Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers.

By Amir Goren, Oren Ram, Maayan Amit, Hadas Keren, Galit Lev-Maor, Ida Vig, Tal Pupko, Gil Ast. Molecules and Cells, 2006

330 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/38591f745b58818cf6357729fe74fe8ac5472399

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Citations in the corpus

An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells (2009, neutral): “Consistent with the previously published bioinformatics analyses showing that composite functional RNA elements tend to be more evolutionarily conserved than other genomic regions that contain just the consensu”
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. (2008, background): “A recent report suggested the counterintuitive result that some elements (designated ‘‘ESRs’’) can function as both ESSs and ESEs depending on exonic context (Goren et al. 2006).”
Expansion of the eukaryotic proteome by alternative splicing (2010, background): “and by pinpointing sequences within coding exons (those translated into protein) that are more highly conserved than expected given the flexibility of the genetic cod”
Variation Interpretation Predictors: Principles, Types, Performance, and Choice (2016, background): “, 2001; Yeo and Burge, 2004] and splicing regulatory sites [Fairbrother et al., 2002; Wang et al., 2004; Goren et al., 2006; Smith et al., 2006].”
Dido3-dependent SFPQ recruitment maintains efficiency in mammalian alternative splicing (2019, background): “Earlier studies reported that sequences surrounding the actual splice sites might control splicing in higher vertebrates; both regional AT content and short SF recognition motifs can impose regulation (55,56).”
Learning the sequence determinants of alternative splicing from millions of random sequences. (2015, methodology): “Examples of SREs have been identified computationally by analyzing motif enrichment near splice sites (Castle et al., 2008; Fairbrother et al., 2002; Zhang and Chasin, 2004) or sequence conservation between species (Goren et al., 2006).”
Human Splicing Finder: an online bioinformatics tool to predict splicing signals (2009, methodology): “To maximize the detection of auxiliary motifs, HSF integrated: (i) matrices for SR proteins (SRp40, SC35, SF2/ ASF, SF2/ASF IgM/BRCA1 and SRp55) from the ESE Finder tool (19,27); (ii) sequence motifs shown to be differentially present in exons and introns, such as the RESCUE-ESE hexamers (18), the p”
SFmap: a web server for motif analysis and prediction of splicing factor binding sites (2010, background): “In recent years, several methodologies for identifying SF binding sites have been developed (6–10); for review see (11).”