IRESite_Id:329 negative control plasmid pXLJCon

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `329`	Version: `5`
Originaly submitted by: Tomáš Mašek
Reviewed by: Tomáš Mašek	Last change: `2008-05-28 17:59:29`

IRESite record type:

negative_control_plasmid_with_promoter_and_without_putative_IRES

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:

In vitro transcribed bicistronic mRNA encoding B2 cyclin and NS protein as the first and the second cistron,
respectively.

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 CGACGAGCTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GGTACCATGG ATCCCAGCTT TCAGGTAGAT TGCTTTCTTT GGCATGTCCG CAAACGAGTT GCAGACCAAG AACTAGGTGA TGCCCCATTC CTTGATCGGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTCGCCGAGA TCAGAAATCC CTAAGAGGAA GGGGCAGCAC CCTCGGTCTG GACATCGAGA CAGCCACACG TGCTGGAAAG CAGATAGTGG AGCGGATTCT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GAAAGAAGAA TCCGATGAGG CACTTAAAAT GACCATGGCC TCTGTACCTG CGTCGCGTTA CCTAACTGAC ATGACTCTTG AGGAAATGTC AAGGGACTGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TCCATGCTCA TACCCAAGCA GAAAGTGGCA GGCCCTCTTT GTATCAGAAT GGACCAGGCG ATCATGGATA AGAACATCAT ACTGAAAGCG AACTTCAGTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGATTTTTGA CCGGCTGGAG ACTCTAATAT TGCTAAGGGC TTTCACCGAA GAGGGAGCAA TTGTTGGCGA AATTTCACCA TTGCCTTCTC TTCCAGGACA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TACTGCTGAG GATGTCAAAA ATGCAGTTGG AGTCCTCATC GGGGGACTTG AATGGAATGA TAACACAGTT CGAGTCTCTG AAACTCTACA GAGATTCGCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGGAGAAGCA GTAATGAGAA TGGGAGACCT CCACTCACTC CAAAACAGAA ACGAGAAATG GCGGGAACAA TTAGGTCAGA AGTTTGAAGA AATAAGATGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TTGATTGAAG AAGTGAGACA CAAACTGAAG ATAACAGAGA ATAGTTTTGA GCAAATAACA TTTATGCAAG CCTTACATCT ATTGCTTGAA GTGGAGCAAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AGATAAGAAC TTTCTCGTTT CAGCTTATTT AATAATAAAA AACACCCTTG TTTCTACTGG
^2201      ^2211      ^2221      ^2231      ^2241      ^2251

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pXLJCon The name of the promoter used to express this mRNA:
T7

Aliases of the plasmid name:

Alias: pXLJ0

Description of the plasmid (facultative for promoter-less plasmid records):
pXLJCon is derived from pGEM-2 (Promega) backbone (GI: 58197). It 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

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 GACGAGCTCG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GTACCATGGA TCCCAGCTTT CAGGTAGATT GCTTTCTTTG GCATGTCCGC AAACGAGTTG CAGACCAAGA ACTAGGTGAT GCCCCATTCC TTGATCGGCT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TCGCCGAGAT CAGAAATCCC TAAGAGGAAG GGGCAGCACC CTCGGTCTGG ACATCGAGAC AGCCACACGT GCTGGAAAGC AGATAGTGGA GCGGATTCTG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AAAGAAGAAT CCGATGAGGC ACTTAAAATG ACCATGGCCT CTGTACCTGC GTCGCGTTAC CTAACTGACA TGACTCTTGA GGAAATGTCA AGGGACTGGT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CCATGCTCAT ACCCAAGCAG AAAGTGGCAG GCCCTCTTTG TATCAGAATG GACCAGGCGA TCATGGATAA GAACATCATA CTGAAAGCGA ACTTCAGTGT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GATTTTTGAC CGGCTGGAGA CTCTAATATT GCTAAGGGCT TTCACCGAAG AGGGAGCAAT TGTTGGCGAA ATTTCACCAT TGCCTTCTCT TCCAGGACAT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ACTGCTGAGG ATGTCAAAAA TGCAGTTGGA GTCCTCATCG GGGGACTTGA ATGGAATGAT AACACAGTTC GAGTCTCTGA AACTCTACAG AGATTCGCTT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GGAGAAGCAG TAATGAGAAT GGGAGACCTC CACTCACTCC AAAACAGAAA CGAGAAATGG CGGGAACAAT TAGGTCAGAA GTTTGAAGAA ATAAGATGGT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TGATTGAAGA AGTGAGACAC AAACTGAAGA TAACAGAGAA TAGTTTTGAG CAAATAACAT TTATGCAAGC CTTACATCTA TTGCTTGAAG TGGAGCAAGA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GATAAGAACT TTCTCGTTTC AGCTTATTTA ATAATAAAAA ACACCCTTGT TTCTACTGGA ATTCCGTGTA TTC
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071

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

Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks):

part of the yet unknown plasmid sequence determined by IRESite curators

A promoter reported in cDNA corresponding to IRES sequence:
not tested 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: `1`	Last change: `2007-10-23 00:00:00`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek

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: `1`	Last change: `2007-10-23 00:00:00`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek

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

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):

1407-2087

Remarks:

IRESite notes about verification of plasmid sequence:
Plasmid DNA was digested by EcoRI/SalI giving fragments 4202/699 bp. Amplification with T7 and NS gene
specific primers (T7, ATACGACTCACTATAGGG,position within plasmid sequence:2785, NS_revseq,
CTGCAACTCGTTTGCGGAC, position within plasmid sequence:4263) gave one band of expected size. The partial
sequence of the vector and the partial sequence encoding bicistronic RNA was determined by sequencing (regions
2050-4584 and 4830-350 of plasmid sequence respectively). The rest of the sequence presented here was
reverse engineered with the help of authors description and Genbank entries (GI:58197 and GI:21693177).
There is one mutation detected in the vector backbone. More detailed data are annotated in the GenBank
formatted plasmid sequence file provided on this page above.

Citations:

Borman A., Jackson R. J. (1992) Initiation of translation of human rhinovirus RNA: mapping the internal ribosome entry site. Virology. 188(2):685-696

Meignin C., Bailly J. L., Arnaud F., Dastugue B., Vaury C. (2003) The 5' untranslated region and Gag product of Idefix, a long terminal repeat-retrotransposon from Drosophila melanogaster, act together to initiate a switch between translated and untranslated states of the genomic mRNA. Mol. Cell. Biol. 23(22):8246-8254

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