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Our pairwise sequence alignment confirmed the prominent sequence similarity of RfCasp10 with its fish homologs, and phylogenetic reconstruction affirmed its homology and substantial evolutionary relationship with known caspases 10 similitudes, in particular with those of teleosts.
While the occurrence of TATA-related motifs was established reliably among highly expressed genes, other more prominent sequence motifs distinct from BRE and DPE have been identified in smaller subsets of TATA-less Arabidopsis genes (Figure 1).
Sequence fragments from the segmentation regions of transcripts classified as cleaved were analyzed with the Gibbs Sequence Sampler [31] and revealed several prominent sequence motifs (Figure 5A; Additional results are available in Figure S7).
However, a striking difference between the most prominent sequence changes noted in this study of inhibin evolution and those noted in many other studies is the importance of indels rather than amino acid substitutions [10].
Thus, while the nature of this study does not allow us to distinguish between direct and indirect SRC substrates, this motif analysis of the Y561-dependent phosphorylation sites suggest that many are in fact direct SRC substrates since the most prominent sequence motif closely matches known c-SRC consensus motifs [36], [37].
More specifically, the profile-based sequence alignment revealed prominent sequence similarities between mouse PrP, Dpl and ZIP10 (Figure 1A), which allowed the threading of the sequence of the PL domain of ZIP10 onto the structures of both PrP and Dpl (Figure 1B).
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This effect is prominent in sequence 13, which results in higher distance measures for this sequence (Fig. 16 a).
A prominent conserved sequence found in maize ID1 and most other IDD genes is the TR/L/Q/DFLG sequence located near the C-terminus.
A prominent earthquake sequence could be observed in the east of the study area (Figure 3, box d).
Given the prominent GAGA sequence within motif 12 0, we compared it to known GAGA-factor binding sites.
Another prominent 601 sequence-related feature that we observed for both remodelers was a 10 bp periodicity of the reaction products.
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