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Table 3 RT-negative introns supported by ASPIC

From: ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences

Encode Region Gene Intron position Prediction Method
   Chr Start End  
ENm004 SLC5A1 22 30779886 30787475 ASPIC (3), ECgene, acembly
ENm004 PISD 22 30350425 30351061 ASPIC (1), ensEstGene
ENm004 PISD 22 30337622 30338657 acembly
ENm004 PISD 22 30346557 30351299 acembly
ENm004 PISD 22 30365972 30366216 acembly
ENm004 RFPL3 22 31075439 31078694 acembly
ENm004 SYN3 22 31727364 31734939 acembly
ENm004 TIMP3 22 31521971 31522263 acembly
ENm004 TIMP3 22 31521971 31522271 acembly
ENr223 MTO1 6 74249065 74253041 ASPIC (6), ECgene, acembly
ENr223 MTO1 6 74253206 74258677 ASPIC (5), ECgene, acembly
ENr231 PSMD4 1 148044771 148047709 ASPIC (2), ECgene, acembly
ENr231 PIP5K1A 1 148035078 148039516 acembly
ENr231 PIP5K1A 1 148035192 148035350 acembly
ENr231 PSMB4 1 148187431 148194586 acembly
ENr231 PSMD4 1 148040228 148047741 acembly
ENr231 PSMD4 1 148040358 148044611 acembly
ENr231 PSMD4 1 148044684 148047709 acembly
ENr231 PSMD4 1 148046796 148047709 acembly
ENr231 SNX27 1 148423496 148424527 acembly
ENr231 TUFT1 1 148350164 148356015 acembly
ENr231 TUFT1 1 148356492 148372163 acembly
ENr232 CRAT 9 128949911 128950731 ASPIC (1), acembly, softberryGene
ENr232 PPP2R4 9 128953625 128962345 ASPIC (1), ECgene
ENr232 PPP2R4 9 128952305 128953168 acembly
ENr232 PPP2R4 9 128952336 128953268 acembly
ENr232 PPP2R4 9 128952981 128953304 acembly
ENr232 PPP2R4 9 128953105 128953150 acembly
ENr232 SH3GLB2 9 128835746 128849868 acembly
ENr232 SH3GLB2 9 128860722 128862923 acembly
ENr323 LACE1 6 108794230 108829892 ASPIC (5), sgpGene
ENr323 LACE1 6 108747689 108751721 acembly
ENr323 SNX3 6 108688727 108690771 acembly
ENr333 RNPC2 20 33764744 33765167 ASPIC (1), ECgene, acembly
ENr333 RNPC2 20 33786418 33787848 ASPIC (1), ECgene
ENr333 CEP2 20 33527835 33529106 acembly
ENr333 CEP2 20 33554537 33568378 acembly
ENr333 CEP2 20 33561298 33568224 acembly
ENr333 ITGB4BP 20 33335958 33343927 acembly
ENr333 RNPC2 20 33776436 33777255 acembly
ENr333 RNPC2 20 33780699 33780701 acembly
ENr333 SDBCAG84 20 33585738 33593682 acembly
ENr334 TFEB 6 41766952 41811861 ASPIC (5), ECgene, acembly
ENr334 TFEB 6 41766952 41799176 ASPIC (3), ECgene, acembly
  1. List of computationally predicted introns of 22 genes contained in 13 Encode regions (see the GENCODE annotations in the Additional file 2) but not validated by RT-PCR analysis. For each intron are shown the Encode region, the gene ID, location (NCBI 35 assembly) and prediction methods (Acembly/AceView, http://www.aceview.org; ECgene [17]; ensEstGene [28]; softberryGene [35]. For ASPIC predictions the number of supporting in shown in the brackets.