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Our approach was to be conservative, and only change gene models where the evidence was clear.
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The DNA bait position with respect to the gene model may change as gene models are updated.
Since only the WormBase ID is always maintained (i.e. the names and sequence may change as gene models and functional annotations improve), we use it as a key for the annotations.
Remarkably, allele-specific splicing changes often lead to qualitative changes in gene models, yielding many isoforms not previously annotated.
Effects of the observed changes in gene models on the encoded proteins were predicted to be modest.
Furthermore, we do not understand how stop codon variants first arise within populations, leading to changes in gene models over evolutionary time.
We did not have the capacity to annotate and analyze exact molecular outcomes of changes in gene models at that time.
One of these, PlantGDB, serves community annotations via Distributed Annotation Service (DAS) wherein the changes to gene models are stored at PlantGDB, and DAS web services are used to serve the data for display within the context of the MaizeGDB Genome Browser.
One of the most dramatic changes to gene models supported by the RNA-Seq coverage data is the length of 3′ UTRs: a number of genes have alternative transcripts with very long 3′ UTRs, up to 18 kb (Table S6, File S5).
Overall, the average change in gene model size was 27.9%, a substantial general increase in the sequence length of the Myc-GeneModel set, although not necessarily a change in the translated sequence.
Others were not used in annotations because they were low frequency and did not change the gene model significantly or because they created frameshifts and lacked corroborating evidence (see below).
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