IRESite_Id:334 characteristics of FMDV IRES studied in pGEM3-FMDV-IRES plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `334`	Version: `0`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-02-12 18:22:15`

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:
only_IRES_fragment

The mRNA/+RNA description:

In vitro T7 run-off transcript with just FMDV IRES (transription runs off at cleaved XhoI site, FMDV IRES is
between EcoRI and XhoI sites).

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

gggagaccgg aattcAGCAG GTTTCCCCAA CTGACACAAA ACGTGCAACT TGAAACTCCG CCTGGTCTTT CCAGGTCTAG AGGGGTAACA CTTTGTACTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGTTTGGCTC CACGCTCGAT CCACTGGCGA GTGTTAGTAA CAGCACTGTT GCTTCGTAGC GGAGCATGAC GGCCGTGGGA ACTCCTCCTT GGTAACAAGG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ACCCACGGGG CCAAAAGCCA CGCCCACACG GGCCCGTCAT GTGTGCAACC CCAGCACGGC GACTTTACTG CGAAACCCAC TTTAAAGTGA CATTGAAACT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GGTACCCACA CACTGGTGAC AGGCTAAGGA TGCCCTTCAG GTACCCCGAG GTAACACGCG ACACTCGGGA TCTGAGAAGG GGACTGGGGC TTCTATAAAA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GCGCTCGGTT TAAAAAGCTT CTACGCCTGA ATAGGTGACC GGAGGTCGGC ACCTTTCCTT TACAATTAAT GACCCTgagc t
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pGEM3-FMDV-IRES 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:
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:

tatagtgtca cctaaatcgt atgtgtatga tacataaggt tatgtattaa ttgtagccgc gttctaacga caatatgtac aagcctaatt gtgtagcatc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tggcttactg aagcagaccc tatcatctct ctcgtaaact gccgtcagag tcggtttggt tggacgaacc ttctgagttt ctggtaacgc cgttccgcac 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

cccggaaatg gtcagcgaac caatcagcag ggtcatcgct agccagatcc tctacgccgg acgcatcgtg gccggcatca ccggcgccac aggtgcggtt 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gctggcgcct atatcgccga catcaccgat ggggaagatc gggctcgcca cttcgggctc atgagcgctt gtttcggcgt gggtatggtg gcaggccccg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

tggccggggg actgttgggc gccatctcct tgcaccattc cttgcggcgg cggtgctcaa cggcctcaac ctactactgg gctgcttcct aatgcaggag 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

tcgcataagg gagagcgtcg atatggtgca ctctcagtac aatctgctct gatgccgcat agttaagcca gccccgacac ccgccaacac ccgctgacgc 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

gccctgacgg gcttgtctgc tcccggcatc cgcttacaga caagctgtga ccgtctccgg gagctgcatg tgtcagaggt tttcaccgtc atcaccgaaa 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

cgcgcgagac gaaagggcct cgtgatacgc ctatttttat aggttaatgt catgataata atggtttctt agacgtcagg tggcactttt cggggaaatg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

tgcgcggaac ccctatttgt ttatttttct aaatacattc aaatatgtat ccgctcatga gacaataacc ctgataaatg cttcaataat attgaaaaag 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

gaagagtatg agtattcaac atttccgtgt cgcccttatt cccttttttg cggcattttg ccttcctgtt tttgctcacc cagaaacgct ggtgaaagta 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

aaagatgctg aagatcagtt gggtgcacga gtgggttaca tcgaactgga tctcaacagc ggtaagatcc ttgagagttt tcgccccgaa gaacgttttc 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

caatgatgag cacttttaaa gttctgctat gtggcgcggt attatcccgt attgacgccg ggcaagagca actcggtcgc cgcatacact attctcagaa 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tgacttggtt gagtactcac cagtcacaga aaagcatctt acggatggca tgacagtaag agaattatgc agtgctgcca taaccatgag tgataacact 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

gcggccaact tacttctgac aacgatcgga ggaccgaagg agctaaccgc ttttttgcac aacatggggg atcatgtaac tcgccttgat cgttgggaac 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

cggagctgaa tgaagccata ccaaacgacg agcgtgacac cacgatgcct gtagcaatgg caacaacgtt gcgcaaacta ttaactggcg aactacttac 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tctagcttcc cggcaacaat taatagactg gatggaggcg gataaagttg caggaccact tctgcgctcg gcccttccgg ctggctggtt tattgctgat 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

aaatctggag ccggtgagcg tgggtctcgc ggtatcattg cagcactggg gccagatggt aagccctccc gtatcgtagt tatctacacg acggggagtc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

aggcaactat ggatgaacga aatagacaga tcgctgagat aggtgcctca ctgattaagc attggtaact gtcagaccaa gtttactcat atatacttta 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gattgattta aaacttcatt tttaatttaa aaggatctag gtgaagatcc tttttgataa tctcatgacc aaaatccctt aacgtgagtt ttcgttccac 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

tgagcgtcag accccgtaga aaagatcaaa ggatcttctt gagatccttt ttttctgcgc gtaatctgct gcttgcaaac aaaaaaacca ccgctaccag 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

cggtggtttg tttgccggat caagagctac caactctttt tccgaaggta actggcttca gcagagcgca gataccaaat actgtccttc tagtgtagcc 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gtagttaggc caccacttca agaactctgt agcaccgcct acatacctcg ctctgctaat cctgttacca gtggctgctg ccagtggcga taagtcgtgt 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

cttaccgggt tggactcaag acgatagtta ccggataagg cgcagcggtc gggctgaacg gggggttcgt gcacacagcc cagcttggag cgaacgacct 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

acaccgaact gagataccta cagcgtgagc tatgagaaag cgccacgctt cccgaaggga gaaaggcgga caggtatccg gtaagcggca gggtcggaac 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

aggagagcgc acgagggagc ttccaggggg aaacgcctgg tatctttata gtcctgtcgg gtttcgccac ctctgacttg agcgtcgatt tttgtgatgc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

tcgtcagggg ggcggagcct atggaaaaac gccagcaacg cggccttttt acggttcctg gccttttgct ggccttttgc tcacatgttc tttcctgcgt 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

tatcccctga ttctgtggat aaccgtatta ccgcctttga gtgagctgat accgctcgcc gcagccgaac gaccgagcgc agcgagtcag tgagcgagga 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

agcggaagag cgcccaatac gcaaaccgcc tctccccgcg cgttggccga ttcattaatg cagctggctt atcgaaatta atacgactca ctatagggag 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

accggaattc AGCAGGTTTC CCCAACTGAC ACAAAACGTG CAACTTGAAA CTCCGCCTGG TCTTTCCAGG TCTAGAGGGG TAACACTTTG TACTGTGTTT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGCTCCACGC TCGATCCACT GGCGAGTGTT AGTAACAGCA CTGTTGCTTC GTAGCGGAGC ATGACGGCCG TGGGAACTCC TCCTTGGTAA CAAGGACCCA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGGGGCCAAA AGCCACGCCC ACACGGGCCC GTCATGTGTG CAACCCCAGC ACGGCGACTT TACTGCGAAA CCCACTTTAA AGTGACATTG AAACTGGTAC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCACACACTG GTGACAGGCT AAGGATGCCC TTCAGGTACC CCGAGGTAAC ACGCGACACT CGGGATCTGA GAAGGGGACT GGGGCTTCTA TAAAAGCGCT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CGGTTTAAAA AGCTTCTACG CCTGAATAGG TGACCGGAGG TCGGCACCTT TCCTTTACAA TTAATGACCC Tgagctcggt acccggggat cctctagagt 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

cgacctgcag gcatgcaagc ttgtattc
^3301      ^3311      ^3321

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

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

0

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

Ramos R., Martinez-Salas E. (1999) Long-range RNA interactions between structural domains of the aphthovirus internal ribosome entry site (IRES). RNA. 5(10):1374-1383

IRESs:

IRES:

Version: `0`
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):

16-476

How IRES boundaries were determined:
experimentally_determined

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

AGCAGGTTTC CCCAACTGAC ACAAAACGTG CAACTTGAAA CTCCGCCTGG TCTTTCCAGG TCTAGAGGGG TAACACTTTG TACTGTGTTT GGCTCCACGC 
^16        ^26        ^36        ^46        ^56        ^66        ^76        ^86        ^96        ^106       

TCGATCCACT GGCGAGTGTT AGTAACAGCA CTGTTGCTTC GTAGCGGAGC ATGACGGCCG TGGGAACTCC TCCTTGGTAA CAAGGACCCA CGGGGCCAAA 
^116       ^126       ^136       ^146       ^156       ^166       ^176       ^186       ^196       ^206       

AGCCACGCCC ACACGGGCCC GTCATGTGTG CAACCCCAGC ACGGCGACTT TACTGCGAAA CCCACTTTAA AGTGACATTG AAACTGGTAC CCACACACTG 
^216       ^226       ^236       ^246       ^256       ^266       ^276       ^286       ^296       ^306       

GTGACAGGCT AAGGATGCCC TTCAGGTACC CCGAGGTAAC ACGCGACACT CGGGATCTGA GAAGGGGACT GGGGCTTCTA TAAAAGCGCT CGGTTTAAAA 
^316       ^326       ^336       ^346       ^356       ^366       ^376       ^386       ^396       ^406       

AGCTTCTACG CCTGAATAGG TGACCGGAGG TCGGCACCTT TCCTTTACAA TTAATGACCC T
^416       ^426       ^436       ^446       ^456       ^466       ^476

Citations:

Fernandez-Miragall O., Martinez-Salas E. (2003) Structural organization of a viral IRES depends on the integrity of the GNRA motif. RNA. 9(11):1333-1344

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