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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.