IRESite: The database of experimentally verified IRES structures
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The nucleic acid data:
IRESite Id:
256
Version:
0
Originaly submitted by:
Martin Mokrejš
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:
3UTR_incomplete
The mRNA/+RNA description:
Putative bicistronic mRNA transcript derived from pBSFLuzPRLuc plasmid through SV40 promoter.
The mRNA/+RNA sequence represented in the +DNA notation:
TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTCCCTC GAGGaactgg aaaaccagaa agttaactgg taagtttagt ^1 ^11 ^21 ^31 ^41 ^51 ^61 ^71 ^81 ^91 ctttttgtct tttatttcag gtcCCGGAAT TGGTTTAAAC GAATTCGAGC TCTTACGCGT GCTAGCCCGG GCTCGAGATC TGCGATCTAA GTAAGCTTGG ^101 ^111 ^121 ^131 ^141 ^151 ^161 ^171 ^181 ^191 CATTCCGGTA CTGTTGGTAA AGCCACCATG GAAGACGCCA AAAACATAAA GAAAGGCCCG GCGCCATTCT ATCCGCTGGA AGATGGAACC GCTGGAGAGC ^201 ^211 ^221 ^231 ^241 ^251 ^261 ^271 ^281 ^291 AACTGCATAA GGCTATGAAG AGATACGCCC TGGTTCCTGG AACAATTGCT TTTACAGATG CACATATCGA GGTGGACATC ACTTACGCTG AGTACTTCGA ^301 ^311 ^321 ^331 ^341 ^351 ^361 ^371 ^381 ^391 AATGTCCGTT CGGTTGGCAG AAGCTATGAA ACGATATGGG CTGAATACAA ATCACAGAAT CGTCGTATGC AGTGAAAACT CTCTTCAATT CTTTATGCCG ^401 ^411 ^421 ^431 ^441 ^451 ^461 ^471 ^481 ^491 GTGTTGGGCG CGTTATTTAT CGGAGTTGCA GTTGCGCCCG CGAACGACAT TTATAATGAA CGTGAATTGC TCAACAGTAT GGGCATTTCG CAGCCTACCG ^501 ^511 ^521 ^531 ^541 ^551 ^561 ^571 ^581 ^591 TGGTGTTCGT TTCCAAAAAG GGGTTGCAAA AAATTTTGAA CGTGCAAAAA AAGCTCCCAA TCATCCAAAA AATTATTATC ATGGATTCTA AAACGGATTA ^601 ^611 ^621 ^631 ^641 ^651 ^661 ^671 ^681 ^691 CCAGGGATTT CAGTCGATGT ACACGTTCGT CACATCTCAT CTACCTCCCG GTTTTAATGA ATACGATTTT GTGCCAGAGT CCTTCGATAG GGACAAGACA ^701 ^711 ^721 ^731 ^741 ^751 ^761 ^771 ^781 ^791 ATTGCACTGA TCATGAACTC CTCTGGATCT ACTGGTCTGC CTAAAGGTGT CGCTCTGCCT CATAGAACTG CCTGCGTGAG ATTCTCGCAT GCCAGAGATC ^801 ^811 ^821 ^831 ^841 ^851 ^861 ^871 ^881 ^891 CTATTTTTGG CAATCAAATC ATTCCGGATA CTGCGATTTT AAGTGTTGTT CCATTCCATC ACGGTTTTGG AATGTTTACT ACACTCGGAT ATTTGATATG ^901 ^911 ^921 ^931 ^941 ^951 ^961 ^971 ^981 ^991 TGGATTTCGA GTCGTCTTAA TGTATAGATT TGAAGAAGAG CTGTTTCTGA GGAGCCTTCA GGATTACAAG ATTCAAAGTG CGCTGCTGGT GCCAACCCTA ^1001 ^1011 ^1021 ^1031 ^1041 ^1051 ^1061 ^1071 ^1081 ^1091 TTCTCCTTCT TCGCCAAAAG CACTCTGATT GACAAATACG ATTTATCTAA TTTACACGAA ATTGCTTCTG GTGGCGCTCC CCTCTCTAAG GAAGTCGGGG ^1101 ^1111 ^1121 ^1131 ^1141 ^1151 ^1161 ^1171 ^1181 ^1191 AAGCGGTTGC CAAGAGGTTC CATCTGCCAG GTATCAGGCA AGGATATGGG CTCACTGAGA CTACATCAGC TATTCTGATT ACACCCGAGG GGGATGATAA ^1201 ^1211 ^1221 ^1231 ^1241 ^1251 ^1261 ^1271 ^1281 ^1291 ACCGGGCGCG GTCGGTAAAG TTGTTCCATT TTTTGAAGCG AAGGTTGTGG ATCTGGATAC CGGGAAAACG CTGGGCGTTA ATCAAAGAGG CGAACTGTGT ^1301 ^1311 ^1321 ^1331 ^1341 ^1351 ^1361 ^1371 ^1381 ^1391 GTGAGAGGTC CTATGATTAT GTCCGGTTAT GTAAACAATC CGGAAGCGAC CAACGCCTTG ATTGACAAGG ATGGATGGCT ACATTCTGGA GACATAGCTT ^1401 ^1411 ^1421 ^1431 ^1441 ^1451 ^1461 ^1471 ^1481 ^1491 ACTGGGACGA AGACGAACAC TTCTTCATCG TTGACCGCCT GAAGTCTCTG ATTAAGTACA AAGGCTATCA GGTGGCTCCC GCTGAATTGG AATCCATCTT ^1501 ^1511 ^1521 ^1531 ^1541 ^1551 ^1561 ^1571 ^1581 ^1591 GCTCCAACAC CCCAACATCT TCGACGCAGG TGTCGCAGGT CTTCCCGACG ATGACGCCGG TGAACTTCCC GCCGCCGTTG TTGTTTTGGA GCACGGAAAG ^1601 ^1611 ^1621 ^1631 ^1641 ^1651 ^1661 ^1671 ^1681 ^1691 ACGATGACGG AAAAAGAGAT CGTGGATTAC GTCGCCAGTC AAGTAACAAC CGCGAAAAAG TTGCGCGGAG GAGTTGTGTT TGTGGACGAA GTACCGAAAG ^1701 ^1711 ^1721 ^1731 ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 GTCTTACCGG AAAACTCGAC GCAAGAAAAA TCAGAGAGAT CCTCATAAAG GCCAAGAAGG GCGGAAAGAT CGCCGTGTAA TTCTAGAGTC GACCTGCAGA ^1801 ^1811 ^1821 ^1831 ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 AGCTTGCGCA GACGTCGCGC GCGGCCGTTT TAAAACAGCT CTGGGGTTGT ACCCACCCCA GAGGCCCACG TGGCGGCTAG TACTCCGGTA TTGCGGTACC ^1901 ^1911 ^1921 ^1931 ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 CTTGTACGCC TGTTTTATAC TCCCTTCCCG TAACTTAGAC GCACAAAACC AAGTTCAATA GAAGGGGGTA CAAACCAGTA CCACCACGAA CAAGCACTTC ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 TGTTTCCCCG GTGATGTCGT ATAGACTGCT TGCGTGGTTG AAAGCGACGG ATCCGTTATC CGCTTATGTA CTTCGAGAAG CCCAGTACCA CCTCGGAATC ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 TTCGATGCGT TGCGCTCAGC ACTCAACCCC AGAGTGTAGC TTAGGCTGAT GAGTCTGGAC ATCCCTCACC GGTGACGGTG GTCCAGGCTG CGTTGGCGGC ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261 ^2271 ^2281 ^2291 CTACCTATGG CTAACGCCAT GGGACGCTAG TTGTGAACAA GGTGTGAAGA GCCTATTGAG CTACATAAGA ATCCTCCGGC CCCTGAATGC GGCTAATCCC ^2301 ^2311 ^2321 ^2331 ^2341 ^2351 ^2361 ^2371 ^2381 ^2391 AACCTCGGAG CAGGTGGTCA CAAACCAGTG ATTGGCCTGT CGTAACGCGC AAGTCCGTGG CGGAACCGAC TACTTTGGGT GTCCGTGTTT CCTTTTATTT ^2401 ^2411 ^2421 ^2431 ^2441 ^2451 ^2461 ^2471 ^2481 ^2491 TATTGTGGCT GCTTATGGTG ACAATCACAG ATTGTTATCA TAAAGCGAAT TGGATTGCGG CGCGCCGAAT TCGAAATGAC TTCGAAAGTT TATGATCCAG ^2501 ^2511 ^2521 ^2531 ^2541 ^2551 ^2561 ^2571 ^2581 ^2591 AACAAAGGAA ACGGATGATA ACTGGTCCGC AGTGGTGGGC CAGATGTAAA CAAATGAATG TTCTTGATTC ATTTATTAAT TATTATGATT CAGAAAAACA ^2601 ^2611 ^2621 ^2631 ^2641 ^2651 ^2661 ^2671 ^2681 ^2691 TGCAGAAAAT GCTGTTATTT TTTTACATGG TAACGCGGCC TCTTCTTATT TATGGCGACA TGTTGTGCCA CATATTGAGC CAGTAGCGCG GTGTATTATA ^2701 ^2711 ^2721 ^2731 ^2741 ^2751 ^2761 ^2771 ^2781 ^2791 CCAGACCTTA TTGGTATGGG CAAATCAGGC AAATCTGGTA ATGGTTCTTA TAGGTTACTT GATCATTACA AATATCTTAC TGCATGGTTT GAACTTCTTA ^2801 ^2811 ^2821 ^2831 ^2841 ^2851 ^2861 ^2871 ^2881 ^2891 ATTTACCAAA GAAGATCATT TTTGTCGGCC ATGATTGGGG TGCTTGTTTG GCATTTCATT ATAGCTATGA GCATCAAGAT AAGATCAAAG CAATAGTTCA ^2901 ^2911 ^2921 ^2931 ^2941 ^2951 ^2961 ^2971 ^2981 ^2991 CGCTGAAAGT GTAGTAGATG TGATTGAATC ATGGGATGAA TGGCCTGATA TTGAAGAAGA TATTGCGTTG ATCAAATCTG AAGAAGGAGA AAAAATGGTT ^3001 ^3011 ^3021 ^3031 ^3041 ^3051 ^3061 ^3071 ^3081 ^3091 TTGGAGAATA ACTTCTTCGT GGAAACCATG TTGCCATCAA AAATCATGAG AAAGTTAGAA CCAGAAGAAT TTGCAGCATA TCTTGAACCA TTCAAAGAGA ^3101 ^3111 ^3121 ^3131 ^3141 ^3151 ^3161 ^3171 ^3181 ^3191 AAGGTGAAGT TCGTCGTCCA ACATTATCAT GGCCTCGTGA AATCCCGTTA GTAAAAGGTG GTAAACCTGA CGTTGTACAA ATTGTTAGGA ATTATAATGC ^3201 ^3211 ^3221 ^3231 ^3241 ^3251 ^3261 ^3271 ^3281 ^3291 TTATCTACGT GCAAGTGATG ATTTACCAAA AATGTTTATT GAATCGGACC CAGGATTCTT TTCCAATGCT ATTGTTGAAG GTGCCAAGAA GTTTCCTAAT ^3301 ^3311 ^3321 ^3331 ^3341 ^3351 ^3361 ^3371 ^3381 ^3391 ACTGAATTTG TCAAAGTAAA AGGTCTTCAT TTTTCGCAAG AAGATGCACC TGATGAAATG GGAAAATATA TCAAATCGTT CGTTGAGCGA GTTCTCAAAA ^3401 ^3411 ^3421 ^3431 ^3441 ^3451 ^3461 ^3471 ^3481 ^3491 ATGAACAATA AGTCGACCTG CAGAAGCTTG CGCAGACGTC GCGCGCGGCC GCTTAAGCTA GCTTCGATCC AGACATGATA AGATACATTG ATGAGTTTGG ^3501 ^3511 ^3521 ^3531 ^3541 ^3551 ^3561 ^3571 ^3581 ^3591 ACAAACCACA ACTAGAATGC AGTGAAAAAA ATGCTTTATT TGTGAAATTT GTGATGCTAT TGCTTTATTT GTAACCATTA TAAGCTGCAA TAAACAAGTT ^3601 ^3611 ^3621 ^3631 ^3641 ^3651 ^3661 ^3671 ^3681 ^3691 AACAACAACA ATTGCATTCA TTTTATGTTT CAGGTTCAGG GGGAGGTGTG GGAGGTTTTT TAAAGCAAGT AAAACCTCTA CAAATGTGGT A ^3701 ^3711 ^3721 ^3731 ^3741 ^3751 ^3761 ^3771 ^3781 ^3791
Credibility of mRNA sequence:
reverse_engineered_sequence_and_should_match_experiment_except_3UTR
The name of the plasmid:
pBSFLuzPRLuc
The name of the promoter used to express this mRNA:
SV40
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:
PV
The origin of IRES in the plasmid:
viral
The donor organism of the IRES segment:
Human poliovirus 1 Mahoney
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:
GCTTCTGTGG AATGTGTGTC AGTTAGGGTG TGGAAAGTCC CCAGGCTCCC CAGCAGGCAG AAGTATGCAA AGCATGCATC TCAATTAGTC AGCAACCAGG ^1 ^11 ^21 ^31 ^41 ^51 ^61 ^71 ^81 ^91 TGTGGAAAGT CCCCAGGCTC CCCAGCAGGC AGAAGTATGC AAAGCATGCA TCTCAATTAG TCAGCAACCA TAGTCCCGCC CCTAACTCCG CCCATCCCGC ^101 ^111 ^121 ^131 ^141 ^151 ^161 ^171 ^181 ^191 CCCTAACTCC GCCCAGTTCC GCCCATTCTC CGCCCCATGG CTGACTAATT TTTTTTATTT ATGCAGAGGC CGAGGCCGCC TCGGCCTCTG AGCTATTCCA ^201 ^211 ^221 ^231 ^241 ^251 ^261 ^271 ^281 ^291 GAAGTAGTGA GGAGGCTTTT TTGGAGGCCT AGGCTTTTGC AAAAAGCTCC CTCGAGGaac tggaaaacca gaaagttaac tggtaagttt agtctttttg ^301 ^311 ^321 ^331 ^341 ^351 ^361 ^371 ^381 ^391 tcttttattt caggtcCCGG AATTGGTTTA AACGAATTCG AGCTCTTACG CGTGCTAGCC CGGGCTCGAG ATCTGCGATC TAAGTAAGCT TGGCATTCCG ^401 ^411 ^421 ^431 ^441 ^451 ^461 ^471 ^481 ^491 GTACTGTTGG TAAAGCCACC ATGGAAGACG CCAAAAACAT AAAGAAAGGC CCGGCGCCAT TCTATCCGCT GGAAGATGGA ACCGCTGGAG AGCAACTGCA ^501 ^511 ^521 ^531 ^541 ^551 ^561 ^571 ^581 ^591 TAAGGCTATG AAGAGATACG CCCTGGTTCC TGGAACAATT GCTTTTACAG ATGCACATAT CGAGGTGGAC ATCACTTACG CTGAGTACTT CGAAATGTCC ^601 ^611 ^621 ^631 ^641 ^651 ^661 ^671 ^681 ^691 GTTCGGTTGG CAGAAGCTAT GAAACGATAT GGGCTGAATA CAAATCACAG AATCGTCGTA TGCAGTGAAA ACTCTCTTCA ATTCTTTATG CCGGTGTTGG ^701 ^711 ^721 ^731 ^741 ^751 ^761 ^771 ^781 ^791 GCGCGTTATT TATCGGAGTT GCAGTTGCGC CCGCGAACGA CATTTATAAT GAACGTGAAT TGCTCAACAG TATGGGCATT TCGCAGCCTA CCGTGGTGTT ^801 ^811 ^821 ^831 ^841 ^851 ^861 ^871 ^881 ^891 CGTTTCCAAA AAGGGGTTGC AAAAAATTTT GAACGTGCAA AAAAAGCTCC CAATCATCCA AAAAATTATT ATCATGGATT CTAAAACGGA TTACCAGGGA ^901 ^911 ^921 ^931 ^941 ^951 ^961 ^971 ^981 ^991 TTTCAGTCGA TGTACACGTT CGTCACATCT CATCTACCTC CCGGTTTTAA TGAATACGAT TTTGTGCCAG AGTCCTTCGA TAGGGACAAG ACAATTGCAC ^1001 ^1011 ^1021 ^1031 ^1041 ^1051 ^1061 ^1071 ^1081 ^1091 TGATCATGAA CTCCTCTGGA TCTACTGGTC TGCCTAAAGG TGTCGCTCTG CCTCATAGAA CTGCCTGCGT GAGATTCTCG CATGCCAGAG ATCCTATTTT ^1101 ^1111 ^1121 ^1131 ^1141 ^1151 ^1161 ^1171 ^1181 ^1191 TGGCAATCAA ATCATTCCGG ATACTGCGAT TTTAAGTGTT GTTCCATTCC ATCACGGTTT TGGAATGTTT ACTACACTCG GATATTTGAT ATGTGGATTT ^1201 ^1211 ^1221 ^1231 ^1241 ^1251 ^1261 ^1271 ^1281 ^1291 CGAGTCGTCT TAATGTATAG ATTTGAAGAA GAGCTGTTTC TGAGGAGCCT TCAGGATTAC AAGATTCAAA GTGCGCTGCT GGTGCCAACC CTATTCTCCT ^1301 ^1311 ^1321 ^1331 ^1341 ^1351 ^1361 ^1371 ^1381 ^1391 TCTTCGCCAA AAGCACTCTG ATTGACAAAT ACGATTTATC TAATTTACAC GAAATTGCTT CTGGTGGCGC TCCCCTCTCT AAGGAAGTCG GGGAAGCGGT ^1401 ^1411 ^1421 ^1431 ^1441 ^1451 ^1461 ^1471 ^1481 ^1491 TGCCAAGAGG TTCCATCTGC CAGGTATCAG GCAAGGATAT GGGCTCACTG AGACTACATC AGCTATTCTG ATTACACCCG AGGGGGATGA TAAACCGGGC ^1501 ^1511 ^1521 ^1531 ^1541 ^1551 ^1561 ^1571 ^1581 ^1591 GCGGTCGGTA AAGTTGTTCC ATTTTTTGAA GCGAAGGTTG TGGATCTGGA TACCGGGAAA ACGCTGGGCG TTAATCAAAG AGGCGAACTG TGTGTGAGAG ^1601 ^1611 ^1621 ^1631 ^1641 ^1651 ^1661 ^1671 ^1681 ^1691 GTCCTATGAT TATGTCCGGT TATGTAAACA ATCCGGAAGC GACCAACGCC TTGATTGACA AGGATGGATG GCTACATTCT GGAGACATAG CTTACTGGGA ^1701 ^1711 ^1721 ^1731 ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 CGAAGACGAA CACTTCTTCA TCGTTGACCG CCTGAAGTCT CTGATTAAGT ACAAAGGCTA TCAGGTGGCT CCCGCTGAAT TGGAATCCAT CTTGCTCCAA ^1801 ^1811 ^1821 ^1831 ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 CACCCCAACA TCTTCGACGC AGGTGTCGCA GGTCTTCCCG ACGATGACGC CGGTGAACTT CCCGCCGCCG TTGTTGTTTT GGAGCACGGA AAGACGATGA ^1901 ^1911 ^1921 ^1931 ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 CGGAAAAAGA GATCGTGGAT TACGTCGCCA GTCAAGTAAC AACCGCGAAA AAGTTGCGCG GAGGAGTTGT GTTTGTGGAC GAAGTACCGA AAGGTCTTAC ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 CGGAAAACTC GACGCAAGAA AAATCAGAGA GATCCTCATA AAGGCCAAGA AGGGCGGAAA GATCGCCGTG TAATTCTAGA GTCGACCTGC AGAAGCTTGC ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 GCAGACGTCG CGCGCGGCCG TTTTAAAACA GCTCTGGGGT TGTACCCACC CCAGAGGCCC ACGTGGCGGC TAGTACTCCG GTATTGCGGT ACCCTTGTAC ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261 ^2271 ^2281 ^2291 GCCTGTTTTA TACTCCCTTC CCGTAACTTA GACGCACAAA ACCAAGTTCA ATAGAAGGGG GTACAAACCA GTACCACCAC GAACAAGCAC TTCTGTTTCC ^2301 ^2311 ^2321 ^2331 ^2341 ^2351 ^2361 ^2371 ^2381 ^2391 CCGGTGATGT CGTATAGACT GCTTGCGTGG TTGAAAGCGA CGGATCCGTT ATCCGCTTAT GTACTTCGAG AAGCCCAGTA CCACCTCGGA ATCTTCGATG ^2401 ^2411 ^2421 ^2431 ^2441 ^2451 ^2461 ^2471 ^2481 ^2491 CGTTGCGCTC AGCACTCAAC CCCAGAGTGT AGCTTAGGCT GATGAGTCTG GACATCCCTC ACCGGTGACG GTGGTCCAGG CTGCGTTGGC GGCCTACCTA ^2501 ^2511 ^2521 ^2531 ^2541 ^2551 ^2561 ^2571 ^2581 ^2591 TGGCTAACGC CATGGGACGC TAGTTGTGAA CAAGGTGTGA AGAGCCTATT GAGCTACATA AGAATCCTCC GGCCCCTGAA TGCGGCTAAT CCCAACCTCG ^2601 ^2611 ^2621 ^2631 ^2641 ^2651 ^2661 ^2671 ^2681 ^2691 GAGCAGGTGG TCACAAACCA GTGATTGGCC TGTCGTAACG CGCAAGTCCG TGGCGGAACC GACTACTTTG GGTGTCCGTG TTTCCTTTTA TTTTATTGTG ^2701 ^2711 ^2721 ^2731 ^2741 ^2751 ^2761 ^2771 ^2781 ^2791 GCTGCTTATG GTGACAATCA CAGATTGTTA TCATAAAGCG AATTGGATTG CGGCGCGCCG AATTCGAAAT GACTTCGAAA GTTTATGATC CAGAACAAAG ^2801 ^2811 ^2821 ^2831 ^2841 ^2851 ^2861 ^2871 ^2881 ^2891 GAAACGGATG ATAACTGGTC CGCAGTGGTG GGCCAGATGT AAACAAATGA ATGTTCTTGA TTCATTTATT AATTATTATG ATTCAGAAAA ACATGCAGAA ^2901 ^2911 ^2921 ^2931 ^2941 ^2951 ^2961 ^2971 ^2981 ^2991 AATGCTGTTA TTTTTTTACA TGGTAACGCG GCCTCTTCTT ATTTATGGCG ACATGTTGTG CCACATATTG AGCCAGTAGC GCGGTGTATT ATACCAGACC ^3001 ^3011 ^3021 ^3031 ^3041 ^3051 ^3061 ^3071 ^3081 ^3091 TTATTGGTAT GGGCAAATCA GGCAAATCTG GTAATGGTTC TTATAGGTTA CTTGATCATT ACAAATATCT TACTGCATGG TTTGAACTTC TTAATTTACC ^3101 ^3111 ^3121 ^3131 ^3141 ^3151 ^3161 ^3171 ^3181 ^3191 AAAGAAGATC ATTTTTGTCG GCCATGATTG GGGTGCTTGT TTGGCATTTC ATTATAGCTA TGAGCATCAA GATAAGATCA AAGCAATAGT TCACGCTGAA ^3201 ^3211 ^3221 ^3231 ^3241 ^3251 ^3261 ^3271 ^3281 ^3291 AGTGTAGTAG ATGTGATTGA ATCATGGGAT GAATGGCCTG ATATTGAAGA AGATATTGCG TTGATCAAAT CTGAAGAAGG AGAAAAAATG GTTTTGGAGA ^3301 ^3311 ^3321 ^3331 ^3341 ^3351 ^3361 ^3371 ^3381 ^3391 ATAACTTCTT CGTGGAAACC ATGTTGCCAT CAAAAATCAT GAGAAAGTTA GAACCAGAAG AATTTGCAGC ATATCTTGAA CCATTCAAAG AGAAAGGTGA ^3401 ^3411 ^3421 ^3431 ^3441 ^3451 ^3461 ^3471 ^3481 ^3491 AGTTCGTCGT CCAACATTAT CATGGCCTCG TGAAATCCCG TTAGTAAAAG GTGGTAAACC TGACGTTGTA CAAATTGTTA GGAATTATAA TGCTTATCTA ^3501 ^3511 ^3521 ^3531 ^3541 ^3551 ^3561 ^3571 ^3581 ^3591 CGTGCAAGTG ATGATTTACC AAAAATGTTT ATTGAATCGG ACCCAGGATT CTTTTCCAAT GCTATTGTTG AAGGTGCCAA GAAGTTTCCT AATACTGAAT ^3601 ^3611 ^3621 ^3631 ^3641 ^3651 ^3661 ^3671 ^3681 ^3691 TTGTCAAAGT AAAAGGTCTT CATTTTTCGC AAGAAGATGC ACCTGATGAA ATGGGAAAAT ATATCAAATC GTTCGTTGAG CGAGTTCTCA AAAATGAACA ^3701 ^3711 ^3721 ^3731 ^3741 ^3751 ^3761 ^3771 ^3781 ^3791 ATAAGTCGAC CTGCAGAAGC TTGCGCAGAC GTCGCGCGCG GCCGCTTAAG CTAGCTTCGA TCCAGACATG ATAAGATACA TTGATGAGTT TGGACAAACC ^3801 ^3811 ^3821 ^3831 ^3841 ^3851 ^3861 ^3871 ^3881 ^3891 ACAACTAGAA TGCAGTGAAA AAAATGCTTT ATTTGTGAAA TTTGTGATGC TATTGCTTTA TTTGTAACCA TTATAAGCTG CAATAAACAA GTTAACAACA ^3901 ^3911 ^3921 ^3931 ^3941 ^3951 ^3961 ^3971 ^3981 ^3991 ACAATTGCAT TCATTTTATG TTTCAGGTTC AGGGGGAGGT GTGGGAGGTT TTTTAAAGCA AGTAAAACCT CTACAAATGT GGTATGGCTG ATTATGATCC ^4001 ^4011 ^4021 ^4031 ^4041 ^4051 ^4061 ^4071 ^4081 ^4091 TGCCTCGCGC GTTTCGGTGA TGACGGTGAA AACCTCTGAC ACATGCAGCT CCCGCCTTAA TTAAGGGTTT AAACCCGGTA CCCAGTCACG TAGCGATAGC ^4101 ^4111 ^4121 ^4131 ^4141 ^4151 ^4161 ^4171 ^4181 ^4191 GGAGTGTACT GCATTAATGA ATCGGCCAAC GCGCGGGGAG AGGCGGTTTG CGTATTGGGC GCTCTTCCGC TTCCTCGCTC ACTGACTCGC TGCGCTCGGT ^4201 ^4211 ^4221 ^4231 ^4241 ^4251 ^4261 ^4271 ^4281 ^4291 CGTTCGGCTG CGGCGAGCGG TATCAGCTCA CTCAAAGGCG GTAATACGGT TATCCACAGA ATCAGGGGAT AACGCAGGAA AGAACATGTG AGCAAAAGGC ^4301 ^4311 ^4321 ^4331 ^4341 ^4351 ^4361 ^4371 ^4381 ^4391 CAGCAAAAGG CCAGGAACCG TAAAAAGGCC GCGTTGCTGG CGTTtTTCCA TAGGCTCCGC CCCCCTGACG AGCATCACAA AAATCGACGC TCAAGTCAGA ^4401 ^4411 ^4421 ^4431 ^4441 ^4451 ^4461 ^4471 ^4481 ^4491 GGTGGCGAAA CCCGACAGGA CTATAAAGAT ACCAGGCGTT TCCCCCTGGA AGCTCCCTCG TGCGCTCTCC TGTTCCGACC CTGCCGCTTA CCGGATACCT ^4501 ^4511 ^4521 ^4531 ^4541 ^4551 ^4561 ^4571 ^4581 ^4591 GTCCGCCTTT CTCCCTTCGG GAAGCGTGGC GCTTTCTCAT AGCTCACGCT GTAGGTATCT CAGTTCGGTG TAGGTCGTTC GCTCCAAGCT GGGCTGTGTG ^4601 ^4611 ^4621 ^4631 ^4641 ^4651 ^4661 ^4671 ^4681 ^4691 CACGAACCCC CCGTTCAGCC CGACCGCTGC GCCTTATCCG GTAACTATCG TCTTGAGTCC AACCCGGTAA GACACGACTT ATCGCCACTG GCAGCAGCCA ^4701 ^4711 ^4721 ^4731 ^4741 ^4751 ^4761 ^4771 ^4781 ^4791 CTGGTAACAG GATTAGCAGA GCGAGGTATG TAGGCGGTGC TACAGAGTTC TTGAAGTGGT GGCCTAACTA CGGCTACACT AGAAGGACAG TATTTGGTAT ^4801 ^4811 ^4821 ^4831 ^4841 ^4851 ^4861 ^4871 ^4881 ^4891 CTGCGCTCTG CTGAAGCCAG TTACCTTCGG AAAAAGAGTT GGTAGCTCTT GATCCGGCAA ACAAACCACC GCTGGTAGCG GTGGTTTTTT TGTTTGCAAG ^4901 ^4911 ^4921 ^4931 ^4941 ^4951 ^4961 ^4971 ^4981 ^4991 CAGCAGATTA CGCGCAGAAA AAAAGGATCT CAAGAAGATC CTTTGATCTT TTCTACGGGG TCTGACGCTC AGTGGAACGA AAACTCACGT TAAGGGATTT ^5001 ^5011 ^5021 ^5031 ^5041 ^5051 ^5061 ^5071 ^5081 ^5091 TGGTCATGAG ATTATCAAAA AGGATCTTCA CCTAGATCCT TTTAAATTAA AAATGAAGTT TTAAATCAAT CTAAAGTATA TATGAGTAAA CTTGGTCTGA ^5101 ^5111 ^5121 ^5131 ^5141 ^5151 ^5161 ^5171 ^5181 ^5191 CAGTTACCAA TGCTTAATCA GTGAGGCACC TATCTCAGCG ATCTGTCTAT TTCGTTCATC CATAGTTGCC TGACTCCCCG TCGTGTAGAT AACTACGATA ^5201 ^5211 ^5221 ^5231 ^5241 ^5251 ^5261 ^5271 ^5281 ^5291 CGGGAGGGCT TACCATCTGG CCCCAGTGCT GCAATGATAC CGCGAGACCC ACGCTCACCG GCTCCAGATT TATCAGCAAT AAACCAGCCA GCCGGAAGGG ^5301 ^5311 ^5321 ^5331 ^5341 ^5351 ^5361 ^5371 ^5381 ^5391 CCGAGCGCAG AAGTGGTCCT GCAACTTTAT CCGCCTCCAT CCAGTCTATT AATTGTTGCC GGGAAGCTAG AGTAAGTAGT TCGCCAGTTA ATAGTTTGCG ^5401 ^5411 ^5421 ^5431 ^5441 ^5451 ^5461 ^5471 ^5481 ^5491 CAACGTTGTT GCCATTGCTA CAGGCATCGT GGTGTCACGC TCGTCGTTTG GTATGGCTTC ATTCAGCTCC GGTTCCCAAC GATCAAGGCG AGTTACATGA ^5501 ^5511 ^5521 ^5531 ^5541 ^5551 ^5561 ^5571 ^5581 ^5591 TCCCCCATGT TGTGCAAAAA AGCGGTTAGC TCCTTCGGTC CTCCGATCGT TGTCAGAAGT AAGTTGGCCG CAGTGTTATC ACTCATGGTT ATGGCAGCAC ^5601 ^5611 ^5621 ^5631 ^5641 ^5651 ^5661 ^5671 ^5681 ^5691 TGCATAATTC TCTTACTGTC ATGCCATCCG TAAGATGCTT TTCTGTGACT GGTGAGTACT CAACCAAGTC ATTCTGAGAA TAGTGTATGC GGCGACCGAG ^5701 ^5711 ^5721 ^5731 ^5741 ^5751 ^5761 ^5771 ^5781 ^5791 TTGCTCTTGC CCGGCGTCAA TACGGGATAA TACCGCGCCA CATAGCAGAA CTTTAAAAGT GCTCATCATT GGAAAACGTT CTTCGGGGCG AAAACTCTCA ^5801 ^5811 ^5821 ^5831 ^5841 ^5851 ^5861 ^5871 ^5881 ^5891 AGGATCTTAC CGCTGTTGAG ATCCAGTTCG ATGTAACCCA CTCGTGCACC CAACTGATCT TCAGCATCTT TTACTTTCAC CAGCGTTTCT GGGTGAGCAA ^5901 ^5911 ^5921 ^5931 ^5941 ^5951 ^5961 ^5971 ^5981 ^5991 AAACAGGAAG GCAAAATGCC GCAAAAAAGG GAATAAGGGC GACACGGAAA TGTTGAATAC TCATACTCTT CCTTTTTCAA TATTATTGAA GCATTTATCA ^6001 ^6011 ^6021 ^6031 ^6041 ^6051 ^6061 ^6071 ^6081 ^6091 GGGTTATTGT CTCATGAGCG GATACATATT TGAATGTATT TAGAAAAATA AACAAATAGG GGTTCCGCGC ACATTTCCCC GAAAAGTGCC ACCTGACGTC ^6101 ^6111 ^6121 ^6131 ^6141 ^6151 ^6161 ^6171 ^6181 ^6191 GGTACCATTT AAATATCGAT AAGCTA ^6201 ^6211 ^6221
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:
1
Last change:
2007-07-13 00:00:00
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The abbreviated name of this ORF/gene:
luc+
The description of the protein encoded in this ORF:
Firefly luciferase with improved codon usage
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):
228-1880
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):
2576-3511
Citations:
Hennecke M., Kwissa M., Metzger K., Oumard A., Kroger A., Schirmbeck R., Reimann J., Hauser H. (2001) Composition and arrangement of genes define the strength of IRES-driven translation in bicistronic mRNAs. Nucleic. Acids Res. 29(16):3327-3334
IRESs:
IRES:
Version:
0
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The IRES name:
PV
The functional status of IRES:
defective
The IRES absolute position (the range includes
START
and
STOP
codons or their equivalents):
1930-2557
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
50
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
677
5'-end of IRES relative to first base of the START codon of the downstream ORF:
-646
3'-end of IRES relative to first base of the START codon of the downstream ORF:
-19
The sequence of IRES region aligned to its secondary structure (if available):
TTAAAACAGC TCTGGGGTTG TACCCACCCC AGAGGCCCAC GTGGCGGCTA GTACTCCGGT ATTGCGGTAC CCTTGTACGC CTGTTTTATA CTCCCTTCCC ^1930 ^1940 ^1950 ^1960 ^1970 ^1980 ^1990 ^2000 ^2010 ^2020 GTAACTTAGA CGCACAAAAC CAAGTTCAAT AGAAGGGGGT ACAAACCAGT ACCACCACGA ACAAGCACTT CTGTTTCCCC GGTGATGTCG TATAGACTGC ^2030 ^2040 ^2050 ^2060 ^2070 ^2080 ^2090 ^2100 ^2110 ^2120 TTGCGTGGTT GAAAGCGACG GATCCGTTAT CCGCTTATGT ACTTCGAGAA GCCCAGTACC ACCTCGGAAT CTTCGATGCG TTGCGCTCAG CACTCAACCC ^2130 ^2140 ^2150 ^2160 ^2170 ^2180 ^2190 ^2200 ^2210 ^2220 CAGAGTGTAG CTTAGGCTGA TGAGTCTGGA CATCCCTCAC CGGTGACGGT GGTCCAGGCT GCGTTGGCGG CCTACCTATG GCTAACGCCA TGGGACGCTA ^2230 ^2240 ^2250 ^2260 ^2270 ^2280 ^2290 ^2300 ^2310 ^2320 GTTGTGAACA AGGTGTGAAG AGCCTATTGA GCTACATAAG AATCCTCCGG CCCCTGAATG CGGCTAATCC CAACCTCGGA GCAGGTGGTC ACAAACCAGT ^2330 ^2340 ^2350 ^2360 ^2370 ^2380 ^2390 ^2400 ^2410 ^2420 GATTGGCCTG TCGTAACGCG CAAGTCCGTG GCGGAACCGA CTACTTTGGG TGTCCGTGTT TCCTTTTATT TTATTGTGGC TGCTTATGGT GACAATCACA ^2430 ^2440 ^2450 ^2460 ^2470 ^2480 ^2490 ^2500 ^2510 ^2520 GATTGTTATC ATAAAGCGAA TTGGATTG ^2530 ^2540 ^2550
Citations:
Hennecke M., Kwissa M., Metzger K., Oumard A., Kroger A., Schirmbeck R., Reimann J., Hauser H. (2001) Composition and arrangement of genes define the strength of IRES-driven translation in bicistronic mRNAs. Nucleic. Acids Res. 29(16):3327-3334
The translation experiments:
Translation results:
IRESite Translation Id:
321
Version:
0
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The translation method used to study IRES function:
in vivo
The organism used for translation:
Mus musculus C243
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this
IRES:
0.600
Name of IRES used as the positive control:
PV
Name of the plasmid used as the positive control.
pBSRLucPFluc
IRESite Id
of the plasmid used as positive control.
246
The relative translation efficiency in % of the positive control:
100.000
The size (length) of intercistronic region in the positive control:
785
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
endogenous_nuclear_RNA_Pol_II_transcript
Citations:
Hennecke M., Kwissa M., Metzger K., Oumard A., Kroger A., Schirmbeck R., Reimann J., Hauser H. (2001) Composition and arrangement of genes define the strength of IRES-driven translation in bicistronic mRNAs. Nucleic. Acids Res. 29(16):3327-3334
Last change to the database: 2019-03-18 09:32:49 GMT+1
plasmid_with_promoter_and_putative_IRES_translationally_characterized
