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The rice trihelix gene of Os03g18330 seems to be a tandem duplication copy of Os03g18340.
We also analyzed the distribution of genomic component, such as segmental duplication, copy number variation regions and ultra conserved elements, which are closely related to conservation.
An allele created by a point mutation in one duplication copy may be subject to a number of genetic processes that determines its allelic state in duplicated DNA.
Therefore, we expect that it will be more frequent for each read of a pair to map to genetically close regions, rather than to another segmental duplication copy in a remote location on the genome.
A total of 3 epileptic cases with CNVs of the MIR155HG/miR-155 gene were observed in the case group, including 1 case with deletion (copy number: 1; 0.40%) and 2 cases with duplication (copy numbers: 3 and 4; 0.80%), but no CNVs were observed in the control group.
Allelic drift can take the newly derived allele through a polymorphic state (that is, SNP in a duplication) and further to fixation, in which the new allele and its counterpart in the other duplication copy are termed paralogous sequence variants (PSVs) [ 29, 35- 37].
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Using a protein protein interaction network, He and Zhang (2005) showed that after gene duplication, duplicate copies can have rapid "subfunctionalization" accompanied by prolonged "neofunctionalization" during evolution.
The type of polymorphisms represented by MSVs involves a variation in duplication copy-number, and presumably indicates that much multisite variation may have originated from point mutational events in paralogous sequences.
In total, 12589 unique pairwise sequence alignments of duplication copies were downloaded from HGSDB (build hg17).
SSD without deletion would lead to either three (post-WGD duplication) or four (pre-WGD duplication) copies.
6587 alignments had both source and target sequences located on the same chromosome (intrachromosomal duplications), the remaining 6002 alignments had their duplication copies on nonhomologous chromosomes (interchromosomal duplications).
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