Table 1.
Input and output statistics of trans-SAs in 10 species
| Species | GoldenPath genome version | Number of orientation-reliable sequences mapped to exact genomic location from NATsDB | Total number of TUs | Number of trans-SA TU pairs | Number of TUs involved in trans-SAsb | Proportion of TUs involved in trans-SAs among all TUs (%) |
|---|---|---|---|---|---|---|
| Human | hg18 | 4 494 665 | 99 919 | 3327 | 2896 | 2.89 |
| Mouse | mm8 | 2 100 305 | 57 416 | 1519 | 1799 | 3.13 |
| Fly | dm2 | 310 319 | 15 375 | 76 | 122 | 0.79 |
| Worm | ce2 | 291 395 | 19 815 | 41 | 69 | 0.35 |
| Sea squirt | ci2 | 414 454 | 14 273 | 1216 | 589 | 4.13 |
| Rata | rn4 | 463 787 | 40 428 | 110 | 188 | 0.47 |
| Cattlea | bosTau2 | 536 939 | 27 102 | 251 | 302 | 1.11 |
| Doga | canFam2 | 203 772 | 16 956 | 31 | 54 | 0.32 |
| Chickena | galGal2 | 299 931 | 21 426 | 37 | 66 | 0.31 |
| Zebrafisha | danRer4 | 522 259 | 23 809 | 185 | 282 | 1.18 |
aDue to the relatively small amount of available ESTs compared to their genome size for these species, the absolute numbers reported for these five species may be low and the percentages may not be accurate. However, the candidate trans-SAs identified should still be reliable.
bPrevious papers reported the number and percentages of genes forming cis-SAs in terms of clusters or transcriptional forests. Here, we reported the number and percentage in terms of TUs.