Welcome to SPLITSdb

Overview of SPLITSdb:
The purpose of this database is to store and retrieve complete set of tRNA sequences in all archaeal species and primitive eukaryotic species to promote the next study of tRNA evolution and tRNA processing. This database contains total 3,741 sequences and secondary structures of various types of tRNA genes (details are shown on the right table), and 783 sequences and secondary structures of tRNA introns. If you use this database in your work you might want to cite: Sugahara J. et al. 2008. Mol Biol Evol.

Data Collection:
In order to collect comprehensive set of tRNA genes from all Archaeal species, we initially conducted multi-directional prediction by using three tRNA prediction software; tRNAscan-SE, ARAGORN and SPLITS. Then all the predicted data were merged and only manually confirmed reliable tRNA sequences were registered in this database.
Types of tRNA genesNum
Intron-containing tRNA671
Split tRNA12
Initiator Met-tRNA93
AUA decoding Ile-tRNA81
Pyrrolisine-tRNA4
Selenocysteine-tRNA8
Other tRNA2872

Background:
In every living organisms, tRNAs are known as a essential molecules to decode initiator codon and 61 sense codons during the translation mechanism and are encoded in the genome sequence. Although, some of these essential tRNA genes are still missing in archaeal species in spite of the use of tRNA predicting softwares. The difficulty of predicting complete set of tRNA genes in a single species has been reaffirmed by the discovery of several types of unique tRNA genes in archaea and in primitive eukaryotes. For example, Archaeal parasite Nanoarchaeum equitans possess 'Split tRNAs', which the 5' and 3' halves are encoded on the separate genes and many Crenarchaeota possesses 'Intron-containing tRNAs'. Here, we have predicted and collected all the above types of tRNAs and further covered selenocysteine tRNAs and pyrrolysine tRNAs which are known to share major stop codons. Further, initiator Methionyl-tRNA, elongator Methionyl-tRNA and isoleucyl-tRNA were distinguished in SPLITSdb for easy interpretation of tRNAs with same CAU anticodon.


tRNA Search Engine

tRNA search engine is an user friendly interface which enables the user to screen and select the required tRNA genes. This system allows you to search the tRNA genes by starting from selecting one of the five search conditions; 'Organism', 'Anticodon', 'tRNA type', 'Intron motif' and 'Intron location'. It is also possible to screen the tRNA genes based on multiple factors. Click here for more detailed explanation and how to use. To start searching, please click following 'Search' icon.





BHB Search Engine

BHB search engine is an user friendly interface to screen and select the required intron sequences located at tRNA genes. This system allows you to search the introns by starting from selecting one of the three search conditions; 'Organism', 'Intron motif' and 'Intron location'. It is also possible to screen the introns based on multiple factors. Click here for more detailed explanation and how to use. To start searching, please click following 'Search' icon.





Download

Download page allows users to download complete set of tRNA sequences in each species (and each phyla). The zipped files containing all the sequences and the secondary structures of tRNA genes and their BHB motifs, and amino acid sequences of tRNA splicing endonucleases in each organisms are available to download respectively.





Research Contributions

  • SPLITS identified novel split tRNA genes in Caldivirga maquilingensis of the Crenarchaea
    Fujishima K., Sugahara J., Kikuta K., Hirano R., Sato A., Tomita M., Kanai A. (2009) Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. PNAS; 106: 2683-2687.


  • SPLITS contributed to identify novel tRNA genes in which the 3' half of the tRNA lies upstream of the 5' half in the genome of red alga
    Soma A., Onodera A., Sugahara J., Kanai A., Yachie N., Tomita M., Kawamura F., Sekine Y. (2007) Permuted tRNA genes expressed via a circular RNA imtermediate in Cyanidioschyzon merolae. Science; 318(5849): 450-453.


  • SPLITS identified novel tRNA genes containing three introns at single gene in Thermofilum pendens of the Crenarchaea
    Sugahara J., Yachie N., Arakawa K., Tomita M. (2007) In silico screening of Archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA; 13: 671-681.


  • SPLITS contributed to the genome project of Cenarchaeum symbiosum by the annotation of the multiple intron-containing tRNAs
    Hallam S.J., Konstantinidis K.T., Putnam N., Schleper C., Watanabe Y.-i., Sugahara J., Preston C., de la Torre J., Richardson P.M., Delong E.F. (2006) Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum. Proc. Natl. Acad. Sci. USA; 28;103(48):18296-301.


  • Our research group developped SPLITS, a program for predicting spliced-tRNA genes
    Sugahara J., Yachie N., Sekine Y., Soma A., Matsui M., Tomita M., Kanai A. (2006) SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biology; 6: 0039.