IRESite_Id:225 summary record describing characteristics of CVB3 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `225`	Version: `5`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-02-01 00:00:00`

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: `CVB3`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
54399972

The mRNA/+RNA description:

Human coxsackievirus B3 strain 20, complete genome.

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

TTAAAACAGC CTGTGGGTTG ATCCCACCCA CAGGGCCCAT TGGGCGCTAG CACTCTGGTA TCACGGTACC TTTGTGCGCC TGTTTTATAC CCCCTCCCCC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AACTGTAACT TAGAAGTAAC ACACACCGAT CAACAGTCAG CGTGGCACAC CAGCCACGTT TTGATCAAGC ACTTCTGTTA CCCCGGACTG AGTATCAATA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GACTGCTCAC GCGGTTGAAG GAGAAAGCGT TCGTTATCCG GCCAACTACT TCGAAAAACC TAGTAACACC GTGGAAGTTG CAGAGTGTTT CGCTCAGCAC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TACCCCAGTG TAGATCAGGT CGATGAGTCA CCGCATTCCC CACGGGCGAC CGTGGCGGTG GCTGCGTTGG CGGCCTGCCC ATGGGGAAAC CCATGGGACG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTCTAATACA GACATGGTGC GAAGAGTCTA TTGAGCTAGT TGGTAGTCCT CCGGCCCCTG AATGCGGCTA ATCCTAACTG CGGAGCACAC ACCCTCAAGC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CAGAGGGCAG TGTGTCGTAA CGGGCAACTC TGCAGCGGAA CCGACTACTT TGGGTGTCCG TGTTTCATTT TATTCCTATA CTGGCTGCTT ATGGTGACAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTGAGAGATT GTTACCATAT AGCTATTGGA TTGGCCATCC GGTGACCAAT AGAGCTATTA TATATCTCTT TGTTGGGTTT ATACCACTTA GCTTGAAAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GGTTAAAACA TTACAATTCA TTGTTAAGTT GAATACAGCA AAATGGGAGC TCAAGTATCA ACGCAAAAGA CTGGGGCACA TGAGACCAGG CTGAATGCTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GCGGCAATTC CATCATTCAC TACACAAATA TTAATTATTA CAAGGATGCC GCATCCAACT CAGCCAATCG GCAGGATTTC ACTCAAGACC CGGGCAAGTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CACAGAACCA GTAAAAGATA TCATGATTAA ATCACTACCA GCTCTCAACT CCCCCACAGT AGAGGAGTGC GGATACAGTG ACAGGGTGAG ATCAATCACA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTAGGTAACT CCACCATAAC GACTCAGGAA TGCGCCAACG TGGTGGTGGG CTATGGAGTA TGGCCAGATT ATCTAAAGGA TAGTGAGGCA ACAGCAGAGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACCAACCGAC CCAACCAGAC GTTGCCACAT GTAGGTTCTA TACCCTTGAC TCTGTGCAAT GGCAGAAAAC CTCACCAGGA TGGTGGTGGA AGCTGCCCGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGCTTTGTCG AACTTAGGAC TGTTTGGGCA GAACATGCAG TACCACTACT TAGGCCGAAC TGGGTATACC GTACATGTGC AGTGCAATGC ATCTAAGTTC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CACCAAGGAT GCTTGCTAGT AGTGTGTGTA CCGGAAGCTG AGATGGGTTG CGCAACGCTA GACAACACCC CATCCAGTGC AGAATTGCTG GGGGGCGATA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCGCAAAAGA GTTTGCGGAC AAACCGGTCG CATCCGGGTC CAACAAGTTG GTACAGAGGG TGGTGTATAA TGCAGGCATG GGGGTGGGTG TTGGAAACCT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CACCATTTTC CCCCACCAAT GGATCAACCT ACGCACCAAT AATAGTGCTA CAATTGTGAT GCCATACACC AACAGTGTAC CTATGGATAA CATGTTTAGG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CATAACAACG TCACCCTAAT GGTTATCCCA TTTGTACCGC TAGATTACTG CCCTGGGTCC ACCACGTACG TCCCAATTAC GGTCACGATA GCCCCAATGT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTGCCGAGTA CAATGGGTTA CGTTTAGCAG GGCACCAGGG CTTACCAACC ATGAATACTC CGGGGAGCTG TCAATTTCTG ACATCAGACG ACTTCCAATC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ACCATCCGCC ATGCCGCAAT ATGACGTCAC ACCAGAGATG AGGATACCTG GTGAGGTGAA AAACTTGATG GAAATAGCTG AGGTTGACTC AGTTGTCCCA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GTCCAAAATG TTGGAGAGAA GGTCAACTCT ATGGAAGCAT ACCAGATACC TGTGAGATCC AATGAAGGAT CTGGAACGCA AGTATTCGGC TTTCCACTGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AACCAGGGTA CTCGAGTGTT TTTAGTCGGA CGCTCCTAGG AGAGATCTTG AACTATTATA CACATTGGTC AGGCAGCATA AAGCTTACGT TTATGTTCTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGGTTCGGCC ATGGCTACTG GAAAATTCCT TTTGGCATAC TCACCACCAG GTGCTGGAGC TCCTACAAAA AGGGTTGATG CCATGCTTGG TACTCATGTA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GTTTGGGACG TGGGGCTACA ATCAAGTTGC GTGCTGTGTA TACCCTGGAT AAGCCAAACA CACTACCGGT TTGTTGCTTC AGATGAGTAT ACCGCAGGGG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GTTTTATTAC GTGCTGGTAT CAAACAAACA TAGTGGTCCC AGCGGATGCC CAAAGCTCCT GTTACATCAT GTGTTTCGTG TCAGCATGCA ATGACTTCTC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGTCAGGCTA TTGAAGGACA CTCCTTTCAT TTCGCAGCAA AACTTTTTCC AGGGCCCAGT GGAAGACGCG ATAACAGCCG CTATAGGGAG AGTTGCGGAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACCGTGGGTA CAGGGCCAAC CAACTCAGAA GCTATACCAG CACTCACTGC TGCTGAGACA GGTCACACGT CACAAGTAGT GCCGGGTGAC ACCATGCAGA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CACGCCACGT TAAGAACTAC CATTCAAGGT CTGAGTCAAC CATAGAGAAC TTCCTATGTA GGTCAGCATG CGTGTACTTT ACGGAGTATA AAAACTCAGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TGCCAAGCGG TATGCTGAAT GGGTATTAAC ACCACGACAA GCAGCACAAC TTAGGAGAAA GCTAGAATTC TTTACCTACG TCCGGTTCGA CCTGGAGCTG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ACGTTTGTCA TAACAAGTAC TCAACAGCCC TCAACCACAC AGAACCAAGA CGCACAGATC CTAACACACC AAATTATGTA CGTACCACCA GGTGGACCTG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TACCAGATAA AGTTGATTCA TACGTGTGGC AAACATCTAC GAATCCCAGT GTGTTTTGGA CCGAGGGAAA CGCCCCGCCG CGCATGTCCA TACCGTTTTT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GAGCATTGGC AACGCCTATT CAAATTTCTA TGACGGATGG TCTGAATTTT CCAGGAACGG AGTTTACGGC ATCAACACGC TAAACAACAT GGGCACGCTA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TATGCAAGAC ATGTCAACGC TGGAAGCACG GGTCCAATAA AAAGCACCAT TAGAATCTAC TTCAAACCGA AGCATGTCAA AGCGTGGATA CCTAGACCAC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CTAGACTCTG CCAATACGAG AAGGCAAAGA ACGTGAACTT CCGACCCAGC GGAGTTACCA CTACTAGGCA AAGCATCACT ACAATGACAA ATACGGGCGC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ATTTGGACAA CAATCAGGGG CAGTGTATGT GGGGAACTAC AGGGTAGTAA ATAGACATCT AGCTACCAGT GCTGACTGGC AAAACTGTGT GTGGGAAAGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TACAACAGAG ACCTCTTAGT GAGCACGACC ACAACACATG GATGTGATAT TATAGCCAGA TGTCAGTGCA CAACGGGAGT GTACTTTTGT GCGTCCAAAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ACAAGCACTA CCCAATTTCG TTTGAAGGAC CAGGTCTAGT AGAGGTCCAA GAGAGTGAAT ACTACCCCAG GAGATACCAA TCCCATGTGC TTTTAGCAGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TGGATTTTCC GAACCAGGTG ACTGTGGCGG TATCCTAAGG TGTGAGCATG GTGTCATTGG CATTGTGACC ATGGGGGGTG AAGGCGTGGT CGGCTTTGCA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GACATCCGTG ATCTCCTGTG GCTGGAAGAT GATGCAATGG AACAGGGAGT GAAGGACTAT GTGGAACAGC TTGGAAATGC ACTCGGCTCC GGCTTTACTA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ACCAAATATG TGAGCAAGTC AACCTCCTGA AAGAATCACT AGTGGGTCAA GACTCCATCT TAGAGAAATC TCTAAAAGCC TTAGTTAAGA TAATATCAGC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CTTAGTAATT GTGGTGAGGA ACCACGATGA CCTGATCACT GTGACTGCCA CACTAGCCCT TATCGGTTGT ACCTCGTCCC CGTGGCGGTG GCTCAAACAG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AAGGTGTCAC AATATTACGG AATCCCTATG GCTGAACGCC AAAACAATAG CTGGCTTAAG AAATTTACTG AAATGACGAA TGCTTGCAAG GGTATGGAAT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GGATAGCTGT CAAAATTCAG AAATTCATTG AATGGCTCAA AGTAAAAATT TTGCCAGAGG TCAGGGAAAA ACACGAATTC CTGAACAGAC TTAAACAACT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CCCCTTATTA GAAAGTCAGA TCGCCACAAT CGAGCAGAGC GCGCCATCCC AAAGTGACCA GGAACAATTA TTTTCCAATG TCCAATACTT TGCCCACTAT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TGCAGAAAGT ACGCTCCCCT CTACGCAGCT GAAGCAAAGA GGGTGTTCTC CCTTGAGAAG AAGATGAGCA ATTACATACA GTTCAAGTCC AAATGCCGTA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TTGAACCTGT ATGTTTGCTC CTGCACGGGA GCCCTGGTGC CGGCAAGTCG GTGGCAACAA ACTTAATTGG AAGGTCGCTT GCTGAGAAAC TCAACAGCTC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AGTGTACTCA CTACCGCCAG ACCCAGATCA CTTCGACGGA TACAAACAGC AGGCCGTGGT GATTATGGAC GATCTATGCC AGAACCCTGA TGGGAAAGAC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GTCTCCTTGT TCTGCCAAAT GGTTTCCAGT GTAGATTTTG TACCACCCAT GGCTGCCCTA GAAGAGAAAG GCATTCTGTT CACCTCACCG TTTGTCTTGG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CATCGACCAA TGCAGGATCT ATTAATGCTC CAACCGTGTC AGATAGCAGA GCCTTGGCAA GGAGATTTCA CTTTGACATG AACATCGAGG TTATTTCCAT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GTACAGTCAG AATGGCAAGA TAAACATGCC CATGTCAGTC AAGACTTGTG ACGATGAGTG TTGCCCGGTC AATTTTAAAA AGTGCTGCCC TCTTGTGTGT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GGGAAGGCTA TACAATTCAT TGATAGAAGA ACACAGGTCA GATACTCTCT AGACATGCTA GTCACCGAGA TGTTTAGGGA GTACAATCAT AGACATAGCG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TGGGGACCAC GCTTGAGGCA CTGTTCCAGG GACCACCAGT ATACAGAGAG ATCAAAATTA GCGTTGCACC AGAGACACCA CCACCGCCCG CCATTGCGGA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CCTGCTCAAA TCGGTAGACA GTGAGGCTGT GAGGGAGTAC TGCAAAGAAA AAGGATGGTT GGTTCCTGAG ATCAACTCCA CCCTCCAAAT TGAGAAACAT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GTCAGTCGGG CTTTCATTTG CTTACAGGCA TTGACCACAT TTGTGTCAGT GGCTGGAATC ATATATATAA TATATAAGCT CTTTGCGGGT TTTCAAGGTG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CTTATACAGG AGTGCCCAAC CAGAAGCCCA GAGTGCCTAC CCTGAGGCAA GCAAAAGTGC AAGGCCCTGC CTTTGAGTTC GCTGTCGCAA TGATGAAAAG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GAACTCAAGC AGGGTGAAAA CTGAATATGG CGAGTTTACC ATGCTGGGCA TCTATGACAG GTGGGCCGTT TTGCCACGCC ACGCCAAACC TGGGCCAACC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ATCTTGATGA ATGATCAAGA GGTTGGTGTG CTAGATGCCA AGGAGCTAGT AGACAAGGAC GGCACCAACT TAGAACTGAC ACTACTCAAA TTGAACCGGA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ATGAGAAGTT CAGAGACATC AGAGGCTTCT TAGCCAAGGA GGAAGTGGAG GTTAATGAGG CAGTGCTAGC AATTAACACC AGCAAGTTTC CCAACATGTA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CATTCCAGTA GGACAGGTCA CAGAATACGG CTTCTTAAAC CTAGGTGGCA CACCCACCAA GAGAATGCTT ATGTACAACT TCCCCACAAG AGCAGGCCAG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TGTGGTGGAG TGCTCATGTC CACCGGCAAG GTACTGGGTA TCCATGTTGG TGGAAATGGC CATCAGGGCT TCTCAGCAGC ACTCCTCAAA CACTACTTCA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ATGATGAGCA AGGTGAAATA GAATTTATTG AGAGCTCAAA GGACGCCGGG TTTCCAGTCA TCAACACACC AAGTAAAACA AAGTTGGAGC CTAGTGTTTT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CCACCAGGTC TTTGAGGGGA ACAAAGAACC AGCAGTACTC AGGAGTGGGG ATCCACGTCT CAAGGCCAAT TTTGAAGAGG CTATATTTTC CAAGTATATA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GGAAATGTCA ACACACACGT GGATGAGTAC ATGCTGGAAG CAGTGGACCA CTACGCAGGC CAACTAGCCA CCCTAGATAT CAGCACTGAA CCAATGAAAC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TGGAGGACGC AGTGTACGGT ACCGAGGGTC TTGAGGCGCT TGATCTAACA ACGAGTGCCG GTTACCCATA TGTTGCACTG GGTATCAAGA AGAGGGACAT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

CCTCTCTAAG AAGACTAAGG ACCTAACAAA GTTAAAGGAA TGTATGGACA AGTATGGCCT GAACCTACCA ATGGTGACTT ATGTAAAAGA TGAGCTCAGG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

TCCATAGAGA AGGTAGCGAA AGGAAAGTCT AGGCTGATTG AGGCGTCCAG TTTGAATGAT TCAGTGGCGA TGAGACAGAC ATTTGGTAAT CTGTACAAAA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CTTTCCACCT AAACCCAGGG GTTGTGACTG GTAGTGCTGT TGGGTGTGAC CCAGACCTCT TTTGGAGCAA GATACCAGTG ATGTTAGATG GACATCTCAT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

AGCATTTGAT TACTCTGGGT ACGATGCTAG CTTAAGCCCT GTCTGGTTTG CTTGCCTAAA AATGTTACTT GAGAAGCTTG GATACACGCA CAAAGAGACA 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

AACTACATTG ACTACTTGTG CAACTCCCAT CACCTGTACA GGGATAAACA TTACTTTGTG AGGGGTGGCA TGCCCTCGGG ATGTTCTGGT ACCAGTATTT 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

TCAACTCAAT GATTAACAAT ATCATAATTA GGACACTAAT GCTAAAAGTG TACAAAGGGA TTGACTTGGA CCAATTCAGG ATGATCGCAT ATGGTGATGA 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

TGTGATCGCA TCGTACCCAT GGCCTATAGA TGCATCTTTA CTCGCTGAAG CTGGTAAGGG TTACGGGCTG ATCATGACAC CAGCAGATAA GGGAGAGTGC 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

TTTAACGAAG TTACCTGGAC CAACGTCACT TTCCTAAAGA GGTATTTTAG AGCAGATGAA CAGTACCCCT TCCTGGTGCA TCCTGTTATG CCCATGAAAG 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

ACATACACGA ATCAATTAGA TGGACCAAGG ATCCAAAGAA CACCCAAGAT CACGTGCGCT CACTGTGTCT ATTAGCTTGG CATAACGGGG AGCACGAATA 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TGAGGAGTTC ATCCGTAAAA TTAGAAGCGT CCCAGTCGGA CGTTGTTTGA CCCTCCCCGC GTTTTCAACT CTACGCAGGA AGTGGTTGGA CTCCTTTTAG 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

ATTAGAGACA ATTTGAAATA ATTTAGATTG GCTTAACCCT ACTGTGCTAA CCGAACCAGA TAACGGTACA GTAGGGGTAA ATTCTCCGCA TTCGGTGCG
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

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

Human coxsackievirus B3 20

A promoter reported in cDNA corresponding to IRES sequence:
no (not convincing) The total number of notable open-reading frames (ORFs):
1

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
heterogeneous_population_of_molecules_found

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
no_promoter_confirmed

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Homo sapiens HeLa (ATCC CCL-2)

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
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:

no

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

743-7300

Remarks:

Jang et al. (2004) have shown that in Fig. 1D and 2A that probably aberrant splicing of pRstCVB3F occurs in
HeLa cell and that the presence of shorter transcripts is not due to a cryptic promoter in CVB3 IRES region.

Jimenez et al. (2005) have shown that in Fig. 2C that aberrant splicing is an issue with pRstCVB3F. Presence
of a promoter was ruled out using promoter-less plasmid (Jang et al., 2004) but for an unknown reason the
promoter-less plasmid (deltaSV40)pRstCVB3F lacks not only SV40 promoter/enhancer region as well as the
chimeric intron and T7 promoter region (the NheI site is just downstream after T7 promoter) but also authors
have intentionally omitted also 45bp long fragment between PacI and NheI sites containing bases 2-46 of CVB3
5'-UTR studied in pRstCVB3F plasmid: taaaacagcctgtgggttgatcccacccacagggcccattgggcg and performed 3-fragment
ligation instead of 2-fragment ligation.

Citations:

Jang G. M., Leong L. E., Hoang L. T., Wang P. H., Gutman G. A., Semler B. L. (2004) Structurally distinct elements mediate internal ribosome entry within the 5'-noncoding region of a voltage-gated potassium channel mRNA. J. Biol. Chem. 279(46):47419-47430

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

IRESs:

IRES:

Version: `5`	Last change: `2009-08-18 16:24:54`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `CVB3`

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

1-750

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

TTAAAACAGC CTGTGGGTTG ATCCCACCCA CAGGGCCCAT TGGGCGCTAG CACTCTGGTA TCACGGTACC TTTGTGCGCC TGTTTTATAC CCCCTCCCCC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AACTGTAACT TAGAAGTAAC ACACACCGAT CAACAGTCAG CGTGGCACAC CAGCCACGTT TTGATCAAGC ACTTCTGTTA CCCCGGACTG AGTATCAATA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GACTGCTCAC GCGGTTGAAG GAGAAAGCGT TCGTTATCCG GCCAACTACT TCGAAAAACC TAGTAACACC GTGGAAGTTG CAGAGTGTTT CGCTCAGCAC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TACCCCAGTG TAGATCAGGT CGATGAGTCA CCGCATTCCC CACGGGCGAC CGTGGCGGTG GCTGCGTTGG CGGCCTGCCC ATGGGGAAAC CCATGGGACG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTCTAATACA GACATGGTGC GAAGAGTCTA TTGAGCTAGT TGGTAGTCCT CCGGCCCCTG AATGCGGCTA ATCCTAACTG CGGAGCACAC ACCCTCAAGC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CAGAGGGCAG TGTGTCGTAA CGGGCAACTC TGCAGCGGAA CCGACTACTT TGGGTGTCCG TGTTTCATTT TATTCCTATA CTGGCTGCTT ATGGTGACAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTGAGAGATT GTTACCATAT AGCTATTGGA TTGGCCATCC GGTGACCAAT AGAGCTATTA TATATCTCTT TGTTGGGTTT ATACCACTTA GCTTGAAAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GGTTAAAACA TTACAATTCA TTGTTAAGTT GAATACAGCA AAATGGGAGC
^701       ^711       ^721       ^731       ^741

Remarks:

The results could be biased by inclusion of FMDV 2A protease in the plasmid vector (IRESite_Id:211). IRESite
annotators  believe the observed reporter protein yields were decreased by the "protease" sequence so the IRES
appears weaker than it actually is. The observed aberrant splicing makes the in vivo of Jang et al. and
Jimenez et al. results hard to interpret.

However, in vitro toe-print assays were done by Bailey and Tapprich (2007).

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

Bailey J. M., Tapprich W. E. (2007) Structure of the 5' nontranslated region of the coxsackievirus b3 genome: Chemical modification and comparative sequence analysis. J. Virol. 81(2):650-668

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `2`	Last change: `2009-08-30 13:01:19`
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):
603-606

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

3.1.2. 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:
HeLa cell lysate

Remarks:

The region 603-606 is a 'GAGA' containing loop, complying the general GNRA motif.

Citations:

Ray PS, Das S (2002) La autoantigen is required for the internal ribosome entry site-mediated translation of Coxsackievirus B3 RNA. Nucleic Acids Res. 20(30):4500-4508

Bhattacharyya S, Das S (2005) Mapping of secondary structure of the spacer region within the 5'-untranslated region of the coxsackievirus B3 RNA: possible role of an apical GAGA loop in binding La protein and influencing internal initiation of translation. Virus Res. 108(1-2):89-100

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 46

Version: `3`	Last change: `2009-08-30 13:01:19`
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):
1-647

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

TTAAAACAGC CTGTGGGTTG ATCCCACCCA CAGGGCCCAT TGGGCGCTAG CACTCTGGTA TCACGGTACC TTTGTGCGCC TGTTTTATAC CCCCTCCCCC 
.((((((((( ((((((((.. .....))))) ))))((((.. .))))((..( (((...(((( (....))))) ...))))))) )))))))... .......... 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AACTGTAACT TAGAAGTAAC ACACACCGAT CAACAGTCAG CGTGGCACAC CAGCCACGTT TTGATCAAGC ACTTCTGTTA CCCCGGACTG AGTATCAATA 
.......... ..((((((.. .......((( ((.......( ((((((.... ..))))))). .))))).... .......... ...(((((.. ....((..(( 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GACTGCTCAC GCGGTTGAAG GAGAAAGCGT TCGTTATCCG GCCAACTACT TCGAAAAACC TAGTAACACC GTGGAAGTTG CAGAGTGTTT CGCTCAGCAC 
((((((.... )))))))).. ))......)) )))....... ((((((((.( ((((...... ......(((( (((...(((. .(((((((.. ......(((( 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TACCCCAGTG TAGATCAGGT CGATGAGTCA CCGCATTCCC CACGGGCGAC CGTGGCGGTG GCTGCGTTGG CGGCCTGCCC ATGGGGAAAC CCATGGGACG 
(.....)))) )....((((( (((((((((( ((((...... (((((....) )))))))))) ))).)))... )))))))((( (((((....) )))))))))) 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTCTAATACA GACATGGTGC GAAGAGTCTA TTGAGCTAGT TGGTAGTCCT CCGGCCCCTG AATGCGGCTA ATCCTAACTG CGGAGCACAC ACCCTCAAGC 
)))))))... ..))))))). .......... ))))).)))) ))))...... .(((.(((.( ((..(((... .(((...((( ((((.((((( .(((((.... 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CAGAGGGCAG TGTGTCGTAA CGGGCAACTC TGCAGCGGAA CCGACTACTT TGGGTGTCCG TGTTTCATTT TATTCCTATA CTGGCTGCTT ATGGTGACAA 
..)))))..) ))))...... .......))) ))))).))). ))).....)) ))))...))) .......... .......... ......(((( ((((((((.( 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTGAGAGATT GTTACCATAT AGCTATTGGA TTGGCCATCC GGTGACC
((....))). ))))))))). )))((((((( (.....)))) ))))...
^601       ^611       ^621       ^631       ^641

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:

.(((((((((((((((((.......)))))))))((((...))))((..((((...(((((....)))))...)))))))))))))).........................((((((.........(((((.......(((((((......)))))))..))))).................(((((......((..((((((((....))))))))..))......))))).......((((((((.(((((............(((((((...(((..(((((((........(((((.....)))))....(((((((((((((((((((......(((((....)))))))))))))).)))...)))))))((((((((....)))))))))))))))))).....)))))))...........))))).)))))))).......(((.(((.(((..(((....(((...(((((((.(((((.(((((......)))))..))))).............)))))))).))).))).....))))))...)))..........................((((((((((((.(((....))).))))))))).)))((((((((.....))))))))...
ERROR: unbalanced brackets in make_pair_table

STDOUT was:

Remarks:

Authors state that they observed no influence on the mapped structure when they used transcripts longer at the
3'-end.

Citations:

Bailey J. M., Tapprich W. E. (2007) Structure of the 5' nontranslated region of the coxsackievirus b3 genome: Chemical modification and comparative sequence analysis. J. Virol. 81(2):650-668

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