IRESite_Id:320 characteristics of FMDV IRES studied in pBIC plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `320`	Version: `2`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2009-04-15 13:38:32`

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:
our_best_guess

The mRNA/+RNA description:

Putative spliced in vivo HSV-TK (thymidine kinase) promoter derived transcript containing CAT and FLuc genes
separated by FMDV IRES

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

AAGCTAAAAT GGAGAAAAAA ATCACTGGAT ATACCACCGT TGATATATCC CAATGGCATC GTAAAGAACA TTTTGAGGCA TTTCAGTCAG TTGCTCAATG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TACCTATAAC CAGACCGTTC AGCTGGATAT TACGGCCTTT TTAAAGACCG TAAAGAAAAA TAAGCACAAG TTTTATCCGG CCTTTATTCA CATTCTTGCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CGCCTGATGA ATGCTCATCC GGAATTCCGT ATGGCAATGA AAGACGGTGA GCTGGTGATA TGGGATAGTG TTCACCCTTG TTACACCGTT TTCCATGAGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AAACTGAAAC GTTTTCATCG CTCTGGAGTG AATACCACGA CGATTTCCGG CAGTTTCTAC ACATATATTC GCAAGATGTG GCGTGTTACG GTGAAAACCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GGCCTATTTC CCTAAAGGGT TTATTGAGAA TATGTTTTTC GTCTCAGCCA ATCCCTGGGT GAGTTTCACC AGTTTTGATT TAAACGTGGC CAATATGGAC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AACTTCTTCG CCCCCGTTTT CACCATGGGC AAATATTATA CGCAAGGCGA CAAGGTGCTG ATGCCGCTGG CGATTCAGGT TCATCATGCC GTCTGTGATG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GCTTCCATGT CGGCAGAATG CTTAATGAAT TACAACAGTA CTGCGATGAG TGGCAGGGCG GGGCGTAATT TTTTTAAGGC AGTTATTGCT GCAGCGACCC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCTTAACAGC GTCAACAGCG TGCCGCagag ctcAGCAGGT TTCCCCAACT GACACAAAAC GTGCAACTTG AAACTCCGCC TGGTCTTTCC AGGTCTAGAG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GGGTAACACT TTGTACTGTG TTTGGCTCCA CGCTCGATCC ACTGGCGAGT GTTAGTAACA GCACTGTTGC TTCGTAGCGG AGCATGACGG CCGTGGGAAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCCTCCTTGG TAACAAGGAC CCACGGGGCC AAAAGCCACG CCCACACGGG CCCGTCATGT GTGCAACCCC AGCACGGCGA CTTTACTGCG AAACCCACTT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TAAAGTGACA TTGAAACTGG TACCCACACA CTGGTGACAG GCTAAGGATG CCCTTCAGGT ACCCCGAGGT AACACGCGAC ACTCGGGATC TGAGAAGGGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACTGGGGCTT CTATAAAAGC GCTCGGTTTA AAAAGCTTCT ACGCCTGAAT AGGTGACCGG AGGTCGGCAC CTTTCCTTTA CAATTAATGA CCCTgagctc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

gagcttgGCA TTCCGGTACT GTTGGTAAAA TGGAAGACGC CAAAAACATA AAGAAAGGCC CGGCGCCATT CTATCCTCTA GAGGATGGAA CCGCTGGAGA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GCAACTGCAT AAGGCTATGA AGAGATACGC CCTGGTTCCT GGAACAATTG CTTTTACAGA TGCACATATC GAGGTGAACA TCACGTACGC GGAATACTTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAAATGTCCG TTCGGTTGGC AGAAGCTATG AAACGATATG GGCTGAATAC AAATCACAGA ATCGTCGTAT GCAGTGAAAA CTCTCTTCAA TTCTTTATGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CGGTGTTGGG CGCGTTATTT ATCGGAGTTG CAGTTGCGCC CGCGAACGAC ATTTATAATG AACGTGAATT GCTCAACAGT ATGAACATTT CGCAGCCTAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CGTAGTGTTT GTTTCCAAAA AGGGGTTGCA AAAAATTTTG AACGTGCAAA AAAAATTACC AATAATCCAG AAAATTATTA TCATGGATTC TAAAACGGAT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TACCAGGGAT TTCAGTCGAT GTACACGTTC GTCACATCTC ATCTACCTCC CGGTTTTAAT GAATACGATT TTGTACCAGA GTCCTTTGAT CGTGACAAAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CAATTGCACT GATAATGAAT TCCTCTGGAT CTACTGGGTT ACCTAAGGGT GTGGCCCTTC CGCATAGAAC TGCCTGCGTC AGATTCTCGC ATGCCAGAGA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TCCTATTTTT GGCAATCAAA TCATTCCGGA TACTGCGATT TTAAGTGTTG TTCCATTCCA TCACGGTTTT GGAATGTTTA CTACACTCGG ATATTTGATA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGTGGATTTC GAGTCGTCTT AATGTATAGA TTTGAAGAAG AGCTGTTTTT ACGATCCCTT CAGGATTACA AAATTCAAAG TGCGTTGCTA GTACCAACCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TATTTTCATT CTTCGCCAAA AGCACTCTGA TTGACAAATA CGATTTATCT AATTTACACG AAATTGCTTC TGGGGGCGCA CCTCTTTCGA AAGAAGTCGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GGAAGCGGTT GCAAAACGCT TCCATCTTCC AGGGATACGA CAAGGATATG GGCTCACTGA GACTACATCA GCTATTCTGA TTACACCCGA GGGGGATGAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAACCGGGCG CGGTCGGTAA AGTTGTTCCA TTTTTTGAAG CGAAGGTTGT GGATCTGGAT ACCGGGAAAA CGCTGGGCGT TAATCAGAGA GGCGAATTAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GTGTCAGAGG ACCTATGATT ATGTCCGGTT ATGTAAACAA TCCGGAAGCG ACCAACGCCT TGATTGACAA GGATGGATGG CTACATTCTG GAGACATAGC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTACTGGGAC GAAGACGAAC ACTTCTTCAT AGTTGACCGC TTGAAGTCTT TAATTAAATA CAAAGGATAT CAGGTGGCCC CCGCTGAATT GGAATCGATA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTGTTACAAC ACCCCAACAT CTTCGACGCG GGCGTGGCAG GTCTTCCCGA CGATGACGCC GGTGAACTTC CCGCCGCCGT TGTTGTTTTG GAGCACGGAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AGACGATGAC GGAAAAAGAG ATCGTGGATT ACGTCGCCAG TCAAGTAACA ACCGCGAAAA AGTTGCGCGG AGGAGTTGTG TTTGTGGACG AAGTACCGAA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AGGTCTTACC GGAAAACTCG ACGCAAGAAA AATCAGAGAG ATCCTCATAA AGGCCAAGAA GGGCGGAAAG TCCAAATTGT AAAATGTAAC TGTATTCAGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GATGACGAAA TTCTTAGCTA TTGTAATgac tctagaggat ctCTTTGTGA AGGAACCTTA CTTCTGTGGT GTGACATAAT TGGACAAACT ACCTACAGAG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ATTTAAAGCT CTAAGATTCC AACCTATGGA ACTGATGAAT GGGAGCAGTG GTGGAATGCC TTTAATGAGG AAAACCTGTT TTGCTCAGAA GAAATGCCAT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CTAGTGATGA TGAGGCTACT GCTGACTCTC AACATTCTAC TCCTCCAAAA AAGAAGAGAA AGGTAGAAGA CCCCAAGGAC TTTCCTTCAG AATTGCTAAG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTTTTTGAGT CATGCTGTGT TTAGTAATAG AACTCTTGCT TGCTTTGCTA TTTACACCAC AAAGGAAAAA GCTGCACTGC TATACAAGAA AATTATGGAA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AAATATTCTG TAACCTTTAT AAGTAGGCAT AACAGTTATA ATCATAACAT ACTGTTTTTT CTTACTCCAC ACAGGCATAG AGTGTCTGCT ATTAATAACT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ATGCTCAAAA ATTGTGTACC TTTAGCTTTT TAATTTGTAA AGGGGTTAAT AAGGAATATT TGATGTATAG TGCCTTGACT AGAGATCATA ATCAGCCATA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CCACATTTGT AGAGGTTTTA CTTGCTTTAA AAAACCTCCC ACACCTCCCC CTGAACCTGA AACATAAAAT GAATGCAATT GTTGTTGTTA ACTTGTTTAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TGCAGCTTAT AATGGTTACA AATAAAGCAA TAGCATCACA AATTTCACAA ATAAAGCATT TTTTTCACTG C
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671

Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_except_both_UTRs

The name of the plasmid:
pBIC The name of the promoter used to express this mRNA:
HSV-TK

Description of the plasmid (facultative for promoter-less plasmid records):
Incomplete pBIC plasmid containing CAT and FLuc genes separated by FMDV IRES under the control of T7 and thymidine kinase promoters

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:
FMDV

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Foot-and-mouth disease virus C-S8c1

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

GGCATCACCG GCGCCACAGG TGCGGTTGCT GGCGCCTATA TCGCCGACAT CACCGATGGG GAAGATCGGG CTCGCCACTT CGGGCTCATG AGCGCTTGTT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TCGGCGTGGG TATGGTGGCA GGCCCCGTGG CCGGGGGACT GTTGGGCGCC ATCTCCTTGC ATGCACCATT CCTTGCGGCG GCGGTGCTCA ACGGCCTCAA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCTACTACTG GGCTGCTTCC TAATGCAGGA GTCGCATAAG GGAGAGCGTC GATATGGTGC ACTCTCAGTA CAATCTGCTC TGATGCCGCA TAGTTAAGCC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGCCCCGACA CCCGCCAACA CCCGCTGACG CGCCCTGACG GGCTTGTCTG CTCCCGGCAT CCGCTTACAG ACAAGCTGTG ACCGTCTCCG GGAGCTGCAT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GTGTCAGAGG TTTTCACCGT CATCACCGAA ACGCGCGAGA CGAAAGGGCC TCGTGATACG CCTATTTTTA TAGGTTAATG TCATGATAAT AATGGTTTCT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TAGACGTCAG GTGGCACTTT TCGGGGAAAT GTGCGCGGAA CCCCTATTTG TTTATTTTTC TAAATACAtt caaatatgta tccgctcatg agacaataac 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

cctgataaat gcttcaataa tattgaaaaa ggaagagtAT GAGTATTCAA CATTTCCGTG TCGCCCTTAT TCCCTTTTTT GCGGCATTTT GCCTTCCTGT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TTTTGCTCAC CCAGAAACGC TGGTGAAAGT AAAAGATGCT GAAGATCAGT TGGGTGCACG AGTGGGTTAC ATCGAACTGG ATCTCAACAG CGGTAAGATC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTTGAGAGTT TTCGCCCCGA AGAACGTTTT CCAATGATGA GCACTTTTAA AGTTCTGCTA TGTGGCGCGG TATTATCCCG TATTGACGCC GGGCAAGAGC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AACTCGGTCG CCGCATACAC TATTCTCAGA ATGACTTGGT TGAGTACTCA CCAGTCACAG AAAAGCATCT TACGGATGGC ATGACAGTAA GAGAATTATG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CAGTGCTGCC ATAACCATGA GTGATAACAC TGCGGCCAAC TTACTTCTGA CAACGATCGG AGGACCGAAG GAGCTAACCG CTTTTTTGCA CAACATGGGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GATCATGTAA CTCGCCTTGA TCGTTGGGAA CCGGAGCTGA ATGAAGCCAT ACCAAACGAC GAGCGTGACA CCACGATGCC TGTAGCAATG GCAACAACGT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGCGCAAACT ATTAACTGGC GAACTACTTA CTCTAGCTTC CCGGCAACAA TTAATAGACT GGATGGAGGC GGATAAAGTT GCAGGACCAC TTCTGCGCTC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGCCCTTCCG GCTGGCTGGT TTATTGCTGA TAAATCTGGA GCCGGTGAGC GTGGGTCTCG CGGTATCATT GCAGCACTGG GGCCAGATGG TAAGCCCTCC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CGTATCGTAG TTATCTACAC GACGGGGAGT CAGGCAACTA TGGATGAACG AAATAGACAG ATCGCTGAGA TAGGTGCCTC ACTGATTAAG CATTGGTAAC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGTCAGACCA AGTTTACTCA TATATACTTT AGATTGATTT AAAACTTCAT TTTTAATTTA AAAGGATCTA GGTGAAGATC CTTTTTGATA ATCTCATGAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CAAAATCCCT TAACGTGAGT TTTCGTTCCA CTGAGCGTCA GACCCCGTAG AAAAGATCAA AGGATCTTCT TGAGATCCTT TTTTTCTGCG CGTAATCTGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGCTTGCAAA CAAAAAAACC ACCGCTACCA GCGGTGGTTT GTTTGCCGGA TCAAGAGCTA CCAACTCTTT TTCCGAAGGT AACTGGCTTC AGCAGAGCGC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGATACCAAA TACTGTCCTT CTAGTGTAGC CGTAGTTAGG CCACCACTTC AAGAACTCTG TAGCACCGCC TACATACCTC GCTCTGCTAA TCCTGTTACC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGTGGCTGCT GCCAGTGGCG ATAAGTCGTG TCTTACCGGG TTGGACTCAA GACGATAGTT ACCGGATAAG GCGCAGCGGT CGGGCTGAAC GGGGGGTTCG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGCACACAGC CCAGCTTGGA GCGAACGACC TACACCGAAC TGAGATACCT ACAGCGTGAG CTATGAGAAA GCGCCACGCT TCCCGAAGGG AGAAAGGCGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACAGGTATCC GGTAAGCGGC AGGGTCGGAA CAGGAGAGCG CACGAGGGAG CTTCCAGGGG GAAACGCCTG GTATCTTTAT AGTCCTGTCG GGTTTCGCCA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCTCTGACTT GAGCGTCGAT TTTTGTGATG CTCGTCAGGG GGGCGGAGCC TATGGAAAAA CGCCAGCAAC GCGGCCTTTT TACGGTTCCT GGCCTTTTGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TGGCCTTTTG CTCACATGTT CTTTCCTGCG TTATCCCCTG ATTCTGTGGA TAACCGTATT ACCGCCTTTG AGTGAGCTGA TACCGCTCGC CGCAGCCGAA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CGACCGAGCG CAGCGAGTCA GTGAGCGAGG AAGCGGAAGA GCGCCCAATA CGCAAACCGC CTCTCCCCGC GCGTTGGCCG ATTCATTAAT GCAGCTGGCT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TATCGAAATT AATACGACTC ACTATAGGGA GACCCAAGCT CGACTCTAGA GGATCCgGCA AACCCCGCCC AGCGTCTTGT CATTGGCGAA TTCGAACACG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CAGATGCAGT CGGGGCGGCG CGGTCCGAGG TCCACTTCGC ATATTAAGGT GACGCGTGTG GCCTCGAACA CCGAGCGACC CTGCAGAAGC TAAAATGGAG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AAAAAAATCA CTGGATATAC CACCGTTGAT ATATCCCAAT GGCATCGTAA AGAACATTTT GAGGCATTTC AGTCAGTTGC TCAATGTACC TATAACCAGA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCGTTCAGCT GGATATTACG GCCTTTTTAA AGACCGTAAA GAAAAATAAG CACAAGTTTT ATCCGGCCTT TATTCACATT CTTGCCCGCC TGATGAATGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TCATCCGGAA TTCCGTATGG CAATGAAAGA CGGTGAGCTG GTGATATGGG ATAGTGTTCA CCCTTGTTAC ACCGTTTTCC ATGAGCAAAC TGAAACGTTT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TCATCGCTCT GGAGTGAATA CCACGACGAT TTCCGGCAGT TTCTACACAT ATATTCGCAA GATGTGGCGT GTTACGGTGA AAACCTGGCC TATTTCCCTA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAGGGTTTAT TGAGAATATG TTTTTCGTCT CAGCCAATCC CTGGGTGAGT TTCACCAGTT TTGATTTAAA CGTGGCCAAT ATGGACAACT TCTTCGCCCC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CGTTTTCACC ATGGGCAAAT ATTATACGCA AGGCGACAAG GTGCTGATGC CGCTGGCGAT TCAGGTTCAT CATGCCGTCT GTGATGGCTT CCATGTCGGC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AGAATGCTTA ATGAATTACA ACAGTACTGC GATGAGTGGC AGGGCGGGGC GTAATTTTTT TAAGGCAGTT ATTGCTGCAG CGACCCGCTT AACAGCGTCA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ACAGCGTGCC GCagagctcA GCAGGTTTCC CCAACTGACA CAAAACGTGC AACTTGAAAC TCCGCCTGGT CTTTCCAGGT CTAGAGGGGT AACACTTTGT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ACTGTGTTTG GCTCCACGCT CGATCCACTG GCGAGTGTTA GTAACAGCAC TGTTGCTTCG TAGCGGAGCA TGACGGCCGT GGGAACTCCT CCTTGGTAAC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AAGGACCCAC GGGGCCAAAA GCCACGCCCA CACGGGCCCG TCATGTGTGC AACCCCAGCA CGGCGACTTT ACTGCGAAAC CCACTTTAAA GTGACATTGA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AACTGGTACC CACACACTGG TGACAGGCTA AGGATGCCCT TCAGGTACCC CGAGGTAACA CGCGACACTC GGGATCTGAG AAGGGGACTG GGGCTTCTAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AAAAGCGCTC GGTTTAAAAA GCTTCTACGC CTGAATAGGT GACCGGAGGT CGGCACCTTT CCTTTACAAT TAATGACCCT gagctcgagc ttgGCATTCC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GGTACTGTTG GTAAAATGGA AGACGCCAAA AACATAAAGA AAGGCCCGGC GCCATTCTAT CCTCTAGAGG ATGGAACCGC TGGAGAGCAA CTGCATAAGG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CTATGAAGAG ATACGCCCTG GTTCCTGGAA CAATTGCTTT TACAGATGCA CATATCGAGG TGAACATCAC GTACGCGGAA TACTTCGAAA TGTCCGTTCG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GTTGGCAGAA GCTATGAAAC GATATGGGCT GAATACAAAT CACAGAATCG TCGTATGCAG TGAAAACTCT CTTCAATTCT TTATGCCGGT GTTGGGCGCG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TTATTTATCG GAGTTGCAGT TGCGCCCGCG AACGACATTT ATAATGAACG TGAATTGCTC AACAGTATGA ACATTTCGCA GCCTACCGTA GTGTTTGTTT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CCAAAAAGGG GTTGCAAAAA ATTTTGAACG TGCAAAAAAA ATTACCAATA ATCCAGAAAA TTATTATCAT GGATTCTAAA ACGGATTACC AGGGATTTCA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GTCGATGTAC ACGTTCGTCA CATCTCATCT ACCTCCCGGT TTTAATGAAT ACGATTTTGT ACCAGAGTCC TTTGATCGTG ACAAAACAAT TGCACTGATA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ATGAATTCCT CTGGATCTAC TGGGTTACCT AAGGGTGTGG CCCTTCCGCA TAGAACTGCC TGCGTCAGAT TCTCGCATGC CAGAGATCCT ATTTTTGGCA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATCAAATCAT TCCGGATACT GCGATTTTAA GTGTTGTTCC ATTCCATCAC GGTTTTGGAA TGTTTACTAC ACTCGGATAT TTGATATGTG GATTTCGAGT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CGTCTTAATG TATAGATTTG AAGAAGAGCT GTTTTTACGA TCCCTTCAGG ATTACAAAAT TCAAAGTGCG TTGCTAGTAC CAACCCTATT TTCATTCTTC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GCCAAAAGCA CTCTGATTGA CAAATACGAT TTATCTAATT TACACGAAAT TGCTTCTGGG GGCGCACCTC TTTCGAAAGA AGTCGGGGAA GCGGTTGCAA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

AACGCTTCCA TCTTCCAGGG ATACGACAAG GATATGGGCT CACTGAGACT ACATCAGCTA TTCTGATTAC ACCCGAGGGG GATGATAAAC CGGGCGCGGT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CGGTAAAGTT GTTCCATTTT TTGAAGCGAA GGTTGTGGAT CTGGATACCG GGAAAACGCT GGGCGTTAAT CAGAGAGGCG AATTATGTGT CAGAGGACCT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ATGATTATGT CCGGTTATGT AAACAATCCG GAAGCGACCA ACGCCTTGAT TGACAAGGAT GGATGGCTAC ATTCTGGAGA CATAGCTTAC TGGGACGAAG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ACGAACACTT CTTCATAGTT GACCGCTTGA AGTCTTTAAT TAAATACAAA GGATATCAGG TGGCCCCCGC TGAATTGGAA TCGATATTGT TACAACACCC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CAACATCTTC GACGCGGGCG TGGCAGGTCT TCCCGACGAT GACGCCGGTG AACTTCCCGC CGCCGTTGTT GTTTTGGAGC ACGGAAAGAC GATGACGGAA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

AAAGAGATCG TGGATTACGT CGCCAGTCAA GTAACAACCG CGAAAAAGTT GCGCGGAGGA GTTGTGTTTG TGGACGAAGT ACCGAAAGGT CTTACCGGAA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AACTCGACGC AAGAAAAATC AGAGAGATCC TCATAAAGGC CAAGAAGGGC GGAAAGTCCA AATTGTAAAA TGTAACTGTA TTCAGCGATG ACGAAATTCT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TAGCTATTGT AATgactcta gaggatctCT TTGTGAAGGA ACCTTACTTC TGTGGTGTGA CATAATTGGA CAAACTACCT ACAGAGATTT AAAGCTCTAA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

GGTAAATATA AAATTTTTAA GTGTATAATG TGTTAAACTA CTGATTCTAA TTGTTTGTGT ATTTTAGATT CCAACCTATG GAACTGATGA ATGGGAGCAG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TGGTGGAATG CCTTTAATGA GGAAAACCTG TTTTGCTCAG AAGAAATGCC ATCTAGTGAT GATGAGGCTA CTGCTGACTC TCAACATTCT ACTCCTCCAA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AAAAGAAGAG AAAGGTAGAA GACCCCAAGG ACTTTCCTTC AGAATTGCTA AGTTTTTTGA GTCATGCTGT GTTTAGTAAT AGAACTCTTG CTTGCTTTGC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

TATTTACACC ACAAAGGAAA AAGCTGCACT GCTATACAAG AAAATTATGG AAAAATATTC TGTAACCTTT ATAAGTAGGC ATAACAGTTA TAATCATAAC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ATACTGTTTT TTCTTACTCC ACACAGGCAT AGAGTGTCTG CTATTAATAA CTATGCTCAA AAATTGTGTA CCTTTAGCTT TTTAATTTGT AAAGGGGTTA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

ATAAGGAATA TTTGATGTAT AGTGCCTTGA CTAGAGATCA TAATCAGCCA TACCACATTT GTAGAGGTTT TACTTGCTTT AAAAAACCTC CCACACCTCC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

CCCTGAACCT GAAACATAAA ATGAATGCAA TTGTTGTTGT TAACTTGTTT ATTGCAGCTT ATAATGGTTA CAAATAAAGC AATAGCATCA CAAATTTCAC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AAATAAAGCA TTTTTTTCAC TGCATTCTAG TTGTGGTTTG TCCAAACTCA TCAATGTATC TTATCATGTC TGGATCCCC
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471

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:

not tested

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

9-668

ORF

ORF position:

2

Version: `1`	Last change: `2008-08-27 11:51:23`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
FLuc

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

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

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

not tested

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

1230-2882

Remarks:

The +1 transcription site is not exactly known to IRESite curator so the 5'-UTR might be slightly wrong. It
seems transcription should terminate after the poly(A) signal from SV40 early region after removal of the SV40
small T antigen intron.

The sequence of the plasmid is not complete. The IRES sequence has been determined by E. Martinez-Salas while
the regions around HSV-TK promoter and intercistronic region were sequenced by IRESite (bp 2227-2802 and
3238-3961). Plasmid DNA was obtained from BCCM database.

Citations:

Martinez-Salas E., Saiz J. C., Davila M., Belsham G. J., Domingo E. (1993) A single nucleotide substitution in the internal ribosome entry site of foot-and-mouth disease virus leads to enhanced cap-independent translation in vivo. J. Virol. 67(7):3748-3755

Additional data: http://bccm.belspo.be/db/lmbp_plasmid_details.php?NM=pBIC

IRESs:

IRES:

Version: `1`	Last change: `2008-08-27 11:51:23`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `FMDV`	The functional status of IRES: `functional`

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

734-1194

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `66`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `526`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-496`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-36`

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

AGCAGGTTTC CCCAACTGAC ACAAAACGTG CAACTTGAAA CTCCGCCTGG TCTTTCCAGG TCTAGAGGGG TAACACTTTG TACTGTGTTT GGCTCCACGC 
^734       ^744       ^754       ^764       ^774       ^784       ^794       ^804       ^814       ^824       

TCGATCCACT GGCGAGTGTT AGTAACAGCA CTGTTGCTTC GTAGCGGAGC ATGACGGCCG TGGGAACTCC TCCTTGGTAA CAAGGACCCA CGGGGCCAAA 
^834       ^844       ^854       ^864       ^874       ^884       ^894       ^904       ^914       ^924       

AGCCACGCCC ACACGGGCCC GTCATGTGTG CAACCCCAGC ACGGCGACTT TACTGCGAAA CCCACTTTAA AGTGACATTG AAACTGGTAC CCACACACTG 
^934       ^944       ^954       ^964       ^974       ^984       ^994       ^1004      ^1014      ^1024      

GTGACAGGCT AAGGATGCCC TTCAGGTACC CCGAGGTAAC ACGCGACACT CGGGATCTGA GAAGGGGACT GGGGCTTCTA TAAAAGCGCT CGGTTTAAAA 
^1034      ^1044      ^1054      ^1064      ^1074      ^1084      ^1094      ^1104      ^1114      ^1124      

AGCTTCTACG CCTGAATAGG TGACCGGAGG TCGGCACCTT TCCTTTACAA TTAATGACCC T
^1134      ^1144      ^1154      ^1164      ^1174      ^1184      ^1194

Citations:

Additional data: http://bccm.belspo.be/db/lmbp_plasmid_details.php?NM=pBIC

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