IRESite: The database of experimentally verified IRES structures
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The nucleic acid data:
IRESite Id:
145
Version:
1
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+14nt-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 aatcaggtac cCGAGAAAAA ^1301 ^1311 ^1321 ^1331 ^1341 ^1351 ^1361 ^1371 ^1381 ^1391 AATCACTGGA TATACCACCG TTGATATATC CCAATGGCAT CGTAAAGAAC ATTTTGAGGC ATTTCAGTCA GTTGCTCAAT GTACCTATAA CCAGACCGTT ^1401 ^1411 ^1421 ^1431 ^1441 ^1451 ^1461 ^1471 ^1481 ^1491 CAGCTGGATA TTACGGCCTT TTTAAAGACC GTAAAGAAAA ATAAGCACAA GTTTTATCCG GCCTTTATTC ACATTCTTGC CCGCCTCATG ATGAATGCTC ^1501 ^1511 ^1521 ^1531 ^1541 ^1551 ^1561 ^1571 ^1581 ^1591 ATCCGGAgTT CCGTATGGCA ATGAAAGACG GTGAGCTGGT GATATGGGAT AGTGTTCACC CTTGTTACAC CGTTTTCCAT GAGCAAACTG AAACGTTTTC ^1601 ^1611 ^1621 ^1631 ^1641 ^1651 ^1661 ^1671 ^1681 ^1691 ATCGCTCTGG AGTGAATACC ACGACGATTT CCGGCAGTTT CTACACATAT ATTCGCAAGA TGTGGCGTGT TACGGTGAAA ACCTGGCCTA TTTCCCTAAA ^1701 ^1711 ^1721 ^1731 ^1741 ^1751 ^1761 ^1771 ^1781 ^1791 GGGTTTATTG AGAATATGTT TTTCGTCTCA GCCAATCCCT GGGTGAGTTT CACCAGTTTT GATTTAAACG TGGCCAATAT GGACAACTTC TTCGCCCCCG ^1801 ^1811 ^1821 ^1831 ^1841 ^1851 ^1861 ^1871 ^1881 ^1891 TTTTCACtAT GGGCAAATAT TATACGCAAG GCGACAAGGT GCTGATGCCG CTGGCGATTC AGGTTCATCA TGCCGTCTGT GATGGCTTCC ATGTCGGCAG ^1901 ^1911 ^1921 ^1931 ^1941 ^1951 ^1961 ^1971 ^1981 ^1991 AATGCTTAAT GAAGTACAAC AATACTGCGA TGAGTGGCAG GGCGGGGCGT AATTTTTTTT AAGGCAGTTA TTGGTGCCCT TAAACGCCTG GTTGCGTACG ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 CCTGAATAAG TGATAATAAG CGGATGAATG GCAGAAATTC GACTCGACAg gatccggctg ctaacaaagc ccgaaaggaa gctgagttgg ctgctgccac ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 cgctgagcaa taactagcat aaccccttgg ggcctctaaa cgggtcttga ggggtttttt g ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261
Credibility of mRNA sequence:
end-to-end_sequence_reverse_engineered_and_should_match_experiment
The name of the plasmid:
pRLuc-CSFV+14-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 ttgaatcagg taccCGAGAA AAAAATCACT GGATATACCA CCGTTGATAT ATCCCAATGG CATCGTAAAG AACATTTTGA ^2001 ^2011 ^2021 ^2031 ^2041 ^2051 ^2061 ^2071 ^2081 ^2091 GGCATTTCAG TCAGTTGCTC AATGTACCTA TAACCAGACC GTTCAGCTGG ATATTACGGC CTTTTTAAAG ACCGTAAAGA AAAATAAGCA CAAGTTTTAT ^2101 ^2111 ^2121 ^2131 ^2141 ^2151 ^2161 ^2171 ^2181 ^2191 CCGGCCTTTA TTCACATTCT TGCCCGCCTC ATGATGAATG CTCATCCGGA gTTCCGTATG GCAATGAAAG ACGGTGAGCT GGTGATATGG GATAGTGTTC ^2201 ^2211 ^2221 ^2231 ^2241 ^2251 ^2261 ^2271 ^2281 ^2291 ACCCTTGTTA CACCGTTTTC CATGAGCAAA CTGAAACGTT TTCATCGCTC TGGAGTGAAT ACCACGACGA TTTCCGGCAG TTTCTACACA TATATTCGCA ^2301 ^2311 ^2321 ^2331 ^2341 ^2351 ^2361 ^2371 ^2381 ^2391 AGATGTGGCG TGTTACGGTG AAAACCTGGC CTATTTCCCT AAAGGGTTTA TTGAGAATAT GTTTTTCGTC TCAGCCAATC CCTGGGTGAG TTTCACCAGT ^2401 ^2411 ^2421 ^2431 ^2441 ^2451 ^2461 ^2471 ^2481 ^2491 TTTGATTTAA ACGTGGCCAA TATGGACAAC TTCTTCGCCC CCGTTTTCAC tATGGGCAAA TATTATACGC AAGGCGACAA GGTGCTGATG CCGCTGGCGA ^2501 ^2511 ^2521 ^2531 ^2541 ^2551 ^2561 ^2571 ^2581 ^2591 TTCAGGTTCA TCATGCCGTC TGTGATGGCT TCCATGTCGG CAGAATGCTT AATGAAGTAC AACAATACTG CGATGAGTGG CAGGGCGGGG CGTAATTTTT ^2601 ^2611 ^2621 ^2631 ^2641 ^2651 ^2661 ^2671 ^2681 ^2691 TTTAAGGCAG TTATTGGTGC CCTTAAACGC CTGGTTGCGT ACGCCTGAAT AAGTGATAAT AAGCGGATGA ATGGCAGAAA TTCGACTCGA CAggatccgg ^2701 ^2711 ^2721 ^2731 ^2741 ^2751 ^2761 ^2771 ^2781 ^2791 ctgctaacaa agcccgaaag gaagctgagt tggctgctgc caccgctgag caataactag cataacccct tggggcctct aaacgggtct tgaggggttt ^2801 ^2811 ^2821 ^2831 ^2841 ^2851 ^2861 ^2871 ^2881 ^2891 tttgctgaaa ggaggaacta tatccggata tcgatatccc gcaagaggcc cggcagtacc ggcataacca agcctatgcc tacagcatcc agggtgacgg ^2901 ^2911 ^2921 ^2931 ^2941 ^2951 ^2961 ^2971 ^2981 ^2991 tgccgaggat gacgatgagc gcattgttag atttcataca cggtgcctga ctgcgttagc aatttaactg tgATAAACTA CCGCATTAaa gcttATCGCC ^3001 ^3011 ^3021 ^3031 ^3041 ^3051 ^3061 ^3071 ^3081 ^3091 AGCTTTTGTT CCCTTTAGTG AGGGTTAATT CCGAGCTTGG CGTAATCATG GTCATAGCTG TTTCCTGTGT GAAATTGTTA TCCGCTCACA ATTCCACACA ^3101 ^3111 ^3121 ^3131 ^3141 ^3151 ^3161 ^3171 ^3181 ^3191 ACATACGAGC CGGAAGCATA AAGTGTAAAG CCTGGGGTGC CTAATGAGTG AGCTAACTCA CATTAATTGC GTTGCGCTCA CTGCCCGCTT TCCAGTCGGG ^3201 ^3211 ^3221 ^3231 ^3241 ^3251 ^3261 ^3271 ^3281 ^3291 AAACCTGTCG TGCCAGCTGC ATTAATGAAT CGGCCAACGC GCGGGGAGAG GCGGTTTGCG TATTGGGCGC TCTTCCGCTT CCTCGCTCAC TGACTCGCTG ^3301 ^3311 ^3321 ^3331 ^3341 ^3351 ^3361 ^3371 ^3381 ^3391 CGCTCGGTCG TTCGGCTGCG GCGAGCGGTA TCAGCTCACT CAAAGGCGGT AATACGGTTA TCCACAGAAT CAGGGGATAA CGCAGGAAAG AACATGTGAG ^3401 ^3411 ^3421 ^3431 ^3441 ^3451 ^3461 ^3471 ^3481 ^3491 CAAAAGGCCA GCAAAAGGCC AGGAACCGTA AAAAGGCCGC GTTGCTGGCG TTTTTCCATA GGCTCCGCCC CCCTGACGAG CATCACAAAA ATCGACGCTC ^3501 ^3511 ^3521 ^3531 ^3541 ^3551 ^3561 ^3571 ^3581 ^3591 AAGTCAGAGG TGGCGAAACC CGACAGGACT ATAAAGATAC CAGGCGTTTC CCCCTGGAAG CTCCCTCGTG CGCTCTCCTG TTCCGACCCT GCCGCTTACC ^3601 ^3611 ^3621 ^3631 ^3641 ^3651 ^3661 ^3671 ^3681 ^3691 GGATACCTGT CCGCCTTTCT CCCTTCGGGA AGCGTGGCGC TTTCTCATAG CTCACGCTGT AGGTATCTCA GTTCGGTGTA GGTCGTTCGC TCCAAGCTGG ^3701 ^3711 ^3721 ^3731 ^3741 ^3751 ^3761 ^3771 ^3781 ^3791 GCTGTGTGCA CGAACCCCCC GTTCAGCCCG ACCGCTGCGC CTTATCCGGT AACTATCGTC TTGAGTCCAA CCCGGTAAGA CACGACTTAT CGCCACTGGC ^3801 ^3811 ^3821 ^3831 ^3841 ^3851 ^3861 ^3871 ^3881 ^3891 AGCAGCCACT GGTAACAGGA TTAGCAGAGC GAGGTATGTA GGCGGTGCTA CAGAGTTCTT GAAGTGGTGG CCTAACTACG GCTACACTAG AAGGACAGTA ^3901 ^3911 ^3921 ^3931 ^3941 ^3951 ^3961 ^3971 ^3981 ^3991 TTTGGTATCT GCGCTCTGCT GAAGCCAGTT ACCTTCGGAA AAAGAGTTGG TAGCTCTTGA TCCGGCAAAC AAACCACCGC TGGTAGCGGT GGTTTTTTTG ^4001 ^4011 ^4021 ^4031 ^4041 ^4051 ^4061 ^4071 ^4081 ^4091 TTTGCAAGCA GCAGATTACG CGCAGAAAAA AAGGATCTCA AGAAGATCCT TTGATCTTTT CTACGGGGTC TGACGCTCAG TGGAACGAAA ACTCACGTTA ^4101 ^4111 ^4121 ^4131 ^4141 ^4151 ^4161 ^4171 ^4181 ^4191 AGGGATTTTG GTCATGAGAT TATCAAAAAG GATCTTCACC TAGATCCTTT TAAATTAAAA ATGAAGTTTT AAATCAATCT AAAGTATATA TGAGTAAACT ^4201 ^4211 ^4221 ^4231 ^4241 ^4251 ^4261 ^4271 ^4281 ^4291 TGGTCTGACA GTTACCAATG CTTAATCAGT GAGGCACCTA TCTCAGCGAT CTGTCTATTT CGTTCATCCA TAGTTGCCTG ACTCCCCGTC GTGTAGATAA ^4301 ^4311 ^4321 ^4331 ^4341 ^4351 ^4361 ^4371 ^4381 ^4391 CTACGATACG GGAGGGCTTA CCATCTGGCC CCAGTGCTGC AATGATACCG CGAGACCCAC GCTCACCGGC TCCAGATTTA TCAGCAATAA ACCAGCCAGC ^4401 ^4411 ^4421 ^4431 ^4441 ^4451 ^4461 ^4471 ^4481 ^4491 CGGAAGGGCC GAGCGCAGAA GTGGTCCTGC AACTTTATCC GCCTCCATCC AGTCTATTAA TTGTTGCCGG GAAGCTAGAG TAAGTAGTTC GCCAGTTAAT ^4501 ^4511 ^4521 ^4531 ^4541 ^4551 ^4561 ^4571 ^4581 ^4591 AGTTTGCGCA ACGTTGTTGC CATTGCTACA GGCATCGTGG TGTCACGCTC GTCGTTTGGT ATGGCTTCAT TCAGCTCCGG TTCCCAACGA TCAAGGCGAG ^4601 ^4611 ^4621 ^4631 ^4641 ^4651 ^4661 ^4671 ^4681 ^4691 TTACATGATC CCCCATGTTG TGCAAAAAAG CGGTTAGCTC CTTCGGTCCT CCGATCGTTG TCAGAAGTAA GTTGGCCGCA GTGTTATCAC TCATGGTTAT ^4701 ^4711 ^4721 ^4731 ^4741 ^4751 ^4761 ^4771 ^4781 ^4791 GGCAGCACTG CATAATTCTC TTACTGTCAT GCCATCCGTA AGATGCTTTT CTGTGACTGG TGAGTACTCA ACCAAGTCAT TCTGAGAATA GTGTATGCGG ^4801 ^4811 ^4821 ^4831 ^4841 ^4851 ^4861 ^4871 ^4881 ^4891 CGACCGAGTT GCTCTTGCCC GGCGTCAATA CGGGATAATA CCGCGCCACA TAGCAGAACT TTAAAAGTGC TCATCATTGG AAAACGTTCT TCGGGGCGAA ^4901 ^4911 ^4921 ^4931 ^4941 ^4951 ^4961 ^4971 ^4981 ^4991 AACTCTCAAG GATCTTACCG CTGTTGAGAT CCAGTTCGAT GTAACCCACT CGTGCACCCA ACTGATCTTC AGCATCTTTT ACTTTCACCA GCGTTTCTGG ^5001 ^5011 ^5021 ^5031 ^5041 ^5051 ^5061 ^5071 ^5081 ^5091 GTGAGCAAAA ACAGGAAGGC AAAATGCCGC AAAAAAGGGA ATAAGGGCGA CACGGAAATG TTGAATACTC ATACTCTTCC TTTTTCAATA TTATTGAAGC ^5101 ^5111 ^5121 ^5131 ^5141 ^5151 ^5161 ^5171 ^5181 ^5191 ATTTATCAGG GTTATTGTCT CATGAGCGGA TACATATTTG AATGTATTTA GAAAAATAAA CAAATAGGGG TTCCGCGCAC ATTTCCCCGA AAAGTGCCAC ^5201 ^5211 ^5221 ^5231 ^5241 ^5251 ^5261 ^5271 ^5281 ^5291 CTG ^5301
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:
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:
CAT
The description of the protein encoded in this ORF:
Chloramphenicol acetyltransferase
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):
1372-2052
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+14
The functional status of IRES:
functional
The IRES absolute position (the range includes
START
and
STOP
codons or their equivalents):
999-1385
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:
417
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:
13
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 tgaatca ^1299 ^1309 ^1319 ^1329 ^1339 ^1349 ^1359 ^1369 ^1379
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:
100
Version:
4
Last change:
2006-07-17 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:
70.000
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
