IRESite_Id:330 characteristics of idefix IRES studied in pXL-Id plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `330`	Version: `6`
Originaly submitted by: Tomáš Mašek
Reviewed by: Tomáš Mašek	Last change: `2008-05-28 18:00:12`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

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 containing Idefix IRES between B2 cyclin and NS protein cistrons.

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 ATCaattcGG TTCGGTGTTC TTCTCAAATA AAAAGATTGT AATCATTTAG TGAAATAAAA ATTATATTTT TTTCACTTAT AAATATTGCA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGTATTTAAT TGGCGCAGTC GGTAGGATCC AATAAAATAA AAGAGTCCTT TTAGTACGGT ACTGATCAAC TGAAGGATAT GCTATACGAC TAGCTATCCA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGATCAGCGA ATTAAAATAG TGATTCAAAA ATATTTTTTA ATCCGCAAAA GAATCTACGT GAAAGTAGTA TTCAAAATAA AATCCCGTGC GGTCGGAAAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAAAATTAAT TTAAATTTTT TAATTCCGAA ACTTAAAACC AAGTTTAAAG AAAACTTAAA ATCAAGAAAA CTTAAAACCA AGTTTAAAGA AAACTTAAAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCAAGAAAAC TAAAgACCAA GTTTAAAGAA AACTTAAgAT CAAGAAAACT TAAAACCAAG TTTAAAGAAA ACTCAAAATC AAGAAAACTT AAAaCCAAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TAAGCTccAG AAAACTAAAA GACATCATGG CAGTCCCACA ACgaattgat cCCAGCTTTC AGGTAGATTG CTTTCTTTGG CATGTCCGCA AACGAGTTGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGACCAAGAA CTAGGTGATG CCCCATTCCT TGATCGGCTT CGCCGAGATC AGAAATCCCT AAGAGGAAGG GGCAGCACCC TCGGTCTGGA CATCGAGACA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCCACACGTG CTGGAAAGCA GATAGTGGAG CGGATTCTGA AAGAAGAATC CGATGAGGCA CTTAAAATGA CCATGGCCTC TGTACCTGCG TCGCGTTACC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TAACTGACAT GACTCTTGAG GAAATGTCAA GGGACTGGTC CATGCTCATA CCCAAGCAGA AAGTGGCAGG CCCTCTTTGT ATCAGAATGG ACCAGGCGAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CATGGATAAG AACATCATAC TGAAAGCGAA CTTCAGTGTG ATTTTTGACC GGCTGGAGAC TCTAATATTG CTAAGGGCTT TCACCGAAGA GGGAGCAATT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GTTGGCGAAA TTTCACCATT GCCTTCTCTT CCAGGACATA CTGCTGAGGA TGTCAAAAAT GCAGTTGGAG TCCTCATCGG GGGACTTGAA TGGAATGATA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACACAGTTCG AGTCTCTGAA ACTCTACAGA GATTCGCTTG GAGAAGCAGT AATGAGAATG GGAGACCTCC ACTCACTCCA AAACAGAAAC GAGAAATGGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GGGAACAATT AGGTCAGAAG TTTGAAGAAA TAAGATGGTT GATTGAAGAA GTGAGACACA AACTGAAGAT AACAGAGAAT AGTTTTGAGC AAATAACATT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TATGCAAGCC TTACATCTAT TGCTTGAAGT GGAGCAAGAG ATAAGAACTT TCTCGTTTCA GCTTATTTAA TAATAAAAAA CACCCTTGTT TCTACTGG
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pXL-Id The name of the promoter used to express this mRNA:
T7

Description of the plasmid (facultative for promoter-less plasmid records):
pXL-Id is derivative of pXLJCon plasmid. It contains T7 and SP6 promoter sites and is typically used in in vitro transcription/translation assays. Bicistronic RNA is transcribed by T7 polymerase after vector linearization by EcoRI. IRES sequence (ranging from 502 to 1024 bp of Idefix sequence, GI: 4165192) was inserted as EcoRI filled-in fragment into BamHI digested and blunted pXLJCon plasmid.

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:
Id

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Drosophila melanogaster

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 TCaattcGGT TCGGTGTTCT TCTCAAATAA AAAGATTGTA ATCATTTAGT GAAATAAAAA TTATATTTTT TTCACTTATA AATATTGCAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GTATTTAATT GGCGCAGTCG GTAGGATCCA ATAAAATAAA AGAGTCCTTT TAGTACGGTA CTGATCAACT GAAGGATATG CTATACGACT AGCTATCCAA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GATCAGCGAA TTAAAATAGT GATTCAAAAA TATTTTTTAA TCCGCAAAAG AATCTACGTG AAAGTAGTAT TCAAAATAAA ATCCCGTGCG GTCGGAAACA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AAAATTAATT TAAATTTTTT AATTCCGAAA CTTAAAACCA AGTTTAAAGA AAACTTAAAA TCAAGAAAAC TTAAAACCAA GTTTAAAGAA AACTTAAAAT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CAAGAAAACT AAAgACCAAG TTTAAAGAAA ACTTAAgATC AAGAAAACTT AAAACCAAGT TTAAAGAAAA CTCAAAATCA AGAAAACTTA AAaCCAAAAT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AAGCTccAGA AAACTAAAAG ACATCATGGC AGTCCCACAA Cgaattgatc CCAGCTTTCA GGTAGATTGC TTTCTTTGGC ATGTCCGCAA ACGAGTTGCA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GACCAAGAAC TAGGTGATGC CCCATTCCTT GATCGGCTTC GCCGAGATCA GAAATCCCTA AGAGGAAGGG GCAGCACCCT CGGTCTGGAC ATCGAGACAG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CCACACGTGC TGGAAAGCAG ATAGTGGAGC GGATTCTGAA AGAAGAATCC GATGAGGCAC TTAAAATGAC CATGGCCTCT GTACCTGCGT CGCGTTACCT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AACTGACATG ACTCTTGAGG AAATGTCAAG GGACTGGTCC ATGCTCATAC CCAAGCAGAA AGTGGCAGGC CCTCTTTGTA TCAGAATGGA CCAGGCGATC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ATGGATAAGA ACATCATACT GAAAGCGAAC TTCAGTGTGA TTTTTGACCG GCTGGAGACT CTAATATTGC TAAGGGCTTT CACCGAAGAG GGAGCAATTG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TTGGCGAAAT TTCACCATTG CCTTCTCTTC CAGGACATAC TGCTGAGGAT GTCAAAAATG CAGTTGGAGT CCTCATCGGG GGACTTGAAT GGAATGATAA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CACAGTTCGA GTCTCTGAAA CTCTACAGAG ATTCGCTTGG AGAAGCAGTA ATGAGAATGG GAGACCTCCA CTCACTCCAA AACAGAAACG AGAAATGGCG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GGAACAATTA GGTCAGAAGT TTGAAGAAAT AAGATGGTTG ATTGAAGAAG TGAGACACAA ACTGAAGATA ACAGAGAATA GTTTTGAGCA AATAACATTT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ATGCAAGCCT TACATCTATT GCTTGAAGTG GAGCAAGAGA TAAGAACTTT CTCGTTTCAG CTTATTTAAT AATAAAAAAC ACCCTTGTTT CTACTGGAAT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TCCGTGTATT C
^5601      ^5611

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

part of the yet unknown plasmid sequence determined by IRESite curators

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: Tomáš Mašek

The abbreviated name of this ORF/gene:
B2

The description of the protein encoded in this ORF:
X. 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: 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 9 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):

1927-2625

Remarks:

IRESite notes about verification of plasmid sequence:
Plasmid DNA was digested by EcoRI/SalI giving fragments 4202/1237 bp. Amplification with T7 and NS gene
specific primers (T7, ATACGACTCACTATAGGG,position within plasmid sequence:2785, NS_revseq,CTGCAACTCGTTTGCGGAC,
position within plasmid sequence:4801) gave one band of expected size. The complete sequence of IRES and 5-
and 3- flanking regions was determined by sequencing (region 3800-5172 of plasmid sequence). The rest of the
sequence presented here was reverse engineered with the help of authors description and IRESite entry 329.
There is one mutation detected in the vector backbone and 5 mutation in Idefix IRES in respect to
GI:4165192. More detailed data are annotated in the GenBank formatted sequence file provided by this page
above.

Citations:

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

IRESs:

IRES:

Version: `3`	Last change: `2007-10-23 00:00:00`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek
The IRES name: `idefix`	The functional status of IRES: `functional`

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

1419-1942

How IRES boundaries were determined:
unknown

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `202`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `725`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-508`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `15`

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

GGTTCGGTGT TCTTCTCAAA TAAAAAGATT GTAATCATTT AGTGAAATAA AAATTATATT TTTTTCACTT ATAAATATTG CAAGTATTTA ATTGGCGCAG 
^1419      ^1429      ^1439      ^1449      ^1459      ^1469      ^1479      ^1489      ^1499      ^1509      

TCGGTAGGAT CCAATAAAAT AAAAGAGTCC TTTTAGTACG GTACTGATCA ACTGAAGGAT ATGCTATACG ACTAGCTATC CAAGATCAGC GAATTAAAAT 
^1519      ^1529      ^1539      ^1549      ^1559      ^1569      ^1579      ^1589      ^1599      ^1609      

AGTGATTCAA AAATATTTTT TAATCCGCAA AAGAATCTAC GTGAAAGTAG TATTCAAAAT AAAATCCCGT GCGGTCGGAA ACAAAAATTA ATTTAAATTT 
^1619      ^1629      ^1639      ^1649      ^1659      ^1669      ^1679      ^1689      ^1699      ^1709      

TTTAATTCCG AAACTTAAAA CCAAGTTTAA AGAAAACTTA AAATCAAGAA AACTTAAAAC CAAGTTTAAA GAAAACTTAA AATCAAGAAA ACTAAAgACC 
^1719      ^1729      ^1739      ^1749      ^1759      ^1769      ^1779      ^1789      ^1799      ^1809      

AAGTTTAAAG AAAACTTAAg ATCAAGAAAA CTTAAAACCA AGTTTAAAGA AAACTCAAAA TCAAGAAAAC TTAAAaCCAA AATAAGCTcc AGAAAACTAA 
^1819      ^1829      ^1839      ^1849      ^1859      ^1869      ^1879      ^1889      ^1899      ^1909      

AAGACATCAT GGCAGTCCCA CAAC
^1919      ^1929      ^1939

Citations:

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