IRESite_Id:598 summary record describing characteristics of PV_type3

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `598`	Version: `1`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-19 00:47:30`
Reviewed by: Martin Mokrejš	Last change: `2009-09-05 13:07:58`

IRESite record type:

natural_transcript

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
332895

The mRNA/+RNA description:

Poliovirus P3/Leon/37 (type 3), complete genome.

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

TTAAAACAGC TCTGGGGTTG TTCCCACCCC AGAGGCCCAC GTGGCGGCTA GTACACTGGT ATCACGGTAC CTTTGTACGC CTGTTTTATA CTCCCTCCCC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGCAACTTAG AAGCATACAA TTCAAGCTCA ATAGGAGGGG GTGCAAGCCA GCGCCTCCGT GGGCAAGCAC TACTGTTTCC CCGGTGAGGC CGCATAGACT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GTTCCCACGG TTGAAAGTGG CCGATCCGTT ATCCGCTCAT GTACTTCGAG AAGCCTAGTA TCGCTCTGGA ATCTTCGACG CGTTGCGCTC AGCACTCAAC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCCGGAGTGT AGCTTGGGCC GATGAGTCTG GACAGTCCCC ACTGGCGACA GTGGTCCAGG CTGCGCTGGC GGCCCACCTG TGGCCCAAAG CCACGGGACG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTAGTTGTGA ACAGGGTGTG AAGAGCCTAT TGAGCTACAT GAGAGTCCTC CGGCCCCTGA ATGCGGCTAA TCCTAACCAT GGAGCAGGCA GCTGCAACCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AGCAGCCAGC CTGTCGTAAC GCGCAAGTCC GTGGCGGAAC CGACTACTTT GGGTGTCCGT GTTTCCTTTT ATTCTTGAAT GGCTGCTTAT GGTGACAATC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATAGATTGTT ATCATAAAGC GAGTTGGATT GGCCATCCAG TGTGAATCAG ATTAATTACT CCCTTGTTTG TTGGATCCAC TCCCGAAACG TTTTACTCCT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TAACTTATTG AAATTGTTTG AAGACAGGAT TTCAGTGTCA CAATGGGAGC TCAAGTATCA TCCCAAAAAG TAGGCGCTCA CGAGAATTCT AACCGAGCCT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ACGGTGGTTC TACGATCAAC TACACCACAA TTAATTATTA TAAAGATTCC GCAAGTAATG CGGCGTCCAA GCAAGATTAC TCACAGGATC CATCAAAATT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CACCGAGCCA CTAAAGGACG TGCTCATAAA AACAGCTCCA GCACTCAATT CACCAAATGT GGAAGCGTGT GGGTATAGTG ATAGAGTGTT GCAACTCACT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTAGGCAATT CCACTATTAC TACACAGGAG GCAGCAAATT CAGTAGTGGC TTACGGACGT TGGCCTGAGT TTATTAGAGA TGACGAAGCA AACCCGGTGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACCAACCAAC TGAACCAGAT GTGGCTACAT GCAGATTCTA CACACTAGAC ACTGTAATGT GGGGTAAGGA GTCGAAAGGC TGGTGGTGGA AGTTACCTGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CGCACTGAGA GACATGGGTC TGTTTGGACA AAACATGTAT TACCACTACC TAGGAAGATC CGGGTACACT GTGCACGTGC AGTGTAATGC ATCCAAATTT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CACCAAGGTG CACTCGGGGT GTTTGCGATT CCTGAGTATT GTCTGGCGGG TGACAGTGAC AAGCAAAGGT ACACTAGTTA TGCAAATGCG AATCCAGGTG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAAGAGGGGG AAAATTTTAC TCCCAATTCA ACAAGGATAA CGCAGTAACA TCCCCAAAAA GAGAGTTCTG CCCAGTGGAT TATCTCCTGG GATGTGGGGT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GTTACTGGGA AATGCCTTTG TATACCCACA TCAAATCATT AATCTGAGGA CCAACAACAG CGCAACTATT GTCCTACCAT ATGTGAATGC TTTGGCCATT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GATTCAATGG TTAAACACAA CAACTGGGGC ATTGCCATTC TGCCCTTATC ACCGCTGGAT TTTGCTCAAG ATTCATCAGT TGAAATTCCA ATTACTGTGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CAATTGCCCC AATGTGTAGC GAGTTCAACG GCCTTCGCAA CGTGACTGCA CCTAAATTTC AAGGACTACC AGTGTTGAAC ACTCCTGGTA GTAACCAGTA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCTGACGTCA GACAACCACC AATCACCATG CGCAATCCCA GAATTTGATG TCACTCCGCC TATTGATATC CCAGGTGAGG TTAAAAACAT GATGGAGCTC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCCGAGATAG ACACCATGAT TCCTCTCAAT TTGGAGAGCA CCAAGAGAAA CACAATGGAC ATGTACAGAG TTACTCTGAG CGACAGTGCC GATCTATCGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AACCAATTTT GTGCTTGTCA CTATCCCCAG CATCTGATCC GCGCTTGTCA CACACCATGC TTGGGGAAGT ACTGAACTAT TATACTCATT GGGCCGGGTC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTTGAAATTT ACCTTCCTGT TCTGTGGTTC AATGATGGCT ACGGGGAAAA TCCTAGTGGC CTATGCACCA CCAGGTGCAC AACCCCCCAC CAGCCGTAAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAGGCTATGT TGGGCACACA TGTCATTTGG GATCTTGGCC TGCAATCATC TTGTACTATG GTGGTGCCGT GGATTAGTAA TGTGACATAC AGACAGACTA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CACAAGATAG TTTCACTGAG GGCGGATATA TCAGCATGTT CTACCAAACA AGAATTGTGG TGCCACTGTC CACCCCTAAG AGTATGAGCA TGCTGGGGTT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGTGTCAGCC TGTAATGATT TCAGTGTGCG ATTGCTGCGA GACACCACTC ACATTTCACA ATCTGCGCTT CCACAGGGTA TTGAAGATTT GATTTCTGAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTTGCACAGG GCGCCCTAAC TTTGTCACTC CCGAAGCAAC AGGATAGCTT ACCTGATACT AAGGCCAGTG GCCCGGCGCA TTCCAAGGAG GTACCTGCAC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TCACTGCAGT CGAGACTGGA GCCACCAATC CTCTGGCACC ATCCGACACA GTTCAAACGC GCCACGTAGT CCAACGACGC AGCAGGTCAG AGTCCACAAT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AGAATCATTC TTCGCACGCG GGGCGTGCGT CGCTATTATT GAGGTGGACA ATGAACAACC AACCACCCGG GCACAGAAAC TATTTGCCAT GTGGCGCATT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ACATACAAAG ATACAGTGCA GTTGCGCCGT AAGTTGGAGT TTTTCACATA CTCTCGTTTT GACATGGAAT TCACCTTCGT GGTAACCGCC AACTTCACCA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ACGCTAATAA TGGGCATGCA CTCAACCAGG TGTACCAGAT AATGTACATC CCCCCAGGGG CACCCACACC AAAGTCATGG GACGACTACA CTTGGCAAAC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ATCTTCCAAC CCGTCCATAT TTTACACCTA TGGGGCTGCC CCGGCGCGAA TCTCAGTGCC ATACGTGGGG TTAGCCAATG CTTACTCGCA CTTTTACGAC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGCTTCGCCA AGGTGCCATT GAAGACAGAT GCCAATGACC AGATTGGTGA TTCCTTGTAC AGCGCCATGA CAGTTGATGA CTTTGGTGTA TTGGCAGTTC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GTGTTGTCAA TGATCACAAC CCCACTAAAG TAACCTCCAA AGTCCGCATT TACATGAAAC CCAAACACGT ACGTGTCTGG TGCCCTAGAC CGCCGCGCGC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GGTACCTTAT TATGGACCAG GGGTGGACTA TAAGAACAAC TTGGACCCCT TATCTGAGAA AGGTTTGACC ACATATGGCT TTGGGCATCA GAATAAAGCT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GTGTACACTG CTGGTTACAA GATCTGCAAC TACCATCTCG CCACTAAGGA GGATTTACAA AATACTGTAA GCATCATGTG GAATAGAGAC CTCTTGGTTG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TTGAATCAAA AGCTCAAGGT ACCGACTCAA TAGCAAGGTG CAATTGCAAT GCAGGGGTGT ACTATTGTGA GTCCAGAAGG AAATACTACC CTGTGTCGTT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TGTGGGACCC ACCTTCCAAT ACATGGAGGC TAATGACTAC TACCCAGCTA GATACCAATC CCACATGTTA ATCGGGCACG GCTTTGCCTC ACCAGGTGAC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TGTGGTGGTA TCCTTAGGTG TCAACATGGC GTCATCGGAA TCGTGACAGC TGGTGGAGAG GGATTAGTCG CATTCTCTGA CATAAGGGAC TTGTATGCTT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ACGAGGAAGA GGCCATGGAG CAGGGCATTT CAAACTATAT TGAGTCACTC GGTGCTGCGT TCGGTAGTGG GTTCACTCAG CAAATAGGGG ATAAGATATC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AGAACTAACC AGCATGGTGA CCAGCACGAT TACAGAGAAG CTACTTAAAA ACCTAATCAA AATTATTTCA TCTCTGGTGA TTATCACTAG AAATTACGAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GATACCACCA CAGTGCTCGC CACTCTAGCT CTTCTTGGGT GTGATGTTTC ACCGTGGCAA TGGTTGAAGA AGAAAGCATG TGACACTTTG GAGATTCCCT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ATGTTATTAG ACAGGGTGAT AGTTGGTTGA AAAAATTTAC TGAGGCGTGC AACGCAGCTA AGGGGTTGGA ATGGGTGTCC AACAAAATCT CAAAATTTAT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TGACTGGTTG AGAGAAAGAA TCATCCCACA AGCCAGGGAC AAGCTTGAGT TTGTAACCAA ATTGAAACAG TTGGAAATGC TAGAGAATCA GATATCCACA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ATACACCAAT CTTGTCCAAG TCAGGAACAC CAGGAAATTT TGTTCAACAA TGTACGCTGG TTGTCCATTC AATCCAAGAG ATTCGCTCCA TTGTACGCAC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TTGAGGCCAA GAGAATACAA AAGTTGGAAC ACACCATTAA TAATTACATA CAGTTCAAGA GCAAACACCG TATTGAGCCA GTATGTTTGT TAGTGCATGG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GAGCCCAGGT ACAGGAAAAT CAGTTGCGAC TAACCTAATT GCTAGAGCCA TAGCTGAGAA AGAGAACACC TCCACCTACT CGCTACCACC GGACCCGTCT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CACTTTGATG GATACAAACA ACAAGGTGTG GTTATCATGG ACGACCTAAA CCAAAACCCG GATGGGGCAG ATATGAAGCT CTTTTGTCAA ATGGTGTCCA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTGTGGAGTT TATCCCACCT ATGGCCTCGC TGGAAGAGAA AGGCATTCTG TTCACATCCA ACTATGTTTT AGCCTCCACC AACTCCAGTC GCATCACACC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ACCTACAGTA GCCCACAGTG ACGCTCTGGC CAGGAGGTTC GCTTTCGATA TGGATATTCA AGTGATGGGC GAGTACTCCA GAGATGGTAA ACTCAACATG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GCAATGGCTA CTGAGACGTG CAAGGACTGC CACCAACCAG CAAACTTCAA AAGATGCTGT CCTTTAGTGT GTGGTAAGGC AATTCAGTTA ATGGACAAAT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CTTCCAGAGT TAGGTACAGT GTTGACCAGA TTACTACAAT GATTATCAAC GAGAGAAACA GAAGATCTAA CATTGGCAAT TGCATGGAGG CTTTGTTCCA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

AGGACCACTC CAGTACAAAG ACCTGAAAAT TGACATCAAG ACGAGGCCCC CCCCTGAATG CATCAATGAT CTGCTTCAAG CAGTTGACTC CCAGGAAGTG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

AGGGATTATT GTGAAAAGAA AGGATGGATC GTCAACATCA CTAGCCAAGT TCAAACAGAG AGAAACATTA ACCGAGCAAT GACCATTTTG CAGGCAGTGA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CAACTTTCGC CGCAGTGGCT GGTGTCGTGT ACGTCATGTA CAAGTTATTC GCTGGACACC AGGGAGCATA CACTGGTCTG CCAAACAAAA GACCCAATGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GCCCACCATT AGAGCAGCAA AAGTGCAAGG GCCTGGGTTT GACTATGCAG TGGCTATGGC TAAAAGAAAC ATTGTTACAG CAACTACTAG CAAAGGGGAG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TTCACAATGC TAGGAGTCCA CGACAACGTG GCCATTTTAC CAACTCATGC CTCACCTGGT GAGAGTATTG TAATTGATGG CAAAGAGGTT GAAATCCTAG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ACGCTAAAGC CCTCGAAGAT CAGGCAGGCA CTAATCTGGA AATCACCATA ATAACCCTCA AAAGAAATGA AAAGTTCAGA GATATCAGAC AACACATACC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CACTCAAATC ACCGAGACGA ATGATGGAGT TCTGATTGTG AACACTAGTA AGTACCCCAA CATGTATGTT CCTGTCGGTG CTGTGACTGA GCAGGGATAC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CTAAATCTCG GTGGGCGCCA GACTGCTCGT ATTCTAATGT ACAACTTTCC AACCAGAGCT GGTCAGTGTG GTGGAGTCAT CACATGCACT GGGAAAGTCA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TCGGGATGCA CGTTGGTGGG AATGGTTCAC ATGGGTTTGC AGCGGCCCTG AAGCGGTCAT ACTTCACTCA GAGCCAAGGT GAAATCCAGT GGATGAGACC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ATCAAAGGAG GCAGGGTATC CAATTATAAA CGCCCCAACC AAGACCAAGC TCGAGCCCAG CGCTTTCCAC TATGTGTTTG AAGGAGTAAA GGAACCAGCA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GTCCTCACAA AGAATGATCC CAGACTTAAA ACAGACTTTG AAGAAGCAAT CTTCTCTAAG TATGTAGGGA ACAAGATCAC TGAGGTGGAT GAGTACATGA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

AAGAGGCAGT GGACCATTAT GCTGGACAAC TTATGTCGCT GGATATCAGC ACAGAGCAAA TGTGTCTAGA AGACGCCATG TATGGTACTG ATGGTCTGGA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

GGCGCTAGAT CTGTCTACCA GTGCCGGGTA CCCCTACGTG GCAATGGGGA AGAAGAAGAG AGATATCCTA AACAAGCAAA CCAGAGACAC CAAAGAAATG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

CAAAGACTTT TGGACGCTTA CGGAATCAAC CTACCATTAG TGACATATGT CAAGGACGAG CTGAGGTCCA AAACAAAAGT GGAACAGGGA AAATCCAGAC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TGATTGAAGC TTCCAGTCTA AATGACTCAG TGGCCATGAG AATGGCATTT GGAAACCTTT ATGCAGCATT CCACAGGAAT CCAGGGGTCG TCACTGGTAG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

TGCAGTTGGA TGCGATCCAG ACCTATTCTG GAGCAAGATC CCAGTGTTGA TGGAAGAAAA GCTATTTGCC TTTGATTACA CAGGATACGA CGCATCACTT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

AGCCCAGCTT GGTTTGAGGC ACTCAAGATG GTGTTAGAGA AAATTGGTTT TGGAGATAGA GTGGATTACA TAGACTACCT TAACCATTCA CACCACTTGT 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ACAAAAACAA GATATATTGT GTTAAGGGCG GCATGCCATC TGGCTGCTCC GGCACTTCAA TTTTTAATTC AATGATTAAC AATTTGATCA TTAGGACGCT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

TTTACTGAAA ACCTACAAGG GCATAGATTT GGACCACTTA AAAATGATTG CCTATGGTGA CGATGTAATA GCTTCCTATC CCCATGAGGT TGACGCTAGT 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CTCCTAGCCC AATCAGGAAA AGACTATGGA CTAACCATGA CTCCGGCAGA TAAATCTGCC ACTTTTGAGA CAGTCACATG GGAGAATGTA ACTTTCTTGA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

AAAGATTCTT CAGAGCAGAT GAGAAATACC CCTTCCTCAT ACATCCAGTA ATGCCAATGA AGGAGATTCA TGAATCAATC AGATGGACAA AAGATCCTCG 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

GAATACGCAG GACCATGTAC GCTCCTTGTG TCTATTGGCT TGGCACAACG GGGAAGAAGA ATACAACAAA TTTTTAGCTA AAATTAGGAG TGTGCCAATC 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

GGAAGAGCTT TGTTGCTCCC AGAGTACTCA ACATTGTACC GCCGTTGGCT TGACTCATTT TAGTAACCCT ACCTCAGTCG AATTGGATTG GGTCATACTG 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

TTGTAGGGGT AAATTTTTCT TTAATTCGGA G
^7401      ^7411      ^7421      ^7431

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

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

Human poliovirus 1 Mahoney

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):

743-7363

Citations:

Stanway G, Hughes PJ, Mountford RC, Reeve P, Minor PD, Schild GC, Almond JW (1984) Comparison of the complete nucleotide sequences of the genomes of the neurovirulent poliovirus P3/Leon/37 and its attenuated Sabin vaccine derivative P3/Leon 12a1b. Proc. Natl. Acad. Sci. U.S.A. 5(81):1539-1543

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `PV_type3_Leon`

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

1-742

Conclusion:
strongly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

TTAAAACAGC TCTGGGGTTG TTCCCACCCC AGAGGCCCAC GTGGCGGCTA GTACACTGGT ATCACGGTAC CTTTGTACGC CTGTTTTATA CTCCCTCCCC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGCAACTTAG AAGCATACAA TTCAAGCTCA ATAGGAGGGG GTGCAAGCCA GCGCCTCCGT GGGCAAGCAC TACTGTTTCC CCGGTGAGGC CGCATAGACT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GTTCCCACGG TTGAAAGTGG CCGATCCGTT ATCCGCTCAT GTACTTCGAG AAGCCTAGTA TCGCTCTGGA ATCTTCGACG CGTTGCGCTC AGCACTCAAC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCCGGAGTGT AGCTTGGGCC GATGAGTCTG GACAGTCCCC ACTGGCGACA GTGGTCCAGG CTGCGCTGGC GGCCCACCTG TGGCCCAAAG CCACGGGACG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTAGTTGTGA ACAGGGTGTG AAGAGCCTAT TGAGCTACAT GAGAGTCCTC CGGCCCCTGA ATGCGGCTAA TCCTAACCAT GGAGCAGGCA GCTGCAACCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AGCAGCCAGC CTGTCGTAAC GCGCAAGTCC GTGGCGGAAC CGACTACTTT GGGTGTCCGT GTTTCCTTTT ATTCTTGAAT GGCTGCTTAT GGTGACAATC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATAGATTGTT ATCATAAAGC GAGTTGGATT GGCCATCCAG TGTGAATCAG ATTAATTACT CCCTTGTTTG TTGGATCCAC TCCCGAAACG TTTTACTCCT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TAACTTATTG AAATTGTTTG AAGACAGGAT TTCAGTGTCA CA
^701       ^711       ^721       ^731       ^741

Citations:

Skinner MA, Racaniello VR, Dunn G, Cooper J, Minor PD, Almond JW (1989) New model for the secondary structure of the 5' non-coding RNA of poliovirus is supported by biochemical and genetic data that also show that RNA secondary structure is important in neurovirulence. J. Mol. Biol. 2(207):379-392

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 43

Version: `1`	Last change: `2009-08-30 03:03:50`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `no`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1-620

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

TTAAAACAGC TCTGGGGTTG TTCCCACCCC AGAGGCCCAC GTGGCGGCTA GTACACTGGT ATCACGGTAC CTTTGTACGC CTGTTTTATA CTCCCTCCCC 
.........( ((((((((.. .....))))) ))))...... .......... (((((..((( (......))) )..))))).. .......... .......... 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CGCAACTTAG AAGCATACAA TTCAAGCTCA ATAGGAGGGG GTGCAAGCCA GCGCCTCCGT GGGCAAGCAC TACTGTTTCC CCGGTGAGGC CGCATAGACT 
.......... .......... .....((((( ......(((( ((((...... )))))))).) ))))...... .......... .......((( (((...(((( 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GTTCCCACGG TTGAAAGTGG CCGATCCGTT ATCCGCTCAT GTACTTCGAG AAGCCTAGTA TCGCTCTGGA ATCTTCGACG CGTTGCGCTC AGCACTCAAC 
((....)))) ))....)))) ))........ .....((((( (((.(((((. ..((...... .(((((((.. .......... .......... ...(((((.. 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCCGGAGTGT AGCTTGGGCC GATGAGTCTG GACAGTCCCC ACTGGCGACA GTGGTCCAGG CTGCGCTGGC GGCCCACCTG TGGCCCAAAG CCACGGGACG 
.....))))) .....((((( ((...((((( ((((...... (((((....) )))))))))) )))....... )))))))((( (((((..... )))))))).. 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTAGTTGTGA ACAGGGTGTG AAGAGCCTAT TGAGCTACAT GAGAGTCCTC CGGCCCCTGA ATGCGGCTAA TCCTAACCAT GGAGCAGGCA GCTGCAACCC 
.......... ..))))))). .....))... ))))).)))) ))))...... .......... .......... .(((...((( ((((.((((( .(((((.... 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AGCAGCCAGC CTGTCGTAAC GCGCAAGTCC GTGGCGGAAC CGACTACTTT GGGTGTCCGT GTTTCCTTTT ATTCTTGAAT GGCTGCTTAT GGTGACAATC 
.)))))..)) )))....... .......))) )))).))).. .......... .......... .......... .......... ....(((((( (((((((((( 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATAGATTGTT ATCATAAAGC
...))))))) ))))).))))
^601       ^611

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 236 and 444 (CA) can't pair!
WARNING: bases 238 and 442 (CA) can't pair!
WARNING: bases 239 and 441 (AG) can't pair!
WARNING: bases 240 and 440 (UU) can't pair!
WARNING: bases 241 and 439 (GA) can't pair!
WARNING: bases 242 and 438 (UC) can't pair!
WARNING: bases 243 and 437 (AA) can't pair!
WARNING: bases 245 and 435 (UC) can't pair!
WARNING: bases 247 and 433 (CA) can't pair!
WARNING: bases 248 and 432 (GG) can't pair!
WARNING: bases 254 and 426 (CC) can't pair!
WARNING: bases 262 and 419 (CU) can't pair!
WARNING: bases 263 and 418 (GG) can't pair!
WARNING: bases 264 and 417 (CU) can't pair!
WARNING: bases 268 and 413 (GA) can't pair!
WARNING: bases 296 and 308 (UU) can't pair!
WARNING: bases 298 and 306 (AA) can't pair!
WARNING: bases 317 and 376 (GA) can't pair!
WARNING: bases 319 and 374 (CC) can't pair!
WARNING: bases 320 and 373 (CC) can't pair!
WARNING: bases 321 and 372 (GG) can't pair!
WARNING: bases 322 and 371 (AG) can't pair!
WARNING: bases 326 and 363 (GG) can't pair!
WARNING: bases 327 and 362 (UU) can't pair!
WARNING: bases 328 and 361 (CC) can't pair!
WARNING: bases 330 and 359 (GG) can't pair!
WARNING: bases 331 and 358 (GA) can't pair!
WARNING: bases 332 and 357 (AC) can't pair!
WARNING: bases 333 and 356 (CC) can't pair!
WARNING: bases 341 and 354 (AG) can't pair!
WARNING: bases 343 and 352 (UU) can't pair!
WARNING: bases 344 and 351 (GG) can't pair!
WARNING: bases 345 and 350 (GA) can't pair!
WARNING: bases 378 and 398 (CA) can't pair!
WARNING: bases 380 and 396 (GG) can't pair!
WARNING: bases 383 and 393 (GA) can't pair!
WARNING: bases 384 and 392 (CC) can't pair!
WARNING: bases 385 and 391 (CC) can't pair!
WARNING: bases 472 and 538 (CA) can't pair!
WARNING: bases 479 and 533 (AG) can't pair!
WARNING: bases 480 and 532 (UU) can't pair!
WARNING: bases 481 and 531 (GG) can't pair!
WARNING: bases 483 and 529 (AC) can't pair!
WARNING: bases 486 and 513 (AG) can't pair!
WARNING: bases 489 and 510 (CC) can't pair!
WARNING: bases 490 and 509 (AG) can't pair!
WARNING: bases 492 and 506 (CC) can't pair!
WARNING: bases 494 and 504 (GA) can't pair!
WARNING: bases 495 and 503 (CC) can't pair!
WARNING: bases 496 and 502 (AG) can't pair!

STDOUT was:

UUAAAACAGCUCUGGGGUUGUUCCCACCCCAGAGGCCCACGUGGCGGCUAGUACACUGGUAUCACGGUACCUUUGUACGCCUGUUUUAUACUCCCUCCCCCGCAACUUAGAAGCAUACAAUUCAAGCUCAAUAGGAGGGGGUGCAAGCCAGCGCCUCCGUGGGCAAGCACUACUGUUUCCCCGGUGAGGCCGCAUAGACUGUUCCCACGGUUGAAAGUGGCCGAUCCGUUAUCCGCUCAUGUACUUCGAGAAGCCUAGUAUCGCUCUGGAAUCUUCGACGCGUUGCGCUCAGCACUCAACCCCGGAGUGUAGCUUGGGCCGAUGAGUCUGGACAGUCCCCACUGGCGACAGUGGUCCAGGCUGCGCUGGCGGCCCACCUGUGGCCCAAAGCCACGGGACGCUAGUUGUGAACAGGGUGUGAAGAGCCUAUUGAGCUACAUGAGAGUCCUCCGGCCCCUGAAUGCGGCUAAUCCUAACCAUGGAGCAGGCAGCUGCAACCCAGCAGCCAGCCUGUCGUAACGCGCAAGUCCGUGGCGGAACCGACUACUUUGGGUGUCCGUGUUUCCUUUUAUUCUUGAAUGGCUGCUUAUGGUGACAAUCAUAGAUUGUUAUCAUAAAGC
.........(((((((((.......)))))))))................(((((..((((......))))..)))))...............................................(((((......((((((((......)))))))).))))).......................((((((...((((((....))))))....)))))).............((((((((.(((((...((.......(((((((.........................(((((.......))))).....(((((((...(((((((((......(((((....)))))))))))))).......)))))))((((((((.....))))))))..............)))))))......))...))))).))))))))...........................(((...(((((((.(((((.(((((.....)))))..)))))..............))))))).)))..............................................((((((((((((((((...)))))))))))).)))) ( -6.70)

Rendering structure of PV mRNA 620 nt long with energy of -6.70 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:

The secondary structure probing data characterize well only two regions: 292-397 and 488-509. Most of the
structure is a prediction.

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

Enzyme or a combination of enzymes used in a single experiment with respective buffer:

ss_experiment_with_enzyme_id: 72

The temperature (in degrees of Celsia):
0 The enzymatic method used to determine the 2D structure:
ribonuclease T1/T2 mix

Enzyme or a combination of enzymes used in a single experiment with respective buffer:

Version: 0

pH `7.80`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `300.00`	Mg²⁺ [mM] `20.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `340.00`	Tris [mM] `30.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Enzyme or a combination of enzymes used in a single experiment with respective buffer:

ss_experiment_with_enzyme_id: 73

The temperature (in degrees of Celsia):
0 The enzymatic method used to determine the 2D structure:
ribonuclease V1

Enzyme or a combination of enzymes used in a single experiment with respective buffer:

Version: 0

pH `7.80`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `300.00`	Mg²⁺ [mM] `0`	Ca²⁺ [mM] `0`
Cl^- [mM] `340.00`	Tris [mM] `30.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

3.1.2. Chemicals used to characterize at least partially the 2D structure.

Chemical reagent used with its respective buffer:

ss_experiment_with_chemical_id: 30

The temperature (in degrees of Celsia):
30 The chemical reagent used to determine the 2D structure:
DMS/kethoxal mix

Chemical reagent used with its respective buffer:

Version: 0

pH `7.40`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `270.00`	Mg²⁺ [mM] `10.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `290.00`	Tris [mM] `0`	BSA [mM] `0`	HEPES [mM] `70.00`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Citations:

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