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In a gene-expression microarray such as the Illumina's gene expression bead chips [ 48] and Affymetrix's gene expression gene chips [ 49], beads or probes are designed to measure the expression levels of multiple transcripts by targeting various transcriptional regions of a gene.
Resulting data indicate that Helitrons not only intertwine the coding regions of different captured genes but also generate multiple transcripts by alternative splicing and by readthrough transcription that captures exons in genes near the Helitron.
This strategy deconvolutes reads mapping to exonic regions shared by multiple transcripts by optimizing a system of linear equations, and thus specifically assigns some reads to each alternative splice form (http://flux.sammeth.net)53.net
Some genomic regions are occasionally used to encode for multiple transcripts, by either overlapping or nested genes.
Whereas multicolor FISH can potentially be used for detecting multiple transcripts by employing different fluorescent tyramide substrates, the method is less efficient, particularly for RNAs expressed at low levels [ 6].
In a study of alternative splicing of SR genes, which undergo extensive alternative splicing in Arabidopsis, it was found that in almost all SR genes the longest intron was involved in generating multiple transcripts by alternative splicing.
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To date, all of the global expression studies in PD have looked at a single transcript per gene, although most genes have multiple transcripts generated by alternative splicing.
Probe sets targeting multiple transcripts represented by suffix (_x_ at, _g_at, _f_at,_r_at,_b_at,_l_at and _i_at) were filtered out and only probe sets with higher specificity represented by suffix (_at and _s_at) were taken into consideration for further analysis.
This analysis also highlighted functional heterogenity within a group of co-localized eQTLs, where colocalization can result not only from multiple transcripts affected by the same locus, but also from independent genetic effets localized on the same chromosome segment.
This research examined the expression and regulation of the catalytic subunit of the vacuolar type H+-ATPase in Arabidopsis thaliana and the effect of environmental stress on multiple transcripts generated by this gene.
The human WNK1 gene (29 exons) covers ∼160 kb on chromosome 12p13 and codes for multiple transcripts initiated by alternative promoters [Delaloy et al., 2003; Wilson et al., 2001; Xu et al., 2000].
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