On the PlantRNA website, the data can be searched with just a few clicks from the starting page to the result table. To help you in your search, 3 examples are given below.
Example 1 : Looking for all nuclear-encoded Arabidopsis thaliana tRNAArg
Possibility 1: From the Home page click on "tRNA"
Select "Arabidopsis thaliana"
Select "Nucleus" (all chromosomes are selected by default, if you wish only one, deselect the ones you do not want)
Select "Arg": (by default, all anticodons are selected, if you wish to restrict your choice, deselect the anticodons you are not interested in)
Go to the bottom of the page, click on "search in database"
Remark : you have several options for display settings !
Results are displayed (you may have several pages), and can be downloaded (xls or fasta format)
For each tRNA, you can click on the "+" button on the right of the screen. This "+" will give you access to important biological information, an example is given below:
Possibility 2: From the Home page click on "Species"
Then click on "Arabidopsis thaliana"
On the "Arg" line, click on the number on the right (total column) to obtain the complete list of A. thaliana tRNAArg genes
By clicking on the "+" button, additional information can be provided, as described in example 1. Clicking on "arath", on the left, will allow you to go back to the summary for the species
Example 2 : Looking for nuclear-encoded Chlamydomonas reinhardtii tRNAArg(ACG) genes containing introns
From the Home page click on "Species"
Then, click on "Chlamydomonas reinhardtii"
This allows you to see the summary table. For each isotype, the first number corresponds to the number of isoacceptors, the second in parenthesis to the number of tRNA isoacceptors with an intron. For instance, there are 6 tRNAArg(ACG) genes out of 14 with an intron in the nuclear genome.
If you click on the number, the whole list of tRNAArg(ACG) genes is given and the "+" button on the right allows you to get details, such as the presence of an intron or the import of the corresponding tRNA into mitochondria, polyT motif...
Example 3 : Looking for Ostreococcus tauri mitochondrial RNAse P
From the Home page click on "Enzymes"
Then, click on "Ostreococcus tauri"
The lists of synthetases and processing enzymes are given one after the other. Go to the list of enzymes involved in "processing, modifications and others" and find the RNase P with a mitochondrial location.
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