Sine Transposable Element Confirmation

Question

[David M]

I've determined a number of repeated regions (using REPET and RepeatModeler), and I'm starting to suspect that a number of the families are SINEs. I'd like to confirm this - how do I go about doing this? Am I correct in assuming that the only unifying features of SINEs are their relatively short size (<500bp) and the presence of a PolIII promoter? I guess my real question is: how do I identify PolIII promoters in these repeat families?

Answer 1

[Casey Bergman]

Odd as it may seem, you can use tRNAscan-SE for this since one of the methods in this pipeline is the EufindtRNA method of Pavesi et al which "searches exclusively for linear sequence signals in the form of eukaryotic RNA polymerase III promoters and terminators."