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Differing start positions of ABL1 can be explained by the missing intron sequences within the data used by deFuse.
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The missing intron contains a CF2-binding site and acts as a repressor for inhibiting Bmglv1 expression in embryonic stage.
For instance, 2.7hPLPΔ212 5810 is missing intron 1 positions 212 to 5810 based on numbering the entire intron from 1 to 8579.
To determine the source of these discrepancies between Tiling Assembly and the FL-cDNA, seven different categories of classification were used: extra exon, missing exon, extra intron, missing intron, missing junction, gap, or multiple discrepancies.
The later duplicate is missing introns II-V and is likely a product of retrotransposition.
Extra or missing introns were the most abundant cause of the discrepancy as would be expected for plants.
We were concerned about the possibility of merging genes or missing introns due to potential genomic contamination in RNASeq experiments.
By comparison the L31 genes in the diatoms T. pseudonana and P. tricornutum seem to be missing introns.
All missing introns were lost precisely from the genome.
Partial deletion constructs were named according to the missing hPLP1 intron 1 sequence, based on numbering the intron from positions 1 to 8579.
Further analysis revealed that the missing sequence stretch lies within the intron sequence.
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