IRESite: The database of experimentally verified IRES structures
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The nucleic acid data:
IRESite Id:
146
Version:
2
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
Last change:
2006-07-16 00:00:00
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:
our_best_guess
The mRNA/+RNA description:
Bicistronic mRNA molecule coding for RLuc-CSFV_IRES+32nt-CAT.
The mRNA/+RNA sequence represented in the +DNA notation:
GGCGAATTGG AGCTCCAccg cggCTAGCCA CCATGACTTC GAAAGTTTAT GATCCAGAAC AAAGGAAACG GATGATAACT GGTCCGCAGT GGTGGGCCAG ^1 ^11 ^21 ^31 ^41 ^51 ^61 ^71 ^81 ^91 ATGTAAACAA ATGAATGTTC TTGATTCATT TATTAATTAT TATGATTCAG AAAAACATGC AGAAAATGCT GTTATTTTTT TACATGGTAA CGCGGCCTCT ^101 ^111 ^121 ^131 ^141 ^151 ^161 ^171 ^181 ^191 TCTTATTTAT GGCGACATGT TGTGCCACAT ATTGAGCCAG TAGCGCGGTG TATTATACCA GACCTTATTG GTATGGGCAA ATCAGGCAAA TCTGGTAATG ^201 ^211 ^221 ^231 ^241 ^251 ^261 ^271 ^281 ^291 GTTCTTATAG GTTACTTGAT CATTACAAAT ATCTTACTGC ATGGTTTGAA CTTCTTAATT TACCAAAGAA GATCATTTTT GTCGGCCATG ATTGGGGTGC ^301 ^311 ^321 ^331 ^341 ^351 ^361 ^371 ^381 ^391 TTGTTTGGCA TTTCATTATA GCTATGAGCA TCAAGATAAG ATCAAAGCAA TAGTTCACGC TGAAAGTGTA GTAGATGTGA TTGAATCATG GGATGAATGG ^401 ^411 ^421 ^431 ^441 ^451 ^461 ^471 ^481 ^491 CCTGATATTG AAGAAGATAT TGCGTTGATC AAATCTGAAG AAGGAGAAAA AATGGTTTTG GAGAATAACT TCTTCGTGGA AACCATGTTG CCATCAAAAA ^501 ^511 ^521 ^531 ^541 ^551 ^561 ^571 ^581 ^591 TCATGAGAAA GTTAGAACCA GAAGAATTTG CAGCATATCT TGAACCATTC AAAGAGAAAG GTGAAGTTCG TCGTCCAACA TTATCATGGC CTCGTGAAAT ^601 ^611 ^621 ^631 ^641 ^651 ^661 ^671 ^681 ^691 CCCGTTAGTA AAAGGTGGTA AACCTGACGT TGTACAAATT GTTAGGAATT ATAATGCTTA TCTACGTGCA AGTGATGATT TACCAAAAAT GTTTATTGAA ^701 ^711 ^721 ^731 ^741 ^751 ^761 ^771 ^781 ^791 TCGGACCCAG GATTCTTTTC CAATGCTATT GTTGAAGGTG CCAAGAAGTT TCCTAATACT GAATTTGTCA AAGTAAAAGG TCTTCATTTT TCGCAAGAAG ^801 ^811 ^821 ^831 ^841 ^851 ^861 ^871 ^881 ^891 ATGCACCTGA TGAAATGGGA AAATATATCA AATCGTTCGT TGAGCGAGTT CTCAAAAATG AACAATAATT CTAGAGCTCT GCAGgaattc agatctatGc ^901 ^911 ^921 ^931 ^941 ^951 ^961 ^971 ^981 ^991 ATACGAGGTT AGTTCATTCT CGTATACACG ATTGGACAAA TCAAAATTAT AATTTGGTTC AGGGCCTCCC TCCAGCGACG GCCGAACTGG GCTAGCCATG ^1001 ^1011 ^1021 ^1031 ^1041 ^1051 ^1061 ^1071 ^1081 ^1091 CCCATAGTAG GACTAGCAAA ACGGAGGGAC TAGCCATAGT GGCGAGCTCC CTGGGTGGTC TAAGTCCTGA GTACAGGACA GTCGTCAGTA GTTCGACGTG ^1101 ^1111 ^1121 ^1131 ^1141 ^1151 ^1161 ^1171 ^1181 ^1191 AGCAGAAGCC CACCTCGAGA TGCTACGTGG ACGAGGGCAT GCCAAGACAC ACCTTAACCC TAGCGGGGGT CGCTAGGGTG AAATCACACC ACGTGATGGG ^1201 ^1211 ^1221 ^1231 ^1241 ^1251 ^1261 ^1271 ^1281 ^1291 AGTACGACCT GATAGGGCGC TGCAGAGGCC CACTATTAGG CTAGTATAAA AATCTCTGCT GTACATGGCA CatGgagttg aatcactttg aacttttata ^1301 ^1311 ^1321 ^1331 ^1341 ^1351 ^1361 ^1371 ^1381 ^1391 caaggtaccC GAGAAAAAAA TCACTGGATA TACCACCGTT GATATATCCC AATGGCATCG TAAAGAACAT TTTGAGGCAT TTCAGTCAGT TGCTCAATGT ^1401 ^1411 ^1421 ^1431 ^1441 ^1451 ^1461 ^1471 ^1481 ^1491 ACCTATAACC AGACCGTTCA GCTGGATATT ACGGCCTTTT TAAAGACCGT AAAGAAAAAT AAGCACAAGT TTTATCCGGC CTTTATTCAC ATTCTTGCCC ^1501 ^1511 ^1521 ^1531 ^1541 ^1551 ^1561 ^1571 ^1581 ^1591 GCCTCATGAT GAATGCTCAT CCGGAgTTCC GTATGGCAAT GAAAGACGGT GAGCTGGTGA TATGGGATAG TGTTCACCCT TGTTACACCG TTTTCCATGA ^1601 ^1611 ^1621 ^1631 ^1641 ^1651 ^1661 ^1671 ^1681 ^1691 GCAAACTGAA ACGTTTTCAT CGCTCTGGAG TGAATACCAC GACGATTTCC GGCAGTTTCT ACACATATAT TCGCAAGATG TGGCGTGTTA CGGTGAAAAC ^1701 ^1711 ^1721 ^1731 ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 CTGGCCTATT TCCCTAAAGG GTTTATTGAG AATATGTTTT TCGTCTCAGC CAATCCCTGG GTGAGTTTCA CCAGTTTTGA TTTAAACGTG GCCAATATGG ^1801 ^1811 ^1821 ^1831 ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 ACAACTTCTT CGCCCCCGTT TTCACtATGG GCAAATATTA TACGCAAGGC GACAAGGTGC TGATGCCGCT GGCGATTCAG GTTCATCATG CCGTCTGTGA ^1901 ^1911 ^1921 ^1931 ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 TGGCTTCCAT GTCGGCAGAA TGCTTAATGA AGTACAACAA TACTGCGATG AGTGGCAGGG CGGGGCGTAA TTTTTTTTAA GGCAGTTATT GGTGCCCTTA ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 AACGCCTGGT TGCGTACGCC TGAATAAGTG ATAATAAGCG GATGAATGGC AGAAATTCGA CTCGACAgga tccggctgct aacaaagccc gaaaggaagc ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 tgagttggct gctgccaccg ctgagcaata actagcataa ccccttgggg cctctaaacg ggtcttgagg ggttttttg ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261 ^2271
Credibility of mRNA sequence:
end-to-end_sequence_reverse_engineered_and_should_match_experiment
The name of the plasmid:
pRLuc-CSFV+32-CAT
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:
CSFV
The origin of IRES in the plasmid:
viral
The donor organism of the IRES segment:
Classical swine fever virus
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:
GGAAATTGTA AACGTTAATA TTTTGTTAAA ATTCGCGTTA AATTTTTGTT AAATCAGCTC ATTTTTTAAC CAATAGGCCG AAATCGGCAA AATCCCTTAT ^1 ^11 ^21 ^31 ^41 ^51 ^61 ^71 ^81 ^91 AAATCAAAAG AATAGACCGA GATAGGGTTG AGTGTTGTTC CAGTTTGGAA CAAGAGTCCA CTATTAAAGA ACGTGGACTC CAACGTCAAA GGGCGAAAAA ^101 ^111 ^121 ^131 ^141 ^151 ^161 ^171 ^181 ^191 CCGTCTATCA GGGCGATGGC CCACTACGTG AACCATCACC CTAATCAAGT TTTTTGGGGT CGAGGTGCCG TAAAGCACTA AATCGGAACC CTAAAGGGAG ^201 ^211 ^221 ^231 ^241 ^251 ^261 ^271 ^281 ^291 CCCCCGATTT AGAGCTTGAC GGGGAAAGCC GGCGAACGTG GCGAGAAAGG AAGGGAAGAA AGCGAAAGGA GCGGGCGCTA GGGCGCTGGC AAGTGTAGCG ^301 ^311 ^321 ^331 ^341 ^351 ^361 ^371 ^381 ^391 GTCACGCTGC GCGTAACCAC CACACCCGCC GCGCTTAATG CGCCGCTACA GGGCGCGTCG CGCCATTCGC CATTCAGGCT GCGCAACTGT TGGGAAGGGC ^401 ^411 ^421 ^431 ^441 ^451 ^461 ^471 ^481 ^491 GATCGGTGCG GGCCTCTTCG CTATTACGCC AGCTGGCGAA AGGGGGATGT GCTGCAAGGC GATTAAGTTG GGTAACGCCA GGGTTTTCCC AGTCACGACG ^501 ^511 ^521 ^531 ^541 ^551 ^561 ^571 ^581 ^591 TTGTAAAACG ACGGCCAGTG AATTGTAATA CGACTCACTA TAGGGCGAAT TGGAGCTCCA ccgcggCTAG CCACCATGAC TTCGAAAGTT TATGATCCAG ^601 ^611 ^621 ^631 ^641 ^651 ^661 ^671 ^681 ^691 AACAAAGGAA ACGGATGATA ACTGGTCCGC AGTGGTGGGC CAGATGTAAA CAAATGAATG TTCTTGATTC ATTTATTAAT TATTATGATT CAGAAAAACA ^701 ^711 ^721 ^731 ^741 ^751 ^761 ^771 ^781 ^791 TGCAGAAAAT GCTGTTATTT TTTTACATGG TAACGCGGCC TCTTCTTATT TATGGCGACA TGTTGTGCCA CATATTGAGC CAGTAGCGCG GTGTATTATA ^801 ^811 ^821 ^831 ^841 ^851 ^861 ^871 ^881 ^891 CCAGACCTTA TTGGTATGGG CAAATCAGGC AAATCTGGTA ATGGTTCTTA TAGGTTACTT GATCATTACA AATATCTTAC TGCATGGTTT GAACTTCTTA ^901 ^911 ^921 ^931 ^941 ^951 ^961 ^971 ^981 ^991 ATTTACCAAA GAAGATCATT TTTGTCGGCC ATGATTGGGG TGCTTGTTTG GCATTTCATT ATAGCTATGA GCATCAAGAT AAGATCAAAG CAATAGTTCA ^1001 ^1011 ^1021 ^1031 ^1041 ^1051 ^1061 ^1071 ^1081 ^1091 CGCTGAAAGT GTAGTAGATG TGATTGAATC ATGGGATGAA TGGCCTGATA TTGAAGAAGA TATTGCGTTG ATCAAATCTG AAGAAGGAGA AAAAATGGTT ^1101 ^1111 ^1121 ^1131 ^1141 ^1151 ^1161 ^1171 ^1181 ^1191 TTGGAGAATA ACTTCTTCGT GGAAACCATG TTGCCATCAA AAATCATGAG AAAGTTAGAA CCAGAAGAAT TTGCAGCATA TCTTGAACCA TTCAAAGAGA ^1201 ^1211 ^1221 ^1231 ^1241 ^1251 ^1261 ^1271 ^1281 ^1291 AAGGTGAAGT TCGTCGTCCA ACATTATCAT GGCCTCGTGA AATCCCGTTA GTAAAAGGTG GTAAACCTGA CGTTGTACAA ATTGTTAGGA ATTATAATGC ^1301 ^1311 ^1321 ^1331 ^1341 ^1351 ^1361 ^1371 ^1381 ^1391 TTATCTACGT GCAAGTGATG ATTTACCAAA AATGTTTATT GAATCGGACC CAGGATTCTT TTCCAATGCT ATTGTTGAAG GTGCCAAGAA GTTTCCTAAT ^1401 ^1411 ^1421 ^1431 ^1441 ^1451 ^1461 ^1471 ^1481 ^1491 ACTGAATTTG TCAAAGTAAA AGGTCTTCAT TTTTCGCAAG AAGATGCACC TGATGAAATG GGAAAATATA TCAAATCGTT CGTTGAGCGA GTTCTCAAAA ^1501 ^1511 ^1521 ^1531 ^1541 ^1551 ^1561 ^1571 ^1581 ^1591 ATGAACAATA ATTCTAGAGC TCTGCAGgaa ttcagatcta tGcATACGAG GTTAGTTCAT TCTCGTATAC ACGATTGGAC AAATCAAAAT TATAATTTGG ^1601 ^1611 ^1621 ^1631 ^1641 ^1651 ^1661 ^1671 ^1681 ^1691 TTCAGGGCCT CCCTCCAGCG ACGGCCGAAC TGGGCTAGCC ATGCCCATAG TAGGACTAGC AAAACGGAGG GACTAGCCAT AGTGGCGAGC TCCCTGGGTG ^1701 ^1711 ^1721 ^1731 ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 GTCTAAGTCC TGAGTACAGG ACAGTCGTCA GTAGTTCGAC GTGAGCAGAA GCCCACCTCG AGATGCTACG TGGACGAGGG CATGCCAAGA CACACCTTAA ^1801 ^1811 ^1821 ^1831 ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 CCCTAGCGGG GGTCGCTAGG GTGAAATCAC ACCACGTGAT GGGAGTACGA CCTGATAGGG CGCTGCAGAG GCCCACTATT AGGCTAGTAT AAAAATCTCT ^1901 ^1911 ^1921 ^1931 ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 GCTGTACATG GCACatGgag ttgaatcact ttgaactttt atacaaggta ccCGAGAAAA AAATCACTGG ATATACCACC GTTGATATAT CCCAATGGCA ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 TCGTAAAGAA CATTTTGAGG CATTTCAGTC AGTTGCTCAA TGTACCTATA ACCAGACCGT TCAGCTGGAT ATTACGGCCT TTTTAAAGAC CGTAAAGAAA ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 AATAAGCACA AGTTTTATCC GGCCTTTATT CACATTCTTG CCCGCCTCAT GATGAATGCT CATCCGGAgT TCCGTATGGC AATGAAAGAC GGTGAGCTGG ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261 ^2271 ^2281 ^2291 TGATATGGGA TAGTGTTCAC CCTTGTTACA CCGTTTTCCA TGAGCAAACT GAAACGTTTT CATCGCTCTG GAGTGAATAC CACGACGATT TCCGGCAGTT ^2301 ^2311 ^2321 ^2331 ^2341 ^2351 ^2361 ^2371 ^2381 ^2391 TCTACACATA TATTCGCAAG ATGTGGCGTG TTACGGTGAA AACCTGGCCT ATTTCCCTAA AGGGTTTATT GAGAATATGT TTTTCGTCTC AGCCAATCCC ^2401 ^2411 ^2421 ^2431 ^2441 ^2451 ^2461 ^2471 ^2481 ^2491 TGGGTGAGTT TCACCAGTTT TGATTTAAAC GTGGCCAATA TGGACAACTT CTTCGCCCCC GTTTTCACtA TGGGCAAATA TTATACGCAA GGCGACAAGG ^2501 ^2511 ^2521 ^2531 ^2541 ^2551 ^2561 ^2571 ^2581 ^2591 TGCTGATGCC GCTGGCGATT CAGGTTCATC ATGCCGTCTG TGATGGCTTC CATGTCGGCA GAATGCTTAA TGAAGTACAA CAATACTGCG ATGAGTGGCA ^2601 ^2611 ^2621 ^2631 ^2641 ^2651 ^2661 ^2671 ^2681 ^2691 GGGCGGGGCG TAATTTTTTT TAAGGCAGTT ATTGGTGCCC TTAAACGCCT GGTTGCGTAC GCCTGAATAA GTGATAATAA GCGGATGAAT GGCAGAAATT ^2701 ^2711 ^2721 ^2731 ^2741 ^2751 ^2761 ^2771 ^2781 ^2791 CGACTCGACA ggatccggct gctaacaaag cccgaaagga agctgagttg gctgctgcca ccgctgagca ataactagca taaccccttg gggcctctaa ^2801 ^2811 ^2821 ^2831 ^2841 ^2851 ^2861 ^2871 ^2881 ^2891 acgggtcttg aggggttttt tgctgaaagg aggaactata tccggatatc gatatcccgc aagaggcccg gcagtaccgg cataaccaag cctatgccta ^2901 ^2911 ^2921 ^2931 ^2941 ^2951 ^2961 ^2971 ^2981 ^2991 cagcatccag ggtgacggtg ccgaggatga cgatgagcgc attgttagat ttcatacacg gtgcctgact gcgttagcaa tttaactgtg ATAAACTACC ^3001 ^3011 ^3021 ^3031 ^3041 ^3051 ^3061 ^3071 ^3081 ^3091 GCATTAaagc ttATCGCCAG CTTTTGTTCC CTTTAGTGAG GGTTAATTCC GAGCTTGGCG TAATCATGGT CATAGCTGTT TCCTGTGTGA AATTGTTATC ^3101 ^3111 ^3121 ^3131 ^3141 ^3151 ^3161 ^3171 ^3181 ^3191 CGCTCACAAT TCCACACAAC ATACGAGCCG GAAGCATAAA GTGTAAAGCC TGGGGTGCCT AATGAGTGAG CTAACTCACA TTAATTGCGT TGCGCTCACT ^3201 ^3211 ^3221 ^3231 ^3241 ^3251 ^3261 ^3271 ^3281 ^3291 GCCCGCTTTC CAGTCGGGAA ACCTGTCGTG CCAGCTGCAT TAATGAATCG GCCAACGCGC GGGGAGAGGC GGTTTGCGTA TTGGGCGCTC TTCCGCTTCC ^3301 ^3311 ^3321 ^3331 ^3341 ^3351 ^3361 ^3371 ^3381 ^3391 TCGCTCACTG ACTCGCTGCG CTCGGTCGTT CGGCTGCGGC GAGCGGTATC AGCTCACTCA AAGGCGGTAA TACGGTTATC CACAGAATCA GGGGATAACG ^3401 ^3411 ^3421 ^3431 ^3441 ^3451 ^3461 ^3471 ^3481 ^3491 CAGGAAAGAA CATGTGAGCA AAAGGCCAGC AAAAGGCCAG GAACCGTAAA AAGGCCGCGT TGCTGGCGTT TTTCCATAGG CTCCGCCCCC CTGACGAGCA ^3501 ^3511 ^3521 ^3531 ^3541 ^3551 ^3561 ^3571 ^3581 ^3591 TCACAAAAAT CGACGCTCAA GTCAGAGGTG GCGAAACCCG ACAGGACTAT AAAGATACCA GGCGTTTCCC CCTGGAAGCT CCCTCGTGCG CTCTCCTGTT ^3601 ^3611 ^3621 ^3631 ^3641 ^3651 ^3661 ^3671 ^3681 ^3691 CCGACCCTGC CGCTTACCGG ATACCTGTCC GCCTTTCTCC CTTCGGGAAG CGTGGCGCTT TCTCATAGCT CACGCTGTAG GTATCTCAGT TCGGTGTAGG ^3701 ^3711 ^3721 ^3731 ^3741 ^3751 ^3761 ^3771 ^3781 ^3791 TCGTTCGCTC CAAGCTGGGC TGTGTGCACG AACCCCCCGT TCAGCCCGAC CGCTGCGCCT TATCCGGTAA CTATCGTCTT GAGTCCAACC CGGTAAGACA ^3801 ^3811 ^3821 ^3831 ^3841 ^3851 ^3861 ^3871 ^3881 ^3891 CGACTTATCG CCACTGGCAG CAGCCACTGG TAACAGGATT AGCAGAGCGA GGTATGTAGG CGGTGCTACA GAGTTCTTGA AGTGGTGGCC TAACTACGGC ^3901 ^3911 ^3921 ^3931 ^3941 ^3951 ^3961 ^3971 ^3981 ^3991 TACACTAGAA GGACAGTATT TGGTATCTGC GCTCTGCTGA AGCCAGTTAC CTTCGGAAAA AGAGTTGGTA GCTCTTGATC CGGCAAACAA ACCACCGCTG ^4001 ^4011 ^4021 ^4031 ^4041 ^4051 ^4061 ^4071 ^4081 ^4091 GTAGCGGTGG TTTTTTTGTT TGCAAGCAGC AGATTACGCG CAGAAAAAAA GGATCTCAAG AAGATCCTTT GATCTTTTCT ACGGGGTCTG ACGCTCAGTG ^4101 ^4111 ^4121 ^4131 ^4141 ^4151 ^4161 ^4171 ^4181 ^4191 GAACGAAAAC TCACGTTAAG GGATTTTGGT CATGAGATTA TCAAAAAGGA TCTTCACCTA GATCCTTTTA AATTAAAAAT GAAGTTTTAA ATCAATCTAA ^4201 ^4211 ^4221 ^4231 ^4241 ^4251 ^4261 ^4271 ^4281 ^4291 AGTATATATG AGTAAACTTG GTCTGACAGT TACCAATGCT TAATCAGTGA GGCACCTATC TCAGCGATCT GTCTATTTCG TTCATCCATA GTTGCCTGAC ^4301 ^4311 ^4321 ^4331 ^4341 ^4351 ^4361 ^4371 ^4381 ^4391 TCCCCGTCGT GTAGATAACT ACGATACGGG AGGGCTTACC ATCTGGCCCC AGTGCTGCAA TGATACCGCG AGACCCACGC TCACCGGCTC CAGATTTATC ^4401 ^4411 ^4421 ^4431 ^4441 ^4451 ^4461 ^4471 ^4481 ^4491 AGCAATAAAC CAGCCAGCCG GAAGGGCCGA GCGCAGAAGT GGTCCTGCAA CTTTATCCGC CTCCATCCAG TCTATTAATT GTTGCCGGGA AGCTAGAGTA ^4501 ^4511 ^4521 ^4531 ^4541 ^4551 ^4561 ^4571 ^4581 ^4591 AGTAGTTCGC CAGTTAATAG TTTGCGCAAC GTTGTTGCCA TTGCTACAGG CATCGTGGTG TCACGCTCGT CGTTTGGTAT GGCTTCATTC AGCTCCGGTT ^4601 ^4611 ^4621 ^4631 ^4641 ^4651 ^4661 ^4671 ^4681 ^4691 CCCAACGATC AAGGCGAGTT ACATGATCCC CCATGTTGTG CAAAAAAGCG GTTAGCTCCT TCGGTCCTCC GATCGTTGTC AGAAGTAAGT TGGCCGCAGT ^4701 ^4711 ^4721 ^4731 ^4741 ^4751 ^4761 ^4771 ^4781 ^4791 GTTATCACTC ATGGTTATGG CAGCACTGCA TAATTCTCTT ACTGTCATGC CATCCGTAAG ATGCTTTTCT GTGACTGGTG AGTACTCAAC CAAGTCATTC ^4801 ^4811 ^4821 ^4831 ^4841 ^4851 ^4861 ^4871 ^4881 ^4891 TGAGAATAGT GTATGCGGCG ACCGAGTTGC TCTTGCCCGG CGTCAATACG GGATAATACC GCGCCACATA GCAGAACTTT AAAAGTGCTC ATCATTGGAA ^4901 ^4911 ^4921 ^4931 ^4941 ^4951 ^4961 ^4971 ^4981 ^4991 AACGTTCTTC GGGGCGAAAA CTCTCAAGGA TCTTACCGCT GTTGAGATCC AGTTCGATGT AACCCACTCG TGCACCCAAC TGATCTTCAG CATCTTTTAC ^5001 ^5011 ^5021 ^5031 ^5041 ^5051 ^5061 ^5071 ^5081 ^5091 TTTCACCAGC GTTTCTGGGT GAGCAAAAAC AGGAAGGCAA AATGCCGCAA AAAAGGGAAT AAGGGCGACA CGGAAATGTT GAATACTCAT ACTCTTCCTT ^5101 ^5111 ^5121 ^5131 ^5141 ^5151 ^5161 ^5171 ^5181 ^5191 TTTCAATATT ATTGAAGCAT TTATCAGGGT TATTGTCTCA TGAGCGGATA CATATTTGAA TGTATTTAGA AAAATAAACA AATAGGGGTT CCGCGCACAT ^5201 ^5211 ^5221 ^5231 ^5241 ^5251 ^5261 ^5271 ^5281 ^5291 TTCCCCGAAA AGTGCCACCT G ^5301 ^5311 ^5321
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:
2006-07-16 00:00:00
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):
33-968
ORF
ORF position:
2
Version:
2
Last change:
2006-07-16 00:00:00
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The abbreviated name of this ORF/gene:
CAT-fusion
The description of the protein encoded in this ORF:
Chloramphenicol acetyltransferase with 32nt from CSFV-Npro followed by KpnI site.
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):
1372-2070
Citations:
Rijnbrand R., Bredenbeek P. J., Haasnoot P. C., Kieft J. S., Spaan W. J., Lemon S. M. (2001) The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA. 7(4):585-597
IRESs:
IRES:
Version:
1
Last change:
2006-07-16 00:00:00
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The IRES name:
CSFV+32
The functional status of IRES:
functional
The IRES absolute position (the range includes
START
and
STOP
codons or their equivalents):
999-1403
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
31
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
435
5'-end of IRES relative to first base of the START codon of the downstream ORF:
-373
3'-end of IRES relative to first base of the START codon of the downstream ORF:
31
The sequence of IRES region aligned to its secondary structure (if available):
GcATACGAGG TTAGTTCATT CTCGTATACA CGATTGGACA AATCAAAATT ATAATTTGGT TCAGGGCCTC CCTCCAGCGA CGGCCGAACT GGGCTAGCCA ^999 ^1009 ^1019 ^1029 ^1039 ^1049 ^1059 ^1069 ^1079 ^1089 TGCCCATAGT AGGACTAGCA AAACGGAGGG ACTAGCCATA GTGGCGAGCT CCCTGGGTGG TCTAAGTCCT GAGTACAGGA CAGTCGTCAG TAGTTCGACG ^1099 ^1109 ^1119 ^1129 ^1139 ^1149 ^1159 ^1169 ^1179 ^1189 TGAGCAGAAG CCCACCTCGA GATGCTACGT GGACGAGGGC ATGCCAAGAC ACACCTTAAC CCTAGCGGGG GTCGCTAGGG TGAAATCACA CCACGTGATG ^1199 ^1209 ^1219 ^1229 ^1239 ^1249 ^1259 ^1269 ^1279 ^1289 GGAGTACGAC CTGATAGGGC GCTGCAGAGG CCCACTATTA GGCTAGTATA AAAATCTCTG CTGTACATGG CACatGgagt tgaatcactt tgaactttta ^1299 ^1309 ^1319 ^1329 ^1339 ^1349 ^1359 ^1369 ^1379 ^1389 tacaa ^1399
Citations:
Rijnbrand R., Bredenbeek P. J., Haasnoot P. C., Kieft J. S., Spaan W. J., Lemon S. M. (2001) The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA. 7(4):585-597
The translation experiments:
Translation results:
IRESite Translation Id:
101
Version:
2
Last change:
2006-06-30 00:00:00
Originaly submitted by:
Martin Mokrejš
Reviewed by:
Martin Mokrejš
The translation method used to study IRES function:
in vitro
The
in vitro
translation system:
rabbit reticulocytes lysate
The organism used for translation:
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this
IRES:
45.000
Name of IRES used as the positive control:
CSFV+55
Name of the plasmid used as the positive control.
pRLuc-CSFV+55-CAT
Name of the plasmid used as the negative control.
pRLuc-CSFV+3-hpCAT
IRESite Id
of the plasmid used as positive control.
144
IRESite Id
of the plasmid used as negative control.
149
The relative translation efficiency in % of the positive control:
100.000
The relative translation efficiency in % of the negative control:
0
The size (length) of intercistronic region in the positive control:
403
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
exogenous_RNA_without_cap_without_polyA_tail
Remarks:
Fig. 8
Citations:
Rijnbrand R., Bredenbeek P. J., Haasnoot P. C., Kieft J. S., Spaan W. J., Lemon S. M. (2001) The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA. 7(4):585-597
Last change to the database: 2019-03-18 09:32:49 GMT+1
plasmid_with_promoter_and_putative_IRES_translationally_characterized
