IRESite_Id:414 characteristics of c-myc IRES studied in pSL-RML plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `414`	Version: `1`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-06-20 14:20:03`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
hopefully_full-length_mRNA

The mRNA/+RNA description:

In vitro T3 run-off transcript produced from bicistronic plasmid pSL-RML 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. A stable stem-loop structure was inserted just behind the T3
promoter close to the 5' end of the first cistron of a bicistronic mRNA.These mRNAs are lacking a poly(A)
tail.

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

GGGAACAAAA GCTGGGTACC CCGGAGCGCC CAGATCTGGG CGCTCCGGGG TACCGGGCCC CCCCTCGAGG TCGACGGTAT CGATAAGCTT ATGACTTCGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAGTTTATGA TCCAGAACAA AGGAAACGGA TGATAACTGG TCCGCAGTGG TGGGCCAGAT GTAAACAAAT GAATGTTCTT GATTCATTTA TTAATTATTA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGATTCAGAA AAACATGCAG AAAATGCTGT TATTTTTTTA CATGGTAACG CGGCCTCTTC TTATTTATGG CGACATGTTG TGCCACATAT TGAGCCAGTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCGCGGTGTA TTATACCAGA CCTTATTGGT ATGGGCAAAT CAGGCAAATC TGGTAATGGT TCTTATAGGT TACTTGATCA TTACAAATAT CTTACTGCAT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GGTTTGAACT TCTTAATTTA CCAAAGAAGA TCATTTTTGT CGGCCATGAT TGGGGTGCTT GTTTGGCATT TCATTATAGC TATGAGCATC AAGATAAGAT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CAAAGCAATA GTTCACGCTG AAAGTGTAGT AGATGTGATT GAATCATGGG ATGAATGGCC TGATATTGAA GAAGATATTG CGTTGATCAA ATCTGAAGAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GGAGAAAAAA TGGTTTTGGA GAATAACTTC TTCGTGGAAA CCATGTTGCC ATCAAAAATC ATGAGAAAGT TAGAACCAGA AGAATTTGCA GCATATCTTG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AACCATTCAA AGAGAAAGGT GAAGTTCGTC GTCCAACATT ATCATGGCCT CGTGAAATCC CGTTAGTAAA AGGTGGTAAA CCTGACGTTG TACAAATTGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TAGGAATTAT AATGCTTATC TACGTGCAAG TGATGATTTA CCAAAAATGT TTATTGAATC GGACCCAGGA TTCTTTTCCA ATGCTATTGT TGAAGGTGCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAGAAGTTTC CTAATACTGA ATTTGTCAAA GTAAAAGGTC TTCATTTTTC GCAAGAAGAT GCACCTGATG AAATGGGAAA ATATATCAAA TCGTTCGTTG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGCGAGTTCT CAAAAATGAA CAATAAACTA GGATCCACTA GAACTCGCTG TAGTAATTCC AGCGAGAGGC AGAGGGAGCG AGCGGGCGGC CGGCTAGGGT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GGAAGAGCCG GGCGAGCAGA GCTGCGCTGC GGGCGTCCTG GGAAGGGAGA TCCGGAGCGA ATAGGGGGCT TCGCCTCTGG CCCAGCCCTC CCGCTGATCC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCCAGCCAGC GGTCCGCAAC CCTTGCCGCA TCCACGAAAC TTTGCCCATA GCAGCGGGCG GGCACTTTGC ACTGGAACTT ACAACACCCG AGCAAGGACG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGACTCTCCC GACGCGGGGA GGCTATTCTG CCCATTTGGG GACACTTCCC CGCCGCTGCC AGGACCCGCT TCTCTGAAAG GCTCTCCTTG CAGCTGCTTA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GACGCTGGAT TTTTTTCGGG TAGTGGAAAA CCAGCAGCCT CCCGCGACCA TGGCCGAAGA CGCCAAAAAC ATAAAGAAAG GCCCGGCGCC ATTCTATCCT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CTAGAGGATG GAACCGCTGG AGAGCAACTG CATAAGGCTA TGAAGAGATA CGCCCTGGTT CCTGGAACAA TTGCTTTTAC AGATGCACAT ATCGAGGTGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACATCACGTA CGCGGAATAC TTCGAAATGT CCGTTCGGTT GGCAGAAGCT ATGAAACGAT ATGGGCTGAA TACAAATCAC AGAATCGTCG TATGCAGTGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAACTCTCTT CAATTCTTTA TGCCGGTGTT GGGCGCGTTA TTTATCGGAG TTGCAGTTGC GCCCGCGAAC GACATTTATA ATGAACGTGA ATTGCTCAAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGTATGAACA TTTCGCAGCC TACCGTAGTG TTTGTTTCCA AAAAGGGGTT GCAAAAAATT TTGAACGTGC AAAAAAAATT ACCAATAATC CAGAAAATTA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TTATCATGGA TTCTAAAACG GATTACCAGG GATTTCAGTC GATGTACACG TTCGTCACAT CTCATCTACC TCCCGGTTTT AATGAATACG ATTTTGTACC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGAGTCCTTT GATCGTGACA AAACAATTGC ACTGATAATG AATTCCTCTG GATCTACTGG GTTACCTAAG GGTGTGGCCC TTCCGCATAG AACTGCCTGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GTCAGATTCT CGCATGCCAG AGATCCTATT TTTGGCAATC AAATCATTCC GGATACTGCG ATTTTAAGTG TTGTTCCATT CCATCACGGT TTTGGAATGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTACTACACT CGGATATTTG ATATGTGGAT TTCGAGTCGT CTTAATGTAT AGATTTGAAG AAGAGCTGTT TTTACGATCC CTTCAGGATT ACAAAATTCA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAGTGCGTTG CTAGTACCAA CCCTATTTTC ATTCTTCGCC AAAAGCACTC TGATTGACAA ATACGATTTA TCTAATTTAC ACGAAATTGC TTCTGGGGGC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GCACCTCTTT CGAAAGAAGT CGGGGAAGCG GTTGCAAAAC GCTTCCATCT TCCAGGGATA CGACAAGGAT ATGGGCTCAC TGAGACTACA TCAGCTATTC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TGATTACACC CGAGGGGGAT GATAAACCGG GCGCGGTCGG TAAAGTTGTT CCATTTTTTG AAGCGAAGGT TGTGGATCTG GATACCGGGA AAACGCTGGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGTTAATCAG AGAGGCGAAT TATGTGTCAG AGGACCTATG ATTATGTCCG GTTATGTAAA CAATCCGGAA GCGACCAACG CCTTGATTGA CAAGGATGGA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TGGCTACATT CTGGAGACAT AGCTTACTGG GACGAAGACG AACACTTCTT CATAGTTGAC CGCTTGAAGT CTTTAATTAA ATACAAAGGA TATCAGGTGG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCCCCGCTGA ATTGGAATCG ATATTGTTAC AACACCCCAA CATCTTCGAC GCGGGCGTGG CAGGTCTTCC CGACGATGAC GCCGGTGAAC TTCCCGCCGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CGTTGTTGTT TTGGAGCACG GAAAGACGAT GACGGAAAAA GAGATCGTGG ATTACGTCGC CAGTCAAGTA ACAACCGCGA AAAAGTTGCG CGGAGGAGTT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GTGTTTGTGG ACGAAGTACC GAAAGGTCTT ACCGGAAAAC TCGACGCAAG AAAAATCAGA GAGATCCTCA TAAAGGCCAA GAAGGGCGGA AAGTCCAAAT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TGTAAGGATC CTCGAGTCTG AG
^3101      ^3111      ^3121

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pSL-RML 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, without the poly(A)tract. A synthetic DNA fragment (5' CCCGGAGCGCCCAGATCTGGGCGCTCCGGGGTAC 3') was inserted into the bicistronic c-myc constructs to introduce a stable stemloop structure (deltaG = - 243 kJ/mol) 19 nts downstream from transcription start site.

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:

GAAATGTGCG CGGAACCCCT ATTTGTTTAT TTTTCTAAAT ACATTCAAAT ATGTATCCGC TCATGAGACA ATAACCCTGA TAAATGCTTC AATAATATTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAAAAGGAAG AGTATGAGTA TTCAACATTT CCGTGTCGCC CTTATTCCCT TTTTTGCGGC ATTTTGCCTT CCTGTTTTTG CTCACCCAGA AACGCTGGTG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AAAGTAAAAG ATGCTGAAGA TCAGTTGGGT GCACGAGTGG GTTACATCGA ACTGGATCTC AACAGCGGTA AGATCCTTGA GAGTTTTCGC CCCGAAGAAC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTTTTCCAAT GATGAGCACT TTTAAAGTTC TGCTATGTGG CGCGGTATTA TCCCGTATTG ACGCCGGGCA AGAGCAACTC GGTCGCCGCA TACACTATTC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TCAGAATGAC TTGGTTGAGT ACTCACCAGT CACAGAAAAG CATCTTACGG ATGGCATGAC AGTAAGAGAA TTATGCAGTG CTGCCATAAC CATGAGTGAT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AACACTGCGG CCAACTTACT TCTGACAACG ATCGGAGGAC CGAAGGAGCT AACCGCTTTT TTGCACAACA TGGGGGATCA TGTAACTCGC CTTGATCGTT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GGGAACCGGA GCTGAATGAA GCCATACCAA ACGACGAGCG TGACACCACG ATGCCTGTAG CAATGGCAAC AACGTTGCGC AAACTATTAA CTGGCGAACT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACTTACTCTA GCTTCCCGGC AACAATTAAT AGACTGGATG GAGGCGGATA AAGTTGCAGG ACCACTTCTG CGCTCGGCCC TTCCGGCTGG CTGGTTTATT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GCTGATAAAT CTGGAGCCGG TGAGCGTGGG TCTCGCGGTA TCATTGCAGC ACTGGGGCCA GATGGTAAGC CCTCCCGTAT CGTAGTTATC TACACGACGG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGAGTCAGGC AACTATGGAT GAACGAAATA GACAGATCGC TGAGATAGGT GCCTCACTGA TTAAGCATTG GTAACTGTCA GACCAAGTTT ACTCATATAT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ACTTTAGATT GATTTAAAAC TTCATTTTTA ATTTAAAAGG ATCTAGGTGA AGATCCTTTT TGATAATCTC ATGACCAAAA TCCCTTAACG TGAGTTTTCG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TTCCACTGAG CGTCAGACCC CGTAGAAAAG ATCAAAGGAT CTTCTTGAGA TCCTTTTTTT CTGCGCGTAA TCTGCTGCTT GCAAACAAAA AAACCACCGC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TACCAGCGGT GGTTTGTTTG CCGGATCAAG AGCTACCAAC TCTTTTTCCG AAGGTAACTG GCTTCAGCAG AGCGCAGATA CCAAATACTG TCCTTCTAGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GTAGCCGTAG TTAGGCCACC ACTTCAAGAA CTCTGTAGCA CCGCCTACAT ACCTCGCTCT GCTAATCCTG TTACCAGTGG CTGCTGCCAG TGGCGATAAG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCGTGTCTTA CCGGGTTGGA CTCAAGACGA TAGTTACCGG ATAAGGCGCA GCGGTCGGGC TGAACGGGGG GTTCGTGCAC ACAGCCCAGC TTGGAGCGAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CGACCTACAC CGAACTGAGA TACCTACAGC GTGAGCTATG AGAAAGCGCC ACGCTTCCCG AAGGGAGAAA GGCGGACAGG TATCCGGTAA GCGGCAGGGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CGGAACAGGA GAGCGCACGA GGGAGCTTCC AGGGGGAAAC GCCTGGTATC TTTATAGTCC TGTCGGGTTT CGCCACCTCT GACTTGAGCG TCGATTTTTG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGATGCTCGT CAGGGGGGCG GAGCCTATGG AAAAACGCCA GCAACGCGGC CTTTTTACGG TTCCTGGCCT TTTGCTGGCC TTTTGCTCAC ATGTTCTTTC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTGCGTTATC CCCTGATTCT GTGGATAACC GTATTACCGC CTTTGAGTGA GCTGATACCG CTCGCCGCAG CCGAACGACC GAGCGCAGCG AGTCAGTGAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGAGGAAGCG GAAGAGCGCC CAATACGCAA ACCGCCTCTC CCCGCGCGTT GGCCGATTCA TTAATGCAGC TGGCACGACA GGTTTCCCGA CTGGAAAGCG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGCAGTGAGC GCAACGCAAT TAATGTGAGT TAGCTCACTC ATTAGGCACC CCAGGCTTTA CACTTTATGC TTCCGGCTCG TATGTTGTGT GGAATTGTGA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCGGATAACA ATTTCACACA GGAAACAGCT ATGACCATGA TTACGCCAAG CGCGCAATTA ACCCTCACTA AAGGGAACAA AAGCTGGGTA CCCCGGAGCG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCCAGATCTG GGCGCTCCGG GGTACCGGGC CCCCCCTCGA GGTCGACGGT ATCGATAAGC TTATGACTTC GAAAGTTTAT GATCCAGAAC AAAGGAAACG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GATGATAACT GGTCCGCAGT GGTGGGCCAG ATGTAAACAA ATGAATGTTC TTGATTCATT TATTAATTAT TATGATTCAG AAAAACATGC AGAAAATGCT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GTTATTTTTT TACATGGTAA CGCGGCCTCT TCTTATTTAT GGCGACATGT TGTGCCACAT ATTGAGCCAG TAGCGCGGTG TATTATACCA GACCTTATTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTATGGGCAA ATCAGGCAAA TCTGGTAATG GTTCTTATAG GTTACTTGAT CATTACAAAT ATCTTACTGC ATGGTTTGAA CTTCTTAATT TACCAAAGAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GATCATTTTT GTCGGCCATG ATTGGGGTGC TTGTTTGGCA TTTCATTATA GCTATGAGCA TCAAGATAAG ATCAAAGCAA TAGTTCACGC TGAAAGTGTA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GTAGATGTGA TTGAATCATG GGATGAATGG CCTGATATTG AAGAAGATAT TGCGTTGATC AAATCTGAAG AAGGAGAAAA AATGGTTTTG GAGAATAACT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TCTTCGTGGA AACCATGTTG CCATCAAAAA TCATGAGAAA GTTAGAACCA GAAGAATTTG CAGCATATCT TGAACCATTC AAAGAGAAAG GTGAAGTTCG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TCGTCCAACA TTATCATGGC CTCGTGAAAT CCCGTTAGTA AAAGGTGGTA AACCTGACGT TGTACAAATT GTTAGGAATT ATAATGCTTA TCTACGTGCA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AGTGATGATT TACCAAAAAT GTTTATTGAA TCGGACCCAG GATTCTTTTC CAATGCTATT GTTGAAGGTG CCAAGAAGTT TCCTAATACT GAATTTGTCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAGTAAAAGG TCTTCATTTT TCGCAAGAAG ATGCACCTGA TGAAATGGGA AAATATATCA AATCGTTCGT TGAGCGAGTT CTCAAAAATG AACAATAAAC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TAGGATCCAC TAGAACTCGC TGTAGTAATT CCAGCGAGAG GCAGAGGGAG CGAGCGGGCG GCCGGCTAGG GTGGAAGAGC CGGGCGAGCA GAGCTGCGCT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GCGGGCGTCC TGGGAAGGGA GATCCGGAGC GAATAGGGGG CTTCGCCTCT GGCCCAGCCC TCCCGCTGAT CCCCCAGCCA GCGGTCCGCA ACCCTTGCCG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CATCCACGAA ACTTTGCCCA TAGCAGCGGG CGGGCACTTT GCACTGGAAC TTACAACACC CGAGCAAGGA CGCGACTCTC CCGACGCGGG GAGGCTATTC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TGCCCATTTG GGGACACTTC CCCGCCGCTG CCAGGACCCG CTTCTCTGAA AGGCTCTCCT TGCAGCTGCT TAGACGCTGG ATTTTTTTCG GGTAGTGGAA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AACCAGCAGC CTCCCGCGAC CATGGCCGAA GACGCCAAAA ACATAAAGAA AGGCCCGGCG CCATTCTATC CTCTAGAGGA TGGAACCGCT GGAGAGCAAC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TGCATAAGGC TATGAAGAGA TACGCCCTGG TTCCTGGAAC AATTGCTTTT ACAGATGCAC ATATCGAGGT GAACATCACG TACGCGGAAT ACTTCGAAAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GTCCGTTCGG TTGGCAGAAG CTATGAAACG ATATGGGCTG AATACAAATC ACAGAATCGT CGTATGCAGT GAAAACTCTC TTCAATTCTT TATGCCGGTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TTGGGCGCGT TATTTATCGG AGTTGCAGTT GCGCCCGCGA ACGACATTTA TAATGAACGT GAATTGCTCA ACAGTATGAA CATTTCGCAG CCTACCGTAG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TGTTTGTTTC CAAAAAGGGG TTGCAAAAAA TTTTGAACGT GCAAAAAAAA TTACCAATAA TCCAGAAAAT TATTATCATG GATTCTAAAA CGGATTACCA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GGGATTTCAG TCGATGTACA CGTTCGTCAC ATCTCATCTA CCTCCCGGTT TTAATGAATA CGATTTTGTA CCAGAGTCCT TTGATCGTGA CAAAACAATT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCACTGATAA TGAATTCCTC TGGATCTACT GGGTTACCTA AGGGTGTGGC CCTTCCGCAT AGAACTGCCT GCGTCAGATT CTCGCATGCC AGAGATCCTA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TTTTTGGCAA TCAAATCATT CCGGATACTG CGATTTTAAG TGTTGTTCCA TTCCATCACG GTTTTGGAAT GTTTACTACA CTCGGATATT TGATATGTGG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ATTTCGAGTC GTCTTAATGT ATAGATTTGA AGAAGAGCTG TTTTTACGAT CCCTTCAGGA TTACAAAATT CAAAGTGCGT TGCTAGTACC AACCCTATTT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TCATTCTTCG CCAAAAGCAC TCTGATTGAC AAATACGATT TATCTAATTT ACACGAAATT GCTTCTGGGG GCGCACCTCT TTCGAAAGAA GTCGGGGAAG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CGGTTGCAAA ACGCTTCCAT CTTCCAGGGA TACGACAAGG ATATGGGCTC ACTGAGACTA CATCAGCTAT TCTGATTACA CCCGAGGGGG ATGATAAACC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GGGCGCGGTC GGTAAAGTTG TTCCATTTTT TGAAGCGAAG GTTGTGGATC TGGATACCGG GAAAACGCTG GGCGTTAATC AGAGAGGCGA ATTATGTGTC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AGAGGACCTA TGATTATGTC CGGTTATGTA AACAATCCGG AAGCGACCAA CGCCTTGATT GACAAGGATG GATGGCTACA TTCTGGAGAC ATAGCTTACT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GGGACGAAGA CGAACACTTC TTCATAGTTG ACCGCTTGAA GTCTTTAATT AAATACAAAG GATATCAGGT GGCCCCCGCT GAATTGGAAT CGATATTGTT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

ACAACACCCC AACATCTTCG ACGCGGGCGT GGCAGGTCTT CCCGACGATG ACGCCGGTGA ACTTCCCGCC GCCGTTGTTG TTTTGGAGCA CGGAAAGACG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ATGACGGAAA AAGAGATCGT GGATTACGTC GCCAGTCAAG TAACAACCGC GAAAAAGTTG CGCGGAGGAG TTGTGTTTGT GGACGAAGTA CCGAAAGGTC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TTACCGGAAA ACTCGACGCA AGAAAAATCA GAGAGATCCT CATAAAGGCC AAGAAGGGCG GAAAGTCCAA ATTGTAAGGA TCCTCGAGTC TGAGCTCCAA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TTCGCCCTAT AGTGAGTCGT ATTACGCGCG CTCACTGGCC GTCGTTTTAC AACGTCGTGA CTGGGAAAAC CCTGGCGTTA CCCAACTTAA TCGCCTTGCA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GCACATCCCC CTTTCGCCAG CTGGCGTAAT AGCGAAGAGG CCCGCACCGA TCGCCCTTCC CAACAGTTGC GCAGCCTGAA TGGCGAATGG GACGCGCCCT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

GTAGCGGCGC ATTAAGCGCG GCGGGTGTGG TGGTTACGCG CAGCGTGACC GCTACACTTG CCAGCGCCCT AGCGCCCGCT CCTTTCGCTT TCTTCCCTTC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CTTTCTCGCC ACGTTCGCCG GCTTTCCCCG TCAAGCTCTA AATCGGGGGC TCCCTTTAGG GTTCCGATTT AGTGCTTTAC GGCACCTCGA CCCCAAAAAA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CTTGATTAGG GTGATGGTTC ACGTAGTGGG CCATCGCCCT GATAGACGGT TTTTCGCCCT TTGACGTTGG AGTCCACGTT CTTTAATAGT GGACTCTTGT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TCCAAACTGG AACAACACTC AACCCTATCT CGGTCTATTC TTTTGATTTA TAAGGGATTT TGCCGATTTC GGCCTATTGG TTAAAAAATG AGCTGATTTA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ACAAAAATTT AACGCGAATT TTAACAAAAT ATTAACGCTT ACAATTTAGG TGGCACTTTT CGGG
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961

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

part of the yet unknown plasmid sequence determined by IRESite curators

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):

91-1026

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):

1450-3105

Remarks:

The plasmid was used as the control for experiments in article Enhancement of IRES-Mediated Translation of the
c-myc and BiP mRNAs by the Poly(A) Tail Is Independent of Intact eIF4G and PABP (Thoma et al., 2004; PMID:
15383282).

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):

1042-1448

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 
^1042      ^1052      ^1062      ^1072      ^1082      ^1092      ^1102      ^1112      ^1122      ^1132      

GAAGGGAGAT CCGGAGCGAA TAGGGGGCTT CGCCTCTGGC CCAGCCCTCC CGCTGATCCC CCAGCCAGCG GTCCGCAACC CTTGCCGCAT CCACGAAACT 
^1142      ^1152      ^1162      ^1172      ^1182      ^1192      ^1202      ^1212      ^1222      ^1232      

TTGCCCATAG CAGCGGGCGG GCACTTTGCA CTGGAACTTA CAACACCCGA GCAAGGACGC GACTCTCCCG ACGCGGGGAG GCTATTCTGC CCATTTGGGG 
^1242      ^1252      ^1262      ^1272      ^1282      ^1292      ^1302      ^1312      ^1322      ^1332      

ACACTTCCCC GCCGCTGCCA GGACCCGCTT CTCTGAAAGG CTCTCCTTGC AGCTGCTTAG ACGCTGGATT TTTTTCGGGT AGTGGAAAAC CAGCAGCCTC 
^1342      ^1352      ^1362      ^1372      ^1382      ^1392      ^1402      ^1412      ^1422      ^1432      

CCGCGAC
^1442

Citations:

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