Table 1.
Number of internally duplicated genes and the new introns associated with internal gene duplications
| Section | Category | A. thaliana | O. sativa | C. elegans | D. melanogaster | M. musculus | H. sapiens |
|---|---|---|---|---|---|---|---|
| I | Total protein-coding genes | 26,514 | 42,802 | 17,830 | 9,221 | 23,739 | 21,481 |
| Internally duplicated protein-coding genes | 2,868 | 6,952 | 1,478 | 978 | 2,703 | 3,571 | |
| Ratio 1 | 10.8% | 16.2% | 8.3% | 10.6% | 11.4% | 16.6% | |
| II | Internally duplicated genes with orthologs in two closely related species (Ratio 2) | 299 (10.4%) | 1,163 (16.7%) | 90 (6.1%) | 155 (15.8%) | 601 (22.2%) | 930 (26.0%) |
| Internally duplicated genes with orthologs and new introns (number of new introns)* | 46 (112) | 90(204) | 27 (55) | 24 (48) | 39 (46) | 68 (105) | |
| Ratio 3 | 15.4% | 7.7% | 30.0% | 15.5% | 6.5% | 7.3% | |
| Ratio 4 | 9.4% | 3.6% | 6.7% | 10.3% | 5.0% | 4.5% |
The total number of protein-coding genes and genes with internal duplications are summarized in section I. The numbers of internally duplicated genes with new introns, and the ratios of genes with intron gain to all internally duplicated genes, are summarized in section II. Ratio 1 = internally duplicated protein-coding genes/total protein-coding genes. Ratio 2 = internally duplicated genes with orthologs in two closely related species/internally duplicated protein-coding genes. Ratio 3 = internally duplicated genes with orthologs and new introns/internally duplicated genes with orthologs in two closely related species. Ratio 4 = cDNA-supported internally duplicated genes with orthologs and new introns (Table 3)/internally duplicated genes with orthologs in two closely related species.
*The numbers of new introns identified from internally duplicated genes with orthologs are listed in parentheses. Some genes have multiple new introns.