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Deep sequencing of the 5' ends of gene transcripts using DeepCAGE delivers detailed information about the architecture and expression level of gene promoters.
Each alternative transcript 3′ end is represented by discrete count data and has the potential to add layers of functional annotation to sequence at the 3′ ends of gene models.
Hence, of these 43,990 ESTs in reference transcriptome, it is likely that several ESTs are sequenced from a common gene which only generates a type of tag by NlaIII from the 3′-most ends of gene.
Two F-ESTs provide top-tier matches to the internal region of gene site 4, while two other F-ESTs (including the probe source [GenBank: DV439384]) provide top-tier matches to the 5' and 3' ends of gene site 6, providing evidence that these two genes are transcribed.
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The papers show that the regulatory regions differ from one cell type to another, that they cluster around the ends of genes, and that they are organized into 'superclusters' spanning hundreds of thousands of base pairs.
(10) 3' ends of genes within operons typically signaled by AATAA.
H3K27me3 are found to be distributed in the 5′ ends of genes in euchromatic regions in Arabidopsis (Turck et al. 2007; Zhang et al. 2007b).
Consequently, multiple mechanisms have evolved to terminate transcription efficiently at the ends of genes.
Similar structural classes were obtained for 5' and 3' ends of genes, and 5' and 3' splice sites.
The 5' ends of genes are not highly conserved, and genomic databases are full of genes with incorrect start calls [22].
It is interesting to speculate that the targeted phosphorylation of Npl3 at 3' ends of genes might help trigger termination.
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