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We found that NE-determined cut-off value varies among different duplicate pairs, suggesting that empirical cutoff value is not suitable for every case.
The graph shows the results of six different duplicate experiments (p < 0.01, t test).
However, different duplicate gene pairs might have different levels of functional similarity.
For example, Gm04.2, Gm04.1, and Gm04.3 located in different duplicate regions of the same chromosome, all have two introns flanked by three exons.
A fifth gene, dopa decarboxylase (Ddc) produced sequence data likely to be from different duplicate loci in some of the taxa, and so was excluded.
The gene duplication can result in the loss of AS because the functions of different AS isoforms may be kept by different duplicate genes.
Similar(51)
In both Arabidopsis and rice, locally duplicated ohnologs are widely distributed in different duplicated chromosomal segments that cover all chromosomes (fig. 2), suggesting that local duplications of ohnologs are not specific to certain chromosomal regions.
For two post-duplication outgroups, the KNST branch length is e2-e1 (if both outgroups retain the same duplicate; Figure 3b,e) or 2d-e2-e1 (if different duplicates are retained; Figure 3c,d).
The total expected NST internal branch length is then equal to (i) the probability that X1 and C retain the same duplicate, 0.5(1+r2), times e1, plus (ii) the probability that X1 and C retain different duplicates, 0.5(1−r2), times the average of e2 and 2d-e2 (which is d).
Locally duplicated ohnologs are widely distributed in different duplicated chromosomal segments and functionally biased.
3D-JIGSAW program [ 51, 52] was used to model the 3D structure of the different duplicates.
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