Table 2.
Intra- and Interspecific Sequence Variations of 25 Noncoding Regions in Mice
| Region name1 | Chromos. no. | Nucleotide position2 | length (nt)3 | Within M. musculus |
Within M. domesticus |
Between species |
|||||||||
| S4 | θ (×104)5 | π (×104)6 | Tajima's D7 | Fu and Li's D*7 | S4 | θ (×104)5 | π (×104)6 | Tajima's D7 | Fu and Li's D*7 | K8 | d (×104)9 | ||||
| 032 | 3 | 61421835–61422742 | 908 | 1 | 3.5 | 1.6 | −1.16 | −1.40 | 10 | 34.6 | 26.4 | −0.93 | 0.58 | 2 | 85.7 |
| con1 | 5 | 4750295–4751185 | 885 | 4 | 14.2 | 22.4 | 1.89 | 1.16 | 5 | 17.8 | 23.6 | 1.14 | 1.23 | 0 | 44.7 |
| con2 | 5 | 4177067–4178013 | 948 | 6 | 19.9 | 26.9 | 1.26 | 1.29 | 4 | 13.3 | 11.1 | −0.53 | 1.16 | 0 | 40.0 |
| 062 | 6 | 13370671–13371601 | 930 | 1 | 3.6 | 5.7 | 1.38 | 0.75 | 5 | 16.9 | 17.7 | 0.17 | 0.51 | 9 | 122.8 |
| 063 | 6 | 13335122–13336060 | 940 | 0 | 0.0 | 0.0 | 0.00 | 0.00 | 7 | 23.5 | 32.5 | 1.41 | 0.77 | 7 | 93.5 |
| 071 | 7 | 34198101–34199051 | 951 | 6 | 19.8 | 14.9 | −0.89 | −0.61 | 8 | 26.5 | 29.5 | 0.43 | 1.37 | 9 | 150.0 |
| 072 | 7 | 1485242–1486253 | 1,012 | 2 | 6.2 | 5.2 | −0.44 | 0.94 | 1 | 3.1 | 4.9 | 1.21 | 0.72 | 11 | 117.9 |
| 073 | 7 | 14736902–14737811 | 902 | 15 | 55.1 | 90.7 | 2.78 | 1.51 | 7 | 24.2 | 30.1 | 0.90 | 0.21 | 4 | 148.9 |
| 074 | 7 | 13161241–13162059 | 818 | 1 | 3.8 | 1.7 | −1.16 | −1.40 | 10 | 38.4 | 65.4 | 2.73 | 1.42 | 1 | 71.6 |
| con3 | 7 | 12877447–12878480 | 1,034 | 3 | 9.1 | 12.4 | 0.07 | 0.30 | 4 | 12.2 | 10.5 | −0.44 | −0.55 | 1 | 26.2 |
| 102 | 10 | 54958829–54959659 | 812 | 0 | 0.0 | 0.0 | 0.00 | 0.00 | 1 | 3.8 | 1.7 | −1.16 | −1.40 | 9 | 111.7 |
| 131 | 13 | 4938296–4939215 | 920 | 2 | 6.8 | 10.5 | 1.46 | 0.94 | 3 | 10.3 | 13.3 | 0.90 | 0.02 | 9 | 117.2 |
| con4 | 13 | 5177266–5178204 | 939 | 3 | 10.0 | 14.4 | 1.32 | 1.07 | 6 | 20.1 | 28.8 | 1.55 | 1.29 | 4 | 81.4 |
| 133 | 13 | 14942772–14943791 | 1,021 | 1 | 3.1 | 5.3 | 1.51 | 0.72 | 7 | 21.6 | 18.1 | −0.60 | 1.33 | 4 | 60.9 |
| con5 | 13 | 10340883–10341849 | 984 | 3 | 9.6 | 8.3 | −0.42 | −1.04 | 8 | 25.5 | 21.9 | −0.53 | 0.86 | 6 | 86.4 |
| con6 | 14 | 12999764–13000706 | 948 | 5 | 16.6 | 15.1 | −0.32 | 0.51 | 2 | 6.6 | 4.3 | −0.96 | −0.45 | 1 | 39.9 |
| con7 | 14 | 55603471–55604414 | 944 | 3 | 10.5 | 5.3 | −1.63 | −1.95 | 17 | 56.6 | 29.3 | −1.99 | −2.45 | 1 | 45.9 |
| con8 | 17 | 1418876–1419796 | 921 | 5 | 17.1 | 13.2 | −0.78 | −0.95 | 5 | 17.1 | 13.6 | −0.70 | −0.22 | 2 | 42.7 |
| 173 | 17 | 27883797–27884681 | 885 | 2 | 7.1 | 6.6 | −0.20 | −0.45 | 1 | 3.6 | 5.1 | 0.84 | 0.72 | 15 | 181.6 |
| con9 | 17 | 64305167–64306026 | 860 | 10 | 36.6 | 30.2 | −0.68 | −1.52 | 3 | 11.0 | 6.4 | −1.28 | −1.04 | 0 | 64.8 |
| GGH | 4 | 20166795–201667294 | 499 | 1 | 5.0 | 3.5 | −0.34 | 0.72 | 4 | 18.3 | 19.3 | 0.00 | 0.00 | 0 | 2.9 |
| MELK | 4 | 2162811–2163729 | 918 | 0 | 0.0 | 0.0 | 0.00 | 0.00 | 14 | 50.6 | 75.0 | 2.06 | 1.20 | 5 | 116.2 |
| NKD1 | 8 | 91403263–91404440 | 1,178 | 8 | 16.9 | 14.9 | −0.87 | −0.22 | 11 | 21.1 | 12.8 | 0.83 | 0.02 | 0 | 26.7 |
| PUM1 | 4 | 130022004–130023187 | 1,183 | 4 | 8.8 | 2.2 | 0.00 | 0.00 | 5 | 10.0 | 3.9 | −1.16 | −1.40 | 0 | 7.9 |
| SFRP1 | 8 | 2480594–2481312 | 1,071 | 1 | 3.0 | 5.0 | 1.43 | 0.72 | 12 | 30.1 | 24.3 | −0.75 | −0.68 | 10 | 122.0 |
| Mean | 936.4 | 3.5 | 11.7 | 12.6 | 0.17 | 0.04 | 160 | 20.7 | 21.2 | 0.13 | 0.21 | 4 | 80.4 | ||
NOTE.—1Most noncoding regions do not have standard names, and the names listed are the idendification numbers used in our laboratory.
2
Nucleotide positions in the mouse genome sequence of National Center for Biotechnology Information Build 37.
3
Length in M. musculus. Length in M. domesticus may be slightly different due to indels.
4
Number of polymorphic sites.
5
Watterson's polymorphism per site.
6
Nucleotide diversity per site.
7
Values significantly different from 0 at the 5% level are underlined. Significance is determined by 10,000 coalescent simulations.
8
Number of fixed nucleotide differences between species.
9
Mean number of nucleotide differences between species.