A recent review in last month's Genome Biology sets out the progress made in identifying non-coding conserved regions of the genome. These areas are conserved, or highly similar in the genome of different vertebrates, but non-coding, which means that they are not translated into protein. In some cases these sequences are shared between animals, like fish and humans, whose last commmon ancestor lived 300 million years in the past. Other sorts of sequences are shared between nearer neighbors such as rat and human. Both levels of conservation imply that these non-coding regions are important for survival of the organism.
Non-coding conserved stretches occur both in the near vicinity of "gene territories" and also remote from any known gene, although the latter tend to be less well conserved. It is proposed that non-coding conserved regions near gene territories help control that gene. However, early functional tests of this idea, by making mutations in the non-coding conserved stretches near the gene singleminded have not led to obvious abnormalities in that gene's activity.The review concludes by showing that at least the evolutionary distance between rat and human is near enough that at least some of the time sequences would not drift very far even without active measures (that is, under neutral selection).
A second paper on this topic from the folks at Hinxton tackles regions of DNA sequence similarity between the puffer fish Fugu and humans. Fugu has an incredibly compact genome (400 Mb versus 3000 Mb for humans), which is thought to enrich its sequences for critical genomic regions relative to organisms with big floppy genomes. Recent computer work had found about 1400 non-coding regions, conserved between humans and fugu, placed in clusters throughout the human genome. The current work took a closer look at the boundary regions around these stretches and found a sharp dropoff between the conserved sequences and their non-conserved neighbors. This pretty strongly suggests that these little regions are being actively husbanded while the genomic neighborhood is allowed to drift. Still, there's no known function.