[coriny]

Sorry, I'm going to nit pick, but non-coding and "junk" aren't the same thing:

Non-coding just refers to not being translated to protein, and we know (as you list, more for the benefit of others) that there are many non-coding functional elements.

Junk DNA is non-conserved DNA (e.g. shows only neutral selection). And if it's not being selected for or against, then it probably doesn't have much effect either way.