I am trying to figure out a way to find a complete list of genes that are located inside of the introns of other genes. I know that this is fairly common for small non-coding RNAs, but we want to find all instances of this sort of overlap among RefSeq genes (in Drosophila). It is fairly easy to do an intersection of intervals between all exons and all introns, but that lists every annotated alternatively spliced exon (every annotated exon that overlaps any region that is also annotated as an intron in some RefSeq gene model). What I want is to find exons that overlap introns of DIFFERENT genes. Is there any way to construct such a query in the Table Browser - or use a Galaxy tool, a trick in Excel, or anything else anyone can think of?
Thanks for your thoughts. Stuart M. Brown, Ph.D. Associate Professor Center for Health Informatics and Bioinformatics NYU School of Medicine 550 First Ave, NY, NY 10016 [email protected] (212)263-7689 FAX (212) 263-8139 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. ================================= _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
