IRESite_Id:351 characteristics of HAV IRES studied in pHAV.IRES-luc plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `351`	Version: `3`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-06-04 15:43:01`

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:
end-to-end_full-length_mRNA

The mRNA/+RNA description:

In vitro T3 run-off transcript containing 5' region of HAV (HM-175/7 MK-5 strain) containing the IRES (-699 to
-1) plus the region encoding the first 51 amino acids of the viral nucleocapsid cloned upstream of the
luciferase reporter RNA lacking a poly(A) tail.

The mRNA/+RNA sequence represented in the +DNA notation:

GGGAACAAAA GCTGGTACCG GGCCCCCCCT CCCTCTTGGA AGTCCCTGGT GAGGGGACTT GATACCTCAC CGCCGTTTGC CTAGGCTATA GGCTAAATTT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TCCCTTTCCC TTTTCCCTTT CCCATTCCCT TTTGCTTGTA AATATTGATT CCTGCAGGTT CAGGGTTCTT AAATCTGTTT CTCTATAAGA ACACTCATTT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCACGCTTTC TGTCTTCTTT CTTCCAGGGC TCTCCCCTTG CCCTAGGCTC TGGCCGTTGC GCCCGGCGGG GTCAACTCCA TGATTAGCAT GGAGCTGTAG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GAGTCTAAAT TGGGGACACA GATGTTTGGA ACGTCACCTT GCAGTGTTAA CTTGGCTTTC ATGAATCTCT TTGATCTTCC ACAAGGGGTA GGCTACGGGT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GAAACCTCTT AGGCTAATAC TTCTATGAAG AGATGCCTTG GATAGGGTAA CAGCGGCGGA TATTGGTGAG TTGTTAAGAC AAAAACCATT CAACGCCGGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GGACTGACTC TCATCCAGTG GATGCATTGA GTGGATTGAC TGTCAGGGCT GTCTTTAGGC TTAATTCCAG ACCTCTCTGT GCTTAGGGCA AACATCATTT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GGCCTTAAAT GGGATTCTGT GAGAGGGGAT CCCTCCATTG ACAGCTGGAC TGTTCTTTGG GGCCTTATGT GGTGTTTGCC TCTGAGGTAC TCAGGGGCAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TTAGGTTTTT CCTCATTCTT AAATAATAAT GAACATGTCT AGACAAGGTA TTTTCCAGAC TGTTGGGAGT GGTCTTGACC ACATCCTGTC TTTGGCAGAC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATTGAGGAAG AGCAAATGAT TCAATCAGTT GATAGGACTG CAGTGACTGG TGCTTCTTAT TTTACTTCTG TGGATCAATC TCGAGTCATG GAAGACGCCA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAAACATAAA GAAAGGCCCG GCGCCATTCT ATCCTCTAGA GGATGGAACC GCTGGAGAGC AACTGCATAA GGCTATGAAG AGATACGCCC TGGTTCCTGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AACAATTGCT TTTACAGATG CACATATCGA GGTGAACATC ACGTACGCGG AATACTTCGA AATGTCCGTT CGGTTGGCAG AAGCTATGAA ACGATATGGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTGAATACAA ATCACAGAAT CGTCGTATGC AGTGAAAACT CTCTTCAATT CTTTATGCCG GTGTTGGGCG CGTTATTTAT CGGAGTTGCA GTTGCGCCCG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CGAACGACAT TTATAATGAA CGTGAATTGC TCAACAGTAT GAACATTTCG CAGCCTACCG TAGTGTTTGT TTCCAAAAAG GGGTTGCAAA AAATTTTGAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGTGCAAAAA AAATTACCAA TAATCCAGAA AATTATTATC ATGGATTCTA AAACGGATTA CCAGGGATTT CAGTCGATGT ACACGTTCGT CACATCTCAT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTACCTCCCG GTTTTAATGA ATACGATTTT GTACCAGAGT CCTTTGATCG TGACAAAACA ATTGCACTGA TAATGAATTC CTCTGGATCT ACTGGGTTAC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CTAAGGGTGT GGCCCTTCCG CATAGAACTG CCTGCGTCAG ATTCTCGCAT GCCAGAGATC CTATTTTTGG CAATCAAATC ATTCCGGATA CTGCGATTTT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AAGTGTTGTT CCATTCCATC ACGGTTTTGG AATGTTTACT ACACTCGGAT ATTTGATATG TGGATTTCGA GTCGTCTTAA TGTATAGATT TGAAGAAGAG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CTGTTTTTAC GATCCCTTCA GGATTACAAA ATTCAAAGTG CGTTGCTAGT ACCAACCCTA TTTTCATTCT TCGCCAAAAG CACTCTGATT GACAAATACG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ATTTATCTAA TTTACACGAA ATTGCTTCTG GGGGCGCACC TCTTTCGAAA GAAGTCGGGG AAGCGGTTGC AAAACGCTTC CATCTTCCAG GGATACGACA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGGATATGGG CTCACTGAGA CTACATCAGC TATTCTGATT ACACCCGAGG GGGATGATAA ACCGGGCGCG GTCGGTAAAG TTGTTCCATT TTTTGAAGCG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAGGTTGTGG ATCTGGATAC CGGGAAAACG CTGGGCGTTA ATCAGAGAGG CGAATTATGT GTCAGAGGAC CTATGATTAT GTCCGGTTAT GTAAACAATC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGGAAGCGAC CAACGCCTTG ATTGACAAGG ATGGATGGCT ACATTCTGGA GACATAGCTT ACTGGGACGA AGACGAACAC TTCTTCATAG TTGACCGCTT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAAGTCTTTA ATTAAATACA AAGGATATCA GGTGGCCCCC GCTGAATTGG AATCGATATT GTTACAACAC CCCAACATCT TCGACGCGGG CGTGGCAGGT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CTTCCCGACG ATGACGCCGG TGAACTTCCC GCCGCCGTTG TTGTTTTGGA GCACGGAAAG ACGATGACGG AAAAAGAGAT CGTGGATTAC GTCGCCAGTC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AAGTAACAAC CGCGAAAAAG TTGCGCGGAG GAGTTGTGTT TGTGGACGAA GTACCGAAAG GTCTTACCGG AAAACTCGAC GCAAGAAAAA TCAGAGAGAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CCTCATAAAG GCCAAGAAGG GCGGAAAGTC CAAATTGTAA AATGTAACTG TATTCAGCGA TGACGAAATT CTTAGCTATT GTAATATTAT ATGCAAATTG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATGAATGGTA ATTTTGTAAT TGTGGGTCAC TGTACTATTT TAACGAATAA TAAAATCAGG TATAGGTAAC TAAAAAGGAA TTCCTGCAGC CCGGGGGATC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CACTAGTTCT AGAGC
^2701      ^2711

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pHAV.IRES-luc The name of the promoter used to express this mRNA:
T3

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing the major part of HAV 5' UTR (-699 to -1) plus the region encoding the first 51 amino acids of the viral polyprotein (+1 to +153) and firefly luciferase coding region (luc version of the luciferase gene) without the poly(A)tract.

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:
HAV

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Hepatitis A virus HM-175/7 MK-5

The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:

GACGAAAGGG CCTCGTGATA CGCCTATTTT TATAGGTTAA TGTCATGATA ATAATGGTTT CTTAGGACGG ATCGCTTGCC TGTAACTTAC ACGCGCCTCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TATCTTTTAA TGATGGAATA ATTTGGGAAT TTACTCTGTG TTTATTTATT TTTATGTTTT GTATTTGGAT TTTAGAAAGT AAATAAAGAA GGTAGAAGAG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TTACGGAATG AAGAAAAAAA AATAAACAAA GGTTTAAAAA ATTTCAACAA AAAGCGTACT TTACATATAT ATTTATTAGA CAAGAAAAGC AGATTAAATA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GATATACATT CGATTAACGA TAAGTAAAAT GTAAAATCAC AGGATTTTCG TGTGTGGTCT TCTACACAGA CAAGATGAAA CAATTCGGCA TTAATACCTG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AGAGCAGGAA GAGCAAGATA AAAGGTAGTA TTTGTTGGCG ATCCCCCTAG AGTCTTTTAC ATCTTCGGAA AACAAAAACT ATTTTTTCTT TAATTTCTTT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TTTTACTTTC TATTTTTAAT TTATATATTT ATATTAAAAA ATTTAAATTA TAATTATTTT TATAGCACGT GATGAAAAGG ACCCAGGTGG CACTTTTCGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GGAAATGTGC GCGGAACCCC TATTTGTTTA TTTTTCTAAA TACATTCAAA TATGTATCCG CTCATGAGAC AATAACCCTG ATAAATGCTT CAATAATATT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GAAAAAGGAA GAGTATGAGT ATTCAACATT TCCGTGTCGC CCTTATTCCC TTTTTTGCGG CATTTTGCCT TCCTGTTTTT GCTCACCCAG AAACGCTGGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GAAAGTAAAA GATGCTGAAG ATCAGTTGGG TGCACGAGTG GGTTACATCG AACTGGATCT CAACAGCGGT AAGATCCTTG AGAGTTTTCG CCCCGAAGAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CGTTTTCCAA TGATGAGCAC TTTTAAAGTT CTGCTATGTG GCGCGGTATT ATCCCGTATT GACGCCGGGC AAGAGCAACT CGGTCGCCGC ATACACTATT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CTCAGAATGA CTTGGTTGAG TACTCACCAG TCACAGAAAA GCATCTTACG GATGGCATGA CAGTAAGAGA ATTATGCAGT GCTGCCATAA CCATGAGTGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TAACACTGCG GCCAACTTAC TTCTGACAAC GATCGGAGGA CCGAAGGAGC TAACCGCTTT TTTTCACAAC ATGGGGGATC ATGTAACTCG CCTTGATCGT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGGGAACCGG AGCTGAATGA AGCCATACCA AACGACGAGC GTGACACCAC GATGCCTGTA GCAATGGCAA CAACGTTGCG CAAACTATTA ACTGGCGAAC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TACTTACTCT AGCTTCCCGG CAACAATTAA TAGACTGGAT GGAGGCGGAT AAAGTTGCAG GACCACTTCT GCGCTCGGCC CTTCCGGCTG GCTGGTTTAT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGCTGATAAA TCTGGAGCCG GTGAGCGTGG GTCTCGCGGT ATCATTGCAG CACTGGGGCC AGATGGTAAG CCCTCCCGTA TCGTAGTTAT CTACACGACG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GGCAGTCAGG CAACTATGGA TGAACGAAAT AGACAGATCG CTGAGATAGG TGCCTCACTG ATTAAGCATT GGTAACTGTC AGACCAAGTT TACTCATATA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TACTTTAGAT TGATTTAAAA CTTCATTTTT AATTTAAAAG GATCTAGGTG AAGATCCTTT TTGATAATCT CATGACCAAA ATCCCTTAAC GTGAGTTTTC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTTCCACTGA GCGTCAGACC CCGTAGAAAA GATCAAAGGA TCTTCTTGAG ATCCTTTTTT TCTGCGCGTA ATCTGCTGCT TGCAAACAAA AAAACCACCG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTACCAGCGG TGGTTTGTTT GCCGGATCAA GAGCTACCAA CTCTTTTTCC GAAGGTAACT GGCTTCAGCA GAGCGCAGAT ACCAAATACT GTCCTTCTAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGTAGCCGTA GTTAGGCCAC CACTTCAAGA ACTCTGTAGC ACCGCCTACA TACCTCGCTC TGCTAATCCT GTTACCAGTG GCTGCTGCCA GTGGCGATAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GTCGTGTCTT ACCGGGTTGG ACTCAAGACG ATAGTTACCG GATAAGGCGC AGCGGTCGGG CTGAACGGGG GGTTCGTGCA CACAGCCCAG CTTGGAGCGA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACGACCTACA CCGAACTGAG ATACCTACAG CGTGAGCATT GAGAAAGCGC CACGCTTCCC GAAGGGAGAA AGGCGGACAG GTATCCGGTA AGCGGCAGGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCGGAACAGG AGAGCGCACG AGGGAGCTTC CAGGGGGGAA CGCCTGGTAT CTTTATAGTC CTGTCGGGTT TCGCCACCTC TGACTTGAGC GTCGATTTTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GTGATGCTCG TCAGGGGGGC CGAGCCTATG GAAAAACGCC AGCAACGCGG CCTTTTTACG GTTCCTGGCC TTTTGCTGGC CTTTTGCTCA CATGTTCTTT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCTGCGTTAT CCCCTGATTC TGTGGATAAC CGTATTACCG CCTTTGAGTG AGCTGATACC GCTCGCCGCA GCCGAACGAC CGAGCGCAGC GAGTCAGTGA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GCGAGGAAGC GGAAGAGCGC CCAATACGCA AACCGCCTCT CCCCGCGCGT TGGCCGATTC ATTAATGCAG CTGGCACGAC AGGTTTCCCG ACTGGAAAGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GGGCAGTGAG CGCAACGCAA TTAATGTGAG TTACCTCACT CATTAGGCAC CCCAGGCTTT ACACTTTATG CTTCCGGCTC CTATGTTGTG TGGAATTGTG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AGCGGATAAC AATTTCACAC AGGAAACAGC TATGACCATG ATTACGCCAA GCTCGGAATT AACCCTCACT AAAGGGAACA AAAGCTGGTA CCGGGCCCCC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCTCCCTCTT GGAAGTCCCT GGTGAGGGGA CTTGATACCT CACCGCCGTT TGCCTAGGCT ATAGGCTAAA TTTTCCCTTT CCCTTTTCCC TTTCCCATTC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CCTTTTGCTT GTAAATATTG ATTCCTGCAG GTTCAGGGTT CTTAAATCTG TTTCTCTATA AGAACACTCA TTTTCACGCT TTCTGTCTTC TTTCTTCCAG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GGCTCTCCCC TTGCCCTAGG CTCTGGCCGT TGCGCCCGGC GGGGTCAACT CCATGATTAG CATGGAGCTG TAGGAGTCTA AATTGGGGAC ACAGATGTTT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGAACGTCAC CTTGCAGTGT TAACTTGGCT TTCATGAATC TCTTTGATCT TCCACAAGGG GTAGGCTACG GGTGAAACCT CTTAGGCTAA TACTTCTATG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AAGAGATGCC TTGGATAGGG TAACAGCGGC GGATATTGGT GAGTTGTTAA GACAAAAACC ATTCAACGCC GGAGGACTGA CTCTCATCCA GTGGATGCAT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TGAGTGGATT GACTGTCAGG GCTGTCTTTA GGCTTAATTC CAGACCTCTC TGTGCTTAGG GCAAACATCA TTTGGCCTTA AATGGGATTC TGTGAGAGGG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GATCCCTCCA TTGACAGCTG GACTGTTCTT TGGGGCCTTA TGTGGTGTTT GCCTCTGAGG TACTCAGGGG CATTTAGGTT TTTCCTCATT CTTAAATAAT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AATGAACATG TCTAGACAAG GTATTTTCCA GACTGTTGGG AGTGGTCTTG ACCACATCCT GTCTTTGGCA GACATTGAGG AAGAGCAAAT GATTCAATCA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GTTGATAGGA CTGCAGTGAC TGGTGCTTCT TATTTTACTT CTGTGGATCA ATCTCGAGTC ATGGAAGACG CCAAAAACAT AAAGAAAGGC CCGGCGCCAT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TCTATCCTCT AGAGGATGGA ACCGCTGGAG AGCAACTGCA TAAGGCTATG AAGAGATACG CCCTGGTTCC TGGAACAATT GCTTTTACAG ATGCACATAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CGAGGTGAAC ATCACGTACG CGGAATACTT CGAAATGTCC GTTCGGTTGG CAGAAGCTAT GAAACGATAT GGGCTGAATA CAAATCACAG AATCGTCGTA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TGCAGTGAAA ACTCTCTTCA ATTCTTTATG CCGGTGTTGG GCGCGTTATT TATCGGAGTT GCAGTTGCGC CCGCGAACGA CATTTATAAT GAACGTGAAT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TGCTCAACAG TATGAACATT TCGCAGCCTA CCGTAGTGTT TGTTTCCAAA AAGGGGTTGC AAAAAATTTT GAACGTGCAA AAAAAATTAC CAATAATCCA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GAAAATTATT ATCATGGATT CTAAAACGGA TTACCAGGGA TTTCAGTCGA TGTACACGTT CGTCACATCT CATCTACCTC CCGGTTTTAA TGAATACGAT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TTTGTACCAG AGTCCTTTGA TCGTGACAAA ACAATTGCAC TGATAATGAA TTCCTCTGGA TCTACTGGGT TACCTAAGGG TGTGGCCCTT CCGCATAGAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CTGCCTGCGT CAGATTCTCG CATGCCAGAG ATCCTATTTT TGGCAATCAA ATCATTCCGG ATACTGCGAT TTTAAGTGTT GTTCCATTCC ATCACGGTTT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TGGAATGTTT ACTACACTCG GATATTTGAT ATGTGGATTT CGAGTCGTCT TAATGTATAG ATTTGAAGAA GAGCTGTTTT TACGATCCCT TCAGGATTAC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AAAATTCAAA GTGCGTTGCT AGTACCAACC CTATTTTCAT TCTTCGCCAA AAGCACTCTG ATTGACAAAT ACGATTTATC TAATTTACAC GAAATTGCTT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CTGGGGGCGC ACCTCTTTCG AAAGAAGTCG GGGAAGCGGT TGCAAAACGC TTCCATCTTC CAGGGATACG ACAAGGATAT GGGCTCACTG AGACTACATC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AGCTATTCTG ATTACACCCG AGGGGGATGA TAAACCGGGC GCGGTCGGTA AAGTTGTTCC ATTTTTTGAA GCGAAGGTTG TGGATCTGGA TACCGGGAAA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ACGCTGGGCG TTAATCAGAG AGGCGAATTA TGTGTCAGAG GACCTATGAT TATGTCCGGT TATGTAAACA ATCCGGAAGC GACCAACGCC TTGATTGACA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

AGGATGGATG GCTACATTCT GGAGACATAG CTTACTGGGA CGAAGACGAA CACTTCTTCA TAGTTGACCG CTTGAAGTCT TTAATTAAAT ACAAAGGATA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TCAGGTGGCC CCCGCTGAAT TGGAATCGAT ATTGTTACAA CACCCCAACA TCTTCGACGC GGGCGTGGCA GGTCTTCCCG ACGATGACGC CGGTGAACTT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CCCGCCGCCG TTGTTGTTTT GGAGCACGGA AAGACGATGA CGGAAAAAGA GATCGTGGAT TACGTCGCCA GTCAAGTAAC AACCGCGAAA AAGTTGCGCG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GAGGAGTTGT GTTTGTGGAC GAAGTACCGA AAGGTCTTAC CGGAAAACTC GACGCAAGAA AAATCAGAGA GATCCTCATA AAGGCCAAGA AGGGCGGAAA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GTCCAAATTG TAAAATGTAA CTGTATTCAG CGATGACGAA ATTCTTAGCT ATTGTAATAT TATATGCAAA TTGATGAATG GTAATTTTGT AATTGTGGGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CACTGTACTA TTTTAACGAA TAATAAAATC AGGTATAGGT AACTAAAAAG GAATTCCTGC AGCCCGGGGG ATCCACTAGT TCTAGAGCGG CCGCCACCGC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

GGTGGAGCTC CAATTCGCCC TATAGTGAGT CGTATTACAA TTCACTGGCC GTCGTTTTAC AACGTCGTGA CTGGGAAAAC CCTGGCGTTA CCCAACTTAA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TCGCCTTGCA GCACATCCCC CCTTCGCCAG CTGGCGTAAT AGCGAAGAGG CCCGCACCGA TCGCCCTTCC CAACAGTTGC GCAGCCTGAA TGGCGAATGG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CGCGACGCGC CCTGTAGCGG CGCATTAAGC GCGGCGGGTG TGGTGGTTAC GCGCAGCGTG ACCGCTACAC TTGCCAGCGC CCTAGCGCCC GCTCCTTTCG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CTTTCTTCCC TTCCTTTCTC GCCACGTTCG CCGGCTTTCC CCGTCAAGCT CTAAATCGGG GGCTCCCTTT AGGGTTCCGA TTTAGTGCTT TACGGCACCT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CGACCCCAAA AAACTTGATT AGGGTGATGG TTCACGTAGT GGGCCATCGC CCTGATAGAC GGTTTTTCGC CCTTTGACGT TGGAGTCCAC GTTCTTTAAT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

AGTGGACTCT TGTTCCAAAC TGGAACAACA CTCAACCCTA TCTCGGTCTA TTCTTTTGAT TTATAAGGGA TTTTGCCGAT TTCGGCCTAT TGGTTAAAAA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ATGAGCTGAT TTAACAAAAA TTTAACGCGA ATTTTAACAA AATATTAACG TTTACAATTT CCTGATGCGG TATTTTCTCC TTACGCATCT GTGCGGTATT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TCACACCGCA TATGATCCGT CGAGTTCAAG AGAAAAAAAA AGAAAAAGCA AAAAGAAAAA AGGAAAGCGC GCCTCGTTCA GAATGACACG TATAGAATGA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TGCATTACCT TGTCATCTTC AGTATCATAC TGTTCGTATA CATACTTACT GACATTCATA GGTATACATA TATACACATG TATATATATC GTATGCTGCA 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

GCTTTAAATA ATCGGTGTCA CTACATAAGA ACACCTTTGG TGGAGGGAAC ATCGTTGGTA CCATTGGGCG AGGTGGCTTC TCTTATGGCA ACCGCAAGAG 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CCTTGAACGC ACTCTCACTA CGGTGATGAT CATTCTTGCC TCGCAGACAA TCAACGTGGA GGGTAATTCT GCTAGCCTCT GCAAAGCTTT CAAGAAAATG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CGGGATCATC TCGCAAGAGA GATCTCCTAC TTTCTCCCTT TGCAAACCAA GTTCGACAAC TGCGTACGGC CTGTTCGAAA GATCTACCAC CGCTCTGGAA 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

AGTGCCTCAT CCAAAGGCGC AAATCCTGAT CCAAACCTTT TTACTCCACG CGCCAGTAGG GCCTCTTTAA AAGCTTGACC GAGAGCAATC CCGCAGTCTT 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

CAGTGGTGTG ATGGTCGTCT ATGTGTAAGT CACCAATGCA CTCAACGATT AGCGACCAGC CGGAATGCTT GGCCAGAGCA TGTATCATAT GGTCCAGAAA 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

CCCTATACCT GTGTGGACGT TAATCACTTG CGATTGTGTG GCCTGTTCTG CTACTGCTTC TGCCTCTTTT TCTGGGAAGA TCGAGTGCTC TATCGCTAGG 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

GGACCACCCT TTAAAGAGAT CGCAATCTGA ATCTTGGTTT CATTTGTAAT ACGCTTTACT AGGGCTTTCT GCTCTGTCAT CTTTGCCTTC GTTTATCTTG 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CCTGCTCATT TTTTAGTATA TTCTTCGAAG AAATCACATT ACTTTATATA ATGTATAATT CATTATGTGA TAATGCCAAT CGCTAAGAAA AAAAAAGAGT 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

CATCCGCTAG GTGGAAAAAA AAAAATGAAA ATCATTACCG AGGCATAAAA AAATATAGAG TGTACTAGAG GAGGCCAAGA GTAATAGAAA AAGAAAATTG 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

CGGGAAAGGA CTGTGTTATG ACTTCCCTGA CTAATGCCGT GTTCAAACGA TACCTGGCAG TGACTCCTAG CGCTCACCAA GCTCTTAAAA CGGAATTATG 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

GTGCACTCTC AGTACAATCT GCTCTGATGC CGCATAGTTA AGCCAGCCCC GACACCCGCC AACACCCGCT GACGCGCCCT GACGGGCTTG TCTGCTCCCG 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

GCATCCGCTT ACAGACAAGC TGTGACCGTC TCCGGGAGCT GCATGTGTCA GAGGTTTTCA CCGTCATCAC CGAAACGCGC GA
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581

Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks):

plasmid sequence confirmed by IRESite curators by restriction analysis + parts by PCR + sequencing

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

The total number of notable open-reading frames (ORFs):

1

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `1`	Last change: `2008-06-04 11:46:27`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
FFluc

The description of the protein encoded in this ORF:
firefly 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):

888-2540

Remarks:

IRESite notes about verification of plasmid sequence:
The complete sequence of IRES element was determined by sequencing using M13_reverse primer
(CAGGAAACAGCTATGAC)

Citations:

Bergamini G., Preiss T., Hentze M. W. (2000) Picornavirus IRESes and the poly(A) tail jointly promote cap-independent translation in a mammalian cell-free system. RNA. 6(12):1781-1790

IRESs:

IRES:

Version: `3`	Last change: `2008-06-04 11:46:27`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `HAV`	The functional status of IRES: `functional`

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

30-881

How IRES boundaries were determined:
experimentally_determined

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

TCCCTCTTGG AAGTCCCTGG TGAGGGGACT TGATACCTCA CCGCCGTTTG CCTAGGCTAT AGGCTAAATT TTCCCTTTCC CTTTTCCCTT TCCCATTCCC 
^30        ^40        ^50        ^60        ^70        ^80        ^90        ^100       ^110       ^120       

TTTTGCTTGT AAATATTGAT TCCTGCAGGT TCAGGGTTCT TAAATCTGTT TCTCTATAAG AACACTCATT TTCACGCTTT CTGTCTTCTT TCTTCCAGGG 
^130       ^140       ^150       ^160       ^170       ^180       ^190       ^200       ^210       ^220       

CTCTCCCCTT GCCCTAGGCT CTGGCCGTTG CGCCCGGCGG GGTCAACTCC ATGATTAGCA TGGAGCTGTA GGAGTCTAAA TTGGGGACAC AGATGTTTGG 
^230       ^240       ^250       ^260       ^270       ^280       ^290       ^300       ^310       ^320       

AACGTCACCT TGCAGTGTTA ACTTGGCTTT CATGAATCTC TTTGATCTTC CACAAGGGGT AGGCTACGGG TGAAACCTCT TAGGCTAATA CTTCTATGAA 
^330       ^340       ^350       ^360       ^370       ^380       ^390       ^400       ^410       ^420       

GAGATGCCTT GGATAGGGTA ACAGCGGCGG ATATTGGTGA GTTGTTAAGA CAAAAACCAT TCAACGCCGG AGGACTGACT CTCATCCAGT GGATGCATTG 
^430       ^440       ^450       ^460       ^470       ^480       ^490       ^500       ^510       ^520       

AGTGGATTGA CTGTCAGGGC TGTCTTTAGG CTTAATTCCA GACCTCTCTG TGCTTAGGGC AAACATCATT TGGCCTTAAA TGGGATTCTG TGAGAGGGGA 
^530       ^540       ^550       ^560       ^570       ^580       ^590       ^600       ^610       ^620       

TCCCTCCATT GACAGCTGGA CTGTTCTTTG GGGCCTTATG TGGTGTTTGC CTCTGAGGTA CTCAGGGGCA TTTAGGTTTT TCCTCATTCT TAAATAATAA 
^630       ^640       ^650       ^660       ^670       ^680       ^690       ^700       ^710       ^720       

TGAACATGTC TAGACAAGGT ATTTTCCAGA CTGTTGGGAG TGGTCTTGAC CACATCCTGT CTTTGGCAGA CATTGAGGAA GAGCAAATGA TTCAATCAGT 
^730       ^740       ^750       ^760       ^770       ^780       ^790       ^800       ^810       ^820       

TGATAGGACT GCAGTGACTG GTGCTTCTTA TTTTACTTCT GTGGATCAAT CT
^830       ^840       ^850       ^860       ^870       ^880

Remarks:

DNA fragment (-699 to +153) containing the HAV IRES and 51 amino acids of the capsid protein from Hepatitis A
virus strain HAV HM-175/7 MK-5.

Citations:

Bergamini G., Preiss T., Hentze M. W. (2000) Picornavirus IRESes and the poly(A) tail jointly promote cap-independent translation in a mammalian cell-free system. RNA. 6(12):1781-1790

The translation experiments:

Translation results:

IRESite Translation Id: 422

Version: `1`	Last change: `2008-06-04 11:46:27`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vitro The in vitro translation system:
HeLa cell lysate

The organism used for translation:

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

100.000

	Name of the plasmid used as the negative control. `pT3Luc`
	`IRESite Id` of the plasmid used as negative control. `346`
	The relative translation efficiency in % of the negative control: `0.300`

The effect of 5'-cap analogs on translation:
no

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_ApppG_cap_without_polyA_tail

Remarks:

The translation of the nonpolyadenylated HAV.IRES RNA is sensitive to the addition of m7GpppG, but not ApppG
competitor.
The translation of HAV.IRES RNA is about 10-fold less efficient than the translation of the polyadenylated
counterpart HAV.IRES-pA RNA.
Translational data are derived from Fig. 6A

Citations:

Bergamini G., Preiss T., Hentze M. W. (2000) Picornavirus IRESes and the poly(A) tail jointly promote cap-independent translation in a mammalian cell-free system. RNA. 6(12):1781-1790

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