IRESite_Id:281 characteristics of ERAV_245-961_deltaA2 IRES studied in pE1(245-961)deltaA2 plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `281`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-04 21:59:12`

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:
our_best_guess

The mRNA/+RNA description:

Putative in vivo bicistronic T7 transcript with CAT and GFP cistrons and 5'-UTR containing EMCV IRES
terminated by Tphi transcription terminator. The EMCV-R IRES is located between nucleotides 57-608 of the
putative mRNA and lacks the very rightmost 6 bases immediately preceding the initiator AUG codon of EMCV
polyprotein. A putative ERAV IRES is located in the intercistronic region with its second AUG mutated from
AUG to AUA.

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

GGGAGACCAC AACGGTTTCC CTCTAGCGGG ATCAATTCCG CCCCTCTCCC TCCCCCCCCC CTAACGTTAC TGGCCGAAGC CGCTTGGAAT AAGGCCGGTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGCGTTTGTC TATATGTTAT TTTCCACCAT ATTGCCGTCT TTTGGCAATG TGAGGGCCCG GAAACCTGGC CCTGTCTTCT TGACGAGCAT TCCTAGGGGT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CTTTCCCCTC TCGCCAAAGG AATGCAAGGT CTGTTGAATG TCGTGAAGGA AGCAGTTCCT CTGGAAGCTT CTTGAAGACA AACAACGTCT GTAGCGACCC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTTGCAGGCA GCGGAACCCC CCACCTGGCG ACAGGTGCCT CTGCGGCCAA AAGCCACGTG TATAAGATAC ACCTGCAAAG GCGGCACAAC CCCAGTGCCA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CGTTGTGAGT TGGATAGTTG TGGAAAGAGT CAAATGGCTC TCCTCAAGCG TATTCAACAA GGGGCTGAAG GATGCCCAGA AGGTACCCCA TTGTATGGGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCTGATCTGG GGCCTCGGTG CACATGCTTT ACATGTGTTT AGTCGAGGTT AAAAAACGTC TAGGCCCCCC GAACCACGGG GACGTGGTTT TCCTTTGAAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AACACGATAA TACCATGGAG AAAAAAATCA CTGGATATAC CACCGTTGAT ATATCCCAAT GGCATCGTAA AGAACATTTT GAGGCATTTC AGTCAGTTGC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TCAATGTACC TATAACCAGA CCGTTCAGCT GGATATTACG GCCTTTTTAA AGACCGTAAA GAAAAATAAG CACAAGTTTT ATCCGGCCTT TATTCACATT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTTGCCCGCC TGATGAATGC TCATCCGGAA CTCCGTATGG CAATGAAAGA CGGTGAGCTG GTGATATGGG ATAGTGTTCA CCCTTGTTAC ACCGTTTTCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATGAGCAAAC TGAAACGTTT TCATCGCTCT GGAGTGAATA CCACGACGAT TTCCGGCAGT TTCTACACAT ATATTCGCAA GATGTGGCGT GTTACGGTGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AAACCTGGCC TATTTCCCTA AAGGGTTTAT TGAGAATATG TTTTTCGTCT CAGCCAATCC CTGGGTGAGT TTCACCAGTT TTGATTTAAA CGTGGCCAAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATGGACAACT TCTTCGCCCC CGTTTTCACG ATGGGCAAAT ATTATACGCA AGGCGACAAG GTGCTGATGC CGCTGGCGAT TCAGGTTCAT CATGCCGTTT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTGATGGCTT CCATGTCGGC AGAATGCTTA ATGAATTACA ACAGTACTGC GATGAGTGGC AGGGCGGGGC GTAATCTAGC GCTACCGGTg agaggagccc 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

gttttcgggc acttgtctcc taaacaatgt tggcgcgcat ttgcgcgccc cccccctttt tcagccccct gtcattgact ggtcgaagcg ttcgcaataa 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

gactggtcgt cacttggctg ttctatcgtt tcaggcttta gcgcgccctt gcgcggcggg ccgtcaagcc cgtgcgctgt atagcgccag gtaaccggac 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

agcggcgtgc tggattttcc cggtgccatt gctctggatg gtgtcaccaa gctgacaaat gcggagtgaa cctcacaaag cgacacgcct gtggtagcgc 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tgcccaaaag ggagcggaac tcccccgccg cgaggcggtc ctctctggcc aaaagcccag cgttgatagc gccttttggg atgcaggaac cccacctgcc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

aggtgtgaag tggagtgagc ggatctccaa tttggtctgt tctgaactac accatttact gctgtgaaga atgccctgga ggcaagctgg ttacagccct 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gaccaggccc tgcccgtgac tctcgaccgg cgcagggtca aaaattgtct aagcagcagc aggaacgcgg gagcgtttct tttccttttg tactgacatg 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

atagcggcgt ctaaggtgta tagagtttgc gagcagactc tgctggcagg tgccgttcgc atgatggaca aattcttgca aaagagaact gtttttgtcc 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

cccaACCGGT CGCCACCATG GTGAGCAAGG GCGAGGAGCT GTTCACCGGG GTGCCCATCC TGGTCGAGCT GGACGGCGAC GTAAACGGCC ACAAGTTCAG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGTGTCCGGC GAGGGCGAGG GCGATGCCAC CTACGGCAAG CTGACCCTGA AGTTCATCTG CACCACCGGC AAGCTGCCCG TGCCCTGGCC CACCCTCGTG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ACCACCCTGA CCTACGGCGT GCAGTGCTTC AGCCGCTACC CCGACCACAT GAAGCAGCAC GACTTCTTCA AGTCCGCCAT GCCCGAAGGC TACGTCCAGG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AGCGCACCAT CTTCTTCAAG GACGACGGCA ACTACAAGAC CCGCGCCGAG GTGAAGTTCG AGGGCGACAC CCTGGTGAAC CGCATCGAGC TGAAGGGCAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CGACTTCAAG GAGGACGGCA ACATCCTGGG GCACAAGCTG GAGTACAACT ACAACAGCCA CAACGTCTAT ATCATGGCCG ACAAGCAGAA GAACGGCATC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AAGGTGAACT TCAAGATCCG CCACAACATC GAGGACGGCA GCGTGCAGCT CGCCGACCAC TACCAGCAGA ACACCCCCAT CGGCGACGGC CCCGTGCTGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TGCCCGACAA CCACTACCTG AGCACCCAGT CCGCCCTGAG CAAAGACCCC AACGAGAAGC GCGATCACAT GGTCCTGCTG GAGTTCGTGA CCGCCGCCGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GATCACTCTC GGCATGGACG AGCTGTACAA GTCCGGACTC AGATCTCGAG CTCAAGCTTC GAATTCTGCA GTCGACGGTA CCGCGGGCCC GGGATCCCTG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CAGCTCGAGA GGCCTAATTA ATTAAGTCGA CGATCCGGCT GCTAACAAAG CCCGAAAGGA AGCTGAGTTG GCTGCTGCCA CCGCTGAGCA ATAACTAGCA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TAACCCCTTG GGGCCTCTAA ACGGGTCTTG AGGGGTTTTT TG
^2901      ^2911      ^2921      ^2931      ^2941

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pE1(245-961)deltaA2 The name of the promoter used to express this mRNA:
T7

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:
ERAV

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Equine rhinitis A virus 1 393/76

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

AAGCTTTTGC GATCAATAAA TGGATCACAA CCAGTATCTC TTAACGATGT TCTTCGCAGA TGATGATTCA TTTTTTAAGT ATTTGGCTAG TCAAGATGAT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GAATCTTCAT TATCTGATAT ATTGCAAATC ACTCAATATC TAGACTTTCT GTTATTATTA TTGATCCAAT CAAAAAATAA ATTAGAAGCC GTGGGTCATT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GTTATGAATC TCTTTCAGAG GAATACAGAC AATTGACAAA ATTCACAGAC TTTCAAGATT TTAAAAAACT GTTTAACAAG GTCCCTATTG TTACAGATGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AAGGGTCAAA CTTAATAAAG GATATTTGTT CGACTTTGTG ATTAGTTTGA TGCGATTCAA AAAAGAATCC TCTCTAGCTA CCACCGCAAT AGATCCTGTT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AGATACATAG ATCCTCGTCG CAATATCGCA TTTTCTAACG TGATGGATAT ATTAAAGTCG AATAAAGTGA ACAATAATTA ATTCTTTATT GTCATCATGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACGGCGGACA TATTCAGTTG ATAATCGGCC CCATGTTTTC AGGTAAAAGT ACAGAATTAA TTAGACGAGT TAGACGTTAT CAAATAGCTC AATATAAATG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CGTGACTATA AAATATTCTA ACGATAATAG ATACGGAACG GGACTATGGA CGCATGATAA GAATAATTTT GAAGCATTGG AAGCAACTAA ACTATGTGAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GTCTTGGAAT CAATTACAGA TTTCTCCGTG ATAGGTATCG ATGAAGGACA GTTCTTTCCA GACATTGTTG AATTGATCTC GATCCCGCGA AATTAATACG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ACTCACTATA GGGAGACCAC AACGGTTTCC CTCTAGCGGG ATCAATTCCG CCCCTCTCCC TCCCCCCCCC CTAACGTTAC TGGCCGAAGC CGCTTGGAAT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAGGCCGGTG TGCGTTTGTC TATATGTTAT TTTCCACCAT ATTGCCGTCT TTTGGCAATG TGAGGGCCCG GAAACCTGGC CCTGTCTTCT TGACGAGCAT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TCCTAGGGGT CTTTCCCCTC TCGCCAAAGG AATGCAAGGT CTGTTGAATG TCGTGAAGGA AGCAGTTCCT CTGGAAGCTT CTTGAAGACA AACAACGTCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GTAGCGACCC TTTGCAGGCA GCGGAACCCC CCACCTGGCG ACAGGTGCCT CTGCGGCCAA AAGCCACGTG TATAAGATAC ACCTGCAAAG GCGGCACAAC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCCAGTGCCA CGTTGTGAGT TGGATAGTTG TGGAAAGAGT CAAATGGCTC TCCTCAAGCG TATTCAACAA GGGGCTGAAG GATGCCCAGA AGGTACCCCA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TTGTATGGGA TCTGATCTGG GGCCTCGGTG CACATGCTTT ACATGTGTTT AGTCGAGGTT AAAAAACGTC TAGGCCCCCC GAACCACGGG GACGTGGTTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCCTTTGAAA AACACGATAA TACCATGGAG AAAAAAATCA CTGGATATAC CACCGTTGAT ATATCCCAAT GGCATCGTAA AGAACATTTT GAGGCATTTC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGTCAGTTGC TCAATGTACC TATAACCAGA CCGTTCAGCT GGATATTACG GCCTTTTTAA AGACCGTAAA GAAAAATAAG CACAAGTTTT ATCCGGCCTT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TATTCACATT CTTGCCCGCC TGATGAATGC TCATCCGGAA CTCCGTATGG CAATGAAAGA CGGTGAGCTG GTGATATGGG ATAGTGTTCA CCCTTGTTAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ACCGTTTTCC ATGAGCAAAC TGAAACGTTT TCATCGCTCT GGAGTGAATA CCACGACGAT TTCCGGCAGT TTCTACACAT ATATTCGCAA GATGTGGCGT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTTACGGTGA AAACCTGGCC TATTTCCCTA AAGGGTTTAT TGAGAATATG TTTTTCGTCT CAGCCAATCC CTGGGTGAGT TTCACCAGTT TTGATTTAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGTGGCCAAT ATGGACAACT TCTTCGCCCC CGTTTTCACG ATGGGCAAAT ATTATACGCA AGGCGACAAG GTGCTGATGC CGCTGGCGAT TCAGGTTCAT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CATGCCGTTT GTGATGGCTT CCATGTCGGC AGAATGCTTA ATGAATTACA ACAGTACTGC GATGAGTGGC AGGGCGGGGC GTAATCTAGC GCTACCGGTg 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

agaggagccc gttttcgggc acttgtctcc taaacaatgt tggcgcgcat ttgcgcgccc cccccctttt tcagccccct gtcattgact ggtcgaagcg 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ttcgcaataa gactggtcgt cacttggctg ttctatcgtt tcaggcttta gcgcgccctt gcgcggcggg ccgtcaagcc cgtgcgctgt atagcgccag 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gtaaccggac agcggcgtgc tggattttcc cggtgccatt gctctggatg gtgtcaccaa gctgacaaat gcggagtgaa cctcacaaag cgacacgcct 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gtggtagcgc tgcccaaaag ggagcggaac tcccccgccg cgaggcggtc ctctctggcc aaaagcccag cgttgatagc gccttttggg atgcaggaac 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

cccacctgcc aggtgtgaag tggagtgagc ggatctccaa tttggtctgt tctgaactac accatttact gctgtgaaga atgccctgga ggcaagctgg 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ttacagccct gaccaggccc tgcccgtgac tctcgaccgg cgcagggtca aaaattgtct aagcagcagc aggaacgcgg gagcgtttct tttccttttg 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

tactgacatg atagcggcgt ctaaggtgta tagagtttgc gagcagactc tgctggcagg tgccgttcgc atgatggaca aattcttgca aaagagaact 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

gtttttgtcc cccaACCGGT CGCCACCATG GTGAGCAAGG GCGAGGAGCT GTTCACCGGG GTGCCCATCC TGGTCGAGCT GGACGGCGAC GTAAACGGCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ACAAGTTCAG CGTGTCCGGC GAGGGCGAGG GCGATGCCAC CTACGGCAAG CTGACCCTGA AGTTCATCTG CACCACCGGC AAGCTGCCCG TGCCCTGGCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CACCCTCGTG ACCACCCTGA CCTACGGCGT GCAGTGCTTC AGCCGCTACC CCGACCACAT GAAGCAGCAC GACTTCTTCA AGTCCGCCAT GCCCGAAGGC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TACGTCCAGG AGCGCACCAT CTTCTTCAAG GACGACGGCA ACTACAAGAC CCGCGCCGAG GTGAAGTTCG AGGGCGACAC CCTGGTGAAC CGCATCGAGC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGAAGGGCAT CGACTTCAAG GAGGACGGCA ACATCCTGGG GCACAAGCTG GAGTACAACT ACAACAGCCA CAACGTCTAT ATCATGGCCG ACAAGCAGAA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GAACGGCATC AAGGTGAACT TCAAGATCCG CCACAACATC GAGGACGGCA GCGTGCAGCT CGCCGACCAC TACCAGCAGA ACACCCCCAT CGGCGACGGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CCCGTGCTGC TGCCCGACAA CCACTACCTG AGCACCCAGT CCGCCCTGAG CAAAGACCCC AACGAGAAGC GCGATCACAT GGTCCTGCTG GAGTTCGTGA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CCGCCGCCGG GATCACTCTC GGCATGGACG AGCTGTACAA GTCCGGACTC AGATCTCGAG CTCAAGCTTC GAATTCTGCA GTCGACGGTA CCGCGGGCCC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GGGATCCCTG CAGCTCGAGA GGCCTAATTA ATTAAGTCGA CGATCCGGCT GCTAACAAAG CCCGAAAGGA AGCTGAGTTG GCTGCTGCCA CCGCTGAGCA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ATAACTAGCA TAACCCCTTG GGGCCTCTAA ACGGGTCTTG AGGGGTTTTT TGCTGAAAGG AGGAACTATA TCCGGATCGA GATCAATTCT GTGAGCGTAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GGCAAACGAA GGAAAAATAG TTATAGTAGC CGCACTCGAT GGGACATTTC AACGTAAACC GTTTAATAAT ATTTTGAATC TTATTCCATT ATCTGAAATG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GTGGTAAAAC TAACTGCTGT GTGTATGAAA TGCTTTAAGG AGGCTTCCTT TTCTAAACGA TTGGGTGAGG AAACCGAGAT AGAAATAATA GGAGGTAATG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ATATGTATCA ATCGGTGTGT AGAAAGTGTT ACATCGACTC ATAATATTAT ATTTTTTATC TAAAAAACTA AAAATAAACA TTGCTTAAAT TTTAATATAA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TACTTAAAAA TGGATGTTGT GTCGTTAGAT AAACCGTTTA TGTATTTTGA GGAAATTGAT AATGAGTTAG ATTACGAACC AGAAAGTGCA AATGAGGTCG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CAAAAAAACT GCCGTATCAA GGACAGTTAA AACTATTACT AGGAGAATTA TTTTTTCTTA GTAAGTTACA GCGACACGGT ATATTAGATG GTGCCACCGT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AGTGTATATA GGATCTGCTC CCGGTACACA TATACGTTAT TTGAGAGATC ATTTCTATAA TTTAGGAGTG ATCATCAAAT GGATGCTAAT TGACGGCCGC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CATCATGATC CTATTTTAAA TGGATTGCGT GATGTGACTC TAGTGACTCG GTTCGTTGAT GAGGAATATC TACGATCCAT CAAAAAACAA CTGCATCCTT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CTAAGATTAT TTTAATTTCT GATGTGAGAT CCAAACGAGG AGGAAATGAA CCTAGTACGG CGGATTTACT AAGTAATTAC GCTCTACAAA ATGTCATGAT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TAGTATTTTA AACCCCGTGG CGTCTAGTCT TAAATGGAGA TGCCCGTTTC CAGATCAATG GATCAAGGAC TTTTATATCC CACACGGTAA TAAAATGTTA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CAACCTTTTG CTCCTTCATA TTCAGGGCCG TCGTTTTACA ACGTCGTGAC TGGGAAAACC CTGGCGTTAC CCAACTTAAT CGCCTTGCAG CACATCCCCC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TTTCGCCAGC TGGCGTAATA GCGAAGAGGC CCGCACCGAT CGCCCTTCCC AACAGTTGCG CAGCCTGAAT GGCGAATGGC GCGACGCGCC CTGTAGCGGC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GCATTAAGCG CGGCGGGTGT GGTGGTTACG CGCAGCGTGA CCGCTACACT TGCCAGCGCC CTAGCGCCCG CTCCTTTCGC TTTCTTCCCT TCCTTTCTCG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CCACGTTCGC CGGCTTTCCC CGTCAAGCTC TAAATCGGGG GCTCCCTTTA GGGTTCCGAT TTAGTGCTTT ACGGCACCTC GACCCCAAAA AACTTGATTA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GGGTGATGGT TCACGTAGTG GGCCATCGCC CTGATAGACG GTTTTTCGCC CTTTGACGTT GGAGTCCACG TTCTTTAATA GTGGACTCTT GTTCCAAACT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GGAACAACAC TCAACCCTAT CTCGGTCTAT TCTTTTGATT TATAAGGGAT TTTGCCGATT TCGGCCTATT GGTTAAAAAA TGAGCTGATT TAACAAAAAT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TTAACGCGAA TTTTAACAAA ATATTAACGT TTACAATTTC CCAGGTGGCA CTTTTCGGGG AAATGTGCGC GGAACCCCTA TTTGTTTATT TTTCTAAATA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CATTCAAATA TGTATCCGCT CATGAGACAA TAACCCTGAT AAATGCTTCA ATAATATTGA AAAAGGAAGA GTATGAGTAT TCAACATTTC CGTGTCGCCC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TTATTCCCTT TTTTGCGGCA TTTTGCCTTC CTCTTTTTGC TCACCCAGAA AGCGTGGTGA AAGTAAAAGA TGCTGAAGAT CAGTTGGGTG CACGAGTGGG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TTACATCGAA CTGGATCTCA ACAGCGGTAA GATCCTTGAG AGTTTTCGCC CCGAAGAACG TTTTCCAATG ATGAGCACTT TTAAAGTTCT GCTATGTGGC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

GCGGTATTAT CCCGTATTGA CGCCGGGCAA GAGCAACTCG GTCGCCGCAT ACACTATTCT CAGAATGACT TGGTTGAGTA CTCACCAGTC ACAGAAAAGC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ATCTTACGGA TGGCATGACA GTAAGAGAAT TATGCAGTGC TGCCATAACC ATGAGTGATA ACACTGCGGC CAACTTACTT CTGACAACGA TCGGAGGACC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

GAAGGAGCTA ACCGCTTTTT TGCACAACAT GGGGGATCAT CTAACTCGCC TTGATCGTTG GGAACCGGAG CTGAATGAAG CCATACCAAA CGACGAGCGT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GACACCACGA TGCCTGTAGC AATGGCAACA ACGTTGCGCA AACTATTAAC TGGCGAACTA CTTACTCTAG CTTCCCGGCA ACAATTAATA GACTGGATGG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

AGGCGGATAA AGTTGCAGGA CCACTTCTGC GCTCGGCCCT TCCGGCTGGC TGGTTTATTG CTGATAAATC TGGAGCCGGT GAGCGTGGGT CTCGCGGTAT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

CATTGCAGCA CTGGGGCCAG ATGGTAAGCC CTCCCGTATC GTAGTTATCT ACACGACGGG GAGTCAGGCA ACTATGGATG AACGAAATAG ACAGATCGCT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

GAGATAGGTG CCTCACTGAT TAAGCATTGG TAACTGTCAG ACCAAGTTTA CTCATATATA CTTTAGATTG ATTTAAAACT TCATTTTTAA TTTAAAAGGA 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

TCTAGGTGAA GATCCTTTTT GATAATCTCA TGACCAAAAT CCCTTAACGT GAGTTTTCGT TCCACTGAGC GTCAGACCCC GTAGAAAAGA TCAAAGGATC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TTCTTGAGAT CCTTTTTTTC TGCGCGTAAT CTGCTGCTTG CAAACAAAAA AACCACCGCT ACCAGCGGTG GTTTGTTTGC CGGATCAAGA GCTACCAACT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CTTTTTCCGA AGGTAACTGG CTTCAGCAGA GCGCAGATAC CAAATACTGT CCTTCTAGTG TAGCCGTAGT TAGGCCACCA CTTCAAGAAC TCTGTAGCAC 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CGCCTACATA CCTCGCTCTG CTAATCCTGT TACCAGTGGC TGCTGCCAGT GGCGATAAGT CGTGTCTTAC CGGGTTGGAC TCAAGACGAT AGTTACCGGA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

TAAGGCGCAG CGGTCGGGCT GAACGGGGGG TTCGTGCACA CAGCCCAGCT TGGAGCGAAC GACCTACACC GAACTGAGAT ACCTACAGCG TGAGCTATGA 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

GAAAGCGCCA CGCTTCCCGA AGGGAGAAAG GCGGACAGGT ATCCGGTAAG CGGCAGGGTC GGAACAGGAG AGCGCACGAG GGAGCTTCCA GGGGGAAACG 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CCTGGTATCT TTATAGTCCT GTCGGGTTTC GCCACCTCTG ACTTGAGCGT CGATTTTTGT GATGCTCGTC AGGGGGGCGG AGCCTATGGA AAAACGCCAG 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CAACGCGGCC TTTTTACGGT TCCTGGCCTT TTGCTGGCCT TTTGCTCACA TGTTCTTTCC TGCGTTATCC CCTGATTCTG TGGATAACCG TATTACCGCC 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TTTGAGTGAG CTGATACCGC TCGCCGCAGC CGAACGACCG AGCGCAGCGA GTCAGTGAGC GAGGAAGCGG AAGAGCGCCC AATACGCAAA CCGCCTCTCC 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

CCGCGCGTTG GCCGATTCAT TAATGCAGCT GGCACGACAG GTTTCCCGAC TGGAAAGCGG GCAGTGAGCG CAACGCAATT AATGTGAGTT AGCTCACTCA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

TTAGGCACCC CAGGCTTTAC ACTTTATGCT TCCGGCTCGT ATGTTGTGTG GAATTGTGAG CGGATAACAA TTTCACACAG GAAACAGCTA TGACCATGAT 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

TACGCC
^7501

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

The total number of notable open-reading frames (ORFs):

5

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:
CAT

The description of the protein encoded in this ORF:
chloramphenicol acetyltransferase

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):

615-1274

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
Lab-GFP

The description of the protein encoded in this ORF:
green fluorescent protein extended at its N-terminus by 40 aminoacid residues encoded by 3'-end of ERAV IRES and partly by multiple cloning sequence site (as if initiated from AUG1).

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:

yes

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

1898-2821

ORF

ORF position:

3

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

The abbreviated name of this ORF/gene:
Lb-GFP

The description of the protein encoded in this ORF:
green fluorescent protein extended at its N-terminus by 19 aminoacid residues encoded by 3'-end of ERAV IRES and partly by multiple cloning sequence site (as if initiated from AUG3)

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:

yes

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

1961-2821

ORF

ORF position:

4

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

The abbreviated name of this ORF/gene:
Lb-GFP

The description of the protein encoded in this ORF:
green fluorescent protein extended at its N-terminus by 18 aminoacid residues encoded by 3'-end of ERAV IRES and partly by multiple cloning sequence site (as if initiated from AUG4)

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:

yes

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

1964-2821

ORF

ORF position:

5

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

The abbreviated name of this ORF/gene:
GFP

The description of the protein encoded in this ORF:
green fluorescent protein

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:

yes

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

2018-2821

Remarks:

It appeared the ERAV 5'-UTR region downstream the poly(C) tract contains 5 AUG codons. The first 4 are in
pairs adjacent to each other, while the fifth is the most downstream and is alone. Three types of proteins
were detected from complete ERAV IRES 245-961, called Lab-GFP, Lb-GFP, GFP. The naming Lab and Lb reflects
the fact that possibly viral proteases Lab and Lb are initiated at those respective AUG codons.

In this particular construct the AUG2 was mutated to AUA (Fig. 5C).

Citations:

Hinton T. M., Li F., Crabb B. S. (2000) Internal ribosomal entry site-mediated translation initiation in equine rhinitis A virus: similarities to and differences from that of foot-and-mouth disease virus. J. Virol. 74(24):11708-11716

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `ERAV_245-961_deltaA2`	The functional status of IRES: `functional`

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

1290-2004

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `16`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `730`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-608`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `106`

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

gagaggagcc cgttttcggg cacttgtctc ctaaacaatg ttggcgcgca tttgcgcgcc cccccccttt ttcagccccc tgtcattgac tggtcgaagc 
^1290      ^1300      ^1310      ^1320      ^1330      ^1340      ^1350      ^1360      ^1370      ^1380      

gttcgcaata agactggtcg tcacttggct gttctatcgt ttcaggcttt agcgcgccct tgcgcggcgg gccgtcaagc ccgtgcgctg tatagcgcca 
^1390      ^1400      ^1410      ^1420      ^1430      ^1440      ^1450      ^1460      ^1470      ^1480      

ggtaaccgga cagcggcgtg ctggattttc ccggtgccat tgctctggat ggtgtcacca agctgacaaa tgcggagtga acctcacaaa gcgacacgcc 
^1490      ^1500      ^1510      ^1520      ^1530      ^1540      ^1550      ^1560      ^1570      ^1580      

tgtggtagcg ctgcccaaaa gggagcggaa ctcccccgcc gcgaggcggt cctctctggc caaaagccca gcgttgatag cgccttttgg gatgcaggaa 
^1590      ^1600      ^1610      ^1620      ^1630      ^1640      ^1650      ^1660      ^1670      ^1680      

ccccacctgc caggtgtgaa gtggagtgag cggatctcca atttggtctg ttctgaacta caccatttac tgctgtgaag aatgccctgg aggcaagctg 
^1690      ^1700      ^1710      ^1720      ^1730      ^1740      ^1750      ^1760      ^1770      ^1780      

gttacagccc tgaccaggcc ctgcccgtga ctctcgaccg gcgcagggtc aaaaattgtc taagcagcag caggaacgcg ggagcgtttc ttttcctttt 
^1790      ^1800      ^1810      ^1820      ^1830      ^1840      ^1850      ^1860      ^1870      ^1880      

gtactgacat gatagcggcg tctaaggtgt atagagtttg cgagcagact ctgctggcag gtgccgttcg catgatggac aaattcttgc aaaagagaac 
^1890      ^1900      ^1910      ^1920      ^1930      ^1940      ^1950      ^1960      ^1970      ^1980      

tgtttttgtc cccca
^1990      ^2000

Remarks:

This mutation confirms that Lab-GFP was synthesized mostly from AUG2 and that AUG1 can be used to initiate
Lab-GFP as well.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 359

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens BHK-21 (ATCC CCL-10)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

58.000

Name of IRES used as the positive control:

ERAV_245-961

Name of the plasmid used as the positive control. `pE1(245-961)`
`IRESite Id` of the plasmid used as positive control. `272`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `626`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_cytoplasmic_uncapped_T7_transcript_without_polyA_tail

Remarks:

Mutation of 2nd AUG codon contained within the putative ERAV IRES only decently impaired
IRES activity. The various GFP-fusion protein yields changed as follows in comparison
to the wild-type pE1(245-961):

                     wt                 pE1(245-961)deltaA2
Lab-GFP (AUG1/2)  13.4%                 10.1%
 Lb-GFP (AUG3/4)   1.4%                  4.3%
    GFP (AUG5)     6.7%                  6.1%
_____________________________________________
          21.6% of CAT (100%)           20.4% (58%) of wt activity


The 87% are a sum of all three types of GFP protein forms, initiated from AUG1, AUA2, AUG3, AUG4.
100% is the sum of these products from wild-type pE1(245-961) plasmid having AUG1-4 (Fig. 5C).
BHK-21 cells were infected by recombinant vaccinia virus that expresses T7 polymerase (vTF7-3).

Citations:

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