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For lower-affinity sites, recognition of any "site" by sequence gazing would be remarkable.
RBM10 binding close to splice sites might interfere with splicing sites recognition and/or splice sites pairing.
For the annotation of miRNA binding sites, recognition sequences for human miRNA were obtained from a human miRNA database [ 35].
The combination of both methods has been shown to be effective for large-scale genome transcription factors binding sites recognition [ 19].
A parallel to Exd-Hox has also been described in yeast: the Cbf1-dependent sulfur metabolism genes are specified by an RYAAT DNA motif found adjacent to the Cbf1 sites, recognition of which requires the Met4 and Met28 subunit cofactors of the Met4- Met28- Cbf1 complex (Siggers et al. 2011).
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Example 2. One more example case will be considered, that is involving acceptor splice-site recognition.
Moreover, Surflex-PSIM [34], a novel method combining initial binding site recognition with subsequent binding site comparisons has been developed.
Specifically, the structural details of splice site recognition and the architecture of the spliceosome active site are poorly understood.
Based on these results, we present a simple model for the mechanism of microRNA target site recognition.
Similarly, PUF60 may be required in addition to U2AF65 and U2AF35 to facilitate splice-site recognition.
Recent experiments suggest further context signals involved in miRNA target site recognition and regulation.
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