I had a page hit earlier today for this search: “only 3%of dna does anything.” Perhaps I can shed a little light on this myth. A few years ago, when the entire human genome was sequenced (not really, they missed the highly methylated regions and telomeres, so more like 92%). It was stated that only 3% of the genome encoded proteins. This does not mean the rest of the DNA does nothing. This only means that 3% of the genome contains an open reading frame (ORF) for protein. The genome is not JUST about encoding proteins, though. There are sequences responsible for encoding ribosomes, sequences which promote genes, regulate transcription, regulate genome structure, and possibly many other functions. Other segments are integrated retroviruses (endogenous retroviruses (another 8% of the genome) and retrotransposons) and other transposable elements (transposons). SINES make up about 13% of the genome. At this point, we’re up to 25% of the genome not including promoters, enhancers, suppressors, and silencing sequences. This also doesn’t include telomeres or LTRs either. The genome has quite a few functional elements which make up far more than 3%.
In any event, you cannot equate “no known function” to “functionless.” Just because we do not know what a sequence does only makes the function of it unknown, not absent. In the same light, some of these sequences can be completely removed from other mammals with no obvious effect on the organism. These regions are likely conserved functionless areas, however, these regions may have regained function in some way (either as enhancers or distant promoters).