IRESite_Id:413 characteristics of c-myc IRES studied in pRML-p(A) plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `413`	Version: `2`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-06-24 21:57:26`

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 produced from bicistronic plasmid pRML-p(A) which comprises renilla and firefly
luciferases as the first and the second cistron, respectively and the 5' UTR of human c-myc (nt from -407 to
-2) mRNA transcribed from major P2 promoter. These mRNAs are bearing a poly(A) tail.

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

GGGAACAAAA GCTGGGTACC GGGCCCCCCC TCGAGGTCGA CGGTATCGAT AAGCTTATGA CTTCGAAAGT TTATGATCCA GAACAAAGGA AACGGATGAT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AACTGGTCCG CAGTGGTGGG CCAGATGTAA ACAAATGAAT GTTCTTGATT CATTTATTAA TTATTATGAT TCAGAAAAAC ATGCAGAAAA TGCTGTTATT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TTTTTACATG GTAACGCGGC CTCTTCTTAT TTATGGCGAC ATGTTGTGCC ACATATTGAG CCAGTAGCGC GGTGTATTAT ACCAGACCTT ATTGGTATGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCAAATCAGG CAAATCTGGT AATGGTTCTT ATAGGTTACT TGATCATTAC AAATATCTTA CTGCATGGTT TGAACTTCTT AATTTACCAA AGAAGATCAT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTTTGTCGGC CATGATTGGG GTGCTTGTTT GGCATTTCAT TATAGCTATG AGCATCAAGA TAAGATCAAA GCAATAGTTC ACGCTGAAAG TGTAGTAGAT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GTGATTGAAT CATGGGATGA ATGGCCTGAT ATTGAAGAAG ATATTGCGTT GATCAAATCT GAAGAAGGAG AAAAAATGGT TTTGGAGAAT AACTTCTTCG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TGGAAACCAT GTTGCCATCA AAAATCATGA GAAAGTTAGA ACCAGAAGAA TTTGCAGCAT ATCTTGAACC ATTCAAAGAG AAAGGTGAAG TTCGTCGTCC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AACATTATCA TGGCCTCGTG AAATCCCGTT AGTAAAAGGT GGTAAACCTG ACGTTGTACA AATTGTTAGG AATTATAATG CTTATCTACG TGCAAGTGAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GATTTACCAA AAATGTTTAT TGAATCGGAC CCAGGATTCT TTTCCAATGC TATTGTTGAA GGTGCCAAGA AGTTTCCTAA TACTGAATTT GTCAAAGTAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAGGTCTTCA TTTTTCGCAA GAAGATGCAC CTGATGAAAT GGGAAAATAT ATCAAATCGT TCGTTGAGCG AGTTCTCAAA AATGAACAAT AAACTAGGAT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCACTAGAAC TCGCTGTAGT AATTCCAGCG AGAGGCAGAG GGAGCGAGCG GGCGGCCGGC TAGGGTGGAA GAGCCGGGCG AGCAGAGCTG CGCTGCGGGC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GTCCTGGGAA GGGAGATCCG GAGCGAATAG GGGGCTTCGC CTCTGGCCCA GCCCTCCCGC TGATCCCCCA GCCAGCGGTC CGCAACCCTT GCCGCATCCA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CGAAACTTTG CCCATAGCAG CGGGCGGGCA CTTTGCACTG GAACTTACAA CACCCGAGCA AGGACGCGAC TCTCCCGACG CGGGGAGGCT ATTCTGCCCA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TTTGGGGACA CTTCCCCGCC GCTGCCAGGA CCCGCTTCTC TGAAAGGCTC TCCTTGCAGC TGCTTAGACG CTGGATTTTT TTCGGGTAGT GGAAAACCAG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CAGCCTCCCG CGACCATGGC CGAAGACGCC AAAAACATAA AGAAAGGCCC GGCGCCATTC TATCCTCTAG AGGATGGAAC CGCTGGAGAG CAACTGCATA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGGCTATGAA GAGATACGCC CTGGTTCCTG GAACAATTGC TTTTACAGAT GCACATATCG AGGTGAACAT CACGTACGCG GAATACTTCG AAATGTCCGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TCGGTTGGCA GAAGCTATGA AACGATATGG GCTGAATACA AATCACAGAA TCGTCGTATG CAGTGAAAAC TCTCTTCAAT TCTTTATGCC GGTGTTGGGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCGTTATTTA TCGGAGTTGC AGTTGCGCCC GCGAACGACA TTTATAATGA ACGTGAATTG CTCAACAGTA TGAACATTTC GCAGCCTACC GTAGTGTTTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TTTCCAAAAA GGGGTTGCAA AAAATTTTGA ACGTGCAAAA AAAATTACCA ATAATCCAGA AAATTATTAT CATGGATTCT AAAACGGATT ACCAGGGATT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TCAGTCGATG TACACGTTCG TCACATCTCA TCTACCTCCC GGTTTTAATG AATACGATTT TGTACCAGAG TCCTTTGATC GTGACAAAAC AATTGCACTG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ATAATGAATT CCTCTGGATC TACTGGGTTA CCTAAGGGTG TGGCCCTTCC GCATAGAACT GCCTGCGTCA GATTCTCGCA TGCCAGAGAT CCTATTTTTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCAATCAAAT CATTCCGGAT ACTGCGATTT TAAGTGTTGT TCCATTCCAT CACGGTTTTG GAATGTTTAC TACACTCGGA TATTTGATAT GTGGATTTCG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AGTCGTCTTA ATGTATAGAT TTGAAGAAGA GCTGTTTTTA CGATCCCTTC AGGATTACAA AATTCAAAGT GCGTTGCTAG TACCAACCCT ATTTTCATTC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTCGCCAAAA GCACTCTGAT TGACAAATAC GATTTATCTA ATTTACACGA AATTGCTTCT GGGGGCGCAC CTCTTTCGAA AGAAGTCGGG GAAGCGGTTG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CAAAACGCTT CCATCTTCCA GGGATACGAC AAGGATATGG GCTCACTGAG ACTACATCAG CTATTCTGAT TACACCCGAG GGGGATGATA AACCGGGCGC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GGTCGGTAAA GTTGTTCCAT TTTTTGAAGC GAAGGTTGTG GATCTGGATA CCGGGAAAAC GCTGGGCGTT AATCAGAGAG GCGAATTATG TGTCAGAGGA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CCTATGATTA TGTCCGGTTA TGTAAACAAT CCGGAAGCGA CCAACGCCTT GATTGACAAG GATGGATGGC TACATTCTGG AGACATAGCT TACTGGGACG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AAGACGAACA CTTCTTCATA GTTGACCGCT TGAAGTCTTT AATTAAATAC AAAGGATATC AGGTGGCCCC CGCTGAATTG GAATCGATAT TGTTACAACA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCCCAACATC TTCGACGCGG GCGTGGCAGG TCTTCCCGAC GATGACGCCG GTGAACTTCC CGCCGCCGTT GTTGTTTTGG AGCACGGAAA GACGATGACG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAAAAAGAGA TCGTGGATTA CGTCGCCAGT CAAGTAACAA CCGCGAAAAA GTTGCGCGGA GGAGTTGTGT TTGTGGACGA AGTACCGAAA GGTCTTACCG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GAAAACTCGA CGCAAGAAAA ATCAGAGAGA TCCTCATAAA GGCCAAGAAG GGCGGAAAGT CCAAATTGTA ATAGATCCAC TAGTTCTAGA GCGGCCGCCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCGCGGTGGA GGGGTACAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAG TACCGAG
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pRML-p(A) The name of the promoter used to express this mRNA:
T3

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing 5' UTR of human c-myc transcribed from major P2 promoter (nt from -407 to -2) inserted between renilla and firefly luciferase reporter genes, with 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:
c-myc

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens HeLa (ATCC CCL-2)

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

CGGGCAGTGA GCGCAACGCA ATTAATGTGA GTTAGCTCAC TCATTAGGCA CCCCAGGCTT TACACTTTAT GCTTCCGGCT CGTATGTTGT GTGGAATTGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GAGCGGATAA CAATTTCACA CAGGAAACAG CTATGACCAT GATTACGCCA AGCGCGCAAT TAACCCTCAC TAAAGGGAAC AAAAGCTGGG TACCGGGCCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCCCTCGAGG TCGACGGTAT CGATAAGCTT ATGACTTCGA AAGTTTATGA TCCAGAACAA AGGAAACGGA TGATAACTGG TCCGCAGTGG TGGGCCAGAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTAAACAAAT GAATGTTCTT GATTCATTTA TTAATTATTA TGATTCAGAA AAACATGCAG AAAATGCTGT TATTTTTTTA CATGGTAACG CGGCCTCTTC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTATTTATGG CGACATGTTG TGCCACATAT TGAGCCAGTA GCGCGGTGTA TTATACCAGA CCTTATTGGT ATGGGCAAAT CAGGCAAATC TGGTAATGGT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCTTATAGGT TACTTGATCA TTACAAATAT CTTACTGCAT GGTTTGAACT TCTTAATTTA CCAAAGAAGA TCATTTTTGT CGGCCATGAT TGGGGTGCTT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GTTTGGCATT TCATTATAGC TATGAGCATC AAGATAAGAT CAAAGCAATA GTTCACGCTG AAAGTGTAGT AGATGTGATT GAATCATGGG ATGAATGGCC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGATATTGAA GAAGATATTG CGTTGATCAA ATCTGAAGAA GGAGAAAAAA TGGTTTTGGA GAATAACTTC TTCGTGGAAA CCATGTTGCC ATCAAAAATC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATGAGAAAGT TAGAACCAGA AGAATTTGCA GCATATCTTG AACCATTCAA AGAGAAAGGT GAAGTTCGTC GTCCAACATT ATCATGGCCT CGTGAAATCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CGTTAGTAAA AGGTGGTAAA CCTGACGTTG TACAAATTGT TAGGAATTAT AATGCTTATC TACGTGCAAG TGATGATTTA CCAAAAATGT TTATTGAATC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GGACCCAGGA TTCTTTTCCA ATGCTATTGT TGAAGGTGCC AAGAAGTTTC CTAATACTGA ATTTGTCAAA GTAAAAGGTC TTCATTTTTC GCAAGAAGAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GCACCTGATG AAATGGGAAA ATATATCAAA TCGTTCGTTG AGCGAGTTCT CAAAAATGAA CAATAAACTA GGATCCACTA GAACTCGCTG TAGTAATTCC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGCGAGAGGC AGAGGGAGCG AGCGGGCGGC CGGCTAGGGT GGAAGAGCCG GGCGAGCAGA GCTGCGCTGC GGGCGTCCTG GGAAGGGAGA TCCGGAGCGA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ATAGGGGGCT TCGCCTCTGG CCCAGCCCTC CCGCTGATCC CCCAGCCAGC GGTCCGCAAC CCTTGCCGCA TCCACGAAAC TTTGCCCATA GCAGCGGGCG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GGCACTTTGC ACTGGAACTT ACAACACCCG AGCAAGGACG CGACTCTCCC GACGCGGGGA GGCTATTCTG CCCATTTGGG GACACTTCCC CGCCGCTGCC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGGACCCGCT TCTCTGAAAG GCTCTCCTTG CAGCTGCTTA GACGCTGGAT TTTTTTCGGG TAGTGGAAAA CCAGCAGCCT CCCGCGACCA TGGCCGAAGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CGCCAAAAAC ATAAAGAAAG GCCCGGCGCC ATTCTATCCT CTAGAGGATG GAACCGCTGG AGAGCAACTG CATAAGGCTA TGAAGAGATA CGCCCTGGTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CCTGGAACAA TTGCTTTTAC AGATGCACAT ATCGAGGTGA ACATCACGTA CGCGGAATAC TTCGAAATGT CCGTTCGGTT GGCAGAAGCT ATGAAACGAT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ATGGGCTGAA TACAAATCAC AGAATCGTCG TATGCAGTGA AAACTCTCTT CAATTCTTTA TGCCGGTGTT GGGCGCGTTA TTTATCGGAG TTGCAGTTGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCCCGCGAAC GACATTTATA ATGAACGTGA ATTGCTCAAC AGTATGAACA TTTCGCAGCC TACCGTAGTG TTTGTTTCCA AAAAGGGGTT GCAAAAAATT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TTGAACGTGC AAAAAAAATT ACCAATAATC CAGAAAATTA TTATCATGGA TTCTAAAACG GATTACCAGG GATTTCAGTC GATGTACACG TTCGTCACAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTCATCTACC TCCCGGTTTT AATGAATACG ATTTTGTACC AGAGTCCTTT GATCGTGACA AAACAATTGC ACTGATAATG AATTCCTCTG GATCTACTGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GTTACCTAAG GGTGTGGCCC TTCCGCATAG AACTGCCTGC GTCAGATTCT CGCATGCCAG AGATCCTATT TTTGGCAATC AAATCATTCC GGATACTGCG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATTTTAAGTG TTGTTCCATT CCATCACGGT TTTGGAATGT TTACTACACT CGGATATTTG ATATGTGGAT TTCGAGTCGT CTTAATGTAT AGATTTGAAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AAGAGCTGTT TTTACGATCC CTTCAGGATT ACAAAATTCA AAGTGCGTTG CTAGTACCAA CCCTATTTTC ATTCTTCGCC AAAAGCACTC TGATTGACAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATACGATTTA TCTAATTTAC ACGAAATTGC TTCTGGGGGC GCACCTCTTT CGAAAGAAGT CGGGGAAGCG GTTGCAAAAC GCTTCCATCT TCCAGGGATA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGACAAGGAT ATGGGCTCAC TGAGACTACA TCAGCTATTC TGATTACACC CGAGGGGGAT GATAAACCGG GCGCGGTCGG TAAAGTTGTT CCATTTTTTG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AAGCGAAGGT TGTGGATCTG GATACCGGGA AAACGCTGGG CGTTAATCAG AGAGGCGAAT TATGTGTCAG AGGACCTATG ATTATGTCCG GTTATGTAAA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CAATCCGGAA GCGACCAACG CCTTGATTGA CAAGGATGGA TGGCTACATT CTGGAGACAT AGCTTACTGG GACGAAGACG AACACTTCTT CATAGTTGAC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CGCTTGAAGT CTTTAATTAA ATACAAAGGA TATCAGGTGG CCCCCGCTGA ATTGGAATCG ATATTGTTAC AACACCCCAA CATCTTCGAC GCGGGCGTGG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CAGGTCTTCC CGACGATGAC GCCGGTGAAC TTCCCGCCGC CGTTGTTGTT TTGGAGCACG GAAAGACGAT GACGGAAAAA GAGATCGTGG ATTACGTCGC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CAGTCAAGTA ACAACCGCGA AAAAGTTGCG CGGAGGAGTT GTGTTTGTGG ACGAAGTACC GAAAGGTCTT ACCGGAAAAC TCGACGCAAG AAAAATCAGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GAGATCCTCA TAAAGGCCAA GAAGGGCGGA AAGTCCAAAT TGTAATAGAT CCACTAGTTC TAGAGCGGCC GCCACCGCGG TGGAGGGGTA CAAAAAAAAA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAGTACCGA GCTCGAATTC TAGTTCTAGA GCGGCCGCCA CCGCGGTGGA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GCTCCAATTC GCCCTATAGT GAGTCGTATT ACGCGCGCTC ACTGGCCGTC GTTTTACAAC GTCGTGACTG GGAAAACCCT GGCGTTACCC AACTTAATCG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CCTTGCAGCA CATCCCCCTT TCGCCAGCTG GCGTAATAGC GAAGAGGCCC GCACCGATCG CCCTTCCCAA CAGTTGCGCA GCCTGAATGG CGAATGGGAC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GCGCCCTGTA GCGGCGCATT AAGCGCGGCG GGTGTGGTGG TTACGCGCAG CGTGACCGCT ACACTTGCCA GCGCCCTAGC GCCCGCTCCT TTCGCTTTCT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TCCCTTCCTT TCTCGCCACG TTCGCCGGCT TTCCCCGTCA AGCTCTAAAT CGGGGGCTCC CTTTAGGGTT CCGATTTAGT GCTTTACGGC ACCTCGACCC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CAAAAAACTT GATTAGGGTG ATGGTTCACG TAGTGGGCCA TCGCCCTGAT AGACGGTTTT TCGCCCTTTG ACGTTGGAGT CCACGTTCTT TAATAGTGGA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CTCTTGTTCC AAACTGGAAC AACACTCAAC CCTATCTCGG TCTATTCTTT TGATTTATAA GGGATTTTGC CGATTTCGGC CTATTGGTTA AAAAATGAGC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TGATTTAACA AAAATTTAAC GCGAATTTTA ACAAAATATT AACGCTTACA ATTTAGGTGG CACTTTTCGG GGAAATGTGC GCGGAACCCC TATTTGTTTA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TTTTTCTAAA TACATTCAAA TATGTATCCG CTCATGAGAC AATAACCCTG ATAAATGCTT CAATAATATT GAAAAAGGAA GAGTATGAGT ATTCAACATT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TCCGTGTCGC CCTTATTCCC TTTTTTGCGG CATTTTGCCT TCCTGTTTTT GCTCACCCAG AAACGCTGGT GAAAGTAAAA GATGCTGAAG ATCAGTTGGG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TGCACGAGTG GGTTACATCG AACTGGATCT CAACAGCGGT AAGATCCTTG AGAGTTTTCG CCCCGAAGAA CGTTTTCCAA TGATGAGCAC TTTTAAAGTT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CTGCTATGTG GCGCGGTATT ATCCCGTATT GACGCCGGGC AAGAGCAACT CGGTCGCCGC ATACACTATT CTCAGAATGA CTTGGTTGAG TACTCACCAG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TCACAGAAAA GCATCTTACG GATGGCATGA CAGTAAGAGA ATTATGCAGT GCTGCCATAA CCATGAGTGA TAACACTGCG GCCAACTTAC TTCTGACAAC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GATCGGAGGA CCGAAGGAGC TAACCGCTTT TTTGCACAAC ATGGGGGATC ATGTAACTCG CCTTGATCGT TGGGAACCGG AGCTGAATGA AGCCATACCA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AACGACGAGC GTGACACCAC GATGCCTGTA GCAATGGCAA CAACGTTGCG CAAACTATTA ACTGGCGAAC TACTTACTCT AGCTTCCCGG CAACAATTAA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TAGACTGGAT GGAGGCGGAT AAAGTTGCAG GACCACTTCT GCGCTCGGCC CTTCCGGCTG GCTGGTTTAT TGCTGATAAA TCTGGAGCCG GTGAGCGTGG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GTCTCGCGGT ATCATTGCAG CACTGGGGCC AGATGGTAAG CCCTCCCGTA TCGTAGTTAT CTACACGACG GGGAGTCAGG CAACTATGGA TGAACGAAAT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AGACAGATCG CTGAGATAGG TGCCTCACTG ATTAAGCATT GGTAACTGTC AGACCAAGTT TACTCATATA TACTTTAGAT TGATTTAAAA CTTCATTTTT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

AATTTAAAAG GATCTAGGTG AAGATCCTTT TTGATAATCT CATGACCAAA ATCCCTTAAC GTGAGTTTTC GTTCCACTGA GCGTCAGACC CCGTAGAAAA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GATCAAAGGA TCTTCTTGAG ATCCTTTTTT TCTGCGCGTA ATCTGCTGCT TGCAAACAAA AAAACCACCG CTACCAGCGG TGGTTTGTTT GCCGGATCAA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GAGCTACCAA CTCTTTTTCC GAAGGTAACT GGCTTCAGCA GAGCGCAGAT ACCAAATACT GTCCTTCTAG TGTAGCCGTA GTTAGGCCAC CACTTCAAGA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ACTCTGTAGC ACCGCCTACA TACCTCGCTC TGCTAATCCT GTTACCAGTG GCTGCTGCCA GTGGCGATAA GTCGTGTCTT ACCGGGTTGG ACTCAAGACG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ATAGTTACCG GATAAGGCGC AGCGGTCGGG CTGAACGGGG GGTTCGTGCA CACAGCCCAG CTTGGAGCGA ACGACCTACA CCGAACTGAG ATACCTACAG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CGTGAGCTAT GAGAAAGCGC CACGCTTCCC GAAGGGAGAA AGGCGGACAG GTATCCGGTA AGCGGCAGGG TCGGAACAGG AGAGCGCACG AGGGAGCTTC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CAGGGGGAAA CGCCTGGTAT CTTTATAGTC CTGTCGGGTT TCGCCACCTC TGACTTGAGC GTCGATTTTT GTGATGCTCG TCAGGGGGGC GGAGCCTATG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GAAAAACGCC AGCAACGCGG CCTTTTTACG GTTCCTGGCC TTTTGCTGGC CTTTTGCTCA CATGTTCTTT CCTGCGTTAT CCCCTGATTC TGTGGATAAC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CGTATTACCG CCTTTGAGTG AGCTGATACC GCTCGCCGCA GCCGAACGAC CGAGCGCAGC GAGTCAGTGA GCGAGGAAGC GGAAGAGCGC CCAATACGCA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

AACCGCCTCT CCCCGCGCGT TGGCCGATTC ATTAATGCAG CTGGCACGAC AGGTTTCCCG ACTGGAAAG
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061

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: Václav Vopálenský	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):

57-992

ORF

ORF position:

2

Version: `0`
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):

1416-3071

Remarks:

IRESite notes about verification of plasmid sequence:
PCR amplification of the sequence encoding bicistronic RNA using M13_reverse (CAGGAAACAGCTATGAC) and
M13_forward (GTAAAACGACGGCCAGT) primers gave one band of expected size.
Sequent sequencing of the vector part's and sequencing of the bicistronic transcription unit using
M13_reverse, M13_forward, Fluc_seq_reverse (AGGAACCAGGGCGTATCTC), Fluc_seq_forward (GTGGACGAAGTACCGAAAGG) and
Rluc_seq_rev (CTGCATGTTTTTCTGAATC) primers resulted in final sequence of supposed mRNA which was in silico
combined with backbone plasmid pBluescript-KS+ (GI: 58065) resulting in the final sequence of vector presented
here in IRESite. More detailed data are annotated in the Genbank sequence file 1343.gb provided on this page
above.

Citations:

Thoma C., Bergamini G., Galy B., Hundsdoerfer P., Hentze M. W. (2004) Enhancement of IRES-mediated translation of the c-myc and BiP mRNAs by the poly(A) tail is independent of intact eIF4G and PABP. Mol. Cell. 15(6):925-935

IRESs:

IRES:

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `c-myc`	The functional status of IRES: `functional`

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

1008-1414

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `16`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `422`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-408`	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):

AACTCGCTGT AGTAATTCCA GCGAGAGGCA GAGGGAGCGA GCGGGCGGCC GGCTAGGGTG GAAGAGCCGG GCGAGCAGAG CTGCGCTGCG GGCGTCCTGG 
^1008      ^1018      ^1028      ^1038      ^1048      ^1058      ^1068      ^1078      ^1088      ^1098      

GAAGGGAGAT CCGGAGCGAA TAGGGGGCTT CGCCTCTGGC CCAGCCCTCC CGCTGATCCC CCAGCCAGCG GTCCGCAACC CTTGCCGCAT CCACGAAACT 
^1108      ^1118      ^1128      ^1138      ^1148      ^1158      ^1168      ^1178      ^1188      ^1198      

TTGCCCATAG CAGCGGGCGG GCACTTTGCA CTGGAACTTA CAACACCCGA GCAAGGACGC GACTCTCCCG ACGCGGGGAG GCTATTCTGC CCATTTGGGG 
^1208      ^1218      ^1228      ^1238      ^1248      ^1258      ^1268      ^1278      ^1288      ^1298      

ACACTTCCCC GCCGCTGCCA GGACCCGCTT CTCTGAAAGG CTCTCCTTGC AGCTGCTTAG ACGCTGGATT TTTTTCGGGT AGTGGAAAAC CAGCAGCCTC 
^1308      ^1318      ^1328      ^1338      ^1348      ^1358      ^1368      ^1378      ^1388      ^1398      

CCGCGAC
^1408

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 464

Version: `3`	Last change: `2008-07-08 09:11:25`
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. `pRML`
	`IRESite Id` of the plasmid used as negative control. `410`
	The relative translation efficiency in % of the negative control: `14.100`
	The size (length) of intercistronic region in the negative control: `423`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_GpppG_cap_with_polyA_tail

Remarks:

Whereas the cap-dependent translation of the 5' cistron (RLuc) in the bicistronic reporter mRNAs is strongly
inhibited by adding 7mGpppG analog, the c-myc IRES-driven translation of the 3' cistron (FFLuc) is not
significantly affected. By contrast, addition of ApppG, cap analog that does not bind the translation
initiation factor eIF4E, does not significantly impair translation from either cistron.

The translation of c-myc.IRES-pA RNA is about 7-fold higher efficient than the translation of the
non-polyadenylated counterpart c-myc.IRES RNA (IRESId: 410).

Translational data are derived from Table 1.

Citations:

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