A Genome-Wide Analysis of RNA Pseudoknots That Stimulate Efficient −1 Ribosomal Frameshifting or Readthrough in Animal Viruses
Table 1
Detected pseudoknots downstream from the frameshift site (slippery sequence) or 0 frame stop codon in viruses.
Virus
SS or RT
sp
S1
S2
L1
L2
L3
Rank
CPK1
Artiriviridae
Equine arteritis virus (EAV)
GUUAAAC
5
10
7
2
58
0
43.3
1
Yes
Lelystad virus (LV)
UUUAAAC
5
12
7
4
15
0
48.7
1
Lactate dehydrogenase-elevating virus (LDV)
UUUAAAC
6
11
8
3
17
0
41.7
1
Porcine reproductive and respiratory syndrome virus (PRRSV)
UUUAAAC
4
13
7
4
21
0
47.7
1
Simian hemorrhagic fever virus (SHFV)
UUUAAAC
7
5
7
8
9
1
21.3
78
Coronaviridae
Transmissible gastroenteritis virus (TGEV)
UUUAAAC
3
14
6
2
25
0
34.5
1
Yes
Bovine coronavirus (BCV)
UUUAAAC
5
11
9
2
32
2
38.8
1
Human coronavirus 229E (HCoV-229E)
UUUAAAC
5
12
7
1
164
0
39.0
1
Yes
Human coronavirus OC43 (HCoV-OC43)
UUUAAAC
5
11
9
2
32
2
38.7
1
Porcine epidemic diarrhea virus (PEDV)
UUUAAAC
7
5
6
1
18
0
19.8
>100
Yes
Human coronavirus HKU1 (HCoV-HKU1)
UUUAAAC
5
12
9
1
32
1
39.0
1
Murine hepatitis coronavirus (MHV)
UUUAAAC
5
13
7
1
32
0
37.1
1
Yes
SARS coronavirus (SARS-CoV)
UUUAAAC
5
11
7
1
32
0
28.7
1
Yes
Avian infectious bronchitis coronavirus (IBV)
UUUAAAC
6
11
7
1
32
0
35.6
1
Yes
Bovine torovirus (Breda virus) (BRV)
UUUAAAC
5
11
6
1
11
2
37.1
1
Equine torovirus (Berne Virus) (BEV)
UUUAAAC
5
11
6
2
10
0
37.3
1
Yes
Astroviridae
Chicken astrovirus (CAstV)
AAAAAAC
6
5
5
3
11
0
22.1
10
Turkey astrovirus (TAstV)
AAAAAAC
8
7
6
1
21
0
30.4
2
Yes
Ovine astrovirus (OAstV)
AAAAAAC
6
5
5
8
20
0
26.2
16
Flaviviridae
Japanese encephalitis virus (JEV)
CCCUUUU
5
11
7
7
16
2
39.2
1
Murray Valley encephalitis virus-Alfuy (ALFV)
CCCUUUU
5
11
6
8
16
2
37.3
2
Murray Valley encephalitis virus (MVEV)
UCCUUUU
5
11
8
6
40
2
29.9
1
Usutu virus (USUV)
UCCUUUU
5
11
7
7
16
2
39.2
1
West Nile virus-Kunjin (WNVKUN)
UCCUUUU
5
11
7
6
17
3
37.6
1
West Nile virus H442 (WNV-H442)
UCCUUUU
5
11
8
6
16
2
40.9
1
West Nile virus (WNV)
CCCUUUU
4
11
7
6
17
3
36.9
1
Retroviridae
Avian leukosis virus (ALV)
AAATTTA
2
13
8
11
11
52
35.8
1
Rous sarcoma virus (RSV)
AAATTTA
2
13
8
11
11
52
36.2
1
Jaagsiekte sheep retrovirus (JSRV)
GGGAAAC
7
6
6
1
11
0
33.2
1
Yes
Mason-Pfizer monkey virus (MPMV)
GGGAAAC
7
6
6
1
12
0
33.7
1
Yes
Simian retrovirus 2 (SRV-2)
GGGAAAC
7
6
6
1
12
0
33.7
1
Yes
Simian retrovirus 1 (SRV-1)
GGGAAAC
7
6
6
1
12
0
33.7
1
Yes
Mouse mammary tumor virus (MMTV)
AAAAAAC
7
5
7
1
8
1
29.7
1
Squirrel monkey retrovirus (SMRV)
GGGAAAC
7
6
7
1
14
0
33.8
1
Yes
Human endogenous retrovirus K10 (HERV K10)
GGGAAAC
7
6
6
1
9
0
31.8
1
Yes
Intracisternal A particle, Syrian hamster (IAP-H18)
AAAAAAC
7
7
7
2
7
0
37.7
1
Yes
Intracisternal A particle, Chinese hamster (CHIAP34)
AAAAAAC
7
7
7
2
8
0
37.9
1
Yes
Intracisternal A particle, mouse (m-IAP)
AAAAAAC
8
7
6
1
9
0
33.9
1
Yes
Bovine leukemia virus (BLV)
AAAAAAC
7
6
6
2
63
0
22.4
26
Yes
Primate T-lymphotropic virus 1 (HTLV-I)
AAAAAAC
6
9
6
1
57
0
32.7
1
Yes
Primate T-lymphotropic virus 2 (HTLV-II)
AAAAAAC
7
8
6
1
83
0
28.6
3
Primate T-lymphotropic virus 3 (STLV-I)
AAAAAAC
6
9
6
1
57
0
35.4
1
Yes
Baboon endogenous virus (BaEV)
RT
8
9
6
1
19
0
38.1
1
Yes
Feline leukemia virus (FeLV)
RT
8
8
6
2
18
0
37.2
2
Yes
Gibbon ape leukemia virus (GaLV)
RT
8
8
7
2
17
0
37.0
1
Yes
Moloney murine sarcoma virus (MSV)
RT
8
8
7
1
18
0
40.9
2
Yes
Moloney murine leukemia virus (Mo-MuLV)
RT
8
8
7
1
18
0
40.9
2
Yes
Bovine immunodeficiency virus (BIV)
AAAAAAC
7
11
6
1
29
0
34.4
1
Yes
Jembrana disease virus (JDV)
AAAAAAC
6
12
6
1
8
0
40.8
1
Yes
South African Ovine Maedi Visna virus (SA-OMVV)
GGGAAAC
7
6
6
1
12
0
40.2
1
Yes
Caprine Arthritis Encephalitis virus (CAEV)
GGGAAAC
4
10
7
1
15
0
38.7
1
Yes
Equine infectious anemia virus (EIAV)
AAAAAAC
9
5
5
4
9
0
20.2
42
Feline immunodeficiency virus (FIV)
GGGAAAC
6
7
6
2
9
0
33.9
1
Yes
Puma lentivirus (PLV)
AAAAAAC
8
5
6
2
11
0
24.6
12
Yes
Human immunodeficiency virus 1 (HIV1-HXB2)
UUUUUUA
7
9
5
5
5
0
23.5
10
Human immunodeficiency virus 2 (HIV2)
UUUUUUA
0
5
9
5
6
3
29.6
5
Togaviridae
Barmah Forest virus (BFV)
UUUUUUA
9
9
5
4
29
0
26.7
6
Eastern equine encephalitis virus (EEEV)
UUUUUUA
5
7
5
1
28
3
25.7
8
Fort Morgan virus (FMV)
UUUUUUA
9
9
5
1
49
3
27.9
1
Getah virus (GETV)
UUUUUUA
11
6
10
2
22
3
19.7
26
Highlands J virus (HJV)
UUUUUUA
8
10
5
1
27
3
32.3
1
Mayaro virus (MAYV)
UUUUUUA
3
6
7
5
42
2
23.3
34
Middelburg virus (MIDV)
UUUUUUA
6
10
7
3
13
1
41.0
1
Ndumu virus (NDUV)
UUUUUUA
7
9
6
4
27
3
36.1
1
O'nyong-nyong virus (ONNV)
UUUUUUA
3
6
5
10
34
2
19.9
57
Seal louse virus (SESV)
UUUUUUA
7
11
7
2
9
0
38.0
1
Yes
Salmon pancreas disease virus (SPDV)
UUUUUUA
8
9
6
1
10
2
25.8
27
Whataroa virus (WHAV)
UUUUUUA
9
6
5
10
28
0
24.6
1
SS or RT: slippery sequence or readthrough of stop codon; sp: length of the spacer sequence between the slippery sequence/stop codon and the downstream pseudoknot; S1, S2, L1, L2, and L3: lengths of the sequence elements of the pseudoknot, stem1, stem2, loop1, loop2, and loop3. See Figure 1 for the sequence elements of a typical pseudoknot. Calculated free energy of the stem regions of the pseudoknot is listed in the column “” in minus kcal/mol. “Rank” indicates the relative ranking (according to the calculated free energy of the stems) of the frameshift/readthrough stimulating pseudoknots among all possible pseudoknots detected within the full-length genomic RNAs. “CPK1” indicates whether the pseudoknot belongs to the CPK1 family.
