IRESite_Id:242 summary record describing characteristics of PV_type1

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `242`	Version: `6`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2009-08-30 13:34:34`

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:
61252

The mRNA/+RNA description:

Human poliovirus 1 Mahoney, complete genome.

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

TTAAAACAGC TCTGGGGTTG TACCCACCCC AGAGGCCCAC GTGGCGGCTA GTACTCCGGT ATTGCGGTAC CCTTGTACGC CTGTTTTATA CTCCCTTCCC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GTAACTTAGA CGCACAAAAC CAAGTTCAAT AGAAGGGGGT ACAAACCAGT ACCACCACGA ACAAGCACTT CTGTTTCCCC GGTGATGTCG TATAGACTGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TTGCGTGGTT GAAAGCGACG GATCCGTTAT CCGCTTATGT ACTTCGAGAA GCCCAGTACC ACCTCGGAAT CTTCGATGCG TTGCGCTCAG CACTCAACCC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CAGAGTGTAG CTTAGGCTGA TGAGTCTGGA CATCCCTCAC CGGTGACGGT GGTCCAGGCT GCGTTGGCGG CCTACCTATG GCTAACGCCA TGGGACGCTA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GTTGTGAACA AGGTGTGAAG AGCCTATTGA GCTACATAAG AATCCTCCGG CCCCTGAATG CGGCTAATCC CAACCTCGGA GCAGGTGGTC ACAAACCAGT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GATTGGCCTG TCGTAACGCG CAAGTCCGTG GCGGAACCGA CTACTTTGGG TGTCCGTGTT TCCTTTTATT TTATTGTGGC TGCTTATGGT GACAATCACA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GATTGTTATC ATAAAGCGAA TTGGATTGGC CATCCGGTGA AAGTGAGACT CATTATCTAT CTGTTTGCTG GATCCGCTCC ATTGAGTGTG TTTACTCTAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GTACAATTTC AACAGTTATT TCAATCAGAC AATTGTATCA TAATGGGTGC TCAGGTTTCA TCACAGAAAG TGGGCGCACA TGAAAACTCA AATAGAGCGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATGGTGGTTC TACCATTAAT TACACCACCA TTAATTATTA TAGAGATTCA GCTAGTAACG CGGCTTCGAA ACAGGACTTC TCTCAAGACC CTTCCAAGTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CACCGAGCCC ATCAAGGATG TCCTGATAAA AACAGCCCCA ATGCTAAACT CGCCAAACAT AGAGGCTTGC GGGTATAGCG ATAGAGTACT GCAATTAACA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CTGGGAAACT CCACTATAAC CACACAGGAG GCGGCTAATT CAGTAGTCGC TTATGGGCGT TGGCCTGAAT ATCTGAGGGA CAGCGAAGCC AATCCAGTGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACCAGCCGAC AGAACCAGAC GTCGCTGCAT GCAGGTTTTA TACGCTAGAC ACCGTGTCTT GGACGAAAGA GTCGCGAGGG TGGTGGTGGA AGTTGCCTGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGCACTGAGG GACATGGGAC TCTTTGGGCA AAATATGTAC TACCACTACC TAGGTAGGTC CGGGTACACC GTGCATGTAC AGTGTAACGC CTCCAAATTC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CACCAGGGGG CACTAGGGGT ATTCGCCGTA CCAGAGATGT GTCTGGCCGG GGATAGCAAC ACCACTACCA TGCACACCAG CTATCAAAAT GCCAATCCTG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCGAGAAAGG AGGCACTTTC ACGGGTACGT TCACTCCTGA CAACAACCAG ACATCACCTG CCCGCAGGTT CTGCCCGGTG GATTACCTCC TTGGAAATGG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CACGTTGTTG GGGAATGCCT TTGTGTTCCC GCACCAGATA ATAAACCTAC GGACCAACAA CTGTGCTACA CTGGTACTCC CTTACGTGAA CTCCCTCTCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ATAGATAGTA TGGTAAAGCA CAATAATTGG GGAATTGCAA TATTACCATT GGCCCCATTA AATTTTGCTA GTGAGTCCTC CCCAGAGATT CCAATCACCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGACCATAGC CCCTATGTGC TGTGAGTTCA ATGGATTAAG AAACATCACC CTGCCACGCT TACAGGGCCT GCCGGTCATG AACACCCCTG GTAGCAATCA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ATATCTTACT GCAGACAACT TCCAGTCACC GTGTGCGCTG CCTGAATTTG ATGTGACCCC ACCTATTGAC ATACCCGGTG AAGTAAAGAA CATGATGGAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TTGGCAGAAA TCGACACCAT GATTCCCTTT GACTTAAGTG CCACAAAAAA GAACACCATG GAAATGTATA GGGTTCGGTT AAGTGACAAA CCACATACAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ACGATCCCAT ACTCTGCCTG TCACTCTCTC CAGCTTCAGA TCCTAGGTTG TCACATACTA TGCTTGGAGA AATCCTAAAT TACTACACAC ACTGGGCAGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ATCCCTGAAG TTCACGTTTC TGTTCTGTGG ATTCATGATG GCAACTGGCA AACTGTTGGT GTCATACGCG CCTCCTGGAG CCGACCCACC AAAGAAGCGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AAGGAGGCGA TGTTGGGAAC ACATGTGATC TGGGACATAG GACTGCAGTC CTCATGTACT ATGGTAGTGC CATGGATTAG CAACACCACG TATCGGCAAA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CCATAGATGA TAGTTTCACC GAAGGCGGAT ACATCAGCGT CTTCTACCAA ACTAGAATAG TCGTCCCTCT TTCGACACCC AGAGAGATGG ACATCCTTGG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTTTGTGTCA GCGTGTAATG ACTTCAGCGT GCGCTTGTTG CGAGATACCA CACATATAGA GCAAAAAGCG CTAGCACAGG GGTTAGGTCA GATGCTTGAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AGCATGATTG ACAACACAGT CCGTGAAACG GTGGGGGCGG CAACATCTAG AGACGCTCTC CCAAACACTG AAGCCAGTGG ACCAACACAC TCCAAGGAAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTCCGGCACT CACCGCAGTG GAAACTGGGG CCACAAATCC ACTAGTCCCT TCTGATACAG TGCAAACCAG ACATGTTGTA CAACATAGGT CAAGGTCAGA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GTCTAGCATA GAGTCTTTCT TCGCGCGGGG TGCATGCGTG ACCATTATGA CCGTGGATAA CCCAGCTTCC ACCACGAATA AGGATAAGCT ATTTGCAGTG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TGGAAGATCA CTTATAAAGA TACTGTCCAG TTACGGAGGA AATTGGAGTT CTTCACCTAT TCTAGATTTG ATATGGAACT TACCTTTGTG GTTACTGCAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATTTCACTGA GACTAACAAT GGGCATGCCT TAAATCAAGT GTACCAAATT ATGTACGTAC CACCAGGCGC TCCAGTGCCC GAGAAATGGG ACGACTACAC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ATGGCAAACC TCATCAAATC CATCAATCTT TTACACCTAC GGAACAGCTC CAGCCCGGAT CTCGGTACCG TATGTTGGTA TTTCGAACGC CTATTCACAC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TTTTACGACG GTTTTTCCAA AGTACCACTG AAGGACCAGT CGGCAGCACT AGGTGACTCC CTTTATGGTG CAGCATCTCT AAATGACTTC GGTATTTTGG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CTGTTAGAGT AGTCAATGAT CACAACCCGA CCAAGGTCAC CTCCAAAATC AGAGTGTATC TAAAACCCAA ACACATCAGA GTCTGGTGCC CGCGTCCACC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GAGGGCAGTG GCGTACTACG GCCCTGGAGT GGATTACAAG GATGGTACGC TTACACCCCT CTCCACCAAG GATCTGACCA CATATGGATT CGGACACCAA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

AACAAAGCGG TGTACACTGC AGGTTACAAA ATTTGCAACT ACCACTTGGC CACTCAGGAT GATTTGCAAA ACGCAGTGAA CGTCATGTGG AGTAGAGACC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TCTTAGTCAC AGAATCAAGA GCCCAGGGCA CCGATTCAAT CGCAAGGTGC AATTGCAACG CAGGGGTGTA CTACTGCGAG TCTAGAAGGA AATACTACCC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AGTATCCTTC GTTGGCCCAA CGTTCCAGTA CATGGAGGCT AATAACTATT ACCCAGCTAG GTACCAGTCC CATATGCTCA TTGGCCATGG ATTCGCATCT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CCAGGGGATT GTGGTGGCAT ACTCAGATGT CACCACGGGG TGATAGGGAT CATTACTGCT GGTGGCGAAG GGTTGGTTGC ATTTTCAGAC ATTAGAGACT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TGTATGCCTA CGAAGAAGAA GCCATGGAAC AAGGCATCAC CAATTACATA GAGTCACTTG GGGCCGCATT TGGAAGTGGA TTTACTCAGC AGATTAGCGA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CAAAATAACA GAGTTGACCA ATATGGTGAC CAGTACCATC ACTGAAAAGC TACTTAAGAA CTTGATCAAG ATCATATCCT CACTAGTTAT TATAACTAGG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AACTATGAAG ACACCACAAC AGTGCTCGCT ACCCTGGCCC TTCTTGGGTG TGATGCTTCA CCATGGCAGT GGCTTAGAAA GAAAGCATGC GATGTTCTGG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AGATACCTTA TGTCATCAAG CAAGGTGACA GTTGGTTGAA GAAGTTTACT GAAGCATGCA ACGCAGCTAA GGGACTGGAG TGGGTGTCAA ACAAAATCTC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

AAAATTCATT GATTGGCTCA AGGAGAAAAT TATCCCACAA GCTAGAGATA AGTTGGAATT TGTAACAAAA CTTAGACAAC TAGAAATGCT GGAAAACCAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ATCTCAACTA TACACCAATC ATGCCCTAGT CAGGAACACC AGGAAATTCT ATTCAATAAT GTCAGATGGT TATCCATCCA GTCTAAGAGG TTTGCCCCTC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TTTACGCAGT GGAAGCCAAA AGAATACAGA AACTAGAGCA TACTATTAAC AACTACATAC AGTTCAAGAG CAAACACCGT ATTGAACCAG TATGTTTGCT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AGTACATGGC AGCCCCGGAA CAGGTAAATC TGTAGCAACC AACCTGATTG CTAGAGCCAT AGCTGAAAGA GAAAACACGT CCACGTACTC GCTACCCCCG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GATCCATCAC ACTTCGACGG ATACAAACAA CAGGGAGTGG TGATTATGGA CGACCTGAAT CAAAACCCAG ATGGTGCGGA CATGAAGCTG TTCTGTCAGA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TGGTATCAAC AGTGGAGTTT ATACCACCCA TGGCATCCCT GGAGGAGAAA GGAATCCTGT TTACTTCAAA TTACGTTCTA GCATCCACAA ACTCAAGCAG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AATTTCCCCC CCCACTGTGG CACACAGTGA TGCATTAGCC AGGCGCTTTG CGTTCGACAT GGACATTCAG GTCATGAATG AGTATTCTAG AGATGGGAAA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TTGAACATGG CCATGGCTAC TGAAATGTGT AAGAACTGTC ACCAACCAGC AAACTTTAAG AGATGCTGTC CTTTAGTGTG TGGTAAGGCA ATTCAATTAA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TGGACAAATC TTCCAGAGTT AGATACAGTA TTGACCAGAT CACTACAATG ATTATCAATG AGAGAAACAG AAGATCCAAC ATTGGCAATT GTATGGAGGC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TTTGTTTCAA GGACCACTCC AGTATAAAGA CTTGAAAATT GACATCAAGA CGAGTCCCCC TCCTGAATGT ATCAATGACT TGCTCCAAGC AGTTGACTCC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CAGGAGGTGA GAGATTACTG TGAGAAGAAG GGTTGGATAG TCAACATCAC CAGCCAGGTT CAAACAGAAA GGAACATCAA CAGGGCAATG ACAATTCTAC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

AAGCGGTGAC AACCTTCGCC GCAGTGGCTG GAGTTGTCTA TGTCATGTAT AAACTGTTTG CTGGACACCA GGGAGCATAC ACTGGTTTAC CAAACAAAAA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ACCCAACGTG CCCACCATTC GGACAGCAAA GGTACAAGGA CCAGGGTTCG ATTACGCAGT GGCTATGGCT AAAAGAAACA TTGTTACAGC AACTACTAGC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AAGGGAGAGT TCACTATGTT AGGAGTCCAC GACAACGTGG CTATTTTACC AACCCACGCT TCACCTGGTG AAAGCATTGT GATCGATGGC AAAGAAGTGG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

AGATCTTGGA TGCCAAAGCG CTCGAAGATC AAGCAGGAAC CAATCTTGAA ATCACTATAA TCACTCTAAA GAGAAATGAA AAGTTCAGAG ACATTAGACC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ACATATACCT ACTCAAATCA CTGAGACAAA TGATGGAGTC TTGATCGTGA ACACTAGCAA GTACCCCAAT ATGTATGTTC CTGTCGGTGC TGTGACTGAA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CAGGGATATC TAAATCTCGG TGGGCGCCAA ACTGCTCGTA CTCTAATGTA CAACTTTCCA ACCAGAGCAG GACAGTGTGG TGGAGTCATC ACATGTACTG 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

GGAAAGTCAT CGGGATGCAT GTTGGTGGGA ACGGTTCACA CGGGTTTGCA GCGGCCCTGA AGCGATCATA CTTCACTCAG AGTCAAGGTG AAATCCAGTG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GATGAGACCT TCGAAGGAAG TGGGATATCC AATCATAAAT GCCCCGTCCA AAACCAAGCT TGAACCCAGT GCTTTCCACT ATGTGTTTGA AGGGGTGAAG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GAACCAGCAG TCCTCACTAA AAACGATCCC AGGCTTAAGA CAGACTTTGA GGAGGCAATT TTCTCCAAGT ACGTGGGTAA CAAAATTACT GAAGTGGATG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

AGTACATGAA AGAGGCAGTA GACCACTATG CTGGCCAGCT CATGTCACTA GACATCAACA CAGAACAAAT GTGCTTGGAG GATGCCATGT ATGGCACTGA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TGGTCTAGAA GCACTTGATT TGTCCACCAG TGCTGGCTAC CCTTATGTAG CAATGGGAAA GAAGAAGAGA GACATCTTGA ACAAACAAAC CAGAGACACT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AAGGAAATGC AAAAACTGCT CGACACATAT GGAATCAACC TCCCACTGGT GACTTATGTA AAGGATGAAC TTAGATCCAA AACAAAGGTT GAGCAGGGGA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

AATCCAGATT AATTGAAGCT TCTAGTTTGA ATGACTCAGT GGCAATGAGA ATGGCTTTTG GGAACCTATA TGCTGCTTTT CACAAAAACC CAGGAGTGAT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

AACAGGTTCA GCAGTGGGGT GCGATCCAGA TTTGTTTTGG AGCAAAATTC CGGTATTGAT GGAAGAGAAG CTGTTTGCTT TTGACTACAC AGGGTATGAT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GCATCTCTCA GCCCTGCTTG GTTCGAGGCA CTAAAGATGG TGCTTGAGAA AATCGGATTC GGAGACAGAG TTGACTACAT CGACTACCTA AACCACTCAC 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ACCACCTGTA CAAGAATAAA ACATACTGTG TCAAGGGCGG TATGCCATCT GGCTGCTCAG GCACTTCAAT TTTTAACTCA ATGATTAACA ACTTGATTAT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

CAGGACACTC TTACTGAAAA CCTACAAGGG CATAGATTTA GACCACCTAA AAATGATTGC CTATGGTGAT GATGTAATTG CTTCCTACCC CCATGAAGTT 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

GACGCTAGTC TCCTAGCCCA ATCAGGAAAA GACTATGGAC TAACTATGAC TCCAGCTGAC AAATCAGCTA CATTTGAAAC AGTCACATGG GAGAATGTAA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CATTCTTGAA GAGATTCTTC AGGGCAGACG AGAAATACCC ATTTCTTATT CATCCAGTAA TGCCAATGAA GGAAATTCAT GAATCAATTA GATGGACTAA 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

AGATCCTAGG AACACTCAGG ATCACGTTCG CTCTCTGTGC CTTTTAGCTT GGCACAATGG CGAAGAAGAA TATAACAAAT TCCTAGCTAA AATCAGGAGT 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

GTGCCAATTG GAAGAGCTTT ATTGCTCCCA GAGTACTCAA CATTGTACCG CCGTTGGCTT GACTCATTTT AGTAACCCTA CCTCAGTCGA ATTGGATTGG 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

GTCATACTGT TGTAGGGGTA AATTTTTCTT TAATTCGGAG
^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:
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):

743-7372

Remarks:

The 5'-UTR viral sequence matches the IRES segment used experimentally, for example included in the pSBC-1
(GI:58272) vector from Dirks et al., 1993 who obtained the sequence of the poliovirus type 1 Mahoney strain
from P. Sarnow extending from nt 1 to 628.

Pelletier et al. (1988) reported the IRES activity in the region 320-631.

Citations:

Dirks W., Wirth M., Hauser H. (1993) Dicistronic transcription units for gene expression in mammalian cells. Gene. 128(2):247-249

IRESs:

IRES:

Version: `6`	Last change: `2009-08-30 13:34:34`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `PV_type1_Mahoney`

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

320-631

Conclusion:
strongly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

ATGAGTCTGG ACATCCCTCA CCGGTGACGG TGGTCCAGGC TGCGTTGGCG GCCTACCTAT GGCTAACGCC ATGGGACGCT AGTTGTGAAC AAGGTGTGAA 
^320       ^330       ^340       ^350       ^360       ^370       ^380       ^390       ^400       ^410       

GAGCCTATTG AGCTACATAA GAATCCTCCG GCCCCTGAAT GCGGCTAATC CCAACCTCGG AGCAGGTGGT CACAAACCAG TGATTGGCCT GTCGTAACGC 
^420       ^430       ^440       ^450       ^460       ^470       ^480       ^490       ^500       ^510       

GCAAGTCCGT GGCGGAACCG ACTACTTTGG GTGTCCGTGT TTCCTTTTAT TTTATTGTGG CTGCTTATGG TGACAATCAC AGATTGTTAT CATAAAGCGA 
^520       ^530       ^540       ^550       ^560       ^570       ^580       ^590       ^600       ^610       

ATTGGATTGG CC
^620       ^630

Citations:

Dirks W., Wirth M., Hauser H. (1993) Dicistronic transcription units for gene expression in mammalian cells. Gene. 128(2):247-249

Pelletier J, Kaplan G, Racaniello VR, Sonenberg N (1988) Cap-independent translation of poliovirus mRNA is conferred by sequence elements within the 5' noncoding region. Mol. Cell. Biol. 8(3):1103-1112

Trono D, Pelletier J, Sonenberg N, Baltimore D (1988) Translation in mammalian cells of a gene linked to the poliovirus 5' noncoding region. Science. 241(4864):445-448

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `2`	Last change: `2009-08-30 03:13:28`
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_and_must_be_supplemented

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

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_vivo

The organism where action of this ITAF was studied:

Homo sapiens

Remarks:

Transfected BS-C-1 cells transcripts co-expressing PTB produced 12-fold more reporter protein but only 2.4x
more in HeLa cells which contain more of endogenous PTB (Gosert et al., 2000).

Citations:

Hunt S. L., Hsuan J. J., Totty N., Jackson R. J. (1999) unr, a cellular cytoplasmic RNA-binding protein with five cold-shock domains, is required for internal initiation of translation of human rhinovirus RNA. Genes. Dev. 13(4):437-448

Gosert R, Chang KH, Rijnbrand R, Yi M, Sangar DV, Lemon SM (2000) Transient expression of cellular polypyrimidine-tract binding protein stimulates cap-independent translation directed by both picornaviral and flaviviral internal ribosome entry sites In vivo. Mol. Cell. Biol. 20(5):1583-1595

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: Václav Vopálenský

ITAF abbreviated name:
Unr

ITAF fullname:
upstream of N-ras

ITAF description (long):
Unr protein is known to bind to gaagaaguaa

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_vivo

The organism where action of this ITAF was studied:

Mus musculus ES

Citations:

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 (ITAF):

Version: `5`	Last change: `2009-08-30 14:01:31`
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

OPTIONAL: The interacting RNA base range (if any):
1-95,230-430

ITAF protein characteristics:

Version: `3`	Last change: `2009-08-30 14:16:52`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
PCBP-2

ITAF fullname:
poly(rC)-binding protein 2 (39 kDa)

ITAF description (long):
Required for poliovirus IRES activity (Blyn et al. 1996 and 1997) and replication (Toyoda et al., 2007). Its amount is not limiting in rabbit reticulocyte lysates (RRL) (Hunt and Jackson 1999).

3.3.2. 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:

Cytosines in regions 93-95 and 98-100 are required for viral replication while not translation although they
are present in the cloverleaf structure in region 1-89 (Toyoda et al., 2007).

PCBP2 also binds to domain IV of PV IRES and is required for ts activity (Blyn et al., 1996, 1997; Gamarnik et
al., 1997; Walter et al., 2002). Blyn et al. (1997) reported that PCBP1 cannot functionally replace PCBP2 in
HeLa cells in respect to translation initiation. This is in agreement with Walter et al. (2002) who reported
that PCBP1 can replace PCBP2 only in respect to replication.

Citations:

Hunt S. L., Jackson R. J. (1999) Polypyrimidine-tract binding protein (PTB) is necessary, but not sufficient, for efficient internal initiation of translation of human rhinovirus-2 RNA. RNA. 5(3):344-359

Toyoda H, Franco D, Fujita K, Paul AV, Wimmer E (2007) Replication of poliovirus requires binding of the poly(rC) binding protein to the cloverleaf as well as to the adjacent C-rich spacer sequence between the cloverleaf and the internal ribosomal entry site. J. Virol. 81(18):10017-10028

Blyn LB, Swiderek KM, Richards O, Stahl DC, Semler BL, Ehrenfeld E (1996) Poly(rC) binding protein 2 binds to stem-loop IV of the poliovirus RNA 5' noncoding region: identification by automated liquid chromatography-tandem mass spectrometry. Proc. Natl. Acad. Sci. U.S.A. 93(20):11115-11120

Blyn LB, Towner JS, Semler BL, Ehrenfeld E (1997) Requirement of poly(rC) binding protein 2 for translation of poliovirus RNA. J. Virol. 71(8):6243-6246

Gamarnik AV, Andino R (1997) Two functional complexes formed by KH domain containing proteins with the 5' noncoding region of poliovirus RNA. RNA. 3(8):882-892

Walter BL, Parsley TB, Ehrenfeld E, Semler BL (2002) Distinct poly(rC) binding protein KH domain determinants for poliovirus translation initiation and viral RNA replication. J. Virol. 76(23):12008-12022

IRES trans-acting factor (ITAF):

Version: `1`	Last change: `2009-08-29 12:27:35`
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: `2`	Last change: `2009-08-29 12:19:15`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
La

ITAF fullname:
La autoantigen

ITAF description (long):
La autoantigen (p52), 52 kDa RNA binding protein, predominantly localized to nucleus, unwinds the dsRNA in ATP-dependent manner, forms a dimer

3.4.2. 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_although_in_limiting_concentration

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

Citations:

Craig AW, Svitkin YV, Lee HS, Belsham GJ, Sonenberg N (1997) The La autoantigen contains a dimerization domain that is essential for enhancing translation. Mol. Cell. Biol. 1(17):163-169

Meerovitch K, Svitkin YV, Lee HS, Lejbkowicz F, Kenan DJ, Chan EK, Agol VI, Keene JD, Sonenberg N (1993) La autoantigen enhances and corrects aberrant translation of poliovirus RNA in reticulocyte lysate. J. Virol. 7(67):3798-3807

Svitkin YV, Meerovitch K, Lee HS, Dholakia JN, Kenan DJ, Agol VI, Sonenberg N (1994) Internal translation initiation on poliovirus RNA: further characterization of La function in poliovirus translation in vitro. J. Virol. 3(68):1544-1550

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 37

Version: `1`	Last change: `2009-08-30 03:08:45`
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):
178-224

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

CCCGGTGATG TCGTATAGAC TGCTTGCGTG GTTGAAAGCG ACGGATC
........(( ((((...((( (((....))) )))....))) )))....
^178       ^188       ^198       ^208       ^218

Rendering structure of PV mRNA 47 nt long with energy of -12.00 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:

For the structure probing authors used alpha sarcin or RNase T1 at 30 oC and DMS.

Citations:

Najita L, Sarnow P (1990) Oxidation-reduction sensitive interaction of a cellular 50-kDa protein with an RNA hairpin in the 5' noncoding region of the poliovirus genome. Proc. Natl. Acad. Sci. U.S.A. 15(87):5846-5850

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