Short intron splicing efficiency is increased by secondary structure, and we detect both canonical and non-canonical short introns. These short introns are often alternatively spliced and are found in a variety of RNAs–both mRNAs and lncRNAs. We identify hundreds of short introns conserved among multiple human cell lines. Here, we report an approach to identify RNA short introns from RNA-Seq data, discriminating against small genomic deletions. There have been some efforts to identify additional short introns, but little is known about how many short introns are processed from mRNAs. ![]() Non-canonical splicing–intron excision without the spliceosome–has been documented most notably, some tRNAs and the XBP1 mRNA contain short introns that are not removed by the spliceosome. Canonical pre-mRNA splicing requires snRNPs and associated splicing factors to excise conserved intronic sequences, with a minimum intron length required for efficient splicing.
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