ESEfinder: a web resource to identify exonic splicing enhancers

By Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang, Adrian R. Krainer. Nucleic Acids Res., 2003

1,656 citations recorded by the source corpus.

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Citations in the corpus

F-SNP: computationally predicted functional SNPs for disease association studies (2007, methodology): “Splicing regulation ESEfinder (11) http://rulai.”
Comparative analysis identifies exonic splicing regulatory sequences--The complex definition of enhancers and silencers. (2006, background): “However, hexamer L7 functions as a strong ESE (Figure 3E, lane 9), suggesting that one out of nine hexamers, not identified so far by this and other studies (Cartegni et al., 2003; Fairbrother et al., 2002; Wang et al., 2004; Zhang and Chasin, 2004 ), may be functional ESRs.”
Human Splicing Finder: an online bioinformatics tool to predict splicing signals (2009, methodology): “As a consequence, previous matrices from ESEFinder (19,27) were modified.”
Expanded GGGGCC hexanucleotide repeat in non-coding region of C9ORF72 causes chromosome 9p-linked frontotemporal dementia and amyotrophic lateral sclerosis (2011, neutral): “The GGGGCC sequence motif predicts the potential binding of several RNA-binding proteins, including the serine/arginine-rich splicing factor 1 (SRSF1) and the heterozygous nuclear ribonucleoprotein (hnRNP) A2/B1 (Cartegni et al., 2003; Smith et al., 2006; Sofola et al., 2007).”
Spectrum of mutations in BRCA1, BRCA2, CHEK2, and TP53 in families at high risk of breast cancer. (2006, background): “30 14 (5) 30-39 77 (26) 40-49 127 (42) 50-59 67 (22) 60 6 (2) Ovarian 6 (2) Male breast 3 (1) Breast or ovarian cancers in the family Female breast only 140 (47) Female breast and ovary 135 (45) Female breast and male breast 13 (4) Female breast and ovary and male breast 12 (4)”
In silico prediction of splice-altering single nucleotide variants in the human genome (2014, methodology): “ESEfinder, a tool that predicts exonic splicing enhancers (ESEs) (14), has successfully predicted the loss of a putative ESE motif in the SMN2 gene as the cause of spinal muscular atrophy (15).”
SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies (2009, methodology): “ESE sites were predicted using RESCUE ESE (19) or ESEfinder ( 20 ) methods.”
SFmap: a web server for motif analysis and prediction of splicing factor binding sites (2010, methodology): “The ESEﬁnder web site presents a search interface for detecting signiﬁcant matches of ﬁve ESEs related to four SR proteins: SF2/ASF, SC35, SRp40 and SRp55.”
Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. (2008, background): “It is now well established that ESEs include a diverse range of sequences, and many if not all exons contain internal ESE sequences (Schaal and Maniatis 1999; Fairbrother et al. 2002; Cartegni et al. 2003).”
FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization (2006, methodology): “FASTSNP will ﬁrst invoke the agents for ESEﬁnder (22), RESCUE-ESE (23) and FAS-ESS (24) to predict if the SNP is located in an exonic splicing enhancer or silencer motif.”
Leber congenital amaurosis: genes, proteins and disease mechanisms. (2008, background): “, 1997), or interrupt an exonic splice enhancer (Cartegni et al., 2003).”
RBPmap: a web server for mapping binding sites of RNA-binding proteins (2014, background): “In addition, several dedicated computational approaches have been developed to map binding motifs of RBPs, given a motif or a consensus sequence (19,21,22).”
Convergence of Acquired Mutations and Alternative Splicing of CD19 Enables Resistance to CART-19 Immunotherapy (2015, methodology): “Unfortunately, the commonly used ESE-Finder tool (22) does not include binding motifs for human SRSF3, because the consensus is not well defined.”