IRESite_Id:326 characteristics of EMCV-R_272-831 IRES studied in pBSFLucERLuc plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `326`	Version: `1`
Originaly submitted by: Tomáš Mašek
Reviewed by: Tomáš Mašek	Last change: `2008-06-04 22:06:57`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

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

The mRNA/+RNA description:

Putative bicistronic mRNA transcript derived from pBSRLucEFluc plasmid through SV40 promoter. The plasmid has
in the intercistronic region T7 promoter.

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

TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTCCTCG AGGaactgAa aaaccagaaa gttaactggt aagtttagtc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tttttgtctt ttatttcagg tcCCGGAtcg gaATTGGTTT AAACGAATTC GAGCTCGCCC GGGGATCCTC TAGAGTCggg gatcctctag agtcAGCTTg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GAATTCCTTT GTGTTACATT CTTGAATGTC GCTCGCAGTG ACATTAGCAT TCCGGTACTG TTGGTAAAAT GGAAGACGCC AAAAACATAA AGAAAGGCCC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GGCGCCATTC TATCCTCTAG AGGATGGAAC CGCTGGAGAG CAACTGCATA AGGCTATGAA GAGATACGCC CTGGTTCCTG GAACAATTGC TTTTACAGAT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCACATATCG AGGTGAACAT CACGTACGCG GAATACTTCG AAATGTCCGT TCGGTTGGCA GAAGCTATGA AACGATATGG GCTGAATACA AATCACAGAA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCGTCGTATG CAGTGAAAAC TCTCTTCAAT TCTTTATGCC GGTGTTGGGC GCGTTATTTA TCGGAGTTGC AGTTGCGCCC GCGAACGACA TTTATAATGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ACGTGAATTG CTCAACAGTA TGAACATTTC GCAGCCTACC GTAGTGTTTG TTTCCAAAAA GGGGTTGCAA AAAATTTTGA ACGTGCAAAA AAAATTACCA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATAATCCAGA AAATTATTAT CATGGATTCT AAAACGGATT ACCAGGGATT TCAGTCGATG TACACGTTCG TCACATCTCA TCTACCTCCC GGTTTTAATG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AATACGATTT TGTACCAGAG TCCTTTGATC GTGACAAAAC AATTGCACTG ATAATGAATT CCTCTGGATC TACTGGGTTA CCTAAGGGTG TGGCCCTTCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCATAGAACT GCCTGCGTCA GATTCTCGCA TGCCAGAGAT CCTATTTTTG GCAATCAAAT CATTCCGGAT ACTGCGATTT TAAGTGTTGT TCCATTCCAT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CACGGTTTTG GAATGTTTAC TACACTCGGA TATTTGATAT GTGGATTTCG AGTCGTCTTA ATGTATAGAT TTGAAGAAGA GCTGTTTTTA CGATCCCTTC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AGGATTACAA AATTCAAAGT GCGTTGCTAG TACCAACCCT ATTTTCATTC TTCGCCAAAA GCACTCTGAT TGACAAATAC GATTTATCTA ATTTACACGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AATTGCTTCT GGGGGCGCAC CTCTTTCGAA AGAAGTCGGG GAAGCGGTTG CAAAACGCTT CCATCTTCCA GGGATACGAC AAGGATATGG GCTCACTGAG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ACTACATCAG CTATTCTGAT TACACCCGAG GGGGATGATA AACCGGGCGC GGTCGGTAAA GTTGTTCCAT TTTTTGAAGC GAAGGTTGTG GATCTGGATA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CCGGGAAAAC GCTGGGCGTT AATCAGAGAG GCGAATTATG TGTCAGAGGA CCTATGATTA TGTCCGGTTA TGTAAACAAT CCGGAAGCGA CCAACGCCTT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GATTGACAAG GATGGATGGC TACATTCTGG AGACATAGCT TACTGGGACG AAGACGAACA CTTCTTCATA GTTGACCGCT TGAAGTCTTT AATTAAATAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AAAGGATATC AGGTGGCCCC CGCTGAATTG GAATCGATAT TGTTACAACA CCCCAACATC TTCGACGCGG GCGTGGCAGG TCTTCCCGAC GATGACGCCG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTGAACTTCC CGCCGCCGTT GTTGTTTTGG AGCACGGAAA GACGATGACG GAAAAAGAGA TCGTGGATTA CGTCGCCAGT CAAGTAACAA CCGCGAAAAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTTGCGCGGA GGAGTTGTGT TTGTGGACGA AGTACCGAAA GGTCTTACCG GAAAACTCGA CGCAAGAAAA ATCAGAGAGA TCCTCATAAA GGCCAAGAAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGCGGAAAGT CCAAATTGTA AAATGTAACT GTATTCAGCG ATGACGAAAT TCTTAGCTAT TGTAATGACC TGCAGGCATG CAAGCTTGCG CAGACGTCGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GCGCGGCCGC GAAATTAATA CGACTCACTA TAGGGAGACC ACAACGGTTT CCCTCTAGCG GGATCAATTC CGCCCCCCCC CTAACGTTAC TGGCCGAAGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGCTTGGAAT AAGGCCGGTG TGCGTTTGTC TATATGTTAT TTTCCACCAT ATTGCCGTCT TTTGGCAATG TGAGGGCCCG GAAACCTGGC CCTGTCTTCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGACGAGCAT TCCTAGGGGT CTTTCCCCTC TCGCCAAAGG AATGCAAGGT CTGTTGAATG TCGTGAAGGA AGCAGTTCCT CTGGAAGCTT CTTGAAGACA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AACAACGTCT GTAGCGACCC TTTGCAGGCA GCGGAACCCC CCACCTGGCG ACAGGTGCCT CTGCGGCCAA AAGCCACGTG TATAAGATAC ACCATGCAAA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GGCGGCACAA CCCCAGTGCC ACGTTGTGAG TTGGATAGTT GTGGAAAGAG TCAAATGGCT CTCCTCAAGC GTATTCAACA AGGGGCTGAA GGATGCCCAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AAGGTACCCC ATTGTATGGG ATCTGATCTG GGGCCTCGGT GCACATGCTT TACATGTGTT TAGTCGAGGT TAAAAAACGT CTAGGCCCCC CGAACCACGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GGACGTGGTT TTCCTTTGAA AAACACGATG ATACCATGAC TTCGAAAGTT TATGATCCAG AACAAAGGAA ACGGATGATA ACTGGTCCGC AGTGGTGGGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CAGATGTAAA CAAATGAATG TTCTTGATTC ATTTATTAAT TATTATGATT CAGAAAAACA TGCAGAAAAT GCTGTTATTT TTTTACATGG TAACGCGGCC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TCTTCTTATT TATGGCGACA TGTTGTGCCA CATATTGAGC CAGTAGCGCG GTGTATTATA CCAGACCTTA TTGGTATGGG CAAATCAGGC AAATCTGGTA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATGGTTCTTA TAGGTTACTT GATCATTACA AATATCTTAC TGCATGGTTT GAACTTCTTA ATTTACCAAA GAAGATCATT TTTGTCGGCC ATGATTGGGG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TGCTTGTTTG GCATTTCATT ATAGCTATGA GCATCAAGAT AAGATCAAAG CAATAGTTCA CGCTGAAAGT GTAGTAGATG TGATTGAATC ATGGGATGAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TGGCCTGATA TTGAAGAAGA TATTGCGTTG ATCAAATCTG AAGAAGGAGA AAAAATGGTT TTGGAGAATA ACTTCTTCGT GGAAACCATG TTGCCATCAA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AAATCATGAG AAAGTTAGAA CCAGAAGAAT TTGCAGCATA TCTTGAACCA TTCAAAGAGA AAGGTGAAGT TCGTCGTCCA ACATTATCAT GGCCTCGTGA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AATCCCGTTA GTAAAAGGTG GTAAACCTGA CGTTGTACAA ATTGTTAGGA ATTATAATGC TTATCTACGT GCAAGTGATG ATTTACCAAA AATGTTTATT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GAATCGGACC CAGGATTCTT TTCCAATGCT ATTGTTGAAG GTGCCAAGAA GTTTCCTAAT ACTGAATTTG TCAAAGTAAA AGGTCTTCAT TTTTCGCAAG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AAGATGCACC TGATGAAATG GGAAAATATA TCAAATCGTT CGTTGAGCGA GTTCTCAAAA ATGAACAATA AGTCGACCTG CAGAAGCTTG CGCAGACGTC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GCGCGCGGCC GCTTAAGCTA GCTTCGATCC AGACATGATA AGATACATTG ATGAGTTTGG ACAAACCACA ACTAGAATGC AGTGAAAAAA ATGCTTTATT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TGTGAAATTT GTGATGCTAT TGCTTTATTT GTAACCATTA TAAGCTGCAA TAAACAAGTT AACAACAACA ATTGCATTCA TTTTATGTTT CAGGTTCAGG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GGGAGGTGTG GGAGGTTTTT TAAAGCAAGT AAAACCTCTA CAAATGTGGT A
^3801      ^3811      ^3821      ^3831      ^3841      ^3851

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_maybe_except_3UTR

The name of the plasmid:
pBSFLucERLuc 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:
EMCV-R

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Encephalomyocarditis virus Rueckert

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 CCTCGAGGaa ctgAaaaacc agaaagttaa ctggtaagtt tagtcttttt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

gtcttttatt tcaggtcCCG GAtcggaATT GGTTTAAACG AATTCGAGCT CGCCCGGGGA TCCTCTAGAG TCggggatcc tctagagtcA GCTTgGAATT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCTTTGTGTT ACATTCTTGA ATGTCGCTCG CAGTGACATT AGCATTCCGG TACTGTTGGT AAAATGGAAG ACGCCAAAAA CATAAAGAAA GGCCCGGCGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CATTCTATCC TCTAGAGGAT GGAACCGCTG GAGAGCAACT GCATAAGGCT ATGAAGAGAT ACGCCCTGGT TCCTGGAACA ATTGCTTTTA CAGATGCACA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TATCGAGGTG AACATCACGT ACGCGGAATA CTTCGAAATG TCCGTTCGGT TGGCAGAAGC TATGAAACGA TATGGGCTGA ATACAAATCA CAGAATCGTC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GTATGCAGTG AAAACTCTCT TCAATTCTTT ATGCCGGTGT TGGGCGCGTT ATTTATCGGA GTTGCAGTTG CGCCCGCGAA CGACATTTAT AATGAACGTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AATTGCTCAA CAGTATGAAC ATTTCGCAGC CTACCGTAGT GTTTGTTTCC AAAAAGGGGT TGCAAAAAAT TTTGAACGTG CAAAAAAAAT TACCAATAAT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCAGAAAATT ATTATCATGG ATTCTAAAAC GGATTACCAG GGATTTCAGT CGATGTACAC GTTCGTCACA TCTCATCTAC CTCCCGGTTT TAATGAATAC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GATTTTGTAC CAGAGTCCTT TGATCGTGAC AAAACAATTG CACTGATAAT GAATTCCTCT GGATCTACTG GGTTACCTAA GGGTGTGGCC CTTCCGCATA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GAACTGCCTG CGTCAGATTC TCGCATGCCA GAGATCCTAT TTTTGGCAAT CAAATCATTC CGGATACTGC GATTTTAAGT GTTGTTCCAT TCCATCACGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TTTTGGAATG TTTACTACAC TCGGATATTT GATATGTGGA TTTCGAGTCG TCTTAATGTA TAGATTTGAA GAAGAGCTGT TTTTACGATC CCTTCAGGAT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TACAAAATTC AAAGTGCGTT GCTAGTACCA ACCCTATTTT CATTCTTCGC CAAAAGCACT CTGATTGACA AATACGATTT ATCTAATTTA CACGAAATTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CTTCTGGGGG CGCACCTCTT TCGAAAGAAG TCGGGGAAGC GGTTGCAAAA CGCTTCCATC TTCCAGGGAT ACGACAAGGA TATGGGCTCA CTGAGACTAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ATCAGCTATT CTGATTACAC CCGAGGGGGA TGATAAACCG GGCGCGGTCG GTAAAGTTGT TCCATTTTTT GAAGCGAAGG TTGTGGATCT GGATACCGGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAAACGCTGG GCGTTAATCA GAGAGGCGAA TTATGTGTCA GAGGACCTAT GATTATGTCC GGTTATGTAA ACAATCCGGA AGCGACCAAC GCCTTGATTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ACAAGGATGG ATGGCTACAT TCTGGAGACA TAGCTTACTG GGACGAAGAC GAACACTTCT TCATAGTTGA CCGCTTGAAG TCTTTAATTA AATACAAAGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATATCAGGTG GCCCCCGCTG AATTGGAATC GATATTGTTA CAACACCCCA ACATCTTCGA CGCGGGCGTG GCAGGTCTTC CCGACGATGA CGCCGGTGAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CTTCCCGCCG CCGTTGTTGT TTTGGAGCAC GGAAAGACGA TGACGGAAAA AGAGATCGTG GATTACGTCG CCAGTCAAGT AACAACCGCG AAAAAGTTGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCGGAGGAGT TGTGTTTGTG GACGAAGTAC CGAAAGGTCT TACCGGAAAA CTCGACGCAA GAAAAATCAG AGAGATCCTC ATAAAGGCCA AGAAGGGCGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AAAGTCCAAA TTGTAAAATG TAACTGTATT CAGCGATGAC GAAATTCTTA GCTATTGTAA TGACCTGCAG GCATGCAAGC TTGCGCAGAC GTCGCGCGCG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GCCGCGAAAT TAATACGACT CACTATAGGG AGACCACAAC GGTTTCCCTC TAGCGGGATC AATTCCGCCC CCCCCCTAAC GTTACTGGCC GAAGCCGCTT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GGAATAAGGC CGGTGTGCGT TTGTCTATAT GTTATTTTCC ACCATATTGC CGTCTTTTGG CAATGTGAGG GCCCGGAAAC CTGGCCCTGT CTTCTTGACG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AGCATTCCTA GGGGTCTTTC CCCTCTCGCC AAAGGAATGC AAGGTCTGTT GAATGTCGTG AAGGAAGCAG TTCCTCTGGA AGCTTCTTGA AGACAAACAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGTCTGTAGC GACCCTTTGC AGGCAGCGGA ACCCCCCACC TGGCGACAGG TGCCTCTGCG GCCAAAAGCC ACGTGTATAA GATACACCAT GCAAAGGCGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CACAACCCCA GTGCCACGTT GTGAGTTGGA TAGTTGTGGA AAGAGTCAAA TGGCTCTCCT CAAGCGTATT CAACAAGGGG CTGAAGGATG CCCAAAAGGT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ACCCCATTGT ATGGGATCTG ATCTGGGGCC TCGGTGCACA TGCTTTACAT GTGTTTAGTC GAGGTTAAAA AACGTCTAGG CCCCCCGAAC CACGGGGACG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGGTTTTCCT TTGAAAAACA CGATGATACC ATGACTTCGA AAGTTTATGA TCCAGAACAA AGGAAACGGA TGATAACTGG TCCGCAGTGG TGGGCCAGAT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GTAAACAAAT GAATGTTCTT GATTCATTTA TTAATTATTA TGATTCAGAA AAACATGCAG AAAATGCTGT TATTTTTTTA CATGGTAACG CGGCCTCTTC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TTATTTATGG CGACATGTTG TGCCACATAT TGAGCCAGTA GCGCGGTGTA TTATACCAGA CCTTATTGGT ATGGGCAAAT CAGGCAAATC TGGTAATGGT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TCTTATAGGT TACTTGATCA TTACAAATAT CTTACTGCAT GGTTTGAACT TCTTAATTTA CCAAAGAAGA TCATTTTTGT CGGCCATGAT TGGGGTGCTT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GTTTGGCATT TCATTATAGC TATGAGCATC AAGATAAGAT CAAAGCAATA GTTCACGCTG AAAGTGTAGT AGATGTGATT GAATCATGGG ATGAATGGCC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGATATTGAA GAAGATATTG CGTTGATCAA ATCTGAAGAA GGAGAAAAAA TGGTTTTGGA GAATAACTTC TTCGTGGAAA CCATGTTGCC ATCAAAAATC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATGAGAAAGT TAGAACCAGA AGAATTTGCA GCATATCTTG AACCATTCAA AGAGAAAGGT GAAGTTCGTC GTCCAACATT ATCATGGCCT CGTGAAATCC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CGTTAGTAAA AGGTGGTAAA CCTGACGTTG TACAAATTGT TAGGAATTAT AATGCTTATC TACGTGCAAG TGATGATTTA CCAAAAATGT TTATTGAATC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GGACCCAGGA TTCTTTTCCA ATGCTATTGT TGAAGGTGCC AAGAAGTTTC CTAATACTGA ATTTGTCAAA GTAAAAGGTC TTCATTTTTC GCAAGAAGAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GCACCTGATG AAATGGGAAA ATATATCAAA TCGTTCGTTG AGCGAGTTCT CAAAAATGAA CAATAAGTCG ACCTGCAGAA GCTTGCGCAG ACGTCGCGCG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CGGCCGCTTA AGCTAGCTTC GATCCAGACA TGATAAGATA CATTGATGAG TTTGGACAAA CCACAACTAG AATGCAGTGA AAAAAATGCT TTATTTGTGA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AATTTGTGAT GCTATTGCTT TATTTGTAAC CATTATAAGC TGCAATAAAC AAGTTAACAA CAACAATTGC ATTCATTTTA TGTTTCAGGT TCAGGGGGAG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GTGTGGGAGG TTTTTTAAAG CAAGTAAAAC CTCTACAAAT GTGGTATGGC TGATTATGAT CCTGCCTCGC GCGTTTCGGT GATGACGGTG AAAACCTCTG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ACACATGCAG CTCCCGCCTT AATTAAGGGT TTAAACCCGG TACCCAGTCA CGTAGCGATA GCGGAGTGTA CTGCATTAAT GAATCGGCCA ACGCGCGGGG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AGAGGCGGTT TGCGTATTGG GCGCTCTTCC GCTTCCTCGC TCACTGACTC GCTGCGCTCG GTCGTTCGGC TGCGGCGAGC GGTATCAGCT CACTCAAAGG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CGGTAATACG GTTATCCACA GAATCAGGGG ATAACGCAGG AAAGAACATG TGAGCAAAAG GCCAGCAAAA GGCCAGGAAC CGTAAAAAGG CCGCGTTGCT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GGCGTTtTTC CATAGGCTCC GCCCCCCTGA CGAGCATCAC AAAAATCGAC GCTCAAGTCA GAGGTGGCGA AACCCGACAG GACTATAAAG ATACCAGGCG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TTTCCCCCTG GAAGCTCCCT CGTGCGCTCT CCTGTTCCGA CCCTGCCGCT TACCGGATAC CTGTCCGCCT TTCTCCCTTC GGGAAGCGTG GCGCTTTCTC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ATAGCTCACG CTGTAGGTAT CTCAGTTCGG TGTAGGTCGT TCGCTCCAAG CTGGGCTGTG TGCACGAACC CCCCGTTCAG CCCGACCGCT GCGCCTTATC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CGGTAACTAT CGTCTTGAGT CCAACCCGGT AAGACACGAC TTATCGCCAC TGGCAGCAGC CACTGGTAAC AGGATTAGCA GAGCGAGGTA TGTAGGCGGT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GCTACAGAGT TCTTGAAGTG GTGGCCTAAC TACGGCTACA CTAGAAGGAC AGTATTTGGT ATCTGCGCTC TGCTGAAGCC AGTTACCTTC GGAAAAAGAG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTGGTAGCTC TTGATCCGGC AAACAAACCA CCGCTGGTAG CGGTGGTTTT TTTGTTTGCA AGCAGCAGAT TACGCGCAGA AAAAAAGGAT CTCAAGAAGA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TCCTTTGATC TTTTCTACGG GGTCTGACGC TCAGTGGAAC GAAAACTCAC GTTAAGGGAT TTTGGTCATG AGATTATCAA AAAGGATCTT CACCTAGATC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CTTTTAAATT AAAAATGAAG TTTTAAATCA ATCTAAAGTA TATATGAGTA AACTTGGTCT GACAGTTACC AATGCTTAAT CAGTGAGGCA CCTATCTCAG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CGATCTGTCT ATTTCGTTCA TCCATAGTTG CCTGACTCCC CGTCGTGTAG ATAACTACGA TACGGGAGGG CTTACCATCT GGCCCCAGTG CTGCAATGAT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ACCGCGAGAC CCACGCTCAC CGGCTCCAGA TTTATCAGCA ATAAACCAGC CAGCCGGAAG GGCCGAGCGC AGAAGTGGTC CTGCAACTTT ATCCGCCTCC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ATCCAGTCTA TTAATTGTTG CCGGGAAGCT AGAGTAAGTA GTTCGCCAGT TAATAGTTTG CGCAACGTTG TTGCCATTGC TACAGGCATC GTGGTGTCAC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

GCTCGTCGTT TGGTATGGCT TCATTCAGCT CCGGTTCCCA ACGATCAAGG CGAGTTACAT GATCCCCCAT GTTGTGCAAA AAAGCGGTTA GCTCCTTCGG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TCCTCCGATC GTTGTCAGAA GTAAGTTGGC CGCAGTGTTA TCACTCATGG TTATGGCAGC ACTGCATAAT TCTCTTACTG TCATGCCATC CGTAAGATGC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TTTTCTGTGA CTGGTGAGTA CTCAACCAAG TCATTCTGAG AATAGTGTAT GCGGCGACCG AGTTGCTCTT GCCCGGCGTC AATACGGGAT AATACCGCGC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CACATAGCAG AACTTTAAAA GTGCTCATCA TTGGAAAACG TTCTTCGGGG CGAAAACTCT CAAGGATCTT ACCGCTGTTG AGATCCAGTT CGATGTAACC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CACTCGTGCA CCCAACTGAT CTTCAGCATC TTTTACTTTC ACCAGCGTTT CTGGGTGAGC AAAAACAGGA AGGCAAAATG CCGCAAAAAA GGGAATAAGG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GCGACACGGA AATGTTGAAT ACTCATACTC TTCCTTTTTC AATATTATTG AAGCATTTAT CAGGGTTATT GTCTCATGAG CGGATACATA TTTGAATGTA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TTTAGAAAAA TAAACAAATA GGGGTTCCGC GCACATTTCC CCGAAAAGTG CCACCTGACG TCGGTACCAT TTAAATATCG ATAAGC
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281

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

plasmid sequence confirmed by IRESite curators by restriction analysis + parts by PCR + sequencing

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: Tomáš Mašek	Reviewed by: Tomáš Mašek

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:

no

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

269-1921

ORF

ORF position:

2

Version: `0`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek

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):

2636-3571

Remarks:

Plasmid DNA was digested by EcoRV/SalI and BamHI/SalI giving fragments 4321/1965 bp and 3392/1877(17) bp,
respectively. Amplification with Firefly/Renilla gene specific primers (Fluc_seq, gTg gAC gAA gTA CCg AAA gg,
position within plasmid sequence:2118, Rluc_revseq, CTGCATGTTTTTCTGAATC, position within plasmid
sequence:3060) gave one fragment of expected size. The sequence of promoter and intercistronic regions was
determined by sequencing (regions 54-626 and 2180-2958 of plasmid sequence). More detailed data are annotated
in GenBank sequence file.

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: `2011-04-08 22:02:13`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek
The IRES name: `EMCV-R_272-831`	The functional status of IRES: `functional`

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

2072-2633

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `151`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `712`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-564`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-3`

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

GCCCCCCCCC TAACGTTACT GGCCGAAGCC GCTTGGAATA AGGCCGGTGT GCGTTTGTCT ATATGTTATT TTCCACCATA TTGCCGTCTT TTGGCAATGT 
^2072      ^2082      ^2092      ^2102      ^2112      ^2122      ^2132      ^2142      ^2152      ^2162      

GAGGGCCCGG AAACCTGGCC CTGTCTTCTT GACGAGCATT CCTAGGGGTC TTTCCCCTCT CGCCAAAGGA ATGCAAGGTC TGTTGAATGT CGTGAAGGAA 
^2172      ^2182      ^2192      ^2202      ^2212      ^2222      ^2232      ^2242      ^2252      ^2262      

GCAGTTCCTC TGGAAGCTTC TTGAAGACAA ACAACGTCTG TAGCGACCCT TTGCAGGCAG CGGAACCCCC CACCTGGCGA CAGGTGCCTC TGCGGCCAAA 
^2272      ^2282      ^2292      ^2302      ^2312      ^2322      ^2332      ^2342      ^2352      ^2362      

AGCCACGTGT ATAAGATACA CCATGCAAAG GCGGCACAAC CCCAGTGCCA CGTTGTGAGT TGGATAGTTG TGGAAAGAGT CAAATGGCTC TCCTCAAGCG 
^2372      ^2382      ^2392      ^2402      ^2412      ^2422      ^2432      ^2442      ^2452      ^2462      

TATTCAACAA GGGGCTGAAG GATGCCCAAA AGGTACCCCA TTGTATGGGA TCTGATCTGG GGCCTCGGTG CACATGCTTT ACATGTGTTT AGTCGAGGTT 
^2472      ^2482      ^2492      ^2502      ^2512      ^2522      ^2532      ^2542      ^2552      ^2562      

AAAAAACGTC TAGGCCCCCC GAACCACGGG GACGTGGTTT TCCTTTGAAA AACACGATGA TA
^2572      ^2582      ^2592      ^2602      ^2612      ^2622      ^2632

Citations:

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