I have some data indicating there might be a splicing variant of the Arabidopsis Thaliana protein I'm studying that has not been identified. Is there a database of i.e. RNA sequences (transcriptome?) that I could search for it, knowing a part of its sequence?
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There's not going to be a specific database that's particularly thorough for this. The best you can do is one of the following:
- Search through TAIR (https://www.arabidopsis.org/servlets/Search?action=new_search&type=protein)
- Blast SRA with the full length sequence ( https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&BLAST_SPEC=SRA&SHOW_DEFAULTS=on). This will unfortunately pull up a LOT of related hits for every other related isoform.
- Download some public RNA-seq data from SRA/ENA and see if it has supporting data.
You're probably best off doing all of these, where you use blast to find relevant datasets that you then align. My guess is that TAIR won't have everything, since this has probably been seen before but not reported since the experiment wasn't intending to find new proteins.
answered Dec 16, 2021 at 16:01