I need to analyze several 5’UTRs from C. elegans transcripts. Is there any way to download ONLY 5’UTRs with the corresponding gene names? Or otherwise to download as in the gene’s pages as “view spliced + UTR” with cds in uppercase and UTRs in lowercase? (This last option would be just perfect for my work!)
I’m kinda old school and I’m not as familiar with WormMine yet, but if you go to the legacy site and use WormMart, it’s super easy to grab what you want.
Pick the gene dataset and under attributes pick gene sequences. Click the expansion ‘+’ sign and pick 5’UTR (lots of other cool options there too). Then, it’s as easy as pressing the results button (left hand side, three buttons are there).
The results button will bring you to a new page and you can choose the format of how you want your results to come out as (FASTA, TSV etc.). I think your file will be pretty massive, so be prepared to wait…
Thank you very much, the info was really helpfull