IRESite_Id:197 characteristics of HCV+21 IRES studied in pBL-RLuc-HCV-c22-28-hpCATT plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `197`	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 21nt (including ATG) from HCV polyprotein followed by some crap and KpnI site, followed by hairpin
structure, followed then by the CAT sequence itself (including the so called ACAT sequence (CGAGAAAAAAATCAC)).

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 CATGAGCACG AATCCTAAAC CTgtttctcA AACcaaGgta ccGCCGAGCT CTCGGCGGTA CGTCGAGAAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAAATCACTG GATATACCAC CGTTGATATA TCCCAATGGC ATCGTAAAGA ACATTTTGAG GCATTTCAGT CAGTTGCTCA ATGTACCTAT AACCAGACCG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTCAGCTGGA TATTACGGCC TTTTTAAAGA CCGTAAAGAA AAATAAGCAC AAGTTTTATC CGGCCTTTAT TCACATTCTT GCCCGCCTCA TGATGAATGC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TCATCCGGAg TTCCGTATGG CAATGAAAGA CGGTGAGCTG GTGATATGGG ATAGTGTTCA CCCTTGTTAC ACCGTTTTCC ATGAGCAAAC TGAAACGTTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TCATCGCTCT GGAGTGAATA CCACGACGAT TTCCGGCAGT TTCTACACAT ATATTCGCAA GATGTGGCGT GTTACGGTGA AAACCTGGCC TATTTCCCTA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AAGGGTTTAT TGAGAATATG TTTTTCGTCT CAGCCAATCC CTGGGTGAGT TTCACCAGTT TTGATTTAAA CGTGGCCAAT ATGGACAACT TCTTCGCCCC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGTTTTCACt ATGGGCAAAT ATTATACGCA AGGCGACAAG GTGCTGATGC CGCTGGCGAT TCAGGTTCAT CATGCCGTCT GTGATGGCTT CCATGTCGGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGAATGCTTA ATGAAGTACA ACAATACTGC GATGAGTGGC AGGGCGGGGC GTAATTTTTT TTAAGGCAGT TATTGGTGCC CTTAAACGCC TGGTTGCGTA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGCCTGAATA AGTGATAATA AGCGGATGAA TGGCAGAAAT TCGACTCGAC Aggatccggc tgctaacaaa gcccgaaagg aagctgagtt ggctgctgcc 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

accgctgagc aataactagc ataacccctt ggggcctcta aacgggtctt gaggggtttt ttg
^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:
pBL-RLuc-HCV-c22-28-hpCATT 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 CACCATGAGC ACGAATCCTA AACCTgtttc 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

tcAAACcaaG gtaccGCCGA GCTCTCGGCG GTACGTCGAG AAAAAAATCA CTGGATATAC CACCGTTGAT ATATCCCAAT GGCATCGTAA AGAACATTTT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GAGGCATTTC AGTCAGTTGC TCAATGTACC TATAACCAGA CCGTTCAGCT GGATATTACG GCCTTTTTAA AGACCGTAAA GAAAAATAAG CACAAGTTTT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATCCGGCCTT TATTCACATT CTTGCCCGCC TCATGATGAA TGCTCATCCG GAgTTCCGTA TGGCAATGAA AGACGGTGAG CTGGTGATAT GGGATAGTGT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TCACCCTTGT TACACCGTTT TCCATGAGCA AACTGAAACG TTTTCATCGC TCTGGAGTGA ATACCACGAC GATTTCCGGC AGTTTCTACA CATATATTCG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CAAGATGTGG CGTGTTACGG TGAAAACCTG GCCTATTTCC CTAAAGGGTT TATTGAGAAT ATGTTTTTCG TCTCAGCCAA TCCCTGGGTG AGTTTCACCA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTTTTGATTT AAACGTGGCC AATATGGACA ACTTCTTCGC CCCCGTTTTC ACtATGGGCA AATATTATAC GCAAGGCGAC AAGGTGCTGA TGCCGCTGGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GATTCAGGTT CATCATGCCG TCTGTGATGG CTTCCATGTC GGCAGAATGC TTAATGAAGT ACAACAATAC TGCGATGAGT GGCAGGGCGG GGCGTAATTT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TTTTTAAGGC AGTTATTGGT GCCCTTAAAC GCCTGGTTGC GTACGCCTGA ATAAGTGATA ATAAGCGGAT GAATGGCAGA AATTCGACTC GACAggatcc 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ggctgctaac aaagcccgaa aggaagctga gttggctgct gccaccgctg agcaataact agcataaccc cttggggcct ctaaacgggt cttgaggggt 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tttttgctga aaggaggaac tatatccgga tatcgatatc ccgcaagagg cccggcagta ccggcataac caagcctatg cctacagcat ccagggtgac 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ggtgccgagg atgacgatga gcgcattgtt agatttcata cacggtgcct gactgcgtta gcaatttaac tgtgATAAAC TACCGCATTA aagcttATCG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCAGCTTTTG TTCCCTTTAG TGAGGGTTAA TTCCGAGCTT GGCGTAATCA TGGTCATAGC TGTTTCCTGT GTGAAATTGT TATCCGCTCA CAATTCCACA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CAACATACGA GCCGGAAGCA TAAAGTGTAA AGCCTGGGGT GCCTAATGAG TGAGCTAACT CACATTAATT GCGTTGCGCT CACTGCCCGC TTTCCAGTCG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GGAAACCTGT CGTGCCAGCT GCATTAATGA ATCGGCCAAC GCGCGGGGAG AGGCGGTTTG CGTATTGGGC GCTCTTCCGC TTCCTCGCTC ACTGACTCGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGCGCTCGGT CGTTCGGCTG CGGCGAGCGG TATCAGCTCA CTCAAAGGCG GTAATACGGT TATCCACAGA ATCAGGGGAT AACGCAGGAA AGAACATGTG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGCAAAAGGC CAGCAAAAGG CCAGGAACCG TAAAAAGGCC GCGTTGCTGG CGTTTTTCCA TAGGCTCCGC CCCCCTGACG AGCATCACAA AAATCGACGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TCAAGTCAGA GGTGGCGAAA CCCGACAGGA CTATAAAGAT ACCAGGCGTT TCCCCCTGGA AGCTCCCTCG TGCGCTCTCC TGTTCCGACC CTGCCGCTTA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CCGGATACCT GTCCGCCTTT CTCCCTTCGG GAAGCGTGGC GCTTTCTCAT AGCTCACGCT GTAGGTATCT CAGTTCGGTG TAGGTCGTTC GCTCCAAGCT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GGGCTGTGTG CACGAACCCC CCGTTCAGCC CGACCGCTGC GCCTTATCCG GTAACTATCG TCTTGAGTCC AACCCGGTAA GACACGACTT ATCGCCACTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GCAGCAGCCA CTGGTAACAG GATTAGCAGA GCGAGGTATG TAGGCGGTGC TACAGAGTTC TTGAAGTGGT GGCCTAACTA CGGCTACACT AGAAGGACAG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TATTTGGTAT CTGCGCTCTG CTGAAGCCAG TTACCTTCGG AAAAAGAGTT GGTAGCTCTT GATCCGGCAA ACAAACCACC GCTGGTAGCG GTGGTTTTTT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TGTTTGCAAG CAGCAGATTA CGCGCAGAAA AAAAGGATCT CAAGAAGATC CTTTGATCTT TTCTACGGGG TCTGACGCTC AGTGGAACGA AAACTCACGT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TAAGGGATTT TGGTCATGAG ATTATCAAAA AGGATCTTCA CCTAGATCCT TTTAAATTAA AAATGAAGTT TTAAATCAAT CTAAAGTATA TATGAGTAAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CTTGGTCTGA CAGTTACCAA TGCTTAATCA GTGAGGCACC TATCTCAGCG ATCTGTCTAT TTCGTTCATC CATAGTTGCC TGACTCCCCG TCGTGTAGAT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AACTACGATA CGGGAGGGCT TACCATCTGG CCCCAGTGCT GCAATGATAC CGCGAGACCC ACGCTCACCG GCTCCAGATT TATCAGCAAT AAACCAGCCA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GCCGGAAGGG CCGAGCGCAG AAGTGGTCCT GCAACTTTAT CCGCCTCCAT CCAGTCTATT AATTGTTGCC GGGAAGCTAG AGTAAGTAGT TCGCCAGTTA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATAGTTTGCG CAACGTTGTT GCCATTGCTA CAGGCATCGT GGTGTCACGC TCGTCGTTTG GTATGGCTTC ATTCAGCTCC GGTTCCCAAC GATCAAGGCG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AGTTACATGA TCCCCCATGT TGTGCAAAAA AGCGGTTAGC TCCTTCGGTC CTCCGATCGT TGTCAGAAGT AAGTTGGCCG CAGTGTTATC ACTCATGGTT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ATGGCAGCAC TGCATAATTC TCTTACTGTC ATGCCATCCG TAAGATGCTT TTCTGTGACT GGTGAGTACT CAACCAAGTC ATTCTGAGAA TAGTGTATGC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GGCGACCGAG TTGCTCTTGC CCGGCGTCAA TACGGGATAA TACCGCGCCA CATAGCAGAA CTTTAAAAGT GCTCATCATT GGAAAACGTT CTTCGGGGCG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AAAACTCTCA AGGATCTTAC CGCTGTTGAG ATCCAGTTCG ATGTAACCCA CTCGTGCACC CAACTGATCT TCAGCATCTT TTACTTTCAC CAGCGTTTCT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GGGTGAGCAA AAACAGGAAG GCAAAATGCC GCAAAAAAGG GAATAAGGGC GACACGGAAA TGTTGAATAC TCATACTCTT CCTTTTTCAA TATTATTGAA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GCATTTATCA GGGTTATTGT CTCATGAGCG GATACATATT TGAATGTATT TAGAAAAATA AACAAATAGG GGTTCCGCGC ACATTTCCCC GAAAAGTGCC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

ACCTG
^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: `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:
CAT-fusion

The description of the protein encoded in this ORF:
Chloramphenicol acetyltransferase fused with N-terminal sequence of HCV polyprotein, some crap and hairpin-derived sequence

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):

1332-2054

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+21`	The functional status of IRES: `functional`

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

991-1352

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: `384`
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: `20`

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 CATGAGCACG AATCCTAAAC CT
^1291      ^1301      ^1311      ^1321      ^1331      ^1341      ^1351

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 174

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:

Cercopithecus aethiops BT7-H

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

178.000

Name of IRES used as the positive control:

HCV+32

Name of the plasmid used as the positive control. `pBL-RLuc-HCV+32-hpCATT`
`IRESite Id` of the plasmid used as positive control. `193`
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. 6b

Citations:

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