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Table 1 Combinatorial enhancers and silencers generated by CoSREM. The number of exons each set resides in, and the splicing factors that they may bind to according to SpliceAid-F [9] and ESEfinder tool [36]

From: CoSREM: a graph mining algorithm for the discovery of combinatorial splicing regulatory elements

Combinatorial SREs Number of exons Splicing factors
CGGGAG,GGGAGG 526 hnRNP A1
GAAGGC,AGGCAG 373 9G8,SC35,SF2/ASF
GCTGTC,TGTCAG 254 -
GAGGAC,GGGAGG 233 SF2/ASF*, hnRNP A1
CCGGGA,GGGAGG 229 hnRNP A1
AGAGAC,TAGAGA 218 -
GGAGTC,AGTCAG 217 -
GAAGTC,AGTCAG 213 -
TGAGGA,GGTGAG 200 SF2/ASF
CCGGGAG,GGGAGG 199 hnRNP A1
GCGGGA,GGGAGG 190 hnRNP A1
GATGTC,TGTCAG 171 -
GCGGGAG,GGGAGG 169 hnRNP A1
AGAGGA,AGGCAG 156 FMRP
GCAAGA,GTGCAA 154 -
GTGAAGA,AGGTGA 153 SF2/ASF
GAGGAT,GGGAGG 147 SF2/ASF**,hnRNP A1
AGAGGA,CAGCCA 133 FMRP,hnRNP L
TGAGGA,AGGCAG 129 -
GATGCC,TGCCTA 127 SRp55*
GGAGCC,AGGTGG 114 -
GGAGCC,CCCACC 114 -
TGGACC,AGGTGG 112 -
TTCAAC,CTTTCA 112 SRp40*,hnRNP E1
TTCATC,CTTTCA 110 YB-1,SRp55*,hnRNP E1
GAACAA,AGGTGA 106 -
CAAGGA,CAGCCA 103 FMRP,hnRNP L
TGAGGA,AGGTGG 103 -
TGAGGA,AGGTGA 102 -
CAAGGA,TCCCAA 100 SRp40,FMRP
  1. *identifies splicing factors identified by ESE finde
  2. **means the splicing factors is identified by both methods