IRESite: The database of experimentally verified IRES structures
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The nucleic acid data:
IRESite Id:
547
Version:
0
Originaly submitted by:
Martin Mokrejš
Submission date:
2008-12-20 19:48:51
Reviewed by:
Martin Mokrejš
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:
hopefully_full-length_mRNA
The mRNA/+RNA description:
In vitro T7 promoter based HpaI site run-off transcript of pF/R-wt plasmid.
The mRNA/+RNA sequence represented in the +DNA notation:
GGCTAGCCTC GAGATGGAAG ACGCCAAAAA CATAAAGAAA GGCCCGGCGC CATTCTATCC TCTAGAGGAT GGAACCGCTG GAGAGCAACT GCATAAGGCT ^1 ^11 ^21 ^31 ^41 ^51 ^61 ^71 ^81 ^91 ATGAAGAGAT ACGCCCTGGT TCCTGGAACA ATTGCTTTTA CAGATGCACA TATCGAGGTG AACATCACGT ACGCGGAAta CTTCGAAATG TCCGTTCGGT ^101 ^111 ^121 ^131 ^141 ^151 ^161 ^171 ^181 ^191 TGGCAGAAGC TATGAAACGA TATGGGCTGA ATACAAATCA CAGAATCGTC GTATGCAGTG AAAACTCTCT TCAATTCTTT ATGCCGGTGT TGGGCGCGTT ^201 ^211 ^221 ^231 ^241 ^251 ^261 ^271 ^281 ^291 ATTTATCGGA GTTGCAGTTG CGCCCGCGAA CGACATTTAT AATGAACGTG AATTGCTCAA CAGTATGAAC ATTTCGCAGC CTACCGTAGT GTTTGTTTCC ^301 ^311 ^321 ^331 ^341 ^351 ^361 ^371 ^381 ^391 AAAAAGGGGT TGCAAaAAAT TtTGAACGTG CAAAAAAAAT TACCAATAAT CCAGAAAATT ATTATCATGG ATTCTAAAAC GGATTACCAG GGATTTCAGT ^401 ^411 ^421 ^431 ^441 ^451 ^461 ^471 ^481 ^491 CGATGTACAC GTTCGTCACA TCTCATCTAC CTCCCGGTTT TAATGAATAC GATTTTGTAC CAGAGTCCTT TGATCGTGAC AAAACAATTG CACTGATAAT ^501 ^511 ^521 ^531 ^541 ^551 ^561 ^571 ^581 ^591 GAATTCCTCT GGATCTACTG GGTTACCTAA GGGTGTGGCC CTTCCGCATA GAACTGCCTG cgTCAGATTC TCGCATGCCA GAGATCCTAT TTTTGGCAAT ^601 ^611 ^621 ^631 ^641 ^651 ^661 ^671 ^681 ^691 CAAATCATTC CGGATACTGC GATTTTAAGT GTTGTTCCAT TCCATCACGG TTTTGGAATG TTTACTACAC TCGGATATTT GATATGTGGA TTTCGAGTCG ^701 ^711 ^721 ^731 ^741 ^751 ^761 ^771 ^781 ^791 TCTTAATGTA TAGATTTGAA GAAGAGCTGT TTTTACGATC CCTTCAGGAT TACAAAATTC AAAGTGCGTT GCTAGTACCA ACCCTATTTT CATTCTTCGC ^801 ^811 ^821 ^831 ^841 ^851 ^861 ^871 ^881 ^891 cAAAaGCACT CTGATTGACA AATACGATTT ATCTAATTTA CACGAAATTG CTTCTGGGGG CGCACCTCTT TCGAAAGAAG TCGGGGAAGC GGTTGCAAAA ^901 ^911 ^921 ^931 ^941 ^951 ^961 ^971 ^981 ^991 CGCTTCCATC TTCCAGGGAT ACGACAAGGA TATGGGCTCA CTGAGACTAC ATCAGCTATT CTGATTACAC CCGAGGGGGA TGATAAACCG GGCGCGGTCG ^1001 ^1011 ^1021 ^1031 ^1041 ^1051 ^1061 ^1071 ^1081 ^1091 GTAAAGTTGT TCCATTTTTT GAAGCGAAGG TTGTGGATCT GgaTACCGGG AAAACGCTGG GCGTTAATCA GAGAGGCGAA TTATGTGTCA GAGGACCTAT ^1101 ^1111 ^1121 ^1131 ^1141 ^1151 ^1161 ^1171 ^1181 ^1191 GATTATGTCC GGTTATGTAA ACAATCCGGA AGCGACCAAC GCCTTGATTG ACAAGGATGG ATGGCTACAT TCTGGAGACA TAGCTTACTG GGACGAAGAC ^1201 ^1211 ^1221 ^1231 ^1241 ^1251 ^1261 ^1271 ^1281 ^1291 GAACACTTCT TCATAGTTGA CCGCTTGAAG TCTTTAATTA AATACAAAGG ATATCAGGTG GCCCCCGCTG AATTGGAATC GATatTGTTA CAACACCCCA ^1301 ^1311 ^1321 ^1331 ^1341 ^1351 ^1361 ^1371 ^1381 ^1391 ACATCTTCGA CGCGGGCGTG GCAGGTCTTC CCGACGATGA CGCCGGTGAA CTTCCCGCCG CCGTTGTTGT TTTGGAGCAC GGAAAGACGA TGACGGAAAA ^1401 ^1411 ^1421 ^1431 ^1441 ^1451 ^1461 ^1471 ^1481 ^1491 AGAGATCGTG GATTACGTGG CCAGTCAAGT AACAACCGCG AAAAAGTTGC GCGGAGGAGT TGTGTTTGTG GACGAAGTAC CGAAAGGTCT TACCGGAAAA ^1501 ^1511 ^1521 ^1531 ^1541 ^1551 ^1561 ^1571 ^1581 ^1591 CTCGACGCAA GAAAAATCAG AGAgaTCCTC ATAAAGGCCA AGAAGGGCGG AAAGTCCAAA TTGTAATAAA CGCGTCGAGC ATGCATCTAG GGCGGCCAAT ^1601 ^1611 ^1621 ^1631 ^1641 ^1651 ^1661 ^1671 ^1681 ^1691 TCCGCCCCTC TCCCCCCCAC CCCTCTCCCT CCCCCCCCCC TAACGTTACT GGCCGAAGCC GCTTGGAATA AGGCCGGTGT GCGTTTGTCT ATATGTTATT ^1701 ^1711 ^1721 ^1731 ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 TTCCACCATA TTGCCGTCTT TTGGCAATGT GAGGGCCCGG AAACCTGGCC CTGTCTTCTT GACGAGCATT CCTAGGGGTC TTTCCCCTCT CGCCAAAGGA ^1801 ^1811 ^1821 ^1831 ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 ATGCAAGGTC TGTTGAATGT CGTGAAGGAA GCAGTTCCTC TGGAAGCTTC TTGAAGACAA ACAACGTCTG TAGCGACCCT TTGCAGGCAG CGGAACCCCC ^1901 ^1911 ^1921 ^1931 ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 CACCTGGCGA CAGGTGCCTC TGCGGCCAAA AGCCACGTGT ATAAGATACA CCTGCAAAGG CGGCACAACC CCAGTGCCAC GTTGTGAGTT GGATAGTTGT ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 GGAAAGAGTC AAATGGCTCT CCTCAAGCGT ATTCAACAAG GGGCTGAAGG ATGCCCAGAA GGTACCCCAT TGTATGGGAT CTGATCTGGG GCCTCGGTGC ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 ACATGCTTTA CATGTGTTTA GTCGAGGTTA AAAAACGTCT AGGCCCCCCG AACCACGGGG ACGTGGTTTT CCTTTGAAAA ACACGATGAT AATATGACTT ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261 ^2271 ^2281 ^2291 CGAAAGTTTA TGATCCAGAA CAAAGGAAAC GGATGATAAC TGGTCCGCAG TGGTGGGCCA GATGTAAACA AATGAATGTT CTTGATTCAT TTATTAATTA ^2301 ^2311 ^2321 ^2331 ^2341 ^2351 ^2361 ^2371 ^2381 ^2391 TTATGATTCA GAAAAACATG CAGAAAATGC TGTTATTTTT TTACATGGTA ACGCGGCCTC TTCTTATTTA TGGCGACATG TTGTGCCACA TATTGAGCCA ^2401 ^2411 ^2421 ^2431 ^2441 ^2451 ^2461 ^2471 ^2481 ^2491 GTAGCGCGGT GTATTATACC AGACCTTATT GGTATGGGCA AATCAGGCAA ATCTGGTAAT GGTTCTTATA GGTTACTTGA TCATTACAAA TATCTTACTG ^2501 ^2511 ^2521 ^2531 ^2541 ^2551 ^2561 ^2571 ^2581 ^2591 CATGGTTTGA ACTTCTTAAT TTACCAAAGA AGATCATTTT TGTCGGCCAT GATTGGGGTG CTTGTTTGGC ATTTCATTAT AGCTATGAGC ATCAAGATAA ^2601 ^2611 ^2621 ^2631 ^2641 ^2651 ^2661 ^2671 ^2681 ^2691 GATCAAAGCA ATAGTTCACG CTGAAAGTGT AGTAGATGTG ATTGAATCAT GGGATGAATG GCCTGATATT GAAGAAGATA TTGCGTTGAT CAAATCTGAA ^2701 ^2711 ^2721 ^2731 ^2741 ^2751 ^2761 ^2771 ^2781 ^2791 GAAGGAGAAA AAATGGTTTT GGAGAATAAC TTCTTCGTGG AAACCATGTT GCCATCAAAA ATCATGAGAA AGTTAGAACC AGAAGAATTT GCAGCATATC ^2801 ^2811 ^2821 ^2831 ^2841 ^2851 ^2861 ^2871 ^2881 ^2891 TTGAACCATT CAAAGAGAAA GGTGAAGTTC GTCGTCCAAC ATTATCATGG CCTCGTGAAA TCCCGTTAGT AAAAGGTGGT AAACCTGACG TTGTACAAAT ^2901 ^2911 ^2921 ^2931 ^2941 ^2951 ^2961 ^2971 ^2981 ^2991 TGTTAGGAAT TATAATGCTT ATCTACGTGC AAGTGATGAT TTACCAAAAA TGTTTATTGA ATCGGACCCA GGATTCTTTT CCAATGCTAT TGTTGAAGGT ^3001 ^3011 ^3021 ^3031 ^3041 ^3051 ^3061 ^3071 ^3081 ^3091 GCCAAGAAGT TTCCTAATAC TGAATTTGTC AAAGTAAAAG GTCTTCATTT TTCGCAAGAA GATGCACCTG ATGAAATGGG AAAATATATC AAATCGTTCG ^3101 ^3111 ^3121 ^3131 ^3141 ^3151 ^3161 ^3171 ^3181 ^3191 TTGAGCGAGT TCTCAAAAAT GAACAATAAT AACCCGGGAT CCTCTAGAGT CGACCCGGGC GGCCGCTTCC CTTTAGTGAG GGTTAATGCT TCGAGCAGAC ^3201 ^3211 ^3221 ^3231 ^3241 ^3251 ^3261 ^3271 ^3281 ^3291 ATGATAAGAT ACATTGATGA GTTTGGACAA ACCACAACTA GAATGCAGTG AAAAAAATGC TTTATTTGTG AAATTTGTGA TGCTATTGCT TTATTTGTAA ^3301 ^3311 ^3321 ^3331 ^3341 ^3351 ^3361 ^3371 ^3381 ^3391 CCATTATAAG CTGCAATAAA CAAGTT ^3401 ^3411 ^3421
Credibility of mRNA sequence:
end-to-end_sequence_reverse_engineered_and_should_match_experiment
The name of the plasmid:
pF/R-wt
The name of the promoter used to express this mRNA:
T7
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:
EMCV-R
The origin of IRES in the plasmid:
viral
The donor organism of the IRES segment:
Encephalomyocarditis virus Rueckert
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:
TCAATATTGG CCATTAGCCA TATTATTCAT TGGTTATATA GCATAAATCA ATATTGGCTA TTGGCCATTG CATACGTTGT ATCTATATCA TAATATGTAC ^1 ^11 ^21 ^31 ^41 ^51 ^61 ^71 ^81 ^91 ATTTATATTG GCTCATGTCC AATATGACCG CCATGTTGGC ATTGATTATT GACTAGTTAT TAATAGTAAT CAATTACGGG GTCATTAGTT CATAGCCCAT ^101 ^111 ^121 ^131 ^141 ^151 ^161 ^171 ^181 ^191 ATATGGAGTT CCGCGTTACA TAACTTACGG TAAATGGCCC GCCTGGCTGA CCGCCCAACG ACCCCCGCCC ATTGACGTCA ATAATGACGT ATGTTCCCAT ^201 ^211 ^221 ^231 ^241 ^251 ^261 ^271 ^281 ^291 AGTAACGCCA ATAGGGACTT TCCATTGACG TCAATGGGTG GAGTATTTAC GGTAAACTGC CCACTTGGCA GTACATCAAG TGTATCATAT GCCAAGTCCG ^301 ^311 ^321 ^331 ^341 ^351 ^361 ^371 ^381 ^391 CCCCCTATTG ACGTCAATGA CGGTAAATGG CCCGCCTGGC ATTATGCCCA GTACATGACC TTACGGGACT TTCCTACTTG GCAGTACATC TACGTATTAG ^401 ^411 ^421 ^431 ^441 ^451 ^461 ^471 ^481 ^491 TCATCGCTAT TACCATGGTG ATGCGGTTTT GGCAGTACAC CAATGGGCGT GGATAGCGGT TTGACTCACG GGGATTTCCA AGTCTCCACC CCATTGACGT ^501 ^511 ^521 ^531 ^541 ^551 ^561 ^571 ^581 ^591 CAATGGGAGT TTGTTTTGGC ACCAAAATCA ACGGGACTTT CCAAAATGTC GTAACAACTG CGATCGCCCG CCCCGTTGAC GCAAATGGGC GGTAGGCGTG ^601 ^611 ^621 ^631 ^641 ^651 ^661 ^671 ^681 ^691 TACGGTGGGA GGTCTATATA AGCAGAGCTC GTTTAGTGAA CCGTCAGATC ACTAGAAGCT TTATTGCGGT AGTTTATCAC AGTTAAATTG CTAACGCAGT ^701 ^711 ^721 ^731 ^741 ^751 ^761 ^771 ^781 ^791 CAGTGCTTCT GACACAACAG TCTCGAACTT AAGCTGCAGT GACTCTCTTA AGGTAGCCTT GCAGAAGTTG GTCGTGAGGC ACTGGGCAGG TAAGTATCAA ^801 ^811 ^821 ^831 ^841 ^851 ^861 ^871 ^881 ^891 GGTTACAAGA CAGGTTTAAG GAGACCAATA GAAACTGGGC TTGTCGAGAC AGAGAAGACT CTTGCGTTTC TGATAGGCAC CTATTGGTCT TACTGACATC ^901 ^911 ^921 ^931 ^941 ^951 ^961 ^971 ^981 ^991 CACTTTGCCT TTCTCTCCAC AGGTGTCCAC TCCCAGTTCA ATTACAGCTC TTAAGGCTAG AGTACTTAAT ACGACTCACT ATAGGCTAGC CTCGAGATGG ^1001 ^1011 ^1021 ^1031 ^1041 ^1051 ^1061 ^1071 ^1081 ^1091 AAGACGCCAA AAACATAAAG AAAGGCCCGG CGCCATTCTA TCCTCTAGAG GATGGAACCG CTGGAGAGCA ACTGCATAAG GCTATGAAGA GATACGCCCT ^1101 ^1111 ^1121 ^1131 ^1141 ^1151 ^1161 ^1171 ^1181 ^1191 GGTTCCTGGA ACAATTGCTT TTACAGATGC ACATATCGAG GTGAACATCA CGTACGCGGA AtaCTTCGAA ATGTCCGTTC GGTTGGCAGA AGCTATGAAA ^1201 ^1211 ^1221 ^1231 ^1241 ^1251 ^1261 ^1271 ^1281 ^1291 CGATATGGGC TGAATACAAA TCACAGAATC GTCGTATGCA GTGAAAACTC TCTTCAATTC TTTATGCCGG TGTTGGGCGC GTTATTTATC GGAGTTGCAG ^1301 ^1311 ^1321 ^1331 ^1341 ^1351 ^1361 ^1371 ^1381 ^1391 TTGCGCCCGC GAACGACATT TATAATGAAC GTGAATTGCT CAACAGTATG AACATTTCGC AGCCTACCGT AGTGTTTGTT TCCAAAAAGG GGTTGCAAaA ^1401 ^1411 ^1421 ^1431 ^1441 ^1451 ^1461 ^1471 ^1481 ^1491 AATTtTGAAC GTGCAAAAAA AATTACCAAT AATCCAGAAA ATTATTATCA TGGATTCTAA AACGGATTAC CAGGGATTTC AGTCGATGTA CACGTTCGTC ^1501 ^1511 ^1521 ^1531 ^1541 ^1551 ^1561 ^1571 ^1581 ^1591 ACATCTCATC TACCTCCCGG TTTTAATGAA TACGATTTTG TACCAGAGTC CTTTGATCGT GACAAAACAA TTGCACTGAT AATGAATTCC TCTGGATCTA ^1601 ^1611 ^1621 ^1631 ^1641 ^1651 ^1661 ^1671 ^1681 ^1691 CTGGGTTACC TAAGGGTGTG GCCCTTCCGC ATAGAACTGC CTGcgTCAGA TTCTCGCATG CCAGAGATCC TATTTTTGGC AATCAAATCA TTCCGGATAC ^1701 ^1711 ^1721 ^1731 ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 TGCGATTTTA AGTGTTGTTC CATTCCATCA CGGTTTTGGA ATGTTTACTA CACTCGGATA TTTGATATGT GGATTTCGAG TCGTCTTAAT GTATAGATTT ^1801 ^1811 ^1821 ^1831 ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 GAAGAAGAGC TGTTTTTACG ATCCCTTCAG GATTACAAAA TTCAAAGTGC GTTGCTAGTA CCAACCCTAT TTTCATTCTT CGCcAAAaGC ACTCTGATTG ^1901 ^1911 ^1921 ^1931 ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 ACAAATACGA TTTATCTAAT TTACACGAAA TTGCTTCTGG GGGCGCACCT CTTTCGAAAG AAGTCGGGGA AGCGGTTGCA AAACGCTTCC ATCTTCCAGG ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 GATACGACAA GGATATGGGC TCACTGAGAC TACATCAGCT ATTCTGATTA CACCCGAGGG GGATGATAAA CCGGGCGCGG TCGGTAAAGT TGTTCCATTT ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 TTTGAAGCGA AGGTTGTGGA TCTGgaTACC GGGAAAACGC TGGGCGTTAA TCAGAGAGGC GAATTATGTG TCAGAGGACC TATGATTATG TCCGGTTATG ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261 ^2271 ^2281 ^2291 TAAACAATCC GGAAGCGACC AACGCCTTGA TTGACAAGGA TGGATGGCTA CATTCTGGAG ACATAGCTTA CTGGGACGAA GACGAACACT TCTTCATAGT ^2301 ^2311 ^2321 ^2331 ^2341 ^2351 ^2361 ^2371 ^2381 ^2391 TGACCGCTTG AAGTCTTTAA TTAAATACAA AGGATATCAG GTGGCCCCCG CTGAATTGGA ATCGATatTG TTACAACACC CCAACATCTT CGACGCGGGC ^2401 ^2411 ^2421 ^2431 ^2441 ^2451 ^2461 ^2471 ^2481 ^2491 GTGGCAGGTC TTCCCGACGA TGACGCCGGT GAACTTCCCG CCGCCGTTGT TGTTTTGGAG CACGGAAAGA CGATGACGGA AAAAGAGATC GTGGATTACG ^2501 ^2511 ^2521 ^2531 ^2541 ^2551 ^2561 ^2571 ^2581 ^2591 TGGCCAGTCA AGTAACAACC GCGAAAAAGT TGCGCGGAGG AGTTGTGTTT GTGGACGAAG TACCGAAAGG TCTTACCGGA AAACTCGACG CAAGAAAAAT ^2601 ^2611 ^2621 ^2631 ^2641 ^2651 ^2661 ^2671 ^2681 ^2691 CAGAGAgaTC CTCATAAAGG CCAAGAAGGG CGGAAAGTCC AAATTGTAAT AAACGCGTCG AGCATGCATC TAGGGCGGCC AATTCCGCCC CTCTCCCCCC ^2701 ^2711 ^2721 ^2731 ^2741 ^2751 ^2761 ^2771 ^2781 ^2791 CACCCCTCTC CCTCCCCCCC CCCTAACGTT ACTGGCCGAA GCCGCTTGGA ATAAGGCCGG TGTGCGTTTG TCTATATGTT ATTTTCCACC ATATTGCCGT ^2801 ^2811 ^2821 ^2831 ^2841 ^2851 ^2861 ^2871 ^2881 ^2891 CTTTTGGCAA TGTGAGGGCC CGGAAACCTG GCCCTGTCTT CTTGACGAGC ATTCCTAGGG GTCTTTCCCC TCTCGCCAAA GGAATGCAAG GTCTGTTGAA ^2901 ^2911 ^2921 ^2931 ^2941 ^2951 ^2961 ^2971 ^2981 ^2991 TGTCGTGAAG GAAGCAGTTC CTCTGGAAGC TTCTTGAAGA CAAACAACGT CTGTAGCGAC CCTTTGCAGG CAGCGGAACC CCCCACCTGG CGACAGGTGC ^3001 ^3011 ^3021 ^3031 ^3041 ^3051 ^3061 ^3071 ^3081 ^3091 CTCTGCGGCC AAAAGCCACG TGTATAAGAT ACACCTGCAA AGGCGGCACA ACCCCAGTGC CACGTTGTGA GTTGGATAGT TGTGGAAAGA GTCAAATGGC ^3101 ^3111 ^3121 ^3131 ^3141 ^3151 ^3161 ^3171 ^3181 ^3191 TCTCCTCAAG CGTATTCAAC AAGGGGCTGA AGGATGCCCA GAAGGTACCC CATTGTATGG GATCTGATCT GGGGCCTCGG TGCACATGCT TTACATGTGT ^3201 ^3211 ^3221 ^3231 ^3241 ^3251 ^3261 ^3271 ^3281 ^3291 TTAGTCGAGG TTAAAAAACG TCTAGGCCCC CCGAACCACG GGGACGTGGT TTTCCTTTGA AAAACACGAT GATAATATGA CTTCGAAAGT TTATGATCCA ^3301 ^3311 ^3321 ^3331 ^3341 ^3351 ^3361 ^3371 ^3381 ^3391 GAACAAAGGA AACGGATGAT AACTGGTCCG CAGTGGTGGG CCAGATGTAA ACAAATGAAT GTTCTTGATT CATTTATTAA TTATTATGAT TCAGAAAAAC ^3401 ^3411 ^3421 ^3431 ^3441 ^3451 ^3461 ^3471 ^3481 ^3491 ATGCAGAAAA TGCTGTTATT TTTTTACATG GTAACGCGGC CTCTTCTTAT TTATGGCGAC ATGTTGTGCC ACATATTGAG CCAGTAGCGC GGTGTATTAT ^3501 ^3511 ^3521 ^3531 ^3541 ^3551 ^3561 ^3571 ^3581 ^3591 ACCAGACCTT ATTGGTATGG GCAAATCAGG CAAATCTGGT AATGGTTCTT ATAGGTTACT TGATCATTAC AAATATCTTA CTGCATGGTT TGAACTTCTT ^3601 ^3611 ^3621 ^3631 ^3641 ^3651 ^3661 ^3671 ^3681 ^3691 AATTTACCAA AGAAGATCAT TTTTGTCGGC CATGATTGGG GTGCTTGTTT GGCATTTCAT TATAGCTATG AGCATCAAGA TAAGATCAAA GCAATAGTTC ^3701 ^3711 ^3721 ^3731 ^3741 ^3751 ^3761 ^3771 ^3781 ^3791 ACGCTGAAAG TGTAGTAGAT GTGATTGAAT CATGGGATGA ATGGCCTGAT ATTGAAGAAG ATATTGCGTT GATCAAATCT GAAGAAGGAG AAAAAATGGT ^3801 ^3811 ^3821 ^3831 ^3841 ^3851 ^3861 ^3871 ^3881 ^3891 TTTGGAGAAT AACTTCTTCG TGGAAACCAT GTTGCCATCA AAAATCATGA GAAAGTTAGA ACCAGAAGAA TTTGCAGCAT ATCTTGAACC ATTCAAAGAG ^3901 ^3911 ^3921 ^3931 ^3941 ^3951 ^3961 ^3971 ^3981 ^3991 AAAGGTGAAG TTCGTCGTCC AACATTATCA TGGCCTCGTG AAATCCCGTT AGTAAAAGGT GGTAAACCTG ACGTTGTACA AATTGTTAGG AATTATAATG ^4001 ^4011 ^4021 ^4031 ^4041 ^4051 ^4061 ^4071 ^4081 ^4091 CTTATCTACG TGCAAGTGAT GATTTACCAA AAATGTTTAT TGAATCGGAC CCAGGATTCT TTTCCAATGC TATTGTTGAA GGTGCCAAGA AGTTTCCTAA ^4101 ^4111 ^4121 ^4131 ^4141 ^4151 ^4161 ^4171 ^4181 ^4191 TACTGAATTT GTCAAAGTAA AAGGTCTTCA TTTTTCGCAA GAAGATGCAC CTGATGAAAT GGGAAAATAT ATCAAATCGT TCGTTGAGCG AGTTCTCAAA ^4201 ^4211 ^4221 ^4231 ^4241 ^4251 ^4261 ^4271 ^4281 ^4291 AATGAACAAT AATAACCCGG GATCCTCTAG AGTCGACCCG GGCGGCCGCT TCCCTTTAGT GAGGGTTAAT GCTTCGAGCA GACATGATAA GATACATTGA ^4301 ^4311 ^4321 ^4331 ^4341 ^4351 ^4361 ^4371 ^4381 ^4391 TGAGTTTGGA CAAACCACAA CTAGAATGCA GTGAAAAAAA TGCTTTATTT GTGAAATTTG TGATGCTATT GCTTTATTTG TAACCATTAT AAGCTGCAAT ^4401 ^4411 ^4421 ^4431 ^4441 ^4451 ^4461 ^4471 ^4481 ^4491 AAACAAGTTA ACAACAACAA TTGCATTCAT TTTATGTTTC AGGTTCAGGG GGAGATGTGG GAGGTTTTTT AAAGCAAGTA AAACCTCTAC AAATGTGGTA ^4501 ^4511 ^4521 ^4531 ^4541 ^4551 ^4561 ^4571 ^4581 ^4591 AAATCCGATA AGGATCGATC CGGGCTGGCG TAATAGCGAA GAGGCCCGCA CCGATCGCCC TTCCCAACAG TTGCGCAGCC TGAATGGCGA ATGGACGCGC ^4601 ^4611 ^4621 ^4631 ^4641 ^4651 ^4661 ^4671 ^4681 ^4691 CCTGTAGCGG CGCATTAAGC GCGGCGGGTG TGGTGGTTAC GCGCAGCGTG ACCGCTACAC TTGCCAGCGC CCTAGCGCCC GCTCCTTTCG CTTTCTTCCC ^4701 ^4711 ^4721 ^4731 ^4741 ^4751 ^4761 ^4771 ^4781 ^4791 TTCCTTTCTC GCCACGTTCG CCGGCTTTCC CCGTCAAGCT CTAAATCGGG GGCTCCCTTT AGGGTTCCGA TTTAGAGCTT TACGGCACCT CGACCGCAAA ^4801 ^4811 ^4821 ^4831 ^4841 ^4851 ^4861 ^4871 ^4881 ^4891 AAACTTGATT TGGGTGATGG TTCACGTAGT GGGCCATCGC CCTGATAGAC GGTTTTTCGC CCTTTGACGT TGGAGTCCAC GTTCTTTAAT AGTGGACTCT ^4901 ^4911 ^4921 ^4931 ^4941 ^4951 ^4961 ^4971 ^4981 ^4991 TGTTCCAAAC TGGAACAACA CTCAACCCTA TCTCGGTCTA TTCTTTTGAT TTATAAGGGA TTTTGCCGAT TTCGGCCTAT TGGTTAAAAA ATGAGCTGAT ^5001 ^5011 ^5021 ^5031 ^5041 ^5051 ^5061 ^5071 ^5081 ^5091 TTAACAAATA TTTAACGCGA ATTTTAACAA AATATTAACG TTTACAATTT CGCCTGATGC GGTATTTTCT CCTTACGCAT CTGTGCGGTA TTTCACACCG ^5101 ^5111 ^5121 ^5131 ^5141 ^5151 ^5161 ^5171 ^5181 ^5191 CATACGCGGA TCTGCGCAGC ACCATGGCCT GAAATAACCT CTGAAAGAGG AACTTGGTTA GGTACCTTCT GAGGCGGAAA GAACCAGCTG TGGAATGTGT ^5201 ^5211 ^5221 ^5231 ^5241 ^5251 ^5261 ^5271 ^5281 ^5291 GTCAGTTAGG GTGTGGAAAG TCCCCAGGCT CCCCAGCAGG CAGAAGTATG CAAAGCATGC ATCTCAATTA GTCAGCAACC AGGTGTGGAA AGTCCCCAGG ^5301 ^5311 ^5321 ^5331 ^5341 ^5351 ^5361 ^5371 ^5381 ^5391 CTCCCCAGCA GGCAGAAGTA TGCAAAGCAT GCATCTCAAT TAGTCAGCAA CCATAGTCCC GCCCCTAACT CCGCCCATCC CGCCCCTAAC TCCGCCCAGT ^5401 ^5411 ^5421 ^5431 ^5441 ^5451 ^5461 ^5471 ^5481 ^5491 TCCGCCCATT CTCCGCCCCA TGGCTGACTA ATTTTTTTTA TTTATGCAGA GGCCGAGGCC GCCTCGGCCT CTGAGCTATT CCAGAAGTAG TGAGGAGGCT ^5501 ^5511 ^5521 ^5531 ^5541 ^5551 ^5561 ^5571 ^5581 ^5591 TTTTTGGAGG CCTAGGCTTT TGCAAAAAGC TTGATTCTTC TGACACAACA GTCTCGAACT TAAGGCTAGA GCCACCATGA TTGAACAAGA TGGATTGCAC ^5601 ^5611 ^5621 ^5631 ^5641 ^5651 ^5661 ^5671 ^5681 ^5691 GCAGGTTCTC CGGCCGCTTG GGTGGAGAGG CTATTCGGCT ATGACTGGGC ACAACAGACA ATCGGCTGCT CTGATGCCGC CGTGTTCCGG CTGTCAGCGC ^5701 ^5711 ^5721 ^5731 ^5741 ^5751 ^5761 ^5771 ^5781 ^5791 AGGGGCGCCC GGTTCTTTTT GTCAAGACCG ACCTGTCCGG TGCCCTGAAT GAACTGCAGG ACGAGGCAGC GCGGCTATCG TGGCTGGCCA CGACGGGCGT ^5801 ^5811 ^5821 ^5831 ^5841 ^5851 ^5861 ^5871 ^5881 ^5891 TCCTTGCGCA GCTGTGCTCG ACGTTGTCAC TGAAGCGGGA AGGGACTGGC TGCTATTGGG CGAAGTGCCG GGGCAGGATC TCCTGTCATC TCACCTTGCT ^5901 ^5911 ^5921 ^5931 ^5941 ^5951 ^5961 ^5971 ^5981 ^5991 CCTGCCGAGA AAGTATCCAT CATGGCTGAT GCAATGCGGC GGCTGCATAC GCTTGATCCG GCTACCTGCC CATTCGACCA CCAAGCGAAA CATCGCATCG ^6001 ^6011 ^6021 ^6031 ^6041 ^6051 ^6061 ^6071 ^6081 ^6091 AGCGAGCACG TACTCGGATG GAAGCCGGTC TTGTCGATCA GGATGATCTG GACGAAGAGC ATCAGGGGCT CGCGCCAGCC GAACTGTTCG CCAGGCTCAA ^6101 ^6111 ^6121 ^6131 ^6141 ^6151 ^6161 ^6171 ^6181 ^6191 GGCGCGCATG CCCGACGGCG AGGATCTCGT CGTGACCCAT GGCGATGCCT GCTTGCCGAA TATCATGGTG GAAAATGGCC GCTTTTCTGG ATTCATCGAC ^6201 ^6211 ^6221 ^6231 ^6241 ^6251 ^6261 ^6271 ^6281 ^6291 TGTGGCCGGC TGGGTGTGGC GGACCGCTAT CAGGACATAG CGTTGGCTAC CCGTGATATT GCTGAAGAGC TTGGCGGCGA ATGGGCTGAC CGCTTCCTCG ^6301 ^6311 ^6321 ^6331 ^6341 ^6351 ^6361 ^6371 ^6381 ^6391 TGCTTTACGG TATCGCCGCT CCCGATTCGC AGCGCATCGC CTTCTATCGC CTTCTTGACG AGTTCTTCTG AGCGGGACTC TGGGGTTCGA AATGACCGAC ^6401 ^6411 ^6421 ^6431 ^6441 ^6451 ^6461 ^6471 ^6481 ^6491 CAAGCGACGC CCAACCTGCC ATCACGATGG CCGCAATAAA ATATCTTTAT TTTCATTACA TCTGTGTGTT GGTTTTTTGT GTGAATCGAT AGCGATAAGG ^6501 ^6511 ^6521 ^6531 ^6541 ^6551 ^6561 ^6571 ^6581 ^6591 ATCCGCGTAT GGTGCACTCT CAGTACAATC TGCTCTGATG CCGCATAGTT AAGCCAGCCC CGACACCCGC CAACACCCGC TGACGCGCCC TGACGGGCTT ^6601 ^6611 ^6621 ^6631 ^6641 ^6651 ^6661 ^6671 ^6681 ^6691 GTCTGCTCCC GGCATCCGCT TACAGACAAG CTGTGACCGT CTCCGGGAGC TGCATGTGTC AGAGGTTTTC ACCGTCATCA CCGAAACGCG CGAGACGAAA ^6701 ^6711 ^6721 ^6731 ^6741 ^6751 ^6761 ^6771 ^6781 ^6791 GGGCCTCGTG ATACGCCTAT TTTTATAGGT TAATGTCATG ATAATAATGG TTTCTTAGAC GTCAGGTGGC ACTTTTCGGG GAAATGTGCG CGGAACCCCT ^6801 ^6811 ^6821 ^6831 ^6841 ^6851 ^6861 ^6871 ^6881 ^6891 ATTTGTTTAT TTTTCTAAAT ACATTCAAAT ATGTATCCGC TCATGAGACA ATAACCCTGA TAAATGCTTC AATAATATTG AAAAAGGAAG AGTATGAGTA ^6901 ^6911 ^6921 ^6931 ^6941 ^6951 ^6961 ^6971 ^6981 ^6991 TTCAACATTT CCGTGTCGCC CTTATTCCCT TTTTTGCGGC ATTTTGCCTT CCTGTTTTTG CTCACCCAGA AACGCTGGTG AAAGTAAAAG ATGCTGAAGA ^7001 ^7011 ^7021 ^7031 ^7041 ^7051 ^7061 ^7071 ^7081 ^7091 TCAGTTGGGT GCACGAGTGG GTTACATCGA ACTGGATCTC AACAGCGGTA AGATCCTTGA GAGTTTTCGC CCCGAAGAAC GTTTTCCAAT GATGAGCACT ^7101 ^7111 ^7121 ^7131 ^7141 ^7151 ^7161 ^7171 ^7181 ^7191 TTTAAAGTTC TGCTATGTGG CGCGGTATTA TCCCGTATTG ACGCCGGGCA AGAGCAACTC GGTCGCCGCA TACACTATTC TCAGAATGAC TTGGTTGAGT ^7201 ^7211 ^7221 ^7231 ^7241 ^7251 ^7261 ^7271 ^7281 ^7291 ACTCACCAGT CACAGAAAAG CATCTTACGG ATGGCATGAC AGTAAGAGAA TTATGCAGTG CTGCCATAAC CATGAGTGAT AACACTGCGG CCAACTTACT ^7301 ^7311 ^7321 ^7331 ^7341 ^7351 ^7361 ^7371 ^7381 ^7391 TCTGACAACG ATCGGAGGAC CGAAGGAGCT AACCGCTTTT TTGCACAACA TGGGGGATCA TGTAACTCGC CTTGATCGTT GGGAACCGGA GCTGAATGAA ^7401 ^7411 ^7421 ^7431 ^7441 ^7451 ^7461 ^7471 ^7481 ^7491 GCCATACCAA ACGACGAGCG TGACACCACG ATGCCTGTAG CAATGGCAAC AACGTTGCGC AAACTATTAA CTGGCGAACT ACTTACTCTA GCTTCCCGGC ^7501 ^7511 ^7521 ^7531 ^7541 ^7551 ^7561 ^7571 ^7581 ^7591 AACAATTAAT AGACTGGATG GAGGCGGATA AAGTTGCAGG ACCACTTCTG CGCTCGGCCC TTCCGGCTGG CTGGTTTATT GCTGATAAAT CTGGAGCCGG ^7601 ^7611 ^7621 ^7631 ^7641 ^7651 ^7661 ^7671 ^7681 ^7691 TGAGCGTGGG TCTCGCGGTA TCATTGCAGC ACTGGGGCCA GATGGTAAGC CCTCCCGTAT CGTAGTTATC TACACGACGG GGAGTCAGGC AACTATGGAT ^7701 ^7711 ^7721 ^7731 ^7741 ^7751 ^7761 ^7771 ^7781 ^7791 GAACGAAATA GACAGATCGC TGAGATAGGT GCCTCACTGA TTAAGCATTG GTAACTGTCA GACCAAGTTT ACTCATATAT ACTTTAGATT GATTTAAAAC ^7801 ^7811 ^7821 ^7831 ^7841 ^7851 ^7861 ^7871 ^7881 ^7891 TTCATTTTTA ATTTAAAAGG ATCTAGGTGA AGATCCTTTT TGATAATCTC ATGACCAAAA TCCCTTAACG TGAGTTTTCG TTCCACTGAG CGTCAGACCC ^7901 ^7911 ^7921 ^7931 ^7941 ^7951 ^7961 ^7971 ^7981 ^7991 CGTAGAAAAG ATCAAAGGAT CTTCTTGAGA TCCTTTTTTT CTGCGCGTAA TCTGCTGCTT GCAAACAAAA AAACCACCGC TACCAGCGGT GGTTTGTTTG ^8001 ^8011 ^8021 ^8031 ^8041 ^8051 ^8061 ^8071 ^8081 ^8091 CCGGATCAAG AGCTACCAAC TCTTTTTCCG AAGGTAACTG GCTTCAGCAG AGCGCAGATA CCAAATACTG TCCTTCTAGT GTAGCCGTAG TTAGGCCACC ^8101 ^8111 ^8121 ^8131 ^8141 ^8151 ^8161 ^8171 ^8181 ^8191 ACTTCAAGAA CTCTGTAGCA CCGCCTACAT ACCTCGCTCT GCTAATCCTG TTACCAGTGG CTGCTGCCAG TGGCGATAAG TCGTGTCTTA CCGGGTTGGA ^8201 ^8211 ^8221 ^8231 ^8241 ^8251 ^8261 ^8271 ^8281 ^8291 CTCAAGACGA TAGTTACCGG ATAAGGCGCA GCGGTCGGGC TGAACGGGGG GTTCGTGCAC ACAGCCCAGC TTGGAGCGAA CGACCTACAC CGAACTGAGA ^8301 ^8311 ^8321 ^8331 ^8341 ^8351 ^8361 ^8371 ^8381 ^8391 TACCTACAGC GTGAGCTATG AGAAAGCGCC ACGCTTCCCG AAGGGAGAAA GGCGGACAGG TATCCGGTAA GCGGCAGGGT CGGAACAGGA GAGCGCACGA ^8401 ^8411 ^8421 ^8431 ^8441 ^8451 ^8461 ^8471 ^8481 ^8491 GGGAGCTTCC AGGGGGAAAC GCCTGGTATC TTTATAGTCC TGTCGGGTTT CGCCACCTCT GACTTGAGCG TCGATTTTTG TGATGCTCGT CAGGGGGGCG ^8501 ^8511 ^8521 ^8531 ^8541 ^8551 ^8561 ^8571 ^8581 ^8591 GAGCCTATGG AAAAACGCCA GCAACGCGGC CTTTTTACGG TTCCTGGCCT TTTGCTGGCC TTTTGCTCAC ATGGCTCGAC AGATCT ^8601 ^8611 ^8621 ^8631 ^8641 ^8651 ^8661 ^8671 ^8681
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:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The abbreviated name of this ORF/gene:
FLuc
The description of the protein encoded in this ORF:
Firefly luciferase
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:
not tested
The ORF absolute position (the base range includes
START
and
STOP
codons or their equivalents):
14-1666
ORF
ORF position:
2
Version:
0
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The abbreviated name of this ORF/gene:
RLuc
The description of the protein encoded in this ORF:
Renilla luciferase
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:
not tested
The ORF absolute position (the base range includes
START
and
STOP
codons or their equivalents):
2294-3229
Citations:
Bochkov Y. A., Palmenberg A. C. (2006) Translational efficiency of EMCV IRES in bicistronic vectors is dependent upon IRES sequence and gene location. Biotechniques. 41(3):283-284, 286, 288, 290
IRESs:
IRES:
Version:
1
Last change:
2011-04-08 22:19:39
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The IRES name:
EMCV-R_281-833
The functional status of IRES:
functional
The IRES absolute position (the range includes
START
and
STOP
codons or their equivalents):
1741-2293
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
75
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
627
5'-end of IRES relative to first base of the START codon of the downstream ORF:
-553
3'-end of IRES relative to first base of the START codon of the downstream ORF:
-1
The sequence of IRES region aligned to its secondary structure (if available):
TAACGTTACT GGCCGAAGCC GCTTGGAATA AGGCCGGTGT GCGTTTGTCT ATATGTTATT TTCCACCATA TTGCCGTCTT TTGGCAATGT GAGGGCCCGG ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 ^1801 ^1811 ^1821 ^1831 AAACCTGGCC CTGTCTTCTT GACGAGCATT CCTAGGGGTC TTTCCCCTCT CGCCAAAGGA ATGCAAGGTC TGTTGAATGT CGTGAAGGAA GCAGTTCCTC ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 ^1901 ^1911 ^1921 ^1931 TGGAAGCTTC TTGAAGACAA ACAACGTCTG TAGCGACCCT TTGCAGGCAG CGGAACCCCC CACCTGGCGA CAGGTGCCTC TGCGGCCAAA AGCCACGTGT ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 ^2001 ^2011 ^2021 ^2031 ATAAGATACA CCTGCAAAGG CGGCACAACC CCAGTGCCAC GTTGTGAGTT GGATAGTTGT GGAAAGAGTC AAATGGCTCT CCTCAAGCGT ATTCAACAAG ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 ^2101 ^2111 ^2121 ^2131 GGGCTGAAGG ATGCCCAGAA GGTACCCCAT TGTATGGGAT CTGATCTGGG GCCTCGGTGC ACATGCTTTA CATGTGTTTA GTCGAGGTTA AAAAACGTCT ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 ^2201 ^2211 ^2221 ^2231 AGGCCCCCCG AACCACGGGG ACGTGGTTTT CCTTTGAAAA ACACGATGAT AAT ^2241 ^2251 ^2261 ^2271 ^2281 ^2291
Citations:
Bochkov Y. A., Palmenberg A. C. (2006) Translational efficiency of EMCV IRES in bicistronic vectors is dependent upon IRES sequence and gene location. Biotechniques. 41(3):283-284, 286, 288, 290
Last change to the database: 2019-03-18 09:32:49 GMT+1
plasmid_with_promoter_and_putative_IRES_without_translational_characterization
