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Updated: Jul 12, 2026

Enhanced Northern Blot Detection of Small RNA Species in Drosophila Melanogaster
Published on: August 21, 2014
Similarities and differences of polyadenylation signals in human and fly
Dorota Retelska1, Christian Iseli, Philipp Bucher
1Swiss Institute of Bioinformatics, Batiment Genopode, UNIL, 1015 Lausanne, Switzerland. dorota@binf.ku.dk
Background:
Cleavage of messenger RNA (mRNA) precursors is an essential step in mRNA maturation. The signal recognized by the cleavage enzyme complex has been characterized as an A rich region upstream of the cleavage site containing a motif with consensus AAUAAA, followed by a U or UG rich region downstream of the cleavage site.
Results:
We studied these signals using exhaustive databases of cleavage sites obtained from aligning raw expressed sequence tags (EST) sequences to genomic sequences in Homo sapiens and Drosophila melanogaster. These data show that the polyadenylation signal is highly conserved in human and fly. In addition, de novo motif searches generated a refined description of the U-rich downstream sequence (DSE) element, which shows more divergence between the two species. These refined motifs are applied, within a Hidden Markov Model (HMM) framework, to predict mRNA cleavage sites.
Conclusion:
We demonstrate that the DSE is a specific motif in both human and Drosophila. These findings shed light on the sequence correlates of a highly conserved biological process, and improve in silico prediction of 3' mRNA cleavage and polyadenylation sites.
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