IRESite_Id:207 characteristics of HCV+3 IRES studied in pBL-RLuc-HCV+3-SAPT plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `207`	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:
hopefully_full-length_mRNA

The mRNA/+RNA description:

Bicistronic mRNA transcribed in vitro using T7 polymerase while transcription was supposedly terminated
immediately after the Tphi termination signal sequence. The CAT-fusion ORF sequence contains at its 5'-end
additional 2nt (just the AT from initiator codon) from HCV polyprotein followed by KpnI site, followed then by
the SAP sequence itself. The construct should have been better named pBL-RLuc-HCV+2-SAPT.

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 GCCAGCCCCC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGATGGGGGC GACACTCCAC CATGAATCAC TCCCCTGTGA GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG TGTCGTGCAG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG CGGAACCGGT GAGTACACCG GAATTGCCAG GACGACCGGG TCCTTTCTTG GATAAACCCG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CTCAATGCCT GGAGATTTGG GCGTGCCCCC GCAAGACTGC TAGCCGAGTA GTGTTGGGTC GCGAAAGGCC TTGTGGTACT GCCTGATAGG GTGCTTGCGA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GTGCCCCGGG AGGTCTCGTA GACCGTGCAC CATggtaccG CTGCTGCTGC TGCTGCTGCT GGGCCTGAGG CTACAGCTCT CCCTGGGCAT CATCCCAGTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAGGAGGAGA ACCCGGACTT CTGGAACCGC GAGGCAGCCG AGGCCCTGGG TGCCGCCAAG AAGCTGCAGC CTGCACAGAC AGCCGCCAAG AACCTCATCA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCTTCCTGGG CGATGGGATG GGGGTGTCTA CGGTGACAGC TGCCAGGATC CTAAAAGGGC AGAAGAAGGA CAAACTGGGG CCTGAGATAC CCCTGGCCAT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGACCGCTTC CCATATGTGG CTCTGTCCAA GACATACAAT GTAGACAAAC ATGTGCCAGA CAGTGGAGCC ACAGCCACGG CCTACCTGTG CGGGGTCAAG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GGCAACTTCC AGACCATTGG CTTGAGTGCA GCCGCCCGCT TTAACCAGTG CAACACGACA CGCGGCAACG AGGTCATCTC CGTGATGAAT CGGGCCAAGA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AAGCAGGGAA GTCAGTGGGA GTGGTAACCA CCACACGAGT GCAGCACGCC TCGCCAGCCG GCACCTACGC CCACACGGTG AACCGCAACT GGTACTCGGA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGCCGACGTG CCTGCCTCGG CCCGCCAGGA GGGGTGCCAG GACATCGCTA CGCAGCTCAT CTCCAACATG GACATTGACG TGATCCTAGG TGGAGGCCGA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAGTACATGT TTCCCATGGG AACCCCAGAC CCTGAGTACC CAGATGACTA CAGCCAAGGT GGGACCAGGC TGGACGGGAA GAATCTGGTG CAGGAATGGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGGCGAAGCG CCAGGGTGCC CGGTATGTGT GGAACCGCAC TGAGCTCATG CAGGCTTCCC TGGACCCGTC TGTGACCCAT CTCATGGGTC TCTTTGAGCC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGGAGACATG AAATACGAGA TCCACCGAGA CTCCACACTG GACCCCTCCC TGATGGAGAT GACAGAGGCT GCCCTGCGCC TGCTGAGCAG GAACCCCCGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGCTTCTTCC TCTTCGTGGA GGGTGGTCGC ATCGACCATG GTCATCATGA AAGCAGGGCT TACCGGGCAC TGACTGAGAC GATCATGTTC GACGACGCCA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTGAGAGGGC GGGCCAGCTC ACCAGCGAGG AGGACACGCT GAGCCTCGTC ACTGCCGACC ACTCCCACGT CTTCTCCTTC GGAGGCTACC CCCTGCGAGG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GAGCTCCATC TTCGGGCTGG CCCCTGGCAA GGCCCGGGAC AGGAAGGCCT ACACGGTCCT CCTATACGGA AACGGTCCAG GCTATGTGCT CAAGGACGGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GCCCGGCCGG ATGTTACCGA GAGCGAGAGC GGGAGCCCCG AGTATCGGCA GCAGTCAGCA GTGCCCCTGG ACGAAGAGAC CCACGCAGGC GAGGACGTGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CGGTGTTCGC GCGCGGCCCG CAGGCGCACC TGGTTCACGG CGTGCAGGAG CAGACCTTCA TAGCGCACGT CATGGCCTTC GCCGCCTGCC TGGAGCCCTA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CACCGCCTGC GACCTGGCGC CCCCCGCCGG CACCACCGAC GCCGCGCACC CGGGTTAAcg cgtagatccg gctgctaaca aagcccgaaa ggaagctgag 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ttggctgctg ccaccgctga gcaataacta gcataacccc ttggggcctc taaacgggtc ttgaggggtt ttttg
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pBL-RLuc-HCV+3-SAPT 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:

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 ttcGCCAGCC CCCTGATGGG GGCGACACTC CACCATGAAT CACTCCCCTG TGAGGAACTA CTGTCTTCAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCAGAAAGCG TCTAGCCATG GCGTTAGTAT GAGTGTCGTG CAGCCTCCAG GACCCCCCCT CCCGGGAGAG CCATAGTGGT CTGCGGAACC GGTGAGTACA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCGGAATTGC CAGGACGACC GGGTCCTTTC TTGGATAAAC CCGCTCAATG CCTGGAGATT TGGGCGTGCC CCCGCAAGAC TGCTAGCCGA GTAGTGTTGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GTCGCGAAAG GCCTTGTGGT ACTGCCTGAT AGGGTGCTTG CGAGTGCCCC GGGAGGTCTC GTAGACCGTG CACCATggta ccGCTGCTGC TGCTGCTGCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GCTGGGCCTG AGGCTACAGC TCTCCCTGGG CATCATCCCA GTTGAGGAGG AGAACCCGGA CTTCTGGAAC CGCGAGGCAG CCGAGGCCCT GGGTGCCGCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAGAAGCTGC AGCCTGCACA GACAGCCGCC AAGAACCTCA TCATCTTCCT GGGCGATGGG ATGGGGGTGT CTACGGTGAC AGCTGCCAGG ATCCTAAAAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GGCAGAAGAA GGACAAACTG GGGCCTGAGA TACCCCTGGC CATGGACCGC TTCCCATATG TGGCTCTGTC CAAGACATAC AATGTAGACA AACATGTGCC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AGACAGTGGA GCCACAGCCA CGGCCTACCT GTGCGGGGTC AAGGGCAACT TCCAGACCAT TGGCTTGAGT GCAGCCGCCC GCTTTAACCA GTGCAACACG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ACACGCGGCA ACGAGGTCAT CTCCGTGATG AATCGGGCCA AGAAAGCAGG GAAGTCAGTG GGAGTGGTAA CCACCACACG AGTGCAGCAC GCCTCGCCAG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CCGGCACCTA CGCCCACACG GTGAACCGCA ACTGGTACTC GGACGCCGAC GTGCCTGCCT CGGCCCGCCA GGAGGGGTGC CAGGACATCG CTACGCAGCT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CATCTCCAAC ATGGACATTG ACGTGATCCT AGGTGGAGGC CGAAAGTACA TGTTTCCCAT GGGAACCCCA GACCCTGAGT ACCCAGATGA CTACAGCCAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GGTGGGACCA GGCTGGACGG GAAGAATCTG GTGCAGGAAT GGCTGGCGAA GCGCCAGGGT GCCCGGTATG TGTGGAACCG CACTGAGCTC ATGCAGGCTT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCCTGGACCC GTCTGTGACC CATCTCATGG GTCTCTTTGA GCCTGGAGAC ATGAAATACG AGATCCACCG AGACTCCACA CTGGACCCCT CCCTGATGGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GATGACAGAG GCTGCCCTGC GCCTGCTGAG CAGGAACCCC CGCGGCTTCT TCCTCTTCGT GGAGGGTGGT CGCATCGACC ATGGTCATCA TGAAAGCAGG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GCTTACCGGG CACTGACTGA GACGATCATG TTCGACGACG CCATTGAGAG GGCGGGCCAG CTCACCAGCG AGGAGGACAC GCTGAGCCTC GTCACTGCCG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ACCACTCCCA CGTCTTCTCC TTCGGAGGCT ACCCCCTGCG AGGGAGCTCC ATCTTCGGGC TGGCCCCTGG CAAGGCCCGG GACAGGAAGG CCTACACGGT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CCTCCTATAC GGAAACGGTC CAGGCTATGT GCTCAAGGAC GGCGCCCGGC CGGATGTTAC CGAGAGCGAG AGCGGGAGCC CCGAGTATCG GCAGCAGTCA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GCAGTGCCCC TGGACGAAGA GACCCACGCA GGCGAGGACG TGGCGGTGTT CGCGCGCGGC CCGCAGGCGC ACCTGGTTCA CGGCGTGCAG GAGCAGACCT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TCATAGCGCA CGTCATGGCC TTCGCCGCCT GCCTGGAGCC CTACACCGCC TGCGACCTGG CGCCCCCCGC CGGCACCACC GACGCCGCGC ACCCGGGTTA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

Acgcgtagat ccggctgcta acaaagcccg aaaggaagct gagttggctg ctgccaccgc tgagcaataa ctagcataac cccttggggc ctctaaacgg 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

gtcttgaggg gttttttgct gaaaggagga actatatccg gatatcgata tcccgcaaga ggcccggcag taccggcata accaagccta tgcctacagc 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

atccagggtg acggtgccga ggatgacgat gagcgcattg ttagatttca tacacggtgc ctgactgcgt tagcaattta actgtgATAA ACTACCGCAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TAaagcttAT CGCCAGCTTT TGTTCCCTTT AGTGAGGGTT AATTCCGAGC TTGGCGTAAT CATGGTCATA GCTGTTTCCT GTGTGAAATT GTTATCCGCT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CACAATTCCA CACAACATAC GAGCCGGAAG CATAAAGTGT AAAGCCTGGG GTGCCTAATG AGTGAGCTAA CTCACATTAA TTGCGTTGCG CTCACTGCCC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GCTTTCCAGT CGGGAAACCT GTCGTGCCAG CTGCATTAAT GAATCGGCCA ACGCGCGGGG AGAGGCGGTT TGCGTATTGG GCGCTCTTCC GCTTCCTCGC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TCACTGACTC GCTGCGCTCG GTCGTTCGGC TGCGGCGAGC GGTATCAGCT CACTCAAAGG CGGTAATACG GTTATCCACA GAATCAGGGG ATAACGCAGG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

AAAGAACATG TGAGCAAAAG GCCAGCAAAA GGCCAGGAAC CGTAAAAAGG CCGCGTTGCT GGCGTTTTTC CATAGGCTCC GCCCCCCTGA CGAGCATCAC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AAAAATCGAC GCTCAAGTCA GAGGTGGCGA AACCCGACAG GACTATAAAG ATACCAGGCG TTTCCCCCTG GAAGCTCCCT CGTGCGCTCT CCTGTTCCGA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CCCTGCCGCT TACCGGATAC CTGTCCGCCT TTCTCCCTTC GGGAAGCGTG GCGCTTTCTC ATAGCTCACG CTGTAGGTAT CTCAGTTCGG TGTAGGTCGT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TCGCTCCAAG CTGGGCTGTG TGCACGAACC CCCCGTTCAG CCCGACCGCT GCGCCTTATC CGGTAACTAT CGTCTTGAGT CCAACCCGGT AAGACACGAC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TTATCGCCAC TGGCAGCAGC CACTGGTAAC AGGATTAGCA GAGCGAGGTA TGTAGGCGGT GCTACAGAGT TCTTGAAGTG GTGGCCTAAC TACGGCTACA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTAGAAGGAC AGTATTTGGT ATCTGCGCTC TGCTGAAGCC AGTTACCTTC GGAAAAAGAG TTGGTAGCTC TTGATCCGGC AAACAAACCA CCGCTGGTAG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CGGTGGTTTT TTTGTTTGCA AGCAGCAGAT TACGCGCAGA AAAAAAGGAT CTCAAGAAGA TCCTTTGATC TTTTCTACGG GGTCTGACGC TCAGTGGAAC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GAAAACTCAC GTTAAGGGAT TTTGGTCATG AGATTATCAA AAAGGATCTT CACCTAGATC CTTTTAAATT AAAAATGAAG TTTTAAATCA ATCTAAAGTA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TATATGAGTA AACTTGGTCT GACAGTTACC AATGCTTAAT CAGTGAGGCA CCTATCTCAG CGATCTGTCT ATTTCGTTCA TCCATAGTTG CCTGACTCCC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CGTCGTGTAG ATAACTACGA TACGGGAGGG CTTACCATCT GGCCCCAGTG CTGCAATGAT ACCGCGAGAC CCACGCTCAC CGGCTCCAGA TTTATCAGCA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ATAAACCAGC CAGCCGGAAG GGCCGAGCGC AGAAGTGGTC CTGCAACTTT ATCCGCCTCC ATCCAGTCTA TTAATTGTTG CCGGGAAGCT AGAGTAAGTA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GTTCGCCAGT TAATAGTTTG CGCAACGTTG TTGCCATTGC TACAGGCATC GTGGTGTCAC GCTCGTCGTT TGGTATGGCT TCATTCAGCT CCGGTTCCCA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ACGATCAAGG CGAGTTACAT GATCCCCCAT GTTGTGCAAA AAAGCGGTTA GCTCCTTCGG TCCTCCGATC GTTGTCAGAA GTAAGTTGGC CGCAGTGTTA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TCACTCATGG TTATGGCAGC ACTGCATAAT TCTCTTACTG TCATGCCATC CGTAAGATGC TTTTCTGTGA CTGGTGAGTA CTCAACCAAG TCATTCTGAG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

AATAGTGTAT GCGGCGACCG AGTTGCTCTT GCCCGGCGTC AATACGGGAT AATACCGCGC CACATAGCAG AACTTTAAAA GTGCTCATCA TTGGAAAACG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TTCTTCGGGG CGAAAACTCT CAAGGATCTT ACCGCTGTTG AGATCCAGTT CGATGTAACC CACTCGTGCA CCCAACTGAT CTTCAGCATC TTTTACTTTC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ACCAGCGTTT CTGGGTGAGC AAAAACAGGA AGGCAAAATG CCGCAAAAAA GGGAATAAGG GCGACACGGA AATGTTGAAT ACTCATACTC TTCCTTTTTC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AATATTATTG AAGCATTTAT CAGGGTTATT GTCTCATGAG CGGATACATA TTTGAATGTA TTTAGAAAAA TAAACAAATA GGGGTTCCGC GCACATTTCC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CCGAAAAGTG CCACCTG
^6001      ^6011

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):

33-968

ORF

ORF position:

2

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
SAP

The description of the protein encoded in this ORF:
secreted alkaline phosphatase

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):

1332-2858

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: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `HCV+3`	The functional status of IRES: `defective`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

991-1334

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `23`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `366`
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: `2`

The sequence of IRES region aligned to its secondary structure (if available):

GCCAGCCCCC TGATGGGGGC GACACTCCAC CATGAATCAC TCCCCTGTGA GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG 
^991       ^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      

TGTCGTGCAG CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG CGGAACCGGT GAGTACACCG GAATTGCCAG GACGACCGGG TCCTTTCTTG 
^1091      ^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      

GATAAACCCG CTCAATGCCT GGAGATTTGG GCGTGCCCCC GCAAGACTGC TAGCCGAGTA GTGTTGGGTC GCGAAAGGCC TTGTGGTACT GCCTGATAGG 
^1191      ^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      

GTGCTTGCGA GTGCCCCGGG AGGTCTCGTA GACCGTGCAC CATg
^1291      ^1301      ^1311      ^1321      ^1331

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 185

Version: `0`
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:

34.000

Name of IRES used as the positive control:

HCV+32

Name of the plasmid used as the positive control. `pBL-RLuc-HCV+32-SAPT`
`IRESite Id` of the plasmid used as positive control. `205`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `363`

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. 3b

Citations:

Last change to the database: 2019-03-18 09:32:49 GMT+1