IRESite_Id:321 summary record describing characteristics of FMDV_type

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `321`	Version: `0`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `end-to-end_full-length_mRNA`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `FMDV`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
6318187

The mRNA/+RNA description:

Foot-and-mouth disease virus (FMDV) strain C, isolate c-s8c1, genomic RNA.

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

TTGAAAGGGG GCGCTAGGGT CTCACCCCTA ACATGCCAAC GACAGTCCCT GCATTGCACT CCACACTTAC GTTGTGCGTA CGCGGGGCCC GATGGACCAT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGTTCACCCA CCTACAGCTG GACTCACGAC ACCGCGTGGC CATTTTAGCT GGATTGTGCG GACGAACACC GCTTGCGCTT CTCGCGTGAC CGGTTAGTAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCTTACCACC TTCCGCCTAC TTGGTTGTTA GCGCTGTCCT GGGCACCCCT GTTGGGGGCC GTTCGACGCT CCACGGGTTC CCCCGTGCGG CAACTACGGT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GATGGGGCCG TTTCGCGCGG GCTGATCGCC TGGTTTGCTT CGGCTGTCAC CCGAAACCCG CCTTTCATAA GTTTTACCGT CTGTCCCGAC GTTAAAGGGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GGTAACCACA AGCATACTGC CGCCTTCCCC GGCGTTAACG GGATGCAACC GTAAGACACA CCTTCATCCG GAAGTGAAAC GGCTGCGTCA CATAGTTTTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCCGTTTTCA CGAGAAATGG GACGTCTGCG CACGAAACGC GCCGTCGCTT GAGGAAGACT TGTACAAACA CGATCTAAGC AGGTTTCCCC AACTGACACA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AAACGTGCAA CTTGAAACTC CGCCTGGTCT TTCCAGGTCT AGAGGGGTAA CACTTTGTAC TGTGTTTGGC TCCACGCTCG ATCCACTGGC GAGTGTTAGT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AACAGCACTG TTGCTTCGTA GCGGAGCATG ACGGCCGTGG GAACTCCTCC TTGGTAACAA GGACCCACGG GGCCAAAAGC CACGCCCACA CGGGCCCGTC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATGTGTGCAA CCCCAGCACG GCGACTTTAC TGCGAAACCC ACTTTAAAGT GACATTGAAA CTGGTACCCA CACACTGGTG ACAGGCTAAG GATGCCCTTC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AGGTACCCCG AGGTAACACG CGACACTCGG GATCTGAGAA GGGGACTGGG GCTTCTATAA AAGCGCTCGG TTTAAAAAGC TTCTATGCCT GAATAGGTGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCGGAGGTCG GCACCTTTCC TTTACAATTA ATGACCCTAT GAATACAACT GACTGTTTTA TCGCTGTGGT AAACGCCATC AAAGAGGTAA GAGCACTTTT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCTACCACGG ACTGCAGGAA AAATGGAATT CACGCTACAC GACGGCGAGA AAAAGGTCTT TTACTCCAGA CCCAACAACC ACGACAACTG CTGGTTGAAC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ACCATCCTTC AGTTGTTCAG GTACGTCGAT GAACCTTTCT TCGACTGGGT CTACAATTCG CCCGAGAACC TCACGCTTGA AGCCATCAAG CAACTGGAGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AACTCACAGG GTTGGAGTTG CGCGAGGGTG GACCGCCCGC CCTTGTGATT TGGAACATCA AACACCTGCT CCACACTGGC ATCGGTACCG CTTCGCGACC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CAGCGAGGTG TGTATGGTGG ACGGCACGGA CATGTGTCTT GCTGACTTTC ATGCAGGCAT TTTCATGAAA GGACGGGAAC ACGCTGTCTT TGCGTGTGTC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACCTCCAACG GGTGGTACGC GATTGATGAC GAGGACTTCT ACCCATGGAC GCCAGACCCG TCTGATGTCC TGGTATTTGT TCCATACGAC CAAGAGCCAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TCAATGAAGG GTGGAAGGCC AGCGTTCAGC GAAAGCTCAA GGGAGCTGGG CAATCCAGCC CAGCGACCGG TTCACAGAAC CAATCTGGCA ACACTGGCAG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CATAATTAAC AACTACTATA TGCAGCAGTA CCAAAACTCC ATGGACACAC AACTCGGCGA CAACGCCATC AGTGGAGGCT CCAATGAAGG CTCCACGGAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ACAACCTCTA CACACACAAC CAACACCCAG AACAACGACT GGTTTTCCAA ACTTGCCAGT TCAGCCTTCA GCGGTCTTTT CGGCGCCCTT CTCGCTGATA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGAAAACGGA GGAAACCACT CTCCTTGAAG ACCGCATTCT CACTACCCGT AACGGGCACA CGACCTCGAC AACCCAGTCG AGCGTCGGAG TCACATTCGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GTATGCAACC GCTGAAGATA GCACGTCTGG ACCCAATACA TCTGGTCTAG AGACGCGCGT TCATCAGGCA GAGAGGTTTT TCAAAATGGC ACTTTTTGAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGGGTTCCTT CACAAAATTT TGGACACATG CACAAGGTTG TTCTGCCCCA CGAACCAAAA GGTGTTTACG GGGGTCTCGT CAAGTCATAC GCGTACATGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GCAATGGCTG GGACGTCGAG GTGACCGCTG TTGGAAACCA GTTCAACGGC GGTTGCCTCC TGGTGGCGCT CGTCCCCGAG ATGGGCGACA TCAGTGACAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGAAAAGTAC CAACTAACTC TTTACCCCCA CCAGTTCATC AACCCACGCA CCAACATGAC GGCACACATC ACTGTGCCCT ATGTGGGTGT CAACAGGTAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GACCAGTACA AACAGCACAG GCCCTGGACC CTCGTGGTCA TGGTTGTCGC GCCACTCACC ACAAACACAG CAGGTGCCCA ACAGATCAAA GTGTATGCCA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACATAGCCCC AACCAACGTG CACGTGGCGG GTGAGCTCCC CTCCAAGGAG GGGATCTTCC CCGTTGCGTG TTCTGACGGT TACGGCAACA TGGTGACAAC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TGACCCGAAA ACGGCTGACC CTGCCTACGG GAAGGTTTAC AACCCCCCTC GGACTGCTCT GCCGGGGCGG TTCACAAACT ACCTGGATGT TGCCGAGGCT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TGTCCCACCT TCCTGATGTT CGAGAACGTA CCTTACGTCT CAACACGAAC TGACGGGCAA AGGCTACTGG CCAAGTTCGA CGTGTCGCTG GCAGCGAAAC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ACATGTCAAA CACCTACTTG GCCGGCTTGG CCCAGTACTA CACACAGTAC ACCGGGACAA TCAACCTACA CTTCATGTTC ACTGGGCCGA CCGACGCGAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AGCTCGGTAC ATGGTGGCGT ACGTGCCCCC TGGCATGGAC GCACCAGACA ACCCAGAAGA GGCTGCCCAC TGCATACACG CAGAATGGGA CACTGGTCTG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AACTCCAAGT TCACGTTTTC AATCCCGTAC ATCTCGGCCG CTGACTACGC GTACACCGCG TCCCACGAGG CTGAAACAAC ATGTGTACAG GGGTGGGTCT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GTGTGTACCA AATCACTCAC GGCAAGGCAG ACGCCGACGC GCTCGTCGTC TCCGCATCAG CGGGGAAAGA CTTTGAGCTC CGGCTACCTG TGGACGCTAG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ACAACAAACT ACGACCACTG GTGAATCTGC TGACCCCGTC ACCACTACCG TTGAGAACTA CGGAGGAGAG ACTCAGGTCC AACGTCGCCA CCACACCGAC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GTTGCCTTCG TTCTTGACCG GTTTGTGAAG GTCACAGTGT CGGATAACCA ACACACACTC GACGTGATGC AGGCACACAA AGACAATATC GTGGGCGCGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TTCTTCGCGC AGCCACGTAC TACTTTTCTG ATTTGGAAAT AGCAGTGACC CACACTGGGA AGCTCACATG GGTGCCCAAC GGTGCACCAG TTTCTGCACT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TAACAACACA ACCAATCCCA CTGCCTACCA CAAGGGCCCG GTGACTCGAC TGGCTCTCCC ATACACCGCG CCACACCGTG TGTTGGCTAC GGCGTACACT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GGCACTACGA CCTACACCGC CAGTGCACGC GGGGATTTGG CTCACCTAAC GACGACGCAT GCTCGGCATT TGCCGACATC GTTCAACTTT GGTGCAGTTA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AAGCAGAAAC AATCACTGAG TTGCTCGTGC GCATGAAGCG TGCTGAACTC TATTGTCCTA GGCCGATTCT TCCGATTCAG CCAACGGGCG ATAGACACAA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GCAACCGCTC GTCGCACCTG CAAAACAACT GCTGAACTTT GACCTGCTCA AGTTGGCTGG AGATGTGGAG TCCAACCCTG GGCCCTTCTT CTTCTCTGAC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GTTAGGTCAA ACTTTTCCAA ACTGGTGGAG ACAATTAACC AGATGCAGGA GGACATGTCC ACAAAGCACG GACCTGACTT TAACCGGTTG GTGTCTGCTT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TTGAGGAACT GGCCAGTGGA GTGAAAGCCA TCAGGACCGG TCTCGATGAG GCCAAACCCT GGTACAAGCT TATTAAGCTC CTGAGCCGCT TGTCGTGCAT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GGCCGCTGTA GCAGCGCGGT CAAAGGACCC AGTCCTTGTG GCCATCATGC TGGCTGACAC CGGTCTCGAG ATTCTGGACA GCACGTTTGT CGTGAAGAAG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ATCTCCGACT CGCTCTCCAG TCTCTTTCAC GTGCCGGCCC CCGCCTTCAG CTTCGGAGCC CCGATTCTGT TGGCCGGGTT GGTCAAGGTC GCCTCGAGTT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TCTTCCGGTC CACACCCGAA GACCTTGAGA GAGCAGAGAA ACAACTCAAA GCACGTGACA TCAACGACAT CTTCGCCATT CTCAAGAACG GCGAGTGGCT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GGTCAAGCTG ATCCTTGCCA TCCGCGACTG GATTAAGGCA TGGATCGCCT CAGAAGAGAA GTTTGTCACC ATGACAGACC TGGTGCCTGG TATCCTTGAA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AAACAGCGGG ACCTCAACGA CCCAAGCAAG TACAAGGATG CCAAGGAATG GCTCGACAAC ACGCGCCAAG TGTGTTTGAA GAGCGGGAAC GTCCATATTG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CCAACCTTTG CAAAGTGGTC GCCCCAGCAC CCAGCAAGTC GAGACCCGAG CCCGTGGTCG TTTGCCTCCG CGGCAAGTCT GGCCAGGGCA AGAGTTTCCT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TGCGAACGTG CTTGCACAAG CAATCTCCAC CCACCTCACC GGCAGGACCG ATTCTGTTTG GTACTGCCCG CCTGACCCTG ACCACTTCGA CGGTTACAAC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CAGCAGACCG TTGTTGTGAT GGACGATTTG GGCCAGAACC CTGACGGCAA GGACTTCAAG TACTTCGCCC AAATGGTTTC AACCACGGGG TTCATCCCGC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CCATGGCATC ACTTGAGGAC AAAGGCAAAC CCTTCAGCAG TAAGGTCATC ATTGCAACCA CCAACCTGTA CTCGGGCTTC ACCCCGAAGA CCATGGTGTG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TCCTGATGCT CTGAACCGGA GGTTTCACTT TGACATCGAC GTGAGCGCCA AGGACGGGTA CAAAATCAAC AACAAATTGG ACATCATCAA AGCACTTGAA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GACACCCACA CCAATCCAGT GGCAATGTTT CAGTACGACT GTGCCCTTCT CAACGGCATG GCTGTTGAAA TGAAGAGATT GCAACAGGAT ATGTTCAAGC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CTCAACCACC CCTCCAGAAC GTGTACCAAC TTGTTCAGGA GGTGATTGAG CGGGTCGAGC TTCACGAGAA AGTGTCAAGC CACCCAATTT TTAAGCAAAT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CTCAATACCT TCCCAAAAAT CTGTGTTGTA CTTCCTCATT GAGAAAGGCC AACACGAGGC AGCAATTGAA TTCTTTGAGG GCATGGTACA CGACTCCATT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

AAGGAGGAAC TCCGGCCCCT CATCCAACAA ACTTCATTTG TGAAACGTGC TTTTAAGCGC CTGAAGGAGA ACTTTGAAAT TGTTGCACTG TGCCTAACAC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TTTTGGCCAA CATTGTCATC ATGATCCGCG AGACTCACAA GAGACAGAAG ATGGTGGATG ATGCGGTGAA TGAGTACATC GAGAAAGCAA ACATCACCAC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CGATGACCAG ACACTTGACG AGGCGGAAAA GAACCCTCTG GAAACCAGTG GTGCCAGCAC CGTTGGCTTC AGAGAGAGAA CTCTTCCAGG TCAGAAGGCG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CGCGATGACG TGAACTCTGA GCCCGCCCAG CCGACTGAAG AGCAACCGCA AGCTGAAGGA CCCTACGCCG GGCCACTCGA GCGTCAGAGA CCTCTGAAAG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TGAGAGCCAA GCTCCCGCGA CAAGAGGGAC CTTACGCCGG TCCGATGGAG AGACAGAAGC CGCTGAAAGT GAAAGCAAGA GCCCCGGTCG TCAAGGAAGG 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ACCTTATGAA GGACCGGTGA AGAAGCCTGT CGCTTTGAAA GTGAAAGCTA AGAATTTGAT TGTCACTGAG AGTGGTGCCC CCCCGACTGA CCTGCAAAAG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ATGGTCATGG GCAACACGAA GCCTGTTGAG CTCATCCTCG ACGGGAAGAC AGTAGCCATC TGCTGTGCTA CTGGAGTGTT CGGCACTGCC TACCTCGTGC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CTCGTCATCT TTTCGCTGAG AAGTACGACA AGATCATGTT GGACGGCAGG GCTTTGACAG ACAGTGACTA CAGAGTGTTT GAGTTTGAGA TTAAAGTAAA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

AGGACAGGAC ATGCTCTCAG ACGCTGCGCT CATGGTGCTC CACCGCGGGA ACCGCGTGAG AGACATCACG AAACACTTTC GTGATGTAGC AAGAATGAAG 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

AAAGGTACCC CCGTCGTTGG CGTGATTAAC AACGCTGATG TTGGGAGACT GATTTTCTCT GGTGAGGCCC TTACCTACAA AGACATTGTA GTGTGCATGG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

ACGGAGACAC CATGCCCGGC CTCTTTGCCT ACAAAGCCGC TACCAAGGCT GGCTACTGTG GAGGAGCCGT TCTTGCTAAG GACGGAGCTG ACACCTTCAT 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CGTTGGCACT CACTCTGCTG GAGGCAATGG AGTTGGGTAC TGCTCATGCG TGTCCAGGTC CATGCTTCTC AAAATGAAGG CACACATCGA CCCTGAACCG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CACCACGAGG GGTTGATCGT TGATACCAGA GATGTGGAAG AGCGCGTCCA TGTAATGCGC AAAACCAAGC TTGCACCCAC CGTCGCGCAC GGTGTGTTCA 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

ATCCTGAGTT CGGGCCTGCC GCCTTGTCTA ACAAGGACCC ACGTCTGAAC GAAGGTGTTG TCCTCGATGA AGTCATTTTC TCCAAGCATA AAGGAGACAC 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

AAAGATGTCT GCGGAGGACA AAGCGCTGTT CCGCCGCTGC GCTGCTGACT ACGCGTCACG CCTGCACAGT GTGCTGGGTA CGGCAAATGC CCCACTGAGC 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

ATTTACGAGG CAATCAAGGG CGTTGACGGA CTCGACGCCA TGGAGCCAGA CACCGCACCT GGCCTTCCCT GGGCCCTCCA GGGGAAACGC CGCGGTGCAC 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

TTATCGATTT CGAGAACGGC ACGGTCGGAC CCGAGGTTGA GGCTGCCTTG AAGCTCATGG AGAAAAGAGA ATACAAGTTT GCTTGCCAGA CCTTCCTGAA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

GGACGAAATT CGCCCGATGG AGAAAGTACG TGCCGGCAAG ACTCGCATTG TCGACGTTTT GCCTGTTGAA CACATTCTTT ACACCAGGAT GATGATTGGC 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

AGATTTTGTG CACAAATGCA CTCAAACAAC GGGCCGCAGA TTGGCTCAGC GGTCGGTTGC AACCCTGATG TTGATTGGCA GAGATTCGGC ACACACTTCG 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

CCCAATACAG AAACGTGTGG GACGTGGACT ATTCGGCCTT TGATGCAAAC CACTGCAGCG ATGCCATGAA CATCATGTTT GAAGAGGTGT TCCGCACGGA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

GTTCGGCTTC CACCCGAATG CTGAGTGGAT CCTGAAGACT CTCGTGAACA CGGAACACGC CTATGAGAAC AAGCGCATCA CTGTTGAAGG CGGGATGCCA 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

TCTGGCTGTT CCGCAACAAG CATCATCAAC ACAATTTTGA ATAACATCTA CGTGCTCTAC GCCTTGCGTA GACACTATGA GGGGGTTGAG CTGGACACCT 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

ACACCATGAT CTCCTATGGA GACGACATCG TGGTGGCAAG CGATTATGAT CTGGACTTTG AGGCCCTCAA GCCTCACTTC AAATCTCTTG GCCAAACCAT 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

TACTCCAGCT GACAAAAGCG ACAAAGGTTT TGTTCTTGGT CACTCCATTA CTGACGTCAC TTTCCTCAAA AGACACTTCC ACATGGATTA TGGCACTGGG 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TTTTACAAAC CTGTGATGGC CTCGAAGACC CTCGAGGCTA TCCTCTCCTT TGCACGCCGT GGGACCATCC AGGAGAAGTT GATTTCCGTG GCAGGACTCG 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

CCGTCCACTC CGGACCAGAC GAGTACCGGC GTCTCTTTGA GCCCTTCCAG GGCCTCTTTG AGATTCCAAG CTACAGATCA CTTTACCTGC GTTGGGTGAA 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

CGCCGTGTGC GGCGACGCAT AATCCCCCAA ACATCACAAT TGGCACAATG ATTTTGGGGC GCGCGACGCC GTGGGAGTGA AAAGCCCGAA AGGGCTTTCC 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

CGGCTTCCTT AATCC
^8101      ^8111

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The organism containing this mRNA with IRES segment in its genome:

Foot-and-mouth disease virus C

A promoter reported in cDNA corresponding to IRES sequence:
not tested The total number of notable open-reading frames (ORFs):
1

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:
polyprotein

The description of the protein encoded in this ORF:
viral polyprotein

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):

1039-8022

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: `3`	Last change: `2008-12-10 00:22:05`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `FMDV_type_C`

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

578-1038

Conclusion:
strongly_supported_IRES

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 
^578       ^588       ^598       ^608       ^618       ^628       ^638       ^648       ^658       ^668       

TCGATCCACT GGCGAGTGTT AGTAACAGCA CTGTTGCTTC GTAGCGGAGC ATGACGGCCG TGGGAACTCC TCCTTGGTAA CAAGGACCCA CGGGGCCAAA 
^678       ^688       ^698       ^708       ^718       ^728       ^738       ^748       ^758       ^768       

AGCCACGCCC ACACGGGCCC GTCATGTGTG CAACCCCAGC ACGGCGACTT TACTGCGAAA CCCACTTTAA AGTGACATTG AAACTGGTAC CCACACACTG 
^778       ^788       ^798       ^808       ^818       ^828       ^838       ^848       ^858       ^868       

GTGACAGGCT AAGGATGCCC TTCAGGTACC CCGAGGTAAC ACGCGACACT CGGGATCTGA GAAGGGGACT GGGGCTTCTA TAAAAGCGCT CGGTTTAAAA 
^878       ^888       ^898       ^908       ^918       ^928       ^938       ^948       ^958       ^968       

AGCTTCTATG CCTGAATAGG TGACCGGAGG TCGGCACCTT TCCTTTACAA TTAATGACCC T
^978       ^988       ^998       ^1008      ^1018      ^1028      ^1038

Remarks:

The studied region spans region -461 to -1 relative to initiator AUG. Therefore 577nt of the 5'-most end are
in front of the IRES region.

FMDV IRES does not require Unr protein for its activity (Boussadia et al., 2003).

Citations:

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

Boussadia O., Niepmann M., Creancier L., Prats A. C., Dautry F., Jacquemin-Sablon H. (2003) Unr is required in vivo for efficient initiation of translation from the internal ribosome entry sites of both rhinovirus and poliovirus. J. Virol. 77(6):3353-3359

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

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

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

ITAF protein characteristics:

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

ITAF abbreviated name:
PTB

ITAF fullname:
polypyrimidine-tract binding protein (unspecified isoform)

ITAF description (long):
polypyrimidine-tract binding protein

3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

The requirement for PTB was found by toeprinting in assay of 48S formation.

Citations:

Pilipenko E. V., Pestova T. V., Kolupaeva V. G., Khitrina E. V., Poperechnaya A. N., Agol V. I., Hellen C. U. (2000) A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes. Dev. 14(16):2028-2045

IRES trans-acting factor (ITAF):

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

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

ITAF protein characteristics:

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

ITAF abbreviated name:
ITAF45

ITAF fullname:
ITAF45 (murine proliferation-associated protein, Mpp1)

ITAF description (long):
proliferation-dependent protein that is not expressed in murine brain cells, its human homolog is called PAG24

3.2.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

The requirement for ITAF45 was found by toeprinting in assay of 48S formation.

Citations:

RNA:protein interactions:

The RNA:protein interaction:

Version: `2`	Last change: `2009-09-18 13:13:41`
Originaly submitted by: Zuzana Feketová	Reviewed by: Martin Mokrejš

Abbreviated name of the protein interacting with the RNA:
PCBP1/hnRNP_E1

Full name of the protein interacting with the RNA:
PCBP1 /poly r(C) binding protein/ (hnRNP E1)

The description of the protein interacting with the RNA:
PCBP1 /poly r(C) binding protein/

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.

The RNA:protein interaction:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Item not reviewed

Abbreviated name of the protein interacting with the RNA:
hnRNP_K

Full name of the protein interacting with the RNA:
Heterogeneous ribonucleoprotein K

The description of the protein interacting with the RNA:
Heterogeneous ribonucleoprotein K

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.

Citations:

Pacheco A, Reigadas S, Martínez-Salas E (2008) Riboproteomic analysis of polypeptides interacting with the internal ribosome-entry site element of foot-and-mouth disease viral RNA. Proteomics. 8(22):4782-4790

The RNA:protein interaction:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Item not reviewed

Abbreviated name of the protein interacting with the RNA:
PCBP2/hnRNP_E2

Full name of the protein interacting with the RNA:
PCBP1 /poly r(C) binding protein/ (hnRNP E2)

The description of the protein interacting with the RNA:
PCBP1 /poly r(C) binding protein/

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.

The RNA:protein interaction:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Item not reviewed

Abbreviated name of the protein interacting with the RNA:
PA2G4

Full name of the protein interacting with the RNA:
PA2G4

The description of the protein interacting with the RNA:
PA2G4

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.

The RNA:protein interaction:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Item not reviewed

Abbreviated name of the protein interacting with the RNA:
eIF2c

Full name of the protein interacting with the RNA:
Eukaryotic translation initiation factor 2c

The description of the protein interacting with the RNA:
Eukaryotic translation initiation factor 2c

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.

The RNA:protein interaction:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Item not reviewed

Abbreviated name of the protein interacting with the RNA:
eIF4b

Full name of the protein interacting with the RNA:
Eukaryotic translation initiation factor 4b

The description of the protein interacting with the RNA:
Eukaryotic translation initiation factor 4b

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.

The RNA:protein interaction:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Item not reviewed

Abbreviated name of the protein interacting with the RNA:
eEF2

Full name of the protein interacting with the RNA:
Eukaryotic translation elongation factor 2

The description of the protein interacting with the RNA:
Eukaryotic translation elongation factor 2

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.

The RNA:protein interaction:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Item not reviewed

Abbreviated name of the protein interacting with the RNA:
PABP2

Full name of the protein interacting with the RNA:
Poly(A)-binding protein 2

The description of the protein interacting with the RNA:
Poly(A)-binding protein 2

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 45

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `unknown`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
678-858

The underlying nucleic acid sequence and structure of the mapped region:

TCGATCCACT GGCGAGTGTT AGTAACAGCA CTGTTGCTTC GTAGCGGAGC ATGACGGCCG TGGGAACTCC TCCTTGGTAA CAAGGACCCA CGGGGCCAAA 
((.((..((( ((((((((.( (.((((((.. ...((((((( ......)))( (((((((((( ((((...... ((((((.... )))))))))) )))(((.... 
^678       ^688       ^698       ^708       ^718       ^728       ^738       ^748       ^758       ^768       

AGCCACGCCC ACACGGGCCC GTCATGTGTG CAACCCCAGC ACGGCGACTT TACTGCGAAA CCCACTTTAA AGTGACATTG A
.)))..(((. .....))))) ))))))(... .......... ..)))))... ..)))))))) )))))))).. )))...)).) )
^778       ^788       ^798       ^808       ^818       ^828       ^838       ^848       ^858

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

WARNING: bases 13 and 166 (CU) can't pair!
WARNING: bases 15 and 164 (AA) can't pair!
WARNING: bases 17 and 162 (UC) can't pair!
WARNING: bases 21 and 159 (AA) can't pair!
WARNING: bases 24 and 157 (AG) can't pair!
WARNING: bases 25 and 156 (AC) can't pair!

STDOUT was:

UCGAUCCACUGGCGAGUGUUAGUAACAGCACUGUUGCUUCGUAGCGGAGCAUGACGGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGCCCACACGGGCCCGUCAUGUGUGCAACCCCAGCACGGCGACUUUACUGCGAAACCCACUUUAAAGUGACAUUGA
((.((..(((((((((((.((.((((((.....(((((((......)))(((((((((((((((......((((((....)))))))))))))(((.....)))..(((......)))))))))))(...............))))).....))))))))))))))))..)))...)).)) (-38.70)

Rendering structure of FMDV mRNA 181 nt long with energy of -38.70 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Remarks:

FMDV IRES domain3 as shown in Fig. 6

5.1.1. Enzymes used to characterize at least partially the 2D structure.