Table 1

Number of exons, transcripts and genes analyzed

Exons

Txs

Genes

Exons dup (%)

Txs dup

Genes dup


Total

193,165

28,099

18,850

11,132 (5.76)

3,966

2,445

Studied

178,295

26,383

17,367

10,634 (5.96)

3,642

2,187

De > Di

25,559

16,405

11,059

3,231 (12.64)

2,220

1,387

q < 0.05

625

802

573

226 (31.16)

291

200

q < 0.05, coverage MMU, Di > 0.01

244

319

226

133 (54.51)

173

119

Domains

39

46

36

16 (41.03)

17

14

PPs

35

52

33

19 (54.29)

30

18

Manually rejected

96

140

96

57 (59.38)

84

57

Good

74

86

64

41 (55.41)

43

31


'Exons' refer to the nonredundant list of human coding exons in RefSeq. We define a transcript as a unique combination of RefSeq ID, gene name, and coordinates while genes are determined solely by the gene name. Exons in the 'Studied' category correspond to exons for which a corresponding intronic region was determined. Proportions of duplicated exons (Exons dup) relative to the total set are shown in parentheses. 'De > Di' refers to exons with higher exonic rate of changes than in their neighboring introns. Significant increases are shown as 'q < 0.05'. The coverage of macaque reads in their introns (more than two reads on average) and with an intronic rate greater than 0.01 was also considered. Numbers for exons discarded because of tandem protein domains, processed pseudogenes (PPs), or after visual inspection for even coverage are also shown. Dup, duplicated; MMU,; Txs, transcripts.

Lorente-Galdos et al. Genome Biology 2013 14:R9   doi:10.1186/gb-2013-14-1-r9

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