Primary and hypothetical secondary structure of Drosophila melanogaster U6 RNA.

A comparison of the nucleotide sequence of Drosophila U6 RNA with that of rat (6) reveals a homology of 90.7%. Of the 10 differences, 4 represent sugar and base modifications (positions 64, 69, 71, 73) while 6 are nucleotide replacements (positions 4, 6,18,65,86,102). Multiple alignements show that the nucleotide sequences of broad bean (7) and Physarum polycephalum U6 snRNA (8) have much weaker homologies than those described above. Interestingly, in domains where the U6 sequences show poor homology, the secondary structures seem to be highly conserved. Detailed computer studies are available from the authors or from Ch. Nager, Bio-Informatics, Friedrich Miescher Institut, 4002 Basel, Switzerland.