Table 1.
Four-way human-mouse-rat-chicken synteny blocks based on orthologous genes
| Human | Mouse | Rat | Chicken | |
|---|---|---|---|---|
| Chromosomes included | 1–22, X | 1–19, X | 1–20, X | 1–24, 26–28, 32 W, Z |
| Total length (Mb) | 3020 | 2577 | 2720 | 940 |
| Run gene4 | ||||
| No. of blocks | 627 | 627 | 627 | 627 |
| Mean synteny block length (kb) | 2865 | 2515 | 2644 | 1075 |
| Max synteny block length (kb) | 49,242 | 45,201 | 48,457 | 22,013 |
| Total synteny block length (kb) | 1,796,071 | 1,576,879 | 1,657,662 | 673,793 |
| Total synteny block length (% of genome) | 59.48% | 61.18% | 60.95% | 71.67% |
| No. of breakpoint regions | 604 | 607 | 606 | 596 |
| Mean breakpoint region length (kb) | 1727 | 1436 | 1613 | 410 |
| Max breakpoint region length (kb) | 45,875 | 25,984 | 30,583 | 5725 |
| Total breakpoint region length (kb) | 1,043,037 | 871,671 | 977,759 | 244,635 |
| Total breakpoint region length (% of genome) | 34.54% | 33.82% | 35.95% | 26.02% |
| No. of genes per block | 3–120, mean 9.7 | |||
| Run gene7 | ||||
| No. of blocks | 586 | 586 | 586 | 586 |
| Mean synteny block length (kb) | 3205 | 2794 | 2945 | 1196 |
| Max synteny block length (kb) | 49,242 | 45,201 | 48,457 | 22,013 |
| Total synteny block length (kb) | 1,877,940 | 1,637,099 | 1,725,810 | 700,581 |
| Total synteny block length (% of genome) | 62.19% | 63.52% | 63.45% | 74.52% |
| No. of breakpoint regions | 563 | 566 | 565 | 555 |
| Mean breakpoint region length (kb) | 1731 | 1436 | 1635 | 394 |
| Max breakpoint region length (kb) | 30,387 | 18,196 | 30,583 | 5725 |
| Total breakpoint region length (kb) | 974,336 | 812,924 | 923,608 | 218,520 |
| Total breakpoint region length (% of genome) | 32.26% | 31.54% | 33.96% | 23.24% |
| No. of genes per block | 3–120, mean 10.5 | |||
| Run gene10 | ||||
| No. of blocks | 567 | 567 | 567 | 567 |
| Mean synteny block length (kb) | 3358 | 2930 | 3089 | 1253 |
| Max snyteny block length (kb) | 49,242 | 45,201 | 48,457 | 22,013 |
| Total synteny block length (kb) | 1,903,906 | 1,661,039 | 1,751,281 | 710,366 |
| Total synteny block length (% of genome) | 63.05% | 64.45% | 64.39% | 75.56% |
| No. of breakpoint regions | 544 | 547 | 546 | 536 |
| Mean breakpoint region length (kb) | 1745 | 1442 | 1646 | 390 |
| Max breakpoint region length (kb) | 30,387 | 18,196 | 30,583 | 5725 |
| Total breakpoint region length (kb) | 949,037 | 788,984 | 898,578 | 208,834 |
| Total breakpoint region length (% of genome) | 31.43% | 30.61% | 33.04% | 22.21% |
| No. of genes per block | 3–120, mean 10.9 | |||
| Run gene20 | ||||
| No. of blocks | 518 | 518 | 518 | 518 |
| Mean synteny block length (kb) | 3787 | 3327 | 3495 | 1413 |
| Max synteny block length (kb) | 49,242 | 45,201 | 48,457 | 22,013 |
| Total synteny block length (kb) | 1,961,447 | 1,723,141 | 1,810,421 | 731,745 |
| Total synteny block length (% of genome) | 64.95% | 66.86% | 66.56% | 77.83% |
| No. of breakpoint regions | 495 | 498 | 497 | 487 |
| Mean breakpoint region length (kb) | 1801 | 1460 | 1689 | 392 |
| Max breakpoint region length (kb) | 30,387 | 18,196 | 30,583 | 5725 |
| Total breakpoint region length (kb) | 891,495 | 726,883 | 839,439 | 191,143 |
| Total breakpoint region length (% of genome) | 29.52% | 28.20% | 30.86% | 20.33% |
| No. of genes per block | 3–120, mean 12.0 |
Several sets of four-way synteny blocks were formed from orthologous genes by allowing for various levels of rearrangements of the genes within the blocks. Runs gene4 through gene20 allow an increasing span of rearrangements, as explained in the text under “GRIMM-Synteny parameters.” Statistics are shown on the sizes of the blocks and the breakpoint regions between them (excluding chromosome ends).