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]
| 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 |
*identifies splicing factors identified by ESE finde
**means the splicing factors is identified by both methods