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Repeated DNA sequences protect the chromosome ends from losing coding sequences at cell divisions.
Such partial gene duplications may then lose coding ability, becoming pseudogenic exons (ΨEs), in a similar way.
It has been reported that transcripts losing coding potential could function as ceRNAs in rodents [ 4, 26].
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Even having lost their coding capacity, transduplicated sequences may undergo transcription and have a regulatory function [31].
The induction of host antioxidant proteins by Wolbachia may be an adaptive mechanism for coping with ROS despite having lost genes coding for bacterial antioxidants.
With such an alignment, information of nucleotide position according to the Open Reading Frame (ORF) of the sequences is lost in coding regions.
However, the gibbon PIPSL lost its coding potential by accumulating three nonsense substitutions and one in-frame indel (See Additional file 3).
However, in combination these analyses show that the inactive transcripts appear to be undergoing neutral evolution, indicating that they have indeed lost their coding potential and are not being selectively maintained.
