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Transfer RNA databases | Non-coding transcript data analysis

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GtRNAdb / Genomic tRNA Database
Provides overview statistics of tRNA genes within each analyzed genome, including information by isotype and genetic locus, easily downloadable primary sequences, graphical secondary structures and multiple sequence alignments. Direct links for each gene to UCSC eukaryotic and microbial genome browsers provide graphical display of tRNA genes in the context of all other local genetic information. The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group.
tRNAdb / Transfer RNA database
Contains currently more than 12,000 tRNA genes from 577 species and 623 tRNA sequences from 104 species, classified into families according to amino acid specificity as defined by anticodon triplets. tRNAdb provides various services including graphical representations of tRNA secondary structures, a customizable output of aligned or un-aligned sequences with a variety of individual and combinable search criteria, the construction of consensus sequences for any selected set of tRNAs, as well as the illustration of consensus and derived typical cloverleaf structures with features of conservation for any selected set of tRNAs.
Compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. This includes 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included.
Displays static individual 2D structures of human mitochondrial tRNA genes with location of polymorphisms and pathology-related point mutations. Mamit-tRNA is a database for mammalian mitochondrial genomes and has been developed for deciphering structural features of mammalian mitochondrial tRNAs. The database is expected to facilitate exploration of structure/function relationships of mitochondrial tRNAs and to assist clinicians in the frame of pathology-related mutation assignments.
The L. monocytogenes 10403S BioCyc database
A resource for researchers studying Listeria and related organisms. The L. monocytogenes 10403S BioCyc database allows users to (i) have a comprehensive view of all reactions and pathways predicted to take place within the cell in the cellular overview, as well as to (ii) upload their own data, such as differential expression data, to visualize the data in the scope of predicted pathways and regulatory networks and to carry on enrichment analyses using several different annotations available within the database.
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