Frequently Asked Questions

1. What is IRESite?

IRESite is a freely available database going into details about IRES segments initially found in RNA viruses and eukaryotic organisms.

2. What is IRES?

IRES is an acronym for Internal Ribosome Entry Site. Originally IRES segments were discovered in +RNA viruses and give viral +RNA molecules the ability to functionally mimic mRNA molecules of their eukaryotic host. To date, the IRES elements have been found in over a fifty distinct viruses including those which cause serious diseases of humans and animals (mostly +RNA viruses but also retroviruses and even DNA viruses). The IRES segments have also been discovered in 5' untranslated regions of the cellular mRNA molecules. Although over 70 different cellular IRES elements have been reported untill now, it is not yet clear whether the cellular IRESs are more widespread or not. Moreover, there is an ongoing discussion in the community whether existence of the reported IRESs was demonstrated convincingly. A number of experimental/methodological drawbacks are currently known to affect the results and have to be carefully considered during interpretation of the result.
We believe it is necessary to re-evaluate the very precious experimental data in current context and correlate the accumulated data in larger scale. Unfortunately, the data provided in print are not accessible for efficient computer-based usage and analyses.

3. What does IRESite contain then?

The database was designed to house most (if not all) scientifically relevant characteristics of every individual experiment ever published in scientific literature in the field of IRES elements. At the moment the database contains still rather limited set of manually extracted primary data from selected publications. Some data presented here had to be deduced by curators from the original articles and other published resources to bring all records to a certain level of informational completeness. We wish the database be filled with data directly by scientists with the assistance of our curators. The database can be used to verify the validity of experiments carried in the past in current context of the knowledge.

4. How can I contribute?

Anybody is welcome to submit either his/her own data or even to submit data extracted from already published materials. The latter is what our curators do at the moment. This is unfortunately rather time consuming and therefore we would prefer scientists to submit their own data directly.

5. How long does it take to submit a new record and how do I do it?

Technically, the submission can be done in 7 minutes provided you have all input data readily available. This is, however, not what usually happens. We believe original authors can submit a single record in the time range of 10 mins to a few hrs depending on the fact whether they know the complete plasmid sequence (or at least the sequence from transcription start site to the transcription terminator), where are the ORFs located within the transcript and where IRES is located.

Further, it is necessary to know the relative values of reporter protein yields or their activities or whatever values were used to quantify the IRES activity. The numerical values should be submitted in a relative scale. When used, the positive control yields are defined as 100% and the yields from the newly characterized IRES and of the negative control should be scaled accordingly. If the positive control was not used then the measured value corresponding to the newly reported IRES activity should be set to 100% and the value measured for the negative control should be recalculated (downscaled). If applicable, it is necessary to annotate the name of positive control IRES and names of the plasmids used for positive and negative control expression, size of the intercistronic region in each of them ... and you are almost done!

Optional annotation sections

1. IREStrans-acting factors (ITAFs) affect activity of an IRES segment possibly by multiple mechanisms and the mechanism is still mostly poorly understood. Some ITAFs interact directly with IRES while others indirectly through cooperation with other molecules/adaptors. It was found that certain IRESs function only when ITAF (protein) is available in the translation system, e.g. when ITAF protein is supplemented to rabbit reticulocyte lysates.
2. The option to enter RNA:protein interaction data can be used to annotate any direct interactions between the mRNA and any protein. It is enough to write something like "an unknown protein of MW 160kDa interacts with the mRNA in HeLa cells" but preferably, you can supply detailed data about the protein, point to its GenBank GI:# record (but also to PDB, SWISS-PROT, PFAM and other databases), describe the range on the mRNA molecule which interacts with the protein, etc.
3. Yet another option is to enter the list of regions where the mRNA transcript shows some remarkable sequence complementarity to rRNA. This is used to label the records where "IRES activity" might be attributed to this sequence complementarity. A number of translational enhancers found in plant RNA viruses act by this mechanism.
4. Finally, if there was experimentally studied any secondary or tertiary structure of any region within the mRNA molecule it is possible to annotate this precious information as well.

That's it! Remember our curators will be happy to answer your questions. You always have the possibility to postpone the incomplete submission form and return to it later. You may have even several submission forms postponed simultaneously.