IRESite_Id:59 summary record describing characteristics of PSIV

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `59`	Version: `4`
Originaly submitted by: Zuzana Feketová	Submission date: `2005-08-05 00:00:00`
Reviewed by: Martin Mokrejš	Last change: `2008-06-26 00:38:37`

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
20451012

The mRNA/+RNA description:

Plautia stali intestine virus (Dicistroviridae), complete genome

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

GCAAAATGGG TACGTAGTTA ACCACTGCGT ATCAGGATTG CAGGCCACGA AGGGTATTTG CATATCTTTC TATGCGGTAT TACGGCTTAA AACCCGTTGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATCTTGTAGT TTGACTGCCT GTATCACTAG TGGCCATTTT ATTTAGGTTA GAGACCCCTG ATAGTAGGAG AGTTACAAAC TCTTTAAAAA TTGTTGACCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CGGAAAAGAT GGTGACCCCT GTAAGTAGTT GATCTAGAAG ATCTATGCGC TGGCATAGTA ATCCAGTGTT TCCTGTTTTA GGATGACCTC TGAAAGTAGA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TGACCGTGGA AAGTCACGTA GTGCCCCAAT AAGCACGTTT GGGCAGCGTG CGCTATCACA AGGCTTGATC TCCGAGGAGC CCCTTGTTTT AGCTGGCTGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AAGCCAATGA TCTTAAGTAG ATAAGTGCTG TTGCTTGTAG TTCAACAGAA AGCTTTGAGT ACGTCTTTCT TGCGAGAAAG AACACATGCA TTCTTATGCT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CTCAATTCTA TTATTTTTAT TTTGGGCGAA AGGAAAGCTC TCACGCGAGT ACGAATAGCC AACCCTTTAT ATGATGTTTT CTCTTAATTC TTTAAATAGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CGGACTGATT TTACAGATGA TGATTTAATG CTTTTGGACT TGGAAAAACC TGTTACGTTA TTCGATAAAG AAATCTTTAG ACAAACGTTA GCTGATATGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATGGTAAAGA TTCTTATTCT TATTATTCTA TCGAACGAAT GATTTTTGAG GATCTTCACA ACCCATATCT AGGTAATGTA AATCATGTAA GGAAAAGAAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TTTCATACAA CCTATTAAAA GGTGGTATGA TATGTATAAT CCTGTTTGTG TGTCTTTTGA TAGGAAGGTG CAGGGTTACG GAGTCAATTG GCCCCATTTC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CTCTTCTTAC ATAGACATGA TGAAACTGAA TCTCAATATA ATACTCACCA TTTATTTAGA TCTGATGTAG ACTTAGTTGT AGAGTACGAG AGAAATTGCG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGTGGTTCGA TTTATCCGCC CGTGATGTAG AAACATATAG TTTTATCTTA GGACTCCCTG AAAACATTCA ATATAATTGT CTGGATCAAA TTTTAGATGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TAGGTTTACA TCTGAAGATC TGTTTCATTT AATAGAAAAT TTACAATTTG CGCGAAAATT ACCTTTAGTG GTTTTTGATG GTAAATGGAG GTTTCAACAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCTCATTTAT CTCTTTTTAA ATTTATAGAT AATTATATTT CTTTAACAGA TCTGACAAAA TTTAGGTTAG TTTCCCATAT GGAAAGAGTA TCTAGTAAGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TCCTTTTTCC TCAACGTAGT ACTGTAAGTC TATGCAGTGA TGGTACTATT TTGGTTGAGG ATCCATACAC TTATGTACAA CATCCACAGA CATCCTATAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGTTGTACCC CCACAATTGA ATCTCCAATC TTCAGGTAAT ATATTAGAAG ATTTTATTAG GAAATATGAG ACTGAGTTAA GATTTATGTG TGGTCAAAAG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AAACTTCAAG GTATTAACAT TACACACAAA ATAGATAAGG ATGACCTCCA AGCTGTAATA AATTCAGTTA TGGCAACTGT ATCAGAACAA TGGAGTCAGG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTAAAGGAAA AGTTTTGAAA CTTTTCTTAA TTTTAGTCAA ATTTTTAACT GGTTTATTAC TCGTTTCTCT AGGTCTTAAA ATTTTAAAGG ATTTATCCGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATTAAGTGTA ATTAAAACAT TTTTATTTTT ACTCTTTGGT ATGTGTAGTT TAGACAAATT TTTCATTTAT TTCGAAGAAA GTTTAGTTTG CCAAGATGGT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TTGAAAGATG AATCTCAGTT CCTTAGTCTA TTTTTATTAG ATAAATTATT TTTAAATGGG TGCCCTGTAT CTATGAAAAA TGCAAAAGAT TTTGTGTGGT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TTGTTTCTCA AGCACCACGC TTTAGTCAGG GTATAACACA TATAGTTTCA TATGTAAAAG ATCTGTATGT ACATTGTGAA CATTTCTTTA GAGTTAAAAT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TTTAGGATTA CCTTCTCTGT CCTATGAATC TCCAGTCTGT ACTTGGATAG AAGCTATTCA AGATATATAT GAAAAATATA AGAAAAATAT ATTAGTTTTA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GATGCTAGGT TGTTAGATAA ACTATTCAAT TTATATAAGG AAGGAAATAG ATTTTTGTGC ACTCCTGCAT TCAAAAATCA ATCTCAAATA ATTGTAAAAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATATTAACCT CACTTATAAT CTCATTGATA AAGTTCCTAT TTCTCAAAGA GGTGGATACA AAAATTCTTT GCGACCACCT CCTGTCAGTT TGTTGTTATT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGGAGGAACA GGTCGAGGAA AGACCACAGT AACCTTTCCG CTTACTACTG AAGTCGCCAC GCGAATTTAT CTCGAAGAAC ATGAAGGGGA TATTACTGAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GAAGATATTG CTTCCTCAAT TTATGCTAGA AATTCTGAGC AGGAGTATTG GGATGGTTAT ACTGGTCAAC TCATTACAGT ATTTGATGAT TTCATGCAAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GCGTGGATTC AGCATCAAAT CCAAACTTAG AAATTTTTGA AATGATTAGA GCAAGTAATA TCTTTCCTTA TCCTTTGCAT ATGGCGAATC TCGAAGATAA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AAACAACACG TGGTTCCGTA GTTCTGTTAT TTTAGCGTCT TCCAATCTTA CCGCAGAGAA CTTGCAATCG AAAGTTCATT CGTTAAACTA CCCTGTAGCT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TTACTTAGGA GATTTGATTT AGTTGTAGAA GTAGAAATAG CCCCTGGTTG TACTAAGCCT CGTGCTGGAC AACCTTTTTC CAAAGATATT TACAAGTTCA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CTAAAGTAGA ATATATTTTA GATGAATCTG ATCGTGTCTC TATAGTAAGA TCTGAAATTA GTTATGATGA AATAGTAAAA TTAATGTGCC TTAAGTACAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AGATAATATG ACGACATGCC AGAGTGTTAG CGCTAATATT ACTGAAATGA TTGGTAATGT GCGAAAACAA GTAATGAAGG CAAAGGAGGA ATCTCATTTA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ACAATAGAAC CATCGGAAAA TAATCTTTTG GCTACACAAG GTTGGTTAAG TTGGTTTGTA GATAGCTATG AGGAAGAAAA TGATCTTGGG TATGATAACT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TCTTCGATGA AGTTGTTACA CCCGACCAAT ATATAGAGAA GTTTGAGACT GCTGTTATTG ACATCACTCC TGATCCCAAG CCAGATGAAA TTAGTGCAGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TAAAGAAAGG ACAACGATGA TATGGCGAAC ACACTTCTCC CAAATATGTG AGGAGTACCC TATAGTCCCA TATTTAGCAA CTTTTGGGCT TGTGGTAACG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GCCTTAGGTG TTGGCTACAC TATATATAGA TGTTTCTTTA ATGGTGAGAC TACACCACTG GCAAAATCTG AAATAGTATT ACCAAAATTT CCTGAATCTC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

AAGAAAAGGA GGGCGTTATA TCAAGATGTA AAATAGAATC CCAAGAAAAG ATAGGATCTG TTTCAAGAGT TAGGGTAGAA TCTCAAGAAA AACTTGGCGC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TATTCCACAC GTGAAAATTG AGCAAAGTGT TTTTAACGCC ACAGAGGACA GTGTGAATAT GCAGTGTAAT GGTAATGTAG AGAACTTAGC GCTACAGAAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TATTATTCCA AAGTTAATGA AATGTTGACT GTGGAAGGAT GTTCAGATCA GAATGCCGCG GAAATACTTT CTAAAGTGGT ATGTAGAAAT TATTATGCTT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TATTTGTATG CAGACCTGAT GGACGTGAAT CTCGTTTAGG CCATATTCTG TTCTTAAAAG ACAAAATTGG TTATATGCCT CAACATTTTC TTTTTAGTTT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AAGAAAAGAA ATGGAAGAAT CTCCAGACTC TTTCATTAGT TTAAGATCTA TTTTCCTTCG TGTAAATATG TATGAAATTT ATATCTGTGA TTTTTTAAAT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TATAATATAT TTGTTCCGGA AAATGACGGA GGGAGGTTAG TTGATTCATG TTTAGTTGAC GTAGAAACCG TCACTAAACA CCCTGATATT CTAACTACAT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ATGTTTCACA AACAGAAGTG AAATCTCTTT TGAGATCTGA TGTGTGTCTG CCTTTTATAC ATGTACCTGA AAGCAACAAA TATAAACCTT ATGCAACCAT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AGCATATGGT ACTGGACAAT CTCAGTTGGT GAAAGGAGGT GAAATCTCAT CTATTAGTAC GTATGATGCT ACCTTTTATT TCAGGCAATC CTGGAAGTAC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

AAATTGCAGA CTGCGTCAGG TACATGTGGT GCCCCTGTTA TTTTAATAGG AGCCAAACAA GGACCTGGTC GCATCTGCGG AATGCATGTC ATGGGAGATT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CACAGGGTAA TGGTTACGCT GTAGCCATTA CAAGAGAACT TTTATGTAAA TGGATAAATG ATCTGAACCC GACAATTCAA TCGTCTGAAA TGGAGAAGAA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AATGATTCAA AATGGAGTGT TTGACACTTT GCCTTTTCCA GGCAAATTTA TATCATTGGG AGACTCTCCT ATTAGTATTA GTGCGGCGTC CAAAACCCAA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CTTCGTAAGA GTGTTCTATA TGGAGAGATA GCGCCAGTCC TAACAAAACC AACATGGCTT ACACCTGGGA CGTTGAATGG TGAAGTTTGG GATCCGAGAA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ACTATAGACT GAGTTTATTT GGTAGACCTC GCACATTAGT TAAAATGAAT CTCCTCAACT CAATTAAAGA TAGATTAGTA CAAAGAATAT ATGTAATGGA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ATATGGATCT AATTATAAAT ATGAATCTCG ATATCCTTTT GAAACAGCGT GTGAAGGAAT TGACAGTGAC CCTACTTTCA ATTCAATAAA AAGGAAAACT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TCAGCTGGAT ATCCATTGTG TTCTAAAGTT AAGAATGGCA AACAAGAAAT ATTTGGGAGT GATGGTCCCT TCAATTTTAA AACTAAATTG GCTTTGGATT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TACGGAAGGA CGTAGAACAT ATAGAATCTC TTGCGATGGA TGGAATTTCA TCTGTACACG TATTTATTGA CACACTTAAA GATGAAAGGA AAGCCATTGA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AAAAGCTCAT AAAACTAGAT TATTTTCTGC TTCACCTCTT CCCTATTTAA TCTTATGTCG AATGTATTTA CAAGGAGGAG TATCAAGACT GATTAGAGGG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

AAAATAGTTA ATAACATAGC CGTAGGAACT AATCCTTACT CTGATGACTG GACTCGTGTT GCACACCACC TTCTTCGAAA TAGACATTTC GTAGCAGGTG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ATTTTGCTAG TTACGATTCT TCTCAAGAAA AAGAAATCCT GAGAGCAGCA TGTGAAGTGA TTGTGGAATT GTGCGAAGAT TTATCTTTGC CACAATCTGA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GCGAGACAAA CACAGGCGTG TTAGATGGGT TCTTTTGGAA TCACTTTTAA ATTCTGTACA TTATTCTTAT GGTAAGCTTT ATTATTGGTC AAAATCTCTC 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CCCTCAGGAC ACTTCCTAAC TTCCATTATT AATAGTATTT TTGTAAATAT AGCTATGTGT TATGCGTTTG TAGAATCTCA AGAAAAGGGA AATAGATCTG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AGGAGAACAT ACGTGTTTTC TTCAACGATT TCTCTATAGT AACTTATGGG GATGACCACG TAATTGGTGT CCCTGAGAAG TATGTAGAAG ATTTTAATCA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ACTCACATTG CCAAAACTTC TCAAAACGTT AGGTTTAGAT TATACTATGG AAGATAAGGA CAGGATCTGT GATATCAAAT CTCGTAAGTT AGAAGAAGTT 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ACCTTCATTA AAAGATCTTT TAGATATGTT AAAGAGTTAG ATAGGTGGTT AGCACCTTTA GATTTAAACA GTATTCTAGA TTGTATGAAT TGGCAAAGAT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CTGGAGAGGA TGAAGGATTG AATGCTCAAG CAAACGTTAG CTTTGCTTTA AAGGAATTAT CTCTCCACCC CGAGGATGTG TGGGACCAGT GGTTTCCCCT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CATTCTCAGA GCATGTAATA AACACGGTGT CGAAGTAGAA TTTCTATCTC GACACGCGGC CTTCCAAGCA GTTAGGGAAA CCGACTTCTT TGAAGAAGAA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

AGCTGACTAT GTGATCTTAT TAAAATTAGG TTAAATTTCG AGGTTAAAAA TAGTTTTAAT ATTGCTATAG TCTTAGAGGT CTTGTATATT TATACTTACC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ACACAAGATG GACCGGAGCA GCCCTCCAAT ATCTAGTGTA CCCTCGTGCT CGCTCAAACA TTAAGTGGTG TTGTGCGAAA AGAATCTCAC TTCAAGAAAA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

AGAATTTACA CAAGGCAGAG ATACAACTGC CCAATCAAAG CGTATACCAG GAGCGCAGGC AGGAGAACTC AACAATGGTG TTGAGTATCA AGAACAGATC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

GTGTCTTTCT CAGACGACGC AATGAAAATA GACGAATGTT TAATTTCATG TGCGCCCCAA ACAATGAATG AATCTCGCCC TGCATCAGAT TTCAGAGAAC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

ACACAATAGT GGACTTTCTA GAAAGACCTC GAGTGGTTGC CACCCATATA TGGTCCACCG CTGATGCGAG GAACACAAAC TTAGTAGATC TGGAAATACC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

AAAGGCATTA TTAGACAATA TGAACCTCAA TAAATTCGAT GGTTTTTCAT CATTTTCTGC GACTGTAGAA TTTAAACTTC AAATAAATTC TCAACCTTTT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CAAGCTGGTT TGTTAATAAT GGGGGCTCTG CCATCCAAAG ATCTGATAGG TTCACGTAAT ACAGACGTTA AAGTCGCCGT TGATAAGTCA TTATATATAC 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CACATACTCT TTTCGATATA AGTAAAACAT CTGAAATTAC TTTAAGTGTC CCCTATGTTA GCCCTTTTCC TCAGTATAAT TTAGTCTTAG AACCCATAAA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

TTGGTCTAAT TTCTTTATTA AAGTGTATAG TCCATTAGTA AGTAAGCAGA CAGACCAGCT AGATCTCGTA TTATGGGCTA GATTTAAGGA TATAAAATTA 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

GGTTACCCAA CTGTATTACC TGTTAAGACC CCTACTACAG ATTTAATTTT GCAGTCAGGA GAAACATCTG GTCCAGTTTC CAAAGTTGCC GCAACTATTG 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

TTGATGTAGC TGAGGGAGTT GGTAAAGGTG TTAGCAATTA TATTCCAACA GTCAAACCTT TCGTAAATGG TATGACCACA GTTGGACGAG GAATTCAATC 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

TCTCATAGCA GCTTTTGGTT TTTCAAAACC TCAAAAGTTG GATAACCAAA ATCAAGTAGT TGTTAGGCCT GGCTTTAATT TAGCCAACGT AGATGGAGTA 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

GACACTGGCG TTCCCATGTC AGCTTTTGCT GGCAATGCCT TGCCATTAAT GTCTAGTCTT GGTGGATCTG ATGCAGATGA ACTCTCATTT AAGTACCTTT 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

TGCAACAACC TAATTATATA GATAGTTTTT CATATAGTAG TACAATAACC TCCCCAACTA CCATTTGGTC GACTCATTTG TGTCCTTTCT TCCTTTCGAA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

GACGGACATA CAAGGCCACC CTCAACCCAC GCTTTTGTAT TATTTGTCCA ACTTCTTCTT ATACTGGAGA GGTTCTTTAA AATTTACTTT TAGATTCGTT 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

AAAACGAATT ATCATAGTGG TAGGTTAGAG CTAGTGTTTT CACCTTTTAG TCAAACTCAG AGTAGTGATT TTGTAAATAG ATCTGCTTAT GCTTATAAGG 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

TTGTTATGGA TTTAAGAGAA CAGACTGAAT TTTCTGTAGT TATACCTTAT GTAAATACTC GTAATTATAG TTATTGTGAT ATGCGTACAA CCGGGCCACC 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

AATTGATGCT ACTGTAACTA ACCCCAATAC GGTAATTGCG CATGCTAGCC CGGGGATGAT TGCAATCAAT GCATTGACAC CCTTGCAACT AGCATCGGAA 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TTATTGCCAA CTAGTATAGA TTGTGTTGTA GAGGTTAGCG GAGGTGATGA CTTTGAATTA CAAGCTCCCA TCAATGAAGG GTGGGTAGGC TTTGATTCGG 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

CGTCATCTTC TCAACTAACC TTACAATCCG GAGATACTTT TGGTTCAACG GGCATTAGAG ACAGTAGAGT CAATACTGTG GACAATAAAG TAGATTTTCA 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

AAGTGTGACT GGTAACAATA GATCTTTAGA TGTAGATACT TCACATGCAG AACATTGTAT GGGAGAAAGA ATGGTCTCAA TGAGACCTCT TTTGAAACGT 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

CCTTCCTATG CTTTCACTTC TACTGGTAAT TTATTTACAT ATATAGATAT TTTGCGCTTA AATTCAATAT TTACAGATGA CACCGGTTCC TATTTAGTTG 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

ATTTTGGTGC GACGACTAAA GATAATCCAA TAGCTTGTAA TTTGCTGAGT AGAATAGTAC AAATGTATGC CTTCTATAGA GGTGGTATTA ATATCAAAGT 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

GGCCCCTGAT AAGGGTCAAG TAGTTCCAAA TTTATATTAC GCTTACATTT CAGGCCTTAC CACATCATCT AATACTTATA TGTCATATCC TTTCTCGGTA 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

GAACAATATA ATGCTAAATC CTTATGTGAA TTTAATTATC CATATTATAA TAGTTTTAAA TTTTCTGCAG TAGCCACAAA TCAAACAGTA CCGAATGTAA 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

CTCAACCTTT CTTCAATTTT ATAGCTGCAG GGAGAGTTGC AGTATCCGCT AAAGACGATT TTGATTGCGG TTTCTTTTTG GGTCCCCCAC CATCTGTGTT 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

TAGACCCACA CTCAAAACAA TTTCGTAGAA TGCCTTGCAT TGGCAGTAGA GTTTTTCCCC AGGGAGCTTC ACTGTCTGGG TTTTCTCTAC TTATCACCTC 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

CTCACTTGGA CGGAGGCTCT TCCGGTTAAC AGCTTCACTG TTGATCTGAC AGAATGTTGG TACATAGCTT CACTATGTAT CAAAGTTTCA TTTTTGC
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

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

Plautia stali intestine virus

A promoter reported in cDNA corresponding to IRES sequence:
not tested The total number of notable open-reading frames (ORFs):
2

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

ORF

ORF position:

1

Version: `5`	Last change: `2008-05-01 21:18:21`
Originaly submitted by: Zuzana Feketová	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
PSIVgp1

The description of the protein encoded in this ORF:
Nonstructural protein precursor. Computer analysis revealed that the aminoacid sequence of ORF1 contains core motifs of picornaviral 2C RNA helicase, 3C cysteine protease and 3D RNA dependent RNA polymerase.

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):

571-6006

ORF

ORF position:

2

Version: `5`	Last change: `2008-05-01 21:18:21`
Originaly submitted by: Zuzana Feketová	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
PSIVgp2

The description of the protein encoded in this ORF:
The capsid protein precursor contains coding regions of four capsid proteins: 33, 30, 26, 4.5 kDa. Coding regions of these proteins were mapped by determination of their N-terminal sequences.

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:

yes

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

6193-8628

Remarks:

IRES is a part of the intergenic region of the genome and extends slightly into ORF2 which starts with CAA
codon (Gln). The sequence directly submitted by authors is GI:2344756.

Citations:

Sasaki J., Nakashima N. (1999) Translation Initiation at the CUU Codon Is Mediated by the Internal Ribosome Entry Site of an Insect Picorna-Like Virus In Vitro. J. Virol. 73(2):1219-1226

Sasaki J., Nakashima N., Saito H., Noda H. (1998) An Insect Picorna-like Virus, Plautia stali Intestine Virus, Has Genes of Capsid Proteins in the 3' Part of the Genome. Virology. 244:50-58

IRESs:

IRES:

Version: `10`	Last change: `2009-08-29 23:49:59`
Originaly submitted by: Zuzana Feketová	Reviewed by: Martin Mokrejš
The IRES name: `PSIV_IGR`

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

6002-6146

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GCTGACTATG TGATCTTATT AAAATTAGGT TAAATTTCGA GGTTAAAAAT AGTTTTAATA TTGCTATAGT CTTAGAGGTC TTGTATATTT ATACTTACCA 
^6002      ^6012      ^6022      ^6032      ^6042      ^6052      ^6062      ^6072      ^6082      ^6092      

CACAAGATGG ACCGGAGCAG CCCTCCAATA TCTAGTGTAC CCTCG
^6102      ^6112      ^6122      ^6132      ^6142

Remarks:

Several studies showed secondary and also 3D structure of the IRES (see the references below). Refer also to
PDB:2IL9 entry. Notably, alignment of the sequence deposited in IRESite reveals that we probably picked up
not the best matching genomic sequence:


>IRESite_Id:59 PSIV_IGR virus
          Length = 8797

 Score =  200 bits (114), Expect = 2e-52
 Identities = 136/150 (90%), Gaps = 13/150 (8%)
 Strand = Plus / Plus


2IL9:  1    gctgactatgtgatcttattaaaattaggttaaatttcgaggttaaaaatagttttaata 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 6002 gctgactatgtgatcttattaaaattaggttaaatttcgaggttaaaaatagttttaata 6061


2IL9:  61   ttgctatagtcttagaggtcttgcga-a-----agcttaccacacaagatggaccggagc 114
            |||||||||||||||||||||||  | |     | |||||||||||||||||||||||||
Sbjct: 6062 ttgctatagtcttagaggtcttg-tatatttata-cttaccacacaagatggaccggagc 6119


2IL9:  115  gaaag--ctccaatatctagtgtaccctcg 142
               ||  |||||||||||||||||||||||
Sbjct: 6120 ---agccctccaatatctagtgtaccctcg 6146

Citations:

Sasaki J., Nakashima N. (1999) Translation Initiation at the CUU Codon Is Mediated by the Internal Ribosome Entry Site of an Insect Picorna-Like Virus In Vitro. J. Virol. 73(2):1219-1226

Sasaki J., Nakashima N. (2000) Methionine-independent initiation of translation in the capsid protein of an insect RNA virus. PNAS. 97(4):1512-1515

Kanamori Y., Nakashima N. (2001) A tertiary structure model of the internal ribosome entry site (IRES) for methionine-independent initiation of translation. RNA. 7:266-274

Shibuya N., Nishiyama T., Kanamori Y., Saito H., Nakashima N. (2003) Conditional Rather than Absolute Requirements of the Capsid Coding Sequence for Initiation of Methionine-Independent Translation in Plautia stali Intestine Virus. J. Virol. 77(22):12002-12010

Nishiyama T., Yamamoto H., Shibuya N., Hatakeyama Y., Hachimori A., Uchiumi T., Nakashima N. (2003) Structural elements in the internal ribosome entry site of Plautia stali intestine virus responsible for binding with ribosomes. Nucleic Acids Res. 31(9):2434-2442

Nishiyama T, Yamamoto H, Uchiumi T, Nakashima N (2007) Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviral intergenic internal ribosome entry site. Nucleic Acids Res. 5(35):1514-1521

Pfingsten JS, Costantino DA, Kieft JS (2006) Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science. 314(5804):1450-1454

RNA:protein interactions:

The RNA:protein interaction:

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

Abbreviated name of the protein interacting with the RNA:
RPS25

Full name of the protein interacting with the RNA:
ribosomal protein 25

The description of the protein interacting with the RNA:
ribosomal protein 25

The interacting RNA base range: 6089-6090

The organism where this RNA:protein interaction occurs:

Drosophila melanogaster Canton-S

Citations:

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 5

Version: `2`	Last change: `2006-08-07 00:00:00`
Originaly submitted by: Zuzana Feketová	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):
6005-6192

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

GACTATGTGA TCTTATTAAA ATTAGGTTAA ATTTCGAGGT TAAAAATAGT TTTAATATTG CTATAGTCTT AGAGGTCTTG TATATTTATA CTTACCACAC 
((((((.... ...((((((( ((((...... .......... ......)))) )))))))... ..)))))).. .........( (((....))) ).....(((( 
^6005      ^6015      ^6025      ^6035      ^6045      ^6055      ^6065      ^6075      ^6085      ^6095      

AAGATGGACC GGAGCAGCCC TCCAATATCT AGTGTACCCT CGTGCTCGCT CAAACATTAA GTGGTGTTGT GCGAAAAGAA TCTCACTT
.((((..... ((((.....) )))...)))) .))))..... .....((((. (.(((((... ...)))))). ))))...... ........
^6105      ^6115      ^6125      ^6135      ^6145      ^6155      ^6165      ^6175      ^6185

Rendering structure of PSIV mRNA 188 nt long with energy of -27.30 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:

IRES structure was mapped by mutagenesis studies which were verified by RNA structure probing using DMS, CMCT
(1-cyclohexyl-3-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate) or by hydroxyl radical
modification. The last method was performed at 0oC.

There are three pseudoknots in this IRES element:
1. PK I is formed by base pairing between nts 6163-6167 and 6188-6192
2. PK II is formed by base pairing between nts 6039-6043 and 6142-6146
3. PK III is formed by base pairing between nts 6078-6082 and 6110-6114

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

Chemical reagent used with its respective buffer:

ss_experiment_with_chemical_id: 11

The temperature (in degrees of Celsia):
20 The chemical reagent used to determine the 2D structure:
DMS

Chemical reagent used with its respective buffer:

Version: 0

pH `7.20`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `150.00`	Mg²⁺ [mM] `2.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `100.00`	Tris [mM] `0`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `50.00`

Other buffer components and their relative concentrations:

40 mM DMS

Chemical reagent used with its respective buffer:

ss_experiment_with_chemical_id: 12

The temperature (in degrees of Celsia):
20 The chemical reagent used to determine the 2D structure:
CMCT

Chemical reagent used with its respective buffer:

Version: 0

pH `7.40`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `100.00`	Mg²⁺ [mM] `2.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `100.00`	Tris [mM] `0`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Other buffer components and their relative concentrations:

50 mM sodium borate
20 mM CMCT

Citations:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 42

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):
225-615

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

GTAGTTGATC TAGAAGATCT ATGCGCTGGC ATAGTAATCC AGTGTTTCCT GTTTTAGGAT GACCTCTGAA AGTAGATGAC CGTGGAAAGT CACGTAGTGC 
......(((( (...))))). ..(((((((. ........)) ))))).(((( .....)))). ....((((.. ..)))).... (((((....) ))))...... 
^225       ^235       ^245       ^255       ^265       ^275       ^285       ^295       ^305       ^315       

CCCAATAAGC ACGTTTGGGC AGCGTGCGCT ATCACAAGGC TTGATCTCCG AGGAGCCCCT TGTTTTAGCT GGCTGGAAGC CAATGATCTT AAGTAGATAA 
........(( ((((...... .))))))((( (..((((((. .....(((.. ..)))..))) )))..)))). (((.....)) )......... ........(( 
^325       ^335       ^345       ^355       ^365       ^375       ^385       ^395       ^405       ^415       

GTGCTGTTGC TTGTAGTTCA ACAGAAAGCT TTGAGTACGT CTTTCTTGCG AGAAAGAACA CATGCATTCT TATGCTCTCA ATTCTATTAT TTTTATTTTG 
((.((((((. ........)) ))))...))) ).(((....( ((((((.... )))))))... ...((((... .)))).))). .......... .........( 
^425       ^435       ^445       ^455       ^465       ^475       ^485       ^495       ^505       ^515       

GGCGAAAGGA AAGCTCTCAC GCGAGTACGA ATAGCCAACC CTTTATATGA TGTTTTCTCT TAATTCTTTA AATAGCCGGA CTGATTTTAC A
((........ ..((((.... ..)))).... ........)) )......... .......... .......... .......... .......... .
^525       ^535       ^545       ^555       ^565       ^575       ^585       ^595       ^605       ^615

Rendering structure of PSIV mRNA 391 nt long with energy of -61.00 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.

Citations:

Shibuya N, Nakashima N (2006) Characterization of the 5' internal ribosome entry site of Plautia stali intestine virus. J. Gen. Virol. 12(87):3679-3686

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