses the more explicit 3-letter amino acid code, states the anticodon, and uses logical 2-digit identifying suffixes - the first digit is the same for all tRNA genes of a given anticodon that have identical sequence, and the second digit then increases stepwise for each copy of that sequence in the genome.
(iii) The nomenclature proposed herein mirrors that at the GtRNAdb, with only slight differences in format to satisfy FlyBase nomenclature conventions.