IRESite_Id:32 characteristics of c-myc_delta341-395 IRES studied in pGL3Rutr1-340 plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `32`	Version: `2`
Originaly submitted by: Tomáš Mašek	Submission date: `2005-09-20 00:00:00`
Reviewed by: Martin Pospíšek

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:
both_UTRs_incomplete

The mRNA/+RNA description:

3'-end truncated 5'-UTR (1-340 bp of original sequence) of c-myc mRNA transcribed from major P2 promotor,
where the last 55 bases of UTR were removed. Insert was cloned into pGL3R vector between renilla and firefly
luciferase.

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

TTGGCATTCC GGTACTGAAT TGATATCAAG CTCTAGCCAC CATGACTTCG AAAGTTTATG ATCCAGAACA AAGGAAACGG ATGATAACTG GTCCGCAGTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GTGGGCCAGA TGTAAACAAA TGAATGTTCT TGATTCATTT ATTAATTATT ATGATTCAGA AAAACATGCA GAAAATGCTG TTATTTTTTT ACATGGTAAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCGGCCTCTT CTTATTTATG GCGACATGTT GTGCCACATA TTGAGCCAGT AGCGCGGTGT ATTATACCAG ACCTTATTGG TATGGGCAAA TCAGGCAAAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CTGGTAATGG TTCTTATAGG TTACTTGATC ATTACAAATA TCTTACTGCA TGGTTTGAAC TTCTTAATTT ACCAAAGAAG ATCATTTTTG TCGGCCATGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTGGGGTGCT TGTTTGGCAT TTCATTATAG CTATGAGCAT CAAGATAAGA TCAAAGCAAT AGTTCACGCT GAAAGTGTAG TAGATGTGAT TGAATCATGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GATGAATGGC CTGATATTGA AGAAGATATT GCGTTGATCA AATCTGAAGA AGGAGAAAAA ATGGTTTTGG AGAATAACTT CTTCGTGGAA ACCATGTTGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CATCAAAAAT CATGAGAAAG TTAGAACCAG AAGAATTTGC AGCATATCTT GAACCATTCA AAGAGAAAGG TGAAGTTCGT CGTCCAACAT TATCATGGCC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TCGTGAAATC CCGTTAGTAA AAGGTGGTAA ACCTGACGTT GTACAAATTG TTAGGAATTA TAATGCTTAT CTACGTGCAA GTGATGATTT ACCAAAAATG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TTTATTGAAT CGGACCCAGG ATTCTTTTCC AATGCTATTG TTGAAGGTGC CAAGAAGTTT CCTAATACTG AATTTGTCAA AGTAAAAGGT CTTCATTTTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CGCAAGAAGA TGCACCTGAT GAAATGGGAA AATATATCAA ATCGTTCGTT GAGCGAGTTC TCAAAAATGA ACAATAATTC TAGAGCTTAT CGATACCGTC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GACCTCGAAT CACTAGTCAG CAGGATCCCC CTAATTCCAG CGAGAGGCAG AGGGAGCGAG CGGGCGGCCG GCTAGGGTGG AAGAGCCGGG CGAGCAGAGC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TGCGCTGCGG GCGTCCTGGG AAGGGAGATC CGGAGCGAAT AGGGGGCTTC GCCTCTGGCC CAGCCCTCCC GCTGATCCCC CAGCCAGCGG TCCGCAACCC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTGCCGCATC CACGAAACTT TGCCCATAGC AGCGGGCGGG CACTTTGCAC TGGAACTTAC AACACCCGAG CAAGGACGCG ACTCTCCCGA CGCGGGGAGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CTATTCTGCC CATTTGGGGA CACTTCCCCG CCGCTGCCAG GACCCGCTTC TCTGAAAGGC TCTCCTTGCA GCATGGAAGA CGCCAAAAAC ATAAAGAAAG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCCCGGCGCC ATTCTATCCG CTGGAAGATG GAACCGCTGG AGAGCAACTG CATAAGGCTA TGAAGAGATA CGCCCTGGTT CCTGGAACAA TTGCTTTTAC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGATGCACAT ATCGAGGTGG ACATCACTTA CGCTGAGTAC TTCGAAATGT CCGTTCGGTT GGCAGAAGCT ATGAAACGAT ATGGGCTGAA TACAAATCAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGAATCGTCG TATGCAGTGA AAACTCTCTT CAATTCTTTA TGCCGGTGTT GGGCGCGTTA TTTATCGGAG TTGCAGTTGC GCCCGCGAAC GACATTTATA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATGAACGTGA ATTGCTCAAC AGTATGGGCA TTTCGCAGCC TACCGTGGTG TTCGTTTCCA AAAAGGGGTT GCAAAAAATT TTGAACGTGC AAAAAAAGCT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCCAATCATC CAAAAAATTA TTATCATGGA TTCTAAAACG GATTACCAGG GATTTCAGTC GATGTACACG TTCGTCACAT CTCATCTACC TCCCGGTTTT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AATGAATACG ATTTTGTGCC AGAGTCCTTC GATAGGGACA AGACAATTGC ACTGATCATG AACTCCTCTG GATCTACTGG TCTGCCTAAA GGTGTCGCTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGCCTCATAG AACTGCCTGC GTGAGATTCT CGCATGCCAG AGATCCTATT TTTGGCAATC AAATCATTCC GGATACTGCG ATTTTAAGTG TTGTTCCATT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCATCACGGT TTTGGAATGT TTACTACACT CGGATATTTG ATATGTGGAT TTCGAGTCGT CTTAATGTAT AGATTTGAAG AAGAGCTGTT TCTGAGGAGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTTCAGGATT ACAAGATTCA AAGTGCGCTG CTGGTGCCAA CCCTATTCTC CTTCTTCGCC AAAAGCACTC TGATTGACAA ATACGATTTA TCTAATTTAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACGAAATTGC TTCTGGTGGC GCTCCCCTCT CTAAGGAAGT CGGGGAAGCG GTTGCCAAGA GGTTCCATCT GCCAGGTATC AGGCAAGGAT ATGGGCTCAC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGAGACTACA TCAGCTATTC TGATTACACC CGAGGGGGAT GATAAACCGG GCGCGGTCGG TAAAGTTGTT CCATTTTTTG AAGCGAAGGT TGTGGATCTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GATACCGGGA AAACGCTGGG CGTTAATCAA AGAGGCGAAC TGTGTGTGAG AGGTCCTATG ATTATGTCCG GTTATGTAAA CAATCCGGAA GCGACCAACG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CCTTGATTGA CAAGGATGGA TGGCTACATT CTGGAGACAT AGCTTACTGG GACGAAGACG AACACTTCTT CATCGTTGAC CGCCTGAAGT CTCTGATTAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GTACAAAGGC TATCAGGTGG CTCCCGCTGA ATTGGAATCC ATCTTGCTCC AACACCCCAA CATCTTCGAC GCAGGTGTCG CAGGTCTTCC CGACGATGAC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GCCGGTGAAC TTCCCGCCGC CGTTGTTGTT TTGGAGCACG GAAAGACGAT GACGGAAAAA GAGATCGTGG ATTACGTCGC CAGTCAAGTA ACAACCGCGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AAAAGTTGCG CGGAGGAGTT GTGTTTGTGG ACGAAGTACC GAAAGGTCTT ACCGGAAAAC TCGACGCAAG AAAAATCAGA GAGATCCTCA TAAAGGCCAA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GAAGGGCGGA AAGATCGCCG TGTAA
^3001      ^3011      ^3021

Credibility of mRNA sequence:

unknown

The name of the plasmid:
pGL3Rutr1-340 The name of the promoter used to express this mRNA:
SV40

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

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

GGTACCGAGC TCTTACGCGT GCTAGCCCGG GCTCGAGATC TGCGATCTGC ATCTCAATTA GTCAGCAACC ATAGTCCCGC CCCTAACTCC GCCCATCCCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCCTAACTC CGCCCAGTTC CGCCCATTCT CCGCCCCATC GCTGACTAAT TTTTTTTATT TATGCAGAGG CCGAGGCCGC CTCGGCCTCT GAGCTATTCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGAAGTAGTG AGGAGGCTTT TTTGGAGGCC TAGGCTTTTG CAAAAAGCTG AAGTTGGTCG TGAGGCACTG GGCAGGTAAG TATCAAGGTT ACAAGACAGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTTAAGGAGA CCAATAGAAA CTGGGCTTGT CGAGACAGAG AAGACTCTTG CGTTTCTGAT AGGCACCTAT TGGTCTTACT GACATCCACT TTGCCTTTCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTCCACAGGT GTCCACTCCC AGTTCAATTA CAGCTCTTAA GGCTAGAGTA CTTAATACGA CTCACTATAG GCTAGACTTG GCATTCCGGT ACTGAATTGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TATCAAGCTC TAGCCACCAT GACTTCGAAA GTTTATGATC CAGAACAAAG GAAACGGATG ATAACTGGTC CGCAGTGGTG GGCCAGATGT AAACAAATGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATGTTCTTGA TTCATTTATT AATTATTATG ATTCAGAAAA ACATGCAGAA AATGCTGTTA TTTTTTTACA TGGTAACGCG GCCTCTTCTT ATTTATGGCG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACATGTTGTG CCACATATTG AGCCAGTAGC GCGGTGTATT ATACCAGACC TTATTGGTAT GGGCAAATCA GGCAAATCTG GTAATGGTTC TTATAGGTTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTTGATCATT ACAAATATCT TACTGCATGG TTTGAACTTC TTAATTTACC AAAGAAGATC ATTTTTGTCG GCCATGATTG GGGTGCTTGT TTGGCATTTC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATTATAGCTA TGAGCATCAA GATAAGATCA AAGCAATAGT TCACGCTGAA AGTGTAGTAG ATGTGATTGA ATCATGGGAT GAATGGCCTG ATATTGAAGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGATATTGCG TTGATCAAAT CTGAAGAAGG AGAAAAAATG GTTTTGGAGA ATAACTTCTT CGTGGAAACC ATGTTGCCAT CAAAAATCAT GAGAAAGTTA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAACCAGAAG AATTTGCAGC ATATCTTGAA CCATTCAAAG AGAAAGGTGA AGTTCGTCGT CCAACATTAT CATGGCCTCG TGAAATCCCG TTAGTAAAAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTGGTAAACC TGACGTTGTA CAAATTGTTA GGAATTATAA TGCTTATCTA CGTGCAAGTG ATGATTTACC AAAAATGTTT ATTGAATCGG ACCCAGGATT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CTTTTCCAAT GCTATTGTTG AAGGTGCCAA GAAGTTTCCT AATACTGAAT TTGTCAAAGT AAAAGGTCTT CATTTTTCGC AAGAAGATGC ACCTGATGAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ATGGGAAAAT ATATCAAATC GTTCGTTGAG CGAGTTCTCA AAAATGAACA ATAATTCTAG AGCTTATCGA TACCGTCGAC CTCGAATCAC TAGTCAGCAG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GATCCCCCTA ATTCCAGCGA GAGGCAGAGG GAGCGAGCGG GCGGCCGGCT AGGGTGGAAG AGCCGGGCGA GCAGAGCTGC GCTGCGGGCG TCCTGGGAAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGAGATCCGG AGCGAATAGG GGGCTTCGCC TCTGGCCCAG CCCTCCCGCT GATCCCCCAG CCAGCGGTCC GCAACCCTTG CCGCATCCAC GAAACTTTGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CCATAGCAGC GGGCGGGCAC TTTGCACTGG AACTTACAAC ACCCGAGCAA GGACGCGACT CTCCCGACGC GGGGAGGCTA TTCTGCCCAT TTGGGGACAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TTCCCCGCCG CTGCCAGGAC CCGCTTCTCT GAAAGGCTCT CCTTGCAGCA TGGAAGACGC CAAAAACATA AAGAAAGGCC CGGCGCCATT CTATCCGCTG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GAAGATGGAA CCGCTGGAGA GCAACTGCAT AAGGCTATGA AGAGATACGC CCTGGTTCCT GGAACAATTG CTTTTACAGA TGCACATATC GAGGTGGACA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TCACTTACGC TGAGTACTTC GAAATGTCCG TTCGGTTGGC AGAAGCTATG AAACGATATG GGCTGAATAC AAATCACAGA ATCGTCGTAT GCAGTGAAAA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTCTCTTCAA TTCTTTATGC CGGTGTTGGG CGCGTTATTT ATCGGAGTTG CAGTTGCGCC CGCGAACGAC ATTTATAATG AACGTGAATT GCTCAACAGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATGGGCATTT CGCAGCCTAC CGTGGTGTTC GTTTCCAAAA AGGGGTTGCA AAAAATTTTG AACGTGCAAA AAAAGCTCCC AATCATCCAA AAAATTATTA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TCATGGATTC TAAAACGGAT TACCAGGGAT TTCAGTCGAT GTACACGTTC GTCACATCTC ATCTACCTCC CGGTTTTAAT GAATACGATT TTGTGCCAGA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GTCCTTCGAT AGGGACAAGA CAATTGCACT GATCATGAAC TCCTCTGGAT CTACTGGTCT GCCTAAAGGT GTCGCTCTGC CTCATAGAAC TGCCTGCGTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AGATTCTCGC ATGCCAGAGA TCCTATTTTT GGCAATCAAA TCATTCCGGA TACTGCGATT TTAAGTGTTG TTCCATTCCA TCACGGTTTT GGAATGTTTA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTACACTCGG ATATTTGATA TGTGGATTTC GAGTCGTCTT AATGTATAGA TTTGAAGAAG AGCTGTTTCT GAGGAGCCTT CAGGATTACA AGATTCAAAG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TGCGCTGCTG GTGCCAACCC TATTCTCCTT CTTCGCCAAA AGCACTCTGA TTGACAAATA CGATTTATCT AATTTACACG AAATTGCTTC TGGTGGCGCT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCCCTCTCTA AGGAAGTCGG GGAAGCGGTT GCCAAGAGGT TCCATCTGCC AGGTATCAGG CAAGGATATG GGCTCACTGA GACTACATCA GCTATTCTGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TTACACCCGA GGGGGATGAT AAACCGGGCG CGGTCGGTAA AGTTGTTCCA TTTTTTGAAG CGAAGGTTGT GGATCTGGAT ACCGGGAAAA CGCTGGGCGT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TAATCAAAGA GGCGAACTGT GTGTGAGAGG TCCTATGATT ATGTCCGGTT ATGTAAACAA TCCGGAAGCG ACCAACGCCT TGATTGACAA GGATGGATGG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CTACATTCTG GAGACATAGC TTACTGGGAC GAAGACGAAC ACTTCTTCAT CGTTGACCGC CTGAAGTCTC TGATTAAGTA CAAAGGCTAT CAGGTGGCTC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CCGCTGAATT GGAATCCATC TTGCTCCAAC ACCCCAACAT CTTCGACGCA GGTGTCGCAG GTCTTCCCGA CGATGACGCC GGTGAACTTC CCGCCGCCGT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TGTTGTTTTG GAGCACGGAA AGACGATGAC GGAAAAAGAG ATCGTGGATT ACGTCGCCAG TCAAGTAACA ACCGCGAAAA AGTTGCGCGG AGGAGTTGTG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TTTGTGGACG AAGTACCGAA AGGTCTTACC GGAAAACTCG ACGCAAGAAA AATCAGAGAG ATCCTCATAA AGGCCAAGAA GGGCGGAAAG ATCGCCGTGT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AATTCTAGAG TCGGGGCGGC CGGCCGCTTC GAGCAGACAT GATAAGATAC ATTGATGAGT TTGGACAAAC CACAACTAGA ATGCAGTGAA AAAAATGCTT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TATTTGTGAA ATTTGTGATG CTATTGCTTT ATTTGTAACC ATTATAAGCT GCAATAAACA AGTTAACAAC AACAATTGCA TTCATTTTAT GTTTCAGGTT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CAGGGGGAGG TGTGGGAGGT TTTTTAAAGC AAGTAAAACC TCTACAAATG TGGTAAAATC GATAAGGATC TGAACGATGG AGCGGAGAAT GGGCGGAACT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GGGCGGAGTT AGGGGCGGGA TGGGCGGAGT TAGGGGCGGG ACTATGGTTG CTGACTAATT GAGATGCATG CTTTGCATAC TTCTGCCTGC TGGGGAGCCT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GGGGACTTTC CACACCTGGT TGCTGACTAA TTGAGATGCA TGCTTTGCAT ACTTCTGCCT GCTGGGGAGC CTGGGGACTT TCCACACCCT AACTGACACA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CATTCCACAG CGGATCCGTC GACCGATGCC CTTGAGAGCC TTCAACCCAG TCAGCTCCTT CCGGTGGGCG CGGGGCATGA CTATCGTCGC CGCACTTATG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ACTGTCTTCT TTATCATGCA ACTCGTAGGA CAGGTGCCGG CAGCGCTCTT CCGCTTCCTC GCTCACTGAC TCGCTGCGCT CGGTCGTTCG GCTGCGGCGA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCGGTATCAG CTCACTCAAA GGCGGTAATA CGGTTATCCA CAGAATCAGG GGATAACGCA GGAAAGAACA TGTGAGCAAA AGGCCAGCAA AAGGCCAGGA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ACCGTAAAAA GGCCGCGTTG CTGGCGTTTT TCCATAGGCT CCGCCCCCCT GACGAGCATC ACAAAAATCG ACGCTCAAGT CAGAGGTGGC GAAACCCGAC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AGGACTATAA AGATACCAGG CGTTTCCCCC TGGAAGCTCC CTCGTGCGCT CTCCTGTTCC GACCCTGCCG CTTACCGGAT ACCTGTCCGC CTTTCTCCCT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TCGGGAAGCG TGGCGCTTTC TCAATGCTCA CGCTGTAGGT ATCTCAGTTC GGTGTAGGTC GTTCGCTCCA AGCTGGGCTG TGTGCACGAA CCCCCCGTTC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

AGCCCGACCG CTGCGCCTTA TCCGGTAACT ATCGTCTTGA GTCCAACCCG GTAAGACACG ACTTATCGCC ACTGGCAGCA GCCACTGGTA ACAGGATTAG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CAGAGCGAGG TATGTAGGCG GTGCTACAGA GTTCTTGAAG TGGTGGCCTA ACTACGGCTA CACTAGAAGG ACAGTATTTG GTATCTGCGC TCTGCTGAAG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CCAGTTACCT TCGGAAAAAG AGTTGGTAGC TCTTGATCCG GCAAACAAAC CACCGCTGGT AGCGGTGGTT TTTTTGTTTG CAAGCAGCAG ATTACGCGCA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GAAAAAAAGG ATCTCAAGAA GATCCTTTGA TCTTTTCTAC GGGGTCTGAC GCTCAGTGGA ACGAAAACTC ACGTTAAGGG ATTTTGGTCA TGAGATTATC 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AAAAAGGATC TTCACCTAGA TCCTTTTAAA TTAAAAATGA AGTTTTAAAT CAATCTAAAG TATATATGAG TAAACTTGGT CTGACAGTTA CCAATGCTTA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ATCAGTGAGG CACCTATCTC AGCGATCTGT CTATTTCGTT CATCCATAGT TGCCTGACTC CCCGTCGTGT AGATAACTAC GATACGGGAG GGCTTACCAT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CTGGCCCCAG TGCTGCAATG ATACCGCGAG ACCCACGCTC ACCGGCTCCA GATTTATCAG CAATAAACCA GCCAGCCGGA AGGGCCGAGC GCAGAAGTGG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TCCTGCAACT TTATCCGCCT CCATCCAGTC TATTAATTGT TGCCGGGAAG CTAGAGTAAG TAGTTCGCCA GTTAATAGTT TGCGCAACGT TGTTGCCATT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GCTACAGGCA TCGTGGTGTC ACGCTCGTCG TTTGGTATGG CTTCATTCAG CTCCGGTTCC CAACGATCAA GGCGAGTTAC ATGATCCCCC ATGTTGTGCA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AAAAAGCGGT TAGCTCCTTC GGTCCTCCGA TCGTTGTCAG AAGTAAGTTG GCCGCAGTGT TATCACTCAT GGTTATGGCA GCACTGCATA ATTCTCTTAC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TGTCATGCCA TCCGTAAGAT GCTTTTCTGT GACTGGTGAG TACTCAACCA AGTCATTCTG AGAATAGTGT ATGCGGCGAC CGAGTTGCTC TTGCCCGGCG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TCAATACGGG ATAATACCGC GCCACATAGC AGAACTTTAA AAGTGCTCAT CATTGGAAAA CGTTCTTCGG GGCGAAAACT CTCAAGGATC TTACCGCTGT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TGAGATCCAG TTCGATGTAA CCCACTCGTG CACCCAACTG ATCTTCAGCA TCTTTTACTT TCACCAGCGT TTCTGGGTGA GCAAAAACAG GAAGGCAAAA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TGCCGCAAAA AAGGGAATAA GGGCGACACG GAAATGTTGA ATACTCATAC TCTTCCTTTT TCAATATTAT TGAAGCATTT ATCAGGGTTA TTGTCTCATG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

AGCGGATACA TATTTGAATG TATTTAGAAA AATAAACAAA TAGGGGTTCC GCGCACATTT CCCCGAAAAG TGCCACCTGA CGCGCCCTGT AGCGGCGCAT 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

TAAGCGCGGC GGGTGTGGTG GTTACGCGCA GCGTGACCGC TACACTTGCC AGCGCCCTAG CGCCCGCTCC TTTCGCTTTC TTCCCTTCCT TTCTCGCCAC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

GTTCGCCGGC TTTCCCCGTC AAGCTCTAAA TCGGGGGCTC CCTTTAGGGT TCCGATTTAG TGCTTTACGG CACCTCGACC CCAAAAAACT TGATTAGGGT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

GATGGTTCAC GTAGTGGGCC ATCGCCCTGA TAGACGGTTT TTCGCCCTTT GACGTTGGAG TCCACGTTCT TTAATAGTGG ACTCTTGTTC CAAACTGGAA 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

CAACACTCAA CCCTATCTCG GTCTATTCTT TTGATTTATA AGGGATTTTG CCGATTTCGG CCTATTGGTT AAAAAATGAG CTGATTTAAC AAAAATTTAA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CGCGAATTTT AACAAAATAT TAACGTTTAC AATTTCCCAT TCGCCATTCA GGCTGCGCAA CTGTTGGGAA GGGCGATCGG TGCGGGCCTC TTCGCTATTA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CGCCAGCCCA AGCTACCATG ATAAGTAAGT AATATTAAGG TACGGGAGGT ACTTGGAGCG GCCGCAATAA AATATCTTTA TTTTCATTAC ATCTGTGTGT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

TGGTTTTTTG TGTGAATCGA TAGTACTAAC ATACGCTCTC CATCAAAACA AAACGAAACA AAACAAACTA GCAAAATAGG CTGTCCCCAG TGCAAGTGCA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

GGTGCCAGAA CATTTCTCTA TCGATA
^6801      ^6811      ^6821

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: Tomáš Mašek	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):

42-977

ORF

ORF position:

2

Version: `1`
Originaly submitted by: Tomáš Mašek	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):

1373-3025

Citations:

Stoneley M., Paulin F. E., Le Quesne J. P., Chappell S. A., Willis A. E. (1998) C-Myc 5' untranslated region contains an internal ribosome entry segment. Oncogene. 16(3):423-428

IRESs:

IRES:

Version: `3`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Pospíšek
The IRES name: `c-myc_delta341-395`	The functional status of IRES: `functional`

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

1033-1372

How IRES boundaries were determined:
unknown

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `56`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `395`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-340`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-1`

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

AATTCCAGCG AGAGGCAGAG GGAGCGAGCG GGCGGCCGGC TAGGGTGGAA GAGCCGGGCG AGCAGAGCTG CGCTGCGGGC GTCCTGGGAA GGGAGATCCG 
^1033      ^1043      ^1053      ^1063      ^1073      ^1083      ^1093      ^1103      ^1113      ^1123      

GAGCGAATAG GGGGCTTCGC CTCTGGCCCA GCCCTCCCGC TGATCCCCCA GCCAGCGGTC CGCAACCCTT GCCGCATCCA CGAAACTTTG CCCATAGCAG 
^1133      ^1143      ^1153      ^1163      ^1173      ^1183      ^1193      ^1203      ^1213      ^1223      

CGGGCGGGCA CTTTGCACTG GAACTTACAA CACCCGAGCA AGGACGCGAC TCTCCCGACG CGGGGAGGCT ATTCTGCCCA TTTGGGGACA CTTCCCCGCC 
^1233      ^1243      ^1253      ^1263      ^1273      ^1283      ^1293      ^1303      ^1313      ^1323      

GCTGCCAGGA CCCGCTTCTC TGAAAGGCTC TCCTTGCAGC
^1333      ^1343      ^1353      ^1363

Remarks:

This bicistronic mRNA contains truncated 5'-UTR of c-myc P2 transcript, where last 55 bases of the wild-type
UTR were removed.

Citations:

Stoneley M., Paulin F. E., Le Quesne J. P., Chappell S. A., Willis A. E. (1998) C-Myc 5' untranslated region contains an internal ribosome entry segment. Oncogene. 16(3):423-428

The translation experiments:

Translation results:

IRESite Translation Id: 46

Version: `3`	Last change: `2006-04-13 00:00:00`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Pospíšek

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HeLa (ATCC CCL-2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

107.000

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pGL3Rutr`
`IRESite Id` of the plasmid used as positive control. `25`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `450`

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:

As a positive control was used HeLa cell line transformed by vector pGL3Rutr, which contains full-length 5'UTR
of c-myc P2 transcript inserted between renilla and firefly luciferase.

Citations:

Stoneley M., Paulin F. E., Le Quesne J. P., Chappell S. A., Willis A. E. (1998) C-Myc 5' untranslated region contains an internal ribosome entry segment. Oncogene. 16(3):423-428

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