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The Illumina RNA-seq platform allows for transcript identification and measurement of transcript abundance.
The segregation within subgenomes likely provides additional "noise" that allows for transcripts relevant to the trait to separate clearly from others, focusing the candidate set.
Similarly, each mRNA is assembled into an RNP (mRNP) particle involving a series of complex assembly intermediates, which associate with each species of RNA in a dynamic fashion to allow for precise transcript maturation (Fatica and Tollervey 2002; Hopper and Phizicky 2003; Vinciguerra and Stutz 2004).
The generally permissive chromatin structure of all var genes exon 1 may allow for abortive transcripts to be formed and rapidly degraded and for the generation of antisense transcript directed by the var intron.
Motivation: Alternative splicing and other processes that allow for different transcripts to be derived from the same gene are significant forces in the eukaryotic cell.
Genome assembly may potentially allow for more complete transcript information to be obtained when compared to a de novo transcriptome procedure, thus easing primer design.
There are respective exon/intron boundary consensus sequences to allow for a single transcript that contains the bHLH domain, an orange domain and ends with the WRPW motif (Fig. 4C).
Note that we also tested for another mechanism, which has the potential of producing different-frame proteins: Alternative translation start sites in a transcript allow for the co-existence of multiple alternative reading frames in the same transcript (Kochetov 2008).
The GhExp1 and β-1,3-glucanase-like genes used to design primers for RT-qPCR (Additional file 2) do not share enough homology with the Affymetrix nucleotide sequences in the regions corresponding to the probsets to allow for accurate comparison of transcript abundance between microarray and RT-qPCR.
In contrast, whole transcript (WT) and tiling arrays allow for exon level interrogation of transcripts and splice variants.
In addition, many colleges and universities are in the process of migrating to competency-based models, which will allow for the output of transcripts that better describe the competencies of graduates.
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