5.6 years ago by
Transposable (aka, "mobile") elements are categorized as repeats in most genomes, so you'll need to start by downloading the repeatmasker track from UCSC. How you proceed with that will depend completely on (A) what you want to do and (B) what's known about the biology. In humans and mice, for example, it's known that some ERVs are still mobile, while others seem to not be. The simplest was to get a list of this is to filter repeat masker tracks by homology, length, etc.. You can find an example of that for the mouse here. That's based on a some human settings that someone else came up with (I can probably dig up the reference if needed). Not all of the candidate regions will be mobile, but it's a useful list to start with.
Of course, if it's unknown what, if any, families of repeats are still mobile in sheep then the best you can do is some filtering of some likely candidate families based on other organisms.