IRESite_Id:250 characteristics of PV IRES studied in pBCRLucPFluc plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `250`	Version: `0`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
3UTR_incomplete

The mRNA/+RNA description:

Putative spliced bicistronic mRNA transcript derived from pBCRLucPFluc plasmid through CMV promoter.

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

TCAGATCACT AGAAGCTTTA TTGCGGTAGT TTATCACAGT TAAATTGCTA ACGCAGTCAG TGCTTCTGAC ACAACAGTCT CGAACTTAAG CTGCAGAAGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGGTCGTGAG GCACTGGGCA GGTGTCCACT CCCAGTTCAA TTACAGCTCT TAAGGCTAGA GTACTTAATA CGACTCACTA TAGGctagcc tcgaggaact 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ggaaaaccag aaagttaact ggtaagttta gtctttttgt cttttatttc aggtcccgga attggtttaa acgaattcga aATGACTTCG AAAGTTTATG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATCCAGAACA AAGGAAACGG ATGATAACTG GTCCGCAGTG GTGGGCCAGA TGTAAACAAA TGAATGTTCT TGATTCATTT ATTAATTATT ATGATTCAGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AAAACATGCA GAAAATGCTG TTATTTTTTT ACATGGTAAC GCGGCCTCTT CTTATTTATG GCGACATGTT GTGCCACATA TTGAGCCAGT AGCGCGGTGT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATTATACCAG ACCTTATTGG TATGGGCAAA TCAGGCAAAT CTGGTAATGG TTCTTATAGG TTACTTGATC ATTACAAATA TCTTACTGCA TGGTTTGAAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTCTTAATTT ACCAAAGAAG ATCATTTTTG TCGGCCATGA TTGGGGTGCT TGTTTGGCAT TTCATTATAG CTATGAGCAT CAAGATAAGA TCAAAGCAAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGTTCACGCT GAAAGTGTAG TAGATGTGAT TGAATCATGG GATGAATGGC CTGATATTGA AGAAGATATT GCGTTGATCA AATCTGAAGA AGGAGAAAAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATGGTTTTGG AGAATAACTT CTTCGTGGAA ACCATGTTGC CATCAAAAAT CATGAGAAAG TTAGAACCAG AAGAATTTGC AGCATATCTT GAACCATTCA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAGAGAAAGG TGAAGTTCGT CGTCCAACAT TATCATGGCC TCGTGAAATC CCGTTAGTAA AAGGTGGTAA ACCTGACGTT GTACAAATTG TTAGGAATTA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TAATGCTTAT CTACGTGCAA GTGATGATTT ACCAAAAATG TTTATTGAAT CGGACCCAGG ATTCTTTTCC AATGCTATTG TTGAAGGTGC CAAGAAGTTT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCTAATACTG AATTTGTCAA AGTAAAAGGT CTTCATTTTT CGCAAGAAGA TGCACCTGAT GAAATGGGAA AATATATCAA ATCGTTCGTT GAGCGAGTTC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TCAAAAATGA ACAATAAgtc gacctgcaga agcttgcgca gacgtcgcgc gcggccgttt taaaacagct ctggggttgt acccacccca gaggcccacg 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tggcggctag tactccggta ttgcggtacc cttgtacgcc tgttttatac tcccttcccg taacttagac gcacaaaacc aagttcaata gaagggggta 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

caaaccagta ccaccacgaa caagcacttc tgtttccccg gtgatgtcgt atagactgct tgcgtggttg aaagcgacgg atccgttatc cgcttatgta 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

cttcgagaag cccagtacca cctcggaatc ttcgatgcgt tgcgctcagc actcaacccc agagtgtagc ttaggctgat gagtctggac atccctcacc 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ggtgacggtg gtccaggctg cgttggcggc ctacctatgg ctaacgccat gggacgctag ttgtgaacaa ggtgtgaaga gcctattgag ctacataaga 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

atcctccggc ccctgaatgc ggctaatccc aacctcggag caggtggtca caaaccagtg attggcctgt cgtaacgcgc aagtccgtgg cggaaccgac 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

tactttgggt gtccgtgttt ccttttattt tattgtggct gcttatggtg acaatcacag attgttatca taaagcgaat tggattgcgg cgcgccgaat 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

tcgagctcgc ccggggatcc tctagagtca gcttgaattc ctttgtgtta cattcttgaa tgtcgctcgc agtgacatta gcattccggt actgttggta 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

aaATGGAAGA CGCCAAAAAC ATAAAGAAAG GCCCGGCGCC ATTCTATCCT CTAGAGGATG GAACCGCTGG AGAGCAACTG CATAAGGCTA TGAAGAGATA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGCCCTGGTT CCTGGAACAA TTGCTTTTAC AGATGCACAT ATCGAGGTGA ACATCACGTA CGCGGAATAC TTCGAAATGT CCGTTCGGTT GGCAGAAGCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATGAAACGAT ATGGGCTGAA TACAAATCAC AGAATCGTCG TATGCAGTGA AAACTCTCTT CAATTCTTTA TGCCGGTGTT GGGCGCGTTA TTTATCGGAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTGCAGTTGC GCCCGCGAAC GACATTTATA ATGAACGTGA ATTGCTCAAC AGTATGAACA TTTCGCAGCC TACCGTAGTG TTTGTTTCCA AAAAGGGGTT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GCAAAAAATT TTGAACGTGC AAAAAAAATT ACCAATAATC CAGAAAATTA TTATCATGGA TTCTAAAACG GATTACCAGG GATTTCAGTC GATGTACACG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTCGTCACAT CTCATCTACC TCCCGGTTTT AATGAATACG ATTTTGTACC AGAGTCCTTT GATCGTGACA AAACAATTGC ACTGATAATG AATTCCTCTG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GATCTACTGG GTTACCTAAG GGTGTGGCCC TTCCGCATAG AACTGCCTGC GTCAGATTCT CGCATGCCAG AGATCCTATT TTTGGCAATC AAATCATTCC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GGATACTGCG ATTTTAAGTG TTGTTCCATT CCATCACGGT TTTGGAATGT TTACTACACT CGGATATTTG ATATGTGGAT TTCGAGTCGT CTTAATGTAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AGATTTGAAG AAGAGCTGTT TTTACGATCC CTTCAGGATT ACAAAATTCA AAGTGCGTTG CTAGTACCAA CCCTATTTTC ATTCTTCGCC AAAAGCACTC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGATTGACAA ATACGATTTA TCTAATTTAC ACGAAATTGC TTCTGGGGGC GCACCTCTTT CGAAAGAAGT CGGGGAAGCG GTTGCAAAAC GCTTCCATCT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TCCAGGGATA CGACAAGGAT ATGGGCTCAC TGAGACTACA TCAGCTATTC TGATTACACC CGAGGGGGAT GATAAACCGG GCGCGGTCGG TAAAGTTGTT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCATTTTTTG AAGCGAAGGT TGTGGATCTG GATACCGGGA AAACGCTGGG CGTTAATCAG AGAGGCGAAT TATGTGTCAG AGGACCTATG ATTATGTCCG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GTTATGTAAA CAATCCGGAA GCGACCAACG CCTTGATTGA CAAGGATGGA TGGCTACATT CTGGAGACAT AGCTTACTGG GACGAAGACG AACACTTCTT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CATAGTTGAC CGCTTGAAGT CTTTAATTAA ATACAAAGGA TATCAGGTGG CCCCCGCTGA ATTGGAATCG ATATTGTTAC AACACCCCAA CATCTTCGAC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GCGGGCGTGG CAGGTCTTCC CGACGATGAC GCCGGTGAAC TTCCCGCCGC CGTTGTTGTT TTGGAGCACG GAAAGACGAT GACGGAAAAA GAGATCGTGG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATTACGTCGC CAGTCAAGTA ACAACCGCGA AAAAGTTGCG CGGAGGAGTT GTGTTTGTGG ACGAAGTACC GAAAGGTCTT ACCGGAAAAC TCGACGCAAG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AAAAATCAGA GAGATCCTCA TAAAGGCCAA GAAGGGCGGA AAGTCCAAAT TGTAAaatgt aactgtattc agcgatgacg aaattcttag ctattgtaat 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

agctgcaggc atgcaagctt gcgcagacgt cgcgcgcggc cgcttaagct agcttcgatc CAGACATGAT AAGATACATT GATGAGTTTG GACAAACCAC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AACTAGAATG CAGTGAAAAA AATGCTTTAT TTGTGAAATT TGTGATGCTA TTGCTTTATT TGTAACCATT ATAAGCTGCA ATAAACAAGT TAACAACAAC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AATTGCATTC ATTTTATGTT TCAGGTTCAG GGGGAGGTGT GGGAGGTTTT TTAAAGCAAG TAAAACCTCT ACAAATGTGG TA
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981

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:

reverse_engineered_sequence_and_should_match_experiment_except_3UTR

The name of the plasmid:
pBCRLucPFluc The name of the promoter used to express this mRNA:
CMV

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:
PV

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Human poliovirus 1 Mahoney

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

aaTATTGGCC ATTAGCCATA TTATTCATTG GTTATATAGC ATAAATCAAT ATTGGCTATT GGCCATTGCA TACGTTGTAT CTATATCATA ATATGTACAT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTATATTGGC TCATGTCCAA TATGACCGCC ATGTTGGCAT TGATTATTGA CTAGTTATTA ATAGTAATCA ATTACGGGGT CATTAGTTCA TAGCCCATAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATGGAGTTCC GCGTTACATA ACTTACGGTA AATGGCCCGC CTGGCTGACC GCCCAACGAC CCCCGCCCAT TGACGTCAAT AATGACGTAT GTTCCCATAG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TAACGCCAAT AGGGACTTTC CATTGACGTC AATGGGTGGA GTATTTACGG TAAACTGCCC ACTTGGCAGT ACATCAAGTG TATCATATGC CAAGTCCGCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCCTATTGAC GTCAATGACG GTAAATGGCC CGCCTGGCAT TATGCCCAGT ACATGACCTT ACGGGACTTT CCTACTTGGC AGTACATCTA CGTATTAGTC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATCGCTATTA CCATGGTGAT GCGGTTTTGG CAGTACACCA ATGGGCGTGG ATAGCGGTTT GACTCACGGG GATTTCCAAG TCTCCACCCC ATTGACGTCA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATGGGAGTTT GTTTTGGCAC CAAAATCAAC GGGACTTTCC AAAATGTCGT AATAACCCCG CCCCGTTGAC GCAAATGGGC GGTAGGCGTG TACGGTGGGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GGTCTATATA AGCAGAGCTC GTTTAGTGAA CCGTCAGATC ACTAGAAGCT TTATTGCGGT AGTTTATCAC AGTTAAATTG CTAACGCAGT CAGTGCTTCT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GACACAACAG TCTCGAACTT AAGCTGCAGA AGTTGGTCGT GAGGCACTGG GCAGGTAAGT ATCAAGGTTA CAAGACAGGT TTAAGGAGAC CAATAGAAAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGGGCTTGTC GAGACAGAGA AGACTCTTGC GTTTCTGATA GGCACCTATT GGTCTTACTG ACATCCACTT TGCCTTTCTC TCCACAGGTG TCCACTCCCA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GTTCAATTAC AGCTCTTAAG GCTAGAGTAC TTAATACGAC TCACTATAGG ctagcctcga ggaactggaa aaccagaaag ttaactggta agtttagtct 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ttttgtcttt tatttcaggt cccggaattg gtttaaacga attcgaaATG ACTTCGAAAG TTTATGATCC AGAACAAAGG AAACGGATGA TAACTGGTCC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GCAGTGGTGG GCCAGATGTA AACAAATGAA TGTTCTTGAT TCATTTATTA ATTATTATGA TTCAGAAAAA CATGCAGAAA ATGCTGTTAT TTTTTTACAT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGTAACGCGG CCTCTTCTTA TTTATGGCGA CATGTTGTGC CACATATTGA GCCAGTAGCG CGGTGTATTA TACCAGACCT TATTGGTATG GGCAAATCAG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCAAATCTGG TAATGGTTCT TATAGGTTAC TTGATCATTA CAAATATCTT ACTGCATGGT TTGAACTTCT TAATTTACCA AAGAAGATCA TTTTTGTCGG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCATGATTGG GGTGCTTGTT TGGCATTTCA TTATAGCTAT GAGCATCAAG ATAAGATCAA AGCAATAGTT CACGCTGAAA GTGTAGTAGA TGTGATTGAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TCATGGGATG AATGGCCTGA TATTGAAGAA GATATTGCGT TGATCAAATC TGAAGAAGGA GAAAAAATGG TTTTGGAGAA TAACTTCTTC GTGGAAACCA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGTTGCCATC AAAAATCATG AGAAAGTTAG AACCAGAAGA ATTTGCAGCA TATCTTGAAC CATTCAAAGA GAAAGGTGAA GTTCGTCGTC CAACATTATC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ATGGCCTCGT GAAATCCCGT TAGTAAAAGG TGGTAAACCT GACGTTGTAC AAATTGTTAG GAATTATAAT GCTTATCTAC GTGCAAGTGA TGATTTACCA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AAAATGTTTA TTGAATCGGA CCCAGGATTC TTTTCCAATG CTATTGTTGA AGGTGCCAAG AAGTTTCCTA ATACTGAATT TGTCAAAGTA AAAGGTCTTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ATTTTTCGCA AGAAGATGCA CCTGATGAAA TGGGAAAATA TATCAAATCG TTCGTTGAGC GAGTTCTCAA AAATGAACAA TAAgtcgacc tgcagaagct 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

tgcgcagacg tcgcgcgcgg ccgttttaaa acagctctgg ggttgtaccc accccagagg cccacgtggc ggctagtact ccggtattgc ggtacccttg 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

tacgcctgtt ttatactccc ttcccgtaac ttagacgcac aaaaccaagt tcaatagaag ggggtacaaa ccagtaccac cacgaacaag cacttctgtt 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

tccccggtga tgtcgtatag actgcttgcg tggttgaaag cgacggatcc gttatccgct tatgtacttc gagaagccca gtaccacctc ggaatcttcg 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

atgcgttgcg ctcagcactc aaccccagag tgtagcttag gctgatgagt ctggacatcc ctcaccggtg acggtggtcc aggctgcgtt ggcggcctac 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ctatggctaa cgccatggga cgctagttgt gaacaaggtg tgaagagcct attgagctac ataagaatcc tccggcccct gaatgcggct aatcccaacc 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

tcggagcagg tggtcacaaa ccagtgattg gcctgtcgta acgcgcaagt ccgtggcgga accgactact ttgggtgtcc gtgtttcctt ttattttatt 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

gtggctgctt atggtgacaa tcacagattg ttatcataaa gcgaattgga ttgcggcgcg ccgaattcga gctcgcccgg ggatcctcta gagtcagctt 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

gaattccttt gtgttacatt cttgaatgtc gctcgcagtg acattagcat tccggtactg ttggtaaaAT GGAAGACGCC AAAAACATAA AGAAAGGCCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGCGCCATTC TATCCTCTAG AGGATGGAAC CGCTGGAGAG CAACTGCATA AGGCTATGAA GAGATACGCC CTGGTTCCTG GAACAATTGC TTTTACAGAT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GCACATATCG AGGTGAACAT CACGTACGCG GAATACTTCG AAATGTCCGT TCGGTTGGCA GAAGCTATGA AACGATATGG GCTGAATACA AATCACAGAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TCGTCGTATG CAGTGAAAAC TCTCTTCAAT TCTTTATGCC GGTGTTGGGC GCGTTATTTA TCGGAGTTGC AGTTGCGCCC GCGAACGACA TTTATAATGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ACGTGAATTG CTCAACAGTA TGAACATTTC GCAGCCTACC GTAGTGTTTG TTTCCAAAAA GGGGTTGCAA AAAATTTTGA ACGTGCAAAA AAAATTACCA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ATAATCCAGA AAATTATTAT CATGGATTCT AAAACGGATT ACCAGGGATT TCAGTCGATG TACACGTTCG TCACATCTCA TCTACCTCCC GGTTTTAATG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

AATACGATTT TGTACCAGAG TCCTTTGATC GTGACAAAAC AATTGCACTG ATAATGAATT CCTCTGGATC TACTGGGTTA CCTAAGGGTG TGGCCCTTCC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GCATAGAACT GCCTGCGTCA GATTCTCGCA TGCCAGAGAT CCTATTTTTG GCAATCAAAT CATTCCGGAT ACTGCGATTT TAAGTGTTGT TCCATTCCAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CACGGTTTTG GAATGTTTAC TACACTCGGA TATTTGATAT GTGGATTTCG AGTCGTCTTA ATGTATAGAT TTGAAGAAGA GCTGTTTTTA CGATCCCTTC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AGGATTACAA AATTCAAAGT GCGTTGCTAG TACCAACCCT ATTTTCATTC TTCGCCAAAA GCACTCTGAT TGACAAATAC GATTTATCTA ATTTACACGA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AATTGCTTCT GGGGGCGCAC CTCTTTCGAA AGAAGTCGGG GAAGCGGTTG CAAAACGCTT CCATCTTCCA GGGATACGAC AAGGATATGG GCTCACTGAG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ACTACATCAG CTATTCTGAT TACACCCGAG GGGGATGATA AACCGGGCGC GGTCGGTAAA GTTGTTCCAT TTTTTGAAGC GAAGGTTGTG GATCTGGATA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CCGGGAAAAC GCTGGGCGTT AATCAGAGAG GCGAATTATG TGTCAGAGGA CCTATGATTA TGTCCGGTTA TGTAAACAAT CCGGAAGCGA CCAACGCCTT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GATTGACAAG GATGGATGGC TACATTCTGG AGACATAGCT TACTGGGACG AAGACGAACA CTTCTTCATA GTTGACCGCT TGAAGTCTTT AATTAAATAC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

AAAGGATATC AGGTGGCCCC CGCTGAATTG GAATCGATAT TGTTACAACA CCCCAACATC TTCGACGCGG GCGTGGCAGG TCTTCCCGAC GATGACGCCG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GTGAACTTCC CGCCGCCGTT GTTGTTTTGG AGCACGGAAA GACGATGACG GAAAAAGAGA TCGTGGATTA CGTCGCCAGT CAAGTAACAA CCGCGAAAAA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GTTGCGCGGA GGAGTTGTGT TTGTGGACGA AGTACCGAAA GGTCTTACCG GAAAACTCGA CGCAAGAAAA ATCAGAGAGA TCCTCATAAA GGCCAAGAAG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GGCGGAAAGT CCAAATTGTA Aaatgtaact gtattcagcg atgacgaaat tcttagctat tgtaatagct gcaggcatgc aagcttgcgc agacgtcgcg 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

cgcggccgct taagctagct tcgatcCAGA CATGATAAGA TACATTGATG AGTTTGGACA AACCACAACT AGAATGCAGT GAAAAAAATG CTTTATTTGT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GAAATTTGTG ATGCTATTGC TTTATTTGTA ACCATTATAA GCTGCAATAA ACAAGTTAAC AACAACAATT GCATTCATTT TATGTTTCAG GTTCAGGGGG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AGGTGTGGGA GGTTTTTTAA AGCAAGTAAA ACCTCTACAA ATGTGGTATG GCTGATTATG ATCCTGCCTC GCGCGTTTCG GTGATGACGG TGAAAACCTC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TGACACATGC AGCTCCCGCC TTAATTAAGG GTTTAAACCC GGTACCCAGT CACGTAGCGA TAGCGGAGTG TACTGCATTA ATGAATCGGC CAACGCGCGG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GGAGAGGCGG TTTGCGTATT GGGCGCTCTT CCGCTTCCTC GCTCACTGAC TCGCTGCGCT CGGTCGTTCG GCTGCGGCGA GCGGTATCAG CTCACTCAAA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GGCGGTAATA CGGTTATCCA CAGAATCAGG GGATAACGCA GGAAAGAACA TGTGAGCAAA AGGCCAGCAA AAGGCCAGGA ACCGTAAAAA GGCCGCGTTG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CTGGCGTTtT TCCATAGGCT CCGCCCCCCT GACGAGCATC ACAAAAATCG ACGCTCAAGT CAGAGGTGGC GAAACCCGAC AGGACTATAA AGATACCAGG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CGTTTCCCCC TGGAAGCTCC CTCGTGCGCT CTCCTGTTCC GACCCTGCCG CTTACCGGAT ACCTGTCCGC CTTTCTCCCT TCGGGAAGCG TGGCGCTTTC 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TCATAGCTCA CGCTGTAGGT ATCTCAGTTC GGTGTAGGTC GTTCGCTCCA AGCTGGGCTG TGTGCACGAA CCCCCCGTTC AGCCCGACCG CTGCGCCTTA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TCCGGTAACT ATCGTCTTGA GTCCAACCCG GTAAGACACG ACTTATCGCC ACTGGCAGCA GCCACTGGTA ACAGGATTAG CAGAGCGAGG TATGTAGGCG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

GTGCTACAGA GTTCTTGAAG TGGTGGCCTA ACTACGGCTA CACTAGAAGG ACAGTATTTG GTATCTGCGC TCTGCTGAAG CCAGTTACCT TCGGAAAAAG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

AGTTGGTAGC TCTTGATCCG GCAAACAAAC CACCGCTGGT AGCGGTGGTT TTTTTGTTTG CAAGCAGCAG ATTACGCGCA GAAAAAAAGG ATCTCAAGAA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GATCCTTTga tcttttctac ggggtctgac gctcagtgga acgaaaactc acgttaaggg attttggtca tgagattatc aaaaaggatc ttcacctaga 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

tccttttaaa ttaaaaatga agttttaaat caatctaaag tatatatgag taaacttggt ctgacagTTA CCAATGCTTA ATCAGTGAGG CACCTATCTC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

AGCGATCTGT CTATTTCGTT CATCCATAGT TGCCTGACTC CCCGTCGTGT AGATAACTAC GATACGGGAG GGCTTACCAT CTGGCCCCAG TGCTGCAATG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ATACCGCGAG ACCCACGCTC ACCGGCTCCA GATTTATCAG CAATAAACCA GCCAGCCGGA AGGGCCGAGC GCAGAAGTGG TCCTGCAACT TTATCCGCCT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

CCATCCAGTC TATTAATTGT TGCCGGGAAG CTAGAGTAAG TAGTTCGCCA GTTAATAGTT TGCGCAACGT TGTTGCCATT GCTACAGGCA TCGTGGTGTC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

ACGCTCGTCG TTTGGTATGG CTTCATTCAG CTCCGGTTCC CAACGATCAA GGCGAGTTAC ATGATCCCCC ATGTTGTGCA AAAAAGCGGT TAGCTCCTTC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

GGTCCTCCGA TCGTTGTCAG AAGTAAGTTG GCCGCAGTGT TATCACTCAT GGTTATGGCA GCACTGCATA ATTCTCTTAC TGTCATGCCA TCCGTAAGAT 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

GCTTTTCTGT GACTGGTGAG TACTCAACCA AGTCATTCTG AGAATAGTGT ATGCGGCGAC CGAGTTGCTC TTGCCCGGCG TCAATACGGG ATAATACCGC 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GCCACATAGC AGAACTTTAA AAGTGCTCAT CATTGGAAAA CGTTCTTCGG GGCGAAAACT CTCAAGGATC TTACCGCTGT TGAGATCCAG TTCGATGTAA 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CCCACTCGTG CACCCAACTG ATCTTCAGCA TCTTTTACTT TCACCAGCGT TTCTGGGTGA GCAAAAACAG GAAGGCAAAA TGCCGCAAAA AAGGGAATAA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

GGGCGACACG GAAATGTTGA ATACTCATac tcttcctttt tcaatattat tgaagcattt atcagggtta ttgtctcatg agcggataca tatttgaatg 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

tatttagaaa aataaacaaa taggggttcc gcgcacattt ccccgaaaag tgccacctga cgtcggtacc atttaaatat cgatcttc
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981

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: Martin Mokrejš	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):

282-1217

ORF

ORF position:

2

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
FLuc

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):

2003-3655

Citations:

Hennecke M., Kwissa M., Metzger K., Oumard A., Kroger A., Schirmbeck R., Reimann J., Hauser H. (2001) Composition and arrangement of genes define the strength of IRES-driven translation in bicistronic mRNAs. Nucleic. Acids Res. 29(16):3327-3334

IRESs:

IRES:

Version: `2`	Last change: `2007-01-23 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `PV`	The functional status of IRES: `functional`

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

1260-1887

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `43`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `670`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-743`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-116`

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

ttaaaacagc tctggggttg tacccacccc agaggcccac gtggcggcta gtactccggt attgcggtac ccttgtacgc ctgttttata ctcccttccc 
^1260      ^1270      ^1280      ^1290      ^1300      ^1310      ^1320      ^1330      ^1340      ^1350      

gtaacttaga cgcacaaaac caagttcaat agaagggggt acaaaccagt accaccacga acaagcactt ctgtttcccc ggtgatgtcg tatagactgc 
^1360      ^1370      ^1380      ^1390      ^1400      ^1410      ^1420      ^1430      ^1440      ^1450      

ttgcgtggtt gaaagcgacg gatccgttat ccgcttatgt acttcgagaa gcccagtacc acctcggaat cttcgatgcg ttgcgctcag cactcaaccc 
^1460      ^1470      ^1480      ^1490      ^1500      ^1510      ^1520      ^1530      ^1540      ^1550      

cagagtgtag cttaggctga tgagtctgga catccctcac cggtgacggt ggtccaggct gcgttggcgg cctacctatg gctaacgcca tgggacgcta 
^1560      ^1570      ^1580      ^1590      ^1600      ^1610      ^1620      ^1630      ^1640      ^1650      

gttgtgaaca aggtgtgaag agcctattga gctacataag aatcctccgg cccctgaatg cggctaatcc caacctcgga gcaggtggtc acaaaccagt 
^1660      ^1670      ^1680      ^1690      ^1700      ^1710      ^1720      ^1730      ^1740      ^1750      

gattggcctg tcgtaacgcg caagtccgtg gcggaaccga ctactttggg tgtccgtgtt tccttttatt ttattgtggc tgcttatggt gacaatcaca 
^1760      ^1770      ^1780      ^1790      ^1800      ^1810      ^1820      ^1830      ^1840      ^1850      

gattgttatc ataaagcgaa ttggattg
^1860      ^1870      ^1880

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 310

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Mus musculus C243

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

74.000

Name of IRES used as the positive control:

PV

Name of the plasmid used as the positive control. `pBSRLucPFluc`
`IRESite Id` of the plasmid used as positive control. `246`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `785`

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:

Fig. 3c

Citations:

Translation results:

IRESite Translation Id: 311

Version: `1`	Last change: `2006-12-22 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens BHK-21 (ATCC CCL-10)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

62.300

Name of IRES used as the positive control:

PV

Name of the plasmid used as the positive control. `pBSRLucPFluc`
`IRESite Id` of the plasmid used as positive control. `246`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `785`

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:

Fig. 3d

Citations:

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