FAQ : Frequently Asked Questions

1. What are tRFs??

tRFs are 14-32 base long single-stranded RNA derived from mature or precursor tRNAs distinct from the stress-induced tRNA fragments created by cleavage in the anti-codon loop. They have been shown to be involved in processes ranging from RNA silencing to priming a retroviral reverse transcriptase.

2. Are there different types of tRFs?

Yes! The fragments of tRNAs that we observe only come from three regions: either the 5' end, the 3' end, or the trailer sequence of the precursor tRNA. We refer to fragments from the 5' end as tRF-5s, the 3' end as tRF-3s, and the trailer sequences as tRF-1s. Among these classes of tRFs there are subclasses for tRF-5s and tRF-3s. We clearly see three different lengths of tRF-5s which result from different 3' cleavage sites, and two different lengths of tRF-3s due to different 5' cleavage sites. When more than one subclass is present for a tRF-5 or tRF-3 sequence, they are named with a, b, or c appended, from shortest to longest, for tRF-5s, and with a or b appended for tRF-3s from shortest to longest.

3. What is in tRFdb?

tRFdb comprises official names, sequences, and read counts for tRFs observed in over 200 libraries from 8 different organisms: R. sphaeroides (bacteria), S. pombe, Drosophila, C.elegans, Xenopus, zebra fish, mouse and human.

4. How do you search tRFdb?

To search for tRF sequences click on the "SEARCH TRFDB" tab at the top of the page. tRFs can be searched by tRF type (tRF-1s, tRF-3s, or tRF-5s), tRF ID (tRF-1s begin with 1001, tRF-3s begin with 3001, tRF-5s begin with 5001), or sequence (no mismatches allowed). These three search parameters can be further limited by organism, and the output will be displayed on the same page if html format is selected, or this output plus a link for downloading will be shown if "HTML + excel" is selected. The search results may contain several rows for the same tRF name. This is because each row lists a possible tRNA gene that the tRF was derived from and many tRNA genes have very similar sequences and therefore it is impossible to know which tRNA(s) produce a tRF. Every row will have a link for the sequence of the tRF. This will show an image of the parental tRNA sequence with the tRF sequence in blue. The "Experiments" link will display a table with every dataset that was analyzed for the organism of this tRF. Each row of this table has abundance of the tRF in the dataset, a brief description of the dataset, and multiple links. The GEO link will take you to the GEO page for this library. The "View Alignment" tab will show left alignment of all the reads in the library mapping to the parental tRNA along with read counts and RPMs. The "View Graph" link will show a bar graph with the x-axis the nucleotide positions of the parental tRNA and the y-axis the read coverage.

5. Is tRFdb complete?

No! This is the first version of tRFdb and we expect to add more organisms and features based on user feedback. Any suggestions for the website can be submitted via the feedback tab.

6. What does tRFdb constitute?

We report a comprehensive database of tRFs prepared from publicly available high-throughput sequencing data of >50 short RNA libraries. tRFs originate precisely from the extreme 5' (tRF-5) or 3' ends (tRF-3) of mature tRNAs or from the 3' trailer sequence of precursor tRNA transcripts (tRF-1) and are present in humans, mice, flies, worms and yeasts. tRF-3s are generated by cleavage of mature tRNA between A/U-A/U bases in the T?C loop.

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