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 |