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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.