IRESite: The database of experimentally verified IRES structures
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The nucleic acid data:
IRESite Id:
185
Version:
0
Originaly submitted by:
Martin Mokrejš
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:
Bicistronic mRNA molecule transcribed from ApaI linearized pRL-HL plasmid from the T7 promoter.
The mRNA/+RNA sequence represented in the +DNA notation:
GGCTAGCCAC CATGACTTCG AAAGTTTATG ATCCAGAACA AAGGAAACGG ATGATAACTG GTCCGCAGTG GTGGGCCAGA TGTAAACAAA TGAATGTTCT ^1 ^11 ^21 ^31 ^41 ^51 ^61 ^71 ^81 ^91 TGATTCATTT ATTAATTATT ATGATTCAGA AAAACATGCA GAAAATGCTG TTATTTTTTT ACATGGTAAC GCGGCCTCTT CTTATTTATG GCGACATGTT ^101 ^111 ^121 ^131 ^141 ^151 ^161 ^171 ^181 ^191 GTGCCACATA TTGAGCCAGT AGCGCGGTGT ATTATACCAG ACCTTATTGG TATGGGCAAA TCAGGCAAAT CTGGTAATGG TTCTTATAGG TTACTTGATC ^201 ^211 ^221 ^231 ^241 ^251 ^261 ^271 ^281 ^291 ATTACAAATA TCTTACTGCA TGGTTTGAAC TTCTTAATTT ACCAAAGAAG ATCATTTTTG TCGGCCATGA TTGGGGTGCT TGTTTGGCAT TTCATTATAG ^301 ^311 ^321 ^331 ^341 ^351 ^361 ^371 ^381 ^391 CTATGAGCAT CAAGATAAGA TCAAAGCAAT AGTTCACGCT GAAAGTGTAG TAGATGTGAT TGAATCATGG GATGAATGGC CTGATATTGA AGAAGATATT ^401 ^411 ^421 ^431 ^441 ^451 ^461 ^471 ^481 ^491 GCGTTGATCA AATCTGAAGA AGGAGAAAAA ATGGTTTTGG AGAATAACTT CTTCGTGGAA ACCATGTTGC CATCAAAAAT CATGAGAAAG TTAGAACCAG ^501 ^511 ^521 ^531 ^541 ^551 ^561 ^571 ^581 ^591 AAGAATTTGC AGCATATCTT GAACCATTCA AAGAGAAAGG TGAAGTTCGT CGTCCAACAT TATCATGGCC TCGTGAAATC CCGTTAGTAA AAGGTGGTAA ^601 ^611 ^621 ^631 ^641 ^651 ^661 ^671 ^681 ^691 ACCTGACGTT GTACAAATTG TTAGGAATTA TAATGCTTAT CTACGTGCAA GTGATGATTT ACCAAAAATG TTTATTGAAT CGGACCCAGG ATTCTTTTCC ^701 ^711 ^721 ^731 ^741 ^751 ^761 ^771 ^781 ^791 AATGCTATTG TTGAAGGTGC CAAGAAGTTT CCTAATACTG AATTTGTCAA AGTAAAAGGT CTTCATTTTT CGCAAGAAGA TGCACCTGAT GAAATGGGAA ^801 ^811 ^821 ^831 ^841 ^851 ^861 ^871 ^881 ^891 AATATATCAA ATCGTTCGTT GAGCGAGTTC TCAAAAATGA ACAATAATTC TAGAGCGGCC GCTCTAGAAC TAGTGGATCC CCCGGGCTGC AGGAATTCGA ^901 ^911 ^921 ^931 ^941 ^951 ^961 ^971 ^981 ^991 TATCAAGCTT ATCGATACCG TCGACACGAG CTCGCCAGCC CCCGATTGGG GGCGACACTC CACCATAGAT CACTCCCCTG TGAGGAACTA CTGTCTTCAC ^1001 ^1011 ^1021 ^1031 ^1041 ^1051 ^1061 ^1071 ^1081 ^1091 GCAGAAAGCG TCTAGCCATG GCGTTAGTAT GAGAGTCGTG CAGCCTCCAG GACCCCCCCT CCCGGGAGAG CCATAGTGGT CTGCGGAACC GGTGAGTACA ^1101 ^1111 ^1121 ^1131 ^1141 ^1151 ^1161 ^1171 ^1181 ^1191 CCGGAATTGC CAGGACGACC GGGTCCTTTC TTGGATCAAC CCGCTCAATG CCTGGAGATT TGGGCGTGCC CCCGCAAGAC TGCTAGCCGA GTAGTGTTGG ^1201 ^1211 ^1221 ^1231 ^1241 ^1251 ^1261 ^1271 ^1281 ^1291 GTCGCGAAAG GCCTTGTGGT ACTGCCTGAT AGGGTGCTTG CGAGTGCCCC GGGAGGTCTC GTAGACCGTG CACCATGAGC ACGAATCCTA AACCTCAAAG ^1301 ^1311 ^1321 ^1331 ^1341 ^1351 ^1361 ^1371 ^1381 ^1391 AAAAACCAAA CGTAACACCA ACCGCCGCCC ACAGGACGTC ATGGAAGACG CCAAAAACAT AAAGAAAGGC CCGGCGCCAT TCTATCCTCT AGAGGATGGA ^1401 ^1411 ^1421 ^1431 ^1441 ^1451 ^1461 ^1471 ^1481 ^1491 ACCGCTGGAG AGCAACTGCA TAAGGCTATG AAGAGATACG CCCTGGTTCC TGGAACAATT GCTTTTACAG ATGCACATAT CGAGGTGAAC ATCACGTACG ^1501 ^1511 ^1521 ^1531 ^1541 ^1551 ^1561 ^1571 ^1581 ^1591 CGGAATACTT CGAAATGTCC GTTCGGTTGG CAGAAGCTAT GAAACGATAT GGGCTGAATA CAAATCACAG AATCGTCGTA TGCAGTGAAA ACTCTCTTCA ^1601 ^1611 ^1621 ^1631 ^1641 ^1651 ^1661 ^1671 ^1681 ^1691 ATTCTTTATG CCGGTGTTGG GCGCGTTATT TATCGGAGTT GCAGTTGCGC CCGCGAACGA CATTTATAAT GAACGTGAAT TGCTCAACAG TATGAACATT ^1701 ^1711 ^1721 ^1731 ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 TCGCAGCCTA CCGTAGTGTT TGTTTCCAAA AAGGGGTTGC AAAAAATTTT GAACGTGCAA AAAAAATTAC CAATAATCCA GAAAATTATT ATCATGGATT ^1801 ^1811 ^1821 ^1831 ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 CTAAAACGGA TTACCAGGGA TTTCAGTCGA TGTACACGTT CGTCACATCT CATCTACCTC CCGGTTTTAA TGAATACGAT TTTGTACCAG AGTCCTTTGA ^1901 ^1911 ^1921 ^1931 ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 TCGTGACAAA ACAATTGCAC TGATAATGAA TTCCTCTGGA TCTACTGGGT TACCTAAGGG TGTGGCCCTT CCGCATAGAA CTGCCTGCGT CAGATTCTCG ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 CATGCCAGAG ATCCTATTTT TGGCAATCAA ATCATTCCGG ATACTGCGAT TTTAAGTGTT GTTCCATTCC ATCACGGTTT TGGAATGTTT ACTACACTCG ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 GATATTTGAT ATGTGGATTT CGAGTCGTCT TAATGTATAG ATTTGAAGAA GAGCTGTTTT TACGATCCCT TCAGGATTAC AAAATTCAAA GTGCGTTGCT ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261 ^2271 ^2281 ^2291 AGTACCAACC CTATTTTCAT TCTTCGCCAA AAGCACTCTG ATTGACAAAT ACGATTTATC TAATTTACAC GAAATTGCTT CTGGGGGCGC ACCTCTTTCG ^2301 ^2311 ^2321 ^2331 ^2341 ^2351 ^2361 ^2371 ^2381 ^2391 AAAGAAGTCG GGGAAGCGGT TGCAAAACGC TTCCATCTTC CAGGGATACG ACAAGGATAT GGGCTCACTG AGACTACATC AGCTATTCTG ATTACACCCG ^2401 ^2411 ^2421 ^2431 ^2441 ^2451 ^2461 ^2471 ^2481 ^2491 AGGGGGATGA TAAACCGGGC GCGGTCGGTA AAGTTGTTCC ATTTTTTGAA GCGAAGGTTG TGGATCTGGA TACCGGGAAA ACGCTGGGCG TTAATCAGAG ^2501 ^2511 ^2521 ^2531 ^2541 ^2551 ^2561 ^2571 ^2581 ^2591 AGGCGAATTA TGTGTCAGAG GACCTATGAT TATGTCCGGT TATGTAAACA ATCCGGAAGC GACCAACGCC TTGATTGACA AGGATGGATG GCTACATTCT ^2601 ^2611 ^2621 ^2631 ^2641 ^2651 ^2661 ^2671 ^2681 ^2691 GGAGACATAG CTTACTGGGA CGAAGACGAA CACTTCTTCA TAGTTGACCG CTTGAAGTCT TTAATTAAAT ACAAAGGATA TCAGGTGGCC CCCGCTGAAT ^2701 ^2711 ^2721 ^2731 ^2741 ^2751 ^2761 ^2771 ^2781 ^2791 TGGAATCGAT ATTGTTACAA CACCCCAACA TCTTCGACGC GGGCGTGGCA GGTCTTCCCG ACGATGACGC CGGTGAACTT CCCGCCGCCG TTGTTGTTTT ^2801 ^2811 ^2821 ^2831 ^2841 ^2851 ^2861 ^2871 ^2881 ^2891 GGAGCACGGA AAGACGATGA CGGAAAAAGA GATCGTGGAT TACGTGGCCA GTCAAGTAAC AACCGCGAAA AAGTTGCGCG GAGGAGTTGT GTTTGTGGAC ^2901 ^2911 ^2921 ^2931 ^2941 ^2951 ^2961 ^2971 ^2981 ^2991 GAAGTACCGA AAGGTCTTAC CGGAAAACTC GACGCAAGAA AAATCAGAGA GATCCTCATA AAGGCCAAGA AGGGCGGAAA GTCCAAATTG TAAAATGTAA ^3001 ^3011 ^3021 ^3031 ^3041 ^3051 ^3061 ^3071 ^3081 ^3091 CTGTATTCAG CGATGACGAA ATTCTTAGCT ATTGTAAGGA TCCGGGCC ^3101 ^3111 ^3121 ^3131 ^3141
Credibility of mRNA sequence:
end-to-end_sequence_reverse_engineered_and_should_match_experiment
The name of the plasmid:
pRL-HL
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:
HCV_type_1b
The origin of IRES in the plasmid:
viral
The donor organism of the IRES segment:
Hepatitis C virus type 1b
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:
GACGGATCGG GAGATCTTCA ATATTGGCCA TTAGCCATAT TATTCATTGG TTATATAGCA TAAATCAATA TTGGCTATTG GCCATTGCAT ACGTTGTATC ^1 ^11 ^21 ^31 ^41 ^51 ^61 ^71 ^81 ^91 TATATCATAA TATGTACATT TATATTGGCT CATGTCCAAT ATGACCGCCA TGTTGGCATT GATTATTGAC TAGTTATTAA TAGTAATCAA TTACGGGGTC ^101 ^111 ^121 ^131 ^141 ^151 ^161 ^171 ^181 ^191 ATTAGTTCAT AGCCCATATA TGGAGTTCCG CGTTACATAA CTTACGGTAA ATGGCCCGCC TGGCTGACCG CCCAACGACC CCCGCCCATT GACGTCAATA ^201 ^211 ^221 ^231 ^241 ^251 ^261 ^271 ^281 ^291 ATGACGTATG TTCCCATAGT AACGCCAATA GGGACTTTCC ATTGACGTCA ATGGGTGGAG TATTTACGGT AAACTGCCCA CTTGGCAGTA CATCAAGTGT ^301 ^311 ^321 ^331 ^341 ^351 ^361 ^371 ^381 ^391 ATCATATGCC AAGTCCGCCC CCTATTGACG TCAATGACGG TAAATGGCCC GCCTGGCATT ATGCCCAGTA CATGACCTTA CGGGACTTTC CTACTTGGCA ^401 ^411 ^421 ^431 ^441 ^451 ^461 ^471 ^481 ^491 GTACATCTAC GTATTAGTCA TCGCTATTAC CATGGTGATG CGGTTTTGGC AGTACACCAA TGGGCGTGGA TAGCGGTTTG ACTCACGGGG ATTTCCAAGT ^501 ^511 ^521 ^531 ^541 ^551 ^561 ^571 ^581 ^591 CTCCACCCCA TTGACGTCAA TGGGAGTTTG TTTTGGCACC AAAATCAACG GGACTTTCCA AAATGTCGTA ATAACCCCGC CCCGTTGACG CAAATGGGCG ^601 ^611 ^621 ^631 ^641 ^651 ^661 ^671 ^681 ^691 GTAGGCGTGT ACGGTGGGAG GTCTATATAA GCAGAGCTCG TTTAGTGAAC CGTCAGATCA CTAGAAGCTT TATTGCGGTA GTTTATCACA GTTAAATTGC ^701 ^711 ^721 ^731 ^741 ^751 ^761 ^771 ^781 ^791 TAACGCAGTC AGTGCTTCTG ACACAACAGT CTCGAACTTA AGCTGCAGAA GTTGGTCGTG AGGCACTGGG CAGGTAAGTA TCAAGGTTAC AAGACAGGTT ^801 ^811 ^821 ^831 ^841 ^851 ^861 ^871 ^881 ^891 TAAGGAGACC AATAGAAACT GGGCTTGTCG AGACAGAGAA GACTCTTGCG TTTCTGATAG GCACCTATTG GTCTTACTGA CATCCACTTT GCCTTTCTCT ^901 ^911 ^921 ^931 ^941 ^951 ^961 ^971 ^981 ^991 CCACAGGTGT CCACTCCCAG TTCAATTACA GCTCTTAAGG CTAGAGTACT TAATACGACT CACTATAGGC TAGCCACCAT GACTTCGAAA GTTTATGATC ^1001 ^1011 ^1021 ^1031 ^1041 ^1051 ^1061 ^1071 ^1081 ^1091 CAGAACAAAG GAAACGGATG ATAACTGGTC CGCAGTGGTG GGCCAGATGT AAACAAATGA ATGTTCTTGA TTCATTTATT AATTATTATG ATTCAGAAAA ^1101 ^1111 ^1121 ^1131 ^1141 ^1151 ^1161 ^1171 ^1181 ^1191 ACATGCAGAA AATGCTGTTA TTTTTTTACA TGGTAACGCG GCCTCTTCTT ATTTATGGCG ACATGTTGTG CCACATATTG AGCCAGTAGC GCGGTGTATT ^1201 ^1211 ^1221 ^1231 ^1241 ^1251 ^1261 ^1271 ^1281 ^1291 ATACCAGACC TTATTGGTAT GGGCAAATCA GGCAAATCTG GTAATGGTTC TTATAGGTTA CTTGATCATT ACAAATATCT TACTGCATGG TTTGAACTTC ^1301 ^1311 ^1321 ^1331 ^1341 ^1351 ^1361 ^1371 ^1381 ^1391 TTAATTTACC AAAGAAGATC ATTTTTGTCG GCCATGATTG GGGTGCTTGT TTGGCATTTC ATTATAGCTA TGAGCATCAA GATAAGATCA AAGCAATAGT ^1401 ^1411 ^1421 ^1431 ^1441 ^1451 ^1461 ^1471 ^1481 ^1491 TCACGCTGAA AGTGTAGTAG ATGTGATTGA ATCATGGGAT GAATGGCCTG ATATTGAAGA AGATATTGCG TTGATCAAAT CTGAAGAAGG AGAAAAAATG ^1501 ^1511 ^1521 ^1531 ^1541 ^1551 ^1561 ^1571 ^1581 ^1591 GTTTTGGAGA ATAACTTCTT CGTGGAAACC ATGTTGCCAT CAAAAATCAT GAGAAAGTTA GAACCAGAAG AATTTGCAGC ATATCTTGAA CCATTCAAAG ^1601 ^1611 ^1621 ^1631 ^1641 ^1651 ^1661 ^1671 ^1681 ^1691 AGAAAGGTGA AGTTCGTCGT CCAACATTAT CATGGCCTCG TGAAATCCCG TTAGTAAAAG GTGGTAAACC TGACGTTGTA CAAATTGTTA GGAATTATAA ^1701 ^1711 ^1721 ^1731 ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 TGCTTATCTA CGTGCAAGTG ATGATTTACC AAAAATGTTT ATTGAATCGG ACCCAGGATT CTTTTCCAAT GCTATTGTTG AAGGTGCCAA GAAGTTTCCT ^1801 ^1811 ^1821 ^1831 ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 AATACTGAAT TTGTCAAAGT AAAAGGTCTT CATTTTTCGC AAGAAGATGC ACCTGATGAA ATGGGAAAAT ATATCAAATC GTTCGTTGAG CGAGTTCTCA ^1901 ^1911 ^1921 ^1931 ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 AAAATGAACA ATAATTCTAG AGCGGCCGCT CTAGAACTAG TGGATCCCCC GGGCTGCAGG AATTCGATAT CAAGCTTATC GATACCGTCG ACACGAGCTC ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 GCCAGCCCCC GATTGGGGGC GACACTCCAC CATAGATCAC TCCCCTGTGA GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 AGTCGTGCAG CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG CGGAACCGGT GAGTACACCG GAATTGCCAG GACGACCGGG TCCTTTCTTG ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261 ^2271 ^2281 ^2291 GATCAACCCG CTCAATGCCT GGAGATTTGG GCGTGCCCCC GCAAGACTGC TAGCCGAGTA GTGTTGGGTC GCGAAAGGCC TTGTGGTACT GCCTGATAGG ^2301 ^2311 ^2321 ^2331 ^2341 ^2351 ^2361 ^2371 ^2381 ^2391 GTGCTTGCGA GTGCCCCGGG AGGTCTCGTA GACCGTGCAC CATGAGCACG AATCCTAAAC CTCAAAGAAA AACCAAACGT AACACCAACC GCCGCCCACA ^2401 ^2411 ^2421 ^2431 ^2441 ^2451 ^2461 ^2471 ^2481 ^2491 GGACGTCATG GAAGACGCCA AAAACATAAA GAAAGGCCCG GCGCCATTCT ATCCTCTAGA GGATGGAACC GCTGGAGAGC AACTGCATAA GGCTATGAAG ^2501 ^2511 ^2521 ^2531 ^2541 ^2551 ^2561 ^2571 ^2581 ^2591 AGATACGCCC TGGTTCCTGG AACAATTGCT TTTACAGATG CACATATCGA GGTGAACATC ACGTACGCGG AATACTTCGA AATGTCCGTT CGGTTGGCAG ^2601 ^2611 ^2621 ^2631 ^2641 ^2651 ^2661 ^2671 ^2681 ^2691 AAGCTATGAA ACGATATGGG CTGAATACAA ATCACAGAAT CGTCGTATGC AGTGAAAACT CTCTTCAATT CTTTATGCCG GTGTTGGGCG CGTTATTTAT ^2701 ^2711 ^2721 ^2731 ^2741 ^2751 ^2761 ^2771 ^2781 ^2791 CGGAGTTGCA GTTGCGCCCG CGAACGACAT TTATAATGAA CGTGAATTGC TCAACAGTAT GAACATTTCG CAGCCTACCG TAGTGTTTGT TTCCAAAAAG ^2801 ^2811 ^2821 ^2831 ^2841 ^2851 ^2861 ^2871 ^2881 ^2891 GGGTTGCAAA AAATTTTGAA CGTGCAAAAA AAATTACCAA TAATCCAGAA AATTATTATC ATGGATTCTA AAACGGATTA CCAGGGATTT CAGTCGATGT ^2901 ^2911 ^2921 ^2931 ^2941 ^2951 ^2961 ^2971 ^2981 ^2991 ACACGTTCGT CACATCTCAT CTACCTCCCG GTTTTAATGA ATACGATTTT GTACCAGAGT CCTTTGATCG TGACAAAACA ATTGCACTGA TAATGAATTC ^3001 ^3011 ^3021 ^3031 ^3041 ^3051 ^3061 ^3071 ^3081 ^3091 CTCTGGATCT ACTGGGTTAC CTAAGGGTGT GGCCCTTCCG CATAGAACTG CCTGCGTCAG ATTCTCGCAT GCCAGAGATC CTATTTTTGG CAATCAAATC ^3101 ^3111 ^3121 ^3131 ^3141 ^3151 ^3161 ^3171 ^3181 ^3191 ATTCCGGATA CTGCGATTTT AAGTGTTGTT CCATTCCATC ACGGTTTTGG AATGTTTACT ACACTCGGAT ATTTGATATG TGGATTTCGA GTCGTCTTAA ^3201 ^3211 ^3221 ^3231 ^3241 ^3251 ^3261 ^3271 ^3281 ^3291 TGTATAGATT TGAAGAAGAG CTGTTTTTAC GATCCCTTCA GGATTACAAA ATTCAAAGTG CGTTGCTAGT ACCAACCCTA TTTTCATTCT TCGCCAAAAG ^3301 ^3311 ^3321 ^3331 ^3341 ^3351 ^3361 ^3371 ^3381 ^3391 CACTCTGATT GACAAATACG ATTTATCTAA TTTACACGAA ATTGCTTCTG GGGGCGCACC TCTTTCGAAA GAAGTCGGGG AAGCGGTTGC AAAACGCTTC ^3401 ^3411 ^3421 ^3431 ^3441 ^3451 ^3461 ^3471 ^3481 ^3491 CATCTTCCAG GGATACGACA AGGATATGGG CTCACTGAGA CTACATCAGC TATTCTGATT ACACCCGAGG GGGATGATAA ACCGGGCGCG GTCGGTAAAG ^3501 ^3511 ^3521 ^3531 ^3541 ^3551 ^3561 ^3571 ^3581 ^3591 TTGTTCCATT TTTTGAAGCG AAGGTTGTGG ATCTGGATAC CGGGAAAACG CTGGGCGTTA ATCAGAGAGG CGAATTATGT GTCAGAGGAC CTATGATTAT ^3601 ^3611 ^3621 ^3631 ^3641 ^3651 ^3661 ^3671 ^3681 ^3691 GTCCGGTTAT GTAAACAATC CGGAAGCGAC CAACGCCTTG ATTGACAAGG ATGGATGGCT ACATTCTGGA GACATAGCTT ACTGGGACGA AGACGAACAC ^3701 ^3711 ^3721 ^3731 ^3741 ^3751 ^3761 ^3771 ^3781 ^3791 TTCTTCATAG TTGACCGCTT GAAGTCTTTA ATTAAATACA AAGGATATCA GGTGGCCCCC GCTGAATTGG AATCGATATT GTTACAACAC CCCAACATCT ^3801 ^3811 ^3821 ^3831 ^3841 ^3851 ^3861 ^3871 ^3881 ^3891 TCGACGCGGG CGTGGCAGGT CTTCCCGACG ATGACGCCGG TGAACTTCCC GCCGCCGTTG TTGTTTTGGA GCACGGAAAG ACGATGACGG AAAAAGAGAT ^3901 ^3911 ^3921 ^3931 ^3941 ^3951 ^3961 ^3971 ^3981 ^3991 CGTGGATTAC GTGGCCAGTC AAGTAACAAC CGCGAAAAAG TTGCGCGGAG GAGTTGTGTT TGTGGACGAA GTACCGAAAG GTCTTACCGG AAAACTCGAC ^4001 ^4011 ^4021 ^4031 ^4041 ^4051 ^4061 ^4071 ^4081 ^4091 GCAAGAAAAA TCAGAGAGAT CCTCATAAAG GCCAAGAAGG GCGGAAAGTC CAAATTGTAA AATGTAACTG TATTCAGCGA TGACGAAATT CTTAGCTATT ^4101 ^4111 ^4121 ^4131 ^4141 ^4151 ^4161 ^4171 ^4181 ^4191 GTAAGGATCC GGGCCCTATT CTATAGTGTC ACCTAAATGC TAGAGCTCGC TGATCAGCCT CGACTGTGCC TTCTAGTTGC CAGCCATCTG TTGTTTGCCC ^4201 ^4211 ^4221 ^4231 ^4241 ^4251 ^4261 ^4271 ^4281 ^4291 CTCCCCCGTG CCTTCCTTGA CCCTGGAAGG TGCCACTCCC ACTGTCCTTT CCTAATAAAA TGAGGAAATT GCATCGCATT GTCTGAGTAG GTGTCATTCT ^4301 ^4311 ^4321 ^4331 ^4341 ^4351 ^4361 ^4371 ^4381 ^4391 ATTCTGGGGG GTGGGGTGGG GCAGGACAGC AAGGGGGAGG ATTGGGAAGA CAATAGCAGG CATGCTGGGG ATGCGGTGGG CTCTATGGCT TCTGAGGCGG ^4401 ^4411 ^4421 ^4431 ^4441 ^4451 ^4461 ^4471 ^4481 ^4491 AAAGAACCAG CTGGGGCTCG AGGGGGGATC CCCACGCGCC CTGTAGCGGC GCATTAAGCG CGGCGGGTGT GGTGGTTACG CGCAGCGTGA CCGCTACACT ^4501 ^4511 ^4521 ^4531 ^4541 ^4551 ^4561 ^4571 ^4581 ^4591 TGCCAGCGCC CTAGCGCCCG CTCCTTTCGC TTTCTTCCCT TCCTTTCTCG CCACGTTCGC CGGCTTTCCC CGTCAAGCTC TAAATCGGGG CATCCCTTTA ^4601 ^4611 ^4621 ^4631 ^4641 ^4651 ^4661 ^4671 ^4681 ^4691 GGGTTCCGAT TTAGTGCTTT ACGGCACCTC GACCCCAAAA AACTTGATTA GGGTGATGGT TCACGTAGTG GGCCATCGCC CTGATAGACG GTTTTTCGCC ^4701 ^4711 ^4721 ^4731 ^4741 ^4751 ^4761 ^4771 ^4781 ^4791 CTTTGACGTT GGAGTCCACG TTCTTTAATA GTGGACTCTT GTTCCAAACT GGAACAACAC TCAACCCTAT CTCGGTCTAT TCTTTTGATT TATAAGGGAT ^4801 ^4811 ^4821 ^4831 ^4841 ^4851 ^4861 ^4871 ^4881 ^4891 TTTGGGGATT TCGGCCTATT GGTTAAAAAA TGAGCTGATT TAACAAAAAT TTAACGCGAA TTTTAACAAA ATATTAACGT TTACAATTTA AATATTTGCT ^4901 ^4911 ^4921 ^4931 ^4941 ^4951 ^4961 ^4971 ^4981 ^4991 TATACAATCT TCCTGTTTTT GGGGCTTTTC TGATTATCAA CCGGGGTGGG TACCGAGCTC GAATTCTGTG GAATGTGTGT CAGTTAGGGT GTGGAAAGTC ^5001 ^5011 ^5021 ^5031 ^5041 ^5051 ^5061 ^5071 ^5081 ^5091 CCCAGGCTCC CCAGGCAGGC AGAAGTATGC AAAGCATGCA TCTCAATTAG TCAGCAACCA GGTGTGGAAA GTCCCCAGGC TCCCCAGCAG GCAGAAGTAT ^5101 ^5111 ^5121 ^5131 ^5141 ^5151 ^5161 ^5171 ^5181 ^5191 GCAAAGCATG CATCTCAATT AGTCAGCAAC CATAGTCCCG CCCCTAACTC CGCCCATCCC GCCCCTAACT CCGCCCAGTT CCGCCCATTC TCCGCCCCAT ^5201 ^5211 ^5221 ^5231 ^5241 ^5251 ^5261 ^5271 ^5281 ^5291 GGCTGACTAA TTTTTTTTAT TTATGCAGAG GCCGAGGCCG CCTCGGCCTC TGAGCTATTC CAGAAGTAGT GAGGAGGCTT TTTTGGAGGC CTAGGCTTTT ^5301 ^5311 ^5321 ^5331 ^5341 ^5351 ^5361 ^5371 ^5381 ^5391 GCAAAAAGCT CCCGGGAGCT TGGATATCCA TTTTCGGATC TGATCAAGAG ACAGGATGAG GATCGTTTCG CATGATTGAA CAAGATGGAT TGCACGCAGG ^5401 ^5411 ^5421 ^5431 ^5441 ^5451 ^5461 ^5471 ^5481 ^5491 TTCTCCGGCC GCTTGGGTGG AGAGGCTATT CGGCTATGAC TGGGCACAAC AGACAATCGG CTGCTCTGAT GCCGCCGTGT TCCGGCTGTC AGCGCAGGGG ^5501 ^5511 ^5521 ^5531 ^5541 ^5551 ^5561 ^5571 ^5581 ^5591 CGCCCGGTTC TTTTTGTCAA GACCGACCTG TCCGGTGCCC TGAATGAACT GCAGGACGAG GCAGCGCGGC TATCGTGGCT GGCCACGACG GGCGTTCCTT ^5601 ^5611 ^5621 ^5631 ^5641 ^5651 ^5661 ^5671 ^5681 ^5691 GCGCAGCTGT GCTCGACGTT GTCACTGAAG CGGGAAGGGA CTGGCTGCTA TTGGGCGAAG TGCCGGGGCA GGATCTCCTG TCATCTCACC TTGCTCCTGC ^5701 ^5711 ^5721 ^5731 ^5741 ^5751 ^5761 ^5771 ^5781 ^5791 CGAGAAAGTA TCCATCATGG CTGATGCAAT GCGGCGGCTG CATACGCTTG ATCCGGCTAC CTGCCCATTC GACCACCAAG CGAAACATCG CATCGAGCGA ^5801 ^5811 ^5821 ^5831 ^5841 ^5851 ^5861 ^5871 ^5881 ^5891 GCACGTACTC GGATGGAAGC CGGTCTTGTC GATCAGGATG ATCTGGACGA AGAGCATCAG GGGCTCGCGC CAGCCGAACT GTTCGCCAGG CTCAAGGCGC ^5901 ^5911 ^5921 ^5931 ^5941 ^5951 ^5961 ^5971 ^5981 ^5991 GCATGCCCGA CGGCGAGGAT CTCGTCGTGA CCCATGGCGA TGCCTGCTTG CCGAATATCA TGGTGGAAAA TGGCCGCTTT TCTGGATTCA TCGACTGTGG ^6001 ^6011 ^6021 ^6031 ^6041 ^6051 ^6061 ^6071 ^6081 ^6091 CCGGCTGGGT GTGGCGGACC GCTATCAGGA CATAGCGTTG GCTACCCGTG ATATTGCTGA AGAGCTTGGC GGCGAATGGG CTGACCGCTT CCTCGTGCTT ^6101 ^6111 ^6121 ^6131 ^6141 ^6151 ^6161 ^6171 ^6181 ^6191 TACGGTATCG CCGCTCCCGA TTCGCAGCGC ATCGCCTTCT ATCGCCTTCT TGACGAGTTC TTCTGAGCGG GACTCTGGGG TTCGAAATGA CCGACCAAGC ^6201 ^6211 ^6221 ^6231 ^6241 ^6251 ^6261 ^6271 ^6281 ^6291 GACGCCCAAC CTGCCATCAC GAGATTTCGA TTCCACCGCC GCCTTCTATG AAAGGTTGGG CTTCGGAATC GTTTTCCGGG ACGCCGGCTG GATGATCCTC ^6301 ^6311 ^6321 ^6331 ^6341 ^6351 ^6361 ^6371 ^6381 ^6391 CAGCGCGGGG ATCTCATGCT GGAGTTCTTC GCCCACCCCA ACTTGTTTAT TGCAGCTTAT AATGGTTACA AATAAAGCAA TAGCATCACA AATTTCACAA ^6401 ^6411 ^6421 ^6431 ^6441 ^6451 ^6461 ^6471 ^6481 ^6491 ATAAAGCATT TTTTTCACTG CATTCTAGTT GTGGTTTGTC CAAACTCATC AATGTATCTT ATCATGTCTG GATCCCGTCG ACCTCGAGAG CTTGGCGTAA ^6501 ^6511 ^6521 ^6531 ^6541 ^6551 ^6561 ^6571 ^6581 ^6591 TCATGGTCAT AGCTGTTTCC TGTGTGAAAT TGTTATCCGC TCACAATTCC ACACAACATA CGAGCCGGAA GCATAAAGTG TAAAGCCTGG GGTGCCTAAT ^6601 ^6611 ^6621 ^6631 ^6641 ^6651 ^6661 ^6671 ^6681 ^6691 GAGTGAGCTA ACTCACATTA ATTGCGTTGC GCTCACTGCC CGCTTTCCAG TCGGGAAACC TGTCGTGCCA GCTGCATTAA TGAATCGGCC AACGCGCGGG ^6701 ^6711 ^6721 ^6731 ^6741 ^6751 ^6761 ^6771 ^6781 ^6791 GAGAGGCGGT TTGCGTATTG GGCGCTCTTC CGCTTCCTCG CTCACTGACT CGCTGCGCTC GGTCGTTCGG CTGCGGCGAG CGGTATCAGC TCACTCAAAG ^6801 ^6811 ^6821 ^6831 ^6841 ^6851 ^6861 ^6871 ^6881 ^6891 GCGGTAATAC GGTTATCCAC AGAATCAGGG GATAACGCAG GAAAGAACAT GTGAGCAAAA GGCCAGCAAA AGGCCAGGAA CCGTAAAAAG GCCGCGTTGC ^6901 ^6911 ^6921 ^6931 ^6941 ^6951 ^6961 ^6971 ^6981 ^6991 TGGCGTTTTT CCATAGGCTC CGCCCCCCTG ACGAGCATCA CAAAAATCGA CGCTCAAGTC AGAGGTGGCG AAACCCGACA GGACTATAAA GATACCAGGC ^7001 ^7011 ^7021 ^7031 ^7041 ^7051 ^7061 ^7071 ^7081 ^7091 GTTTCCCCCT GGAAGCTCCC TCGTGCGCTC TCCTGTTCCG ACCCTGCCGC TTACCGGATA CCTGTCCGCC TTTCTCCCTT CGGGAAGCGT GGCGCTTTCT ^7101 ^7111 ^7121 ^7131 ^7141 ^7151 ^7161 ^7171 ^7181 ^7191 CAATGCTCAC GCTGTAGGTA TCTCAGTTCG GTGTAGGTCG TTCGCTCCAA GCTGGGCTGT GTGCACGAAC CCCCCGTTCA GCCCGACCGC TGCGCCTTAT ^7201 ^7211 ^7221 ^7231 ^7241 ^7251 ^7261 ^7271 ^7281 ^7291 CCGGTAACTA TCGTCTTGAG TCCAACCCGG TAAGACACGA CTTATCGCCA CTGGCAGCAG CCACTGGTAA CAGGATTAGC AGAGCGAGGT ATGTAGGCGG ^7301 ^7311 ^7321 ^7331 ^7341 ^7351 ^7361 ^7371 ^7381 ^7391 TGCTACAGAG TTCTTGAAGT GGTGGCCTAA CTACGGCTAC ACTAGAAGGA CAGTATTTGG TATCTGCGCT CTGCTGAAGC CAGTTACCTT CGGAAAAAGA ^7401 ^7411 ^7421 ^7431 ^7441 ^7451 ^7461 ^7471 ^7481 ^7491 GTTGGTAGCT CTTGATCCGG CAAACAAACC ACCGCTGGTA GCGGTGGTTT TTTTGTTTGC AAGCAGCAGA TTACGCGCAG AAAAAAAGGA TCTCAAGAAG ^7501 ^7511 ^7521 ^7531 ^7541 ^7551 ^7561 ^7571 ^7581 ^7591 ATCCTTTGAT CTTTTCTACG GGGTCTGACG CTCAGTGGAA CGAAAACTCA CGTTAAGGGA TTTTGGTCAT GAGATTATCA AAAAGGATCT TCACCTAGAT ^7601 ^7611 ^7621 ^7631 ^7641 ^7651 ^7661 ^7671 ^7681 ^7691 CCTTTTAAAT TAAAAATGAA GTTTTAAATC AATCTAAAGT ATATATGAGT AAACTTGGTC TGACAGTTAC CAATGCTTAA TCAGTGAGGC ACCTATCTCA ^7701 ^7711 ^7721 ^7731 ^7741 ^7751 ^7761 ^7771 ^7781 ^7791 GCGATCTGTC TATTTCGTTC ATCCATAGTT GCCTGACTCC CCGTCGTGTA GATAACTACG ATACGGGAGG GCTTACCATC TGGCCCCAGT GCTGCAATGA ^7801 ^7811 ^7821 ^7831 ^7841 ^7851 ^7861 ^7871 ^7881 ^7891 TACCGCGAGA CCCACGCTCA CCGGCTCCAG ATTTATCAGC AATAAACCAG CCAGCCGGAA GGGCCGAGCG CAGAAGTGGT CCTGCAACTT TATCCGCCTC ^7901 ^7911 ^7921 ^7931 ^7941 ^7951 ^7961 ^7971 ^7981 ^7991 CATCCAGTCT ATTAATTGTT GCCGGGAAGC TAGAGTAAGT AGTTCGCCAG TTAATAGTTT GCGCAACGTT GTTGCCATTG CTACAGGCAT CGTGGTGTCA ^8001 ^8011 ^8021 ^8031 ^8041 ^8051 ^8061 ^8071 ^8081 ^8091 CGCTCGTCGT TTGGTATGGC TTCATTCAGC TCCGGTTCCC AACGATCAAG GCGAGTTACA TGATCCCCCA TGTTGTGCAA AAAAGCGGTT AGCTCCTTCG ^8101 ^8111 ^8121 ^8131 ^8141 ^8151 ^8161 ^8171 ^8181 ^8191 GTCCTCCGAT CGTTGTCAGA AGTAAGTTGG CCGCAGTGTT ATCACTCATG GTTATGGCAG CACTGCATAA TTCTCTTACT GTCATGCCAT CCGTAAGATG ^8201 ^8211 ^8221 ^8231 ^8241 ^8251 ^8261 ^8271 ^8281 ^8291 CTTTTCTGTG ACTGGTGAGT ACTCAACCAA GTCATTCTGA GAATAGTGTA TGCGGCGACC GAGTTGCTCT TGCCCGGCGT CAATACGGGA TAATACCGCG ^8301 ^8311 ^8321 ^8331 ^8341 ^8351 ^8361 ^8371 ^8381 ^8391 CCACATAGCA GAACTTTAAA AGTGCTCATC ATTGGAAAAC GTTCTTCGGG GCGAAAACTC TCAAGGATCT TACCGCTGTT GAGATCCAGT TCGATGTAAC ^8401 ^8411 ^8421 ^8431 ^8441 ^8451 ^8461 ^8471 ^8481 ^8491 CCACTCGTGC ACCCAACTGA TCTTCAGCAT CTTTTACTTT CACCAGCGTT TCTGGGTGAG CAAAAACAGG AAGGCAAAAT GCCGCAAAAA AGGGAATAAG ^8501 ^8511 ^8521 ^8531 ^8541 ^8551 ^8561 ^8571 ^8581 ^8591 GGCGACACGG AAATGTTGAA TACTCATACT CTTCCTTTTT CAATATTATT GAAGCATTTA TCAGGGTTAT TGTCTCATGA GCGGATACAT ATTTGAATGT ^8601 ^8611 ^8621 ^8631 ^8641 ^8651 ^8661 ^8671 ^8681 ^8691 ATTTAGAAAA ATAAACAAAT AGGGGTTCCG CGCACATTTC CCCGAAAAGT GCCACCTGAC GTC ^8701 ^8711 ^8721 ^8731 ^8741 ^8751 ^8761
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:
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):
12-947
ORF
ORF position:
2
Version:
0
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The abbreviated name of this ORF/gene:
FLuc-fusion
The description of the protein encoded in this ORF:
Firefly luciferase fusion protein with 22 aminoacid residues from HCV ORF.
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):
1375-3093
Citations:
Honda M., Kaneko S., Matsushita E., Kobayashi K., Abell G. A., Lemon S. M. (2000) Cell cycle regulation of hepatitis C virus internal ribosomal entry site-directed translation. Gastroenterology. 118(1):152-162
IRESs:
IRES:
Version:
0
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The IRES name:
HCV_type_1b+66
The functional status of IRES:
functional
The IRES absolute position (the range includes
START
and
STOP
codons or their equivalents):
1034-1440
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
87
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
493
5'-end of IRES relative to first base of the START codon of the downstream ORF:
-341
3'-end of IRES relative to first base of the START codon of the downstream ORF:
65
The sequence of IRES region aligned to its secondary structure (if available):
GCCAGCCCCC GATTGGGGGC GACACTCCAC CATAGATCAC TCCCCTGTGA GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG ^1034 ^1044 ^1054 ^1064 ^1074 ^1084 ^1094 ^1104 ^1114 ^1124 AGTCGTGCAG CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG CGGAACCGGT GAGTACACCG GAATTGCCAG GACGACCGGG TCCTTTCTTG ^1134 ^1144 ^1154 ^1164 ^1174 ^1184 ^1194 ^1204 ^1214 ^1224 GATCAACCCG CTCAATGCCT GGAGATTTGG GCGTGCCCCC GCAAGACTGC TAGCCGAGTA GTGTTGGGTC GCGAAAGGCC TTGTGGTACT GCCTGATAGG ^1234 ^1244 ^1254 ^1264 ^1274 ^1284 ^1294 ^1304 ^1314 ^1324 GTGCTTGCGA GTGCCCCGGG AGGTCTCGTA GACCGTGCAC CATGAGCACG AATCCTAAAC CTCAAAGAAA AACCAAACGT AACACCAACC GCCGCCCACA ^1334 ^1344 ^1354 ^1364 ^1374 ^1384 ^1394 ^1404 ^1414 ^1424 GGACGTC ^1434
Citations:
Honda M., Kaneko S., Matsushita E., Kobayashi K., Abell G. A., Lemon S. M. (2000) Cell cycle regulation of hepatitis C virus internal ribosomal entry site-directed translation. Gastroenterology. 118(1):152-162
Last change to the database: 2019-03-18 09:32:49 GMT+1
plasmid_with_promoter_and_putative_IRES_without_translational_characterization
