Research Article
Purifying Selection Bias against Microsatellites in Gene Rich Segmental Duplications in the Rice Genome
Table 1
Occurrence of genes and microsatellite repeats in duplicated regions of the rice genome.
|
| Duplicated segments
(length covered in bp) | Intergenic | Genic | Gene frequency
(bp/gene) | Repeat frequency
(bp/repeat) | | Exon | Intron |
| | Chromosome 1 corresponding chromosome 5 | | Segment 1.1 | 58 (81685) | 46 | 9 | 3 | 6807.08 | 16337 | | Segment 5A1.1 | 50 (75106) | 21 | 20 | 9 | 2589.86 | 8345.11 | | Segment 1.2 | 6 (9866) | 2 | 3 | 1 | 2466.5 | 0 | | Segment 5A1.2 | 4 (5909) | 2 | 1 | 1 | 203.76 | 0.00 | | Segment 1.3 | 163 (244228) | 98 | 42 | 23 | 3757.35 | 9769.12 | | Segment 5A1.3 | 169 (268072) | 110 | 41 | 18 | 9243.86 | 9928.59 | | Segment 1.4 | 3 (4300) | 2 | 0 | 1 | 4300 | 0 | | Segment 5A1.4 | 1 (2247) | 1 | 0 | 0 | 77.48 | 2247.00 |
| | Chromosome 2 corresponding chromosomes 4 and 6 | | Segment 2.1 | 342 (518707) | 200 | 89 | 53 | 3652.87 | 17886.45 | | Segment 4A2.1 | 347 (522868) | 199 | 97 | 51 | 18029.93 | 13071.70 | | Segment 2.2 | 102 (149764) | 49 | 43 | 10 | 2825.74 | 29952.8 | | Segment 6A2.2 | 105 (146574) | 56 | 35 | 14 | 5054.28 | 24429.00 | | Segment 2.3 | 81 (124845) | 50 | 14 | 17 | 4027.26 | 15605.63 | | Segment 6A2.3 | 77 (114157) | 45 | 22 | 10 | 3936.45 | 16308.14 |
| | Chromosome 3 corresponding chromosomes 7, 10, and 12 | | Segment 3.1 | 29 (42425) | 14 | 11 | 4 | 2828.33 | 21212.5 | | Segment 7A3.1 | 31 (47154) | 21 | 9 | 1 | 1626.00 | 23577.00 | | Segment 3.2 | 29 (41410) | 14 | 12 | 3 | 2760.67 | 20705 | | Segment 7A3.2 | 36 (49456) | 22 | 9 | 5 | 1705.38 | 16485.33 | | Segment 3.3 | 37 (59771) | 26 | 5 | 6 | 5433.73 | 11954.2 | | Segment 10A3.3 | 42 (66214) | 24 | 9 | 9 | 2283.24 | 16553.50 | | Segment 3.4 | 23 (28749) | 15 | 1 | 7 | 3593.63 | 28749 | | Segment 10A3.4 | 28 (39198) | 16 | 6 | 6 | 1351.66 | 19599.00 | | Segment 3.5 | 29 (41024) | 15 | 10 | 4 | 2930.29 | 41024 | | Segment 12A3.5 | 24 (37014) | 13 | 8 | 3 | 1276.34 | 18507.00 |
| | Chromosome 4 corresponding chromosomes 8 and 10 | | Segment 4.1 | 17 (26044) | 7 | 6 | 4 | 2604.4 | 8681.33 | | Segment 8A4.1 | 16 (21129) | 11 | 4 | 1 | 728.59 | 0.00 | | Segment 4.2 | 40 (62581) | 22 | 12 | 6 | 3476.72 | 15645.25 | | Segment 10A4.2 | 40 (59065) | 22 | 11 | 7 | 2036.72 | 59065.00 |
| | Chromosome 8 corresponding chromosome 9 | | Segment 8.1 | 28 (36632) | 21 | 4 | 3 | 5233.14 | 6105.33 | | Segment 9A8.1 | 33 (42741) | 28 | 3 | 2 | 1473.83 | 8548.20 | | Segment 8.2 | 130 (191894) | 73 | 47 | 10 | 3366.56 | 31982.33 | | Segment 9A8.2 | 122 (180824) | 72 | 41 | 9 | 6235.31 | 12054.93 |
| | Chromosome 11 corresponding chromosome 12 | | Segment 11.1 | 111 (168247) | 51 | 40 | 20 | 2804.12 | 12017.64 | | Segment 12A11.1 | 101 (158798) | 45 | 39 | 17 | 5475.79 | 14436.18 | | Segment 11.2 | 43 (59793) | 25 | 15 | 3 | 3321.83 | 8541.86 | | Segment 12A11.2 | 47 (65442) | 20 | 18 | 9 | 2256.62 | 21814.00 |
|
|
