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Furthermore short segment scans are less affected by global ocular aberrations that might cause loss of overlap between both beams.
For a START codon present inside the coding region of the gene to be used (a process that could lead to lead to a loss of overlap between OGPs) the original START needs to be lost.
So for this process to lead to a loss of overlap or change in the length of the overlap two events are needed: the loss of the initial START codon and the acquisition of an alternative START inside the protein coding gene sequence in the relevant reading frame.
Our results suggest a relatively high turnover of the properties of adjacent gene pairs, including the creation and loss of overlap between coding sequence of proteins, and relatively rapid variation of the distance separating the coding sequences, including the size of overlaps.
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We determined gain and loss of overlaps using the maximum parsimony principle [ 32] and the species tree.
The observation that less than 30% of the overlaps are shared between human and mouse suggests fast gain and/or loss of overlapping genes.
Therefore lack of strong overlaps conservation between even closely related species may result from the origin of a new, lineage specific overlap as well as from the loss of overlaps in many lineages.
Therefore, it is likely that some of the gains and losses of overlaps seen here are actually annotation artifact.
Moving the START codon downward the sequence, or the STOP codon upward, could lead to a loss of the overlap.
Using this method, we measured a significant loss in GluA1 signal in Arf6 endosomes following TC10CA expression, also reflected by the loss of spatial overlap indicated by the decrease in Pearson's correlation coefficient.
While young gene overlaps can arise from new splice variants, ancient overlaps can disappear due to the loss of the overlapping splice variant.
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