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We have created tRFdb, the first database of transfer RNA fragments (tRFs), available at http://genome.bioch.virginia.edu/trfdb/. With over 100 small RNA libraries analyzed, the database currently contains the sequences and read counts of the three classes of tRFs for eight species: R. sphaeroides, S. pombe, D. melanogaster, C. elegans, Xenopus, zebra fish, mouse and human, for a total of 12,877 tRFs. The database can be searched by tRF ID or tRF sequence, and the results can be limited by organism. The search results show the genome coordinates and names of the tRNAs the sequence may derive from, and there are links for the sequence of the tRF and parental tRNA, and links for the read counts in all the corresponding small RNA libraries. As a case study for how this database may be used, we have shown that a certain class of tRFs, tRF-1s, is highly upregulated in B-cell malignancies.
Figure 1. Illustration of primary tRNA, mature tRNA and tRF-5, -3 and -1. tRF-1 (shown in green) is generated from primary tRNA. tRF-5 and -3 are produced from mature tRNA. The tRF-3s always have ‘CCA’ at their 3′ end.
Figure 2. The patterns of small RNA deep sequencing reads (GSM416733) mapping to tRNA genes. Examples of small RNA reads that mapped to specific tRNAs are shown. More than 80% of reads for a given tRF-1, -3 or -5 represent one or two most abundant reads and this is the read that is included as the main tRF sequence in the database. The most abundant clones are shown in green. Upper: tRF-1-like sequences mapping to the primary tRNA chr17.trna7-SerGCT. Middle: tRF-3-like sequences mapping to the mature tRNA chr6.trna126-LeuAAG. Lower: tRF-5-like sequences mapping to the mature tRNA chr6.trna126-LeuAAG.
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