| (Return to Main) | CONSERVED CIS-ACTING SEQUENCES OF RNA VIRUSES |
Double-stranded, segmented RNA genome: 10 (Reovirus, Orbivirus), 11 (Rotavirus), or 12 (Coltivirus) segments
Sequences shown here are those of the mRNA, sense strand
e.g., reovirus 3, 2, 1, avian orthoreoviruses
Terminal sequences of reovirus serotype 3, strain Dearing [Antczak, et al., 1982]:
Segment 5' end 3' end L1 GCUACACGUU.....UCAACUCAUC REO3LAM3P M31058 L2 ----A-U-GC.....CU--U----- REO3L2 J03488 L3 ----AU---C.....C-G-U----- REOMCPL1A M23747 M1 ----UU--CG.....G-GCU----- REO3M1B M27261 M2 G----AU-UGC.....G---A----- REO3M2C M19408 M3 ----A-GUGA.....C-C-U----- REO3M3C M27262 S1 ----UUG--C.....G--UU----- REOS1C M10262 S2 ----UU--C-.....CAC-U----- REOS2T4A M25780 S3 ----A-GUCA.....C-U-A----- REHS3NS X01627 S4 ----UUUU-G.....-UC-U----- REOS4 K02739
Terminal sequences are conserved among reovirus type 1, 2 and 3
e.g., S1 segments
Type 5' end 3' end 3 GCUAUUGGUC.....GCAUUUCAUC REOS1C M10262 1 ------C-CG.....-UCAA----- REOS1A M10260 2 ------C-CA.....--GAC----- REOS1B M10261
e.g., bluetongue virus (BTV) 1 [Roy, et al., 1990], and at least 23 other serotypes, epizootic hemorraghic disease virus (EHDV), Broadhaven virus (BRD, [Moss, et al., 1990]), and African horse sickness virus (AHSV)
Terminal sequences of bluetongue virus, BTV serotype 10 [Roy, 1989]:
Segment 5' end 3' end L1 GUUAAAAUG.....UUACACUUAC BTV10VP1 X12819 L2 --A-U--AA.....---------- BTVL2 M11787 L3 ------U-U.....A--------- BTVL3 K02369 M4 -------CA.....-ACA------ BTVVP4LZIP L13726 M5 -------A-.....--C------- BTVVP5 D12532 M6 -------AA.....--CA------ BTVNS1 Y00422 S7 -------AU.....---------- BTVP7 X06463 S8 -------AA.....---------- BTV10S8 X13374 S9 -------AA.....-C-U------ BTV10VP6 L08669 S10 -------A-.....AC-------- BTVNS3II L08628
Terminal sequences are conserved among orbiviruses
e.g., segment 10 [Moss, et al., 1992; van Staden and Huisman, 1991]:
Virus 5' end 3' end BTV-10 GUUAAAAAG.....ACACACUUAC BTVNS3II L08628 EHDV ---------.....---------- EHDEHDV1A L29023 AHSV ---U---UU.....-ACG------ AHV3NS3 D12479 BRD --A---CUU.....-UUAGGA--- TBOBRD10NS M83197
e.g. simian rotavirus SA11, other human and animal rotaviruses.
Terminal sequences of simian SA11 rotavirus:
Segment 5' end 3' end 1 GGCUAUUAAAG.....GAUGUG ACC ROSIVP1 X16830 2 -----------.....---A-- --- ROSIVP2 X16831 3 ----U------.....------ G-- ROSIVP3 X16387 4 ------A---U.....------ --- ROSA11G4 Y00336 5 ----U--UUUU.....AC----A--- RSA115NS X14914 6 ----U-----C.....------ --- ROSRV6 X00421 7 ---AU----U-.....U----- G-- ROSA11 X00355 8 ----U------.....U----- --- RO1G8 J02353 9 ----U-A----.....------ --- REROT1 J02354 10 --G-U-----A.....A----- --- RO1G10 K01138 11 ----U------.....UU---- --- ROTNS26 M28347
Comparison of 5' and 3' termini of gene 9 of these viruses with that of simian (SA11) and human (WA) rotaviruses:
Virus 5' end 3' end Si SA11 GGC UUUAAAAGAGAGAAUUU.....UAGAAUUGUAUGAUGUGACC REROT1 J02354 Hu WA --- -----------------.....---------UC--------- RO29 K02033 Po OSU --- -----------------.....-----C-------------- ROOSUVP7 X04613 Ch Ch2 ---A-------C---A- --C.....G-U--AG--U---------- BRRNAVP7 X56784 Rh RRV --- --------C--------.....-----A-------------- RORVP7 M21650
e.g., Colorado tick fever virus (CTFV) (Florio strain; European-American subgroup A1), Eyach (European-American subgroup A2), Coltivirus JKT-7075 (Asian subgroup B1), Coltivirus JKT-6423 and Banna (BAN; Asian subgroup B2) viruses. [See Attoui, et al., 1998 for subgroups].
Comparison of terminal sequences of various segments.
CTFV sequences:
Segment 5' end 3' end CTFV VP12 GACAUUUUGUCUCAGAA.....GACGGGUAAUUGCAGUC CTU53227 U53227 CTFV VP9 ----------G---CG-.....AGG-AA-CC-------- AF000720 AF000720 CTFV VP11 C------------U-UG.....UGGAUAC--A------G CTU72694 U72694
Asian subgroup B viruses:
Segment 5' end 3' end JKT-7075 VP7 GUAGAAAAUUUGUUGAG.....UGAGUUUAAAGAACGAC AF052023 AF052023 JKT-6423 VP8 ---UUU--AA-UGAU-U.....GAUACAAUUU--C---- AF052017 AF052017 BAN VP12 ---UUA--AA-UGAU--.....-CCAA--U-GA-CU--- AF052030 AF052030
Comparison of CTFV and JKT-7075 sequences. CTFV is clearly different from the Asian subgroup B viruses:
Segment 5' end 3' end CTFV VP12 GACAUUUUGUCUCAGAA.....GACGGGUAAUUGCAGUC CTU53227 U53227 JKT-7075 VP7 -UAGAAAAU-UGUU--G.....UGA-UU---AGAAC-A- AF052023 AF052023
| (Return to Main) | Conserved cis-acting sequences of RNA viruses |
| Send suggestions and comments to: huang@borcim.wustl.edu Henry V. Huang Department of Molecular Microbiology, Box 8230 Washington University School of Medicine St. Louis, MO 63110-1093 USA | Tel 314-362-2755 FAX 314-362-1232 | |