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miRNA sequences were checked to compensate for the mis annotation of miR168 type and miR403-type sequences in miRBase.
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While we identified 1,439 pseudogenes in this study, these represent only a partial set of pseudogenes in the rice genome as we deliberately designed a conservative approach to annotating pseudogenes to prevent mis-annotation of true functional genes.
The region between two stop codons (O SS) encompassing a potential open reading frame that could have produced a particular orphan peptide appears highlighted in light gray to give the user an intuitive feel regarding whether the orphan peptide indicates the potential mis-annotation of a unique open reading frame or an extension of an annotated gene (i.e., a missed start).
However, there are several problematic aspects in the GeneChip technology, related especially to the mis-annotation of many probes.
This finding may be the result of mis-annotation of these sequences as miRNAs or that processing of the hairpins is somehow suppressed in ES cells.
This has led historically to the mis-annotation of many proteins.
A small number of introns were supported at only one end, suggesting mis-annotation of the gene models.
This could be a result of the loss of a clade member or a mis-annotation of the Vitis genome.
We understand that there may be a mis-annotation of eel sequences if using the other available model species databases.
Possibilities for these failures include functional mis-annotation of genes or protection from loss-of-function phenotypes due to gene redundancy.
Quality of probes, probes directed at minor splice variants, and mis-annotation of probes can also lead to errors in conclusions (e.g., [ 23]).
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CEO of Professional Science Editing for Scientists @ prosciediting.com