IRESite_Id:278 characteristics of ERAV_245-858 IRES studied in pE1(245-858) plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `278`	Version: `2`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-04 22:00:22`

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 and is retained only to the 2nd
AUG codon (nucleotides 1901-1903) which starts the GFP ORF. Thus, there is no remaining sequence from
MCS between putative ERAV IRES and GFP ORF.

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      

atgGTGAGCA AGGGCGAGGA GCTGTTCACC GGGGTGCCCA TCCTGGTCGA GCTGGACGGC GACGTAAACG GCCACAAGTT CAGCGTGTCC GGCGAGGGCG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGGGCGATGC CACCTACGGC AAGCTGACCC TGAAGTTCAT CTGCACCACC GGCAAGCTGC CCGTGCCCTG GCCCACCCTC GTGACCACCC TGACCTACGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGTGCAGTGC TTCAGCCGCT ACCCCGACCA CATGAAGCAG CACGACTTCT TCAAGTCCGC CATGCCCGAA GGCTACGTCC AGGAGCGCAC CATCTTCTTC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AAGGACGACG GCAACTACAA GACCCGCGCC GAGGTGAAGT TCGAGGGCGA CACCCTGGTG AACCGCATCG AGCTGAAGGG CATCGACTTC AAGGAGGACG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GCAACATCCT GGGGCACAAG CTGGAGTACA ACTACAACAG CCACAACGTC TATATCATGG CCGACAAGCA GAAGAACGGC ATCAAGGTGA ACTTCAAGAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCGCCACAAC ATCGAGGACG GCAGCGTGCA GCTCGCCGAC CACTACCAGC AGAACACCCC CATCGGCGAC GGCCCCGTGC TGCTGCCCGA CAACCACTAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CTGAGCACCC AGTCCGCCCT GAGCAAAGAC CCCAACGAGA AGCGCGATCA CATGGTCCTG CTGGAGTTCG TGACCGCCGC CGGGATCACT CTCGGCATGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ACGAGCTGTA CAAGTCCGGA CTCAGATCTC GAGCTCAAGC TTCGAATTCT GCAGTCGACG GTACCGCGGG CCCGGGATCC CTGCAGCTCG AGAGGCCTAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TTAATTAAGT CGACGATCCG GCTGCTAACA AAGCCCGAAA GGAAGCTGAG TTGGCTGCTG CCACCGCTGA GCAATAACTA GCATAACCCC TTGGGGCCTC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TAAACGGGTC TTGAGGGGTT TTTTG
^2801      ^2811      ^2821

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pE1(245-858) 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 atgGTGAGCA AGGGCGAGGA GCTGTTCACC GGGGTGCCCA TCCTGGTCGA GCTGGACGGC GACGTAAACG GCCACAAGTT CAGCGTGTCC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GGCGAGGGCG AGGGCGATGC CACCTACGGC AAGCTGACCC TGAAGTTCAT CTGCACCACC GGCAAGCTGC CCGTGCCCTG GCCCACCCTC GTGACCACCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGACCTACGG CGTGCAGTGC TTCAGCCGCT ACCCCGACCA CATGAAGCAG CACGACTTCT TCAAGTCCGC CATGCCCGAA GGCTACGTCC AGGAGCGCAC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CATCTTCTTC AAGGACGACG GCAACTACAA GACCCGCGCC GAGGTGAAGT TCGAGGGCGA CACCCTGGTG AACCGCATCG AGCTGAAGGG CATCGACTTC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAGGAGGACG GCAACATCCT GGGGCACAAG CTGGAGTACA ACTACAACAG CCACAACGTC TATATCATGG CCGACAAGCA GAAGAACGGC ATCAAGGTGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ACTTCAAGAT CCGCCACAAC ATCGAGGACG GCAGCGTGCA GCTCGCCGAC CACTACCAGC AGAACACCCC CATCGGCGAC GGCCCCGTGC TGCTGCCCGA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CAACCACTAC CTGAGCACCC AGTCCGCCCT GAGCAAAGAC CCCAACGAGA AGCGCGATCA CATGGTCCTG CTGGAGTTCG TGACCGCCGC CGGGATCACT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CTCGGCATGG ACGAGCTGTA CAAGTCCGGA CTCAGATCTC GAGCTCAAGC TTCGAATTCT GCAGTCGACG GTACCGCGGG CCCGGGATCC CTGCAGCTCG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGAGGCCTAA TTAATTAAGT CGACGATCCG GCTGCTAACA AAGCCCGAAA GGAAGCTGAG TTGGCTGCTG CCACCGCTGA GCAATAACTA GCATAACCCC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTGGGGCCTC TAAACGGGTC TTGAGGGGTT TTTTGCTGAA AGGAGGAACT ATATCCGGAT CGAGATCAAT TCTGTGAGCG TATGGCAAAC GAAGGAAAAA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TAGTTATAGT AGCCGCACTC GATGGGACAT TTCAACGTAA ACCGTTTAAT AATATTTTGA ATCTTATTCC ATTATCTGAA ATGGTGGTAA AACTAACTGC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TGTGTGTATG AAATGCTTTA AGGAGGCTTC CTTTTCTAAA CGATTGGGTG AGGAAACCGA GATAGAAATA ATAGGAGGTA ATGATATGTA TCAATCGGTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TGTAGAAAGT GTTACATCGA CTCATAATAT TATATTTTTT ATCTAAAAAA CTAAAAATAA ACATTGCTTA AATTTTAATA TAATACTTAA AAATGGATGT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TGTGTCGTTA GATAAACCGT TTATGTATTT TGAGGAAATT GATAATGAGT TAGATTACGA ACCAGAAAGT GCAAATGAGG TCGCAAAAAA ACTGCCGTAT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CAAGGACAGT TAAAACTATT ACTAGGAGAA TTATTTTTTC TTAGTAAGTT ACAGCGACAC GGTATATTAG ATGGTGCCAC CGTAGTGTAT ATAGGATCTG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CTCCCGGTAC ACATATACGT TATTTGAGAG ATCATTTCTA TAATTTAGGA GTGATCATCA AATGGATGCT AATTGACGGC CGCCATCATG ATCCTATTTT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AAATGGATTG CGTGATGTGA CTCTAGTGAC TCGGTTCGTT GATGAGGAAT ATCTACGATC CATCAAAAAA CAACTGCATC CTTCTAAGAT TATTTTAATT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TCTGATGTGA GATCCAAACG AGGAGGAAAT GAACCTAGTA CGGCGGATTT ACTAAGTAAT TACGCTCTAC AAAATGTCAT GATTAGTATT TTAAACCCCG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TGGCGTCTAG TCTTAAATGG AGATGCCCGT TTCCAGATCA ATGGATCAAG GACTTTTATA TCCCACACGG TAATAAAATG TTACAACCTT TTGCTCCTTC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATATTCAGGG CCGTCGTTTT ACAACGTCGT GACTGGGAAA ACCCTGGCGT TACCCAACTT AATCGCCTTG CAGCACATCC CCCTTTCGCC AGCTGGCGTA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ATAGCGAAGA GGCCCGCACC GATCGCCCTT CCCAACAGTT GCGCAGCCTG AATGGCGAAT GGCGCGACGC GCCCTGTAGC GGCGCATTAA GCGCGGCGGG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TGTGGTGGTT ACGCGCAGCG TGACCGCTAC ACTTGCCAGC GCCCTAGCGC CCGCTCCTTT CGCTTTCTTC CCTTCCTTTC TCGCCACGTT CGCCGGCTTT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CCCCGTCAAG CTCTAAATCG GGGGCTCCCT TTAGGGTTCC GATTTAGTGC TTTACGGCAC CTCGACCCCA AAAAACTTGA TTAGGGTGAT GGTTCACGTA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GTGGGCCATC GCCCTGATAG ACGGTTTTTC GCCCTTTGAC GTTGGAGTCC ACGTTCTTTA ATAGTGGACT CTTGTTCCAA ACTGGAACAA CACTCAACCC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TATCTCGGTC TATTCTTTTG ATTTATAAGG GATTTTGCCG ATTTCGGCCT ATTGGTTAAA AAATGAGCTG ATTTAACAAA AATTTAACGC GAATTTTAAC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

AAAATATTAA CGTTTACAAT TTCCCAGGTG GCACTTTTCG GGGAAATGTG CGCGGAACCC CTATTTGTTT ATTTTTCTAA ATACATTCAA ATATGTATCC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GCTCATGAGA CAATAACCCT GATAAATGCT TCAATAATAT TGAAAAAGGA AGAGTATGAG TATTCAACAT TTCCGTGTCG CCCTTATTCC CTTTTTTGCG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GCATTTTGCC TTCCTCTTTT TGCTCACCCA GAAAGCGTGG TGAAAGTAAA AGATGCTGAA GATCAGTTGG GTGCACGAGT GGGTTACATC GAACTGGATC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TCAACAGCGG TAAGATCCTT GAGAGTTTTC GCCCCGAAGA ACGTTTTCCA ATGATGAGCA CTTTTAAAGT TCTGCTATGT GGCGCGGTAT TATCCCGTAT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TGACGCCGGG CAAGAGCAAC TCGGTCGCCG CATACACTAT TCTCAGAATG ACTTGGTTGA GTACTCACCA GTCACAGAAA AGCATCTTAC GGATGGCATG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ACAGTAAGAG AATTATGCAG TGCTGCCATA ACCATGAGTG ATAACACTGC GGCCAACTTA CTTCTGACAA CGATCGGAGG ACCGAAGGAG CTAACCGCTT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TTTTGCACAA CATGGGGGAT CATCTAACTC GCCTTGATCG TTGGGAACCG GAGCTGAATG AAGCCATACC AAACGACGAG CGTGACACCA CGATGCCTGT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AGCAATGGCA ACAACGTTGC GCAAACTATT AACTGGCGAA CTACTTACTC TAGCTTCCCG GCAACAATTA ATAGACTGGA TGGAGGCGGA TAAAGTTGCA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GGACCACTTC TGCGCTCGGC CCTTCCGGCT GGCTGGTTTA TTGCTGATAA ATCTGGAGCC GGTGAGCGTG GGTCTCGCGG TATCATTGCA GCACTGGGGC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CAGATGGTAA GCCCTCCCGT ATCGTAGTTA TCTACACGAC GGGGAGTCAG GCAACTATGG ATGAACGAAA TAGACAGATC GCTGAGATAG GTGCCTCACT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

GATTAAGCAT TGGTAACTGT CAGACCAAGT TTACTCATAT ATACTTTAGA TTGATTTAAA ACTTCATTTT TAATTTAAAA GGATCTAGGT GAAGATCCTT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TTTGATAATC TCATGACCAA AATCCCTTAA CGTGAGTTTT CGTTCCACTG AGCGTCAGAC CCCGTAGAAA AGATCAAAGG ATCTTCTTGA GATCCTTTTT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

TTCTGCGCGT AATCTGCTGC TTGCAAACAA AAAAACCACC GCTACCAGCG GTGGTTTGTT TGCCGGATCA AGAGCTACCA ACTCTTTTTC CGAAGGTAAC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TGGCTTCAGC AGAGCGCAGA TACCAAATAC TGTCCTTCTA GTGTAGCCGT AGTTAGGCCA CCACTTCAAG AACTCTGTAG CACCGCCTAC ATACCTCGCT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CTGCTAATCC TGTTACCAGT GGCTGCTGCC AGTGGCGATA AGTCGTGTCT TACCGGGTTG GACTCAAGAC GATAGTTACC GGATAAGGCG CAGCGGTCGG 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GCTGAACGGG GGGTTCGTGC ACACAGCCCA GCTTGGAGCG AACGACCTAC ACCGAACTGA GATACCTACA GCGTGAGCTA TGAGAAAGCG CCACGCTTCC 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

CGAAGGGAGA AAGGCGGACA GGTATCCGGT AAGCGGCAGG GTCGGAACAG GAGAGCGCAC GAGGGAGCTT CCAGGGGGAA ACGCCTGGTA TCTTTATAGT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

CCTGTCGGGT TTCGCCACCT CTGACTTGAG CGTCGATTTT TGTGATGCTC GTCAGGGGGG CGGAGCCTAT GGAAAAACGC CAGCAACGCG GCCTTTTTAC 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

GGTTCCTGGC CTTTTGCTGG CCTTTTGCTC ACATGTTCTT TCCTGCGTTA TCCCCTGATT CTGTGGATAA CCGTATTACC GCCTTTGAGT GAGCTGATAC 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CGCTCGCCGC AGCCGAACGA CCGAGCGCAG CGAGTCAGTG AGCGAGGAAG CGGAAGAGCG CCCAATACGC AAACCGCCTC TCCCCGCGCG TTGGCCGATT 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

CATTAATGCA GCTGGCACGA CAGGTTTCCC GACTGGAAAG CGGGCAGTGA GCGCAACGCA ATTAATGTGA GTTAGCTCAC TCATTAGGCA CCCCAGGCTT 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

TACACTTTAT GCTTCCGGCT CGTATGTTGT GTGGAATTGT GAGCGGATAA CAATTTCACA CAGGAAACAG CTATGACCAT GATTACGCC
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381

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:
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: `2`	Last change: `2007-04-11 00:00:00`
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 inefficiently initiated from 4th AUG codon encoded by ERAV IRES

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):

1901-2704

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 1-961, 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.

Plasmid constructs lacking a MCS between the cloned ERAV IRES and GFP ORF were described in Fig. 7A.
Results shown in Fig. 7C demonstrate that not all GFP protein fusion variants could be detected in
certain truncations of putative ERAV IRES. In this particular case, no Lab-GFP nor Lb-GFP was detected.
Authors claim the GFP corresponds in size to the one initiated in wild-type from AUG2, although chance
to distinguish from the polypeptide initiated at AUG1 which is longer by one aminoacid residue on 12%
PAA gel is questionable. It seems sequences downstream the second pair of AUG codons (not present in this
construct) are required to allow use of AUG codons 3 and 4.

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: `1`	Last change: `2007-04-04 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `ERAV_245-858`	The functional status of IRES: `defective`

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

1290-1903

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: `629`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-611`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `2`

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 gatg
^1890      ^1900

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 356

Version: `1`	Last change: `2007-04-04 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens BHK-21 (ATCC CCL-10)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

18.000

Name of IRES used as the positive control:

ERAV_245-961

Name of the plasmid used as the positive control. `pE1(245-961)`	Name of the plasmid used as the negative control. `pT7CG`
`IRESite Id` of the plasmid used as positive control. `272`	`IRESite Id` of the plasmid used as negative control. `270`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `21.000`
The size (length) of intercistronic region in the positive control: `626`	The size (length) of intercistronic region in the negative control: `22`

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:

BHK-21 cells were infected by recombinant vaccinia virus that expresses T7 polymerase (vTF7-3). Data from Fig.
7B.

Citations:

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