IRESite_Id:546 characteristics of EMCV-R_281-833 IRES studied in pF/R-wt plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `546`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2008-12-20 19:41:39`
Reviewed by: Martin Mokrejš

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_possibly_incomplete

The mRNA/+RNA description:

Putative in vivo CMV IE promoter-derived spliced transcript contain firefly luciferase and renilla luciferase
separated by a wild-type EMCV IRES up to the SV40 poly(A) signal.

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

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

TCTCTTAAGG TAGCCTTGCA GAAGTTGGTC GTGAGGCACT GGGCAGGTGT CCACTCCCAG TTCAATTACA GCTCTTAAGG CTAGAGTACT TAATACGACT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CACTATAGGC TAGCCTCGAG ATGGAAGACG CCAAAAACAT AAAGAAAGGC CCGGCGCCAT TCTATCCTCT AGAGGATGGA ACCGCTGGAG AGCAACTGCA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TAAGGCTATG AAGAGATACG CCCTGGTTCC TGGAACAATT GCTTTTACAG ATGCACATAT CGAGGTGAAC ATCACGTACG CGGAAtaCTT CGAAATGTCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GTTCGGTTGG CAGAAGCTAT GAAACGATAT GGGCTGAATA CAAATCACAG AATCGTCGTA TGCAGTGAAA ACTCTCTTCA ATTCTTTATG CCGGTGTTGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GCGCGTTATT TATCGGAGTT GCAGTTGCGC CCGCGAACGA CATTTATAAT GAACGTGAAT TGCTCAACAG TATGAACATT TCGCAGCCTA CCGTAGTGTT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TGTTTCCAAA AAGGGGTTGC AAaAAATTtT GAACGTGCAA AAAAAATTAC CAATAATCCA GAAAATTATT ATCATGGATT CTAAAACGGA TTACCAGGGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TTTCAGTCGA TGTACACGTT CGTCACATCT CATCTACCTC CCGGTTTTAA TGAATACGAT TTTGTACCAG AGTCCTTTGA TCGTGACAAA ACAATTGCAC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TGATAATGAA TTCCTCTGGA TCTACTGGGT TACCTAAGGG TGTGGCCCTT CCGCATAGAA CTGCCTGcgT CAGATTCTCG CATGCCAGAG ATCCTATTTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGGCAATCAA ATCATTCCGG ATACTGCGAT TTTAAGTGTT GTTCCATTCC ATCACGGTTT TGGAATGTTT ACTACACTCG GATATTTGAT ATGTGGATTT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CGAGTCGTCT TAATGTATAG ATTTGAAGAA GAGCTGTTTT TACGATCCCT TCAGGATTAC AAAATTCAAA GTGCGTTGCT AGTACCAACC CTATTTTCAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCTTCGCcAA AaGCACTCTG ATTGACAAAT ACGATTTATC TAATTTACAC GAAATTGCTT CTGGGGGCGC ACCTCTTTCG AAAGAAGTCG GGGAAGCGGT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGCAAAACGC TTCCATCTTC CAGGGATACG ACAAGGATAT GGGCTCACTG AGACTACATC AGCTATTCTG ATTACACCCG AGGGGGATGA TAAACCGGGC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GCGGTCGGTA AAGTTGTTCC ATTTTTTGAA GCGAAGGTTG TGGATCTGga TACCGGGAAA ACGCTGGGCG TTAATCAGAG AGGCGAATTA TGTGTCAGAG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GACCTATGAT TATGTCCGGT TATGTAAACA ATCCGGAAGC GACCAACGCC TTGATTGACA AGGATGGATG GCTACATTCT GGAGACATAG CTTACTGGGA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CGAAGACGAA CACTTCTTCA TAGTTGACCG CTTGAAGTCT TTAATTAAAT ACAAAGGATA TCAGGTGGCC CCCGCTGAAT TGGAATCGAT atTGTTACAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CACCCCAACA TCTTCGACGC GGGCGTGGCA GGTCTTCCCG ACGATGACGC CGGTGAACTT CCCGCCGCCG TTGTTGTTTT GGAGCACGGA AAGACGATGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CGGAAAAAGA GATCGTGGAT TACGTGGCCA GTCAAGTAAC AACCGCGAAA AAGTTGCGCG GAGGAGTTGT GTTTGTGGAC GAAGTACCGA AAGGTCTTAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CGGAAAACTC GACGCAAGAA AAATCAGAGA gaTCCTCATA AAGGCCAAGA AGGGCGGAAA GTCCAAATTG TAATAAACGC GTCGAGCATG CATCTAGGGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGCCAATTCC GCCCCTCTCC CCCCCACCCC TCTCCCTCCC CCCCCCCTAA CGTTACTGGC CGAAGCCGCT TGGAATAAGG CCGGTGTGCG TTTGTCTATA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGTTATTTTC CACCATATTG CCGTCTTTTG GCAATGTGAG GGCCCGGAAA CCTGGCCCTG TCTTCTTGAC GAGCATTCCT AGGGGTCTTT CCCCTCTCGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CAAAGGAATG CAAGGTCTGT TGAATGTCGT GAAGGAAGCA GTTCCTCTGG AAGCTTCTTG AAGACAAACA ACGTCTGTAG CGACCCTTTG CAGGCAGCGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AACCCCCCAC CTGGCGACAG GTGCCTCTGC GGCCAAAAGC CACGTGTATA AGATACACCT GCAAAGGCGG CACAACCCCA GTGCCACGTT GTGAGTTGGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TAGTTGTGGA AAGAGTCAAA TGGCTCTCCT CAAGCGTATT CAACAAGGGG CTGAAGGATG CCCAGAAGGT ACCCCATTGT ATGGGATCTG ATCTGGGGCC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TCGGTGCACA TGCTTTACAT GTGTTTAGTC GAGGTTAAAA AACGTCTAGG CCCCCCGAAC CACGGGGACG TGGTTTTCCT TTGAAAAACA CGATGATAAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATGACTTCGA AAGTTTATGA TCCAGAACAA AGGAAACGGA TGATAACTGG TCCGCAGTGG TGGGCCAGAT GTAAACAAAT GAATGTTCTT GATTCATTTA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTAATTATTA TGATTCAGAA AAACATGCAG AAAATGCTGT TATTTTTTTA CATGGTAACG CGGCCTCTTC TTATTTATGG CGACATGTTG TGCCACATAT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TGAGCCAGTA GCGCGGTGTA TTATACCAGA CCTTATTGGT ATGGGCAAAT CAGGCAAATC TGGTAATGGT TCTTATAGGT TACTTGATCA TTACAAATAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CTTACTGCAT GGTTTGAACT TCTTAATTTA CCAAAGAAGA TCATTTTTGT CGGCCATGAT TGGGGTGCTT GTTTGGCATT TCATTATAGC TATGAGCATC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AAGATAAGAT CAAAGCAATA GTTCACGCTG AAAGTGTAGT AGATGTGATT GAATCATGGG ATGAATGGCC TGATATTGAA GAAGATATTG CGTTGATCAA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ATCTGAAGAA GGAGAAAAAA TGGTTTTGGA GAATAACTTC TTCGTGGAAA CCATGTTGCC ATCAAAAATC ATGAGAAAGT TAGAACCAGA AGAATTTGCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GCATATCTTG AACCATTCAA AGAGAAAGGT GAAGTTCGTC GTCCAACATT ATCATGGCCT CGTGAAATCC CGTTAGTAAA AGGTGGTAAA CCTGACGTTG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TACAAATTGT TAGGAATTAT AATGCTTATC TACGTGCAAG TGATGATTTA CCAAAAATGT TTATTGAATC GGACCCAGGA TTCTTTTCCA ATGCTATTGT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TGAAGGTGCC AAGAAGTTTC CTAATACTGA ATTTGTCAAA GTAAAAGGTC TTCATTTTTC GCAAGAAGAT GCACCTGATG AAATGGGAAA ATATATCAAA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TCGTTCGTTG AGCGAGTTCT CAAAAATGAA CAATAATAAC CCGGGATCCT CTAGAGTCGA CCCGGGCGGC CGCTTCCCTT TAGTGAGGGT TAATGCTTCG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGCAGACATG ATAAGATACA TTGATGAGTT TGGACAAACC ACAACTAGAA TGCAGTGAAA AAAATGCTTT ATTTGTGAAA TTTGTGATGC TATTGCTTTA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTTGTAACCA TTATAAGCTG CAATAAACAA GTTAACAACA ACAATTGCAT TCATTTTATG TTTCAGGTTC AGGGGGAGAT GTGGGAGGTT TTTTAAAGCA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AGTAAAACCT CTACAAATGT GGTA
^3701      ^3711      ^3721

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_maybe_except_3UTR

The name of the plasmid:
pF/R-wt The name of the promoter used to express this mRNA:
CMV_IE

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:

TCAATATTGG CCATTAGCCA TATTATTCAT TGGTTATATA GCATAAATCA ATATTGGCTA TTGGCCATTG CATACGTTGT ATCTATATCA TAATATGTAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATTTATATTG GCTCATGTCC AATATGACCG CCATGTTGGC ATTGATTATT GACTAGTTAT TAATAGTAAT CAATTACGGG GTCATTAGTT CATAGCCCAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATATGGAGTT CCGCGTTACA TAACTTACGG TAAATGGCCC GCCTGGCTGA CCGCCCAACG ACCCCCGCCC ATTGACGTCA ATAATGACGT ATGTTCCCAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGTAACGCCA ATAGGGACTT TCCATTGACG TCAATGGGTG GAGTATTTAC GGTAAACTGC CCACTTGGCA GTACATCAAG TGTATCATAT GCCAAGTCCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCCCCTATTG ACGTCAATGA CGGTAAATGG CCCGCCTGGC ATTATGCCCA GTACATGACC TTACGGGACT TTCCTACTTG GCAGTACATC TACGTATTAG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCATCGCTAT TACCATGGTG ATGCGGTTTT GGCAGTACAC CAATGGGCGT GGATAGCGGT TTGACTCACG GGGATTTCCA AGTCTCCACC CCATTGACGT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CAATGGGAGT TTGTTTTGGC ACCAAAATCA ACGGGACTTT CCAAAATGTC GTAACAACTG CGATCGCCCG CCCCGTTGAC GCAAATGGGC GGTAGGCGTG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

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

CAGTGCTTCT GACACAACAG TCTCGAACTT AAGCTGCAGT GACTCTCTTA AGGTAGCCTT GCAGAAGTTG GTCGTGAGGC ACTGGGCAGG TAAGTATCAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGTTACAAGA CAGGTTTAAG GAGACCAATA GAAACTGGGC TTGTCGAGAC AGAGAAGACT CTTGCGTTTC TGATAGGCAC CTATTGGTCT TACTGACATC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CACTTTGCCT TTCTCTCCAC AGGTGTCCAC TCCCAGTTCA ATTACAGCTC TTAAGGCTAG AGTACTTAAT ACGACTCACT ATAGGCTAGC CTCGAGATGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AAGACGCCAA AAACATAAAG AAAGGCCCGG CGCCATTCTA TCCTCTAGAG GATGGAACCG CTGGAGAGCA ACTGCATAAG GCTATGAAGA GATACGCCCT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GGTTCCTGGA ACAATTGCTT TTACAGATGC ACATATCGAG GTGAACATCA CGTACGCGGA AtaCTTCGAA ATGTCCGTTC GGTTGGCAGA AGCTATGAAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGATATGGGC TGAATACAAA TCACAGAATC GTCGTATGCA GTGAAAACTC TCTTCAATTC TTTATGCCGG TGTTGGGCGC GTTATTTATC GGAGTTGCAG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TTGCGCCCGC GAACGACATT TATAATGAAC GTGAATTGCT CAACAGTATG AACATTTCGC AGCCTACCGT AGTGTTTGTT TCCAAAAAGG GGTTGCAAaA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AATTtTGAAC GTGCAAAAAA AATTACCAAT AATCCAGAAA ATTATTATCA TGGATTCTAA AACGGATTAC CAGGGATTTC AGTCGATGTA CACGTTCGTC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACATCTCATC TACCTCCCGG TTTTAATGAA TACGATTTTG TACCAGAGTC CTTTGATCGT GACAAAACAA TTGCACTGAT AATGAATTCC TCTGGATCTA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CTGGGTTACC TAAGGGTGTG GCCCTTCCGC ATAGAACTGC CTGcgTCAGA TTCTCGCATG CCAGAGATCC TATTTTTGGC AATCAAATCA TTCCGGATAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGCGATTTTA AGTGTTGTTC CATTCCATCA CGGTTTTGGA ATGTTTACTA CACTCGGATA TTTGATATGT GGATTTCGAG TCGTCTTAAT GTATAGATTT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GAAGAAGAGC TGTTTTTACG ATCCCTTCAG GATTACAAAA TTCAAAGTGC GTTGCTAGTA CCAACCCTAT TTTCATTCTT CGCcAAAaGC ACTCTGATTG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACAAATACGA TTTATCTAAT TTACACGAAA TTGCTTCTGG GGGCGCACCT CTTTCGAAAG AAGTCGGGGA AGCGGTTGCA AAACGCTTCC ATCTTCCAGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GATACGACAA GGATATGGGC TCACTGAGAC TACATCAGCT ATTCTGATTA CACCCGAGGG GGATGATAAA CCGGGCGCGG TCGGTAAAGT TGTTCCATTT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTTGAAGCGA AGGTTGTGGA TCTGgaTACC GGGAAAACGC TGGGCGTTAA TCAGAGAGGC GAATTATGTG TCAGAGGACC TATGATTATG TCCGGTTATG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TAAACAATCC GGAAGCGACC AACGCCTTGA TTGACAAGGA TGGATGGCTA CATTCTGGAG ACATAGCTTA CTGGGACGAA GACGAACACT TCTTCATAGT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGACCGCTTG AAGTCTTTAA TTAAATACAA AGGATATCAG GTGGCCCCCG CTGAATTGGA ATCGATatTG TTACAACACC CCAACATCTT CGACGCGGGC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTGGCAGGTC TTCCCGACGA TGACGCCGGT GAACTTCCCG CCGCCGTTGT TGTTTTGGAG CACGGAAAGA CGATGACGGA AAAAGAGATC GTGGATTACG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TGGCCAGTCA AGTAACAACC GCGAAAAAGT TGCGCGGAGG AGTTGTGTTT GTGGACGAAG TACCGAAAGG TCTTACCGGA AAACTCGACG CAAGAAAAAT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CAGAGAgaTC CTCATAAAGG CCAAGAAGGG CGGAAAGTCC AAATTGTAAT AAACGCGTCG AGCATGCATC TAGGGCGGCC AATTCCGCCC CTCTCCCCCC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CACCCCTCTC CCTCCCCCCC CCCTAACGTT ACTGGCCGAA GCCGCTTGGA ATAAGGCCGG TGTGCGTTTG TCTATATGTT ATTTTCCACC ATATTGCCGT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CTTTTGGCAA TGTGAGGGCC CGGAAACCTG GCCCTGTCTT CTTGACGAGC ATTCCTAGGG GTCTTTCCCC TCTCGCCAAA GGAATGCAAG GTCTGTTGAA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TGTCGTGAAG GAAGCAGTTC CTCTGGAAGC TTCTTGAAGA CAAACAACGT CTGTAGCGAC CCTTTGCAGG CAGCGGAACC CCCCACCTGG CGACAGGTGC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CTCTGCGGCC AAAAGCCACG TGTATAAGAT ACACCTGCAA AGGCGGCACA ACCCCAGTGC CACGTTGTGA GTTGGATAGT TGTGGAAAGA GTCAAATGGC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TCTCCTCAAG CGTATTCAAC AAGGGGCTGA AGGATGCCCA GAAGGTACCC CATTGTATGG GATCTGATCT GGGGCCTCGG TGCACATGCT TTACATGTGT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TTAGTCGAGG TTAAAAAACG TCTAGGCCCC CCGAACCACG GGGACGTGGT TTTCCTTTGA AAAACACGAT GATAATATGA CTTCGAAAGT TTATGATCCA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GAACAAAGGA AACGGATGAT AACTGGTCCG CAGTGGTGGG CCAGATGTAA ACAAATGAAT GTTCTTGATT CATTTATTAA TTATTATGAT TCAGAAAAAC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATGCAGAAAA TGCTGTTATT TTTTTACATG GTAACGCGGC CTCTTCTTAT TTATGGCGAC ATGTTGTGCC ACATATTGAG CCAGTAGCGC GGTGTATTAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ACCAGACCTT ATTGGTATGG GCAAATCAGG CAAATCTGGT AATGGTTCTT ATAGGTTACT TGATCATTAC AAATATCTTA CTGCATGGTT TGAACTTCTT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AATTTACCAA AGAAGATCAT TTTTGTCGGC CATGATTGGG GTGCTTGTTT GGCATTTCAT TATAGCTATG AGCATCAAGA TAAGATCAAA GCAATAGTTC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ACGCTGAAAG TGTAGTAGAT GTGATTGAAT CATGGGATGA ATGGCCTGAT ATTGAAGAAG ATATTGCGTT GATCAAATCT GAAGAAGGAG AAAAAATGGT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TTTGGAGAAT AACTTCTTCG TGGAAACCAT GTTGCCATCA AAAATCATGA GAAAGTTAGA ACCAGAAGAA TTTGCAGCAT ATCTTGAACC ATTCAAAGAG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AAAGGTGAAG TTCGTCGTCC AACATTATCA TGGCCTCGTG AAATCCCGTT AGTAAAAGGT GGTAAACCTG ACGTTGTACA AATTGTTAGG AATTATAATG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CTTATCTACG TGCAAGTGAT GATTTACCAA AAATGTTTAT TGAATCGGAC CCAGGATTCT TTTCCAATGC TATTGTTGAA GGTGCCAAGA AGTTTCCTAA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TACTGAATTT GTCAAAGTAA AAGGTCTTCA TTTTTCGCAA GAAGATGCAC CTGATGAAAT GGGAAAATAT ATCAAATCGT TCGTTGAGCG AGTTCTCAAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AATGAACAAT AATAACCCGG GATCCTCTAG AGTCGACCCG GGCGGCCGCT TCCCTTTAGT GAGGGTTAAT GCTTCGAGCA GACATGATAA GATACATTGA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TGAGTTTGGA CAAACCACAA CTAGAATGCA GTGAAAAAAA TGCTTTATTT GTGAAATTTG TGATGCTATT GCTTTATTTG TAACCATTAT AAGCTGCAAT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AAACAAGTTA ACAACAACAA TTGCATTCAT TTTATGTTTC AGGTTCAGGG GGAGATGTGG GAGGTTTTTT AAAGCAAGTA AAACCTCTAC AAATGTGGTA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

AAATCCGATA AGGATCGATC CGGGCTGGCG TAATAGCGAA GAGGCCCGCA CCGATCGCCC TTCCCAACAG TTGCGCAGCC TGAATGGCGA ATGGACGCGC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CCTGTAGCGG CGCATTAAGC GCGGCGGGTG TGGTGGTTAC GCGCAGCGTG ACCGCTACAC TTGCCAGCGC CCTAGCGCCC GCTCCTTTCG CTTTCTTCCC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TTCCTTTCTC GCCACGTTCG CCGGCTTTCC CCGTCAAGCT CTAAATCGGG GGCTCCCTTT AGGGTTCCGA TTTAGAGCTT TACGGCACCT CGACCGCAAA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

AAACTTGATT TGGGTGATGG TTCACGTAGT GGGCCATCGC CCTGATAGAC GGTTTTTCGC CCTTTGACGT TGGAGTCCAC GTTCTTTAAT AGTGGACTCT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TGTTCCAAAC TGGAACAACA CTCAACCCTA TCTCGGTCTA TTCTTTTGAT TTATAAGGGA TTTTGCCGAT TTCGGCCTAT TGGTTAAAAA ATGAGCTGAT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TTAACAAATA TTTAACGCGA ATTTTAACAA AATATTAACG TTTACAATTT CGCCTGATGC GGTATTTTCT CCTTACGCAT CTGTGCGGTA TTTCACACCG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CATACGCGGA TCTGCGCAGC ACCATGGCCT GAAATAACCT CTGAAAGAGG AACTTGGTTA GGTACCTTCT GAGGCGGAAA GAACCAGCTG TGGAATGTGT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GTCAGTTAGG GTGTGGAAAG TCCCCAGGCT CCCCAGCAGG CAGAAGTATG CAAAGCATGC ATCTCAATTA GTCAGCAACC AGGTGTGGAA AGTCCCCAGG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CTCCCCAGCA GGCAGAAGTA TGCAAAGCAT GCATCTCAAT TAGTCAGCAA CCATAGTCCC GCCCCTAACT CCGCCCATCC CGCCCCTAAC TCCGCCCAGT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TCCGCCCATT CTCCGCCCCA TGGCTGACTA ATTTTTTTTA TTTATGCAGA GGCCGAGGCC GCCTCGGCCT CTGAGCTATT CCAGAAGTAG TGAGGAGGCT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TTTTTGGAGG CCTAGGCTTT TGCAAAAAGC TTGATTCTTC TGACACAACA GTCTCGAACT TAAGGCTAGA GCCACCATGA TTGAACAAGA TGGATTGCAC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

GCAGGTTCTC CGGCCGCTTG GGTGGAGAGG CTATTCGGCT ATGACTGGGC ACAACAGACA ATCGGCTGCT CTGATGCCGC CGTGTTCCGG CTGTCAGCGC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

AGGGGCGCCC GGTTCTTTTT GTCAAGACCG ACCTGTCCGG TGCCCTGAAT GAACTGCAGG ACGAGGCAGC GCGGCTATCG TGGCTGGCCA CGACGGGCGT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TCCTTGCGCA GCTGTGCTCG ACGTTGTCAC TGAAGCGGGA AGGGACTGGC TGCTATTGGG CGAAGTGCCG GGGCAGGATC TCCTGTCATC TCACCTTGCT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CCTGCCGAGA AAGTATCCAT CATGGCTGAT GCAATGCGGC GGCTGCATAC GCTTGATCCG GCTACCTGCC CATTCGACCA CCAAGCGAAA CATCGCATCG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

AGCGAGCACG TACTCGGATG GAAGCCGGTC TTGTCGATCA GGATGATCTG GACGAAGAGC ATCAGGGGCT CGCGCCAGCC GAACTGTTCG CCAGGCTCAA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

GGCGCGCATG CCCGACGGCG AGGATCTCGT CGTGACCCAT GGCGATGCCT GCTTGCCGAA TATCATGGTG GAAAATGGCC GCTTTTCTGG ATTCATCGAC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TGTGGCCGGC TGGGTGTGGC GGACCGCTAT CAGGACATAG CGTTGGCTAC CCGTGATATT GCTGAAGAGC TTGGCGGCGA ATGGGCTGAC CGCTTCCTCG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

TGCTTTACGG TATCGCCGCT CCCGATTCGC AGCGCATCGC CTTCTATCGC CTTCTTGACG AGTTCTTCTG AGCGGGACTC TGGGGTTCGA AATGACCGAC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CAAGCGACGC CCAACCTGCC ATCACGATGG CCGCAATAAA ATATCTTTAT TTTCATTACA TCTGTGTGTT GGTTTTTTGT GTGAATCGAT AGCGATAAGG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

ATCCGCGTAT GGTGCACTCT CAGTACAATC TGCTCTGATG CCGCATAGTT AAGCCAGCCC CGACACCCGC CAACACCCGC TGACGCGCCC TGACGGGCTT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GTCTGCTCCC GGCATCCGCT TACAGACAAG CTGTGACCGT CTCCGGGAGC TGCATGTGTC AGAGGTTTTC ACCGTCATCA CCGAAACGCG CGAGACGAAA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

GGGCCTCGTG ATACGCCTAT TTTTATAGGT TAATGTCATG ATAATAATGG TTTCTTAGAC GTCAGGTGGC ACTTTTCGGG GAAATGTGCG CGGAACCCCT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

ATTTGTTTAT TTTTCTAAAT ACATTCAAAT ATGTATCCGC TCATGAGACA ATAACCCTGA TAAATGCTTC AATAATATTG AAAAAGGAAG AGTATGAGTA 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

TTCAACATTT CCGTGTCGCC CTTATTCCCT TTTTTGCGGC ATTTTGCCTT CCTGTTTTTG CTCACCCAGA AACGCTGGTG AAAGTAAAAG ATGCTGAAGA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

TCAGTTGGGT GCACGAGTGG GTTACATCGA ACTGGATCTC AACAGCGGTA AGATCCTTGA GAGTTTTCGC CCCGAAGAAC GTTTTCCAAT GATGAGCACT 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TTTAAAGTTC TGCTATGTGG CGCGGTATTA TCCCGTATTG ACGCCGGGCA AGAGCAACTC GGTCGCCGCA TACACTATTC TCAGAATGAC TTGGTTGAGT 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

ACTCACCAGT CACAGAAAAG CATCTTACGG ATGGCATGAC AGTAAGAGAA TTATGCAGTG CTGCCATAAC CATGAGTGAT AACACTGCGG CCAACTTACT 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

TCTGACAACG ATCGGAGGAC CGAAGGAGCT AACCGCTTTT TTGCACAACA TGGGGGATCA TGTAACTCGC CTTGATCGTT GGGAACCGGA GCTGAATGAA 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

GCCATACCAA ACGACGAGCG TGACACCACG ATGCCTGTAG CAATGGCAAC AACGTTGCGC AAACTATTAA CTGGCGAACT ACTTACTCTA GCTTCCCGGC 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

AACAATTAAT AGACTGGATG GAGGCGGATA AAGTTGCAGG ACCACTTCTG CGCTCGGCCC TTCCGGCTGG CTGGTTTATT GCTGATAAAT CTGGAGCCGG 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

TGAGCGTGGG TCTCGCGGTA TCATTGCAGC ACTGGGGCCA GATGGTAAGC CCTCCCGTAT CGTAGTTATC TACACGACGG GGAGTCAGGC AACTATGGAT 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

GAACGAAATA GACAGATCGC TGAGATAGGT GCCTCACTGA TTAAGCATTG GTAACTGTCA GACCAAGTTT ACTCATATAT ACTTTAGATT GATTTAAAAC 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

TTCATTTTTA ATTTAAAAGG ATCTAGGTGA AGATCCTTTT TGATAATCTC ATGACCAAAA TCCCTTAACG TGAGTTTTCG TTCCACTGAG CGTCAGACCC 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

CGTAGAAAAG ATCAAAGGAT CTTCTTGAGA TCCTTTTTTT CTGCGCGTAA TCTGCTGCTT GCAAACAAAA AAACCACCGC TACCAGCGGT GGTTTGTTTG 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

CCGGATCAAG AGCTACCAAC TCTTTTTCCG AAGGTAACTG GCTTCAGCAG AGCGCAGATA CCAAATACTG TCCTTCTAGT GTAGCCGTAG TTAGGCCACC 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

ACTTCAAGAA CTCTGTAGCA CCGCCTACAT ACCTCGCTCT GCTAATCCTG TTACCAGTGG CTGCTGCCAG TGGCGATAAG TCGTGTCTTA CCGGGTTGGA 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

CTCAAGACGA TAGTTACCGG ATAAGGCGCA GCGGTCGGGC TGAACGGGGG GTTCGTGCAC ACAGCCCAGC TTGGAGCGAA CGACCTACAC CGAACTGAGA 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

TACCTACAGC GTGAGCTATG AGAAAGCGCC ACGCTTCCCG AAGGGAGAAA GGCGGACAGG TATCCGGTAA GCGGCAGGGT CGGAACAGGA GAGCGCACGA 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

GGGAGCTTCC AGGGGGAAAC GCCTGGTATC TTTATAGTCC TGTCGGGTTT CGCCACCTCT GACTTGAGCG TCGATTTTTG TGATGCTCGT CAGGGGGGCG 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

GAGCCTATGG AAAAACGCCA GCAACGCGGC CTTTTTACGG TTCCTGGCCT TTTGCTGGCC TTTTGCTCAC ATGGCTCGAC AGATCT
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681

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):

221-1873

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):

2501-3436

Citations:

Bochkov Y. A., Palmenberg A. C. (2006) Translational efficiency of EMCV IRES in bicistronic vectors is dependent upon IRES sequence and gene location. Biotechniques. 41(3):283-284, 286, 288, 290

IRESs:

IRES:

Version: `1`	Last change: `2011-04-08 22:18:55`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `EMCV-R_281-833`	The functional status of IRES: `functional`

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

1948-2500

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `75`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `627`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-553`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-1`

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

TAACGTTACT GGCCGAAGCC GCTTGGAATA AGGCCGGTGT GCGTTTGTCT ATATGTTATT TTCCACCATA TTGCCGTCTT TTGGCAATGT GAGGGCCCGG 
^1948      ^1958      ^1968      ^1978      ^1988      ^1998      ^2008      ^2018      ^2028      ^2038      

AAACCTGGCC CTGTCTTCTT GACGAGCATT CCTAGGGGTC TTTCCCCTCT CGCCAAAGGA ATGCAAGGTC TGTTGAATGT CGTGAAGGAA GCAGTTCCTC 
^2048      ^2058      ^2068      ^2078      ^2088      ^2098      ^2108      ^2118      ^2128      ^2138      

TGGAAGCTTC TTGAAGACAA ACAACGTCTG TAGCGACCCT TTGCAGGCAG CGGAACCCCC CACCTGGCGA CAGGTGCCTC TGCGGCCAAA AGCCACGTGT 
^2148      ^2158      ^2168      ^2178      ^2188      ^2198      ^2208      ^2218      ^2228      ^2238      

ATAAGATACA CCTGCAAAGG CGGCACAACC CCAGTGCCAC GTTGTGAGTT GGATAGTTGT GGAAAGAGTC AAATGGCTCT CCTCAAGCGT ATTCAACAAG 
^2248      ^2258      ^2268      ^2278      ^2288      ^2298      ^2308      ^2318      ^2328      ^2338      

GGGCTGAAGG ATGCCCAGAA GGTACCCCAT TGTATGGGAT CTGATCTGGG GCCTCGGTGC ACATGCTTTA CATGTGTTTA GTCGAGGTTA AAAAACGTCT 
^2348      ^2358      ^2368      ^2378      ^2388      ^2398      ^2408      ^2418      ^2428      ^2438      

AGGCCCCCCG AACCACGGGG ACGTGGTTTT CCTTTGAAAA ACACGATGAT AAT
^2448      ^2458      ^2468      ^2478      ^2488      ^2498

Citations:

Bochkov Y. A., Palmenberg A. C. (2006) Translational efficiency of EMCV IRES in bicistronic vectors is dependent upon IRES sequence and gene location. Biotechniques. 41(3):283-284, 286, 288, 290

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