IRESite_Id:72 characteristics of n-myc IRES studied in pRNF plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `72`	Version: `7`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-09-20 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2008-07-03 12:54:42`

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:
our_best_guess

The mRNA/+RNA description:

Putative spliced in vivo SV40 promoter-derived transcript produced from bicistronic plasmid pRL which
comprises renilla and firefly luciferases as the first and the second cistron, respectively and the 5' UTR (nt
8 to nt 300) plus first 27 bp from human n-myc mRNA.
The sequence ends at its 3'-end right after the poly(A) signal from SV40 mRNA and thus the 3'-UTR might be
slightly wrong.

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

TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTGAAGT TGGTCGTGAG GCACTGGGCA GGTGTCCACT CCCAGTTCAA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTACAGCTCT TAAGGCTAGA GTACTTAATA CGACTCACTA TAGGCTAGGC TTGGCATTCC GGTACTGAAT TGATATCAAG CTCTAGCCAC CATGACTTCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AAAGTTTATG ATCCAGAACA AAGGAAACGG ATGATAACTG GTCCGCAGTG GTGGGCCAGA TGTAAACAAA TGAATGTTCT TGATTCATTT ATTAATTATT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATGATTCAGA AAAACATGCA GAAAATGCTG TTATTTTTTT ACATGGTAAC GCGGCCTCTT CTTATTTATG GCGACATGTT GTGCCACATA TTGAGCCAGT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AGCGCGGTGT ATTATACCAG ACCTTATTGG TATGGGCAAA TCAGGCAAAT CTGGTAATGG TTCTTATAGG TTACTTGATC ATTACAAATA TCTTACTGCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TGGTTTGAAC TTCTTAATTT ACCAAAGAAG ATCATTTTTG TCGGCCATGA TTGGGGTGCT TGTTTGGCAT TTCATTATAG CTATGAGCAT CAAGATAAGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCAAAGCAAT AGTTCACGCT GAAAGTGTAG TAGATGTGAT TGAATCATGG GATGAATGGC CTGATATTGA AGAAGATATT GCGTTGATCA AATCTGAAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGGAGAAAAA ATGGTTTTGG AGAATAACTT CTTCGTGGAA ACCATGTTGC CATCAAAAAT CATGAGAAAG TTAGAACCAG AAGAATTTGC AGCATATCTT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GAACCATTCA AAGAGAAAGG TGAAGTTCGT CGTCCAACAT TATCATGGCC TCGTGAAATC CCGTTAGTAA AAGGTGGTAA ACCTGACGTT GTACAAATTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTAGGAATTA TAATGCTTAT CTACGTGCAA GTGATGATTT ACCAAAAATG TTTATTGAAT CGGACCCAGG ATTCTTTTCC AATGCTATTG TTGAAGGTGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CAAGAAGTTT CCTAATACTG AATTTGTCAA AGTAAAAGGT CTTCATTTTT CGCAAGAAGA TGCACCTGAT GAAATGGGAA AATATATCAA ATCGTTCGTT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAGCGAGTTC TCAAAAATGA ACAATAATTC TAGAGCTTAT CGATACCGTC GACCTCGAAT CACTAGTCAG CTGGAATTCG TCTGGACGCG CTGGGTGGAT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GCGGGGGGCT CCTGGGAACT GTGTTGGAGC CGAGCAAGCG CTAGCCAGGC GCAAGCGCGC ACAGACTGTA GCCATCCGAG GACACCCCCG CCCCCCCGGC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCACCCGGAG ACACCCGCGC AGAATCGCCT CCGGATCCCC TGCAGTCGGC GGGAGTGTTG GAGGTCGGCG CCGGCCCCCG CCTTCCGCGC CCCCCACGGG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAGGAAGCAC CCCCGGTATT AAAACGAACG GGGCGGAAAG AAGCCCTCAG TCGCCGGCCG GGAGGCGAGC CGATGCCGAG CTGCTCCACG TCCACCATGG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AAGACGCCAA AAACATAAAG AAAGGCCCGG CGCCATTCTA TCCGCTGGAA GATGGAACCG CTGGAGAGCA ACTGCATAAG GCTATGAAGA GATACGCCCT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGTTCCTGGA ACAATTGCTT TTACAGATGC ACATATCGAG GTGGACATCA CTTACGCTGA GTACTTCGAA ATGTCCGTTC GGTTGGCAGA AGCTATGAAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CGATATGGGC TGAATACAAA TCACAGAATC GTCGTATGCA GTGAAAACTC TCTTCAATTC TTTATGCCGG TGTTGGGCGC GTTATTTATC GGAGTTGCAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TTGCGCCCGC GAACGACATT TATAATGAAC GTGAATTGCT CAACAGTATG GGCATTTCGC AGCCTACCGT GGTGTTCGTT TCCAAAAAGG GGTTGCAAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AATTTTGAAC GTGCAAAAAA AGCTCCCAAT CATCCAAAAA ATTATTATCA TGGATTCTAA AACGGATTAC CAGGGATTTC AGTCGATGTA CACGTTCGTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACATCTCATC TACCTCCCGG TTTTAATGAA TACGATTTTG TGCCAGAGTC CTTCGATAGG GACAAGACAA TTGCACTGAT CATGAACTCC TCTGGATCTA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTGGTCTGCC TAAAGGTGTC GCTCTGCCTC ATAGAACTGC CTGCGTGAGA TTCTCGCATG CCAGAGATCC TATTTTTGGC AATCAAATCA TTCCGGATAC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGCGATTTTA AGTGTTGTTC CATTCCATCA CGGTTTTGGA ATGTTTACTA CACTCGGATA TTTGATATGT GGATTTCGAG TCGTCTTAAT GTATAGATTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GAAGAAGAGC TGTTTCTGAG GAGCCTTCAG GATTACAAGA TTCAAAGTGC GCTGCTGGTG CCAACCCTAT TCTCCTTCTT CGCCAAAAGC ACTCTGATTG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ACAAATACGA TTTATCTAAT TTACACGAAA TTGCTTCTGG TGGCGCTCCC CTCTCTAAGG AAGTCGGGGA AGCGGTTGCC AAGAGGTTCC ATCTGCCAGG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TATCAGGCAA GGATATGGGC TCACTGAGAC TACATCAGCT ATTCTGATTA CACCCGAGGG GGATGATAAA CCGGGCGCGG TCGGTAAAGT TGTTCCATTT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTTGAAGCGA AGGTTGTGGA TCTGGATACC GGGAAAACGC TGGGCGTTAA TCAAAGAGGC GAACTGTGTG TGAGAGGTCC TATGATTATG TCCGGTTATG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TAAACAATCC GGAAGCGACC AACGCCTTGA TTGACAAGGA TGGATGGCTA CATTCTGGAG ACATAGCTTA CTGGGACGAA GACGAACACT TCTTCATCGT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TGACCGCCTG AAGTCTCTGA TTAAGTACAA AGGCTATCAG GTGGCTCCCG CTGAATTGGA ATCCATCTTG CTCCAACACC CCAACATCTT CGACGCAGGT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GTCGCAGGTC TTCCCGACGA TGACGCCGGT GAACTTCCCG CCGCCGTTGT TGTTTTGGAG CACGGAAAGA CGATGACGGA AAAAGAGATC GTGGATTACG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TCGCCAGTCA AGTAACAACC GCGAAAAAGT TGCGCGGAGG AGTTGTGTTT GTGGACGAAG TACCGAAAGG TCTTACCGGA AAACTCGACG CAAGAAAAAT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CAGAGAGATC CTCATAAAGG CCAAGAAGGG CGGAAAGATC GCCGTGTAAT TCTAGAGTCG GGGCGGCCGG CCGCTTCGAG CAGACATGAT AAGATACATT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GATGAGTTTG GACAAACCAC AACTAGAATG CAGTGAAAAA AATGCTTTAT TTGTGAAATT TGTGATGCTA TTGCTTTATT TGTAACCATT ATAAGCTGCA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ATAAACAAGT TAACAACAAC AATTGCATTC ATTTTATGTT TCAGGTTCAG GGGGAGGTGT GGGAGGTTTT TTAAAGCAAG TAAAACCTCT ACAAATGTGG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TA
^3401

Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pRNF 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?):

no

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

no

A promoter reported in cDNA corresponding to IRES sequence:

no

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
not_tested

Integrity (uniformity) of mRNA tested using RNase protection:
homogeneous_population_of_molecules_confirmed

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
not_tested

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Homo sapiens HeLa (ATCC CCL-2)

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
n-myc

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens SH-SY5Y (ATCC CRL-2266)

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

CCGATCGTTG TCAGAAGTAA GTTGGCCGCA GTGTTATCAC TCATGGTTAT GGCAGCACTG CATAATTCTC TTACTGTCAT GCCATCCGTA AGATGCTTTT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CTGTGACTGG TGAGTACTCA ACCAAGTCAT TCTGAGAATA GTGTATGCGG CGACCGAGTT GCTCTTGCCC GGCGTCAATA CGGGATAATA CCGCGCCACA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TAGCAGAACT TTAAAAGTGC TCATCATTGG AAAACGTTCT TCGGGGCGAA AACTCTCAAG GATCTTACCG CTGTTGAGAT CCAGTTCGAT GTAACCCACT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CGTGCACCCA ACTGATCTTC AGCATCTTTT ACTTTCACCA GCGTTTCTGG GTGAGCAAAA ACAGGAAGGC AAAATGCCGC AAAAAAGGGA ATAAGGGCGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CACGGAAATG TTGAATACTC ATACTCTTCC TTTTTCAATA TTATTGAAGC ATTTATCAGG GTTATTGTCT CATGAGCGGA TACATATTTG AATGTATTTA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GAAAAATAAA CAAATAGGGG TTCCGCGCAC ATTTCCCCGA AAAGTGCCAC CTGACGCGCC CTGTAGCGGC GCATTAAGCG CGGCGGGTGT GGTGGTTACG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CGCAGCGTGA CCGCTACACT TGCCAGCGCC CTAGCGCCCG CTCCTTTCGC TTTCTTCCCT TCCTTTCTCG CCACGTTCGC CGGCTTTCCC CGTCAAGCTC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TAAATCGGGG GCTCCCTTTA GGGTTCCGAT TTAGTGCTTT ACGGCACCTC GACCCCAAAA AACTTGATTA GGGTGATGGT TCACGTAGTG GGCCATCGCC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTGATAGACG GTTTTTCGCC CTTTGACGTT GGAGTCCACG TTCTTTAATA GTGGACTCTT GTTCCAAACT GGAACAACAC TCAACCCTAT CTCGGTCTAT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCTTTTGATT TATAAGGGAT TTTGCCGATT TCGGCCTATT GGTTAAAAAA TGAGCTGATT TAACAAAAAT TTAACGCGAA TTTTAACAAA ATATTAACGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTACAATTTG CCATTCGCCA TTCAGGCTGC GCAACTGTTG GGAAGGGCGA TCGGTGCGGG CCTCTTCGCT ATTACGCCAG CCCAAGCTAC CATGATAAGT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AAGTAATATT AAGGTACGGG AGGTACTTGG AGCGGCCGCA ATAAAATATC TTTATTTTCA TTACATCTGT GTGTTGGTTT TTTGTGTGAA TCGATAGTAC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TAACATACGC TCTCCATCAA AACAAAACGA AACAAAACAA ACTAGCAAAA TAGGCTGTCC CCAGTGCAAG TGCAGGTGCC AGAACATTTC TCTATCGATA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGTACCGAGC TCTTACGCGT GCTAGCCCGG GCTCGAGATC TGCGATCTGC ATCTCAATTA GTCAGCAACC ATAGTCCCGC CCCTAACTCC GCCCATCCCG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CCCCTAACTC CGCCCAGTTC CGCCCATTCT CCGCCCCATC GCTGACTAAT TTTTTTTATT TATGCAGAGG CCGAGGCCGC CTCGGCCTCT GAGCTATTCC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGAAGTAGTG AGGAGGCTTT TTTGGAGGCC TAGGCTTTTG CAAAAAGCTG AAGTTGGTCG TGAGGCACTG GGCAGGTAAG TATCAAGGTT ACAAGACAGG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTTAAGGAGA CCAATAGAAA CTGGGCTTGT CGAGACAGAG AAGACTCTTG CGTTTCTGAT AGGCACCTAT TGGTCTTACT GACATCCACT TTGCCTTTCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CTCCACAGGT GTCCACTCCC AGTTCAATTA CAGCTCTTAA GGCTAGAGTA CTTAATACGA CTCACTATAG GCTAGGCTTG GCATTCCGGT ACTGAATTGA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TATCAAGCTC TAGCCACCAT GACTTCGAAA GTTTATGATC CAGAACAAAG GAAACGGATG ATAACTGGTC CGCAGTGGTG GGCCAGATGT AAACAAATGA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATGTTCTTGA TTCATTTATT AATTATTATG ATTCAGAAAA ACATGCAGAA AATGCTGTTA TTTTTTTACA TGGTAACGCG GCCTCTTCTT ATTTATGGCG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACATGTTGTG CCACATATTG AGCCAGTAGC GCGGTGTATT ATACCAGACC TTATTGGTAT GGGCAAATCA GGCAAATCTG GTAATGGTTC TTATAGGTTA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTTGATCATT ACAAATATCT TACTGCATGG TTTGAACTTC TTAATTTACC AAAGAAGATC ATTTTTGTCG GCCATGATTG GGGTGCTTGT TTGGCATTTC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATTATAGCTA TGAGCATCAA GATAAGATCA AAGCAATAGT TCACGCTGAA AGTGTAGTAG ATGTGATTGA ATCATGGGAT GAATGGCCTG ATATTGAAGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AGATATTGCG TTGATCAAAT CTGAAGAAGG AGAAAAAATG GTTTTGGAGA ATAACTTCTT CGTGGAAACC ATGTTGCCAT CAAAAATCAT GAGAAAGTTA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GAACCAGAAG AATTTGCAGC ATATCTTGAA CCATTCAAAG AGAAAGGTGA AGTTCGTCGT CCAACATTAT CATGGCCTCG TGAAATCCCG TTAGTAAAAG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTGGTAAACC TGACGTTGTA CAAATTGTTA GGAATTATAA TGCTTATCTA CGTGCAAGTG ATGATTTACC AAAAATGTTT ATTGAATCGG ACCCAGGATT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTTTTCCAAT GCTATTGTTG AAGGTGCCAA GAAGTTTCCT AATACTGAAT TTGTCAAAGT AAAAGGTCTT CATTTTTCGC AAGAAGATGC ACCTGATGAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ATGGGAAAAT ATATCAAATC GTTCGTTGAG CGAGTTCTCA AAAATGAACA ATAATTCTAG AGCTTATCGA TACCGTCGAC CTCGAATCAC TAGTCAGCTG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GAATTCGTCT GGACGCGCTG GGTGGATGCG GGGGGCTCCT GGGAACTGTG TTGGAGCCGA GCAAGCGCTA GCCAGGCGCA AGCGCGCACA GACTGTAGCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATCCGAGGAC ACCCCCGCCC CCCCGGCCCA CCCGGAGACA CCCGCGCAGA ATCGCCTCCG GATCCCCTGC AGTCGGCGGG AGTGTTGGAG GTCGGCGCCG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GCCCCCGCCT TCCGCGCCCC CCACGGGAAG GAAGCACCCC CGGTATTAAA ACGAACGGGG CGGAAAGAAG CCCTCAGTCG CCGGCCGGGA GGCGAGCCGA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TGCCGAGCTG CTCCACGTCC ACCATGGAAG ACGCCAAAAA CATAAAGAAA GGCCCGGCGC CATTCTATCC GCTGGAAGAT GGAACCGCTG GAGAGCAACT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GCATAAGGCT ATGAAGAGAT ACGCCCTGGT TCCTGGAACA ATTGCTTTTA CAGATGCACA TATCGAGGTG GACATCACTT ACGCTGAGTA CTTCGAAATG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TCCGTTCGGT TGGCAGAAGC TATGAAACGA TATGGGCTGA ATACAAATCA CAGAATCGTC GTATGCAGTG AAAACTCTCT TCAATTCTTT ATGCCGGTGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGGGCGCGTT ATTTATCGGA GTTGCAGTTG CGCCCGCGAA CGACATTTAT AATGAACGTG AATTGCTCAA CAGTATGGGC ATTTCGCAGC CTACCGTGGT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GTTCGTTTCC AAAAAGGGGT TGCAAAAAAT TTTGAACGTG CAAAAAAAGC TCCCAATCAT CCAAAAAATT ATTATCATGG ATTCTAAAAC GGATTACCAG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GGATTTCAGT CGATGTACAC GTTCGTCACA TCTCATCTAC CTCCCGGTTT TAATGAATAC GATTTTGTGC CAGAGTCCTT CGATAGGGAC AAGACAATTG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CACTGATCAT GAACTCCTCT GGATCTACTG GTCTGCCTAA AGGTGTCGCT CTGCCTCATA GAACTGCCTG CGTGAGATTC TCGCATGCCA GAGATCCTAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TTTTGGCAAT CAAATCATTC CGGATACTGC GATTTTAAGT GTTGTTCCAT TCCATCACGG TTTTGGAATG TTTACTACAC TCGGATATTT GATATGTGGA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TTTCGAGTCG TCTTAATGTA TAGATTTGAA GAAGAGCTGT TTCTGAGGAG CCTTCAGGAT TACAAGATTC AAAGTGCGCT GCTGGTGCCA ACCCTATTCT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CCTTCTTCGC CAAAAGCACT CTGATTGACA AATACGATTT ATCTAATTTA CACGAAATTG CTTCTGGTGG CGCTCCCCTC TCTAAGGAAG TCGGGGAAGC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GGTTGCCAAG AGGTTCCATC TGCCAGGTAT CAGGCAAGGA TATGGGCTCA CTGAGACTAC ATCAGCTATT CTGATTACAC CCGAGGGGGA TGATAAACCG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GGCGCGGTCG GTAAAGTTGT TCCATTTTTT GAAGCGAAGG TTGTGGATCT GGATACCGGG AAAACGCTGG GCGTTAATCA AAGAGGCGAA CTGTGTGTGA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GAGGTCCTAT GATTATGTCC GGTTATGTAA ACAATCCGGA AGCGACCAAC GCCTTGATTG ACAAGGATGG ATGGCTACAT TCTGGAGACA TAGCTTACTG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GGACGAAGAC GAACACTTCT TCATCGTTGA CCGCCTGAAG TCTCTGATTA AGTACAAAGG CTATCAGGTG GCTCCCGCTG AATTGGAATC CATCTTGCTC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CAACACCCCA ACATCTTCGA CGCAGGTGTC GCAGGTCTTC CCGACGATGA CGCCGGTGAA CTTCCCGCCG CCGTTGTTGT TTTGGAGCAC GGAAAGACGA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TGACGGAAAA AGAGATCGTG GATTACGTCG CCAGTCAAGT AACAACCGCG AAAAAGTTGC GCGGAGGAGT TGTGTTTGTG GACGAAGTAC CGAAAGGTCT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TACCGGAAAA CTCGACGCAA GAAAAATCAG AGAGATCCTC ATAAAGGCCA AGAAGGGCGG AAAGATCGCC GTGTAATTCT AGAGTCGGGG CGGCCGGCCG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CTTCGAGCAG ACATGATAAG ATACATTGAT GAGTTTGGAC AAACCACAAC TAGAATGCAG TGAAAAAAAT GCTTTATTTG TGAAATTTGT GATGCTATTG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CTTTATTTGT AACCATTATA AGCTGCAATA AACAAGTTAA CAACAACAAT TGCATTCATT TTATGTTTCA GGTTCAGGGG GAGGTGTGGG AGGTTTTTTA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AAGCAAGTAA AACCTCTACA AATGTGGTAA AATCGATAAG GATCTGAACG ATGGAGCGGA GAATGGGCGG AACTGGGCGG AGTTAGGGGC GGGATGGGCG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GAGTTAGGGG CGGGACTATG GTTGCTGACT AATTGAGATG CATGCTTTGC ATACTTCTGC CTGCTGGGGA GCCTGGGGAC TTTCCACACC TGGTTGCTGA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CTAATTGAGA TGCATGCTTT GCATACTTCT GCCTGCTGGG GAGCCTGGGG ACTTTCCACA CCCTAACTGA CACACATTCC ACAGCGGATC CGTCGACCGA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TGCCCTTGAG AGCCTTCAAC CCAGTCAGCT CCTTCCGGTG GGCGCGGGGC ATGACTATCG TCGCCGCACT TATGACTGTC TTCTTTATCA TGCAACTCGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

AGGACAGGTG CCGGCAGCGC TCTTCCGCTT CCTCGCTCAC TGACTCGCTG CGCTCGGTCG TTCGGCTGCG GCGAGCGGTA TCAGCTCACT CAAAGGCGGT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AATACGGTTA TCCACAGAAT CAGGGGATAA CGCAGGAAAG AACATGTGAG CAAAAGGCCA GCAAAAGGCC AGGAACCGTA AAAAGGCCGC GTTGCTGGCG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TTTTTCCATA GGCTCCGCCC CCCTGACGAG CATCACAAAA ATCGACGCTC AAGTCAGAGG TGGCGAAACC CGACAGGACT ATAAAGATAC CAGGCGTTTC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CCCCTGGAAG CTCCCTCGTG CGCTCTCCTG TTCCGACCCT GCCGCTTACC GGATACCTGT CCGCCTTTCT CCCTTCGGGA AGCGTGGCGC TTTCTCATAG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CTCACGCTGT AGGTATCTCA GTTCGGTGTA GGTCGTTCGC TCCAAGCTGG GCTGTGTGCA CGAACCCCCC GTTCAGCCCG ACCGCTGCGC CTTATCCGGT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AACTATCGTC TTGAGTCCAA CCCGGTAAGA CACGACTTAT CGCCACTGGC AGCAGCCACT GGTAACAGGA TTAGCAGAGC GAGGTATGTA GGCGGTGCTA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CAGAGTTCTT GAAGTGGTGG CCTAACTACG GCTACACTAG AAGAACAGTA TTTGGTATCT GCGCTCTGCT GAAGCCAGTT ACCTTCGGAA AAAGAGTTGG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

TAGCTCTTGA TCCGGCAAAC AAACCACCGC TGGTAGCGGT GGTTTTTTTG TTTGCAAGCA GCAGATTACG CGCAGAAAAA AAGGATCTCA AGAAGATCCT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TTGATCTTTT CTACGGGGTC TGACGCTCAG TGGAACGAAA ACTCACGTTA AGGGATTTTG GTCATGAGAT TATCAAAAAG GATCTTCACC TAGATCCTTT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TAAATTAAAA ATGAAGTTTT AAATCAATCT AAAGTATATA TGAGTAAACT TGGTCTGACA GTTACCAATG CTTAATCAGT GAGGCACCTA TCTCAGCGAT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

CTGTCTATTT CGTTCATCCA TAGTTGCCTG ACTCCCCGTC GTGTAGATAA CTACGATACG GGAGGGCTTA CCATCTGGCC CCAGTGCTGC AATGATACCG 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CGAGACCCAC GCTCACCGGC TCCAGATTTA TCAGCAATAA ACCAGCCAGC CGGAAGGGCC GAGCGCAGAA GTGGTCCTGC AACTTTATCC GCCTCCATCC 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

AGTCTATTAA TTGTTGCCGG GAAGCTAGAG TAAGTAGTTC GCCAGTTAAT AGTTTGCGCA ACGTTGTTGC CATTGCTACA GGCATCGTGG TGTCACGCTC 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GTCGTTTGGT ATGGCTTCAT TCAGCTCCGG TTCCCAACGA TCAAGGCGAG TTACATGATC CCCCATGTTG TGCAAAAAAG CGGTTAGCTC CTTCGGTCCT
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791

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: Václav Vopálenský

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):

1-936

ORF

ORF position:

2

Version: `0`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

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):

1306-2958

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

IRESs:

IRES:

Version: `6`	Last change: `2008-07-03 12:54:42`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `n-myc`	The functional status of IRES: `functional`

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

989-1308

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `53`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `372`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-317`	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):

TGTTGAAGGT GCCAAGAAGT TTCCTAATAC TGAATTTGTC AAAGTAAAAG GTCTTCATTT TTCGCAAGAA GATGCACCTG ATGAAATGGG AAAATATATC 
^989       ^999       ^1009      ^1019      ^1029      ^1039      ^1049      ^1059      ^1069      ^1079      

AAATCGTTCG TTGAGCGAGT TCTCAAAAAT GAACAATAAT TCTAGAGCTT ATCGATACCG TCGACCTCGA ATCACTAGTC AGCTGGAATT CGTCTGGACG 
^1089      ^1099      ^1109      ^1119      ^1129      ^1139      ^1149      ^1159      ^1169      ^1179      

CGCTGGGTGG ATGCGGGGGG CTCCTGGGAA CTGTGTTGGA GCCGAGCAAG CGCTAGCCAG GCGCAAGCGC GCACAGACTG TAGCCATCCG AGGACACCCC 
^1189      ^1199      ^1209      ^1219      ^1229      ^1239      ^1249      ^1259      ^1269      ^1279      

CGCCCCCCCG GCCCACCCGG
^1289      ^1299

Remarks:

n-myc 5' UTR (293 nt) and open reading frame (27 nt)

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

The translation experiments:

Translation results:

IRESite Translation Id: 55

Version: `6`	Last change: `2008-07-06 13:36:51`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

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:

145.000

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pRMF`
`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: `446`

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 transfected by vector pRMF (alias pRmycF; formerly pGL3Rutr),
which contains full-length 5' UTR of c-myc P2 transcript inserted between renilla and firefly luciferase (see
IRESite Id #25).

As a negative control was used HeLa cell line transfected by control vector pRF (formerly pGL3R) without
insertion.

Data from Figure 3.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

Translation results:

IRESite Translation Id: 56

Version: `4`	Last change: `2008-07-06 13:14:49`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens MCF7 (ATCC HTB-22)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

175.000

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pRMF`
`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: `446`

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 MCF7 cell line transfected by vector pRMF (alias pRmycF; formerly pGL3Rutr),
which contains full-length 5' UTR of c-myc P2 transcript inserted between renilla and firefly luciferase.

Data from Figure 3.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

Translation results:

IRESite Translation Id: 57

Version: `4`	Last change: `2008-07-06 13:14:49`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HEK 293T/17 (ATCC CRL-11268)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

375.000

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pRMF`
`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: `446`

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

Rapamycin affects translation:
no

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

As a positive control was used HEK293 cell line transfected by vector pRMF (alias pRmycF; formerly pGL3Rutr),
which contains full-length 5' UTR of c-myc P2 transcript inserted between renilla and firefly luciferase.

Data from Figure 3.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

Translation results:

IRESite Translation Id: 58

Version: `4`	Last change: `2008-07-06 13:14:49`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The translation method used to study IRES function:
in vivo

The organism used for translation:

Mus musculus Neuro-2a [N2a] (ATCC CCL-131)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

540.000

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pRMF`
`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: `446`

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

Rapamycin affects translation:
no

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

As a positive control was used NB2a cell line transfected by vector pRMF (alias pRmycF; formerly pGL3Rutr),
which contains full-length 5' UTR of c-myc P2 transcript inserted between renilla and firefly luciferase.

Data from Figure 3.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

Translation results:

IRESite Translation Id: 59

Version: `4`	Last change: `2008-07-06 13:14:49`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens NTERA-2 cl.D1 [NT2/D1] (ATCC CRL-1973)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

383.000

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pRMF`
`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: `446`

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

Rapamycin affects translation:
no

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

As a positive control was used NT2 cell line transfected by vector pRMF (alias pRmycF; formerly pGL3Rutr),
which contains full-length 5' UTR of c-myc P2 transcript inserted between renilla and firefly luciferase.

ATCC number of used cell line - CRL-1973; Designation - NTERA-2 cl.D1, NT2/D1

Data from Figure 3.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

Translation results:

IRESite Translation Id: 60

Version: `4`	Last change: `2008-07-06 13:14:49`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens SH-SY5Y (ATCC CRL-2266)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

670.000

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pRMF`
`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: `446`

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

Rapamycin affects translation:
no

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

As a positive control was used SH-SY5Y cell line transfected by vector pRMF (alias pRmycF; formerly pGL3Rutr),
which contains full-length 5' UTR of c-myc P2 transcript inserted between renilla and firefly luciferase.

Data from Figure 3.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

Translation results:

IRESite Translation Id: 498

Version: `1`	Last change: `2008-07-06 14:32:07`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

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:

132.000

Name of IRES used as the positive control:

c-myc

Name of the plasmid used as the positive control. `pRMF`	Name of the plasmid used as the negative control. `pRF`
`IRESite Id` of the plasmid used as positive control. `25`	`IRESite Id` of the plasmid used as negative control. `184`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `1.500`
The size (length) of intercistronic region in the positive control: `446`	The size (length) of intercistronic region in the negative control: `67`

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:

Translational data are derived from Fig. 1B.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

Translation results:

IRESite Translation Id: 499

Version: `1`	Last change: `2008-07-06 14:32:07`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

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:

315.000

Name of IRES used as the positive control:

EMCV-R

Name of the plasmid used as the positive control. `pREMCVF`	Name of the plasmid used as the negative control. `pRF`
`IRESite Id` of the plasmid used as positive control. `349`	`IRESite Id` of the plasmid used as negative control. `184`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `1.700`
The size (length) of intercistronic region in the positive control: `619`	The size (length) of intercistronic region in the negative control: `67`

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:

Translational data are derived from Fig. 1B.

Citations:

Jopling C. L., Willis A. E. (2001) N-myc translation is initiated via an internal ribosome entry segment that displays enhanced activity in neuronal cells. Oncogene. 20(21):2664-2670

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