IRESite_Id:210 characteristics of CVB3 IRES studied in pRSTF-CVB3 plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `210`	Version: `8`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-01-23 00:00:00`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
hopefully_full-length_mRNA

The mRNA/+RNA description:

In vitro T7 transcript containing renilla_luciferase - hairpin_from_multiple_cloning_site -
CVB3_nt1-750 - 45_nt_of_FMDV_2A_protease - firefly_luciferase and terminated at XbaI site immediately after
the STOP codon. A fusion protein CVB3+FMDV+Fluc should be translated from the second cistron (N-terminal 31
additional aminoacids fused to FLuc).

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

GGctagccac catGacttcg aaagtttatg atccagaaca aaggaaacgg atgataactg gtccgcagtg gtgggccaga tgtaaacaaa tgaatgttct 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tgattcattt attaattatt atgattcaga aaaacatgca gaaaatgctg ttattttttt acatggtaac gcggcctctt cttatttatg gcgacatgtt 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

gtgccacata ttgagccagt agcgcggtgt attataccag accttattgg tatgggcaaa tcaggcaaat ctggtaatgg ttcttatagg ttacttgatc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

attacaaata tcttactgca tggtttgaac ttcttaattt accaaagaag atcatttttg tcggccatga ttggggtgct tgtttggcat ttcattatag 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ctatgagcat caagataaga tcaaagcaat agttcacgct gaaagtgtag tagatgtgat tgaatcatgg gatgaatggc ctgatattga agaagatatt 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

gcgttgatca aatctgaaga aggagaaaaa atggttttgg agaataactt cttcgtggaa accatgttgc catcaaaaat catgagaaag ttagaaccag 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

aagaatttgc agcatatctt gaaccattca aagagaaagg tgaagttcgt cgtccaacat tatcatggcc tcgtgaaatc ccgttagtaa aaggtggtaa 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

acctgacgtt gtacaaattg ttaggaatta taatgcttat ctacgtgcaa gtgatgattt accaaaaatg tttattgaat cggacccagg attcttttcc 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

aatgctattg ttgaaggtgc caagaagttt cctaatactg aatttgtcaa agtaaaaggt cttcattttt cgcaagaaga tgcacctgat gaaatgggaa 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

aatatatcaa atcgttcgtt gagcgagttc tcaaaaatga acaaatGTCG Acctaggctt ttgcaaaAAG CTTctcgagg cgaggtggcg accgcgcatg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

cgcggtcgcc acctcgcctc gagAAGCTTA Attaaaacag cctgtgggtt gatcccaccc acagggccca ttgggcgcta gcactctggt atcacggtac 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ctttgtgcgc ctgttttata ccccctcccc caactgtaac ttagaagtaa cacacaccga tcaacagtca gcgtggcaca ccagccacgt tttgatcaag 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

cacttctgtt accccggact gagtatcaat agactgctca cgcggttgaa ggagaaagcg ttcgttatcc ggccaactac ttcgaaaaac ctagtaacac 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

cgtggaagtt gcagagtgtt tcgctcagca ctaccccagt gtagatcagg tcgatgagtc accgcattcc ccacgggcga ccgtggcggt ggctgcgttg 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

gcggcctgcc catggggaaa cccatgggac gctctaatac agacatggtg cgaagagtct attgagctag ttggtagtcc tccggcccct gaatgcggct 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

aatcctaact gcggagcaca caccctcaag ccagagggca gtgtgtcgta acgggcaact ctgcagcgga accgactact ttgggtgtcc gtgtttcatt 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ttattcctat actggctgct tatggtgaca attgagagat tgttaccata tagctattgg attggccatc cggtgaccaa tagagctatt atatatctct 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ttgttgggtt tataccactt agcttgaaag aggttaaaac attacaattc attgttaagt tgaatacagc aaaatgggaG CGGCCGCaaa ttttgacctt 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ctcaagttgg cgggagacgt cgagtccaac cctGGGCCCc taggagatct agcgctGgat cGATCCATGG aagacgccaa aaacataaag aaaggcccgg 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

cgccattcta tccgctggaa gatggaaccg ctggagagca actgcataag gctatgaaga gatacgccct ggttcctgga acaattgctt ttacagatgc 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

acatatcgag gtggacatca cttacgctga gtacttcgaa atgtccgttc ggttggcaga agctatgaaa cgatatgggc tgaatacaaa tcacagaatc 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gtcgtatgca gtgaaaactc tcttcaattc tttatgccgg tgttgggcgc gttatttatc ggagttgcag ttgcgcccgc gaacgacatt tataatgaac 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

gtgaattgct caacagtatg ggcatttcgc agcctaccgt ggtgttcgtt tccaaaaagg ggttgcaaaa aattttgaac gtgcaaaaaa agctcccaat 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

catccaaaaa attattatca tggattctaa aacggattac cagggatttc agtcgatgta cacgttcgtc acatctcatc tacctcccgg ttttaatgaa 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

tacgattttg tgccagagtc cttcgatagg gacaagacaa ttgcactgat catgaactcc tctggatcta ctggtctgcc taaaggtgtc gctctgcctc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

atagaactgc ctgcgtgaga ttctcgcatg ccagagatcc tatttttggc aatcaaatca ttccggatac tgcgatttta agtgttgttc cattccatca 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

cggttttgga atgtttacta cactcggata tttgatatgt ggatttcgag tcgtcttaat gtatagattt gaagaagagc tgtttctgag gagccttcag 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

gattacaaga ttcaaagtgc gctgctggtg ccaaccctat tctccttctt cgccaaaagc actctgattg acaaatacga tttatctaat ttacacgaaa 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ttgcttctgg tggcgctccc ctctctaagg aagtcgggga agcggttgcc aagaggttcc atctgccagg tatcaggcaa ggatatgggc tcactgagac 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tacatcagct attctgatta cacccgaggg ggatgataaa ccgggcgcgg tcggtaaagt tgttccattt tttgaagcga aggttgtgga tctggatacc 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

gggaaaacgc tgggcgttaa tcaaagaggc gaactgtgtg tgagaggtcc tatgattatg tccggttatg taaacaatcc ggaagcgacc aacgccttga 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ttgacaagga tggatggcta cattctggag acatagctta ctgggacgaa gacgaacact tcttcatcgt tgaccgcctg aagtctctga ttaagtacaa 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

aggctatcag gtggctcccg ctgaattgga atccatcttg ctccaacacc ccaacatctt cgacgcaggt gtcgcaggtc ttcccgacga tgacgccggt 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

gaacttcccg ccgccgttgt tgttttggag cacggaaaga cgatgacgga aaaagagatc gtggattacg tcgccagtca agtaacaacc gcgaaaaagt 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

tgcgcggagg agttgtgttt gtggacgaag taccgaaagg tcttaccgga aaactcgacg caagaaaaat cagagagatc ctcataaagg ccaagaaggg 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

cggaaagatc gccgtgtaat T
^3501      ^3511      ^3521

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pRSTF-CVB3 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:
CVB3

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Human coxsackievirus B3

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

agatcgatct gcgcagcacc atggcctgaa ataacctctg aaagaggaac ttggttaggt accttctgag gcggaaagaa ccagctgtgg aatgtgtgtc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

agttagggtg tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa agcatgcatc tcaattagtc agcaaccagg tgtggaaagt ccccaggctc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

cccagcaggc agaagtatgc aaagcatgca tctcaattag tcagcaacca tagtcccgcc cctaactccg cccatcccgc ccctaactcc gcccagttcc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gcccattctc cgccccatgg ctgactaatt ttttttattt atgcagaggc cgaggccgcc tcggcctctg agctattcca gaagtagtga ggaggctttt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ttggaggcct aggcttttgc aaaaagcttg attcttctga cacaacagtc tcgaacttaa gctgcagaag ttggtcgtga ggcactgggc aggtaagtat 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

caaggttaca agacaggttt aaggagacca atagaaactg ggcttgtcga gacagagaag actcttgcgt ttctgatagg cacctattgg tcttactgac 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

atccactttg cctttctctc cacaggtgtc cactcccagt tcaattacag ctcttaaggc tagagtacTT AATACGACTC ACTATAGGct agccaccatG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

acttcgaaag tttatgatcc agaacaaagg aaacggatga taactggtcc gcagtggtgg gccagatgta aacaaatgaa tgttcttgat tcatttatta 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

attattatga ttcagaaaaa catgcagaaa atgctgttat ttttttacat ggtaacgcgg cctcttctta tttatggcga catgttgtgc cacatattga 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

gccagtagcg cggtgtatta taccagacct tattggtatg ggcaaatcag gcaaatctgg taatggttct tataggttac ttgatcatta caaatatctt 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

actgcatggt ttgaacttct taatttacca aagaagatca tttttgtcgg ccatgattgg ggtgcttgtt tggcatttca ttatagctat gagcatcaag 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ataagatcaa agcaatagtt cacgctgaaa gtgtagtaga tgtgattgaa tcatgggatg aatggcctga tattgaagaa gatattgcgt tgatcaaatc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tgaagaagga gaaaaaatgg ttttggagaa taacttcttc gtggaaacca tgttgccatc aaaaatcatg agaaagttag aaccagaaga atttgcagca 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tatcttgaac cattcaaaga gaaaggtgaa gttcgtcgtc caacattatc atggcctcgt gaaatcccgt tagtaaaagg tggtaaacct gacgttgtac 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

aaattgttag gaattataat gcttatctac gtgcaagtga tgatttacca aaaatgttta ttgaatcgga cccaggattc ttttccaatg ctattgttga 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

aggtgccaag aagtttccta atactgaatt tgtcaaagta aaaggtcttc atttttcgca agaagatgca cctgatgaaa tgggaaaata tatcaaatcg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ttcgttgagc gagttctcaa aaatgaacaa atGTCGAcct aggcttttgc aaaAAGCTTc tcgaggcgag gtggcgaccg cgcatgcgcg gtcgccacct 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

cgcctcgagA AGCTTAAtta aaacagcctg tgggttgatc ccacccacag ggcccattgg gcgctagcac tctggtatca cggtaccttt gtgcgcctgt 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

tttatacccc ctcccccaac tgtaacttag aagtaacaca caccgatcaa cagtcagcgt ggcacaccag ccacgttttg atcaagcact tctgttaccc 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

cggactgagt atcaatagac tgctcacgcg gttgaaggag aaagcgttcg ttatccggcc aactacttcg aaaaacctag taacaccgtg gaagttgcag 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

agtgtttcgc tcagcactac cccagtgtag atcaggtcga tgagtcaccg cattccccac gggcgaccgt ggcggtggct gcgttggcgg cctgcccatg 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gggaaaccca tgggacgctc taatacagac atggtgcgaa gagtctattg agctagttgg tagtcctccg gcccctgaat gcggctaatc ctaactgcgg 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

agcacacacc ctcaagccag agggcagtgt gtcgtaacgg gcaactctgc agcggaaccg actactttgg gtgtccgtgt ttcattttat tcctatactg 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gctgcttatg gtgacaattg agagattgtt accatatagc tattggattg gccatccggt gaccaataga gctattatat atctctttgt tgggtttata 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ccacttagct tgaaagaggt taaaacatta caattcattg ttaagttgaa tacagcaaaa tgggaGCGGC CGCaaatttt gaccttctca agttggcggg 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

agacgtcgag tccaaccctG GGCCCctagg agatctagcg ctGgatcGAT CCATGGaaga cgccaaaaac ataaagaaag gcccggcgcc attctatccg 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ctggaagatg gaaccgctgg agagcaactg cataaggcta tgaagagata cgccctggtt cctggaacaa ttgcttttac agatgcacat atcgaggtgg 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

acatcactta cgctgagtac ttcgaaatgt ccgttcggtt ggcagaagct atgaaacgat atgggctgaa tacaaatcac agaatcgtcg tatgcagtga 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

aaactctctt caattcttta tgccggtgtt gggcgcgtta tttatcggag ttgcagttgc gcccgcgaac gacatttata atgaacgtga attgctcaac 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

agtatgggca tttcgcagcc taccgtggtg ttcgtttcca aaaaggggtt gcaaaaaatt ttgaacgtgc aaaaaaagct cccaatcatc caaaaaatta 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ttatcatgga ttctaaaacg gattaccagg gatttcagtc gatgtacacg ttcgtcacat ctcatctacc tcccggtttt aatgaatacg attttgtgcc 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

agagtccttc gatagggaca agacaattgc actgatcatg aactcctctg gatctactgg tctgcctaaa ggtgtcgctc tgcctcatag aactgcctgc 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

gtgagattct cgcatgccag agatcctatt tttggcaatc aaatcattcc ggatactgcg attttaagtg ttgttccatt ccatcacggt tttggaatgt 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ttactacact cggatatttg atatgtggat ttcgagtcgt cttaatgtat agatttgaag aagagctgtt tctgaggagc cttcaggatt acaagattca 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

aagtgcgctg ctggtgccaa ccctattctc cttcttcgcc aaaagcactc tgattgacaa atacgattta tctaatttac acgaaattgc ttctggtggc 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

gctcccctct ctaaggaagt cggggaagcg gttgccaaga ggttccatct gccaggtatc aggcaaggat atgggctcac tgagactaca tcagctattc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

tgattacacc cgagggggat gataaaccgg gcgcggtcgg taaagttgtt ccattttttg aagcgaaggt tgtggatctg gataccggga aaacgctggg 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

cgttaatcaa agaggcgaac tgtgtgtgag aggtcctatg attatgtccg gttatgtaaa caatccggaa gcgaccaacg ccttgattga caaggatgga 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

tggctacatt ctggagacat agcttactgg gacgaagacg aacacttctt catcgttgac cgcctgaagt ctctgattaa gtacaaaggc tatcaggtgg 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ctcccgctga attggaatcc atcttgctcc aacaccccaa catcttcgac gcaggtgtcg caggtcttcc cgacgatgac gccggtgaac ttcccgccgc 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

cgttgttgtt ttggagcacg gaaagacgat gacggaaaaa gagatcgtgg attacgtcgc cagtcaagta acaaccgcga aaaagttgcg cggaggagtt 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

gtgtttgtgg acgaagtacc gaaaggtctt accggaaaac tcgacgcaag aaaaatcaga gagatcctca taaaggccaa gaagggcgga aagatcgccg 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

tgtaatTCTA GAgcggccgg ccgcttcgag cagacatgat aagatacatt gatgagtttg gacaaaccac aactagaatg cagtgaaaaa aatgctttat 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ttgtgaaatt tgtgatgcta ttgctttatt tgtaaccatt ataagctgca ataaacaagt taacaacaac aattgcattc attttatgtt tcaggttcag 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ggggaggtgt gggaggtttt ttaaagcaag taaaacctct acaaatgtgg taaaatcgat aagtttaaac agatccaggt ggcacttttc ggggaaatgt 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

gcgcggaacc cctatttgtt tatttttcta aatacattca aatatgtatc cgctcatgag acaataaccc tgataaatgc ttcaataata ttgaaaaagg 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

aagagtatga gtattcaaca tttccgtgtc gcccttattc ccttttttgc ggcattttgc cttcctgttt ttgctcaccc agaaacgctg gtgaaagtaa 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

aagatgctga agatcagttg ggtgcacgag tgggttacat cgaactggat ctcaacagcg gtaagatcct tgagagtttt cgccccgaag aacgttttcc 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

aatgatgagc acttttaaag ttctgctatg tggcgcggta ttatcccgta ttgacgccgg gcaagagcaa ctcggtcgcc gcatacacta ttctcagaat 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

gacttggttg agtactcacc agtcacagaa aagcatctta cggatggcat gacagtaaga gaattatgca gtgctgccat aaccatgagt gataacactg 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cggccaactt acttctgaca acgatcggag gaccgaagga gctaaccgct tttttgcaca acatggggga tcatgtaact cgccttgatc gttgggaacc 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ggagctgaat gaagccatac caaacgacga gcgtgacacc acgatgcctg tagcaatggc aacaacgttg cgcaaactat taactggcga actacttact 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ctagcttccc ggcaacaatt aatagactgg atggaggcgg ataaagttgc aggaccactt ctgcgctcgg cccttccggc tggctggttt attgctgata 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

aatctggagc cggtgagcgt gggtctcgcg gtatcattgc agcactgggg ccagatggta agccctcccg tatcgtagtt atctacacga cggggagtca 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ggcaactatg gatgaacgaa atagacagat cgctgagata ggtgcctcac tgattaagca ttggtaactg tcagaccaag tttactcata tatactttag 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

attgatttaa aacttcattt ttaatttaaa aggatctagg tgaagatcct ttttgataat ctcatgacca aaatccctta acgtgagttt tcgttccact 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

gagcgtcaga ccccgtagaa aagatcaaag gatcttcttg agatcctttt tttctgcgcg taatctgctg cttgcaaaca aaaaaaccac cgctaccagc 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ggtggtttgt ttgccggatc aagagctacc aactcttttt ccgaaggtaa ctggcttcag cagagcgcag ataccaaata ctgtccttct agtgtagccg 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

tagttaggcc accacttcaa gaactctgta gcaccgccta catacctcgc tctgctaatc ctgttaccag tggctgctgc cagtggcgat aagtcgtgtc 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ttaccgggtt ggactcaaga cgatagttac cggataaggc gcagcggtcg ggctgaacgg ggggttcgtg cacacagccc agcttggagc gaacgaccta 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

caccgaactg agatacctac agcgtgagct atgagaaagc gccacgcttc ccgaagggag aaaggcggac aggtatccgg taagcggcag ggtcggaaca 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ggagagcgca cgagggagct tccaggggga aacgcctggt atctttatag tcctgtcggg tttcgccacc tctgacttga gcgtcgattt ttgtgatgct 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

cgtcaggggg gcggagccta tggaaaaacg ccagcaacgc ggccttttta cggttcctgg ccttttgctg gccttttgct cacatggctc gac
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291

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

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

2

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
RLuc

The description of the protein encoded in this ORF:
Renilla luciferase

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

not tested

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

12-956

ORF

ORF position:

2

Version: `1`	Last change: `2006-07-22 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
FLuc-fusion

The description of the protein encoded in this ORF:
Firefly luciferase to which is fused coding part of CVB3 IRES (atgggaGCGGCCGC) which is followed by FMDV 2A protease fragment aattttgaccttctcaagttggcgggagacgtcgagtccaaccct and additional 34 bases of unknown origin and then finally comes the FLuc ORF.

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

not tested

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

1774-3519

Remarks:

The plasmid with one mismatch encodes complete protease except the very last aminoacid residue fused to the
firefly-luciferase reporter protein. The cleavage protein causes release of the N-terminal
part of the protein while some ribosomes can resume protein synthesis with prolyl-tRNA.

>gi|4007043|emb|AJ007572.1|FMV7572  Foot-and-mouth disease virus, derived from C3Arg85, clone 15
Length=8161

 Score = 81.8 bits (41),  Expect = 1e-13
 Identities = 44/45 (97%), Gaps = 0/45 (0%)
 Strand=Plus/Plus

Query  1     AATTTTGACCTTCTCAAGTTGGCGGGAGACGTCGAGTCCAACCCT  45
             |||||||||||||| ||||||||||||||||||||||||||||||
Sbjct  3881  AATTTTGACCTTCTTAAGTTGGCGGGAGACGTCGAGTCCAACCCT  3925


LOCUS       FMV7572                 8161 bp    RNA     linear   VRL 15-APR-2005
DEFINITION  Foot-and-mouth disease virus, derived from C3Arg85, clone 15.
ACCESSION   AJ007572
VERSION     AJ007572.1  GI:4007043
[...]
FEATURES             Location/Qualifiers
     source          1..8161
                     /organism="Foot-and-mouth disease virus"
                     /virion
                     /mol_type="genomic RNA"
                     /strain="C3Arg85"
                     /isolate="clone 15"
                     /db_xref="taxon:12110"
     source          1..8161
                     /organism="Foot-and-mouth disease virus"
                     /virion
                     /mol_type="genomic RNA"
                     /strain="C3Arg85"
                     /isolate="clone 15"
                     /db_xref="taxon:12110"
     CDS             1082..8068
                     /codon_start=1
                     /product="polyprotein"
                     /protein_id="CAA07561.1"
                     /db_xref="GI:4007044"
[...]
     mat_peptide     3881..3928
                     /product="2A protein"

Citations:

Jang G. M., Leong L. E., Hoang L. T., Wang P. H., Gutman G. A., Semler B. L. (2004) Structurally distinct elements mediate internal ribosome entry within the 5'-noncoding region of a voltage-gated potassium channel mRNA. J. Biol. Chem. 279(46):47419-47430

IRESs:

IRES:

Version: `4`	Last change: `2007-01-23 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `CVB3`	The functional status of IRES: `functional`

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

1032-1781

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `76`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `825`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-742`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `7`

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

ttaaaacagc ctgtgggttg atcccaccca cagggcccat tgggcgctag cactctggta tcacggtacc tttgtgcgcc tgttttatac cccctccccc 
^1032      ^1042      ^1052      ^1062      ^1072      ^1082      ^1092      ^1102      ^1112      ^1122      

aactgtaact tagaagtaac acacaccgat caacagtcag cgtggcacac cagccacgtt ttgatcaagc acttctgtta ccccggactg agtatcaata 
^1132      ^1142      ^1152      ^1162      ^1172      ^1182      ^1192      ^1202      ^1212      ^1222      

gactgctcac gcggttgaag gagaaagcgt tcgttatccg gccaactact tcgaaaaacc tagtaacacc gtggaagttg cagagtgttt cgctcagcac 
^1232      ^1242      ^1252      ^1262      ^1272      ^1282      ^1292      ^1302      ^1312      ^1322      

taccccagtg tagatcaggt cgatgagtca ccgcattccc cacgggcgac cgtggcggtg gctgcgttgg cggcctgccc atggggaaac ccatgggacg 
^1332      ^1342      ^1352      ^1362      ^1372      ^1382      ^1392      ^1402      ^1412      ^1422      

ctctaataca gacatggtgc gaagagtcta ttgagctagt tggtagtcct ccggcccctg aatgcggcta atcctaactg cggagcacac accctcaagc 
^1432      ^1442      ^1452      ^1462      ^1472      ^1482      ^1492      ^1502      ^1512      ^1522      

cagagggcag tgtgtcgtaa cgggcaactc tgcagcggaa ccgactactt tgggtgtccg tgtttcattt tattcctata ctggctgctt atggtgacaa 
^1532      ^1542      ^1552      ^1562      ^1572      ^1582      ^1592      ^1602      ^1612      ^1622      

ttgagagatt gttaccatat agctattgga ttggccatcc ggtgaccaat agagctatta tatatctctt tgttgggttt ataccactta gcttgaaaga 
^1632      ^1642      ^1652      ^1662      ^1672      ^1682      ^1692      ^1702      ^1712      ^1722      

ggttaaaaca ttacaattca ttgttaagtt gaatacagca aaatgggaGC
^1732      ^1742      ^1752      ^1762      ^1772

Citations:

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