IRESite_Id:448 characteristics of CSFV_1-442_349UUU IRES studied in pXLCSFV1-442.NS349UUU plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `448`	Version: `0`
Originaly submitted by: Tomáš Mašek
Reviewed by: Martin Mokrejš

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
end-to-end_full-length_mRNA

The mRNA/+RNA description:

Bicistronic RNA encoding B2 and NS´proteins as the first and the second cistron, respectively, with mutated
CSFV IRES inserted between them. Capped T7 promoter-derived transcript has been transcribed in vitro.

The mRNA/+RNA sequence represented in the +DNA notation:

GGGAGACCCA AGCTTGGGCA AACGTTATTT TACCGGAGAT GGCTACTCGT CGCGCTGCTA TTCCCCGTGA AGCGGATAAT ATCCTTGGGG GTGCAATGCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATCCAAAGTT CAAATGAATA GCAGACGAGC TGCTTTGGGA GAGATTGGCA ACAAAGTGAC TGTGCGAGGA AAACCACCTG CAGTAAAGCA GTCTTCCAAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCTGTGGCAA AGCCTTCAAA GATGGCAGCA ACTAAAGTGG CAAATGTTAA GACTAAGCAT GTACCTGTGA AACCAGTTGT AGCTGAAGCT GCCCCCAAAG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TGCCTTCCCC TGTGCCGATG GATGTGTCCT TGAAAGAGGA AGAGCTGTGC CAGGCATTCT CCGATGCACT GACCAGTGTT GAAGACATTG ATGCAGATGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TGGTGGAAAC CCTCAATTGT GCAGTGACTA TGTGATGGAC ATCTATAACT ACCTTAAGCA ACTGGAAGTT CAACAGTCTG TACATCCTTG CTATCTTGAA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GGAAAAGAAA TTAATGAGCG TATGAGAGCT ATCCTAGTTG ACTGGCTTGT TCAAGTGCAT TCTAGGTTTC AGCTTCTTCA GGAGACTTTA TACATGGGCG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTGCAATCAT GGATCGCTTC TTACAAGTTC AGCCAGTCTC CCGCAGTAAG CTTCAGTTGG TTGGTGTTAC TTCCCTACTA ATTGCTTCAA AATATGAAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GATGTACACT CCAGAGGTTG CAGACTTTGT TTATATCACC GATAATGCCT ATACTGCATC TCAGATCAGA GAAATGGAAA TGATTATCCT TCGACTCCTC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AACTTTGACC TTGGACGGCC ATTACCTCTC CACTTCCTCA GACGGGCTTC AAAATCTTGC AGTGCTGATG CAGAGCAACA TACCCTTGCA AAATATTTGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGGAGCTTAC ACTCATAGAC TATGAAATGG TCCACATCAA GCCTTCAGAA ATTGCAGCTG CTGCCCTCTG CCTATCTCAA AAAATTCTTG GCCAGGGAAC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CTGGGGTACC ACTCAGCACT ATTACACAGG CTACACAGAA GGTGACTTGC AACTGATCAT GAAGCATATG GCTAAGAACA TAACCAAAGT CAACCAGAAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTAACAAAGC ATGTGGCTGT GAGGAACAAG TATGCTAGCA GTAAACTGAT GAAGATCAGC ACCCTTCCTC AGCTTATGGC TCCTCTAATC ACAGAGCTTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CTGCAAGTCT CTCTTAGAAC TGTTAAGTGA CCCTTTCAAA GAGAACCACT AATTGCACTT TTAACGTTGC TGCTGGCAAA TGCTGCTGTT CCTGTAAATA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TGTTTGTATT TTTATTGACT CATTTGTGAA CTTTGAGTAA TCAATGCTGT AATGTCAGTA TGAAATAAAA CTTCACATTT TTTATTTGGT CGACGAGGTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AGCTCTTTCT CGTATACGAT ATTGGATACA CTAAATTTCG ATTTGGTCTA GGGCACCCCT CCAGCGACGG CCGAAATGGG CTAGCCATGC CCATAGTAGG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACTAGCAAAC GGAGGGACTA GCCGTAGTGG CGAGCTCCCT GGGTGGTCTA AGTCCTGAGT ACAGGACAGT CGTCAGTAGT TCGACGTGAG CACTAGCCCA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CCTCGAGATG CTACGTGGAC GAGGGCATGC CCAAGACACA CCTTAACCCT GGCGGGGGTC GCTAGGGTGA AATCACATTA TGTGATGGGG GTACGACCTG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATAGGGTGCT GCAGAGGCCC ACTAGCAGGC TAGTATTTTA ATCTCTGCTG TACATGGCAC ATGGAGTTGA ATCATTTTGA ATTATTATAC AAAACAAGCA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AACAAAAACC AGTGGGAGTG GAGGAACCGG GTACCATGGA TCCCAGCTTT CAGGTAGATT GCTTTCTTTG GCATGTCCGC AAACGAGTTG CAGACCAAGA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ACTAGGTGAT GCCCCATTCC TTGATCGGCT TCGCCGAGAT CAGAAATCCC TAAGAGGAAG GGGCAGCACC CTCGGTCTGG ACATCGAGAC AGCCACACGT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GCTGGAAAGC AGATAGTGGA GCGGATTCTG AAAGAAGAAT CCGATGAGGC ACTTAAAATG ACCATGGCCT CTGTACCTGC GTCGCGTTAC CTAACTGACA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGACTCTTGA GGAAATGTCA AGGGACTGGT CCATGCTCAT ACCCAAGCAG AAAGTGGCAG GCCCTCTTTG TATCAGAATG GACCAGGCGA TCATGGATAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAACATCATA CTGAAAGCGA ACTTCAGTGT GATTTTTGAC CGGCTGGAGA CTCTAATATT GCTAAGGGCT TTCACCGAAG AGGGAGCAAT TGTTGGCGAA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATTTCACCAT TGCCTTCTCT TCCAGGACAT ACTGCTGAGG ATGTCAAAAA TGCAGTTGGA GTCCTCATCG GGGGACTTGA ATGGAATGAT AACACAGTTC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GAGTCTCTGA AACTCTACAG AGATTCGCTT GGAGAAGCAG TAATGAGAAT GGGAGACCTC CACTCACTCC AAAACAGAAA CGAGAAATGG CGGGAACAAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TAGGTCAGAA GTTTGAAGAA ATAAGATGGT TGATTGAAGA AGTGAGACAC AAACTGAAGA TAACAGAGAA TAGTTTTGAG CAAATAACAT TTATGCAAGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTTACATCTA TTGCTTGAAG TGGAGCAAGA GATAAGAACT TTCTCGTTTC AGCTTATTTA ATAATAAAAA ACACCCTTGT TTCTACTGG
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pXLCSFV1-442.NS349UUU The name of the promoter used to express this mRNA:
T7

Description of the plasmid (facultative for promoter-less plasmid records):
pXLCSFV1-442.NS349U is a derivative of pXL10S. CSFV IRES corresponding to 1-442 bp of viral genomic RNA and carrying mutation at position 349 has been inserted between the two cistrons using SalI and SnaBI enzymes. The pXLJ0S contains T7 and SP6 promoter sites and is typically used in in vitro transcription/translation assays. Bicistronic RNA, which contains B2 and NS cistrons (GI:214094, GI:21693177), is transcribed by T7 polymerase after vector linearization by EcoRI.

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

not tested

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

not tested

A promoter reported in cDNA corresponding to IRES sequence:

not tested

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
CSFV

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Classical swine fever virus Alfort/Tuebingen

The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:

TATAGTGTCA CCTAAATCGT ATGTGTATGA TACATAAGGT TATGTATTAA TTGTAGCCGC GTTCTAACGA CAATATGTAC AAGCCTAATT GTGTAGCATC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGGCTTACTG AAGCAGACCC TATCATCTCT CTCGTAAACT GCCGTCAGAG TCGGTTTGGT TGGACGAACC TTCTGAGTTT CTGGTAACGC CGTTCCGCAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCCGGAAATG GTCAGCGAAC CAATCAGCAG GGTCATCGCT AGCCAGATCC TCTACGCCGG ACGCATCGTG GCCGGCATCA CCGGCGCCAC AGGTGCGGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCTGGCGCCT ATATCGCCGA CATCACCGAT GGGGAAGATC GGGCTCGCCA CTTCGGGCTC ATGAGCGCTT GTTTCGGCGT GGGTATGGTG GCAGGCCCCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TGGCCGGGGG ACTGTTGGGC GCCATCTCCT TGCATGCACC ATTCCTTGCG GCGGCGGTGC TCAACGGCCT CAACCTACTA CTGGGCTGCT TCCTAATGCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GGAGTCGCAT AAGGGAGAGC GTCGATATGG TGCACTCTCA GTACAATCTG CTCTGATGCC GCATAGTTAA GCCAGCCCCG ACACCCGCCA ACACCCGCTG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ACGCGCCCTG ACGGGCTTGT CTGCTCCCGG CATCCGCTTA CAGACAAGCT GTGACCGTCT CCGGGAGCTG CATGTGTCAG AGGTTTTCAC CGTCATCACC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GAAACGCGCG AGACGAAAGG GCCTCGTGAT ACGCCTATTT TTATAGGTTA ATGTCATGAT AATAATGGTT TCTTAGACGT CAGGTGGCAC TTTTCGGGGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AATGTGCGCG GAACCCCTAT TTGTTTATTT TTCTAAATAC ATTCAAATAT GTATCCGCTC ATGAGACAAT AACCCTGATA AATGCTTCAA TAATATTGAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAAGGAAGAG TATGAGTATT CAACATTTCC GTGTCGCCCT TATTCCCTTT TTTGCGGCAT TTTGCCTTCC TGTTTTTGCT CACCCAGAAA CGCTGGTGAA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGTAAAAGAT GCTGAAGATC AGTTGGGTGC ACGAGTGGGT TACATCGAAC TGGATCTCAA CAGCGGTAAG ATCCTTGAGA GTTTTCGCCC CGAAGAACGT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TTTCCAATGA TGAGCACTTT TAAAGTTCTG CTATGTGGCG CGGTATTATC CCGTATTGAC GCCGGGCAAG AGCAACTCGG TCGCCGCATA CACTATTCTC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGAATGACTT GGTTGAGTAC TCACCAGTCA CAGAAAAGCA TCTTACGGAT GGCATGACAG TAAGAGAATT ATGCAGTGCT GCCATAACCA TGAGTGATAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CACTGCGGCC AACTTACTTC TGACAACGAT CGGAGGACCG AAGGAGCTAA CCGCTTTTTT GCACAACATG GGGGATCATG TAACTCGCCT TGATCGTTGG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAACCGGAGC TGAATGAAGC CATACCAAAC GACGAGCGTG ACACCACGAT GCCTGTAGCA ATGGCAACAA CGTTGCGCAA ACTATTAACT GGCGAACTAC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTACTCTAGC TTCCCGGCAA CAATTAATAG ACTGGATGGA GGCGGATAAA GTTGCAGGAC CACTTCTGCG CTCGGCCCTT CCGGCTGGCT GGTTTATTGC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TGATAAATCT GGAGCCGGTG AGCGTGGGTC TCGCGGTATC ATTGCAGCAC TGGGGCCAGA TGGTAAGCCC TCCCGTATCG TAGTTATCTA CACGACGGGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGTCAGGCAA CTATGGATGA ACGAAATAGA CAGATCGCTG AGATAGGTGC CTCACTGATT AAGCATTGGT AACTGTCAGA CCAAGTTTAC TCATATATAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TTTAGATTGA TTTAAAACTT CATTTTTAAT TTAAAAGGAT CTAGGTGAAG ATCCTTTTTG ATAATCTCAT GACCAAAATC CCTTAACGTG AGTTTTCGTT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CCACTGAGCG TCAGACCCCG TAGAAAAGAT CAAAGGATCT TCTTGAGATC CTTTTTTTCT GCGCGTAATC TGCTGCTTGC AAACAAAAAA ACCACCGCTA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCAGCGGTGG TTTGTTTGCC GGATCAAGAG CTACCAACTC TTTTTCCGAA GGTAACTGGC TTCAGCAGAG CGCAGATACC AAATACTGTC CTTCTAGTGT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AGCCGTAGTT AGGCCACCAC TTCAAGAACT CTGTAGCACC GCCTACATAC CTCGCTCTGC TAATCCTGTT ACCAGTGGCT GCTGCCAGTG GCGATAAGTC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GTGTCTTACC GGGTTGGACT CAAGACGATA GTTACCGGAT AAGGCGCAGC GGTCGGGCTG AACGGGGGGT TCGTGCACAC AGCCCAGCTT GGAGCGAACG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACCTACACCG AACTGAGATA CCTACAGCGT GAGCTATGAG AAAGCGCCAC GCTTCCCGAA GGGAGAAAGG CGGACAGGTA TCCGGTAAGC GGCAGGGTCG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GAACAGGAGA GCGCACGAGG GAGCTTCCAG GGGGAAACGC CTGGTATCTT TATAGTCCTG TCGGGTTTCG CCACCTCTGA CTTGAGCGTC GATTTTTGTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATGCTCGTCA GGGGGGCGGA GCCTATGGAA AAACGCCAGC AACGCGGCCT TTTTACGGTT CCTGGCCTTT TGCTGGCCTT TTGCTCACAT GTTCTTTCCT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GCGTTATCCC CTGATTCTGT GGATAACCGT ATTACCGCCT TTGAGTGAGC TGATACCGCT CGCCGCAGCC GAACGACCGA GCGCAGCGAG TCAGTGAGCG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AGGAAGCGGA AGAGCGCCCA ATACGCAAAC CGCCTCTCCC CGCGCGTTGG CCGATTCATT AATGCAGCTG GCTTATCGAA ATTAATACGA CTCACTATAG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GGAGACCCAA GCTTGGGCAA ACGTTATTTT ACCGGAGATG GCTACTCGTC GCGCTGCTAT TCCCCGTGAA GCGGATAATA TCCTTGGGGG TGCAATGCGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TCCAAAGTTC AAATGAATAG CAGACGAGCT GCTTTGGGAG AGATTGGCAA CAAAGTGACT GTGCGAGGAA AACCACCTGC AGTAAAGCAG TCTTCCAATG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CTGTGGCAAA GCCTTCAAAG ATGGCAGCAA CTAAAGTGGC AAATGTTAAG ACTAAGCATG TACCTGTGAA ACCAGTTGTA GCTGAAGCTG CCCCCAAAGT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GCCTTCCCCT GTGCCGATGG ATGTGTCCTT GAAAGAGGAA GAGCTGTGCC AGGCATTCTC CGATGCACTG ACCAGTGTTG AAGACATTGA TGCAGATGAT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GGTGGAAACC CTCAATTGTG CAGTGACTAT GTGATGGACA TCTATAACTA CCTTAAGCAA CTGGAAGTTC AACAGTCTGT ACATCCTTGC TATCTTGAAG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GAAAAGAAAT TAATGAGCGT ATGAGAGCTA TCCTAGTTGA CTGGCTTGTT CAAGTGCATT CTAGGTTTCA GCTTCTTCAG GAGACTTTAT ACATGGGCGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGCAATCATG GATCGCTTCT TACAAGTTCA GCCAGTCTCC CGCAGTAAGC TTCAGTTGGT TGGTGTTACT TCCCTACTAA TTGCTTCAAA ATATGAAGAG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATGTACACTC CAGAGGTTGC AGACTTTGTT TATATCACCG ATAATGCCTA TACTGCATCT CAGATCAGAG AAATGGAAAT GATTATCCTT CGACTCCTCA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ACTTTGACCT TGGACGGCCA TTACCTCTCC ACTTCCTCAG ACGGGCTTCA AAATCTTGCA GTGCTGATGC AGAGCAACAT ACCCTTGCAA AATATTTGAT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GGAGCTTACA CTCATAGACT ATGAAATGGT CCACATCAAG CCTTCAGAAA TTGCAGCTGC TGCCCTCTGC CTATCTCAAA AAATTCTTGG CCAGGGAACC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TGGGGTACCA CTCAGCACTA TTACACAGGC TACACAGAAG GTGACTTGCA ACTGATCATG AAGCATATGG CTAAGAACAT AACCAAAGTC AACCAGAATC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TAACAAAGCA TGTGGCTGTG AGGAACAAGT ATGCTAGCAG TAAACTGATG AAGATCAGCA CCCTTCCTCA GCTTATGGCT CCTCTAATCA CAGAGCTTGC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TGCAAGTCTC TCTTAGAACT GTTAAGTGAC CCTTTCAAAG AGAACCACTA ATTGCACTTT TAACGTTGCT GCTGGCAAAT GCTGCTGTTC CTGTAAATAT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GTTTGTATTT TTATTGACTC ATTTGTGAAC TTTGAGTAAT CAATGCTGTA ATGTCAGTAT GAAATAAAAC TTCACATTTT TTATTTGGTC GACGAGGTTA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCTCTTTCTC GTATACGATA TTGGATACAC TAAATTTCGA TTTGGTCTAG GGCACCCCTC CAGCGACGGC CGAAATGGGC TAGCCATGCC CATAGTAGGA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CTAGCAAACG GAGGGACTAG CCGTAGTGGC GAGCTCCCTG GGTGGTCTAA GTCCTGAGTA CAGGACAGTC GTCAGTAGTT CGACGTGAGC ACTAGCCCAC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CTCGAGATGC TACGTGGACG AGGGCATGCC CAAGACACAC CTTAACCCTG GCGGGGGTCG CTAGGGTGAA ATCACATTAT GTGATGGGGG TACGACCTGA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TAGGGTGCTG CAGAGGCCCA CTAGCAGGCT AGTATTTTAA TCTCTGCTGT ACATGGCACA TGGAGTTGAA TCATTTTGAA TTATTATACA AAACAAGCAA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ACAAAAACCA GTGGGAGTGG AGGAACCGGG TACCATGGAT CCCAGCTTTC AGGTAGATTG CTTTCTTTGG CATGTCCGCA AACGAGTTGC AGACCAAGAA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTAGGTGATG CCCCATTCCT TGATCGGCTT CGCCGAGATC AGAAATCCCT AAGAGGAAGG GGCAGCACCC TCGGTCTGGA CATCGAGACA GCCACACGTG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CTGGAAAGCA GATAGTGGAG CGGATTCTGA AAGAAGAATC CGATGAGGCA CTTAAAATGA CCATGGCCTC TGTACCTGCG TCGCGTTACC TAACTGACAT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GACTCTTGAG GAAATGTCAA GGGACTGGTC CATGCTCATA CCCAAGCAGA AAGTGGCAGG CCCTCTTTGT ATCAGAATGG ACCAGGCGAT CATGGATAAG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AACATCATAC TGAAAGCGAA CTTCAGTGTG ATTTTTGACC GGCTGGAGAC TCTAATATTG CTAAGGGCTT TCACCGAAGA GGGAGCAATT GTTGGCGAAA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TTTCACCATT GCCTTCTCTT CCAGGACATA CTGCTGAGGA TGTCAAAAAT GCAGTTGGAG TCCTCATCGG GGGACTTGAA TGGAATGATA ACACAGTTCG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

AGTCTCTGAA ACTCTACAGA GATTCGCTTG GAGAAGCAGT AATGAGAATG GGAGACCTCC ACTCACTCCA AAACAGAAAC GAGAAATGGC GGGAACAATT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

AGGTCAGAAG TTTGAAGAAA TAAGATGGTT GATTGAAGAA GTGAGACACA AACTGAAGAT AACAGAGAAT AGTTTTGAGC AAATAACATT TATGCAAGCC 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TTACATCTAT TGCTTGAAGT GGAGCAAGAG ATAAGAACTT TCTCGTTTCA GCTTATTTAA TAATAAAAAA CACCCTTGTT TCTACTGGAA TTCCGTGTAT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TC
^5501

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

The total number of notable open-reading frames (ORFs):

2

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `0`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
B2

The description of the protein encoded in this ORF:
Xenopus laevis B2 cyclin

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

no

The ORF absolute position (the base range includes START and STOP codons or their equivalents):

39-1217

ORF

ORF position:

2

Version: `0`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
NS

The description of the protein encoded in this ORF:
Truncated form of influenza NS1 protein which is N-terminally fused with 3 amino acids originating from polylinker and with N-terminal part of viral NPro protein.

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

no

The ORF absolute position (the base range includes START and STOP codons or their equivalents):

1761-2516

Remarks:

IRESite notes about verification of plasmid sequence:
The sequence of pXLCSFV1-442.NS349UUU(pXLJ0S respectively) was derived from the pXLJCon sequence which
has been experimentally determined by IRESite curators (please see the IRESite entry 329). The sequence of
pXLJ0S differs from pXLJCon in a creation of SnaBI restriction site at position 4202 of plasmid sequence.  A
mutation in vector backbone at position 2808 is indicated in pXLCSFV1-442.NS349UUU.gb file provided by
IRESite. This mutation has been detected by sequencing of pXLJCon, thus it is not clear if it is present in
pXLJ0S series as well.

Citations:

Fletcher S. P., Jackson R. J. (2002) Pestivirus internal ribosome entry site (IRES) structure and function: elements in the 5' untranslated region important for IRES function. J. Virol. 76(10):5024-5033

IRESs:

IRES:

Version: `0`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Mokrejš
The IRES name: `CSFV_1-442_349UUU`	The functional status of IRES: `defective`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

1389-1830

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `172`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `613`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-372`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `69`

The sequence of IRES region aligned to its secondary structure (if available):

GTCGACGAGG TTAGCTCTTT CTCGTATACG ATATTGGATA CACTAAATTT CGATTTGGTC TAGGGCACCC CTCCAGCGAC GGCCGAAATG GGCTAGCCAT 
^1389      ^1399      ^1409      ^1419      ^1429      ^1439      ^1449      ^1459      ^1469      ^1479      

GCCCATAGTA GGACTAGCAA ACGGAGGGAC TAGCCGTAGT GGCGAGCTCC CTGGGTGGTC TAAGTCCTGA GTACAGGACA GTCGTCAGTA GTTCGACGTG 
^1489      ^1499      ^1509      ^1519      ^1529      ^1539      ^1549      ^1559      ^1569      ^1579      

AGCACTAGCC CACCTCGAGA TGCTACGTGG ACGAGGGCAT GCCCAAGACA CACCTTAACC CTGGCGGGGG TCGCTAGGGT GAAATCACAT TATGTGATGG 
^1589      ^1599      ^1609      ^1619      ^1629      ^1639      ^1649      ^1659      ^1669      ^1679      

GGGTACGACC TGATAGGGTG CTGCAGAGGC CCACTAGCAG GCTAGTATTT TAATCTCTGC TGTACATGGC ACATGGAGTT GAATCATTTT GAATTATTAT 
^1689      ^1699      ^1709      ^1719      ^1729      ^1739      ^1749      ^1759      ^1769      ^1779      

ACAAAACAAG CAAACAAAAA CCAGTGGGAG TGGAGGAACC GG
^1789      ^1799      ^1809      ^1819      ^1829

Remarks:

Changing AAA to UUU in pseudoknot loop at position 349 of CSFV IRES decreases the IRES activity.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 491

Version: `1`	Last change: `2008-07-04 13:49:40`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vitro The in vitro translation system:
rabbit reticulocytes lysate

The organism used for translation:

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

52.000

Name of IRES used as the positive control:

CSFV_1-442

Name of the plasmid used as the positive control. `pXLCSFV1-442.NS`	Name of the plasmid used as the negative control. `pXL0S`
`IRESite Id` of the plasmid used as positive control. `359`	`IRESite Id` of the plasmid used as negative control. `356`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0`
The size (length) of intercistronic region in the positive control: `543`	The size (length) of intercistronic region in the negative control: `193`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_GpppG_cap_without_polyA_tail

Remarks:

Data from Table 2.

Citations:

Last change to the database: 2019-03-18 09:32:49 GMT+1