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Many alternative splicing processes are associated with RNA secondary structure formation in pre-mRNA.
Up to date, many alternative splicing databases have been developed [ 33- 37, 41, 42], the main purpose is to collect all the alternative splicing candidates.
Unlike other classes, a low level of variance was observed in the number of CRY-DASH genes, which suggests that these genes do not have many alternative splicing isoforms.
Analysis of gene models predicted from assembled EST and full-length cDNA genomic alignments from rice and Arabidopsis discovered that many alternative splicing sites are separated by a small number of bases, typically four or three bases in the case of alternative donor and acceptor sites, respectively [ 12].
However, though we detected many alternative splicing events using the whole exon chip, we are aware that these microarrays are not be able to detect exhaustively all alternative splicing in a given tissue.
It is important to note that many alternative splicing events display precise tissue and developmental regulation, underlining the requirement for the correct biological context when examining functional and therapeutic insights into alternative splicing (Takeuchi et al., 2010; Calarco et al., 2011).
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Simultaneously, this analysis implies that many alternative splice forms may accumulate to different levels, possibly resulting in accumulation of varying amounts of protein products with different functions.
This approach can identify many alternative splice variants if sufficient sequence reads are carried out [13], [14].
Such an arrangement helps in accurate splice site selection especially across large introns that may have many alternative splice sites [ 36].
Second, models for quantifying full-length isoforms with single-end RNA-Seq data are often not identifiable for genes with many alternative splice forms (Hiller et al., 2009; Lacroix et al., 2008).
The NOS gene in vertebrates is known to generate many alternative splice variants with importance to differential tissue expression, enzyme activity [ 67] and even, erection of the penis [ 68].
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