|MadSci Network: Genetics|
Thanks for the question. It is true that only ~10% of the human genome encodes proteins or functional RNA's. This is how the cell differentiates between 'the good stuff' and the 'junk' - by only transcribing and translating this small fraction of the genome. However, as you guessed, not all the 'junk' is dispensable. Non-coding sequence includes 1) intervening sequences (or introns) within the gene, 2) spacers between genes, and 3) repetitive DNA sequences.
Introns, which are transcribed into RNA but then removed at splicing, provide extra versatility to the genome- by splicing in different patterns, one gene can in fact encode more than one protein. Both introns and the spacer regions between genes can contain control regions that determine where and when in the body a given gene is transcribed; this is especially true of the region just upstream of each gene. These control regions are called promoters and enhancers.
Spacers between the genes are also needed to prevent cross-talk between the control regions of each gene. Repetitive DNA sequences are not known to play any functional role in the activities of the genome. 30% of the genome is made up of repetitive elements. 18% of the genome consists of repetitive elements present in 100,000 or more copies. One theory is that these repetitive arose from transposable elements capable of copying themselves and jumping in the genome. While some of the elements might still be active, others have mutated and are dormant. Transposable elements are parasites within the genome - playing no helpful role but using the genome to perpetuate themselves. Its possible that they exist in our genomes because evolutionary selective pressure against them is not too great - in an organism with a long generation time like humans the burden of copying all this extra DNA is not too high.