SNPs in the B6 and BTBR Pdi cDNA sequences and their predicted impact on mRNA secondary structure
| Position (B6-BTBR) . | Region . | B6 . | . | . | BTBR . | . | . | Impact . | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| . | . | Base . | Paired with . | Structure . | Base . | Paired with . | Structure . | . | ||||
| 831(U-C) | ORF | 831-U | 952-A | start of a 9-bp stem | 831-C | none | next to a 8-bp stem | Decrease stem size by 1 | ||||
| 1077(U-C) | ORF | 1077-U | none | loop | 1077-C | none | loop | No change | ||||
| 1209(A-G) | ORF | 1209-A | 2487-U | start of a 15-bp stem | 1209-G | 2487-U | start of a 15-bp stem | No change | ||||
| 1509(C-U) | ORF | 1509-C | none | loop | 1509-U | 2170-A | 10-bp stem | Structure change | ||||
| 2049(C-U) | 3′-UTR | 2049-C | none | loop | 2049-U | none | loop | No change | ||||
| 2098(C-U) | 3′-UTR | 2098-C | 2127-G | 5-bp stem | 2098-U | 2127-G | 5-bp stem | No change | ||||
| 2240(A-G) | 3′-UTR | 2240-A | 2203-U | 14-bp stem | 2204-G | 2203-U | 14-bp stem | No change | ||||
| Position (B6-BTBR) . | Region . | B6 . | . | . | BTBR . | . | . | Impact . | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| . | . | Base . | Paired with . | Structure . | Base . | Paired with . | Structure . | . | ||||
| 831(U-C) | ORF | 831-U | 952-A | start of a 9-bp stem | 831-C | none | next to a 8-bp stem | Decrease stem size by 1 | ||||
| 1077(U-C) | ORF | 1077-U | none | loop | 1077-C | none | loop | No change | ||||
| 1209(A-G) | ORF | 1209-A | 2487-U | start of a 15-bp stem | 1209-G | 2487-U | start of a 15-bp stem | No change | ||||
| 1509(C-U) | ORF | 1509-C | none | loop | 1509-U | 2170-A | 10-bp stem | Structure change | ||||
| 2049(C-U) | 3′-UTR | 2049-C | none | loop | 2049-U | none | loop | No change | ||||
| 2098(C-U) | 3′-UTR | 2098-C | 2127-G | 5-bp stem | 2098-U | 2127-G | 5-bp stem | No change | ||||
| 2240(A-G) | 3′-UTR | 2240-A | 2203-U | 14-bp stem | 2204-G | 2203-U | 14-bp stem | No change | ||||
The table shows the most probable structure predicted by mFOLD. The positions in column 1 are indexed with coordinates of the Pdi mRNA sequence in the Genebank (J05185).