IRESite_Id:274 characteristics of ERAV_434-961 IRES studied in pE1(434-961) plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `274`	Version: `6`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-04 22:02:12`

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 truncated putative ERAV IRES is located in the intercistronic region.

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 tatagcgcca 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ggtaaccgga cagcggcgtg ctggattttc ccggtgccat tgctctggat ggtgtcacca agctgacaaa tgcggagtga acctcacaaa gcgacacgcc 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

tgtggtagcg ctgcccaaaa gggagcggaa ctcccccgcc gcgaggcggt cctctctggc caaaagccca gcgttgatag cgccttttgg gatgcaggaa 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ccccacctgc caggtgtgaa gtggagtgag cggatctcca atttggtctg ttctgaacta caccatttac tgctgtgaag aatgccctgg aggcaagctg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

gttacagccc tgaccaggcc ctgcccgtga ctctcgaccg gcgcagggtc aaaaattgtc taagcagcag caggaacgcg ggagcgtttc ttttcctttt 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

gtactgacat gatggcggcg tctaaggtgt atagagtttg cgagcagact ctgctggcag gtgccgttcg catgatggac aaattcttgc aaaagagaac 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

tgtttttgtc ccccaACCGG TCGCCACCAT GGTGAGCAAG GGCGAGGAGC TGTTCACCGG GGTGCCCATC CTGGTCGAGC TGGACGGCGA CGTAAACGGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CACAAGTTCA GCGTGTCCGG CGAGGGCGAG GGCGATGCCA CCTACGGCAA GCTGACCCTG AAGTTCATCT GCACCACCGG CAAGCTGCCC GTGCCCTGGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCACCCTCGT GACCACCCTG ACCTACGGCG TGCAGTGCTT CAGCCGCTAC CCCGACCACA TGAAGCAGCA CGACTTCTTC AAGTCCGCCA TGCCCGAAGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTACGTCCAG GAGCGCACCA TCTTCTTCAA GGACGACGGC AACTACAAGA CCCGCGCCGA GGTGAAGTTC GAGGGCGACA CCCTGGTGAA CCGCATCGAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTGAAGGGCA TCGACTTCAA GGAGGACGGC AACATCCTGG GGCACAAGCT GGAGTACAAC TACAACAGCC ACAACGTCTA TATCATGGCC GACAAGCAGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AGAACGGCAT CAAGGTGAAC TTCAAGATCC GCCACAACAT CGAGGACGGC AGCGTGCAGC TCGCCGACCA CTACCAGCAG AACACCCCCA TCGGCGACGG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCCCGTGCTG CTGCCCGACA ACCACTACCT GAGCACCCAG TCCGCCCTGA GCAAAGACCC CAACGAGAAG CGCGATCACA TGGTCCTGCT GGAGTTCGTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACCGCCGCCG GGATCACTCT CGGCATGGAC GAGCTGTACA AGTCCGGACT CAGATCTCGA GCTCAAGCTT CGAATTCTGC AGTCGACGGT ACCGCGGGCC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGGGATCCCT GCAGCTCGAG AGGCCTAATT AATTAAGTCG ACGATCCGGC TGCTAACAAA GCCCGAAAGG AAGCTGAGTT GGCTGCTGCC ACCGCTGAGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AATAACTAGC ATAACCCCTT GGGGCCTCTA AACGGGTCTT GAGGGGTTTT TTG
^2701      ^2711      ^2721      ^2731      ^2741      ^2751

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pE1(434-961) 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      

tatagcgcca ggtaaccgga cagcggcgtg ctggattttc ccggtgccat tgctctggat ggtgtcacca agctgacaaa tgcggagtga acctcacaaa 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

gcgacacgcc tgtggtagcg ctgcccaaaa gggagcggaa ctcccccgcc gcgaggcggt cctctctggc caaaagccca gcgttgatag cgccttttgg 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gatgcaggaa ccccacctgc caggtgtgaa gtggagtgag cggatctcca atttggtctg ttctgaacta caccatttac tgctgtgaag aatgccctgg 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

aggcaagctg gttacagccc tgaccaggcc ctgcccgtga ctctcgaccg gcgcagggtc aaaaattgtc taagcagcag caggaacgcg ggagcgtttc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ttttcctttt gtactgacat gatggcggcg tctaaggtgt atagagtttg cgagcagact ctgctggcag gtgccgttcg catgatggac aaattcttgc 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

aaaagagaac tgtttttgtc ccccaACCGG TCGCCACCAT GGTGAGCAAG GGCGAGGAGC TGTTCACCGG GGTGCCCATC CTGGTCGAGC TGGACGGCGA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CGTAAACGGC CACAAGTTCA GCGTGTCCGG CGAGGGCGAG GGCGATGCCA CCTACGGCAA GCTGACCCTG AAGTTCATCT GCACCACCGG CAAGCTGCCC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GTGCCCTGGC CCACCCTCGT GACCACCCTG ACCTACGGCG TGCAGTGCTT CAGCCGCTAC CCCGACCACA TGAAGCAGCA CGACTTCTTC AAGTCCGCCA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGCCCGAAGG CTACGTCCAG GAGCGCACCA TCTTCTTCAA GGACGACGGC AACTACAAGA CCCGCGCCGA GGTGAAGTTC GAGGGCGACA CCCTGGTGAA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CCGCATCGAG CTGAAGGGCA TCGACTTCAA GGAGGACGGC AACATCCTGG GGCACAAGCT GGAGTACAAC TACAACAGCC ACAACGTCTA TATCATGGCC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GACAAGCAGA AGAACGGCAT CAAGGTGAAC TTCAAGATCC GCCACAACAT CGAGGACGGC AGCGTGCAGC TCGCCGACCA CTACCAGCAG AACACCCCCA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TCGGCGACGG CCCCGTGCTG CTGCCCGACA ACCACTACCT GAGCACCCAG TCCGCCCTGA GCAAAGACCC CAACGAGAAG CGCGATCACA TGGTCCTGCT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GGAGTTCGTG ACCGCCGCCG GGATCACTCT CGGCATGGAC GAGCTGTACA AGTCCGGACT CAGATCTCGA GCTCAAGCTT CGAATTCTGC AGTCGACGGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ACCGCGGGCC CGGGATCCCT GCAGCTCGAG AGGCCTAATT AATTAAGTCG ACGATCCGGC TGCTAACAAA GCCCGAAAGG AAGCTGAGTT GGCTGCTGCC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ACCGCTGAGC AATAACTAGC ATAACCCCTT GGGGCCTCTA AACGGGTCTT GAGGGGTTTT TTGCTGAAAG GAGGAACTAT ATCCGGATCG AGATCAATTC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TGTGAGCGTA TGGCAAACGA AGGAAAAATA GTTATAGTAG CCGCACTCGA TGGGACATTT CAACGTAAAC CGTTTAATAA TATTTTGAAT CTTATTCCAT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TATCTGAAAT GGTGGTAAAA CTAACTGCTG TGTGTATGAA ATGCTTTAAG GAGGCTTCCT TTTCTAAACG ATTGGGTGAG GAAACCGAGA TAGAAATAAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AGGAGGTAAT GATATGTATC AATCGGTGTG TAGAAAGTGT TACATCGACT CATAATATTA TATTTTTTAT CTAAAAAACT AAAAATAAAC ATTGCTTAAA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TTTTAATATA ATACTTAAAA ATGGATGTTG TGTCGTTAGA TAAACCGTTT ATGTATTTTG AGGAAATTGA TAATGAGTTA GATTACGAAC CAGAAAGTGC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AAATGAGGTC GCAAAAAAAC TGCCGTATCA AGGACAGTTA AAACTATTAC TAGGAGAATT ATTTTTTCTT AGTAAGTTAC AGCGACACGG TATATTAGAT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GGTGCCACCG TAGTGTATAT AGGATCTGCT CCCGGTACAC ATATACGTTA TTTGAGAGAT CATTTCTATA ATTTAGGAGT GATCATCAAA TGGATGCTAA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TTGACGGCCG CCATCATGAT CCTATTTTAA ATGGATTGCG TGATGTGACT CTAGTGACTC GGTTCGTTGA TGAGGAATAT CTACGATCCA TCAAAAAACA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ACTGCATCCT TCTAAGATTA TTTTAATTTC TGATGTGAGA TCCAAACGAG GAGGAAATGA ACCTAGTACG GCGGATTTAC TAAGTAATTA CGCTCTACAA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AATGTCATGA TTAGTATTTT AAACCCCGTG GCGTCTAGTC TTAAATGGAG ATGCCCGTTT CCAGATCAAT GGATCAAGGA CTTTTATATC CCACACGGTA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ATAAAATGTT ACAACCTTTT GCTCCTTCAT ATTCAGGGCC GTCGTTTTAC AACGTCGTGA CTGGGAAAAC CCTGGCGTTA CCCAACTTAA TCGCCTTGCA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GCACATCCCC CTTTCGCCAG CTGGCGTAAT AGCGAAGAGG CCCGCACCGA TCGCCCTTCC CAACAGTTGC GCAGCCTGAA TGGCGAATGG CGCGACGCGC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

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

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

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

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

TTAACAAAAA TTTAACGCGA ATTTTAACAA AATATTAACG TTTACAATTT CCCAGGTGGC ACTTTTCGGG GAAATGTGCG CGGAACCCCT ATTTGTTTAT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TTTTCTAAAT ACATTCAAAT ATGTATCCGC TCATGAGACA ATAACCCTGA TAAATGCTTC AATAATATTG AAAAAGGAAG AGTATGAGTA TTCAACATTT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CCGTGTCGCC CTTATTCCCT TTTTTGCGGC ATTTTGCCTT CCTCTTTTTG CTCACCCAGA AAGCGTGGTG AAAGTAAAAG ATGCTGAAGA TCAGTTGGGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GCACGAGTGG GTTACATCGA ACTGGATCTC AACAGCGGTA AGATCCTTGA GAGTTTTCGC CCCGAAGAAC GTTTTCCAAT GATGAGCACT TTTAAAGTTC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TGCTATGTGG CGCGGTATTA TCCCGTATTG ACGCCGGGCA AGAGCAACTC GGTCGCCGCA TACACTATTC TCAGAATGAC TTGGTTGAGT ACTCACCAGT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CACAGAAAAG CATCTTACGG ATGGCATGAC AGTAAGAGAA TTATGCAGTG CTGCCATAAC CATGAGTGAT AACACTGCGG CCAACTTACT TCTGACAACG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ATCGGAGGAC CGAAGGAGCT AACCGCTTTT TTGCACAACA TGGGGGATCA TCTAACTCGC CTTGATCGTT GGGAACCGGA GCTGAATGAA GCCATACCAA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ACGACGAGCG TGACACCACG ATGCCTGTAG CAATGGCAAC AACGTTGCGC AAACTATTAA CTGGCGAACT ACTTACTCTA GCTTCCCGGC AACAATTAAT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AGACTGGATG GAGGCGGATA AAGTTGCAGG ACCACTTCTG CGCTCGGCCC TTCCGGCTGG CTGGTTTATT GCTGATAAAT CTGGAGCCGG TGAGCGTGGG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

TCTCGCGGTA TCATTGCAGC ACTGGGGCCA GATGGTAAGC CCTCCCGTAT CGTAGTTATC TACACGACGG GGAGTCAGGC AACTATGGAT GAACGAAATA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GACAGATCGC TGAGATAGGT GCCTCACTGA TTAAGCATTG GTAACTGTCA GACCAAGTTT ACTCATATAT ACTTTAGATT GATTTAAAAC TTCATTTTTA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

ATTTAAAAGG ATCTAGGTGA AGATCCTTTT TGATAATCTC ATGACCAAAA TCCCTTAACG TGAGTTTTCG TTCCACTGAG CGTCAGACCC CGTAGAAAAG 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

ATCAAAGGAT CTTCTTGAGA TCCTTTTTTT CTGCGCGTAA TCTGCTGCTT GCAAACAAAA AAACCACCGC TACCAGCGGT GGTTTGTTTG CCGGATCAAG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AGCTACCAAC TCTTTTTCCG AAGGTAACTG GCTTCAGCAG AGCGCAGATA CCAAATACTG TCCTTCTAGT GTAGCCGTAG TTAGGCCACC ACTTCAAGAA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CTCTGTAGCA CCGCCTACAT ACCTCGCTCT GCTAATCCTG TTACCAGTGG CTGCTGCCAG TGGCGATAAG TCGTGTCTTA CCGGGTTGGA CTCAAGACGA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

TAGTTACCGG ATAAGGCGCA GCGGTCGGGC TGAACGGGGG GTTCGTGCAC ACAGCCCAGC TTGGAGCGAA CGACCTACAC CGAACTGAGA TACCTACAGC 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GTGAGCTATG AGAAAGCGCC ACGCTTCCCG AAGGGAGAAA GGCGGACAGG TATCCGGTAA GCGGCAGGGT CGGAACAGGA GAGCGCACGA GGGAGCTTCC 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

AGGGGGAAAC GCCTGGTATC TTTATAGTCC TGTCGGGTTT CGCCACCTCT GACTTGAGCG TCGATTTTTG TGATGCTCGT CAGGGGGGCG GAGCCTATGG 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

AAAAACGCCA GCAACGCGGC CTTTTTACGG TTCCTGGCCT TTTGCTGGCC TTTTGCTCAC ATGTTCTTTC CTGCGTTATC CCCTGATTCT GTGGATAACC 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

GTATTACCGC CTTTGAGTGA GCTGATACCG CTCGCCGCAG CCGAACGACC GAGCGCAGCG AGTCAGTGAG CGAGGAAGCG GAAGAGCGCC CAATACGCAA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

ACCGCCTCTC CCCGCGCGTT GGCCGATTCA TTAATGCAGC TGGCACGACA GGTTTCCCGA CTGGAAAGCG GGCAGTGAGC GCAACGCAAT TAATGTGAGT 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TAGCTCACTC ATTAGGCACC CCAGGCTTTA CACTTTATGC TTCCGGCTCG TATGTTGTGT GGAATTGTGA GCGGATAACA ATTTCACACA GGAAACAGCT 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

ATGACCATGA TTACGCC
^7301      ^7311

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

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

6

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `1`	Last change: `2007-04-04 00:00:00`
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: `5`	Last change: `2007-04-11 00:00:00`
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 artificially extended at its N-terminus by some 40 aminoacid residues

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):

1709-2632

ORF

ORF position:

3

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 artificially extended at its N-terminus by some 39 aminoacid residues

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):

1712-2632

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 artificially extended at its N-terminus by some 19 aminoacid residues

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):

1772-2632

ORF

ORF position:

5

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 artificially extended at its N-terminus by some 18 aminoacid residues

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):

1775-2632

ORF

ORF position:

6

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):

1829-2632

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.

Also results shown in Fig. 7C show that when the 3'end of ERAV was deleted the Lab-GFP remained the
only translation product detected. It is not clear which fusion proteins remained when 5'-end of
ERAV IRES was deleted. In particular case IRESite annotation contains all 5 ORF annotated, although some ORF
might not be translated anymore (compared to the wild-types pE1(1-961) and pE1(245-961)).

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: `2`	Last change: `2007-04-04 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `ERAV_434-961`	The functional status of IRES: `defective`

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

1290-1815

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: `541`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-419`	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):

gtatagcgcc aggtaaccgg acagcggcgt gctggatttt cccggtgcca ttgctctgga tggtgtcacc aagctgacaa atgcggagtg aacctcacaa 
^1290      ^1300      ^1310      ^1320      ^1330      ^1340      ^1350      ^1360      ^1370      ^1380      

agcgacacgc ctgtggtagc gctgcccaaa agggagcgga actcccccgc cgcgaggcgg tcctctctgg ccaaaagccc agcgttgata gcgccttttg 
^1390      ^1400      ^1410      ^1420      ^1430      ^1440      ^1450      ^1460      ^1470      ^1480      

ggatgcagga accccacctg ccaggtgtga agtggagtga gcggatctcc aatttggtct gttctgaact acaccattta ctgctgtgaa gaatgccctg 
^1490      ^1500      ^1510      ^1520      ^1530      ^1540      ^1550      ^1560      ^1570      ^1580      

gaggcaagct ggttacagcc ctgaccaggc cctgcccgtg actctcgacc ggcgcagggt caaaaattgt ctaagcagca gcaggaacgc gggagcgttt 
^1590      ^1600      ^1610      ^1620      ^1630      ^1640      ^1650      ^1660      ^1670      ^1680      

cttttccttt tgtactgaca tgatggcggc gtctaaggtg tatagagttt gcgagcagac tctgctggca ggtgccgttc gcatgatgga caaattcttg 
^1690      ^1700      ^1710      ^1720      ^1730      ^1740      ^1750      ^1760      ^1770      ^1780      

caaaagagaa ctgtttttgt ccccca
^1790      ^1800      ^1810

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 352

Version: `2`	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:

14.000

Name of IRES used as the positive control:

ERAV_1-961

Name of the plasmid used as the positive control. `pE1(1-961)`	Name of the plasmid used as the negative control. `pT7CG`
`IRESite Id` of the plasmid used as positive control. `271`	`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: `868`	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.
3B.

Citations:

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