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As for many alternatively spliced exons, it comprises an imperfect polypyrimidine tract interrupted by purines (Figure S1).
For example, the Drosophila homolog of the human Down Syndrome Cell Adhesion Molecule (DSCAM) gene potentially encodes three times as many alternatively spliced transcripts (∼38,000) as the total number of predicted genes (∼13,600) in the fruitfly [3], [4].
On the other hand, expression of many alternatively spliced exons is highly regulated through development, including the precise regulation of exon inclusion levels (i.e. the fraction of transcripts from a given locus that include an exon; [14] [16]).
An effect of Tat-SF1 depletion on HIV-1 RNA ratios is also consistent with recent unpublished data from our laboratory that demonstrate that Tat-SF1 depletion changes the relative levels many alternatively spliced transcripts in human cells without affecting the total amount of these transcripts (H.B. Miller et al., unpublished results).
c Many alternatively spliced genes.
CAPN3 exists in many alternatively spliced isoforms.
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The proposed nomenclature encompasses forty-three distinct proteoglycan-encoding genes and many alternatively-spliced variants.
It has previously been noted that many such alternatively spliced exons (perhaps up to ~30%) harbour premature stop codons [ 11, 12], and thus may be considered 'pseudogenic' alternative transcripts.
Although we cannot readily estimate how many additional alternatively spliced variants C. elegans may have, we have shown that SAGE data can be efficiently used for discovery of novel transcript isoforms.
Several possibilities for the discrepancy between the lack of positive effects on CVD and the beneficial effects on surrogate markers exist, including chance due to low power and short duration of many studies; alternatively, surrogates such as CRP or measures of atherosclerosis may not be informative for TZDs, as was the case with the HDL-raising medication torcetrapib (35, 36).
Since the microarrays included constitutive and alternative splice variant probes, we examined how many genes were alternatively spliced in response to HAL-PDT (Table 3).
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