To summarize, we have demonstrated that older genes tend to be bound by more TFs, have more conserved upstream sequences, use more alternative TSSs, produce more alternative splicing isoforms, use more alternative polyadenylation sites, and contain more miRNA-binding sites and that they are also more likely targets of NMD and RNA editing.
Trinity focuses more on splice isoforms.
Second, aided by improved sequencing technology and increasing EST and cDNA experimental data, many more alternative splice isoforms had been identified [ 17, 18].
We found that older genes tend to be bound by more TFs, have more conserved upstream sequences, use more alternative transcription start sites (TSSs), produce more alternative splicing isoforms, and use more alternative polyadenylation sites.
We searched gene loci with two or more alternative splicing isoforms supported by FL-cDNAs to determine whether alternative splicing mechanisms affect gene expression during Pi stress.
The system allows users to compute isoform signatures for one or more alternative splicing isoforms at the same time, offering a variety of different methods to describe the isoform structure, and provides its results as a web page or as a downloadable delimited file.
This way we obtained a set of 804 proteins whose genes encode for one or more alternative splicing isoforms distinct from the reference protein sequence.
To search for more alternatively spliced isoforms of the CALU gene, we designed a pair of primers localized in the first and last exon (Supplementary Figure S1a), and performed PCR analysis.
Independent and in silico genome-wide assessments have identified genes expressing particular splice isoforms more frequently in glioma than in normal brain.
The analysis of differential splice isoforms is more complex than the analysis of differential gene expression, due to a higher variation in thermodynamic conditions and possible cross-hybridization and folding of sub-optimally designed oligonucleotides.
