Molecular Biology and Evolution, Vol 15, 820-826, Copyright © 1998 by Society for Molecular Biology and Evolution
J Parsch, W Stephan and S Tanda
The potential for long-range base pairing between the 5' and 3' ends of
mRNA molecules was examined for 134 Drosophila and 204 human sequences
collected from the GenBank database. Each sequence was divided into two
parts, a 5' sequence taken from the start of the protein-encoding region
and a 3' sequence taken from the end of the transcript. The strongest RNA
pairing stem between each pair of 5' and 3' sequences was identified and
scored using an alignment program modified to incorporate RNA base pairing.
The observed pairing scores were then compared with a random distribution
of scores generated by aligning each 5' sequence to random permutations of
its corresponding 3' sequence. For both the Drosophila and the human mRNAs,
the observed pairing scores were significantly biased toward the upper tail
of the random distributions, with 61% of the Drosophila sequences and 64%
of the human sequences falling within the upper half of the random
distributions. This suggests that a pattern of long-range base pairing may
be a common feature of eukaryotic mRNAs. We have also analyzed a subset of
Drosophila and human mRNAs which show the greatest potential for long-range
pairing. The human pairings appear to be stronger and localized to more
specific regions near the ends of the mRNA sequence than those of
Drosophila.
ORIGINAL ARTICLE
Long-range base pairing in Drosophila and human mRNA sequences
Molecular and Cell Biology Program, University of Maryland, College Park, USA.
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