Gilliland et al. 10.1073/pnas.0606221103. |
Table 5. Sequence polymorphisms between Ler and Cvi accessions within the 91,910-101,450 bp region of chromosome 3
ID | Polymorphism Ler > Cvi | Position Chr3, bp | Details of position | Col resembles |
- | GACAGAGGA > - | 101,990 | 5' UTR/promoter At3g01310 | Ler |
- | - > G | 101,445 | Intron, external to recombination site | Ler |
1 | A > G | 101,091 | Intron At3g01310 / cT22N4w CAPS | Cvi |
2 | A > G | 101,067 | Intron At3g01310 | Ler |
3 | A > G | 100,602 | Amino acid 99 - silent At3g01310 | Ler |
4 | - > TCCAAAATTTG | 100,517 | Intron At3g01310 | Ler |
5 | T > A | 100,487 | Intron At3g01310 | Ler |
6 | A > T | 100,216 | Intron At3g01310 | Ler |
7 | A > T | 100,210 | Intron At3g01310 | Ler |
8 | TTTT > AA | 100,204 | Intron At3g01310 | Ler |
9 | T > C | 100,029 | Intron At3g01310 | Ler |
10 | A > C | 100,007 | Intron At3g01310 | Ler |
11 | G > A | 99,979 | Intron At3g01310 | Ler |
12 | T > G | 99,921 | Amino acid 207 - silent At3g01310 | Ler |
13 | A > G | 99,884 | Ile>Thr amino acid 219, At3g01310 | Cvi |
14 | C > T | 99,775 | Intron At3g01310 | Ler |
15 | G > T | 99,629 | Intron At3g01310 | Ler |
16 | C > A | 99,621 | Intron At3g01310 | Ler |
17 | C > T | 99,424 | Intron At3g01310 | Ler |
18 | C > T | 99,413 | Intron At3g01310 | Ler |
19 | T > A | 99,353 | Intron At3g01310 | Ler |
20 | A > T | 99,266 | Amino acid 266 - silent At3g01310 | Ler |
21 | A > T | 99,200 | Intron At3g01310 | Ler |
22 | - > AAT | 99,191 | Intron At3g01310 | Ler |
23 | C > A | 99,152 | Intron At3g01310 | Ler |
24 | G > A | 99,132 | Intron At3g01310 | Ler |
25 | - > AA | 99,114 | Intron At3g01310 | Ler |
26 | T > C | 99,017 | Amino acid 308 - silent At3g01310 | Ler |
27 | - > A | 99,001 | Intron At3g01310 | Ler |
28 | G > A | 98,999 | Intron At3g01310 | Ler |
29 | T > C | 98,989 | Intron At3g01310 | Ler |
30 | C > A | 98,965 | Intron At3g01310 | Ler |
31 | CTCN24TAT > - | 98,930-98,959 | 30-bp deletion, intron At3g01310 | Ler |
32 | C > T | 98,812 | Amino acid 318 - silent At3g01310 | Ler |
33 | T > C | 98,785 | Amino acid 327 - silent At3g01310 | Ler |
34 | G > T | 98,559 | Intron At3g01310 | Ler |
35 | A > C | 98,262 | Intron At3g01310 | Ler |
36 | C > T | 98,247 | Intron At3g01310 | Ler |
37 | C > A | 98,189 | Intron At3g01310 | Ler |
38 | T > C | 98,145 | Intron At3g01310 | Ler |
39 | T > C | 97,927 | Intron At3g01310 | Ler |
40 | A > C | 97,880 | Intron At3g01310 | Ler |
41 | A > T | 97,694 | Asp>Glu amino acid 490, At3g01310 | Ler |
42 | G > A | 97,048 | Amino acid 570 - silent At3g01310 | Ler |
43 | - > G | 97,003 | Intron At3g01310 | Ler |
44 | G > T | 96,943 | Intron -4th base 3' At3g01310 | Ler |
45 | T > A | 96,440 | Intron At3g01310 | Ler |
46 | G > T | 96,385 | Intron At3g01310 | Ler |
47 | G > A | 96,354 | Intron -3rd base 3' At3g01310 | Ler |
48 | G > C | 96,021 | Intron At3g01310 | Ler |
49 | - > C | 95,953 | Intron At3g01310 | Ler |
50 | - > GCTAAAAACA | 95,948 | Intron At3g01310 | Ler |
51 | T > C | 95,939 | Intron At3g01310 | Ler |
52 | GTA > T | 95,932-95,934 | Intron At3g01310 | Ler |
53 | T > A | 95,769 | Intron At3g01310 | Ler |
54 | T > C | 95,589 | Intron At3g01310 | Ler |
55 | C > T | 95,583 | Intron At3g01310 | Ler |
56 | C > T | 95,576 | Intron At3g01310 | Ler |
57 | G > C | 95,556 | Intron At3g01310 | Ler |
58 | A > T | 95,521 | Intron At3g01310 | Ler |
59 | G > C | 95,506 | Intron At3g01310 | Ler |
60 | G > A | 95,420 | Amino acid 812 - silent At3g01310 | Ler |
61 | AGCA > CT | 94,806-94,809 | Intron At3g01310 | Ler |
62 | C > - | 94,228 | 3'UTR At3g01310 | Ler |
63 | A > T | 94,203 | 3'UTR At3g01310 | Cvi |
64 | T > G | 94,163 | Intergenic region (-571 bp At3g01300) | Cvi |
65 | C > A | 93,880 | Promoter region At3g01300 (-288 bp) | Ler |
66 | T > G | 93,832 | Promoter region At3g01300 (-240 bp) | Ler |
67 | GTATC > - | 93,782-93,786 | Promoter region At3g01300 (-190 bp) | Ler |
68 | GTTTTT > TTAA | 93,759-93,761 | Promoter region At3g01300 (-167 bp) | Cvi |
69 | - > GTAGTTTTTTA | 93,687-93,697 | Promoter region At3g01300 (-95 bp) | Cvi |
70 | TA > - | 92,662 | Intron At3g01300 | Cvi |
- | - > A | 91,917 | Intron, external to recombination site | Ler |
Each polymorphism, its position relative to the published Col chromosome 3 sequence (www.arabidopsis.org) and the Col allele are listed along with placement and inferred effect on the associated gene. Changes predicted to have the most influence on the gene model are in bold and correspond to the bold arrows in Fig. 3B. The sequence changes that are external to recombination events in the NILs (8E5 and 4-212) are indicated in italics and are not given a polymorphism identification number. The translational start of the shorter gene model of At3g01310 proposed by MAtDB is located between polymorphisms 41 and 42.