IRESite_Id:6 characteristics of HCV_type_4a IRES studied in pRL

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `6`	Version: `5`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-08-02 00:00:00`
Reviewed by: Martin Pospíšek	Last change: `2006-10-04 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:
3UTR_incomplete

The mRNA/+RNA description:

5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus (HCV) type 4a cloned
between renilla and firefly luciferase. This sequence was hand-crafted according to Figure 1 in cited article.

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

GGGAATTCGA GCTCATGACT TCGAAAGTTT ATGATCCAGA ACAAAGGAAA CGGATGATAA CTGGTCCGCA GTGGTGGGCC AGATGTAAAC AAATGAATGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TCTTGATTCA TTTATTAATT ATTATGATTC AGAAAAACAT GCAGAAAATG CTGTTATTTT TTTACATGGT AACGCGGCCT CTTCTTATTT ATGGCGACAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GTTGTGCCAC ATATTGAGCC AGTAGCGCGG TGTATTATAC CAGACCTTAT TGGTATGGGC AAATCAGGCA AATCTGGTAA TGGTTCTTAT AGGTTACTTG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATCATTACAA ATATCTTACT GCATGGTTTG AACTTCTTAA TTTACCAAAG AAGATCATTT TTGTCGGCCA TGATTGGGGT GCTTGTTTGG CATTTCATTA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TAGCTATGAG CATCAAGATA AGATCAAAGC AATAGTTCAC GCTGAAAGTG TAGTAGATGT GATTGAATCA TGGGATGAAT GGCCTGATAT TGAAGAAGAT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATTGCGTTGA TCAAATCTGA AGAAGGAGAA AAAATGGTTT TGGAGAATAA CTTCTTCGTG GAAACCATGT TGCCATCAAA AATCATGAGA AAGTTAGAAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CAGAAGAATT TGCAGCATAT CTTGAACCAT TCAAAGAGAA AGGTGAAGTT CGTCGTCCAA CATTATCATG GCCTCGTGAA ATCCCGTTAG TAAAAGGTGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TAAACCTGAC GTTGTACAAA TTGTTAGGAA TTATAATGCT TATCTACGTG CAAGTGATGA TTTACCAAAA ATGTTTATTG AATCGGACCC AGGATTCTTT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TCCAATGCTA TTGTTGAAGG TGCCAAGAAG TTTCCTAATA CTGAATTTGT CAAAGTAAAA GGTCTTCATT TTTCGCAAGA AGATGCACCT GATGAAATGG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GAAAATATAT CAAATCGTTC GTTGAGCGAG TTCTCAAAAA TGAACAATAA GGATCCGGCG ACACTCCACC ATAGATCACT CCCCTGTGAG GAACTACTGT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CTTCACGCAG AAAGCGTCTA GCCATGGCGT TAGTATGAGT GTTGTACAGC CTCCAGGACC CCCCCTCCCG GGAGAGCCAT AGTGGTCTTC GGAACCGGTG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AGTACACCGG AATCGCCGGG ATGACCGGGT CCTTTCTTGG ATTAACCCGC TCAATGCCCG GAAATTTGGG CGTGCCCCCG CAAGACTGCT AGCCGAGTAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGTTGGGTCG CGAAAGGCCT TGCGGTACTG CCTGATAGGG TGCTTGCGAG TGCCCCGGGA GGTCTCGTAG ACCGTGCACC ATGAGCACGA ATCCTGGATC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGAAGACGCC AAAAACATAA AGAAAGGCCC GGCGCCATTC TATCCTCTAG AGGATGGAAC CGCTGGAGAG CAACTGCATA AGGCTATGAA GAGATACGCC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTGGTTCCTG GAACAATTGC TTTTACAGAT GCACATATCG AGGTGAACAT CACGTACGCG GAATACTTCG AAATGTCCGT TCGGTTGGCA GAAGCTATGA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AACGATATGG GCTGAATACA AATCACAGAA TCGTCGTATG CAGTGAAAAC TCTCTTCAAT TCTTTATGCC GGTGTTGGGC GCGTTATTTA TCGGAGTTGC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGTTGCGCCC GCGAACGACA TTTATAATGA ACGTGAATTG CTCAACAGTA TGAACATTTC GCAGCCTACC GTAGTGTTTG TTTCCAAAAA GGGGTTGCAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAAATTTTGA ACGTGCAAAA AAAATTACCA ATAATCCAGA AAATTATTAT CATGGATTCT AAAACGGATT ACCAGGGATT TCAGTCGATG TACACGTTCG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCACATCTCA TCTACCTCCC GGTTTTAATG AATACGATTT TGTACCAGAG TCCTTTGATC GTGACAAAAC AATTGCACTG ATAATGAATT CCTCTGGATC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TACTGGGTTA CCTAAGGGTG TGGCCCTTCC GCATAGAACT GCCTGCGTCA GATTCTCGCA TGCCAGAGAT CCTATTTTTG GCAATCAAAT CATTCCGGAT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACTGCGATTT TAAGTGTTGT TCCATTCCAT CACGGTTTTG GAATGTTTAC TACACTCGGA TATTTGATAT GTGGATTTCG AGTCGTCTTA ATGTATAGAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TTGAAGAAGA GCTGTTTTTA CGATCCCTTC AGGATTACAA AATTCAAAGT GCGTTGCTAG TACCAACCCT ATTTTCATTC TTCGCCAAAA GCACTCTGAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGACAAATAC GATTTATCTA ATTTACACGA AATTGCTTCT GGGGGCGCAC CTCTTTCGAA AGAAGTCGGG GAAGCGGTTG CAAAACGCTT CCATCTTCCA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGGATACGAC AAGGATATGG GCTCACTGAG ACTACATCAG CTATTCTGAT TACACCCGAG GGGGATGATA AACCGGGCGC GGTCGGTAAA GTTGTTCCAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTTTTGAAGC GAAGGTTGTG GATCTGGATA CCGGGAAAAC GCTGGGCGTT AATCAGAGAG GCGAATTATG TGTCAGAGGA CCTATGATTA TGTCCGGTTA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TGTAAACAAT CCGGAAGCGA CCAACGCCTT GATTGACAAG GATGGATGGC TACATTCTGG AGACATAGCT TACTGGGACG AAGACGAACA CTTCTTCATA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GTTGACCGCT TGAAGTCTTT AATTAAATAC AAAGGATATC AGGTGGCCCC CGCTGAATTG GAATCGATAT TGTTACAACA CCCCAACATC TTCGACGCGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCGTGGCAGG TCTTCCCGAC GATGACGCCG GTGAACTTCC CGCCGCCGTT GTTGTTTTGG AGCACGGAAA GACGATGACG GAAAAAGAGA TCGTGGATTA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CGTCGCCAGT CAAGTAACAA CCGCGAAAAA GTTGCGCGGA GGAGTTGTGT TTGTGGACGA AGTACCGAAA GGTCTTACCG GAAAACTCGA CGCAAGAAAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATCAGAGAGA TCCTCATAAA GGCCAAGAAG GGCGGAAAGT CCAAATTGTA AAAAAAAAAA AAAAAAA
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

The name of the plasmid:
pRL_4a 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_4a

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Hepatitis C virus type 4a

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

AAATTGTAAA CGTTTAATAT TTTGTTAAAA TTCGCGTTAA ATTTTTGTTA AATCAGCTCA TTTTTTAACC AATAGGCCGA AATCGGCAAA ATCCCTTATA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AATCAAAAGA ATAGACCGAG ATAGGGTTGA GTGTTGTTCC AGTTTGGAAC AAGAGTCCAC TATTAAAGAA CGTGGACTCC AACGTCAAAG GGCGAAAAAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CGTCTATCAG GGCGATGGCC CACTACGTGA ACCATCACCC TAATCAAGTT TTTTGGGGTC GAGGTGCCGT AAAGCACTAA ATCGGAACCC TAAAGGGATG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCCCGATTTA GAGCTTGACG GGGAAAGCCG GCGAACGTGG CGAGAAAGGA AGGGAAGAAA GCGAAAGGAG CGGGCGCTAG GGCGCTGGCA AGTGTAGCGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TCACGCTGCG CGTAACCACC ACACCCGCCG CGCTTAATGC GCCGCTACAG GGCGCGTCAG GTGGCACTTT TCGGGGAAAT GTGCGCGGAA CCCCTATTTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TTTATTTTTC TAAATACATT CAAATATGTA TCCGCTCATG AGACAATAAC CCTGATAAAT GCTTCAATAA TATTGAAAAA GGAAGAGTAT GAGTATTCAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CATTTCCGTG TCGCCCTTAT TCCCTTTTTT GCGGCATTTT GCCTTCCTGT TTTTGCTCAC CCAGAAACGC TGGTGAAAGT AAAAGATGCT GAAGATCAGT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGGGTGCACG AGTGGGTTAC ATCGAACTGG ATCTCAACAG CGGTAAGATC CTTGAGAGTT TTCGCCCCGA AGAACGTTTT CCAATGATGA GCACTTTTAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AGTTCTGCTA TGTGGCGCGG TATTATCCCG TATTGACGCC GGGCAAGAGC AACTCGGTCG CCGCATACAC TATTCTCAGA ATGACTTGGT TGAGTACTCA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CCAGTCACAG AAAAGCATCT TACGGATGGC ATGACAGTAA GAGAATTATG CAGTGCTGCC ATAACCATGA GTGATAACAC TGCGGCCAAC TTACTTCTGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CAACGATCGG AGGACCGAAG GAGCTAACCG CTTTTTTGCA CAACATGGGG GATCATGTAA CTCGCCTTGA TCGTTGGGAA CCGGAGCTGA ATGAAGCCAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACCAAACGAC GAGCGTGACA CCACGATGCC TGTAGCAATG GCAACAACGT TGCGCAAACT ATTAACTGGC GAACTACTTA CTCTAGCTTC CCGGCAACAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTAATAGACT GGATGGAGGC GGATAAAGTT GCAGGACCAC TTCTGCGCTC GGCCCTTCCG GCTGGCTGGT TTATTGCTGA TAAATCTGGA GCCGGTGAGC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GTGGGTCTCG CGGTATCATT GCAGCACTGG GGCCAGATGG TAAGCCCTCC CGTATCGTAG TTATCTACAC GACGGGGAGT CAGGCAACTA TGGATGAACG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAATAGACAG ATCGCTGAGA TAGGTGCCTC ACTGATTAAG CATTGGTAAC TGTCAGACCA AGTTTACTCA TATATACTTT AGATTGATTT AAAACTTCAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTTTAATTTA AAAGGATCTA GGTGAAGATC CTTTTTGATA ATCTCATGAC CAAAATCCCT TAACGTGAGT TTTCGTTCCA CTGAGCGTCA GACCCCGTAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AAAAGATCAA AGGATCTTCT TGAGATCCTT TTTTTCTGCG CGTAATCTGC TGCTTGCAAA CAAAAAAACC ACCGCTACCA GCGGTGGTTT GTTTGCCGGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TCAAGAGCTA CCAACTCTTT TTCCGAAGGT AACTGGCTTC AGCAGAGCGC AGATACCAAA TACTGTTCTT CTAGTGTAGC CGTAGTTAGG CCACCACTTC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AAGAACTCTG TAGCACCGCC TACATACCTC GCTCTGCTAA TCCTGTTACC AGTGGCTGCT GCCAGTGGCG ATAAGTCGTG TCTTACCGGG TTGGACTCAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GACGATAGTT ACCGGATAAG GCGCAGCGGT CGGGCTGAAC GGGGGGTTCG TGCACACAGC CCAGCTTGGA GCGAACGACC TACACCGAAC TGAGATACCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACAGCGTGAG CATTGAGAAA GCGCCACGCT TCCCGAAGGG AGAAAGGCGG ACAGGTATCC GGTAAGCGGC AGGGTCGGAA CAGGAGAGCG CACGAGGGAG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTTCCAGGGG GAAACGCCTG GTATCTTTAT AGTCCTGTCG GGTTTCGCCA CCTCTGACTT GAGCGTCGAT TTTTGTGATG CTCGTCAGGG GGGCGGAGCC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TATGGAAAAA CGCCAGCAAC GCGGCCTTTT TACGGTTCCT GGCCTTTTGC TGGCCTTTTG CTCACATGTT CTTTCCTGCG TTATCCCCTG ATTCTGTGGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TAACCGTATT ACCGCCTTTG AGTGAGCTGA TACCGCTCGC CGCAGCCGAA CGACCGAGCG CAGCGAGTCA GTGAGCGAGG AAGCGGAAGA GCGCCCAATA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CGCAAACCGC CTCTCCCCGC GCGTTGGCCG ATTCATTAAT GCAGCTGGCA CGACAGGTTT CCCGACTGGA AAGCGGGCAG TGAGCGCAAC GCAATTAATG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TGAGTTAGCT CACTCATTAG GCACCCCAGG CTTTACACTT TATGCTTCCG GCTCGTATGT TGTGTGGAAT TGTGAGCGGA TAACAATTTC ACACAGGAAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CAGCTATGAC CATGATTACG AATTTAATAC GACTCACTAT AGGGAATTCG AGCTCATGAC TTCGAAAGTT TATGATCCAG AACAAAGGAA ACGGATGATA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ACTGGTCCGC AGTGGTGGGC CAGATGTAAA CAAATGAATG TTCTTGATTC ATTTATTAAT TATTATGATT CAGAAAAACA TGCAGAAAAT GCTGTTATTT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TTTTACATGG TAACGCGGCC TCTTCTTATT TATGGCGACA TGTTGTGCCA CATATTGAGC CAGTAGCGCG GTGTATTATA CCAGACCTTA TTGGTATGGG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CAAATCAGGC AAATCTGGTA ATGGTTCTTA TAGGTTACTT GATCATTACA AATATCTTAC TGCATGGTTT GAACTTCTTA ATTTACCAAA GAAGATCATT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TTTGTCGGCC ATGATTGGGG TGCTTGTTTG GCATTTCATT ATAGCTATGA GCATCAAGAT AAGATCAAAG CAATAGTTCA CGCTGAAAGT GTAGTAGATG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TGATTGAATC ATGGGATGAA TGGCCTGATA TTGAAGAAGA TATTGCGTTG ATCAAATCTG AAGAAGGAGA AAAAATGGTT TTGGAGAATA ACTTCTTCGT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GGAAACCATG TTGCCATCAA AAATCATGAG AAAGTTAGAA CCAGAAGAAT TTGCAGCATA TCTTGAACCA TTCAAAGAGA AAGGTGAAGT TCGTCGTCCA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ACATTATCAT GGCCTCGTGA AATCCCGTTA GTAAAAGGTG GTAAACCTGA CGTTGTACAA ATTGTTAGGA ATTATAATGC TTATCTACGT GCAAGTGATG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ATTTACCAAA AATGTTTATT GAATCGGACC CAGGATTCTT TTCCAATGCT ATTGTTGAAG GTGCCAAGAA GTTTCCTAAT ACTGAATTTG TCAAAGTAAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGGTCTTCAT TTTTCGCAAG AAGATGCACC TGATGAAATG GGAAAATATA TCAAATCGTT CGTTGAGCGA GTTCTCAAAA ATGAACAATA AGGATCCGGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GACACTCCAC CATAGATCAC TCCCCTGTGA GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG TGTTGTACAG CCTCCAGGAC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CCCCCCTCCC GGGAGAGCCA TAGTGGTCTT CGGAACCGGT GAGTACACCG GAATCGCCGG GATGACCGGG TCCTTTCTTG GATTAACCCG CTCAATGCCC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GGAAATTTGG GCGTGCCCCC GCAAGACTGC TAGCCGAGTA GTGTTGGGTC GCGAAAGGCC TTGCGGTACT GCCTGATAGG GTGCTTGCGA GTGCCCCGGG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AGGTCTCGTA GACCGTGCAC CATGAGCACG AATCCTGGAT CCGAAGACGC CAAAAACATA AAGAAAGGCC CGGCGCCATT CTATCCTCTA GAGGATGGAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CCGCTGGAGA GCAACTGCAT AAGGCTATGA AGAGATACGC CCTGGTTCCT GGAACAATTG CTTTTACAGA TGCACATATC GAGGTGAACA TCACGTACGC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GGAATACTTC GAAATGTCCG TTCGGTTGGC AGAAGCTATG AAACGATATG GGCTGAATAC AAATCACAGA ATCGTCGTAT GCAGTGAAAA CTCTCTTCAA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TTCTTTATGC CGGTGTTGGG CGCGTTATTT ATCGGAGTTG CAGTTGCGCC CGCGAACGAC ATTTATAATG AACGTGAATT GCTCAACAGT ATGAACATTT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CGCAGCCTAC CGTAGTGTTT GTTTCCAAAA AGGGGTTGCA AAAAATTTTG AACGTGCAAA AAAAATTACC AATAATCCAG AAAATTATTA TCATGGATTC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TAAAACGGAT TACCAGGGAT TTCAGTCGAT GTACACGTTC GTCACATCTC ATCTACCTCC CGGTTTTAAT GAATACGATT TTGTACCAGA GTCCTTTGAT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CGTGACAAAA CAATTGCACT GATAATGAAT TCCTCTGGAT CTACTGGGTT ACCTAAGGGT GTGGCCCTTC CGCATAGAAC TGCCTGCGTC AGATTCTCGC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATGCCAGAGA TCCTATTTTT GGCAATCAAA TCATTCCGGA TACTGCGATT TTAAGTGTTG TTCCATTCCA TCACGGTTTT GGAATGTTTA CTACACTCGG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ATATTTGATA TGTGGATTTC GAGTCGTCTT AATGTATAGA TTTGAAGAAG AGCTGTTTTT ACGATCCCTT CAGGATTACA AAATTCAAAG TGCGTTGCTA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GTACCAACCC TATTTTCATT CTTCGCCAAA AGCACTCTGA TTGACAAATA CGATTTATCT AATTTACACG AAATTGCTTC TGGGGGCGCA CCTCTTTCGA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

AAGAAGTCGG GGAAGCGGTT GCAAAACGCT TCCATCTTCC AGGGATACGA CAAGGATATG GGCTCACTGA GACTACATCA GCTATTCTGA TTACACCCGA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GGGGGATGAT AAACCGGGCG CGGTCGGTAA AGTTGTTCCA TTTTTTGAAG CGAAGGTTGT GGATCTGGAT ACCGGGAAAA CGCTGGGCGT TAATCAGAGA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GGCGAATTAT GTGTCAGAGG ACCTATGATT ATGTCCGGTT ATGTAAACAA TCCGGAAGCG ACCAACGCCT TGATTGACAA GGATGGATGG CTACATTCTG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GAGACATAGC TTACTGGGAC GAAGACGAAC ACTTCTTCAT AGTTGACCGC TTGAAGTCTT TAATTAAATA CAAAGGATAT CAGGTGGCCC CCGCTGAATT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GGAATCGATA TTGTTACAAC ACCCCAACAT CTTCGACGCG GGCGTGGCAG GTCTTCCCGA CGATGACGCC GGTGAACTTC CCGCCGCCGT TGTTGTTTTG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GAGCACGGAA AGACGATGAC GGAAAAAGAG ATCGTGGATT ACGTCGCCAG TCAAGTAACA ACCGCGAAAA AGTTGCGCGG AGGAGTTGTG TTTGTGGACG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AAGTACCGAA AGGTCTTACC GGAAAACTCG ACGCAAGAAA AATCAGAGAG ATCCTCATAA AGGCCAAGAA GGGCGGAAAG TCCAAATTGT AAAAAAAAAA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

AAAAAAAAGC TTGGCACTGG CCGTCGTTTT ACAACGTCGT GACTGGGAAA ACCCTGGCGT TACCCAACTT AATCGCCTTG CAGCACATCC CCCTTTCGCC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

AGCTGGCGTA ATAGCGAAGA GGCCCGCACC GATCGCCCTT CCCAACAGTT GCGCAGCCTG AATGGCGAAT GGG
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771

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`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek

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:

no

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

15-950

ORF

ORF position:

2

Version: `1`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek

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:

no

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

1302-2951

Remarks:

This item is labeled as 3'UTR incomplete because the mRNA sequence deposited here ends at the stop codon of
the second cistron.

Citations:

Collier A. J., Tang S., Elliott R. M. (1998) Translation efficiencies of the 5' untranslated region from representatives of the six major genotypes of hepatitis C virus using a novel bicistronic reporter assay system. J. Gen. Virol. 79(Pt 10):2359-2366

IRESs:

IRES:

Version: `2`	Last change: `2006-01-15 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek
The IRES name: `HCV_type_4a`	The functional status of IRES: `functional`

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

957-1295

How IRES boundaries were determined:
unknown

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `7`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `345`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-345`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-7`

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

GGCGACACTC CACCATAGAT CACTCCCCTG TGAGGAACTA CTGTCTTCAC GCAGAAAGCG TCTAGCCATG GCGTTAGTAT GAGTGTTGTA CAGCCTCCAG 
^957       ^967       ^977       ^987       ^997       ^1007      ^1017      ^1027      ^1037      ^1047      

GACCCCCCCT CCCGGGAGAG CCATAGTGGT CTTCGGAACC GGTGAGTACA CCGGAATCGC CGGGATGACC GGGTCCTTTC TTGGATTAAC CCGCTCAATG 
^1057      ^1067      ^1077      ^1087      ^1097      ^1107      ^1117      ^1127      ^1137      ^1147      

CCCGGAAATT TGGGCGTGCC CCCGCAAGAC TGCTAGCCGA GTAGTGTTGG GTCGCGAAAG GCCTTGCGGT ACTGCCTGAT AGGGTGCTTG CGAGTGCCCC 
^1157      ^1167      ^1177      ^1187      ^1197      ^1207      ^1217      ^1227      ^1237      ^1247      

GGGAGGTCTC GTAGACCGTG CACCATGAGC ACGAATCCT
^1257      ^1267      ^1277      ^1287

Remarks:

HCV UTR (324 nt) and open reading frame (15 nt)

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 17

Version: `4`	Last change: `2006-10-04 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens BHK-21 (ATCC CCL-10)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

100.000

Name of IRES used as the positive control:

HCV_type_1a

Name of the plasmid used as the positive control. `pRL_1a`
`IRESite Id` of the plasmid used as positive control. `224`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `352`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

positive control: 5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus
(HCV) type 1a (gi:329737) in the same bicistronic vector

Citations:

Translation results:

IRESite Translation Id: 18

Version: `4`	Last change: `2006-10-04 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HuH7

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

95.000

Name of IRES used as the positive control:

HCV_type_1a

Name of the plasmid used as the positive control. `pRL_1a`
`IRESite Id` of the plasmid used as positive control. `224`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `352`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

positive control: 5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus
(HCV) type 1a (gi:329737) in the same bicistronic vector

Citations:

Translation results:

IRESite Translation Id: 19

Version: `4`	Last change: `2006-10-04 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HepG2 (ATCC HB-8065)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

88.000

Name of IRES used as the positive control:

HCV_type_1a

Name of the plasmid used as the positive control. `pRL_1a`
`IRESite Id` of the plasmid used as positive control. `224`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `352`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

positive control: 5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus
(HCV) type 1a (gi:329737) in the same bicistronic vector

Citations:

Translation results:

IRESite Translation Id: 20

Version: `4`	Last change: `2006-10-04 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HeLa-T4+

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

72.000

Name of IRES used as the positive control:

HCV_type_1a

Name of the plasmid used as the positive control. `pRL_1a`
`IRESite Id` of the plasmid used as positive control. `224`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `352`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

positive control: 5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus
(HCV) type 1a (gi:329737) in the same bicistronic vector

Citations:

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