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Most often, APA generates transcript variants with different length of 3′ untranslated regions (3′UTR), though it could affect the coding region occasionally.
Alternative splicing is an important mechanism that generates transcript diversity.
RNA-Seq rapidly generates transcript sequences and provides more detailed information than microarray-based technologies.
As shown in the cartoon in Figure 1A, inclusion of the ASE in the final spliced mRNA product generates transcript N1 and exclusion of the ASE generates transcript N2.
Here, we describe Rnnotator, an automated software pipeline that generates transcript models by de novo assembly of RNA-Seq data without the need for a reference genome.
Oases generates transcript "loci", which is Oases terminology for the de-Brujin graph clusters meant to represent genes and their splice variants or highly-similar paralogs.
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At genes, RNA Pol II generates transcripts in one direction.
The BLCAP/ Blcap locus generates transcripts from distinct promoters downstream (BLCAP_V1/ Blcandv1) and upstream (BLCAP_V2/ Blcap_v2) of NNAT/ Nnat (Fig. 1).
The approach, without a specific design, generates transcripts with slight variations in intergenic regions that change RNAase cleavage sites, ribosomal binding sites sequestering sequences and mRNA secondary structures.
However, these previous analyses did not recognize the presence of yar, likely because yar generates transcripts that lack a large ORF (Soshnev et al. 2008).
To this end, we found that miRNAs contributed only marginally to generating transcript rhythms at the post-transcriptional level.
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