One of the main reasons that the "junk" DNA is believed to be
junk is that it doesn't look like protein coding sequence. A large
proportion of it consists of the same short bit repeated over
and over (GGCGGCGGCGGC and so on for thousands of bases). This
cannot be translated into protein--it lacks the start and stop
signals and control signals, and would produce a very boring
protein anyway.
There are some gene-like stretches in the junk DNA, but the bulk of
it, if it has any function at all, must be doing something different.
In many organisms another substantial portion of the junk consists of
thousands of copies of sequences which have the ability to duplicate
themselves. These may or may not be useful in some way to the organism;
they could survive even if they are not useful, as a sort of genetic
parasite, because of that copying ability.
Mary Kuhner mkkuhner at genetics.washington.edu
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