The 19 nt of the genomic (+)RNA immediately adjacent to the poly-A sequence are very well conserved,
while sequences upstream are variable, helping to distinguish between subgroups of the alphaviruses.
Abbreviations:
VEE = Venezuelan equine encephalitis virus
EEE = eastern equine encephalitis virus
WEE = western equine encephalitis virus
SPD = salmon pancreas disease virus
SDV = rainbow trout sleeping disease virus
Plus-strand sequence is shown. Sequence identities are indicated by dashes.
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: | : | : | : | :
Sindbis CUUUUAUUAUUUCUUUUAUUAAUCAAC AAAAUUUUG UUUUUAACAUUU C poly-A J02363
AR86 U-------------------------- --------- ------------ - U38305
Girdwood U-------------------------- --------- ------------ N U38304
YN87448 U-------------------------- --------- ------------ - AF103734
Ockelbo U-------------------------- --------- ------------ - M69205
Whataroa U-A-A---U--CU------A-UC---- --------- ------------ - AF023292
Babanki U---AU-AU--CU--------------A--------- ------------ - AF023290
Xinjiang-160 -C---UA-UA---------C---U---C--------- ------------ - AF103728
Kyzylagach UC---UA-UA---------C---U---C--------- -------U---- - AF023291
Aura AA-C-U--G---U-C--U-AUUAUUU- --------- -------U---- - AF126284 S78478
EEE AAAA-CA----AA----UC-UU-AUGUUUUU------ -------U---- - X63135 X67111
WEE UAAA-UC-U--AUAA--U--CU-UUGUUUUU------ -------A---- - AF214040 AF143811
Highlands J AC-A----U--CU---CU---U-UUU-UUUU------ -------A---- - AF023289
Buggy Creek U---CU------UA----G-CUAUU-GAUU-G----- -------U---- - AF023287
Fort Morgan U-A-CC------UA----G-CUA-U-GAUU-G----- -------U---- - AF023288
VEE TRD A-------U--------C--UUC-G-AUCGG------ -------U---- - J04332
VEE Everglades U-A--U-AU--------C--UUC---AUUGG------ -------U---- - AF023293
VEE Ag80-663 AGA--U--U---U----UA--UA-C-AUUGG------ -------U---- - AF023299
VEE Pixuna U--A--A-U--CUC-GCCAAU--U-GAUUGG------ -------U---- - AF023294
VEE Cabassou -CA-----U-A-U--C-U-ACCAAC-AUUGG------ -------U---- - AF023300
VEE 78V-3531 AAAA-U--UA--UGA--U-CCGAUU-AUUGG------ -------U---- - AF023298
VEE Mucambo AAAA-U--UA--U-C--U-ACCAAU-AUUGG------ -------U---- - AF023295
VEE 71D-1252 AACAAU--UA--U-C--U-ACCAAC-AUUGG------ -------U---- - AF023297
VEE Tonate ACAAAU--U-A-U--C-U--CCAAU-AUUGG------ -------U---- - AF023296
Mayaro A-AGGGCACC-A--AACCA--GAAGUAAUUC------ -------U---- - AF023285
Chikungunya UC-CCGAACCCA-AGGG-CGU-GG-GAUGUU------ -------U---- - AF023283
ONN (Gulu) AA--CUCCGACG-AGGG-CGU-GG-GAAGUU------ -------U---- - M20303 M33999
ONN (SG650) UC-CCGAACCCG-AGGG-CGU-GG-GAAGUU------ -------U---- - AF079456
ONN (Igbo Ora) UC-CCGAACCCG-AGGG-CGU-GG-GAAGUU------ -------U--- - AF079457
Middelburg GGAAAUAAUA-CGCGACGA-UGG-U-GUCGC-A--G- ------U--- C- AF023284
Ndumu UAAAAU--UG--U--A-U--UUGAUU-G-UC-A--G- -------U---- C- AF023281
Bebaru AAAAAC--UAA--AGAA--AU-AUUGGAC--CA--G- -------U---- C- AF023282
Semliki Forest GACGA--A---GGA---U-AUU-U-UUUUGC-A--G- -------U---- C- X04129
Una GCAGAU-A---GA--AA--AU-AUUCGAUUG-A--G- -------U---- C- AF023280
SPD A-CCG--CCCACAGGGAG-AGGAUG-GUC-UC-A--- G------A----U -AAUAC AJ012631
SDV A-CCG--CCCACAGGGAG-AGGAUG-GUC-UC-A--- G----U-A-A--UU-AAU AJ238578
Ross River ACCCC--A-CAC-GGGG-CGU-GGCGU CU----- -UU-------U----UA- J02337
Sagiyama ACCCC-GACCA--GGGG-CGU-GGCGU CU----- -UU-------U----UA- AF023301
Getah ACCCC-GACCAC-GGGG-CGU-GGCGU CU----- -UU-------U----UA- AF023279
Barmah Forest ACCCC-GA-CAC-GGGG-CGU-GGCGU CU----- -UU-------U----UA- U73745
: | : | : | : | :
-40 -30 -20 -10 (Sindbis virus coordinates)
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| Send suggestions and comments to: huang@borcim.wustl.edu WWW 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 | |