IRESite_Id:597 summary record describing characteristics of TMEV IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `597`	Version: `1`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-18 22:42:30`
Reviewed by: Martin Mokrejš	Last change: `2009-08-18 23:09:29`

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
335239

The mRNA/+RNA description:

Theiler's murine encephalomyelitis virus (TMEV) RNA polyprotein, complete genome.

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

TTGAAAGGGG GCCCGGGGGA TCTCCCCCGC GGTAACTGGT GACAGTTGTC GCGGACGGAG ATCATCCCCC GGTTACCCCC TTTCGACGCG GGTACTGCGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TAGTGCCACC CCAGTCTTTC CTACTCCCGA CTCCCGACCC TAACCCAGGT TCCTCGGAAC AGGAACACCA ATTTACTCAT CCCCTGGATG CTGACTAATC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGAGGAACGT CAGCATTTTC CGGCCCAGGC TAAGAGAAGT AGATAAGTTA GAATCCAAAT TGATTTATCA TCCCCTTGAC GAATTCGCGT TGGAAAAACA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCTCTCACTT GCCGCTCTTC ACACCCATTA ATTTAATTCG GCCTCTGTGT TGAGCCCCTT GTTGAAGTGT TTCCCTCCAT CGCGACGTGG TTGGAGATCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AAGTCAACCG ACTCCGACGA AACTACCATC ATGCCTCCCC GATTATGTGA TGCTTTCTGC CCTGCTGGGT GGAGCACCCT CGGGTTGAGA AAACCTTCTT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCTTTTTCCT TGGACTCCGG TCCCCCGGTC TAAGCCGCTC GGAATATGAC AGGGTTATTT TCACCTCTTC TTTTCTACTC CACAGTGTTC TATACTGTGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AAGGGTATGT GTTGCCCCTT CCTTCTTGGA GAACGTGCGC GGCGGTCTTT CCGTCTCTCG ACAAGCGCGC GTGCAACATA CAGAGTAACG CGAAGAAAGC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGTTCTCGGT CTAGCTCTAG TGCCCACAAG AAAACAGCTG TAGCGACCAC ACAAAGGCAG CGGAACCCCC CTCCTGGTAA CAGGAGCCTC TGCGGCCAAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AGCCACGTGG ATAAGATCCA CCTTTGTGTG CGGTGCAACC CCAGCACCCT GGTTTCTTGG TGACACTCTA GTGAACCCCT GAATGGCAAT CTCAAGCGCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCTGTAGGGA AGCCAAGAAT GTCCAGGAGG TACCCCTTCC TCTCGGAAGG GATCTGACCT GGAGACACAT CACACGTGCT TTACACCTGT GCTTGTGTTT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AAAAATTGTT ACAGCTTCCC CGAACCAAGT GGTCTTGGTT TTCACTTTTT ATCACACTGT CAATATGGCC TGCAAACATG GATACCCAGA TGTGTGCCCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATTTGCACAG CCGTTGACGC TACTCCCGGC TTTGAATATT TGCTCATGGC AGACGGAGAA TGGTACCCTA CGGACCTTCT TTGTGTGGAC TTGGACGATG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ACGTCTTCTG GCCTTCGGAC ACGAGCAATC AATCTCAAAC AATGGACTGG ACTGACGTAC CGCTCATACG CGATATTGTC ATGGAACCCC AGGGAAACTC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CTCGTCATCT GACAAGAGTA ACTCCCAGTC CTCAGGAAAT GAAGGGGTTA TTATTAACAA CTTCTATTCC AATCAATACC AAAACTCAAT TGATTTGTCT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCCAGTGGTG GCAACGCTGG CGATGCTCCC CAGACCAATG GACAACTGTC CAACATCCTG GGTGGAGCTG CAAATGCTTT TGCTACTATG GCACCTCTCC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTTTGGACCA AAACACAGAG GAGATGGAAA ACCTCTCTGA CAGAGTAGCT TCTGATAAAG CAGGAAATTC GGCCACAAAC ACACAATCTA CTGTTGGTCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACTCTGTGGT TACGGAAAGT CCCACCACGG AGAACATCCT GCTTCTTGTG CTGACACCGC GACTGACAAG GTGCTCGCGG CTGAACGCTA CTACACCATT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GACCTGGCTA GTTGGACTAC TTCCCAAGAA GCTTTCTCTC ACATCAGAAT CCCTCTCCCC CACGTCCTTG CTGGCGAGGA CGGAGGGGTT TTTGGAGCTA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CGCTGAGGAG GCACTACCTC TGCAAGACTG GTTGGCGTGT GCAAGTTCAG TGCAATGCTT CCCAGTTTCA TGCTGGCTCC CTTCTTGTTT TCATGGCTCC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGAGTTCTAT ACTGGAAAAG GAACAAAAAC GGGCACCATG GAGCCTTCGG ATCCATTTAC CATGGATACC GAGTGGCGCA GCCCGCAGGG TGCACCCACA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGCTACCGCT ATGACAGTCG AACCGGCTTC TTTGCCACGA ACCACCAGAA CCAATGGCAA TGGACTGTGT ACCCCCACCA GATTCTGAAT CTGCGCACAA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACACCACTGT TGATTTGGAA GTCCCCTACG TCAATGTGGC ACCTTCTAGC TCATGGACCC AACATGCAAA CTGGACTCTC GTTGTCGCCG TGCTCAGTCC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCTCCAGTAC GCCACCGGTT CTTCACCGGA TGTCCAAATT ACAGCCTCCC TACAACCTGT CAATCCCGTG TTTAATGGTT TGAGACACGA GACTGTAATT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GCACAGAGTC CTATTCCAGT CACAGTGCGT GAGCACAAGG GTTGCTTCTA CTCCACCAAC CCTGACACCA CTGTCCCCAT CTATGGAAAA ACCATTTCTA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCCCGAGTGA CTATATGTGT GGTGAGTTTT CCGACCTCCT TGAATTGTGC AAGCTCCCCA CTTTCCTTGG TAACCCCAAC ACCAACAACA AGCGTTACCC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CTATTTCTCT GCCACCAATT CTGTACCAGC CACTTCCATG GTTGATTACC AAGTTGCTCT CTCATGCTCT TGTATGGCTA ATTCAATGCT TGCTGCTGTT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GCTCGTAATT TTAATCAGTA CCGTGGTTCT TTAAACTTCC TCTTTGTTTT CACTGGTGCT GCTATGGTTA AAGGTAAGTT CCTCATAGCT TACACGCCGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CTGGTGCGGG AAAACCCACC ACCCGGGACC AAGCTATGCA GTCTACCTAC GCCATCTGGG ACTTGGGCTT GAATTCCAGC TTCAATTTCA CTGCCCCTTT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TATTTCTCCC ACTCATTACC GCCAGACTAG TTATACCAGC CCCACTATCA CCTCTGTGGA CGGCTGGGTT ACCGTTTGGA AACTGACTCC CTTGACTTAC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CCCTCTGGAA CTCCCACCAA TTCTGACATT CTCACCCTTG TTTCCGCTGG CGATGATTTC ACGCTCAGGA TGCCGATTTC ACCCACCAAG TGGGTTCCAC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AAGGAGTTGA CAATGCTGAG AAAGGTAAAG TCTCCAACGA TGATGCTTCG GTTGACTTTG TCGCCGAACC AGTCAAGCTG CCCGAGAACC AAACCCGGGT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGCCTTCTTC TATGACAGAG CTGTCCCTAT AGGTATGTTG AGGCCCGGCC AAAATATGGA AACCACTTTT AACTACCAAG AAAATGATTA CCGCCTCAAT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGTCTTTTGC TAACCCCTCT CCCTTCCTTT TGTCCTGACA GTTCTTCCGG GCCCCAAAAA ACAAAGGCTC CCGTTCAATG GCGATGGGTG CGATCTGGCG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GCGTCAACGG CGCCAACTTT CCGCTCATGA CTAAGCAGGA CTATGCCTTC CTTTGTTTTT CTCCCTTTAC CTTTTACAAG TGTGACCTTG AGGTCACAGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CAGTGCCCTG GGCATGACAC GGGTTGCCTC CGTGCTCCGT TGGGCCCCTA CCGGCGCCCC TGCGGATGTT ACTGACCAGC TAATAGGTTA CACACCCAGC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CTTGGTGAGA CGCGTAATCC GCATATGTGG CTCGTTGGTG CTGGCAACTC ACAAGTTTCT TTTGTGGTTC CCTATAACTC CCCTCTCTCC GTCCTCCCTG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CCGCTTGGTT TAATGGATGG TCCGACTTTG GAAACACTAA GGACTTTGGA GTCGCCCCTA ACGCAGACTT CGGGCGTCTC TGGATCCAGG GCAATACCTC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TGCCTCCGTC CGGATCAGGT ACAAGAAAAT GAAGGTCTTC TGCCCCCGCC CGACCCTCTT CTTCCCCTGG CCTACGCCCA CCACCACCAA GATCAATGCT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GACAACCCAG TCCCCATTCT TGAACTCGAG AATCCCGCTG CTCTCTACCG CATTGATCTC TTCATCACCT TCACTGATGA GTTCATCACC TTTGATTACA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AGGTTCACGG ACGTCCTGTG CTTACCTTCC GGATCCCAGG CTTCGGCCTG ACCCCGGCAG GTAGGATGCT CGTGTGCATG GGCGAACAAC CCGCACATGG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TCCGTTCACC TCCTCTAGAT CCCTCTATCA TGTCATTTTT ACTGCTACTT GCTCTTCCTT TAGCTTTAGT ATCTACAAGG GGCGGTACCG CTCCTGGAAA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AAGCCCATCC ATGACGAGCT TGTGGATCGT GGTTACACCA CTTTCGGCGA GTTCTTCAAG GCTGTGCGCG GATACCATGC TGACTATTAC AGACAGAGAC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TCATACACGA TGTGGAAACA AATCCAGGCC CTGTGCAGTC GGTTTTTCAG CCACAAGGTG CGGTGCTAAC TAAATCCCTA GCACCCCAGG CAGGAATTCA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AAACCTCCTT CTACGCCTCC TCGGCATAGA CGGTGACTGT TCAGAAGTTA GTAAAGCAAT CACAGTCGTC ACCGACTTAG TTGCTGCATG GGAAAAGGCA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AAAACCACCC TGGTTTCCCC TGAATTCTGG TCAAAACTCA TATTAAAAAC CACCAAATTC ATTGCTGCCT CTGTGCTTTA CCTACACAAC CCTGATTTTA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CCACCACTGT TTGTCTTTCA TTGATGACTG GTGTGGACCT CCTCACCAAC GATTCTGTTT TTGATTGGCT CAAACAAAAA TTGTCTTCCT TCTTTCGCAC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CCCTCCCCCA GCTTGCCCCA ATGTTATGCA GCCTCAGGGA CCTCTACGCG AGGCCAATGA AGGCTTCACC TTTGCTAAGA ACATTGAGTG GGCTATGAAA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ACCATCCAGT CTGTTGTTAA TTGGCTTACT AGTTGGTTTA AACAAGAAGA GGATCACCCC CAATCAAAAT TAGACAAACT GCTCATGGAA TTCCCCGACC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ATTGCAGGAA CATCATGGAT ATGAGAAACG GTCGAAAGGC CTATTGTGAG TGCACTGCTT CCTTTAAGTA TTTTGATGAA CTTTACAATC TTGCTGTTAC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TTGCAAAAGA ATTCCATTGG CCTCCCTATG TGAAAAATTT AAGAATAGAC ATGATCACTC TGTCACTAGA CCCGAGCCGG TGGTTGTCGT TCTTCGCGGC 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GCCGCTGGGC AAGGTAAGTC TGTGACCAGC CAAATTATCG CCCAATCCGT GTCAAAGATG GCCTTTGGTC GTCAGTCTGT CTATTCAATG CCCCCCGATT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CGGAATATTT TGATGGCTAT GAAAATCAAT TTTCTGTGAT TATGGATGAT CTAGGACAAA ATCCTGATGG CGAAGACTTC ACTGTCTTTT GTCAAATGGT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TTCTAGCACA AATTTTCTTC CGAATATGGC TCACCTGGAA AGAAAAGGCA CTCCTTTTAC CTCTAGCTTC ATTGTTGCTA CAACAAATTT GCCCAAATTC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CGCCCTGTTA CGGTTGCCCA CTACCCCGCT GTTGATAGGC GAATCACCTT TGATTTTACT GTTACTGCTG GACCCCACTG CAAAACGCCT GCTGGAATGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TGGATGTTGA GAAAGCTTTT GATGAGATAC CTGGCTCCAA ACCTCAGCTT GCCTGCTTCA GTGCTGATTG CCCCCTCCTA CACAAAAGAG GAGTCATGTT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

CACCTGCAAT CGCACCCAGA CCGTTTACAA CCTCCAACAA GTTGTAAAAA TGGTCAACGA CACCATTACC CGCAAGACTG AAAATGTGAA GAAAATGAAT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

AGCCTGGTTG CTCAGTCTCC ACCAGACTGG GAGCACTTTG AGAACATCCT CACCTGTCTC CGTCAGAACA ACGCCGCTCT CCAGGACCAA CTCGATGAGT 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TACAGGAAGC GTTTGCTCAA GCGCGCGAGC GCTCTGACTT TCTTTCTGAT TGGTTGAAGG TTTCTGCTAT CATTTTTGCT GGTATTGCCT CACTTTCTGC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TGTTATAAAA CTAGCCTCCA AATTTAAAGA ATCAATTTGG CCCACACCCG TGAGAGTTGA GCTCTCTGAG GGTGAACAGG CCGCGTACGC TGGTCGTGCG 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CGCGCCCAAA AGCAAGCCCT TCAGGTATTG GACATTCAAG GAGGCGGGAA GGTTCTAGCC CAGGCCGGCA ACCCCGTCAT GGACTTTGAG CTTTTCTGTG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CCAAGAATAT AGTTGCCCCC ATCACCTTCT ATTACCCTGA CAAGGCTGAA GTGACCCAGA GTTGTTTGCT ACTCCGAGCT CATCTCTTCG TGGTTAACCG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CCACGTTGCA GAGACAGATT GGACCGCTTT CAAACTCAAG GATGTGAGAC ACGAGCGCCA CACTGTCGCC CTTCGCTCCG TCAATAGATC AGGAGCCAAG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

ACTGACCTCA CATTCATAAA AGTCACAAAG GGACCTCTCT TCAAAGACAA CGTTAACAAA TTTTGCTCCA ACAAGGACGA CTTCCCAGCA AGGAACGACA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

CCGTCACTGG AATCATGAAC ACCGGCCTGG CTTTCGTGTA CTCTGGCAAC TTCTTGATTG GCAACCAACC TGTTAACACC ACAACTGGAG CCTGTTTCAA 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

CCACTGCCTC CACTACCGGG CTCAAACCCG ACGTGGTTGG TGTGGATCTG CCATTATCTG CAATGTCAAT GGTAAGAAAG CTGTTTATGG AATGCATTCT 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

GCTGGAGGTG GAGGCCTCGC TGCCGCTACC ATCATCACCA AGGAATTGAT TGAAGCAGCT GAAAAGTCTA TGCTGGCACT GGAACCTCAG GGAGCCATTG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

TTGACATAGC CACAGGATCT GTTGTACATG TCCCTAGAAA AACTAAATTG AGGAGGACAG TCGCCCACGA CGTCTTCCAA CCCAAATTCG AACCTGCAGT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

TCTGTCCCGT TATGACCCTC GGACCGATAA AGATGTGGAT GTTGTAGCCT TCTCCAAACA CACTACCAAC ATGGAAAGCT TGCCCCCAAT CTTTGATGTC 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

GTCTGCGGTG AATACGCTAA TCGTGTTTTC ACCATCCTTG GCAAAGAGAA CGGTCTCCTG ACTGTTGAAC AAGCCGTGCT TGGCTTGCCG GGTATGGATC 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

CCATGGAGAA AGACACCTCC CCTGGATTGC CCTACACCCA ACAAGGACTC AGACGAACTG ATCTTCTGAA TTTCATCACT GCTAAAATGA CCCCTCAATT 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

GGACTACGCT CATTCCAAAT TGGTGATCGG TGTTTATGAT GATGTTGTTT ACCAATCATT TTTGAAAGAT GAAATTCGGC CTATAGAAAA GATCCATGAA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

GCGAAAACCC GGATCGTTGA CGTACCCCCG TTTGCTCACT GCATTTGGGG AAGACAGCTT CTGGGACGCT TCGCTTCCAA ATTTCAAACC AAACCCGGAC 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TTGAACTCGG ATCTGCAATT GGAACTGACC CAGATGTTGA TTGGACACGC TACGCTGTCG AGCTGAGCGG ATTCAATTAT GTCTATGATG TTGATTACTC 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

TAACTTTGAT GCTTCCCACT CCACTGCGAT GTTTGAATGC TTAATTAACA ATTTCTTTAC AGAGCAAAAT GGATTTGACA GACGCATCGC CGAGTATCTT 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

AGATCTCTGG CTGTGTCACG ACATGCCTAT GAGGACCGCC GTGTCCTTAT ACGTGGGGGC CTGCCCTCGG GCTGTGCTGC CACCAGCATG TTAAACACCA 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

TCATGAACAA TGTCATAATT CGTGCTGCCC TGTACCTTAC CTATTCAAAT TTTGATTTTG ATGATATTAA GGTCCTTTCC TATGGAGATG ACCTATTAAT 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

TGGAACTAAT TACCAAATTG ATTTTAATCT TGTTAAAGAA AGATTAGCCC CCTTCGGTTA TAAGATTACT CCTGCCAACA AGACCACCAC CTTTCCTCTG 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

ACCTCCCATT TGCAAGATGT TACCTTTCTA AAGAGGAGAT TTGTGAGATT CAATTCTTAC TTGTTTAGAC CTCAAATGGA TGCTGTCAAT TTGAAAGCGA 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TGGTTAGCTA CTGTAAACCA GGAACACTCA AGGAGAAACT AATGTCCATT GCTCTTCTGG CCGTTCACTC TGGACCAGAT ATCTATGATG AGATTTTCCT 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

TCCCTTTAGG AATGTTGGAA TAGTTGTCCC TACCTATAGT TCTATGCTTT ATAGATGGCT TAGCTTATTT AGATGAACAT CCCCTCGATC GGATCGCAAC 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

GCTTTACCCT AGAAGCCACT AGGGTGTACG CGGCCGTTCT GACGTTGGAA TTCTTTTAGG CAAAAGTTGT GTAGATGCTT ATAATTGGAA ATGAGAAC
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091

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:

Theiler's encephalomyelitis virus BeAn 8386

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: `1`	Last change: `2009-08-18 23:09:29`
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):

1065-7976

Remarks:

The strain GDVII is stored in Genbank under GI:62039

Citations:

Pevear DC, Calenoff M, Rozhon E, Lipton HL (1987) Analysis of the complete nucleotide sequence of the picornavirus Theiler's murine encephalomyelitis virus indicates that it is closely related to cardioviruses. J. Virol. 5(61):1507-1516

IRESs:

IRES:

Version: `3`	Last change: `2009-08-18 23:14:29`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `TMEV`

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

1-1040

Conclusion:
strongly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

TTGAAAGGGG GCCCGGGGGA TCTCCCCCGC GGTAACTGGT GACAGTTGTC GCGGACGGAG ATCATCCCCC GGTTACCCCC TTTCGACGCG GGTACTGCGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TAGTGCCACC CCAGTCTTTC CTACTCCCGA CTCCCGACCC TAACCCAGGT TCCTCGGAAC AGGAACACCA ATTTACTCAT CCCCTGGATG CTGACTAATC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGAGGAACGT CAGCATTTTC CGGCCCAGGC TAAGAGAAGT AGATAAGTTA GAATCCAAAT TGATTTATCA TCCCCTTGAC GAATTCGCGT TGGAAAAACA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCTCTCACTT GCCGCTCTTC ACACCCATTA ATTTAATTCG GCCTCTGTGT TGAGCCCCTT GTTGAAGTGT TTCCCTCCAT CGCGACGTGG TTGGAGATCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AAGTCAACCG ACTCCGACGA AACTACCATC ATGCCTCCCC GATTATGTGA TGCTTTCTGC CCTGCTGGGT GGAGCACCCT CGGGTTGAGA AAACCTTCTT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCTTTTTCCT TGGACTCCGG TCCCCCGGTC TAAGCCGCTC GGAATATGAC AGGGTTATTT TCACCTCTTC TTTTCTACTC CACAGTGTTC TATACTGTGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AAGGGTATGT GTTGCCCCTT CCTTCTTGGA GAACGTGCGC GGCGGTCTTT CCGTCTCTCG ACAAGCGCGC GTGCAACATA CAGAGTAACG CGAAGAAAGC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGTTCTCGGT CTAGCTCTAG TGCCCACAAG AAAACAGCTG TAGCGACCAC ACAAAGGCAG CGGAACCCCC CTCCTGGTAA CAGGAGCCTC TGCGGCCAAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AGCCACGTGG ATAAGATCCA CCTTTGTGTG CGGTGCAACC CCAGCACCCT GGTTTCTTGG TGACACTCTA GTGAACCCCT GAATGGCAAT CTCAAGCGCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCTGTAGGGA AGCCAAGAAT GTCCAGGAGG TACCCCTTCC TCTCGGAAGG GATCTGACCT GGAGACACAT CACACGTGCT TTACACCTGT GCTTGTGTTT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AAAAATTGTT ACAGCTTCCC CGAACCAAGT GGTCTTGGTT
^1001      ^1011      ^1021      ^1031

Remarks:

Bandyopadhyay et al. (1992) initially reported the IRES in BeAn strain.

Citations:

Pilipenko EV, Gmyl AP, Maslova SV, Belov GA, Sinyakov AN, Huang M, Brown TD, Agol VI (1994) Starting window, a distinct element in the cap-independent internal initiation of translation on picornaviral RNA. J. Mol. Biol. 3(241):398-414

Pilipenko EV, Gmyl AP, Maslova SV, Khitrina EV, Agol VI (1995) Attenuation of Theiler's murine encephalomyelitis virus by modifications of the oligopyrimidine/AUG tandem, a host-dependent translational cis element. J. Virol. 2(69):864-870

Bandyopadhyay PK, Wang C, Lipton HL (1992) Cap-independent translation by the 5' untranslated region of Theiler's murine encephalomyelitis virus. J. Virol. 11(66):6249-6256

Pilipenko EV, Blinov VM, Chernov BK, Dmitrieva TM, Agol VI (1989) Conservation of the secondary structure elements of the 5'-untranslated region of cardio- and aphthovirus RNAs. Nucleic Acids Res. 14(17):5701-5711

Pilipenko EV, Pestova TV, Kolupaeva VG, Khitrina EV, Poperechnaya AN, Agol VI, Hellen CU (2000) A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes Dev. 16(14):2028-2045

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 39

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):
599-1040

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

GGAAGGGTAT GTGTTGCCCC TTCCTTCTTG GAGAACGTGC GCGGCGGTCT TTCCGTCTCT CGACAAGCGC GCGTGCAACA TACAGAGTAA CGCGAAGAAA 
(((.(((((. ....))))). )))....((( ....(((((( (((((((... ..)))))... ......)))) )))).))).. (((((((... (((..(((.. 
^599       ^609       ^619       ^629       ^639       ^649       ^659       ^669       ^679       ^689       

GCAGTTCTCG GTCTAGCTCT AGTGCCCACA AGAAAACAGC TGTAGCGACC ACACAAAGGC AGCGGAACCC CCCTCCTGGT AACAGGAGCC TCTGCGGCCA 
((..(((..( ((((((.... ((((....(( (((((.(((. .((....))( (((((((((( ((.((..... ..((((((.. ..)))))))) .))))(((.. 
^699       ^709       ^719       ^729       ^739       ^749       ^759       ^769       ^779       ^789       

AAAGCCACGT GGATAAGATC CACCTTTGTG TGCGGTGCAA CCCCAGCACC CTGGTTTCTT GGTGACACTC TAGTGAACCC CTGAATGGCA ATCTCAAGCG 
...)))..(( ((((...))) )))))))))) )).(((((.. .....))))) ))).)))))) )....))))) )))...))). ..)))..)). .)))...))) 
^799       ^809       ^819       ^829       ^839       ^849       ^859       ^869       ^879       ^889       

CCTCTGTAGG GAAGCCAAGA ATGTCCAGGA GGTACCCCTT CCTCTCGGAA GGGATCTGAC CTGGAGACAC ATCACACGTG CTTTACACCT GTGCTTGTGT 
.)))))))(( (((((.((.( ((.((((((( (((..((((( ((....)))) )))))))..) ))))).(((( (.((((.((( .....))).) )))..))))) 
^899       ^909       ^919       ^929       ^939       ^949       ^959       ^969       ^979       ^989       

TTAAAAATTG TTACAGCTTC CCCGAACCAA GTGGTCTTGG TT
......))). ))...))))) ))..(((((( (....))))) ))
^999       ^1009      ^1019      ^1029      ^1039

Rendering structure of TMEV mRNA 442 nt long with energy of -156.40 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:

This actually a prediction model based on the EMCV structure probing data.

Citations:

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