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
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
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.