IRESite_Id:148 summary record describing characteristics of CSFV IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `148`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2006-06-29 00:00:00`

IRESite record type:

natural_transcript

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
1220145

The mRNA/+RNA description:

Hog cholera virus (Classical swine fever virus) 'Chinese' strain (C-strain; EP 0 351 901 B1) encoding
polyprotein.

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

GTATACGAGG TTAGTTCATT CTCGTATACA CGATTGGACA AATCAAAATT ATAATTTGGT TCAGGGCCTC CCTCCAGCGA CGGCCGAACT GGGCTAGCCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGCCCATAGT AGGACTAGCA AAACGGAGGG ACTAGCCATA GTGGCGAGCT CCCTGGGTGG TCTAAGTCCT GAGTACAGGA CAGTCGTCAG TAGTTCGACG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGAGCAGAAG CCCACCTCGA GATGCTACGT GGACGAGGGC ATGCCAAGAC ACACCTTAAC CCTAGCGGGG GTCGCTAGGG TGAAATCACA CCACGTGATG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GGAGTACGAC CTGATAGGGC GCTGCAGAGG CCCACTATTA GGCTAGTATA AAAATCTCTG CTGTACATGG CACATGGAGT TGAATCACTT TGAACTTTTA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TACAAAACAA ACAAACAAAA ACCAATGGGA GTGGAGGAAC CGGTGTACGA TGCCACGGGG AGACCGTTGT TCGGAGACCC GAGTGAGGTA CACCCACAAT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CAACACTGAA GCTACCACAT GATAGGGGTA GAGGCAACAT TAAAACAACA CTGAAGAACC TACCTAGGAA AGGCGACTGC AGGAGCGGCA ACCATCTAGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCCGGTCAGT GGGATATATG TAAAACCCGG CCCTGTCTTT TACCAGGACT ACATGGGCCC GGTCTACCAT AGAGCCCCTC TGGAGTTTTT TGACGAAGTG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CAGTTCTGCG AGGTGACCAA AAGGATAGGT AGGGTGACAG GTAGCGACGG AAAGCTTTAC CATACATATG TGTGCATCGA TGGCTGCATA CTGCTGAAGC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TGGCCAAGAG GGGTGAGCCA AGAACCCTGA AGTGGATTAG AAATTTCACC GACTGTCCAT TGTGGGTTAC CAGTTGCTCC GATGATGGCG CAAGTGGGAG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TAAAGAGAAG AAGCCAGATA GGATCAACAA AGGCAAATTA AAAATAGCCC CAAAAGAGCA TGAGAAGGAC AGCAGAACTA GGCCACCTGA CGCTACGATC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GTGGTGGAAG GAGTAAAATA CCAGGTCAAA AAGAAAGGTA AAGTTAAAGG AAAGAATACC CAAGACGGCC TGTACCACAA CAAGAATAAA CCACCAGAAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTAGGAAGAA ACTAGAAAAA GCCCTATTGG CATGGGCGGT GATAGCAATT ATGTTGTACC AACCAGTTGA AGCCGAAAAT ATAACTCAAT GGAACCTGAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGACAACGGC ACTAATGGTA TCCAGCATGC TATGTACCTT AGAGGGGTTA ACAGAAGCTT GCATGGGATC TGGCCGGGGA AAATATGCAA AGGAGTCCCA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ACCCACCTGG CCACAGACGT GGAGCTGAAA GAAATACAGG GAATGATGGA TGCCAGCGAG GGGACAAACT ATACGTGCTG TAAGTTACAG AGACATGAAT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GGAACAAACA TGGATGGTGT AACTGGCACA ATATAGACCC CTGGATACAG CTGATGAATA GAACCCAAGC AGACTTGGCA GAAGGCCCTC CGGTCAAGGA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GTGCGCTGTG ACTTGCAGGT ACGATAAAGA TGCTGACATC AACGTGGTTA CCCAGGCTAG AAACAGGCCA ACAACCCTGA CCGGCTGCAA GAAAGGGAAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AATTTTTCTT TTGCGGGTAC AGTTATAGAG AGCCCATGTA ATTTCAATGT TTCCGTGGAG GATACCTTGT ATGGGGATCA TGAGTGCGGC AGTTTGCTCC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGGACGCAGC TCTGTACCTA GTAGATGGAA TGACCAACAC TATAGAGAAT GCCAGACAGG GAGCAGCGAG GGTGACATCC TGGCTCGGGA GGCAACTCAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AACTGCTGGG AAGAGGTTGG AGGGTAGAAG CAAAACCTGG TTTGGCGCTT ATGCCCTATC GCCTTACTGT AATGTAACAA GCAAAATAGG GTACATATGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TACACTAACA ACTGCACCCC AGCTTGCCTC CCCAAAAACA CAAAGATAAT AGGCCCTGGT AAATTTGACA CTAATGCAGA AGACGGAAAG ATTCTCCATG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGATGGGGGG CCACCTATCA GAATTTCTGC TGCTTTCTCT GGTTGTTCTG TCTGACTTCG CCCCTGAAAC AGCCAGCGCG TTATACCTCA TTTTGCACTA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGTGATTCCT CAACCCCATG ATGAACCTGA AGGCTGCGAT ACGAACCAGC TGAATCTAAC AGTAGAACTC AGGACTGAAG ACGTAATACC GTCATCAGTC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGGAATGTTG GTAAATATGT GTGTGTTAGA CCAGACTGGT GGCCATATGA AACCGAGGTG GCTCTGTTAT TTGAAGAGGT AGGACAGGTC GTAAAGTTAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CCTTACGGGC GCTGAGGGAT TTGACTAGGG TCTGGAATAG CGCATCAACC ATTGCATTCC TCATCTGCTT GATAAAAGTA TTAAGAGGAC AGATCGTGCA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AGGTGTGGTA TGGCTGTTAC TAGTAACTGG GGCACAAGGC CGGCTAGCCT GCAAGGAAGA TTACAGGTAC GCAATATCGT CAACCGATGA GATAGGGCTA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CTTGGGGCCG GAGGTCTCAC CACCACCTGG AAGGAATACA ACCACGATTT GCAACTGAAT GACGGGACCG TTAAGGCCAG TTGCGTGGCA GGTTCCTTTA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AAGTCACAGC ACTTAATGTG GTCAGTAGGA GGTATTTGGC ATCATTGCAT AAGAAGGCTT TACCCACTTC CGTGACATTC GAGCTCCTGT TCGACGGGAC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CAACCCATCA ACTGAGGAAA TGGGAGATGA CTTCAGGTCC GGGCTGTGCC CGTTTGATAC GAGTCCTGTT GTTAAGGGAA AGTACAATAC GACCTTGTTG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AACGGTAGTG CTTTCTATCT TGTCTGCCCA ATAGGGTGGA CGGGTGTCAT AGAGTGCACA GCAGTGAGCC CAACAACTCT GAGAACAGAA GTGGTAAAGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CCTTCAGGAG AGACAAGCCC TTTCCGCACA GAATGGATTG TGTGACCACC ACAGTGGAAA ATGAAGATTT ATTCTATTGT AAGTTGGGGG GCAACTGGAC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ATGTGTGAAA GGCGAGCCAG TGGTCTACAC AGGGGGGCTA GTAAAACAAT GTAGATGGTG TGGCTTCGAC TTCGATGGGC CTGACGGACT CCCGCATTAC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CCCATAGGTA AGTGCATTTT GGCAAATGAG ACAGGTTACA GAATAGTAGA TTCAACGGAC TGTAACAGAG ATGGCGTTGT AATCAGCACA GAGGGGAGTC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ATGAGTGCTT GATCGGTAAC ACGACTGTCA AGGTGCATGC ATCAGATGAA AGATTGGGCC CTATGCCATG CAGACCTAAA GAGATTGTCT CTAGTGCTGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ACCTGTAAAG AAAACCTCCT GTACATTCAA CTACACAAAA ACTTTGAAGA ACAGGTACTA TGAGCCCAGG GACAGCTACT TCCAGCAATA TATGCTTAAG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GGTGAGTATC AGTACTGGTT TGACCTGGAT GCGACTGACC GCCACTCAGA TTACTTCGCA GAATTTGTTG TCTTGGTGGT GGTAGCACTG TTAGGAGGAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GATATGTCCT GTGGCTGATA GTGACCTACG TAGTTCTAAC AGAACAACTC GCCGCTGGTT TACCATTGGG CCAGGGTGAG GTAGTGTTGA TAGGGAACTT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AATTACCCAT ACAGACATTG AGGTCGTAGT ATATTTTTTA CTACTCTATT TGGTCATGAG GGATGAACCT ATAAAGAAAT GGATACTGCT GCTGTTCCAT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GCTATGACTA ACAATCCAGT CAAGACCATA ACAGTGGCAT TGCTCATGGT TAGTGGAGTT GCCAAGGGTG GAAAGATAGA TGGCGGTTGG CAGCGACTGC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CGGGGACCAG CTTTGACATC CAACTCGCGC TGACAGTTAT AGTAGTCGCT GTGATGTTGC TGGCAAAGAG AGATCCGACT ACTGTCCCCT TGGTTATAAC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AGTGGCACCC CTGAGGACAG CTAAGATGAC TAACGGACTT AGTACGGATA TAGCCATAGC CACAGTGTCA GCAGCGTTGC TAACCTGGAC CTACATTAGT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GACTATTACA GATACAAGAC CTGGCTACAG TACCTTATCA GCACAGTGAC AGGTATCTTT TTAATAAGGG TACTGAAGGG AATAGGTGAG TTGGATTTAC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ACACTCCGAC CTTGCCATCT CATAGACCCC TCTTTTTCAT TCTCGTGTAC CTTATTTCCA CTGCAGTGGT AACAAGATGG AATCTGGACA TAGCCGGATT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCTGTTGCAG TGTGTCCCAA CCCTTTTGAT GGTTTTTACG ATGTGGGCAG ACATTCTCAC CCTGATCCTC ATACTGCCCA CTTACGAGTT AACGAAGCTA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TATTATCTTA AGGAAGTGAG GATTGGGGCA GAAAAGGGCT GGTTATGGAA AACCAACTTC AAGAGGGTAA ACGACATATA CGAAGTTGAC CAAGCTGGTG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AAGGGGTATA CCTATTCCCG TCAAAACAAA AGACAAGTTC AATGACAGGC ACCATGTTGC CATTGATCAA AGCCATACTT ATCAGCTGCG TCAGTAATAA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GTGGCAGTTC ATATATCTAC TGTACTTGAT ATTTGAAGTA TCTTACTACC TCCACAAGAA GATCATAGAT GAAATAGCAG GAGGGACCAA CTTCATCTCA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

AGACTTGTAG CCGCTTTGAT CGAAGTCAAT TGGGCCTTTG ACAACGAAGA AGTTAGGGGT TTGAAGAAGT TCTTCCTGTT GTCTAGTAGG GTTAAAGAAC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TGATCATCAA ACACAAAGTG AGGAATGAAG TAATGGTCCG CTGGTTTGGT GACGAAGAGG TCTATGGGAT GCCGAAGTTG GTTGGCCTAG TCAAGGCAGC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AACATTGAGT AAAAATAAAC ATTGTATTTT GTGCACCGTC TGTGAAGACA GAGAGTGGAG AGGAGAAACC TGCCCAAAAT GCGGGCGTTT TGGGCCACCA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

ATGACCTGTG GCATGACCCT AGCCGACTTT GAAGAGAAAC ACTATAAGAG GATCTTTTTT AGAGAGGATC AATCAGAAGG GCCGGTTAGG GAGGAGTACG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CAGGGTATCT GCAATATAGA GCCAGAGGGC AATTGTTCCT GAGGAATCTC CCAGTGCTAG CAACAAAAGT CAAGATGCTC CTGGTCGGCA ATCTTGGGAC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GGAGGTGGGA GATTTGGAAC ACCTTGGCTG GGTGCTTAGA GGGCCTGCCG TTTGCAAGAA GGTCACTGAA CATGAGAAAT GTACCACATC CATGATGGAC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

AAATTGACTG CTTTTTTCGG TGTTATGCCG AGGGGCACCA CACCTAGAGC CCCTGTGAGA TTCCCTACCT CTCTCTTAAA GATAAGAAGG GGTTTGGAAA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CTGGCTGGGC GTACACACAC CAAGGTGGCA TCAGTTCAGT GGACCATGTC ACTTGTGGAA AAGACTTACT GGTATGTGAC ACTATGGGCC GGACAAGGGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TGTTTGCCAG TCAAATAATA AGATGACAGA TGAGTCCGAG TATGGAGTTA AAACTGACTC CGGATGCCCG GAAGGAGCTA GGTGTTATGT GTTTAACCCA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

GAGGCGGTTA ACATATCAGG GACTAAAGGA GCCATGGTCC ACTTACAAAA AACTGGAGGA GAATTCACCT GTGTGACAGC ATCAGGAACT CCGGCTTTCT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TTGATCTTAA AAACCTTAAA GGCTGGTCAG GGCTACCGAT ATTTGAGGCA TCAAGTGGAA GGGTAGTCGG CAGGGTCAAG GTCGGTAAGA ATGAGGACTC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TAAACCAACC AAGCTTATGA GTGGAATACA AACAGTTTCC AAAAGTACCA CAGACTTGAC AGAAATGGTA AAGAAAATAA CTACCATGAG CAGGGGAGAA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TTCAGACAAA TAACCCTTGC TACAGGTGCC GGAAAAACCA CGGAACTCCC TAGGTCAGTC ATAGAAGAGA TAGGGAGGCA TAAGAGAGTC TTGGTCTTGA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TTCCTCTGAG GGCGGCAGCA GAGTCAGTAT ACCAATATAT GAGACAAAAA CATCCAAGCA TCGCATTTAA CCTGAGGATA GGGGAGATGA AGGAAGGGGA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CATGGCCACA GGGATAACTT ATGCTTCATA CGGTTACTTC TGTCAGATGC CACAACCTAA GTTGCGAGCC GCAATGGTTG AGTACTCCTT CATATTTCTT 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GATGAGTACC ACTGTGCCAC CCCTGAACAA TTGGCTATCA TGGGAAAGAT TCACAGATTT TCAGAGAACC TGCGGGTGGT GGCCATGACC GCAACACCAG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TAGGCACGGT AACGACCACA GGGCAGAAAC ACCCTATAGA AGAATTCATA GCCCCAGATG TGATGAAAGG GAAAGACTTA GGTTCAGAGT ACTTGGACAT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TGCTGGATTA AAGATACCAG TAGAGGAGAT GAAGAGCAAT ATGCTGGTTT TTGTGCCCAC CAGGAACATG GCAGTGGAGA CAGCAAAGAA ATTGAAAGCT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AAGGGTTATA ACTCAGGCTA CTATTATAGT GGTGAGGATC CATCTAACCT GAGGGTGGTA ACATCGCAGT CCCCGTACGT GGTGGTGGCA ACCAACGCGA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TAGAATCAGG TGTTACTCTC CCGGACTTGG ATGTGGTTGT CGATACAGGG CTTAAGTGTG AAAAGAGAAT ACGGCTGTCA CCTAAGATGC CCTTCATAGT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GACGGGCCTG AAGAGAATGG CTGTCACGAT TGGGGAACAA GCCCAGAGAA GGGGGAGAGT TGGGAGAGTA AAGCCTGGAA GATACTACAG GAGTCAAGAA 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

ACTCCCGTTG GTTCTAAAGA TTACCATTAT GATTTACTGC AAGCACAGAG GTACGGTATT GAAGATGGGA TAAACATCAC CAAATCCTTT AGAGAGATGA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ACTATGATTG GAGCCTTTAT GAGGAGGACA GTCTGATGAT TACACAATTG GAAATTCTTA ATAATTTGTT GATATCAGAT GAACTACCAA TGGCAGTAAA 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

AAATATAATG GCCAGGACTG ACCACCCAGA ACCAATTCAG CTGGCGTACA ACAGCTACGA AACACAAGTG CCAGTGCTAT TCCCAAAAAT AAAGAATGGA 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

GAGGTGACTG ACAGTTACGA TAACTATACC TTCCTCAACG CAAGAAAATT AGGGGATGAT GTACCCCCTT ACGTGTATGC CACAGAGGAT GAGGACTTAG 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CGGTAGAGCT GCTGGGCTTA GACTGGCCGG ACCCTGGAAA CCAAGGGACC GTAGAGACTG GCAGAGCACT AAAACAGGTA GTTGGTCTAT CAACAGCTGA 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

GAATGCCCTG TTAGTAGCCT TATTCGGCTA CGTAGGATAT CAGGCGCTTT CAAAGAGGCA TATACCAGTA GTCACAGACA TATATTCAAT TGAAGATCAC 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

AGGTTGGAAG ACACCACACA CCTACAGTAC GCCCCAAATG CTATCAAGAC GGAGGGGAAG GAGACAGAAT TGAAAGAGCT AGCTCAGGGG GATGTGCAGA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

GATGTGTGGA AGCCATGACC AATTATGCAA GAGAGGGTAT CCAATTTATG AAGTCTCAGG CACTGAAGGT GAAGGAAACC CCTACTTACA AGGAGACAAT 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

GGACACTGTG ACGGACTATG TAAAGAAATT CATGGAGGCG CTGGCAGACA GTAAAGAAGA CATCATAAAA TATGGGCTGT GGGGGACGCA CACAGCCTTA 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

TATAAGAGCA TCAGTGCCAG GCTTGGGGGT GAGACTGCGT TCGCTACCCT GGTAGTGAAG TGGCTGGCAT TTGGGGGTGA ATCAATAGCA GACCATGTCA 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

AACAAGCGGC CACAGACTTG GTCGTTTACT ATATCATCAA CAGACCTCAG TTCCCAGGAG ACACGGAGAC ACAACAAGAC GGAAGGAAAT TTGTGGCCAG 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

CCTACTGGCC TCAGCTCTAG CTACTTACAC ATACAAAAGC TGGAATTACA ATAACCTGTC CAAGATAGTT GAACCGGCTT TGGCCACTCT GCCCTATGCC 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

GCCACAGCTC TCAAATTATT CGCCCCCACC CGATTGGAGA GCGTTGTCAT ATTAAGTACC GCAATCTACA AAACCTACCT ATCAATCAGG CGCGGAAAAA 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

GCGATGGTTT GCTAGGCACG GGGGTTAGTG CGGCTATGGA GATCATGTCA CAAAATCCAG TATCCGTGGG CATAGCAGTC ATGCTAGGGG TAGGGGCCGT 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

GGCAGCCCAC AATGCAATCG AAGCCAGTGA GCAGAAAAGA ACACTACTCA TGAAAGTCTT TGTAAAGAAC TTCTTGGACC AGGCAGCCAC AGATGAATTA 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

GTCAAGGAGA GTCCTGAAAA AATAATAATG GCTTTGTTTG AAGCAGTGCA GACAGTCGGC AACCCTCTTA GACTTGTATA CCACCTTTAT GGAGTTTTTT 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

ATAAAGGGTG GGAGGCAAAA GAGTTGGCCC AAAGGACAGC CGGTAGGAAC CTTTTCACTT TAATCATGTT CGAGGCTGTG GAACTGCTGG GAGTAGACAG 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

TGAAGGAAAG GTCCGCCAGC TATCAAGTAA TTACATACTA GAGCTTTTGT ATAAGTTCCG TGACAGTATC AAGTCTAGCG TGAGGGAGAT GGCAATCAGC 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

TGGGCCCCTG CCCCTTTCAG TTGTGATTGG ACACCGACGG ATGACAGAAT AGGGCTCCCC CAAGACAATT TCCACCAAGT GGAGACGAAA TGCCCCTGTG 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

GTTACAAGAT GAAGGCAGTT AAGAATTGTG CTGGAGAACT GAGACTCTTG GAGGAGGAGG GTTCATTTCT CTGCAGAAAT AAATTCGGGA GAGGTTCACG 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

GAACTACAGA GTGACAAAAT ATTATGATGA CAACCTATTA GAAATAAAGC CAGTGATAAG AATGGAAGGG CATGTGGAAC TCTACTACAA GGGGGCCACC 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

ATCAAACTGG ATTTCAACAA CAGCAAAACA ATATTGGCAA CCGATAAATG GGAGGTTGAT CACTCCACTC TGGTCAGGGT GCTCAAGAGG CACACAGGGG 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

CTGGATATCA TGGGGCATAC CTGGGCGAGA AACCGAACCA CAAACACCTG ATAGAGAGGG ACTGTGCAAC CATCACCAAA GATAAGGTCT GTTTTCTCAA 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

AATGAAGAGA GGGTGCGCAT TTACTTATGA CTTATCCCTT CACAACCTTA CCCGACTGAT TGAATTGGTA CACAAGAATA ACTTGGAAGA CAAAGAGATT 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

CCCGCTGCTA CGGTTACAAC CTGGCTGGCT TACACATTTG TAAATGAAGA TATAGGGACC ATAAAACCAG CCTTCGGGGA GAAAGTAACG CTGGAGATGC 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

AGGAGGAGAT AACCTTGCAG CCTGCTGTTG TGGTGGATAC AACAGACGTA GCCGTGACTG TGGTAGGGGA AGCCCCCACT ATGACTACAG GGGAGACACC 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

GACAGTGTTC ACCAGCTCAG GTTCAGGCCT GAAAAGCCAA CAAGTTTTGA AACTAGGGGT AGGTGAAGGC CAATATCCAG GGACTAATCC ACAGAGGGCA 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

AGCCTGCACG AAGCCATACA AGGTGCAGAT GAGAGGCCCT CGGTGCTGAT ATTGGGGTCT GATAAAGCCA CCTCTAATAG AGTGAAGACT GCAAAGAATG 
^9401      ^9411      ^9421      ^9431      ^9441      ^9451      ^9461      ^9471      ^9481      ^9491      

TAAAGGTATA CAGAGGCAGG GACCCACTAG AAGTGAGAGA TATGATGAGG AGGGGAAAGA TCCTGGTCGT AGCCCTGTCT AGGGTTGATA ATGCTCTATT 
^9501      ^9511      ^9521      ^9531      ^9541      ^9551      ^9561      ^9571      ^9581      ^9591      

GAAATTTGTT GACTACAAAG GCACCTTTCT AACTAGGGAG GCCCTAGAGG CATTAAGTTT GGGCAGGCCT AAAAAGAAAA ACATAACCAA GGCAGAAGCG 
^9601      ^9611      ^9621      ^9631      ^9641      ^9651      ^9661      ^9671      ^9681      ^9691      

CAGTGGTTGC TGTGCCCCGA GGACCAAATG GAAGAGCTAC CCGACTGGTT CGCAGCCGGG GAACCCATTT TTTTAGAGGC CAACATTAAA CATGACAGGT 
^9701      ^9711      ^9721      ^9731      ^9741      ^9751      ^9761      ^9771      ^9781      ^9791      

ACCATCTGGT GGGGGATATA GCTACCATCA AGGAAAAAGC CAAACAGTTG GGGGCTACAG ACTCCACAAA GATATCTAAG GAGGTTGGTG CTAAAGTGTA 
^9801      ^9811      ^9821      ^9831      ^9841      ^9851      ^9861      ^9871      ^9881      ^9891      

TTCTATGAAA CTGAGTAATT GGGTGATGCA AGAAGAAAAT AAACAGGGCA ATCTGACCCC CTTGTTTGAA GAGCTCCTGC AACAGTGTCC ACCCGGGGGC 
^9901      ^9911      ^9921      ^9931      ^9941      ^9951      ^9961      ^9971      ^9981      ^9991      

CAGAACAAAA CTGCACACAT GGTCTCTGCT TACCAACTAG CTCAAGGGAA CTGGATGCCG ACCAGCTGCC ATGTTTTCAT GGGGACCGTA TCTGCCAGGA 
^10001     ^10011     ^10021     ^10031     ^10041     ^10051     ^10061     ^10071     ^10081     ^10091     

GAACCAAGAC CCACCCATAC GAAGCATACG TTAAGTTAAG GGAGTTGGTA GAGGAGCACA AGATGAAAAC ACTGTGTCCC GGATCAAGCC TGGGTAGGCA 
^10101     ^10111     ^10121     ^10131     ^10141     ^10151     ^10161     ^10171     ^10181     ^10191     

CAACGATTGG ATAATTGGAA AAATTAAATA CCAGGGAAAC CTGAGGACCA AACACATGTT GAACCCCGGC AAGGTGGCAG AGCAACTGTG CAGAGAGGGA 
^10201     ^10211     ^10221     ^10231     ^10241     ^10251     ^10261     ^10271     ^10281     ^10291     

CACAGACACA ATGTGTATAA CAAGACAATA AGCTCAGTAA TGACAGCTAC TGGTATCAGG TTGGAGAAGT TGCCCGTGGT TAGGGCCCAG ACAGACCCAA 
^10301     ^10311     ^10321     ^10331     ^10341     ^10351     ^10361     ^10371     ^10381     ^10391     

CCAACTTCCA CCAAGCAATA AGGGATAAGA TAGACAAGGA AGAGAACCTA CAAACCCCGG GTTTACATAA GAAATTAATG GAAGTTTTCA ACGCATTGAA 
^10401     ^10411     ^10421     ^10431     ^10441     ^10451     ^10461     ^10471     ^10481     ^10491     

ACGACCCGAG TTAGAGTCCT CCTACGACGC CGTGGAATGG GAGGAACTGG AGAGAGGAAT AAACAGGAAG GGTGCTGCTG GTTTTTTCGA ACGCAAAAAT 
^10501     ^10511     ^10521     ^10531     ^10541     ^10551     ^10561     ^10571     ^10581     ^10591     

ATAGGGGAAA TATTGGATTC AGAGAAAAAT AAAGTCGAAG AGATTATTGA CAATCTGAAA AAAGGTAGAA ACATTAAATA TTATGAAACC GCGATCCCAA 
^10601     ^10611     ^10621     ^10631     ^10641     ^10651     ^10661     ^10671     ^10681     ^10691     

AGAATGAGAA GAGGGACGTC AACGATGACT GGACCGCCGG TGATTTCGTG GACGAGAAGA AACCTAGAGT CATACAATAC CCTGAAGCAA AAACAAGACT 
^10701     ^10711     ^10721     ^10731     ^10741     ^10751     ^10761     ^10771     ^10781     ^10791     

GGCCATCACC AAGGTGATGT ATAAGTGGGT GAAGCAGAAG CCAGTAGTTA TACCCGGGTA TGAAGGGAAG ACACCTCTAT TCCAAATTTT TGACAAAGTA 
^10801     ^10811     ^10821     ^10831     ^10841     ^10851     ^10861     ^10871     ^10881     ^10891     

AAGAAGGAAT GGGATCAATT TCAAAATCCA GTGGCAGTGA GCTTCGACAC TAAGGCGTGG GACACCCAGG TAACCACAAA AGATTTGGAG CTGATAAGGG 
^10901     ^10911     ^10921     ^10931     ^10941     ^10951     ^10961     ^10971     ^10981     ^10991     

ACATACAAAA GTATTATTTC AAGAAGAAAT GGCACAAATT TATTGACACC CTGACCACGC ATATGTCAGA AGTACCCGTG ATCAGTGCTG ATGGGGAAGT 
^11001     ^11011     ^11021     ^11031     ^11041     ^11051     ^11061     ^11071     ^11081     ^11091     

ATACATAAGG AAAGGGCAAA GAGGCAGTGG ACAACCTGAC ACAAGTGCGG GCAACAGCAT GCTAAATGTC TTAACAATGG TTTACGCCTT CTGCGAGGCC 
^11101     ^11111     ^11121     ^11131     ^11141     ^11151     ^11161     ^11171     ^11181     ^11191     

ACAGGAGTAC CCTACAAGAG CTTTGACAGG GTGGCAAAAA TTCATGTGTG CGGGGATGAT GGCTTCCTGA TCACAGAAAG AGCTCTCGGT GAGAAATTTG 
^11201     ^11211     ^11221     ^11231     ^11241     ^11251     ^11261     ^11271     ^11281     ^11291     

CAAGTAAGGG AGTCCAGATC CTTTATGAAG CTGGGAAGCC CCAGAAGATC ACTGAAGGGG ACAAAATGAA AGTGGCCTAC CAATTTGATG ATATTGAGTT 
^11301     ^11311     ^11321     ^11331     ^11341     ^11351     ^11361     ^11371     ^11381     ^11391     

TTGCTCCCAT ACACCAATAC AAGTAAGATG GTCAGATAAC ACTTCTAGTT ACATGCCGGG GAGAAATACA ACCACAATCC TGGCAAAGAT GGCCACGAGG 
^11401     ^11411     ^11421     ^11431     ^11441     ^11451     ^11461     ^11471     ^11481     ^11491     

TTAGATTCCA GCGGTGAAAG GGGTACCATA GCATATGAGA AAGCAGTAGC ATTTAGCTTC CTGCTGATGT ACTCCTGGAA CCCACTAATT AGAAGGATCT 
^11501     ^11511     ^11521     ^11531     ^11541     ^11551     ^11561     ^11571     ^11581     ^11591     

GCTTACTGGT GCTATCAACT GAACTGCAAG TGAAACCAGG GAAGTCAACT ACTTACTATT ATGAAGGAGA CCCGATATCT GCCTACAAGG AAGTCATCGG 
^11601     ^11611     ^11621     ^11631     ^11641     ^11651     ^11661     ^11671     ^11681     ^11691     

CCACAACCTT TTTGATCTTA AGAGAACAAG CTTTGAGAAG CTGGCCAAGT TAAATCTTAG CATGTCTGTA CTCGGGGCCT GGACTAGACA CACCAGTAAA 
^11701     ^11711     ^11721     ^11731     ^11741     ^11751     ^11761     ^11771     ^11781     ^11791     

AGACTACTAC AAGACTGTGT CAATATAGGT GTTAAAGAGG GCAATTGGCT AGTCAATGCA GACAGACTAG TAAGTAGCAA GACCGGGAAT AGGTACATAC 
^11801     ^11811     ^11821     ^11831     ^11841     ^11851     ^11861     ^11871     ^11881     ^11891     

CCGGAGAGGG TCACACCCTG CAAGGAAGAC ATTATGAAGA ACTGGTGTTG GCAAGAAAAC AGATCAACAA CTTTCAAGGG ACAGACAGGT ACAACCTAGG 
^11901     ^11911     ^11921     ^11931     ^11941     ^11951     ^11961     ^11971     ^11981     ^11991     

CCCAATAGTC AACATGGTGT TAAGGAGGCT GAGAGTCATG ATGATGACGC TGATAGGGAG AGGGGCATGA GCGCGGGTAA CCCGGGATCT GAACCCGCCA 
^12001     ^12011     ^12021     ^12031     ^12041     ^12051     ^12061     ^12071     ^12081     ^12091     

GTAGGACCCT ATTGTAGATA ACACTAATTT TCTTTTTTTT CTTTTTTATT TATTTAGATA TTATTATTTA TTTATTTATT TATTTATTGA ATGAGTAAGA 
^12101     ^12111     ^12121     ^12131     ^12141     ^12151     ^12161     ^12171     ^12181     ^12191     

ACTGGTATAA ACTACCTCAA GTTACCACAC TACACTCATT TTTAACAGCA CTTTAGCTGG AAGGAAAATT CCTGACGTCC ACAGTTGGAC TAAGGTAATT 
^12201     ^12211     ^12221     ^12231     ^12241     ^12251     ^12261     ^12271     ^12281     ^12291     

TCTAACGGCC C
^12301     ^12311

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

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

Classical swine fever virus - C Chinese strain (C-strain, EP 0 351 901 B1)

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:

no

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

374-12070

Citations:

Moormann R. J., van Gennip H. G., Miedema G. K., Hulst M. M., van Rijn P. A. (1996) Infectious RNA transcribed from an engineered full-length cDNA template of the genome of a pestivirus. J. Virol. 70(2):763-770

IRESs:

IRES:

Version: `2`	Last change: `2009-08-30 04:48:09`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `CSFV`

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

1-373

Conclusion:
strongly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

GTATACGAGG TTAGTTCATT CTCGTATACA CGATTGGACA AATCAAAATT ATAATTTGGT TCAGGGCCTC CCTCCAGCGA CGGCCGAACT GGGCTAGCCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGCCCATAGT AGGACTAGCA AAACGGAGGG ACTAGCCATA GTGGCGAGCT CCCTGGGTGG TCTAAGTCCT GAGTACAGGA CAGTCGTCAG TAGTTCGACG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGAGCAGAAG CCCACCTCGA GATGCTACGT GGACGAGGGC ATGCCAAGAC ACACCTTAAC CCTAGCGGGG GTCGCTAGGG TGAAATCACA CCACGTGATG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GGAGTACGAC CTGATAGGGC GCTGCAGAGG CCCACTATTA GGCTAGTATA AAAATCTCTG CTGTACATGG CAC
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371

Citations:

Rijnbrand R., Bredenbeek P. J., Haasnoot P. C., Kieft J. S., Spaan W. J., Lemon S. M. (2001) The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA. 7(4):585-597

RNA:protein interactions:

The RNA:protein interaction:

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

The description of the protein interacting with the RNA:
eIF3

The interacting RNA base range: 182-234

The organism where this RNA:protein interaction occurs:

Remarks:

The interaction was studied in vitro with isolated ribosomes from rabbit reticulocyte lysates.

Citations:

Sizova D. V., Kolupaeva V. G., Pestova T. V., Shatsky I. N., Hellen C. U. (1998) Specific interaction of eukaryotic translation initiation factor 3 with the 5' nontranslated regions of hepatitis C virus and classical swine fever virus RNAs. J. Virol. 72(6):4775-4782

The RNA:protein interaction:

Version: `2`	Last change: `2009-08-29 13:01:59`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Abbreviated name of the protein interacting with the RNA:
RPS9

Full name of the protein interacting with the RNA:
ribosomal protein S9

The description of the protein interacting with the RNA:
ribosomal protein S9

The organism where this RNA:protein interaction occurs:

Oryctolagus cuniculus RRL

Remarks:

The interaction with RPS9 was shown in RRL-based toe-printing assay (Pestova et al., 1998). It could be that
the RPS9 protein was misplaced instead of RPS5 (Fukushi et al., 2001).

Citations:

Pestova TV, Shatsky IN, Fletcher SP, Jackson RJ, Hellen CU (1998) A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes Dev. 1(12):67-83

Fukushi S, Okada M, Stahl J, Kageyama T, Hoshino FB, Katayama K (2001) Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus. J. Biol. Chem. 24(276):20824-20826

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