IRESite_Id:248 characteristics of PV IRES studied in pBSFLucPRLuc plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `248`	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 bicistronic mRNA transcript derived from pBSFLucPRluc plasmid through SV40 promoter.

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

TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTCCCTC GAGGaactgg aaaaccagaa agttaactgg taagtttagt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ctttttgtct tttatttcag gtcCCGGAAT TGGTTTAAAC GAATTCGAGC TCGCCCGGGG ATCCTCTAGA GTCAGCTTGA ATTCCTTTGT GTTACATTCT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGAATGTCGC TCGCAGTGAC ATTAGCATTC CGGTACTGTT GGTAAAATGG AAGACGCCAA AAACATAAAG AAAGGCCCGG CGCCATTCTA TCCTCTAGAG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GATGGAACCG CTGGAGAGCA ACTGCATAAG GCTATGAAGA GATACGCCCT GGTTCCTGGA ACAATTGCTT TTACAGATGC ACATATCGAG GTGAACATCA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CGTACGCGGA ATACTTCGAA ATGTCCGTTC GGTTGGCAGA AGCTATGAAA CGATATGGGC TGAATACAAA TCACAGAATC GTCGTATGCA GTGAAAACTC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCTTCAATTC TTTATGCCGG TGTTGGGCGC GTTATTTATC GGAGTTGCAG TTGCGCCCGC GAACGACATT TATAATGAAC GTGAATTGCT CAACAGTATG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AACATTTCGC AGCCTACCGT AGTGTTTGTT TCCAAAAAGG GGTTGCAAAA AATTTTGAAC GTGCAAAAAA AATTACCAAT AATCCAGAAA ATTATTATCA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGGATTCTAA AACGGATTAC CAGGGATTTC AGTCGATGTA CACGTTCGTC ACATCTCATC TACCTCCCGG TTTTAATGAA TACGATTTTG TACCAGAGTC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTTTGATCGT GACAAAACAA TTGCACTGAT AATGAATTCC TCTGGATCTA CTGGGTTACC TAAGGGTGTG GCCCTTCCGC ATAGAACTGC CTGCGTCAGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTCTCGCATG CCAGAGATCC TATTTTTGGC AATCAAATCA TTCCGGATAC TGCGATTTTA AGTGTTGTTC CATTCCATCA CGGTTTTGGA ATGTTTACTA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CACTCGGATA TTTGATATGT GGATTTCGAG TCGTCTTAAT GTATAGATTT GAAGAAGAGC TGTTTTTACG ATCCCTTCAG GATTACAAAA TTCAAAGTGC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GTTGCTAGTA CCAACCCTAT TTTCATTCTT CGCCAAAAGC ACTCTGATTG ACAAATACGA TTTATCTAAT TTACACGAAA TTGCTTCTGG GGGCGCACCT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CTTTCGAAAG AAGTCGGGGA AGCGGTTGCA AAACGCTTCC ATCTTCCAGG GATACGACAA GGATATGGGC TCACTGAGAC TACATCAGCT ATTCTGATTA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CACCCGAGGG GGATGATAAA CCGGGCGCGG TCGGTAAAGT TGTTCCATTT TTTGAAGCGA AGGTTGTGGA TCTGGATACC GGGAAAACGC TGGGCGTTAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCAGAGAGGC GAATTATGTG TCAGAGGACC TATGATTATG TCCGGTTATG TAAACAATCC GGAAGCGACC AACGCCTTGA TTGACAAGGA TGGATGGCTA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CATTCTGGAG ACATAGCTTA CTGGGACGAA GACGAACACT TCTTCATAGT TGACCGCTTG AAGTCTTTAA TTAAATACAA AGGATATCAG GTGGCCCCCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CTGAATTGGA ATCGATATTG TTACAACACC CCAACATCTT CGACGCGGGC GTGGCAGGTC TTCCCGACGA TGACGCCGGT GAACTTCCCG CCGCCGTTGT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGTTTTGGAG CACGGAAAGA CGATGACGGA AAAAGAGATC GTGGATTACG TCGCCAGTCA AGTAACAACC GCGAAAAAGT TGCGCGGAGG AGTTGTGTTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTGGACGAAG TACCGAAAGG TCTTACCGGA AAACTCGACG CAAGAAAAAT CAGAGAGATC CTCATAAAGG CCAAGAAGGG CGGAAAGTCC AAATTGTAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATGTAACTGT ATTCAGCGAT GACGAAATTC TTAGCTATTG TAATAGCTGC AGGCATGCAA GCTTGCGCAG ACGTCGCGCG CGGCCGTTTT AAAACAGCTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGGGGTTGTA CCCACCCCAG AGGCCCACGT GGCGGCTAGT ACTCCGGTAT TGCGGTACCC TTGTACGCCT GTTTTATACT CCCTTCCCGT AACTTAGACG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CACAAAACCA AGTTCAATAG AAGGGGGTAC AAACCAGTAC CACCACGAAC AAGCACTTCT GTTTCCCCGG TGATGTCGTA TAGACTGCTT GCGTGGTTGA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AAGCGACGGA TCCGTTATCC GCTTATGTAC TTCGAGAAGC CCAGTACCAC CTCGGAATCT TCGATGCGTT GCGCTCAGCA CTCAACCCCA GAGTGTAGCT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TAGGCTGATG AGTCTGGACA TCCCTCACCG GTGACGGTGG TCCAGGCTGC GTTGGCGGCC TACCTATGGC TAACGCCATG GGACGCTAGT TGTGAACAAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GTGTGAAGAG CCTATTGAGC TACATAAGAA TCCTCCGGCC CCTGAATGCG GCTAATCCCA ACCTCGGAGC AGGTGGTCAC AAACCAGTGA TTGGCCTGTC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTAACGCGCA AGTCCGTGGC GGAACCGACT ACTTTGGGTG TCCGTGTTTC CTTTTATTTT ATTGTGGCTG CTTATGGTGA CAATCACAGA TTGTTATCAT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AAAGCGAATT GGATTGCGGC GCGCCGAATT CGAAATGACT TCGAAAGTTT ATGATCCAGA ACAAAGGAAA CGGATGATAA CTGGTCCGCA GTGGTGGGCC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AGATGTAAAC AAATGAATGT TCTTGATTCA TTTATTAATT ATTATGATTC AGAAAAACAT GCAGAAAATG CTGTTATTTT TTTACATGGT AACGCGGCCT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CTTCTTATTT ATGGCGACAT GTTGTGCCAC ATATTGAGCC AGTAGCGCGG TGTATTATAC CAGACCTTAT TGGTATGGGC AAATCAGGCA AATCTGGTAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGGTTCTTAT AGGTTACTTG ATCATTACAA ATATCTTACT GCATGGTTTG AACTTCTTAA TTTACCAAAG AAGATCATTT TTGTCGGCCA TGATTGGGGT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GCTTGTTTGG CATTTCATTA TAGCTATGAG CATCAAGATA AGATCAAAGC AATAGTTCAC GCTGAAAGTG TAGTAGATGT GATTGAATCA TGGGATGAAT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGCCTGATAT TGAAGAAGAT ATTGCGTTGA TCAAATCTGA AGAAGGAGAA AAAATGGTTT TGGAGAATAA CTTCTTCGTG GAAACCATGT TGCCATCAAA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AATCATGAGA AAGTTAGAAC CAGAAGAATT TGCAGCATAT CTTGAACCAT TCAAAGAGAA AGGTGAAGTT CGTCGTCCAA CATTATCATG GCCTCGTGAA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ATCCCGTTAG TAAAAGGTGG TAAACCTGAC GTTGTACAAA TTGTTAGGAA TTATAATGCT TATCTACGTG CAAGTGATGA TTTACCAAAA ATGTTTATTG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

AATCGGACCC AGGATTCTTT TCCAATGCTA TTGTTGAAGG TGCCAAGAAG TTTCCTAATA CTGAATTTGT CAAAGTAAAA GGTCTTCATT TTTCGCAAGA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGATGCACCT GATGAAATGG GAAAATATAT CAAATCGTTC GTTGAGCGAG TTCTCAAAAA TGAACAATAA GTCGACCTGC AGAAGCTTGC GCAGACGTCG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CGCGCGGCCG CTTAAGCTAG CTTCGATCCA GACATGATAA GATACATTGA TGAGTTTGGA CAAACCACAA CTAGAATGCA GTGAAAAAAA TGCTTTATTT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GTGAAATTTG TGATGCTATT GCTTTATTTG TAACCATTAT AAGCTGCAAT AAACAAGTTA ACAACAACAA TTGCATTCAT TTTATGTTTC AGGTTCAGGG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GGAGGTGTGG GAGGTTTTTT AAAGCAAGTA AAACCTCTAC AAATGTGGTA
^3801      ^3811      ^3821      ^3831      ^3841

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_except_3UTR

The name of the plasmid:
pBSFLucPRLuc 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:
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:

TAGCTTCTGT GGAATGTGTG TCAGTTAGGG TGTGGAAAGT CCCCAGGCTC CCCAGCAGGC AGAAGTATGC AAAGCATGCA TCTCAATTAG TCAGCAACCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GGTGTGGAAA GTCCCCAGGC TCCCCAGCAG GCAGAAGTAT GCAAAGCATG CATCTCAATT AGTCAGCAAC CATAGTCCCG CCCCTAACTC CGCCCATCCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCCCCTAACT CCGCCCAGTT CCGCCCATTC TCCGCCCCAT GGCTGACTAA TTTTTTTTAT TTATGCAGAG GCCGAGGCCG CCTCGGCCTC TGAGCTATTC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CAGAAGTAGT GAGGAGGCTT TTTTGGAGGC CTAGGCTTTT GCAAAAAGCT CCCTCGAGGa actggaaaac cagaaagtta actggtaagt ttagtctttt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

tgtcttttat ttcaggtcCC GGAATTGGTT TAAACGAATT CGAGCTCGCC CGGGGATCCT CTAGAGTCAG CTTGAATTCC TTTGTGTTAC ATTCTTGAAT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GTCGCTCGCA GTGACATTAG CATTCCGGTA CTGTTGGTAA AATGGAAGAC GCCAAAAACA TAAAGAAAGG CCCGGCGCCA TTCTATCCTC TAGAGGATGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AACCGCTGGA GAGCAACTGC ATAAGGCTAT GAAGAGATAC GCCCTGGTTC CTGGAACAAT TGCTTTTACA GATGCACATA TCGAGGTGAA CATCACGTAC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCGGAATACT TCGAAATGTC CGTTCGGTTG GCAGAAGCTA TGAAACGATA TGGGCTGAAT ACAAATCACA GAATCGTCGT ATGCAGTGAA AACTCTCTTC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AATTCTTTAT GCCGGTGTTG GGCGCGTTAT TTATCGGAGT TGCAGTTGCG CCCGCGAACG ACATTTATAA TGAACGTGAA TTGCTCAACA GTATGAACAT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTCGCAGCCT ACCGTAGTGT TTGTTTCCAA AAAGGGGTTG CAAAAAATTT TGAACGTGCA AAAAAAATTA CCAATAATCC AGAAAATTAT TATCATGGAT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TCTAAAACGG ATTACCAGGG ATTTCAGTCG ATGTACACGT TCGTCACATC TCATCTACCT CCCGGTTTTA ATGAATACGA TTTTGTACCA GAGTCCTTTG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATCGTGACAA AACAATTGCA CTGATAATGA ATTCCTCTGG ATCTACTGGG TTACCTAAGG GTGTGGCCCT TCCGCATAGA ACTGCCTGCG TCAGATTCTC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GCATGCCAGA GATCCTATTT TTGGCAATCA AATCATTCCG GATACTGCGA TTTTAAGTGT TGTTCCATTC CATCACGGTT TTGGAATGTT TACTACACTC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGATATTTGA TATGTGGATT TCGAGTCGTC TTAATGTATA GATTTGAAGA AGAGCTGTTT TTACGATCCC TTCAGGATTA CAAAATTCAA AGTGCGTTGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TAGTACCAAC CCTATTTTCA TTCTTCGCCA AAAGCACTCT GATTGACAAA TACGATTTAT CTAATTTACA CGAAATTGCT TCTGGGGGCG CACCTCTTTC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GAAAGAAGTC GGGGAAGCGG TTGCAAAACG CTTCCATCTT CCAGGGATAC GACAAGGATA TGGGCTCACT GAGACTACAT CAGCTATTCT GATTACACCC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GAGGGGGATG ATAAACCGGG CGCGGTCGGT AAAGTTGTTC CATTTTTTGA AGCGAAGGTT GTGGATCTGG ATACCGGGAA AACGCTGGGC GTTAATCAGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAGGCGAATT ATGTGTCAGA GGACCTATGA TTATGTCCGG TTATGTAAAC AATCCGGAAG CGACCAACGC CTTGATTGAC AAGGATGGAT GGCTACATTC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGGAGACATA GCTTACTGGG ACGAAGACGA ACACTTCTTC ATAGTTGACC GCTTGAAGTC TTTAATTAAA TACAAAGGAT ATCAGGTGGC CCCCGCTGAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TTGGAATCGA TATTGTTACA ACACCCCAAC ATCTTCGACG CGGGCGTGGC AGGTCTTCCC GACGATGACG CCGGTGAACT TCCCGCCGCC GTTGTTGTTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGGAGCACGG AAAGACGATG ACGGAAAAAG AGATCGTGGA TTACGTCGCC AGTCAAGTAA CAACCGCGAA AAAGTTGCGC GGAGGAGTTG TGTTTGTGGA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGAAGTACCG AAAGGTCTTA CCGGAAAACT CGACGCAAGA AAAATCAGAG AGATCCTCAT AAAGGCCAAG AAGGGCGGAA AGTCCAAATT GTAAAATGTA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ACTGTATTCA GCGATGACGA AATTCTTAGC TATTGTAATA GCTGCAGGCA TGCAAGCTTG CGCAGACGTC GCGCGCGGCC GTTTTAAAAC AGCTCTGGGG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTGTACCCAC CCCAGAGGCC CACGTGGCGG CTAGTACTCC GGTATTGCGG TACCCTTGTA CGCCTGTTTT ATACTCCCTT CCCGTAACTT AGACGCACAA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AACCAAGTTC AATAGAAGGG GGTACAAACC AGTACCACCA CGAACAAGCA CTTCTGTTTC CCCGGTGATG TCGTATAGAC TGCTTGCGTG GTTGAAAGCG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACGGATCCGT TATCCGCTTA TGTACTTCGA GAAGCCCAGT ACCACCTCGG AATCTTCGAT GCGTTGCGCT CAGCACTCAA CCCCAGAGTG TAGCTTAGGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TGATGAGTCT GGACATCCCT CACCGGTGAC GGTGGTCCAG GCTGCGTTGG CGGCCTACCT ATGGCTAACG CCATGGGACG CTAGTTGTGA ACAAGGTGTG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AAGAGCCTAT TGAGCTACAT AAGAATCCTC CGGCCCCTGA ATGCGGCTAA TCCCAACCTC GGAGCAGGTG GTCACAAACC AGTGATTGGC CTGTCGTAAC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GCGCAAGTCC GTGGCGGAAC CGACTACTTT GGGTGTCCGT GTTTCCTTTT ATTTTATTGT GGCTGCTTAT GGTGACAATC ACAGATTGTT ATCATAAAGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAATTGGATT GCGGCGCGCC GAATTCGAAA TGACTTCGAA AGTTTATGAT CCAGAACAAA GGAAACGGAT GATAACTGGT CCGCAGTGGT GGGCCAGATG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TAAACAAATG AATGTTCTTG ATTCATTTAT TAATTATTAT GATTCAGAAA AACATGCAGA AAATGCTGTT ATTTTTTTAC ATGGTAACGC GGCCTCTTCT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TATTTATGGC GACATGTTGT GCCACATATT GAGCCAGTAG CGCGGTGTAT TATACCAGAC CTTATTGGTA TGGGCAAATC AGGCAAATCT GGTAATGGTT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CTTATAGGTT ACTTGATCAT TACAAATATC TTACTGCATG GTTTGAACTT CTTAATTTAC CAAAGAAGAT CATTTTTGTC GGCCATGATT GGGGTGCTTG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TTTGGCATTT CATTATAGCT ATGAGCATCA AGATAAGATC AAAGCAATAG TTCACGCTGA AAGTGTAGTA GATGTGATTG AATCATGGGA TGAATGGCCT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GATATTGAAG AAGATATTGC GTTGATCAAA TCTGAAGAAG GAGAAAAAAT GGTTTTGGAG AATAACTTCT TCGTGGAAAC CATGTTGCCA TCAAAAATCA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TGAGAAAGTT AGAACCAGAA GAATTTGCAG CATATCTTGA ACCATTCAAA GAGAAAGGTG AAGTTCGTCG TCCAACATTA TCATGGCCTC GTGAAATCCC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GTTAGTAAAA GGTGGTAAAC CTGACGTTGT ACAAATTGTT AGGAATTATA ATGCTTATCT ACGTGCAAGT GATGATTTAC CAAAAATGTT TATTGAATCG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GACCCAGGAT TCTTTTCCAA TGCTATTGTT GAAGGTGCCA AGAAGTTTCC TAATACTGAA TTTGTCAAAG TAAAAGGTCT TCATTTTTCG CAAGAAGATG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CACCTGATGA AATGGGAAAA TATATCAAAT CGTTCGTTGA GCGAGTTCTC AAAAATGAAC AATAAGTCGA CCTGCAGAAG CTTGCGCAGA CGTCGCGCGC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GGCCGCTTAA GCTAGCTTCG ATCCAGACAT GATAAGATAC ATTGATGAGT TTGGACAAAC CACAACTAGA ATGCAGTGAA AAAAATGCTT TATTTGTGAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ATTTGTGATG CTATTGCTTT ATTTGTAACC ATTATAAGCT GCAATAAACA AGTTAACAAC AACAATTGCA TTCATTTTAT GTTTCAGGTT CAGGGGGAGG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TGTGGGAGGT TTTTTAAAGC AAGTAAAACC TCTACAAATG TGGTATGGCT GATTATGATC CTGCCTCGCG CGTTTCGGTG ATGACGGTGA AAACCTCTGA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CACATGCAGC TCCCGCCTTA ATTAAGGGTT TAAACCCGGT ACCCAGTCAC GTAGCGATAG CGGAGTGTAC TGCATTAATG AATCGGCCAA CGCGCGGGGA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GAGGCGGTTT GCGTATTGGG CGCTCTTCCG CTTCCTCGCT CACTGACTCG CTGCGCTCGG TCGTTCGGCT GCGGCGAGCG GTATCAGCTC ACTCAAAGGC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GGTAATACGG TTATCCACAG AATCAGGGGA TAACGCAGGA AAGAACATGT GAGCAAAAGG CCAGCAAAAG GCCAGGAACC GTAAAAAGGC CGCGTTGCTG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GCGTTtTTCC ATAGGCTCCG CCCCCCTGAC GAGCATCACA AAAATCGACG CTCAAGTCAG AGGTGGCGAA ACCCGACAGG ACTATAAAGA TACCAGGCGT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TTCCCCCTGG AAGCTCCCTC GTGCGCTCTC CTGTTCCGAC CCTGCCGCTT ACCGGATACC TGTCCGCCTT TCTCCCTTCG GGAAGCGTGG CGCTTTCTCA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TAGCTCACGC TGTAGGTATC TCAGTTCGGT GTAGGTCGTT CGCTCCAAGC TGGGCTGTGT GCACGAACCC CCCGTTCAGC CCGACCGCTG CGCCTTATCC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GGTAACTATC GTCTTGAGTC CAACCCGGTA AGACACGACT TATCGCCACT GGCAGCAGCC ACTGGTAACA GGATTAGCAG AGCGAGGTAT GTAGGCGGTG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CTACAGAGTT CTTGAAGTGG TGGCCTAACT ACGGCTACAC TAGAAGGACA GTATTTGGTA TCTGCGCTCT GCTGAAGCCA GTTACCTTCG GAAAAAGAGT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TGGTAGCTCT TGATCCGGCA AACAAACCAC CGCTGGTAGC GGTGGTTTTT TTGTTTGCAA GCAGCAGATT ACGCGCAGAA AAAAAGGATC TCAAGAAGAT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CCTTTGATCT TTTCTACGGG GTCTGACGCT CAGTGGAACG AAAACTCACG TTAAGGGATT TTGGTCATGA GATTATCAAA AAGGATCTTC ACCTAGATCC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TTTTAAATTA AAAATGAAGT TTTAAATCAA TCTAAAGTAT ATATGAGTAA ACTTGGTCTG ACAGTTACCA ATGCTTAATC AGTGAGGCAC CTATCTCAGC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GATCTGTCTA TTTCGTTCAT CCATAGTTGC CTGACTCCCC GTCGTGTAGA TAACTACGAT ACGGGAGGGC TTACCATCTG GCCCCAGTGC TGCAATGATA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CCGCGAGACC CACGCTCACC GGCTCCAGAT TTATCAGCAA TAAACCAGCC AGCCGGAAGG GCCGAGCGCA GAAGTGGTCC TGCAACTTTA TCCGCCTCCA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TCCAGTCTAT TAATTGTTGC CGGGAAGCTA GAGTAAGTAG TTCGCCAGTT AATAGTTTGC GCAACGTTGT TGCCATTGCT ACAGGCATCG TGGTGTCACG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CTCGTCGTTT GGTATGGCTT CATTCAGCTC CGGTTCCCAA CGATCAAGGC GAGTTACATG ATCCCCCATG TTGTGCAAAA AAGCGGTTAG CTCCTTCGGT 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CCTCCGATCG TTGTCAGAAG TAAGTTGGCC GCAGTGTTAT CACTCATGGT TATGGCAGCA CTGCATAATT CTCTTACTGT CATGCCATCC GTAAGATGCT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TTTCTGTGAC TGGTGAGTAC TCAACCAAGT CATTCTGAGA ATAGTGTATG CGGCGACCGA GTTGCTCTTG CCCGGCGTCA ATACGGGATA ATACCGCGCC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ACATAGCAGA ACTTTAAAAG TGCTCATCAT TGGAAAACGT TCTTCGGGGC GAAAACTCTC AAGGATCTTA CCGCTGTTGA GATCCAGTTC GATGTAACCC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ACTCGTGCAC CCAACTGATC TTCAGCATCT TTTACTTTCA CCAGCGTTTC TGGGTGAGCA AAAACAGGAA GGCAAAATGC CGCAAAAAAG GGAATAAGGG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CGACACGGAA ATGTTGAATA CTCATACTCT TCCTTTTTCA ATATTATTGA AGCATTTATC AGGGTTATTG TCTCATGAGC GGATACATAT TTGAATGTAT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TTAGAAAAAT AAACAAATAG GGGTTCCGCG CACATTTCCC CGAAAAGTGC CACCTGACGT CGGTACCATT TAAATATCGA TAAGC
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281

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:
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):

247-1899

ORF

ORF position:

2

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):

2635-3570

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: `3`	Last change: `2007-01-11 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `PV`	The functional status of IRES: `defective`

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

1989-2616

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `90`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `717`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-646`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-19`

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

TTAAAACAGC TCTGGGGTTG TACCCACCCC AGAGGCCCAC GTGGCGGCTA GTACTCCGGT ATTGCGGTAC CCTTGTACGC CTGTTTTATA CTCCCTTCCC 
^1989      ^1999      ^2009      ^2019      ^2029      ^2039      ^2049      ^2059      ^2069      ^2079      

GTAACTTAGA CGCACAAAAC CAAGTTCAAT AGAAGGGGGT ACAAACCAGT ACCACCACGA ACAAGCACTT CTGTTTCCCC GGTGATGTCG TATAGACTGC 
^2089      ^2099      ^2109      ^2119      ^2129      ^2139      ^2149      ^2159      ^2169      ^2179      

TTGCGTGGTT GAAAGCGACG GATCCGTTAT CCGCTTATGT ACTTCGAGAA GCCCAGTACC ACCTCGGAAT CTTCGATGCG TTGCGCTCAG CACTCAACCC 
^2189      ^2199      ^2209      ^2219      ^2229      ^2239      ^2249      ^2259      ^2269      ^2279      

CAGAGTGTAG CTTAGGCTGA TGAGTCTGGA CATCCCTCAC CGGTGACGGT GGTCCAGGCT GCGTTGGCGG CCTACCTATG GCTAACGCCA TGGGACGCTA 
^2289      ^2299      ^2309      ^2319      ^2329      ^2339      ^2349      ^2359      ^2369      ^2379      

GTTGTGAACA AGGTGTGAAG AGCCTATTGA GCTACATAAG AATCCTCCGG CCCCTGAATG CGGCTAATCC CAACCTCGGA GCAGGTGGTC ACAAACCAGT 
^2389      ^2399      ^2409      ^2419      ^2429      ^2439      ^2449      ^2459      ^2469      ^2479      

GATTGGCCTG TCGTAACGCG CAAGTCCGTG GCGGAACCGA CTACTTTGGG TGTCCGTGTT TCCTTTTATT TTATTGTGGC TGCTTATGGT GACAATCACA 
^2489      ^2499      ^2509      ^2519      ^2529      ^2539      ^2549      ^2559      ^2569      ^2579      

GATTGTTATC ATAAAGCGAA TTGGATTG
^2589      ^2599      ^2609

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 308

Version: `2`	Last change: `2006-12-23 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:

Mus musculus C243

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

2.600

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,e, 4b and 5a

Citations:

Translation results:

IRESite Translation Id: 313

Version: `1`	Last change: `2006-12-23 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:

Mus musculus C243

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

2.700

Name of IRES used as the positive control:

PV

Name of the plasmid used as the positive control. `pBSRLucEFluc`
`IRESite Id` of the plasmid used as positive control. `245`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `666`

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. 3e

Citations:

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