Sequence features responsible for intron retention in human

BMC Genomics

Table 4 Conservation of human intron retention events in the mouse.

	low-RIF	high-RIF
1. mean %ID (human retained introns versus mouse genome)¹	59% ± 10 (1582 introns)	81% ± 9 (408 introns)
2. mean %ID (exons)	91% ± 3	91% ± 3
3. number of events presenting only the non-retaining form	1252/1297³ (97%)	16/201³ (8%)
4. number of events presenting only the retaining form	16/1297³ (1%)	177/201³ (88%)
5. number of conserved events²	29/1297³ (2%)	8/201³ (4%)
6. number of conserved events with conserved RIF	22/29	7/8
7. mean %ID of conserved retained introns with conserved RIF	86% ± 10 (22 retained introns)	91% ± 9 (7 retained introns)
8. mean %ID of non-conserved retained introns²	59% ± 9 (no retention in mouse; 1252 introns)	82% ± 9 (no non-retained form in mouse; 177 introns)
9. mean length of conserved retained intron	152 ± 83 (22 introns)	142 ± 87 (7 introns)
10. information content of splice sites⁴	7.2 bits ± 0.2/9.7 bits ± 0.4 (22 introns, all GT..AG)	5.4 bits ± 1.3/7.4 bits ± 1.3(7 introns, all GT..AG)

¹ only introns with similar lengths and borders in human and mouse were considered
² conserved in the mouse if the event presented ≥ 1 cDNA with the retained intron and ≥ 1 without. Non-conserved: only the major form was found in mouse cDNAs
³ the total number of events (1297 and 201) corresponds only to those events from row 1 with a least one mouse cDNA aligned to the genomic region corresponding to the event
⁴ with the exception of the high information content of the 3'ss of the low-RIF group, values were very similar to those observed for human

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