IRESite_Id:620 summary record describing characteristics of BQCV

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `620`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-29 20:19:10`
Reviewed by: Martin Mokrejš

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
8100530

The mRNA/+RNA description:

Black queen cell virus nonstructural polyprotein (orf1) and structural polyprotein (orf2) genes, complete cds.

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

CGCAAAATTG CGTATAGTAT ATAAAATACT ATACGCGCTT GGTTGTTTTC ACATATCAAG TGGGTTAAAA GCCCCGTATG CTTGGAGACC AGGTTTGTTT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCCGACTTAC GGAATGTCGT TAAACTCTAG GCTTTCCGGA TGGCTTCTAA TTATCCGAGG CCCGTACGTG GGCTCGAAGT TTAGTAGAGA GTACGCGTAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AAAAGTCCTA GTTGTTTTCA TACATCAAGT GGGTTAAAAG CCCCGTGTAC TTGGAGGCTA GGCAACACGA TTACAGTAGC CTGTACTACC TGAAGCATGT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGTAAAACTG CACAGTTGAA AATTGTCACA AACGGGCTGA AAGCGTAGGG CTGGATTGTT GAGGGATAGC ATTCTGCGGG ATGTGAAAGA ACATGTTAGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CATGTATTAT GGTTTTTCCC AATACGCAGT CTTTGCTGTG CGTGTGTAGG CAAAAGGAAG TGAGAGAGCT GACCGTCTCT CATGGGTATC TAGGTTATTC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AGAGTACGCT GCTACTGCGG TAGCGGACAC AACCCAGGTG TTCGGGTCTC TGTCTTAGAA CTATTATTGA TGGCGAAAGT TGTTAATGGG CTCTCTAACG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCACTCTTAA ATGGTACGTG TCGATTGAGT TTATTGCAAT GAATAGCCAA CCCTATAATG ATGGAACCAA TTTACGAGAA TACTAAAACT GTAACTGAAC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CAATACTTTA CTACCCATTC CGTTACAACT GGAATATTAA GATTCTTGAC CTCACAGATA AGGAGGGTCA AGAGAGTGTC AATAAGAAGT TTTTAAGGAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GTTTACTAAA CTTAGGAAGC TTTGTTTGAG ACTTCAAAAG GACACTGCCT TCTGGAAAAA TACTAGAAGT AGGTTAGATA TGATTCAGGA TGACATAGAC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAAATGGTCG CACAAAGTGG CCCTGTTATG AGTCAGAGCT TAAGTGACAG GGTTGACCGC ATGTACCATG AGTTAATACA TACGAATGTC GCTCAAATGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ATTTCTCTAT ACCGTTTTCA CATAATTTGT CCAAGGATTC AAAGGCGTTT CTTACTCAAA CAGTAGACAC TTCTCTTGAT GGTATGAAGC AGATTTCTAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TGAAACAGTG AATACCATTA AGGAAGTGTT CGAAACGTTT TTGACTAAAA TGACGACTAC ATTTGAACAA TGTGCAGAAG CTCATTGTAA AATTAAAAGC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTCTGCACAT TGTTCAAATG TAGTCGTCAT TTTAACAATG TGCAGGAAGC TTTTAATTTT ACAATGAGCT TTATGAGATT TTTAGCTTTG GCTTATGCCA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TCTTTTTCCT CATTTCACGA GCAACTAAGT TCTTTGGAGC GTCATTTTCT ACGATATCTA CTGTTCTGAT AACTCTTATT ACTATGACAG TAACTGACAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GTTAGTTAAG AAATTTTTGG TCGATTACTA CTCAAAACAC ATGGAAAATG CTAAAATGTT AGCCCAAGCA GGAGAGGAAG ACTCGTCTTT TCTATCCTAC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GTCATTCCCC CATTGTTTTT AGAATCAGTT GTAGATACAA AATCTAACTT GTTTAAGAGG ATTTGGAAGA GTAAAGACCT GGACCTTGTT GTTAAGAGGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TGTCGTATTT TGGTGATGCT AAAATATACA ATGCCTTTGA CAATATAGGC ACGTGGTTGA CTACGATGAT CAACAAGACA GTAAATTATG TAAAGGTTAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ACTCTTGGGC CATGATCCTG AAGAATTTTT GGAGAATCAG AGTGACCCTC TGGTGGATTG GGAAGAGCAG TGCAGGAAAC ATTTCGTTTC AGACACTGAT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGAATAGCGA TCTATACAGA GTCCACGTTA GCGGACATTA AACGTCTGTA CAATATGGGC GTTAGTTATA TGCGGCATCC TCTGTATAAA CCCCACCAGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GTGTTATTTC TGAGATTCTG AATCAGTTAC TCAGGTTTGC TGATAAGATC AAAAAGAAGG TAGGCACGGA TGCTTCTGTT CGAAATCCCC CAGTTACTCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ATATTTATAT GGAGAAACAG GAGTAGGTAA ATCTACTTTG ACGTATCCTT TGTGTGCCAC TCTTCTTAAA ACCATCTTTA CAAGAGAGGG GAATACAGTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ATGCTTGAAT CTCTTAAACA ACATTACAAA GAGATGATAT ACGTGAGAGC TGCAGAACAA GAGTTCTGGG ACGGCTACAC GCAGCAATTA GTCACTGTAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTGATGATTT CAATCAGCAA GTTGATTCTT CCGCAAACCC AAGTTTGGAG TTATTTGAAA TTATTAGGAG TTCTAATATA TTTCCTTATC CATTACACAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGCATCGATT GAAGAGAAGG CTAATACCGT TTTTCAATCA AAGGTGATAT TGTGTTCTTC TAATAATAAG ACTCCAAAAA CTGAATCTCT AAATTATCCG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AAGGCTTTGT TAAGAAGGTT CGCGAAATTC GTCGAAGTTA AGAGGGCTCC TTCTGAAAGT GGTACATTCT CTACTGATTG TTATACTTTC GTGGAATATG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATCCATTTGA CCACTGCAAC ATCGTTAAAT CAATGTCTTT CAATGAATTG ATAGATGAGG TGGTTGCCAT GTATTTCCAC GAAGGAGAGT TTGTATCTTC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGTAGATAAA TTTATTATGG AGAATGTATT TGCTCAGGGA GGAGGCTCTT TATCAGACGA AGAAGATGAT TTTATTGAAG CTAGTTCTTA TGGTGACAGT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AATCTGGATG AAGCCTTGAC ACGTGAAGAA AAGAAAGAAA TTATTGAGTG TATCAACGAT CAATTTAAGA ATGAGAATGA TACTAGAACT TCCTTCCAGT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TGATTAGAGA CTATTTCCAT TGTGCTAAGG ACTCGTTACA AGAGAAATTT TTAGCTTATC GCCGAAAGTA CTCTTTCGAC GATTGGTTTA GTTTCTCAAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AGCGTCCAAA GTAGTATTGG GAATACTTTC TCTCGTATTG GTTGGGTATG GCATATATTC ATATGTCAAA GGAAATCCTG CAAAAGACTC AGCTGAATCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TACGAGCCAA AGGTGGCGAG TAAGGCCAAG GTTGAGGGAA GTAATGGCGT TCCCGAGGCA TATGAATCTA AAGTCAACAG AAAGATCAAT GTTGAAGGGT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ATAATGCGAG AGATCTTAAG CGTAAAGTAG AGGCTTATGC TCCTAAAGTT AATCGAACTG TGCGCGTGGA ATCTAGTGAG GTGATAATAC ATCCTAATTC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TCTGATCGAG AAAGGTGATG ATATTGTACA GTCTGAAGCA TGTAGCGATA TAAATGCTTC GGAACAACTC ACTGCTGTTA CGACTAATAA CACCTATGTA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ATGACTATCT TATCTAAAGA ATCTGTTATT AGAGTGGGGC ACTGCATTTT TCTGAAAGGA AAGATTGCAG TAGCTCCTGG TCATTATCTT CGTATACTCC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

AACGCGCATA TGAGTTAGAT GACGGTGCTA TTTTACAATT TAATCATCCT TACGGTAAGA GAAACTTCTT TACGTTTATC GGTGATATCC AGTTCTCGTT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GTATAAAACG AAAAATATAT CCAAAACGAA CGATTTGGAT TCTCGTGACT TGATGCATTT TGTTGTTGAT AAGTCAGTAG TTCACAGAGA TATTTCTTCG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TATTTCTGTG AACGTTTAGA ACTGCAATCT GTTGGTTCTA CTCGAATCCA ATTACCTGTT ATGCGATGGG TAAGAGATGT TGGATATATT TTCGTTAAGT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CGGGACAAGG TACTAGTTGT ATAAAGAACG TTTCCAACGT TAGTTATATG ACTGATACTG ATCCCGACGC TCGAGAAATT CGATTGAGGG AAGCATGGGA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GTATTCTTTA GAAACAATAT CTGGTGATTG CGGAGCTCCC CTTTTTGTAA CCAATAGTAA AATAGGACCT GGTAAAATTA TAGGAATTCA CACAGCTGGG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GGTCATCGAT TCGGAGTTGG CAGTTGCTTT GCCACTCCGT TTTACTTAGA GGACGTGAAA GAGATCTTGT CTCGGTACGA TTATAAAGCA CAGTCTTGTG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CTTTTGAGTT AGTATTGCGA CAGGATCTTG AACCATGTGC TCTACCTAAC CACTTGGATG AATGCGAATT CATCTTGATG GGAAAGGTAA AGGATCCTCC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AGTTCAACCA TCTAGAAGTA AAATATCTCC ATCTCCCTTG TACGGACACA TAACTGAACC CTCTAGTGCC CCAACTTGGT TATATCCTAG GGAGCTTGAT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GGACAGATTT TTGACCCTTT AAAATATAGA ACTGCTAGAC TTGGAAAAGA TAGCGTTCCT ATTAGAAGTA AGTTAATTAA TCTGGCCAAA ATGGCTCTTA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TAGATGATAT ATATTCCGTG TACTTGCAAA AGAAAGATCT TTTGGACGGA CGATTTCCAT CATCGTTGAC CTTTGATCAA GCAGTGTTGG GGATACCTGG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AGAAGACTAT GTCAATTCAA TAAAACGTGA TACCTCTTGC GGTTATCCTT TCGTTAAGGA AGGATGGACA CGAGCTAAAA TCTTCGGTAA CGGTGATGAA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TATGACATGT CTACCTCGGG TGTTCAAATG TTACGAGAGA AAGTACAGGA ATGCATAGAG GCGGCGAGAC AAGGGAAGAT ATTGGACCAT TATTTTATAG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATACATTAAA GGACGAAAGG AAGCCTAAAC ATAAGGCTCA TAAGTCTCGA ATGTTTTCTA ATGGACCAAT AGATTATCTT GTTTGGAGTA AGATGTATTT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TAATCCGATA GTAGCGGTGT TGTCTGAGCT TAAAAATGTA GACCATATTT CCGTGGGGTC CAATGTGTAT TCTACGGACT GGGACGTTAT TGCAAGGTAC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TTGAAGTCGA AATCTCACCA TATGGTGGCT GGAGACTTCG AGGGCTTTGA TGCTTCGGAA CAGTCCGACA TATTGTACGC TGCGGGAGAG GTTCTGCAAG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

AGTTGAGTAA GAAAATCTTT AACTCAACTG AGGATGAGAT GTTGCAACAG AGGGCTATCA TCCACTCGTT GGTCAATTCA CTTCATATCA ATGAGAACGG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GATTGTTCTT CAATGGTGCA AGTCTCTTCC TAGTGGCCAT TATCTCACCG CTATTATTAA TTCCGTCTTT GTGAATTTGG TTATGTGTCT TGTATTTATG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GAAGCCAATC AAAAATATTC ATTTACGACT GCTTCTTCAT TTTTCCGTGA ATGTGGTATA GTAGCATATG GAGACGACCA TGTTGTCTCT GTTCCCGAAA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

AATACTTGTC TGTGTTTAAT CAACAGACAC TACCAGTGTT GATGAGTAAA TTCGGGATGT TCTATACCAT AGAAACCAAG GATGACACAG AGATTGATTT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CCTTTCGAGG AGATTAGAGG ATGTGTCGTA CTTGAAACGG AATTTTGTTT ATGACGAATC TAGGCAACGT TATATTGCTC CTCTCTCTTT GGATGTTGTA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TTGGAAATGC CTATGTGGAC CAAATCCAGC AAGGACATTG TAACTAATGT ATTCTGTAAT TTGGAACACG CCCTCAAGGA GTTATCATTG CATGATAAAG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AATTGTGGGA AAAATGGAGT CCTGTATTGC ATTCAAAGAG TGAGGAAGTC CTGAAAATGG TTTCTTCTCT GAAATTTCAA GATGAGGTCA GGGAGATTGC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TCTTGGCCTT TCAGGTTATG AGTAGTTTTC TTGACTTCTC TTAAAACCAA CAATGTGATC TTGCTTGCGG AGGCAAAATT TGCACAGTAT AAAATCTGCA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

AGTAGTGCTA TTGTTGGAAT CACCGTACCT ATTTAGGTTT ACGCTCCAAG ATCGGTGGAT AGCAGCCCTA TCAATATCTA GGAGAACTGT GCTATGTTTA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GAAGATTAGG TAGTCTCTAA ACAGAACAAT TTACCTGCTG AACAAATTAA TGAAAATTAT GAAAATAAAC AACAACTTGT TGAACAGACT GAAATTACCA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CCTTTGAAAA CGATTTGATA GTGCTTGAAG ATGGACCGCA GATGGAAGAA CCTCTTCCTT ATGCATTCCA TGGACAGCAT ACTGATAATC GTCAACATAC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GGTGGTTAAT TTCTTGCAAC GTCCCCAGGT TATTTTCGAT TCGTCTTGGG CGTCTGATCT CCCTCGAAAC AAACAATTTA TGGATTCGAT TATGATACCA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GATGATATCA TTTCTTTTCC AATGTTTGCG GAAAAACTCA AAGGATTTTC TTCTTTGAGA GCAACAGCTG TAATAACAGT GCAATTTCAG ACGCAACCAT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TTCAAGCGGG AAGGGTCATG TTGGGATCAT TTCCATTACC AACACTCAAC CCAACTAGAG TTAAGTTTGC CACCAATCAT GTGTCTCGTT TAATGCTTTT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

AAACCATGTC CAGTGTGATA TTGCCAAGGA AACTGAAGTA TCCTTACGGA TTCCTTTTGT TTCTCCATAC AATTCATACG ACTTGGTGTC GAAGCGTTTT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

CCGTGGGCTA AAGTGGTTGG TTTGGTGTAC TCACCTCTTA CTACGACCAT TCCCGTAGAT TATATAGTAT ACGGTCATTT TGAGGACGTG GAGTTGGGTT 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

GTCCAACTTC AGGAATGTTG GCTCAAGCAG GTCTTAAAGT GCAACCTCCT ACGAACTCTG ACTCTCGACA GCGTGCCAAA GAGAGTAAGG GAAAGAAGGA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

TTACTCTAAG ACAGGCGCAG CTTTTAAACA ATCTGTTTCA AAGCTGGGCG AACATTTACC TTTCCTCAAA TCTGGAGCGA ACTGGGTCAG TGAGAACATT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CTACAACCTG CAGATGAAAT CATAGGACCT ATTTTATCTC TTTTTGGGTT CTCGAAGCCC CTTTTGCCCA TTACCAATCC CACCGTTTTA CGGCCAGCGA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ATACCTTTGC TATCACTGAT ACAAATGATA TGTCGCATAG TCTGGCGCTT TCTAATGATA CCAATGTACC ATTTGTTAAG GCGCTGGATG GTTCTGGTTT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

GGACGAAATG AGCTTCGATT ACCTGAAGAA GATACCCCAA TTCATACAGT CAAAATTCTT CACCACCACG ACAAAACCTC AAGAGGTTTT GTTTCAGACT 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

AAAGTAATGC CTCATTACTT TGTCCCGGCT GGCGATGTAA CTGTCGCCAT GGATAAAGAT AAAACTAGAA CTATTTGGCA ACCTAGCCAT TTAGCCTATA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

TCACTTCCAT GTTTAAGTAT TGGACGGGTT CGCTCGTGTA TACATTCAAA TTTGTTAAAA CAGACTACCA TTCTGGTAGG GTGGAGATTT CTTTCCACCC 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TTTTTCTGAT TATACCGCTA ACTCCTATTC GGATTATACC TATAGGATTA TAGTGGATTT GAGGGAAAAG TCTGAGTTTT CGGTTACAAT ACCCTTCATT 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

TCTCCAGTAC CATACAAACG CATATCTAGG CCAGATTGGG ATAAACCTTA TTCCAAGTAC GCTCATGCTA GTACAGGAAC TCTGGTGTTG AAGGCGTTGA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

CATCGTTAAA GGCGACTAAT ACCGTGGTTT CCAATTCTGT GGAAATCTTG ATAGAAGTCA ATGCTGGCGA CGATTTCAAC GTTATCGCTC CTATCGAAAA 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

CATCTTCTTC CCCTTCTCTC TCTCTCCAGG GAGGAAGGGG ATGGTTGCTC AATCCAATTC GGGGACTGAA CAACAAAACC CCAGAGGATC ATCTTTGTTA 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

ACTGATCCAG AATCTATTAC AAAGTCTGAT CCTTACAATC CGAATATTTC TCTCTTGATT AGTGGAGAAG TTTTCACGAA CTTCAGAAAT TTGATCAAGA 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

GGGTAAATTT CAGAAAGGCT ACTACGTTGA ATGGAAAACG TATCTCAGAT ACGTTTGACA TCAACAGCCT GATTGAAGCA CCCCGTCTTG ATATAGCGCA 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

ATATGTCGAT ACTGAAACAA AGGAGGCTAA ATATGGATTT AGCTACTTTT GGTCAGCTCC CACTACCTTA AACATAGTGG CGGAGATGTA TGCGCTTTAT 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

CGAGGAGGAG TTCGAGTTAA AGTAGTTACT GAGAAGGGTG TAGATTTCGT CAGAGCTACC GTTAGTCCTC AACAGACTTA TGGTAGCGAT GTCGCTCCTA 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

CTACTCACAT CAGTACTCCT TTGGCAATAG AACAAATACC TATAAAGGGA GTCGCAGAGT TCCAAATACC GTACTATGCT CCATGTTTGT CATCTTCGTT 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

TAGAGCGAAT TCGGAAACAT TTTACTATAG TTCAGGTCGG AATAATCTCG ATATAGCCAC TTCACCTCCC ACCGTCAATC GCTATTATGC GGTTGGTGCG 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

GGAGATGATA TGGACTTTTC CATCTTTATC GGTACGCCGC CCTGTATTCA TGCATCTCAG ACGGCCCAGT TTACCAAGAT AAAACAAGGT AAAGTGTATG 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

ATTTGAGGTA TGATCAGTAC GACCCTTTTA GGGAAGTCCA GGACGGTACG GCGTTCCTCA ATGCTCGTAG TATTGAGGAT AGCGATTTGT TGTGAGCTCC 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

TTTAGAGGGA GGGCTCACTT TATCTATTGC TTAATTCGGT AAGCCACAAA TTTTTCTAAG TGTCATGAGT TTCTTCTCGG TTCTTCTCAT GATTACTAAT 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

CGAACCGTGT GTAGAGTCAG AATGTTGTGG TTTACGTTTC TTCTTGTTGC
^8501      ^8511      ^8521      ^8531      ^8541

Credibility of mRNA sequence:

unknown

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

Black queen cell virus South African

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

The abbreviated name of this ORF/gene:
ORF1

The description of the protein encoded in this ORF:
nonstructural polyprotein

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

not tested

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

658-5625

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
CP

The description of the protein encoded in this ORF:
capsid protein

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
no

The alternative forms of this protein occur by the alternative initiation of translation:

not tested

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

5834-8395

Citations:

Leat N, Ball B, Govan V, Davison S (2000) Analysis of the complete genome sequence of black queen-cell virus, a picorna-like virus of honey bees. J. Gen. Virol. 8(81):2111-2119

IRESs:

IRES:

Version: `1`	Last change: `2009-08-29 21:27:38`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `BQCV_IGRpred`

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

5647-5836

Conclusion:
putative_IRES

How IRES boundaries were determined:
guessed

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `22`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `211`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-187`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `2`

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

CCAACAATGT GATCTTGCTT GCGGAGGCAA AATTTGCACA GTATAAAATC TGCAAGTAGT GCTATTGTTG GAATCACCGT ACCTATTTAG GTTTACGCTC 
^5647      ^5657      ^5667      ^5677      ^5687      ^5697      ^5707      ^5717      ^5727      ^5737      

CAAGATCGGT GGATAGCAGC CCTATCAATA TCTAGGAGAA CTGTGCTATG TTTAGAAGAT TAGGTAGTCT CTAAACAGAA CAATTTACCT
^5747      ^5757      ^5767      ^5777      ^5787      ^5797      ^5807      ^5817      ^5827

Remarks:

The IRES was NOT characterized experimentally. The presumed IRES region was taken over from Nakashima and
Uchiumi (2009) from Table 1.

Citations:

Nakashima N, Uchiumi T (2009) Functional analysis of structural motifs in dicistroviruses. Virus Res. 2(139):137-147

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