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Table 5 Number of introns that contain functional RNAs based on various criteria

From: Intronic RNAs constitute the major fraction of the non-coding RNA in mammalian cells

Criterion

Threshold used

Number of introns detected *

Number of ensembl-specific snoRNAs detected

p-value** of overlap with ensembl-specific snoRNAs

“Sense” introns (> = 63 % sense reads)

“Sense-antisense” introns ([37 %; 63 %) sense reads)

“Antisense” introns (<37 % sense reads)

Fraction of introns with abundant antisense transcription

1. Correlation between RNAseq densities of each intron and the corresponding exons (Figure 2 B)

≤ 0

30,141

111

0.009

28,617

1,258

266

5.1 %

2. Correlation with other introns (Figure 2 C)

≤ −0.3

8,989

39

0.019

8,529

384

76

5.1 %

3. Intronic density relative to the minimal intronic density in a transcript*** (Figure 2 D)

≥ 10

18,863

104

2.34E-10

17,491

1,101

271

7.3 %

4. Maximum Intron/Exon Density Ratio (Figure 2 E)

≥ 1

5,753

95

1.37E-42

4,936

594

223

14.2 %

5. Coefficient of variation of each intron (Text)

≤ that of exons

40,948

201

4.31E-16

39,146

1,107

695

4.4 %

6. DE in any timepoint (Table 3 )

Presence of a DE bin

25,739

159

1.34E-22

24,626

714

387

4.3 %

Total number that pass at least one criterion

 

82,481

349

4.49E-27

77,611

3,517

1,341

5.9 %

Maximum number that pass at least two criteria

 

35,979

229

1.90E-40

34,315

1,248

416

4.6 %

Maximum number that pass at least three criteria

 

10,111

103

2.02E-30

9,671

319

121

4.4 %

  1. * With unique coordinates.
  2. ** Based on 534 Ensembl-specific snoRNAs (see Methods).
  3. *** See Methods.
  4. **** The following was done: 1. Average intronic density was calculated per each time point, introns were sorted based on this value and an intron with minimal value for each time point was identified. 2. Per each time and each intron, the ration of the density for this intron versus the minimal intronic value in this locus was calculated. 3. Introns passing the threshold in at least one timepoint were taken.