Table 3.
Comparison of predicted clustered and non-clustered constitutive A-to-I sites
|
A | ||||||
|---|---|---|---|---|---|---|
| A-to-I conversions | A-to-Is in H9 and HeLa | Numbers of validated sites | ||||
| Clustered sites |
2,245 |
296 |
22 of 22 |
|||
| Non-clustered sites |
10,220 |
1,542 |
7 of 15 |
|||
|
B | ||||||
| Predicted A-to-I sites |
Predicted A-to-I ratios |
Validation |
||||
| Chr. location |
Altered base |
Gene location |
H9 |
HeLa |
H9 |
HeLa |
| chr1:40041484 |
A- > G (+) |
Coding |
28.1% |
29.5% |
− |
− |
| chr4:184186228 |
A- > G (+) |
Coding |
30.8% |
28.1% |
− |
− |
| chr6:159187882 |
A- > G (+) |
3′UTR |
46.2% |
50% |
− |
− |
| chr7:44841489 |
A- > G (+) |
3′UTR |
78.4% |
69.2% |
+ |
+ |
| chr8:48890109 |
A- > G (+) |
3′UTR |
29.6% |
32.5% |
+ |
+ |
| chr10:75008955 |
A- > G (−) |
3′UTR |
59.5% |
65.8% |
+ |
+ |
| chr17:4068050 |
A- > G (+) |
3′UTR |
31.8% |
31.7% |
− |
− |
| chr17:61898921 |
A- > G (−) |
Coding |
27.5% |
16.9% |
+ |
+ |
| chr17:80445942 |
A- > G (+) |
Coding |
34.4% |
32.1% |
− |
− |
| chr19:10755103 |
A- > G (−) |
3′UTR |
95.3% |
96.7% |
− |
− |
| chr19:34718735 |
A- > G (+) |
3′UTR |
46.5% |
27.9% |
+ |
+ |
| chr19:39874895 |
A- > G (+) |
3′UTR |
36.1% |
38.9% |
− |
− |
| chr20:30253695 |
A- > G (+) |
3′UTR |
20.0% |
29.9% |
− |
− |
| chrX:54589730 |
A- > G (+) |
3′UTR |
30.0% |
46.3% |
+ |
+ |
| chrX:54589774 | A- > G (+) | 3′UTR | 6.9% | 8.8% | + | + |
(A) Comparison of clustered and non-clustered constitutive A-to-I sites identified with or without STEP4 cutoff. Editing sites detected in HeLa and H9 cells were further used for validation with Sanger sequencing. (B) Validation results of randomly selected non-clustered A-to-I editing sites. “+”, validated to be an editing site; “-”, validated not to be an editing site.