IRESite_Id:37 summary record describing characteristics of BVDV1

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `37`	Version: `4`
Originaly submitted by: Václav Vopálenský	Submission date: `2006-01-12 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2006-08-03 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: `BVDV1`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
9626649

The mRNA/+RNA description:

Bovine viral diarrhea virus 1, complete genome.

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

GTATACGAGA ATTAGAAAAG GCACTCGTAT ACGTATTGGG CAATTAAAAA TAATAATTAG GCCTAGGGAA CAAATCCCTC TCAGCGAAGG CCGAAAAGAG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCTAGCCATG CCCTTAGTAG GACTAGCATA ATGAGGGGGG TAGCAACAGT GGTGAGTTCG TTGGATGGCT TAAGCCCTGA GTACAGGGTA GTCGTCAGTG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GTTCGACGCC TTGGAATAAA GGTCTCGAGA TGCCACGTGG ACGAGGGCAT GCCCAAAGCA CATCTTAACC TGAGCGGGGG TCGCCCAGGT AAAAGCAGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTAACCGACT GTTACGAATA CAGCCTGATA GGGTGCTGCA GAGGCCCACT GTATTGCTAC TAAAAATCTC TGCTGTACAT GGCACATGGA GTTGATCACA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AATGAACTTT TATACAAAAC ATACAAACAA AAACCCGTCG GGGTGGAGGA ACCTGTTTAT GATCAGGCAG GTGATCCCTT ATTTGGTGAA AGGGGAGCAG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCCACCCTCA ATCGACGCTA AAGCTCCCAC ACAAGAGAGG GGAACGCGAT GTTCCAACCA ACTTGGCATC CTTACCAAAA AGAGGTGACT GCAGGTCGGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TAATAGCAGA GGACCTGTGA GCGGGATCTA CCTGAAGCCA GGGCCACTAT TTTACCAGGA CTATAAAGGT CCCGTCTATC ACAGGGCCCC GCTGGAGCTC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TTTGAGGAGG GATCCATGTG TGAAACGACT AAACGGATAG GGAGAGTAAC TGGAAGTGAC GGAAAGCTGT ACCACATTTA TGTGTGTATA GATGGATGTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TAATAATAAA AAGTGCCACG AGAAGTTACC AAAGGGTGTT CAGGTGGGTC CATAATAGGC TTGACTGCCC TCTATGGGTC ACAACTTGCT CAGACACGAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AGAAGAGGGA GCAACAAAAA AGAAAACACA GAAACCCGAC AGACTAGAAA GGGGGAAAAT GAAAATAGTG CCCAAAGAAT CTGAAAAAGA CAGCAAAACT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AAACCTCCGG ATGCTACAAT AGTGGTGGAA GGAGTCAAAT ACCAGGTGAG GAAGAAGGGA AAAACCAAGA GTAAAAACAC TCAGGACGGC TTGTACCATA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACAAAAACAA ACCTCAGGAA TCACGCAAGA AACTGGAAAA AGCATTGTTG GCGTGGGCAA TAATAGCTAT AGTTTTGTTT CAAGTTACAA TGGGAGAAAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CATAACACAG TGGAACCTAC AAGATAATGG GACGGAAGGG ATACAACGGG CAATGTTCCA AAGGGGTGTG AATAGAAGTT TACATGGAAT CTGGCCAGAG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AAAATCTGTA CTGGCGTCCC TTCCCATCTA GCCACCGATA TAGAACTAAA AACAATTCAT GGTATGATGG ATGCAAGTGA GAAGACCAAC TACACGTGTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCAGACTTCA ACGCCATGAG TGGAACAAGC ATGGTTGGTG CAACTGGTAC AATATTGAAC CCTGGATTCT AGTCATGAAT AGAACCCAAG CCAATCTCAC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGAGGGACAA CCACCAAGGG AGTGCGCAGT CACTTGTAGG TATGATAGGG CTAGTGACTT AAACGTGGTA ACACAAGCTA GAGATAGCCC CACACCCTTA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACAGGTTGCA AGAAAGGAAA GAACTTCTCC TTTGCAGGCA TATTGATGCG GGGCCCCTGC AACTTTGAAA TAGCTGCAAG TGATGTATTA TTCAAAGAAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATGAACGCAT TAGTATGTTC CAGGATACCA CTCTTTACCT TGTTGACGGG TTGACCAACT CCTTAGAAGG TGCCAGACAA GGAACCGCTA AACTGACAAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTGGTTAGGC AAGCAGCTCG GGATACTAGG AAAAAAGTTG GAAAACAAGA GTAAGACGTG GTTTGGAGCA TACGCTGCTT CCCCTTACTG TGATGTCGAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGCAAAATTG GCTACATATG GTATACAAAA AATTGCACCC CTGCCTGCTT ACCCAAGAAC ACAAAAATTG TCGGCCCTGG GAAATTTGGC ACCAATGCAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGGACGGCAA GATATTACAT GAGATGGGGG GTCACTTGTC GGAGGTACTA CTACTTTCTT TAGTGGTGCT GTCCGACTTC GCACCGGAAA CAGCTAGTGT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AATGTACCTA ATCCTACATT TTTCCATCCC ACAAAGTCAC GTTGATGTAA TGGATTGTGA TAAGACCCAG TTGAACCTCA CAGTGGAGCT GACAACAGCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAAGTAATAC CAGGGTCGGT CTGGAATCTA GGCAAATATG TATGTATAAG ACCAAATTGG TGGCCTTATG AGACAACTGT AGTGTTGGCA TTTGAAGAGG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TGAGCCAGGT GGTGAAGTTA GTGTTGAGGG CACTCAGAGA TTTAACACGC ATTTGGAACG CTGCAACAAC TACTGCTTTT TTAGTATGCC TTGTTAAGAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AGTCAGGGGC CAGATGGTAC AGGGCATTCT GTGGCTACTA TTGATAACAG GGGTACAAGG GCACTTGGAT TGCAAACCTG AATTCTCGTA TGCCATAGCA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AAGGACGAAA GAATTGGTCA ACTGGGGGCT GAAGGCCTTA CCACCACTTG GAAGGAATAC TCACCTGGAA TGAAGCTGGA AGACACAATG GTCATTGCTT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GGTGCGAAGA TGGGAAGTTA ATGTACCTCC AAAGATGCAC GAGAGAAACC AGATATCTCG CAATCTTGCA TACAAGAGCC TTGCCGACCA GTGTGGTATT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CAAAAAACTC TTTGATGGGC GAAAGCAAGA GGATGTAGTC GAAATGAACG ACAACTTTGA ATTTGGACTC TGCCCATGTG ATGCCAAACC CATAGTAAGA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GGGAAGTTCA ATACAACGCT GCTGAACGGA CCGGCCTTCC AGATGGTATG CCCCATAGGA TGGACAGGGA CTGTAAGCTG TACGTCATTC AATATGGACA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CCTTAGCCAC AACTGTGGTA CGGACATATA GAAGGTCTAA ACCATTCCCT CATAGGCAAG GCTGTATCAC CCAAAAGAAT CTGGGGGAGG ATCTCCATAA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CTGCATCCTT GGAGGAAATT GGACTTGTGT GCCTGGAGAC CAACTACTAT ACAAAGGGGG CTCTATTGAA TCTTGCAAGT GGTGTGGCTA TCAATTTAAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GAGAGTGAGG GACTACCACA CTACCCCATT GGCAAGTGTA AATTGGAGAA CGAGACTGGT TACAGGCTAG TAGACAGTAC CTCTTGCAAT AGAGAAGGTG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGGCCATAGT ACCACAAGGG ACATTAAAGT GCAAGATAGG AAAAACAACT GTACAGGTCA TAGCTATGGA TACCAAACTC GGACCTATGC CTTGCAGACC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ATATGAAATC ATATCAAGTG AGGGGCCTGT AGAAAAGACA GCGTGTACTT TCAACTACAC TAAGACATTA AAAAATAAGT ATTTTGAGCC CAGAGACAGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TACTTTCAGC AATACATGCT AAAAGGAGAG TATCAATACT GGTTTGACCT GGAGGTGACT GACCATCACC GGGATTACTT CGCTGAGTCC ATATTAGTGG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TGGTAGTAGC CCTCTTGGGT GGCAGATATG TACTTTGGTT ACTGGTTACA TACATGGTCT TATCAGAACA GAAGGCCTTA GGGATTCAGT ATGGATCAGG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GGAAGTGGTG ATGATGGGCA ACTTGCTAAC CCATAACAAT ATTGAAGTGG TGACATACTT CTTGCTGCTG TACCTACTGC TGAGGGAGGA GAGCGTAAAG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AAGTGGGTCT TACTCTTATA CCACATCTTA GTGGTACACC CAATCAAATC TGTAATTGTG ATCCTACTGA TGATTGGGGA TGTGGTAAAG GCCGATTCAG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GGGGCCAAGA GTACTTGGGG AAAATAGACC TCTGTTTTAC AACAGTAGTA CTAATCGTCA TAGGTTTAAT CATAGCTAGG CGTGACCCAA CTATAGTGCC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ACTGGTAACA ATAATGGCAG CACTGAGGGT CACTGAACTG ACCCACCAGC CTGGAGTTGA CATCGCTGTG GCGGTCATGA CTATAACCCT ACTGATGGTT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AGCTATGTGA CAGATTATTT TAGATATAAA AAATGGTTAC AGTGCATTCT CAGCCTGGTA TCTGCGGTGT TCTTGATAAG AAGCCTAATA TACCTAGGTA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GAATCGAGAT GCCAGAGGTA ACTATCCCAA ACTGGAGACC ACTAACTTTA ATACTATTAT ATTTGATCTC AACAACAATT GTAACGAGGT GGAAGGTTGA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CGTGGCTGGC CTATTGTTGC AATGTGTGCC TATCTTATTG CTGGTCACAA CCTTGTGGGC CGACTTCTTA ACCCTAATAC TGATCCTGCC TACCTATGAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TTGGTTAAAT TATACTATCT GAAAACTGTT AGGACTGATA CAGAAAGAAG TTGGCTAGGG GGGATAGACT ATACAAGAGT TGACTCCATC TACGACGTTG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ATGAGAGTGG AGAGGGCGTA TATCTTTTTC CATCAAGGCA GAAAGCACAG GGGAATTTTT CTATACTCTT GCCCCTTATC AAAGCAACAC TGATAAGTTG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CGTCAGCAGT AAATGGCAGC TAATATACAT GAGTTACTTA ACTTTGGACT TTATGTACTA CATGCACAGG AAAGTTATAG AAGAGATCTC AGGAGGTACC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

AACATAATAT CCAGGTTAGT GGCAGCACTC ATAGAGCTGA ACTGGTCCAT GGAAGAAGAG GAGAGCAAAG GCTTAAAGAA GTTTTATCTA TTGTCTGGAA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GGTTGAGAAA CCTAATAATA AAACATAAGG TAAGGAATGA GACCGTGGCT TCTTGGTACG GGGAGGAGGA AGTCTACGGT ATGCCAAAGA TCATGACTAT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AATCAAGGCC AGTACACTGA GTAAGAGCAG GCACTGCATA ATATGCACTG TATGTGAGGG CCGAGAGTGG AAAGGTGGCA CCTGCCCAAA ATGTGGACGC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CATGGGAAGC CGATAACGTG TGGGATGTCG CTAGCAGATT TTGAAGAAAG ACACTATAAA AGAATCTTTA TAAGGGAAGG CAACTTTGAG GGTATGTGCA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GCCGATGCCA GGGAAAGCAT AGGAGGTTTG AAATGGACCG GGAACCTAAG AGTGCCAGAT ACTGTGCTGA GTGTAATAGG CTGCATCCTG CTGAGGAAGG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TGACTTTTGG GCAGAGTCGA GCATGTTGGG CCTCAAAATC ACCTACTTTG CGCTGATGGA TGGAAAGGTG TATGATATCA CAGAGTGGGC TGGATGCCAG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CGTGTGGGAA TCTCCCCAGA TACCCACAGA GTCCCTTGTC ACATCTCATT TGGTTCACGG ATGCCTTTCA GGCAGGAATA CAATGGCTTT GTACAATATA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CCGCTAGGGG GCAACTATTT CTGAGAAACT TGCCCGTACT GGCAACTAAA GTAAAAATGC TCATGGTAGG CAACCTTGGA GAAGAAATTG GTAATCTGGA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ACATCTTGGG TGGATCCTAA GGGGGCCTGC CGTGTGTAAG AAGATCACAG AGCACGAAAA ATGCCACATT AATATACTGG ATAAACTAAC CGCATTTTTC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

GGGATCATGC CAAGGGGGAC TACACCCAGA GCCCCGGTGA GGTTCCCTAC GAGCTTACTA AAAGTGAGGA GGGGTCTGGA GACTGCCTGG GCTTACACAC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ACCAAGGCGG GATAAGTTCA GTCGACCATG TAACCGCCGG AAAAGATCTA CTGGTCTGTG ACAGCATGGG ACGAACTAGA GTGGTTTGCC AAAGCAACAA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CAGGTTGACC GATGAGACAG AGTATGGCGT CAAGACTGAC TCAGGGTGCC CAGACGGTGC CAGATGTTAT GTGTTAAATC CAGAGGCCGT TAACATATCA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GGATCCAAAG GGGCAGTCGT TCACCTCCAA AAGACAGGTG GAGAATTCAC GTGTGTCACC GCATCAGGCA CACCGGCTTT CTTCGACCTA AAAAACTTGA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AAGGATGGTC AGGCTTGCCT ATATTTGAAG CCTCCAGCGG GAGGGTGGTT GGCAGAGTCA AAGTAGGGAA GAATGAAGAG TCTAAACCTA CAAAAATAAT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GAGTGGAATC CAGACCGTCT CAAAAAACAG AGCAGACCTG ACCGAGATGG TCAAGAAGAT AACCAGCATG AACAGGGGAG ACTTCAAGCA GATTACTTTG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GCAACAGGGG CAGGCAAAAC CACAGAACTC CCAAAAGCAG TTATAGAGGA GATAGGAAGA CACAAGAGAG TATTAGTTCT TATACCATTA AGGGCAGCGG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

CAGAGTCAGT CTACCAGTAT ATGAGATTGA AACACCCAAG CATCTCTTTT AACCTAAGGA TAGGGGACAT GAAAGAGGGG GACATGGCAA CCGGGATAAC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

CTATGCATCA TACGGGTACT TCTGCCAAAT GCCTCAACCA AAGCTCAGAG CTGCTATGGT AGAATACTCA TACATATTCT TAGATGAATA CCATTGTGCC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

ACTCCTGAAC AACTGGCAAT TATCGGGAAG ATCCACAGAT TTTCAGAGAG TATAAGGGTT GTCGCCATGA CTGCCACGCC AGCAGGGTCG GTGACCACAA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CAGGTCAAAA GCACCCAATA GAGGAATTCA TAGCCCCCGA GGTAATGAAA GGGGAGGATC TTGGTAGTCA GTTCCTTGAT ATAGCAGGGT TAAAAATACC 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

AGTGGATGAG ATGAAAGGCA ATATGTTGGT TTTTGTACCA ACGAGAAACA TGGCAGTAGA GGTAGCAAAG AAGCTAAAAG CTAAGGGCTA TAACTCTGGA 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

TACTATTACA GTGGAGAGGA TCCAGCCAAT CTGAGAGTTG TGACATCACA ATCCCCCTAT GTAATCGTGG CTACAAATGC TATTGAATCA GGAGTGACAC 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

TACCAGATTT GGACACGGTT ATAGACACGG GGTTGAAATG TGAAAAGAGG GTGAGGGTAT CATCAAAGAT ACCCTTCATC GTAACAGGCC TTAAGAGGAT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

GGCCGTGACT GTGGGTGAGC AGGCGCAGCG TAGGGGCAGA GTAGGTAGAG TGAAACCCGG GAGGTATTAT AGGAGCCAGG AAACAGCAAC AGGGTCAAAG 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

GACTACCACT ATGACCTCTT GCAGGCACAA AGATACGGGA TTGAGGATGG AATCAACGTG ACGAAATCCT TTAGGGAGAT GAATTACGAT TGGAGCCTAT 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

ACGAGGAGGA CAGCCTACTA ATAACCCAGC TGGAAATACT AAATAATCTA CTCATCTCAG AAGACTTGCC AGCCGCTGTT AAGAACATAA TGGCCAGGAC 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TGATCACCCA GAGCCAATCC AACTTGCATA CAACAGCTAT GAAGTCCAGG TCCCGGTCCT ATTCCCAAAA ATAAGGAATG GAGAAGTCAC AGACACCTAC 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

GAAAATTACT CGTTTCTAAA TGCCAGAAAG TTAGGGGAGG ATGTGCCCGT GTATATCTAC GCTACTGAAG ATGAGGATCT GGCAGTTGAC CTCTTAGGGC 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

TAGACTGGCC TGATCCTGGG AACCAGCAGG TAGTGGAGAC TGGTAAAGCA CTGAAGCAAG TGACCGGGTT GTCCTCGGCT GAAAATGCCC TACTAGTGGC 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

TTTATTTGGG TATGTGGGTT ACCAGGCTCT CTCAAAGAGG CATGTCCCAA TGATAACAGA CATATATACC ATCGAGGACC AGAGACTAGA AGACACCACC 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

CACCTCCAGT ATGCACCCAA CGCCATAAAA ACCGATGGGA CAGAGACTGA ACTGAAAGAA CTGGCGTCGG GTGACGTGGA AAAAATCATG GGAGCCATTT 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

CAGATTATGC AGCTGGGGGA CTGGAGTTTG TTAAATCCCA AGCAGAAAAG ATAAAAACAG CTCCTTTGTT TAAAGAAAAC GCAGAAGCCG CAAAAGGGTA 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TGTCCAAAAA TTCATTGACT CATTAATTGA AAATAAAGAA GAAATAATCA GATATGGTTT GTGGGGAACA CACACAGCAC TATACAAAAG CATAGCTGCA 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

AGACTGGGGC ATGAAACAGC GTTTGCCACA CTAGTGTTAA AGTGGCTAGC TTTTGGAGGG GAATCAGTGT CAGACCACGT CAAGCAGGCG GCAGTTGATT 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

TAGTGGTCTA TTATGTGATG AATAAGCCTT CCTTCCCAGG TGACTCCGAG ACACAGCAAG AAGGGAGGCG ATTCGTCGCA AGCCTGTTCA TCTCCGCACT 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

GGCAACCTAC ACATACAAAA CTTGGAATTA CCACAATCTC TCTAAAGTGG TGGAACCAGC CCTGGCTTAC CTCCCCTATG CTACCAGCGC ATTAAAAATG 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

TTCACCCCAA CGCGGCTGGA GAGCGTGGTG ATACTGAGCA CCACGATATA TAAAACATAC CTCTCTATAA GGAAGGGGAA GAGTGATGGA TTGCTGGGTA 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

CGGGGATAAG TGCAGCCATG GAAATCCTGT CACAAAACCC AGTATCGGTA GGTATATCTG TGATGTTGGG GGTAGGGGCA ATCGCTGCGC ACAACGCTAT 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

TGAGTCCAGT GAACAGAAAA GGACCCTACT TATGAAGGTG TTTGTAAAGA ACTTCTTGGA TCAGGCTGCA ACAGATGAGC TGGTAAAAGA AAACCCAGAA 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

AAAATTATAA TGGCCTTATT TGAAGCAGTC CAGACAATTG GTAACCCCCT GAGACTAATA TACCACCTGT ATGGGGTTTA CTACAAAGGT TGGGAGGCCA 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

AGGAACTATC TGAGAGGACA GCAGGCAGAA ACTTATTCAC ATTGATAATG TTTGAAGCCT TCGAGTTATT AGGGATGGAC TCACAAGGGA AAATAAGGAA 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

CCTGTCCGGA AATTACATTT TGGATTTGAT ATACGGCCTA CACAAGCAAA TCAACAGAGG GCTGAAGAAA ATGGTACTGG GGTGGGCCCC TGCACCCTTT 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

AGTTGTGACT GGACCCCTAG TGACGAGAGG ATCAGATTGC CAACAGACAA CTATTTGAGG GTAGAAACCA GGTGCCCATG TGGCTATGAG ATGAAAGCTT 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

TCAAAAATGT AGGTGGCAAA CTTACCAAAG TGGAGGAGAG CGGGCCTTTC CTATGTAGAA ACAGACCTGG TAGGGGACCA GTCAACTACA GAGTCACCAA 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

GTATTACGAT GACAACCTCA GAGAGATAAA ACCAGTAGCA AAGTTGGAAG GACAGGTAGA GCACTACTAC AAAGGGGTCA CAGCAAAAAT TGACTACAGT 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

AAAGGAAAAA TGCTCTTGGC CACTGACAAG TGGGAGGTGG AACATGGTGT CATAACCAGG TTAGCTAAGA GATATACTGG GGTCGGGTTC AATGGTGCAT 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

ACTTAGGTGA CGAGCCCAAT CACCGTGCTC TAGTGGAGAG GGACTGTGCA ACTATAACCA AAAACACAGT ACAGTTTCTA AAAATGAAGA AGGGGTGTGC 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

GTTCACCTAT GACCTGACCA TCTCCAATCT GACCAGGCTC ATCGAACTAG TACACAGGAA CAATCTTGAA GAGAAGGAAA TACCCACCGC TACGGTCACC 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

ACATGGCTAG CTTACACCTT CGTGAATGAA GACGTAGGGA CTATAAAACC AGTACTAGGA GAGAGAGTAA TCCCCGACCC TGTAGTTGAT ATCAATTTAC 
^9401      ^9411      ^9421      ^9431      ^9441      ^9451      ^9461      ^9471      ^9481      ^9491      

AACCAGAGGT GCAAGTGGAC ACGTCAGAGG TTGGGATCAC AATAATTGGA AGGGAAACCC TGATGACAAC GGGAGTGACA CCTGTCTTGG AAAAAGTAGA 
^9501      ^9511      ^9521      ^9531      ^9541      ^9551      ^9561      ^9571      ^9581      ^9591      

GCCTGACGCC AGCGACAACC AAAACTCGGT GAAGATCGGG TTGGATGAGG GTAATTACCC AGGGCCTGGA ATACAGACAC ATACACTAAC AGAAGAAATA 
^9601      ^9611      ^9621      ^9631      ^9641      ^9651      ^9661      ^9671      ^9681      ^9691      

CACAACAGGG ATGCGAGGCC CTTCATCATG ATCCTGGGCT CAAGGAATTC CATATCAAAT AGGGCAAAGA CTGCTAGAAA TATAAATCTG TACACAGGAA 
^9701      ^9711      ^9721      ^9731      ^9741      ^9751      ^9761      ^9771      ^9781      ^9791      

ATGACCCCAG GGAAATACGA GACTTGATGG CTGCAGGGCG CATGTTAGTA GTAGCACTGA GGGATGTCGA CCCTGAGCTG TCTGAAATGG TCGATTTCAA 
^9801      ^9811      ^9821      ^9831      ^9841      ^9851      ^9861      ^9871      ^9881      ^9891      

GGGGACTTTT TTAGATAGGG AGGCCCTGGA GGCTCTAAGT CTCGGGCAAC CTAAACCGAA GCAGGTTACC AAGGAAGCTG TTAGGAATTT GATAGAACAG 
^9901      ^9911      ^9921      ^9931      ^9941      ^9951      ^9961      ^9971      ^9981      ^9991      

AAAAAAGATG TGGAGATCCC TAACTGGTTT GCATCAGATG ACCCAGTATT TCTGGAAGTG GCCTTAAAAA ATGATAAGTA CTACTTAGTA GGAGATGTTG 
^10001     ^10011     ^10021     ^10031     ^10041     ^10051     ^10061     ^10071     ^10081     ^10091     

GAGAGCTAAA AGATCAAGCT AAAGCACTTG GGGCCACGGA TCAGACAAGA ATTATAAAGG AGGTAGGCTC AAGGACGTAT GCCATGAAGC TATCTAGCTG 
^10101     ^10111     ^10121     ^10131     ^10141     ^10151     ^10161     ^10171     ^10181     ^10191     

GTTCCTCAAG GCATCAAACA AACAGATGAG TTTAACTCCA CTGTTTGAGG AATTGTTGCT ACGGTGCCCA CCTGCAACTA AGAGCAATAA GGGGCACATG 
^10201     ^10211     ^10221     ^10231     ^10241     ^10251     ^10261     ^10271     ^10281     ^10291     

GCATCAGCTT ACCAATTGGC ACAGGGTAAC TGGGAGCCCC TCGGTTGCGG GGTGCACCTA GGTACAATAC CAGCCAGAAG GGTGAAGATA CACCCATATG 
^10301     ^10311     ^10321     ^10331     ^10341     ^10351     ^10361     ^10371     ^10381     ^10391     

AAGCTTACCT GAAGTTGAAA GATTTCATAG AAGAAGAAGA GAAGAAACCT AGGGTTAAGG ATACAGTAAT AAGAGAGCAC AACAAATGGA TACTTAAAAA 
^10401     ^10411     ^10421     ^10431     ^10441     ^10451     ^10461     ^10471     ^10481     ^10491     

AATAAGGTTT CAAGGAAACC TCAACACCAA GAAAATGCTC AACCCAGGGA AACTATCTGA ACAGTTGGAC AGGGAGGGGC GCAAGAGGAA CATCTACAAC 
^10501     ^10511     ^10521     ^10531     ^10541     ^10551     ^10561     ^10571     ^10581     ^10591     

CACCAGATTG GTACTATAAT GTCAAGTGCA GGCATAAGGC TGGAGAAATT GCCAATAGTG AGGGCCCAAA CCGACACCAA AACCTTTCAT GAGGCAATAA 
^10601     ^10611     ^10621     ^10631     ^10641     ^10651     ^10661     ^10671     ^10681     ^10691     

GAGATAAGAT AGACAAGAGT GAAAACCGGC AAAATCCAGA ATTGCACAAC AAATTGTTGG AGATTTTCCA CACGATAGCC CAACCCACCC TGAAACACAC 
^10701     ^10711     ^10721     ^10731     ^10741     ^10751     ^10761     ^10771     ^10781     ^10791     

CTACGGTGAG GTGACGTGGG AGCAACTTGA GGCGGGGGTA AATAGAAAGG GGGCAGCAGG CTTCCTGGAG AAGAAGAACA TCGGAGAAGT ATTGGATTCA 
^10801     ^10811     ^10821     ^10831     ^10841     ^10851     ^10861     ^10871     ^10881     ^10891     

GAAAAGCACC TGGTAGAACA ATTGGTCAGG GATCTGAAGG CCGGGAGAAA GATAAAATAT TATGAAACTG CAATACCAAA AAATGAGAAG AGAGATGTCA 
^10901     ^10911     ^10921     ^10931     ^10941     ^10951     ^10961     ^10971     ^10981     ^10991     

GTGATGACTG GCAGGCAGGG GACCTGGTGG TTGAGAAGAG GCCAAGAGTT ATCCAATACC CTGAAGCCAA GACAAGGCTA GCCATCACTA AGGTCATGTA 
^11001     ^11011     ^11021     ^11031     ^11041     ^11051     ^11061     ^11071     ^11081     ^11091     

TAACTGGGTG AAACAGCAGC CCGTTGTGAT TCCAGGATAT GAAGGAAAGA CCCCCTTGTT CAACATCTTT GATAAAGTGA GAAAGGAATG GGACTCGTTC 
^11101     ^11111     ^11121     ^11131     ^11141     ^11151     ^11161     ^11171     ^11181     ^11191     

AATGAGCCAG TGGCCGTAAG TTTTGACACC AAAGCCTGGG ACACTCAAGT GACTAGTAAG GATCTGCAAC TTATTGGAGA AATCCAGAAA TATTACTATA 
^11201     ^11211     ^11221     ^11231     ^11241     ^11251     ^11261     ^11271     ^11281     ^11291     

AGAAGGAGTG GCACAAGTTC ATTGACACCA TCACCGACCA CATGACAGAA GTACCAGTTA TAACAGCAGA TGGTGAAGTA TATATAAGAA ATGGGCAGAG 
^11301     ^11311     ^11321     ^11331     ^11341     ^11351     ^11361     ^11371     ^11381     ^11391     

AGGGAGCGGC CAGCCAGACA CAAGTGCTGG CAACAGCATG TTAAATGTCC TGACAATGAT GTACGGCTTC TGCGAAAGCA CAGGGGTACC GTACAAGAGT 
^11401     ^11411     ^11421     ^11431     ^11441     ^11451     ^11461     ^11471     ^11481     ^11491     

TTCAACAGGG TGGCAAGGAT CCACGTCTGT GGGGATGATG GCTTCTTAAT AACTGAAAAA GGGTTAGGGC TGAAATTTGC TAACAAAGGG ATGCAGATTC 
^11501     ^11511     ^11521     ^11531     ^11541     ^11551     ^11561     ^11571     ^11581     ^11591     

TTCATGAAGC AGGCAAACCT CAGAAGATAA CGGAAGGGGA AAAGATGAAA GTTGCCTATA GATTTGAGGA TATAGAGTTC TGTTCTCATA CCCCAGTCCC 
^11601     ^11611     ^11621     ^11631     ^11641     ^11651     ^11661     ^11671     ^11681     ^11691     

TGTTAGGTGG TCCGACAACA CCAGTAGTCA CATGGCCGGG AGAGACACCG CTGTGATACT ATCAAAGATG GCAACAAGAT TGGATTCAAG TGGAGAGAGG 
^11701     ^11711     ^11721     ^11731     ^11741     ^11751     ^11761     ^11771     ^11781     ^11791     

GGTACCACAG CATATGAAAA AGCGGTAGCC TTCAGTTTCT TGCTGATGTA TTCCTGGAAC CCGCTTGTTA GGAGGATTTG CCTGTTGGTC CTTTCGCAAC 
^11801     ^11811     ^11821     ^11831     ^11841     ^11851     ^11861     ^11871     ^11881     ^11891     

AGCCAGAGAC AGACCCATCA AAACATGCCA CTTATTATTA CAAAGGTGAT CCAATAGGGG CCTATAAAGA TGTAATAGGT CGGAATCTAA GTGAACTGAA 
^11901     ^11911     ^11921     ^11931     ^11941     ^11951     ^11961     ^11971     ^11981     ^11991     

GAGAACAGGC TTTGAGAAAT TGGCAAATCT AAACCTAAGC CTGTCCACGT TGGGGGTCTG GACTAAGCAC ACAAGCAAAA GAATAATTCA GGACTGTGTT 
^12001     ^12011     ^12021     ^12031     ^12041     ^12051     ^12061     ^12071     ^12081     ^12091     

GCCATTGGGA AAGAAGAGGG CAACTGGCTA GTTAAGCCCG ACAGGCTGAT ATCCAGCAAA ACTGGCCACT TATACATACC TGATAAAGGC TTTACATTAC 
^12101     ^12111     ^12121     ^12131     ^12141     ^12151     ^12161     ^12171     ^12181     ^12191     

AAGGAAAGCA TTATGAGCAA CTGCAGCTAA GAACAGAGAC AAACCCGGTC ATGGGGGTTG GGACTGAGAG ATACAAGTTA GGTCCCATAG TCAATCTGCT 
^12201     ^12211     ^12221     ^12231     ^12241     ^12251     ^12261     ^12271     ^12281     ^12291     

GCTGAGAAGG TTGAAAATTC TGCTCATGAC GGCCGTCGGC GTCAGCAGCT GAGACAAAAT GTATATATTG TAAATAAATT AATCCATGTA CATAGTGTAT 
^12301     ^12311     ^12321     ^12331     ^12341     ^12351     ^12361     ^12371     ^12381     ^12391     

ATAAATATAG TTGGGACCGT CCACCTCAAG AAGACGACAC GCCCAACACG CACAGCTAAA CAGTAGTCAA GATTATCTAC CTCAAGATAA CACTACATTT 
^12401     ^12411     ^12421     ^12431     ^12441     ^12451     ^12461     ^12471     ^12481     ^12491     

AATGCACACA GCACTTTAGC TGTATGAGGA TACGCCCGAC GTCTATAGTT GGACTAGGGA AGACCTCTAA CAG
^12501     ^12511     ^12521     ^12531     ^12541     ^12551     ^12561     ^12571

Credibility of mRNA sequence:

unknown

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

Bovine viral diarrhea virus 1 NADL

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`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
BVDV_1

The description of the protein encoded in this ORF:
Bovine viral diarrhea virus 1 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):

386-12352

Remarks:

T7 derived transcripts containing BVDV IRES functional also in rabbit reticulocyte lysates (CAT and LUC were
detectable). In contrast, direct mRNA transfection of uncapped T7 transcripts yielded only LUC signal (second
cistron) in vivo. A series of 11 20b long DNA oligos was used to map which oligos inhibit in vitro
translation. The inhibitory effect was observed when they annealed to bases 154-261 (numbers not recalculated
to match the sequence used herein) of BVDV genome.

Citations:

Poole T. L., Wang C., Popp R. A., Potgieter L. N., Siddiqui A., Collett M. S. (1995) Pestivirus translation initiation occurs by internal ribosome entry. Virology. 206(1):750-754

IRESs:

IRES:

Version: `8`	Last change: `2007-01-11 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `BVDV1_1-385`

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

1-385

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GTATACGAGA ATTAGAAAAG GCACTCGTAT ACGTATTGGG CAATTAAAAA TAATAATTAG GCCTAGGGAA CAAATCCCTC TCAGCGAAGG CCGAAAAGAG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCTAGCCATG CCCTTAGTAG GACTAGCATA ATGAGGGGGG TAGCAACAGT GGTGAGTTCG TTGGATGGCT TAAGCCCTGA GTACAGGGTA GTCGTCAGTG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GTTCGACGCC TTGGAATAAA GGTCTCGAGA TGCCACGTGG ACGAGGGCAT GCCCAAAGCA CATCTTAACC TGAGCGGGGG TCGCCCAGGT AAAAGCAGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTAACCGACT GTTACGAATA CAGCCTGATA GGGTGCTGCA GAGGCCCACT GTATTGCTAC TAAAAATCTC TGCTGTACAT GGCAC
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381

Remarks:

Deletion of the 5' end to nt 31 had no effect on the IRES activity.

Citations:

Chon S. K., Perez D. R., Donis R. O. (1998) Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology. 251(2):370-382

IRES:

Version: `3`	Last change: `2007-01-11 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `BVDV1_29-391`

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

29-391

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

ATACGTATTG GGCAATTAAA AATAATAATT AGGCCTAGGG AACAAATCCC TCTCAGCGAA GGCCGAAAAG AGGCTAGCCA TGCCCTTAGT AGGACTAGCA 
^29        ^39        ^49        ^59        ^69        ^79        ^89        ^99        ^109       ^119       

TAATGAGGGG GGTAGCAACA GTGGTGAGTT CGTTGGATGG CTTAAGCCCT GAGTACAGGG TAGTCGTCAG TGGTTCGACG CCTTGGAATA AAGGTCTCGA 
^129       ^139       ^149       ^159       ^169       ^179       ^189       ^199       ^209       ^219       

GATGCCACGT GGACGAGGGC ATGCCCAAAG CACATCTTAA CCTGAGCGGG GGTCGCCCAG GTAAAAGCAG TTTTAACCGA CTGTTACGAA TACAGCCTGA 
^229       ^239       ^249       ^259       ^269       ^279       ^289       ^299       ^309       ^319       

TAGGGTGCTG CAGAGGCCCA CTGTATTGCT ACTAAAAATC TCTGCTGTAC ATGGCACATG GAG
^329       ^339       ^349       ^359       ^369       ^379       ^389

Remarks:

The IRES region annotated here spans 385b of BVDV 5' UTR and 6b of the open reading frame.

Citations:

Poole T. L., Wang C., Popp R. A., Potgieter L. N., Siddiqui A., Collett M. S. (1995) Pestivirus translation initiation occurs by internal ribosome entry. Virology. 206(1):750-754

RNA:protein interactions:

The RNA:protein interaction:

Version: `4`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The description of the protein interacting with the RNA:
In UV cross-link assay p72 protein from RRL (Rabbit Reticulocyte Lysate System) binds to the BVDV IRES.

The organism where this RNA:protein interaction occurs:

Oryctolagus cuniculus RRL

Remarks:

PTB binds weakly to the BVDV IRES when added to wheat germ extract that normally does not contain PTB (but the
binding of PTB to the BVDV IRES is probably nonspecifc). PTB did not bind to the BVDV IRES in RRL, although
endogenous PTB is present in this extract in sufficient amounts.
BVDV IRES binds specifically and precisely to a ribosomal 40S (at bases 361 (U), 381 (G), 388 (G), 395-397
(AUC), 400-402 (AAA), G (404)) and 48S subunits (388 (G) and 403-405 (UGA)) respectively. BVDV IRES binds
specifically eIF3 (260-261 (AC) and also 320 (A)).

Citations:

Pestova T. V., Hellen C. U. (1999) Internal initiation of translation of bovine viral diarrhea virus RNA. Virology. 258(2):249-256

Sanderbrand S. A., Tautz N., Thiel H. J., Ochs K., Beck E., Niepmann M. (2000) Translation from the internal ribosome entry site of bovine viral diarrhea virus is independent of the interaction with polypyrimidine tract-binding protein. Vet. Microbiol. 77(1-2):215-227

Myers T. M., Kolupaeva V. G., Mendez E., Baginski S. G., Frolov I., Hellen C. U., Rice C. M. (2001) Efficient translation initiation is required for replication of bovine viral diarrhea virus subgenomic replicons. J Virol. 75(9):4226-4238

The RNA:protein interaction:

Version: `1`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

The description of the protein interacting with the RNA:
In UV cross-link assay p65 protein from RRL (Rabbit Reticulocyte Lysate System) binds to the BVDV IRES.

The organism where this RNA:protein interaction occurs:

Oryctolagus cuniculus RRL

Citations:

Pestova T. V., Hellen C. U. (1999) Internal initiation of translation of bovine viral diarrhea virus RNA. Virology. 258(2):249-256

The RNA:protein interaction:

Version: `1`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

The description of the protein interacting with the RNA:
In UV cross-link assay p50 protein from RRL (Rabbit Reticulocyte Lysate System) binds to the BVDV IRES.

The organism where this RNA:protein interaction occurs:

Oryctolagus cuniculus RRL

Citations:

Pestova T. V., Hellen C. U. (1999) Internal initiation of translation of bovine viral diarrhea virus RNA. Virology. 258(2):249-256

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 2

Version: `4`	Last change: `2006-04-09 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
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):
1-38

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

GTATACGAGA ATTAGAAAAG GCACTCGTAT ACGTATTG
(((((((((. .......... ...))))))) ))......
^1         ^11        ^21        ^31

Rendering structure of BVDV1 mRNA 38 nt long with energy of -10.50 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:

Chemical probing of RNA secondary structure used the following buffers:
- probing agents DMS (buffer components: 20 mM HEPES-KOH (pH 7.9), 60 mM KCl, 12 mM MgCl2; for 5 min at 30 oC)
- probing agents CMCT (buffer components: 80 mM sodium borate (pH 8.1), 60 mM KCl, 12 mM MgCl2; 10 min at 30
oC)

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

Enzyme or a combination of enzymes used in a single experiment with respective buffer:

ss_experiment_with_enzyme_id: 2

The temperature (in degrees of Celsia):
0 The enzymatic method used to determine the 2D structure:
other

Enzyme or a combination of enzymes used in a single experiment with respective buffer:

Version: 0

pH `7.50`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `30.00`	Mg²⁺ [mM] `20.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `50.00`	Tris [mM] `30.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Other buffer components and their relative concentrations:

1 mM dithiothreitol (DTT)
RNases T1 (0.7 U), U2 (4 U), and PhyM (4 U) and Bacillus cereus RNase (1 U)

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

Chemical reagent used with its respective buffer:

ss_experiment_with_chemical_id: 3

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

Chemical reagent used with its respective buffer:

Version: 0

pH `7.90`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `60.00`	Mg²⁺ [mM] `12.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `84.00`	Tris [mM] `0`	BSA [mM] `0`	HEPES [mM] `20.00`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Chemical reagent used with its respective buffer:

ss_experiment_with_chemical_id: 4

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

Chemical reagent used with its respective buffer:

Version: 0

pH `8.10`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `60.00`	Mg²⁺ [mM] `12.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `84.00`	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:

80 mM sodium borate (pH 8.1)

Citations:

Yu H., Isken O., Grassmann C. W., Behrens S. E. (2000) A stem-loop motif formed by the immediate 5' terminus of the bovine viral diarrhea virus genome modulates translation as well as replication of the viral RNA. J. Virol. 74(13):5825-5835

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