BLAT alignment of the 5'RACE products led to three main observations: (1) multiple distinct p110δ transcripts exist within each cell line investigated; (2) most transcripts contains two untranslated exons (Figure 4A), which we have named exon -1 and -2 (to indicate their relative locations with respect to exon 1, which contains the putative ATG translation start site as defined in [13], [54]).
Our finding that the most downregulated transcripts contain a short 3'UTR is possibly linked to the fact that most of these transcripts represent housekeeping genes [42].
For example, most mRNA transcripts contain a stop codon, but some do not, and these non-stop mRNA transcripts result in a non-stop polypeptide that remains tethered to the ribosome.
Since most FMR1 transcripts contain the 195-bp exon 14 [ 34], and all contain exons3/4, both assays target FMR1 transcripts of a similar size and abundance, which is experimentally reflected by the highly significant correlation between the two assays for high quality total RNA samples from the peripheral blood of patients with small to intermediate size expansions (Additional file 1).
Analysis of flanking regions also revealed that most of these transcripts contain a PHR1-binding sequence (P1BS) in the 1-kb upstream or downstream region (Supplementary Table S5).
Most of these transcripts contain identifiable ORFs but no recognized Pfam motifs, and represent genes of unknown function.
In most tissues, transcripts containing exon IXL were relatively more abundant than transcripts containing exon IXS.
However, for the other components, IDBA-Tran did a good job: 6353 components, each of which contained at most 5 transcripts, contained 9082 transcripts all together.
Excluding operons that were made up only of ribosomal transcripts, most polycistronic transcripts contained two or three genes (Table 2).> -wrap-foot> Genes are reported in order, starting from the 5′ of the polycistronic transcript.
