I am working on RNA translation and I must identify uORF, so How to find an upstream open reading frames (uORF) or small reading frames in the untranslated 5' region (5' UTR) of messenger RNA? Are there any specialized databases?
maybe try to find a kozack sequence 5'ATG
either, take the full lenght cDNA , in vitro translate in rabbit lysate and analyse by gel and autoradio....look if you detect a translation product compatible with the lenght of the uORF
Try ORF finder http://www.ncbi.nlm.nih.gov/projects/gorf/ and then ,,manually'' investigate results for possible uORFs. Keep in mind Kozak context of uORF AUGs and whether uORF AUGs are in frame with main ORF. If you find something you can check it in RRL.
The free program / download ApE (A Plasmid Editor) can do this. Just use the ORF finder from the beginning of your transcript sequence and it will find them.
hi, Amine Bouchareb , did you find the uORFs? I am doing this now, could you please me some suggestion?
Hi Xiaojie, I'm really sorry but I didn't find any accurate tool that helps to find uORFs. However, you can look at ribosome-profiling screening from other teams and see if you gene of interest is there.
Good luck
I developed a tool (uorf-finder) which can find all uORFs within a genome, it's available for download here: https://bitbucket.org/TabeaK/uorf-finder/
http://bioinfo.unl.edu/mediawiki/images/d/d5/UORF_Presentation_2014-09-02.pdf
How about the new uorf-tools?
https://uorf-tools.readthedocs.io/en/latest/preprocessing-workflow.html
- Badges
- Science topic