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L1MC4 may be a fecund source of octamer binding sites.

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posted on 20.02.2013, 00:18 by Craig B. Lowe, David Haussler

The probability density of each base in the L1MC4 consensus being present in a genomic copy (gray) or an exapted copy (red) is plotted (top plot). When zooming in to the second highest peak of exaptation probability we show the consensus sequence as well. By using motif finding software on the exaptation events in the extant human genome that contributed to this peak, we obtained a profile describing the selection acting on paralogous exaptations of this small region. This profile is easily alignable to the consensus, but it is interesting to note the ‘C’ in the consensus (bold type) that routinely changes to a ‘T’ in the exaptations. The profile describing the selective pressure acting on these paralogs is similar to the octamer binding profile, which is consistent with this section of the L1MC4 consensus often being exapted on the human lineage to act as a binding site for a member of the octamer family of proteins.