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Table 3 Densities of putative cis-regulatory motifs in exons, retained and non-retained introns of genes of the low and high-RIF groups.

From: Sequence features responsible for intron retention in human

  

introns

exons

 

cis-regulatory motif

retained

non-retained

flanking upstream

flanking downstream

all other

 

SF2/ASF

0.0415 +i

0.0365

0.0458

0.0451

0.0430

 

SC35

0.0457+i

0.0413

0.0445

0.0450

0.0425

 

SRp40

0.0388

0.0384

0.0399

0.0395

0.0394

low

SRp55

0.0219

0.0220

0.0272

0.0264

0.0261

 

RESCUE-ESEs

0.0442 -i

0.0541

0.0837

0.0850

0.0951

 

GAA (ESE)

0.0115 -i

0.0142

0.0191

0.0197

0.0219

 

GGG (ISE)

0.0397 +i

0.0333

0.0185

0.0190

0.0165

 

FAS-ESS hex-3 class 1

0.0047 -i

0.0069

0.0010

0.0009

0.0011

 

FAS-ESS hex-3 class 2

0.0294 +i

0.0276

0.0110

0.0115

0.0101

 

SF2/ASF

0.0383 +i

0.0345

0.0445

0.0458

0.0423

 

SC35

0.0409

0.0387

0.0447

0.0412

0.0428

 

SRp40

0.0394+i

0.0371

0.0404

0.0397

0.0408

high

SRp55

0.0231

0.0219

0.0256

0.0241

0.0250

 

RESCUE-ESEs

0.0548

0.0591

0.0952

0.0971

0.0974

 

GAA (ESE)

0.0137 -i

0.0156

0.0227

0.0206

0.0224

 

GGG (ISE)

0.0264 -i

0.0300

0.0164

0.0173

0.0165

 

FAS-ESS hex-3 class 1

0.0043 -i

0.0074

0.0017

0.0007

0.0013

 

FAS-ESS hex-3 class 2

0.0208 -i

0.0253

0.0095

0.0106

0.0098

  1. mean densities in italics are lower than in exons (P ≤ 0.05), mean densities in boldface are higher than in exons (P ≤ 0.05). The sign +i indicates that the density of the motif in retained introns is significantly higher (P ≤ 0.05) than in non-retained introns, -i indicates it is lower.