GtRNAdb

The Genomic tRNA Database (GtRNAdb) is a comprehensive repository for transfer RNA gene predictions made by tRNAscan-SE on complete or nearly complete genomes across all three domains of life. Created and maintained by Todd Lowe and Patricia Chan at UC Santa Cruz, GtRNAdb has become the most commonly cited web-based source of tRNA gene information.

As of Data Release 22 (September 2024), the database contains 431,433 tRNA gene predictions from 4,867 genomes, including 609 eukaryotes (178,889 tRNAs), 220 archaea (10,476 tRNAs), and 4,038 bacteria (242,068 tRNAs). The database focuses on high-quality predictions, excluding predicted pseudogenes and, for large eukaryotes, primary and secondary filtered predictions.

GtRNAdb provides rich annotations for each tRNA gene, including primary sequences, predicted secondary structures (both from covariance model alignment and minimum free energy prediction), isotype-specific scoring, genomic coordinates with direct links to UCSC Genome Browsers, flanking sequences for regulatory motif identification, and detailed scoring breakdowns to identify potential pseudogenes.

The database integrates extensive functional data from external sources including RNA modification data from MODOMICS, tRNA fragment expression profiles from ARM-seq studies, single nucleotide polymorphisms from dbSNP with predicted structural impacts, epigenetic data from ENCODE showing RNA polymerase III transcription factor binding, and evolutionary conservation through multi-genome alignments.

Search capabilities include the tRNA Sifter for querying by phylogenetic domain, species name, chromosome, amino acid isotype, anticodon, number of introns, tRNA score thresholds, and structural mismatches. A BLAST server enables sequence similarity searches across all tRNAs in the database. Additional tools include tRNAscan-SE for custom predictions, tRAX for tRNA-derived RNA sequencing analysis, tDRnamer for standardized naming, and tRAP for predicting tRNA gene activity.

GtRNAdb serves as an indispensable platform for comparative genomics, tRNA biology research, and understanding the regulatory roles of tRNAs across all domains of life.