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The last exon (exon 9) is the main protein-coding exon, and several distinct transcript classes are formed when transcription is initiated at various other exons [Pruunsild et al., 2007].
Contrary to the expectation that antisense transcription or processing regulates alternative polyadenylation of the sense gene, we find that the two alternative sense transcript classes are independent of antisense transcription.
Some transcript classes were of particular interest in this analysis (Table 2).
Analyses of transcript databases via bioinformatic approaches have described and uncovered numerous transcript classes.
Our gene set enrichment analysis suggested that NMD is essential for the proper regulation of selected transcript classes.
These include differential requirements for NMD in proliferating cells, regulation of distinct transcript classes as well as more systemic effects on alternative splicing.
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The class transcription represents the production (relationship produced by) of a primary transcript (class primary transcript) from the information codified (relationship has participant) by a gene (class gene).
The merged assembly transcripts provide a uniform basis for calculating transcript expression in each condition and the transcript class code.
To examine the distribution of hits for a particular protein across all members of a transcript class (e.g., Cbc1 hits in mRNAs), we used two related approaches, both performed on the most abundantly bound members of the transcript class.
A breakdown of hits by transcript class revealed a broad range of substrate specificities for the tested proteins.
Long non-protein-coding RNAs (lncRNAs) are proposed to be the largest transcript class in the mouse and human transcriptomes.
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