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Our analysis of transcript 5' ends suggests that transcription initiation and transcript processing in Anabaena is often complex, and that many transcripts have long 5' UTRs with unclear transcriptional start sites or processing sites.
Many transcripts have multiple antisense transcripts in plant.
Many transcripts have correlated expression to only a small number of other transcripts (see Additional file 2: Figure S5).
Many transcripts have been found in intergenic regions, particularly the long intergenic noncoding RNAs (lincRNAs) (Derrien et al. 2012).
From the NAT-network, we found that many transcripts have more than one partners and are involved in several NAT pairs.
To date, many transcripts have been evaluated as 'tumor-specific' markers, such as CK18, CK19, CK20, Mucin-1 (MUC1), and carcinoembryonic antigen [ 35].
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How many transcripts had homology to the fire ant and/or the honey bee?
The presence of pleiotropic hotspots affecting the expression of many transcripts has already been described in yeast [ 14], where no more than 200 trans-eQTLs explained transcript variation for 1,716 traits.
One possible reason for the longer last exons observed in the current study is that the sequence data necessary to determine the true 3'-end of many transcripts has become available only recently.
Further work would be needed to assess whether LNA-mediated template-switching could be preferable for digital expression profiling starting from partially degraded RNA samples, where the cap structure of many transcripts has been lost.
However, recent studies of the human transcriptome indicate pervasive transcription in previously unannotated regions of the genome and that many RNA transcripts have short or lack 3' poly(A) ends.
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