IRESite_Id:245 characteristics of EMCV-R_271-831 IRES studied in pBSRLucEFluc plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `245`	Version: `2`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-09-11 00:00:00`

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 FLuc ORF has one additional aminoacid and one putative
sequencing error.

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 GAATTCGAAA TGACTTCGAA AGTTTATGAT CCAGAACAAA GGAAACGGAT GATAACTGGT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCGCAGTGGT GGGCCAGATG TAAACAAATG AATGTTCTTG ATTCATTTAT TAATTATTAT GATTCAGAAA AACATGCAGA AAATGCTGTT ATTTTTTTAC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATGGTAACGC GGCCTCTTCT TATTTATGGC GACATGTTGT GCCACATATT GAGCCAGTAG CGCGGTGTAT TATACCAGAC CTTATTGGTA TGGGCAAATC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AGGCAAATCT GGTAATGGTT CTTATAGGTT ACTTGATCAT TACAAATATC TTACTGCATG GTTTGAACTT CTTAATTTAC CAAAGAAGAT CATTTTTGTC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GGCCATGATT GGGGTGCTTG TTTGGCATTT CATTATAGCT ATGAGCATCA AGATAAGATC AAAGCAATAG TTCACGCTGA AAGTGTAGTA GATGTGATTG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AATCATGGGA TGAATGGCCT GATATTGAAG AAGATATTGC GTTGATCAAA TCTGAAGAAG GAGAAAAAAT GGTTTTGGAG AATAACTTCT TCGTGGAAAC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CATGTTGCCA TCAAAAATCA TGAGAAAGTT AGAACCAGAA GAATTTGCAG CATATCTTGA ACCATTCAAA GAGAAAGGTG AAGTTCGTCG TCCAACATTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TCATGGCCTC GTGAAATCCC GTTAGTAAAA GGTGGTAAAC CTGACGTTGT ACAAATTGTT AGGAATTATA ATGCTTATCT ACGTGCAAGT GATGATTTAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CAAAAATGTT TATTGAATCG GACCCAGGAT TCTTTTCCAA TGCTATTGTT GAAGGTGCCA AGAAGTTTCC TAATACTGAA TTTGTCAAAG TAAAAGGTCT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TCATTTTTCG CAAGAAGATG CACCTGATGA AATGGGAAAA TATATCAAAT CGTTCGTTGA GCGAGTTCTC AAAAATGAAC AATAAGTCGA CCTGCAGAAG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTTGCGCAGA CGTCGCGCGC GGCCGCGAAA TTAATACGAC TCACTATAGG GAGACCACAA CGGTTTCCCT CTAGCGGGAT CATTCCGCCC CCCCCCCTAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CGTTACTGGC CGAAGCCGCT TGGAATAAGG CCGGTGTGCG TTTGTCTATA TGTTATTTTC CACCATATTG CCGTCTTTTG GCAATGTGAG GGCCCGGAAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCTGGCCCTG TCTTCTTGAC GAGCATTCCT AGGGGTCTTT CCCCTCTCGC CAAAGGAATG CAAGGTCTGT TGAATGTCGT GAAGGAAGCA GTTCCTCTGG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAGCTTCTTG AAGACAAACA ACGTCTGTAG CGACCCTTTG CAGGCAGCGG AACCCCCCAC CTGGCGACAG GTGCCTCTGC GGCCAAAAGC CACGTGTATA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGATACACCA TGCAAAGGCG GCACAACCCC AGTGCCACGT TGTGAGTTGG ATAGTTGTGG AAAGAGTCAA ATGGCTCTCC TCAAGCGTAT TCAACAAGGG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCTGAAGGAT GCCCAGAAGG TACCCCATTG TATGGGATCT GATCTGGGGC CTCGGTGCAC ATGCTTTACA TGTGTTTAGT CGAGGTTAAA AAACGTCTAG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCCCCCCGAA CCACGGGGAC GTGGTTTTCC TTTGAAAAAC ACGATGATAC CATGGCCGAA GACGCCAAAA ACATAAAGAA AGGCCCGGCA CCATTCTATC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CACTAGAGGA TGGAACCGCT GGAGAGCAAC TGCATAAGGC TATGAAGAGA TACGCCCTGG TTCCTGGAAC AATTGCTTTT ACAGATGCAC ATATCGAGGT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GAACATCACG TACGCGGAAT ACTTCGAAAT GTCCGTTCGG TTGGCAGAAG CTATGAAACG ATATGGGCTG AATACAAATC ACAGAATCGT CGTATGCAGT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GAAAACTCTC TTCAATTCTT TATGCCGGTG TTGGGCGCGT TATTTATCGG AGTTGCAGTT GCGCCCGCGA ACGACATTTA TAATGAACGT GAATTGCTCA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACAGTATGAA CATTTCGCAG CCTACCGTAG TGTTTGTTTC CAAAAAGGGG TTGCAAAAAA TTTTGAACGT GCAAAAAAAA TTACCAATAA TCCAGAAAAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TATTATCATG GATTCTAAAA CGGATTACCA GGGATTTCAG TCGATGTACA CGTTCGTCAC ATCTCATCTA CCTCCCGGTT TTAATGAATA CGATTTTGTA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CCAGAGTCCT TTGATCGTGA CAAAACAATT GCACTGATAA TGAATTCCTC TGGATCTACT GGGTTACCTA AGGGTGTGGC CCTTCCGCAT AGAACTGCCT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GCGTCAGATT CTCGCATGCC AGAGATCCTA TTTTTGGCAA TCAAATCATT CCGGATACTG CGATTTTAAG TGTTGTTCCA TTCCATCACG GTTTTGGAAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTTTACTACA CTCGGATATT TGATATGTGG ATTTCGAGTC GTCTTAATGT ATAGATTTGA AGAAGAGCTG TTTTTACGAT CCCTTCAGGA TTACAAAATT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CAAAGTGCGT TGCTAGTACC AACCCTATTT TCATTCTTCG CCAAAAGCAC TCTGATTGAC AAATACGATT TATCTAATTT ACACGAAATT GCTTCTGGGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCGCACCTCT TTCGAAAGAA GTCGGGGAAG CGGTTGCAAA ACGCTTCCAT CTTCCAGGGA TACGACAAGG ATATGGGCTC ACTGAGACTA CATCAGCTAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TCTGATTACA CCCGAGGGGG ATGATAAACC GGGCGCGGTC GGTAAAGTTG TTCCATTTTT TGAAGCGAAG GTTGTGGATC TGGATACCGG GAAAACGCTG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGCGTTAATC AGAGAGGCGA ATTATGTGTC AGAGGACCTA TGATTATGTC CGGTTATGTA AACAATCCGG AAGCGACCAA CGCCTTGATT GACAAGGATG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GATGGCTACA TTCTGGAGAC ATAGCTTACT GGGACGAAGA CGAACACTTC TTCATAGTTG ACCGCTTGAA GTCTTTAATT AAATACAAAG GGTATCAGGT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGCCCCCGCT GAATTGGAAT CGATATTGTT ACAACACCCC AACATCTTCG ACGCGGGCGT GGCAGGTCTT CCCGACGATG ACGCCGGTGA ACTTCCCGCC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GCCGTTGTTG TTTTGGAGCA CGGAAAGACG ATGACGGAAA AAGAGATCGT GGATTACGTC GCCAGTCAAG TAACAACCGC GAAAAAGTTG CGCGGAGGAG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TTGTGTTTGT GGACGAAGTA CCGAAAGGTC TTACCGGAAA ACTCGACGCA AGAAAAATCA GAGAGATCCT CATAAAGGCC AAGAAGGGCG GAAAGTCCAA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ATTGTAAGCG GCCGCTTAAG CTAGCTTCGA TCCAGACATG ATAAGATACA TTGATGAGTT TGGACAAACC ACAACTAGAA TGCAGTGAAA AAAATGCTTT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATTTGTGAAA TTTGTGATGC TATTGCTTTA TTTGTAACCA TTATAAGCTG CAATAAACAA GTTAACAACA ACAATTGCAT TCATTTTATG TTTCAGGTTC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AGGGGGAGGT GTGGGAGGTT TTTTAAAGCA AGTAAAACCT CTACAAATGT GGTA
^3601      ^3611      ^3621      ^3631      ^3641      ^3651

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_except_3UTR

The name of the plasmid:
pBSRLucEFluc The name of the promoter used to express this mRNA:
SV40

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

no (not convincing)

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

not tested

A promoter reported in cDNA corresponding to IRES sequence:

no (not convincing)

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

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

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

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

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

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

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

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

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

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

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

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

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

The organism used:

Mus musculus C243

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 CCCTCGAGGa actggaaaac cagaaagtta actggtaagt ttagtctttt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

tgtcttttat ttcaggtcCC GGAATTGGTT TAAACGAATT CGAAATGACT TCGAAAGTTT ATGATCCAGA ACAAAGGAAA CGGATGATAA CTGGTCCGCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GTGGTGGGCC AGATGTAAAC AAATGAATGT TCTTGATTCA TTTATTAATT ATTATGATTC AGAAAAACAT GCAGAAAATG CTGTTATTTT TTTACATGGT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AACGCGGCCT CTTCTTATTT ATGGCGACAT GTTGTGCCAC ATATTGAGCC AGTAGCGCGG TGTATTATAC CAGACCTTAT TGGTATGGGC AAATCAGGCA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AATCTGGTAA TGGTTCTTAT AGGTTACTTG ATCATTACAA ATATCTTACT GCATGGTTTG AACTTCTTAA TTTACCAAAG AAGATCATTT TTGTCGGCCA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TGATTGGGGT GCTTGTTTGG CATTTCATTA TAGCTATGAG CATCAAGATA AGATCAAAGC AATAGTTCAC GCTGAAAGTG TAGTAGATGT GATTGAATCA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGGGATGAAT GGCCTGATAT TGAAGAAGAT ATTGCGTTGA TCAAATCTGA AGAAGGAGAA AAAATGGTTT TGGAGAATAA CTTCTTCGTG GAAACCATGT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGCCATCAAA AATCATGAGA AAGTTAGAAC CAGAAGAATT TGCAGCATAT CTTGAACCAT TCAAAGAGAA AGGTGAAGTT CGTCGTCCAA CATTATCATG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GCCTCGTGAA ATCCCGTTAG TAAAAGGTGG TAAACCTGAC GTTGTACAAA TTGTTAGGAA TTATAATGCT TATCTACGTG CAAGTGATGA TTTACCAAAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ATGTTTATTG AATCGGACCC AGGATTCTTT TCCAATGCTA TTGTTGAAGG TGCCAAGAAG TTTCCTAATA CTGAATTTGT CAAAGTAAAA GGTCTTCATT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TTTCGCAAGA AGATGCACCT GATGAAATGG GAAAATATAT CAAATCGTTC GTTGAGCGAG TTCTCAAAAA TGAACAATAA GTCGACCTGC AGAAGCTTGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCAGACGTCG CGCGCGGCCG CGAAATTAAT ACGACTCACT ATAGGGAGAC CACAACGGTT TCCCTCTAGC GGGATCATTC CGCCCCCCCC CCTAACGTTA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CTGGCCGAAG CCGCTTGGAA TAAGGCCGGT GTGCGTTTGT CTATATGTTA TTTTCCACCA TATTGCCGTC TTTTGGCAAT GTGAGGGCCC GGAAACCTGG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CCCTGTCTTC TTGACGAGCA TTCCTAGGGG TCTTTCCCCT CTCGCCAAAG GAATGCAAGG TCTGTTGAAT GTCGTGAAGG AAGCAGTTCC TCTGGAAGCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TCTTGAAGAC AAACAACGTC TGTAGCGACC CTTTGCAGGC AGCGGAACCC CCCACCTGGC GACAGGTGCC TCTGCGGCCA AAAGCCACGT GTATAAGATA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CACCATGCAA AGGCGGCACA ACCCCAGTGC CACGTTGTGA GTTGGATAGT TGTGGAAAGA GTCAAATGGC TCTCCTCAAG CGTATTCAAC AAGGGGCTGA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGGATGCCCA GAAGGTACCC CATTGTATGG GATCTGATCT GGGGCCTCGG TGCACATGCT TTACATGTGT TTAGTCGAGG TTAAAAAACG TCTAGGCCCC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCGAACCACG GGGACGTGGT TTTCCTTTGA AAAACACGAT GATACCATGG CCGAAGACGC CAAAAACATA AAGAAAGGCC CGGCACCATT CTATCCACTA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GAGGATGGAA CCGCTGGAGA GCAACTGCAT AAGGCTATGA AGAGATACGC CCTGGTTCCT GGAACAATTG CTTTTACAGA TGCACATATC GAGGTGAACA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCACGTACGC GGAATACTTC GAAATGTCCG TTCGGTTGGC AGAAGCTATG AAACGATATG GGCTGAATAC AAATCACAGA ATCGTCGTAT GCAGTGAAAA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CTCTCTTCAA TTCTTTATGC CGGTGTTGGG CGCGTTATTT ATCGGAGTTG CAGTTGCGCC CGCGAACGAC ATTTATAATG AACGTGAATT GCTCAACAGT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ATGAACATTT CGCAGCCTAC CGTAGTGTTT GTTTCCAAAA AGGGGTTGCA AAAAATTTTG AACGTGCAAA AAAAATTACC AATAATCCAG AAAATTATTA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TCATGGATTC TAAAACGGAT TACCAGGGAT TTCAGTCGAT GTACACGTTC GTCACATCTC ATCTACCTCC CGGTTTTAAT GAATACGATT TTGTACCAGA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GTCCTTTGAT CGTGACAAAA CAATTGCACT GATAATGAAT TCCTCTGGAT CTACTGGGTT ACCTAAGGGT GTGGCCCTTC CGCATAGAAC TGCCTGCGTC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AGATTCTCGC ATGCCAGAGA TCCTATTTTT GGCAATCAAA TCATTCCGGA TACTGCGATT TTAAGTGTTG TTCCATTCCA TCACGGTTTT GGAATGTTTA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CTACACTCGG ATATTTGATA TGTGGATTTC GAGTCGTCTT AATGTATAGA TTTGAAGAAG AGCTGTTTTT ACGATCCCTT CAGGATTACA AAATTCAAAG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGCGTTGCTA GTACCAACCC TATTTTCATT CTTCGCCAAA AGCACTCTGA TTGACAAATA CGATTTATCT AATTTACACG AAATTGCTTC TGGGGGCGCA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CCTCTTTCGA AAGAAGTCGG GGAAGCGGTT GCAAAACGCT TCCATCTTCC AGGGATACGA CAAGGATATG GGCTCACTGA GACTACATCA GCTATTCTGA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TTACACCCGA GGGGGATGAT AAACCGGGCG CGGTCGGTAA AGTTGTTCCA TTTTTTGAAG CGAAGGTTGT GGATCTGGAT ACCGGGAAAA CGCTGGGCGT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TAATCAGAGA GGCGAATTAT GTGTCAGAGG ACCTATGATT ATGTCCGGTT ATGTAAACAA TCCGGAAGCG ACCAACGCCT TGATTGACAA GGATGGATGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CTACATTCTG GAGACATAGC TTACTGGGAC GAAGACGAAC ACTTCTTCAT AGTTGACCGC TTGAAGTCTT TAATTAAATA CAAAGGGTAT CAGGTGGCCC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CCGCTGAATT GGAATCGATA TTGTTACAAC ACCCCAACAT CTTCGACGCG GGCGTGGCAG GTCTTCCCGA CGATGACGCC GGTGAACTTC CCGCCGCCGT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TGTTGTTTTG GAGCACGGAA AGACGATGAC GGAAAAAGAG ATCGTGGATT ACGTCGCCAG TCAAGTAACA ACCGCGAAAA AGTTGCGCGG AGGAGTTGTG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTTGTGGACG AAGTACCGAA AGGTCTTACC GGAAAACTCG ACGCAAGAAA AATCAGAGAG ATCCTCATAA AGGCCAAGAA GGGCGGAAAG TCCAAATTGT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AAGCGGCCGC TTAAGCTAGC TTCGATCCAG ACATGATAAG ATACATTGAT GAGTTTGGAC AAACCACAAC TAGAATGCAG TGAAAAAAAT GCTTTATTTG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TGAAATTTGT GATGCTATTG CTTTATTTGT AACCATTATA AGCTGCAATA AACAAGTTAA CAACAACAAT TGCATTCATT TTATGTTTCA GGTTCAGGGG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GAGGTGTGGG AGGTTTTTTA AAGCAAGTAA AACCTCTACA AATGTGGTAT GGCTGATTAT GATCCTGCCT CGCGCGTTTC GGTGATGACG GTGAAAACCT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CTGACACATG CAGCTCCCGC CTTAATTAAG GGTTTAAACC CGGTACCCAG TCACGTAGCG ATAGCGGAGT GTACTGCATT AATGAATCGG CCAACGCGCG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GGGAGAGGCG GTTTGCGTAT TGGGCGCTCT TCCGCTTCCT CGCTCACTGA CTCGCTGCGC TCGGTCGTTC GGCTGCGGCG AGCGGTATCA GCTCACTCAA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

AGGCGGTAAT ACGGTTATCC ACAGAATCAG GGGATAACGC AGGAAAGAAC ATGTGAGCAA AAGGCCAGCA AAAGGCCAGG AACCGTAAAA AGGCCGCGTT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GCTGGCGTTt TTCCATAGGC TCCGCCCCCC TGACGAGCAT CACAAAAATC GACGCTCAAG TCAGAGGTGG CGAAACCCGA CAGGACTATA AAGATACCAG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GCGTTTCCCC CTGGAAGCTC CCTCGTGCGC TCTCCTGTTC CGACCCTGCC GCTTACCGGA TACCTGTCCG CCTTTCTCCC TTCGGGAAGC GTGGCGCTTT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CTCATAGCTC ACGCTGTAGG TATCTCAGTT CGGTGTAGGT CGTTCGCTCC AAGCTGGGCT GTGTGCACGA ACCCCCCGTT CAGCCCGACC GCTGCGCCTT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATCCGGTAAC TATCGTCTTG AGTCCAACCC GGTAAGACAC GACTTATCGC CACTGGCAGC AGCCACTGGT AACAGGATTA GCAGAGCGAG GTATGTAGGC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GGTGCTACAG AGTTCTTGAA GTGGTGGCCT AACTACGGCT ACACTAGAAG GACAGTATTT GGTATCTGCG CTCTGCTGAA GCCAGTTACC TTCGGAAAAA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GAGTTGGTAG CTCTTGATCC GGCAAACAAA CCACCGCTGG TAGCGGTGGT TTTTTTGTTT GCAAGCAGCA GATTACGCGC AGAAAAAAAG GATCTCAAGA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

AGATCCTTTG ATCTTTTCTA CGGGGTCTGA CGCTCAGTGG AACGAAAACT CACGTTAAGG GATTTTGGTC ATGAGATTAT CAAAAAGGAT CTTCACCTAG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

ATCCTTTTAA ATTAAAAATG AAGTTTTAAA TCAATCTAAA GTATATATGA GTAAACTTGG TCTGACAGTT ACCAATGCTT AATCAGTGAG GCACCTATCT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CAGCGATCTG TCTATTTCGT TCATCCATAG TTGCCTGACT CCCCGTCGTG TAGATAACTA CGATACGGGA GGGCTTACCA TCTGGCCCCA GTGCTGCAAT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GATACCGCGA GACCCACGCT CACCGGCTCC AGATTTATCA GCAATAAACC AGCCAGCCGG AAGGGCCGAG CGCAGAAGTG GTCCTGCAAC TTTATCCGCC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TCCATCCAGT CTATTAATTG TTGCCGGGAA GCTAGAGTAA GTAGTTCGCC AGTTAATAGT TTGCGCAACG TTGTTGCCAT TGCTACAGGC ATCGTGGTGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CACGCTCGTC GTTTGGTATG GCTTCATTCA GCTCCGGTTC CCAACGATCA AGGCGAGTTA CATGATCCCC CATGTTGTGC AAAAAAGCGG TTAGCTCCTT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

CGGTCCTCCG ATCGTTGTCA GAAGTAAGTT GGCCGCAGTG TTATCACTCA TGGTTATGGC AGCACTGCAT AATTCTCTTA CTGTCATGCC ATCCGTAAGA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TGCTTTTCTG TGACTGGTGA GTACTCAACC AAGTCATTCT GAGAATAGTG TATGCGGCGA CCGAGTTGCT CTTGCCCGGC GTCAATACGG GATAATACCG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CGCCACATAG CAGAACTTTA AAAGTGCTCA TCATTGGAAA ACGTTCTTCG GGGCGAAAAC TCTCAAGGAT CTTACCGCTG TTGAGATCCA GTTCGATGTA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ACCCACTCGT GCACCCAACT GATCTTCAGC ATCTTTTACT TTCACCAGCG TTTCTGGGTG AGCAAAAACA GGAAGGCAAA ATGCCGCAAA AAAGGGAATA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AGGGCGACAC GGAAATGTTG AATACTCATA CTCTTCCTTT TTCAATATTA TTGAAGCATT TATCAGGGTT ATTGTCTCAT GAGCGGATAC ATATTTGAAT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GTATTTAGAA AAATAAACAA ATAGGGGTTC CGCGCACATT TCCCCGAAAA GTGCCACCTG ACGTCGGTAC CATTTAAATA TCGATAAGC
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081

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):

150-1085

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):

1752-3407

Remarks:

For Northern blot please see Fig. 2b.

Citations:

Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759

IRESs:

IRES:

Version: `4`	Last change: `2011-04-08 22:03:26`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `EMCV-R_271-831`	The functional status of IRES: `functional`

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

1188-1749

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `103`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `664`
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):

CCCCCCCCCC TAACGTTACT GGCCGAAGCC GCTTGGAATA AGGCCGGTGT GCGTTTGTCT ATATGTTATT TTCCACCATA TTGCCGTCTT TTGGCAATGT 
^1188      ^1198      ^1208      ^1218      ^1228      ^1238      ^1248      ^1258      ^1268      ^1278      

GAGGGCCCGG AAACCTGGCC CTGTCTTCTT GACGAGCATT CCTAGGGGTC TTTCCCCTCT CGCCAAAGGA ATGCAAGGTC TGTTGAATGT CGTGAAGGAA 
^1288      ^1298      ^1308      ^1318      ^1328      ^1338      ^1348      ^1358      ^1368      ^1378      

GCAGTTCCTC TGGAAGCTTC TTGAAGACAA ACAACGTCTG TAGCGACCCT TTGCAGGCAG CGGAACCCCC CACCTGGCGA CAGGTGCCTC TGCGGCCAAA 
^1388      ^1398      ^1408      ^1418      ^1428      ^1438      ^1448      ^1458      ^1468      ^1478      

AGCCACGTGT ATAAGATACA CCATGCAAAG GCGGCACAAC CCCAGTGCCA CGTTGTGAGT TGGATAGTTG TGGAAAGAGT CAAATGGCTC TCCTCAAGCG 
^1488      ^1498      ^1508      ^1518      ^1528      ^1538      ^1548      ^1558      ^1568      ^1578      

TATTCAACAA GGGGCTGAAG GATGCCCAGA AGGTACCCCA TTGTATGGGA TCTGATCTGG GGCCTCGGTG CACATGCTTT ACATGTGTTT AGTCGAGGTT 
^1588      ^1598      ^1608      ^1618      ^1628      ^1638      ^1648      ^1658      ^1668      ^1678      

AAAAAACGTC TAGGCCCCCC GAACCACGGG GACGTGGTTT TCCTTTGAAA AACACGATGA TA
^1688      ^1698      ^1708      ^1718      ^1728      ^1738      ^1748

Remarks:

The IRES segment includes part of the polyC tract. The minimal EMCV-R IRES is located in 1273-1749.

Citations:

Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759

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