TABLE 3.
Structural elements and sequence motifs in group A, group B, and group C HP-like IRESs
| IRES group and virus | Data for indicated structural element
|
||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Domain II
|
Pseudoknot
|
Domain III
|
|||||||||||
| Length (nt) | Presence of:
|
Length (nt) of:
|
Presence of:
|
III1 mispair | |||||||||
| Loop E motif | UANCCAU loop | Stem 1 | Stem 2 | Linker | Spacer | IIIa AGUA loop | IIIc | IIId G loop | IIId2 | IIIe | |||
| A | |||||||||||||
| HCV | 75 | + | + | 9/9 | 6/6 | 1 | 11 | + | + | + | − | + | A-A |
| GBVB | 174 | + | (+) | 9/9 | 6/6 | 1 | 11 | − | + | + | − | + | A-A |
| AEV | 64 | + | + | 9/9 | 5/5 | 3 | 11 | + | + | + | − | + | A-A |
| SVV | 79 | + | − | 11/11a | 5/5 | 1 | 13 | + | + | + | + | + | A-A |
| B | |||||||||||||
| PEV-8 | 54 | − | − | 12/12 | 8/8 | 3 | 10 | − | − | + | − | + | A-A |
| PTV-1 | 29 | − | − | 12/12 | 8/8 | 3 | 9 | − | − | + | − | + | A-G |
| SPV-9 | 119 | + | − | 12/12 | 8/8a | 3 | 9 | − | − | + | − | + | A-G |
| DHV-1 | 76 | + | − | 12/12a | 8/8 | 5 | 11 | − | − | + | − | + | A-A |
| DPV | 66 | + | − | 12/12a | 8/8 | 3 | 17 | − | + | + | − | + | A-A |
| C | |||||||||||||
| CSFV | 59 | + | + | 14/16a | 7/7 | 7 | 12 | + | + | + | + | + | A-A |
| BVDV | 64 | + | + | 13/15a | 7/7 | 6 | 12 | + | + | + | + | + | A-A |
a
Numbers defining the lengths of helices in the pseudoknot include internal mispairs and internal bulges as appropriate. “Spacer” refers to the nucleotides between the pseudoknot and the initiation codon.