Table 1.
Overview of gene retrotransposition analysis for eight vertebrates
| Species | Number of genes * | Number of PRs | PR matches retrotransposed TE ** | PR overlaps pseudogene annotation | FLE ≤ 0.8 *** | Number of retro- pseudogenes (RψGs) | PRs passing local gene order test | Matching Refseq mRNA or Unigene consensus **** |
| Human | 22219 | 631 (3%) | 78 (12%) | 36 (6%) | 504 | 2493 | 545 | 145/631 (23%) |
| Chimp | 20980 | 476 (2%) | 17 (4%) | 5 (1%) | 339 | 1889 | ---- | |
| Dog | 18199 | 409 (2%) | 18 (4%) | 25 (6%) | 363 | 3505 | ---- | |
| Cow | 23147 | 790 (3%) | 46 (6%) | 104 (13%) | 479 | 1996 | ---- | |
| Mouse | 25021 | 663 (3%) | 31 (5%) | 75 (11%) | 518 | 2969 | 533 | 58/663 (9%) |
| Rat | 22157 | 567 (3%) | 21 (4%) | 62 (11%) | 492 | 4520 | ---- | |
| Chicken | 17707 | 321 (2%) | 15 (5%) | 26 (8%) | 267 | 720 | ---- | |
| Tetraodon | 28005 | 227 (1%) | 4 (2%) | 10 (4%) | 203 | 644 | ---- |
* The number of gene annotations (both those labelled 'known' and 'novel') for the genome version downloaded from Ensembl [[15]; see Methods for details].
** TE = transposable element ; see Methods for details.
*** FLE = fraction of largest exon ; see Methods for details.
**** Number of PRs with complete Refseq mRNAs or complete Unigene consensus sequences (percentage of these in brackets); see Methods for details. PRs have significantly much less mapping of this transcription information than the whole annotated proteome for these organisms.