| (Return to Main) | CONSERVED CIS-ACTING SEQUENCES OF RNA VIRUSES |
Single-stranded, plus-sense RNA genome
e.g., Sindbis (SIN), Sindbis-like AR86 (AR8) and Girdwood (GIR) viruses from South Africa, Sindbis-like YN87448 (YN8) virus from China, Ocklebo (OCK), Whataroa, Babanki, Kyzylagach, Xinjiang-160 (XJ1), Aura (AUR), eastern equine encephalitis (EEE), western equine encephalitis (WEE), Venezuelan equine encephalitis (VEE), Highland J (HJ), Buggy Creek, Fort Morgan, Semliki Forest (SFV), Middelburg (MID), Ndumu, Bebaru, Una, Mayaro, chickungunya, o'nyong nyong (ONN, Gulu strain), o'nyong nyong-like Igbo Ora (IGB), o'nyong nyong-like SG650 (SG6), Ross River (RRV), Sagiyama (SAG), Getah, Barma Forest (BFV), salmon pancreatic disease (SPD), rainbow trout sleeping disease (SDV) viruses.
Probably recognized for initiating synthesis of viral minus-strand RNA [Ou, et al., 1981; Levis, et al., 1986; Kuhn, et al., 1990]
Plus-strand sequence is shown
-40 -30 -20 -10 (Sindbis virus coordinates)
: | : | : | : | :
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 (Igbo Ora) UC-CCGAACCCG-AGGG-CGU-GG-GAAGUU------ -------U--- - AF079457
ONN (SG650) UC-CCGAACCCG-AGGG-CGU-GG-GAAGUU------ -------U---- - AF079456
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)
Recognized for initiating synthesis of viral subgenomic mRNA [Ou, et al., 1982; Levis, et al., 1990; Raju and Huang, 1991]
The sequence from -19 to +5 (relative to the initiation site of the mRNA) is sufficient for directing subgenomic mRNA synthesis. It is about 3-6 fold less active than the sequence from -40 to +14.
Minus-strand sequence is shown
|--> subgenomic mRNA
-50 -40 -30 -20 -10 +1 +10
: | : | : | : | : | : | : |
nsP4 SerLysArgAlaPheGlnAlaIleArgGlyGluIleLysHisLeuTyrGlyGlyProLystrm
SIN UCGUUUUCUCGUAAGGUUCGGUAGUCUCCCCUUUAUUUCGUAGAGAUGCCACCAGGAUUUAUCA GUCGUAUCA SINCG J02363
A86 --------------A------------------------------------------------- --------- ACU38305 U38305
Gir --------------A------------------------------------------------- --------G ACU38304 U38304
YN8 --------------A----------------------C-------------------------- --------- AF103734 AF103734
OCK ------G----------------U-----A---------------------------------- --------- SINOCK82 M69205
XJ1 -------UAA-C--A--------A-----U-----------U---------------------- --------G AF103728 AF103728
AUR ---C-A-U------AU----UG-UG-G---UCGGG--CU--G---------------------U -C-AC---G AF126284 AF126284 S78478
SFV CU--AA-UC--C--AU-CUUUA-C-----UGGAC-A-AU--G--------G----------A-C ACGCA--U- ALSFV42S X04129
MBV -UAA-AGUGUUA----C-GUAG-U-----UGGGC-A-AAC-G--------G------------- ACGCAC-U- MBVCP J02246
BFV -U-AAC-UCA-G---UC-UU---U------U--GG--AU------------------------- ACG-C-AUC BFU73745 U73745
RRV ---GAC-UCUUA--AU--UUCG-CG-A--UGGG--GCAU--G--------G------------U ACGUCUCUG RRVNBCG J02337
SAG -UAAAC-UCA-A--AUCCUUU--U-----AGGG--G-AU-----C-----G------------U ACGUCC-A- AB032553 AB032553
ONN ------CU-UUG--AU-CUUUG-U------GGGC-GCAUUGGA-C-----G--U---------C A-GCGUGAU ONNCG M20303 M33999
IGB --A---CU-UUG--AU--UUUG-U------GGGC-GCAUUGGA-C-----G--U---------C A-GCGUAAU AF079457 AF079457
SG6 ------CU-UUG--AU--UUUG-U------GGGC-GCAUUGGA-C--------U---------C A-GCGUGAU AF079456 AF079456
WEE ---CAA-UCUUG---U-CUC---U------U-GGG--AGUGG--------GA-U---------C ACU-C---- AF214040 AF214040 AF143811
EEE AGUCAA--GUUG--AU--GU---U-----AG-GGGG-AUUGG--------GA-U---------C AA-ACG-A- EEEVIRNA X63135 X67111
VEE --ACAA-U-A-----UCGAU-G-C-------GGGGA-AUUG---------GAUU---C---C-U -AU-CUGU- EEVNSPENV J04332
SPD CU-AAC---A-C-U--AC-C-CGCG-------CAUGCAUAGG-------AGAUU---A----A-AA-A----GU- SPA012631 AJ012631
SDV CUAGAC---A-C-U-AAC-C-CGCG-------CAUGCAUAGG-------GGAUU---A----A-AA-A----GU- SDI238578 AJ238578
|- minimal promoter -|
|------------------- full promoter ---------------------|
Probably recognized (on the minus-strand) for initiating synthesis of viral plus-strand RNA, and for translation regulation [Ou, et al., 1983; Levis, et al., 1986; Niesters and Strauss, 1990a].
Function of the conserved sequences is unknown [Ou, et al., 1983; Niesters and Strauss, 1990b].
Plus-strand sequence is shown
stem 1 loop 1 stem 1 stem 2 loop 2 stem 2
-------> <-------- -------> <--------
SIN CACAGCAGGUCACUCCAAAUGACCAUGCUAAUGCCAGAGCAUUUUCGCAUCUGGCCAGUAAA 3' SINCG J02363
SFV --UU---------A--------------A--------------------C-----U-CC--- ALSFV42S X04129
HJ ---------AG-C-----------------------G---------G----T-CA--G HJV01 K00700
RRV -------------A--U-----------------------U----------------CA--G RRVNBCG M20162
EEE -CAC---------CGAC-----------------U-----G--------------U-CA--- EEEVIRNA X63135 X67111
ONN --A----------G--------------A--C--U-----------------A--A-UA--- ONNCG M20303
VEE -CA-----------GAU-----------------------G------------G-UUCA--- EEVCOMGEN L04653