IRESite_Id:306 characteristics of GBV-B IRES studied in RepDBla plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `306`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-04 21:43:24`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
hopefully_full-length_mRNA

The mRNA/+RNA description:

In vitro bicistronic transcript (non-capped non-poly(A)-tailed) containing
5' -GBV-B_IRES - 63nt_of_GBV-B_core_gene - beta-lactamase - EMCV-R_IRES - NS3-NS5B_GBV-B_polyprotein - 3'

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

Gaccacaaac actccagttt gttacactcc gctaggaatg ctcctggagc acccccccta gcagggcgtg ggggatttcc cctgcccgtc tgcagaaggg 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tggagccaac caccttagta tgtaggcggc gggactcatg acgctcgcgt gatgacaagc gccaagcttg acttggatgg ccctgatggg cgttcatggg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ttcggtggtg gtggcgcttt aggcagcctc cacgcccacc acctcccaga tagagcggcg gcactgtagg gaagaccggg gaccggtcac taccaaggac 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gcagacctct ttttgagtat cacgcctccg gaagtagttg ggcaagccca cctatatgtg ttgggatggt tggggttagc catccatacc gtactgcctg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

atagggtcct tgcgagggga tctgggagtc tcgtagaccg tagcacatgc ctgttatttc tactcaaaca agtcctgtac ctgcgcccag aacgcgcaag 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

aacaagcaga cggggcgcgc catgcaccca gaaacgctgg tgaaagtaaa agatgctgaa gatcagttgg gtgcacgagt gggttacatc gaactggatc 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tcaacagcgg taagatcctt gagagttttc gccccgaaga acgttttcca atgatgagca cttttaaagt tctgctatgt ggcgcggtat tatcccgtat 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

tgacgccggg caagagcaac tcggtcgccg catacactat tctcagaatg acttggttga gtattcacca gtcacagaaa agcatcttac ggatggcatg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

acagtaagag aattatgcag tgctgccata accatgagtg ataacactgc ggccaactta cttctgacaa cgatcggagg accgaaggag ctaaccgctt 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ttttgcacaa catgggggat catgtaactc gccttgatcg ttgggaaccg gagctgaatg aagccatacc aaacgacgag cgtgacacca cgatgcctgt 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

agcaatggca acaacgttgc gcaaactatt aactggcgaa ctacttactc tagcttcccg gcaacaatta atagactgga tggaggcgga taaagttgca 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ggaccacttc tgcgctcggc ccttccggct ggctggttta ttgctgataa atctggagcc ggtgagcgtg ggtctcgcgg tatcattgca gcactggggc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

cagatggtaa gccctcccgt atcgtagtta tctacacgac ggggagtcag gcaactatgg atgaacgaaa tagacagatc gctgagatag gtgcctcact 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

gattaagcat tggtaagttt aaacagacca caacggtttc cctctagcgg gatcaattcc gcccctctcc ctcccccccc cctaacgtta ctggccgaag 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ccgcttggaa taaggccggt gtgcgtttgt ctatatgtta ttttccacca tattgccgtc ttttggcaat gtgagggccc ggaaacctgg ccctgtcttc 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ttgacgagca ttcctagggg tctttcccct ctcgccaaag gaatgcaagg tctgttgaat gtcgtgaagg aagcagttcc tctggaagct tcttgaagac 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

aaacaacgtc tgtagcgacc ctttgcaggc agcggaaccc cccacctggc gacaggtgcc tctgcggcca aaagccacgt gtataagata cacctgcaaa 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ggcggcacaa ccccagtgcc acgttgtgag ttggatagtt gtggaaagag tcaaatggct ctcctcaagc gtattcaaca aggggctgaa ggatgcccag 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

aaggtacccc attgtatggg atctgatctg gggcctcggt gcacatgctt tacatgtgtt tagtcgaggt taaaaaacgt ctaggccccc cgaaccacgg 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ggacgtggtt ttcctttgaa aaacacgata ataccatggc accttttacg ctgcagtgtc tctctgaacg tggcacgctg tcagcgatgg cagtggtcat 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gactggtata gacccccgaa cttggactgg aactatcttc agattaggat ctctggccac tagctacatg ggatttgttt gtgacaacgt gttgtatact 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gctcaccatg gcagcaaggg gcgccggttg gctcatccca caggctccat acacccaata accgttgacg cggctaatga ccaggacatc tatcaaccac 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

catgtggagc tgggtccctt actcggtgct cttgcgggga gaccaagggg tatctggtaa cacgactggg gtcattggtt gaggtcaata aatccgatga 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

cccttattgg tgtgtgtgcg gggcccttcc catggctgtt gccaagggtt cttcaggtgc cccgattctg tgctcctccg ggcatgttat tgggatgttc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

accgctgcta gaaattctgg cggttcagtc agccagatta gggttaggcc gttggtgtgt gctggatacc atccccagta cacagcacat gccactcttg 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

atacaaaacc tactgtgcct aacgagtatt cagtgcaaat tttaattgcc cccactggca gcggcaagtc aaccaaatta ccactttctt acatgcagga 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

gaagtatgag gtcttggtcc taaatcccag tgtggctaca acagcatcaa tgccaaagta catgcacgcg acgtacggcg tgaatccaaa ttgctatttt 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

aatggcaaat gtaccaacac aggggcttca cttacgtaca gcacatatgg catgtacctg accggagcat gttcccggaa ctatgatgta atcatttgtg 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

acgaatgcca tgctaccgat gcaaccaccg tgttgggcat tggaaaggtc ctaaccgaag ctccatccaa aaatgttagg ctagtggttc ttgccacggc 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

taccccccct ggagtaatcc ctacaccaca tgccaacata actgagattc aattaaccga tgaaggcact atcccctttc atggaaaaaa gattaaggag 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

gaaaatctga agaaagggag acaccttatc tttgaggcta ccaaaaaaca ctgtgatgag cttgctaacg agttagctcg aaagggaata acagctgtct 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

cttactatag gggatgtgac atctcaaaaa tccctgaggg cgactgtgta gtagttgcca ctgatgcctt gtgtacaggg tacactggtg actttgattc 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

cgtgtatgac tgcagcctca tggtagaagg cacatgccat gttgaccttg accctacttt caccatgggt gttcgtgtgt gcggggtttc agcaatagtt 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

aaaggccagc gtaggggccg cacaggccgt gggagagctg gcatatacta ctatgtagac gggagttgta ccccttcggg tatggttcct gaatgcaaca 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ttgttgaagc cttcgacgca gccaaggcat ggtatggttt gtcatcaaca gaagctcaaa ctattctgga cacctatcgc acccaacctg ggttacctgc 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

gataggagca aatttggacg agtgggctga tctcttttca atggtcaacc ccgaaccttc atttgtcaat actgcaaaaa gaactgctga caattatgtt 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ttgttgactg cagcccaact acaactgtgt catcagtatg gctatgctgc tcccaatgac gcaccacggt ggcagggagc ccggcttggg aaaaaacctt 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

gtggggttct gtggcgcttg gacggcgctg acgcctgtcc tggcccagag cccagcgagg tgaccagata ccaaatgtgc ttcactgaag tcaatacttc 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

tgggacagcc gcactcgctg ttggcgttgg agtggctatg gcttatctag ccattgacac ttttggcgcc acttgtgtgc ggcgttgctg gtctattaca 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

tcagtcccta ccggtgctac tgtcgcccca gtggttgacg aagaagaaat cgtggaggag tgtgcatcat tcattccctt ggaggccatg gttgctgcaa 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ttgacaagct gaagagtaca atcaccacaa ctagtccttt cacattggaa accgcccttg aaaaacttaa cacctttctt gggcctcatg cagctacaat 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ccttgctatc atagagtatt gctgtggctt agtcacttta cctgacaatc cctttgcatc atgcgtgttt gctttcattg cgggtattac taccccacta 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

cctcacaaga tcaaaatgtt cctgtcatta tttggaggcg caattgcgtc caagcttaca gacgctagag gcgcactggc gttcatgatg gccggggctg 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

cgggaacagc tcttggtaca tggacatcgg tgggttttgt ctttgacatg ctaggcggct atgctgccgc ctcatccact gcttgcttga catttaaatg 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

cttgatgggt gagtggccca ctatggatca gcttgctggt ttagtctact ccgcgttcaa cccggccgca ggagttgtgg gcgttttgtc agcttgtgca 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

atgtttgctt tgacaacagc agggccagat cactggccca acagacttct tactatgctt gctaggagca acactgtatg taatgagtac tttattgcca 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ctcgtgacat ccgcaggaag atactgggca ttctggaggc atctaccccc tggagtgtca tatcagcttg catccgttgg ctccacaccc cgacggagga 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

tgattgcggc ctcattgctt ggggtctaga gatttggcag tacgtgtgca atttctttgt gatttgcttt aatgtcctta aagctggagt tcagagcatg 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

gttaacattc ctggttgtcc tttctacagc tgccagaagg ggtacaaggg cccctggatt ggatcaggta tgctccaagc acgctgtcca tgcggtgctg 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

aactcatctt ttctgttgag aatggttttg caaaacttta caaaggaccc agaacttgtt caaattactg gagaggggct gttccagtca acgctaggct 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

gtgtgggtcg gctagaccgg acccaactga ttggactagt cttgtcgtca attatggcgt tagggactac tgtaaatatg agaaattggg agatcacatc 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

tttgttacag cagtatcctc tccaaatgtc tgtttcaccc aggtgccccc aaccttgaga gctgcagtgg ccgtggacgg cgtacaggtt cagtgttatc 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

taggtgagcc caaaactcct tggacgacat ctgcttgctg ttacggtcct gacggtaagg gtaaaactgt taagcttccc ttccgcgttg acggtcacac 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

acctggtgtg cgcatgcaac ttaatttgcg tgatgcactt gagacaaatg actgtaattc cacaaacaac actcctagtg atgaagccgc agtgtccgct 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

cttgttttca aacaggagtt gcggcgtaca aaccaattgc ttgaggcaat ttcagctggc gttgacacca ccaaactgcc agccccctcc atcgaagagg 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

tagtggtaag aaagcgccag ttccgggcaa gaactggttc gcttaccttg cccccccctc cgagatccgt cccaggagtg tcatgtcctg aaagcctgca 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

acgaagtgac ccgttagaag gtccttcaaa cctccctcct tcaccacctg ttctacagtt ggccatgccg atgcccctgt tgggagcggg tgagtgtaac 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

cctttcactg caattggatg tgcaatgacc gaaacaggcg gaggccctga tgatttaccc agttaccctc ccaaaaagga ggtctctgaa tggtcagacg 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

aaagttggtc aacggctaca accgcttcca gctacgttac tggccccccg taccctaaga tacggggaaa ggattccact cagtcagccc ccgccaaacg 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

gcctacaaaa aagaagttgg gaaagagtga gttttcgtgc agcatgagct acacttggac cgacgtgatt agcttcaaaa ctgcttctaa agttctgtct 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

gcaactcggg ccatcactag tggtttcctc aaacaaagat cattggtgta tgtgactgag ccgcgggatg cggagcttag aaaacaaaaa gtcactatta 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

atagacaacc tctgttcccc ccatcatacc acaagcaagt gagattggct aaggagaaag cttcaaaagt tgtcggtgtc atgtgggact atgatgaagt 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

agcagctcac acgccctcta agtctgctaa gtcccacatc actggccttc ggggcactga tgttcgttct ggagcagccc gcaaggctgt tctggacttg 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

cagaagtgtg tcgaggcagg tgagataccg agtcattatc ggcaaacagt gatagttcca aaggaggagg tcttcgtgaa gaccccccag aaaccaacaa 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

agaaaccccc aaggctcatc tcgtaccccc accttgaaat gagatgtgtt gagaagatgt actacggtca ggttgctcct gacgtagtta aagctgtcat 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

gggagatgcg tacgggtttg tagatccacg tacccgtgtc aagcgtctgt tgtcgatgtg gtcacccgat gcagtcggag ccacatgcga tacagtgtgt 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

tttgacagta ccatcacacc cgaggatatc atggtggaga cagacatcta ctcagcagct aaactcagtg accaacaccg agctggcatt cacaccattg 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

cgaggcagtt atacgctgga ggaccgatga tcgcttatga tggccgagag atcggatatc gtaggtgtag gtcttccggc gtctatacta cctcaagttc 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

caacagtttg acctgctggc tgaaggtaaa tgctgcagcc gaacaggctg gcatgaagaa ccctcgcttc cttatttgcg gcgatgattg caccgtaatt 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

tggaaaagcg ccggagcaga tgcagacaaa caagcaatgc gtgtctttgc tagctggatg aaggtgatgg gtgcaccaca agattgtgtg cctcaaccca 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

aatacagttt ggaagaatta acatcatgct catcaaatgt tacctctgga attaccaaaa gtggcaagcc ttactacttt cttacaagag atcctcgtat 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

cccccttggc aggtgctctg ccgagggtct gggatacaac cccagtgctg cgtggattgg gtatctaata catcactacc catgtttgtg ggttagccgt 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

gtgttggctg tccatttcat ggagcagatg ctctttgagg acaaacttcc cgagactgtg acctttgact ggtatgggaa aaattatacg gtgcctgtag 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

aagatctgcc cagcatcatt gctggtgtgc acggtattga ggctttctcg gtggtgcgct acaccaacgc tgagatcctc agagtttccc aatcactaac 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

agacatgacc atgccccccc tgcgagcctg gcgaaagaaa gccagggcgg tcctcgccag cgccaagagg cgtggcggag cacacgcaaa attggctcgc 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

ttccttctct ggcatgctac atctagacct ctaccagatt tggataagac gagcgtggct cggtacacca ctttcaatta ttgtgatgtt tactccccgg 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

agggggatgt gtttgttaca ccacagagaa gattgcagaa gtttcttgtg aagtatttgg ctgtcattgt ttttgcccta gggctcattg ctgttggatt 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

agccatcagc tgaaccccca aattcaaaat taactaacag tttttttttt tttttttttt tagggcagcg gcaacagggg agaccccggg cttaacgacc 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

ccgccgatgt gagtttggcg accatggtgg atcagaaccg tttcgggtga agccatggtc tgaaggggat gacgtccctt ctggctcatc cacaaaaacc 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

gtctcgggtg ggtgaggagt cctggctgtg tgggaagcag tcagtataat tcccgtcgtg tgtggtgacg cctcacgacg tacttgtccg ctgtgcagag 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

cgtagtacca agggctgcac cccggttttt gttccaagcg gagggcaacc cccgcttgga attaaaaact
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
RepDBla The name of the promoter used to express this mRNA:
T7

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

not tested

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

not tested

A promoter reported in cDNA corresponding to IRES sequence:

not tested

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
GBV-B

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Hepatitis GB virus B ACY/GBV-B/FL-3

The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:

ggatccggta aTACGACTCA CTATAGacca caaacactcc agtttgttac actccgctag gaatgctcct ggagcacccc ccctagcagg gcgtggggga 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tttcccctgc ccgtctgcag aagggtggag ccaaccacct tagtatgtag gcggcgggac tcatgacgct cgcgtgatga caagcgccaa gcttgacttg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

gatggccctg atgggcgttc atgggttcgg tggtggtggc gctttaggca gcctccacgc ccaccacctc ccagatagag cggcggcact gtagggaaga 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ccggggaccg gtcactacca aggacgcaga cctctttttg agtatcacgc ctccggaagt agttgggcaa gcccacctat atgtgttggg atggttgggg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ttagccatcc ataccgtact gcctgatagg gtccttgcga ggggatctgg gagtctcgta gaccgtagca catgcctgtt atttctactc aaacaagtcc 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

tgtacctgcg cccagaacgc gcaagaacaa gcagacgggg cgcgccatgc acccagaaac gctggtgaaa gtaaaagatg ctgaagatca gttgggtgca 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

cgagtgggtt acatcgaact ggatctcaac agcggtaaga tccttgagag ttttcgcccc gaagaacgtt ttccaatgat gagcactttt aaagttctgc 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

tatgtggcgc ggtattatcc cgtattgacg ccgggcaaga gcaactcggt cgccgcatac actattctca gaatgacttg gttgagtatt caccagtcac 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

agaaaagcat cttacggatg gcatgacagt aagagaatta tgcagtgctg ccataaccat gagtgataac actgcggcca acttacttct gacaacgatc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ggaggaccga aggagctaac cgcttttttg cacaacatgg gggatcatgt aactcgcctt gatcgttggg aaccggagct gaatgaagcc ataccaaacg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

acgagcgtga caccacgatg cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg gcgaactact tactctagct tcccggcaac aattaataga 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ctggatggag gcggataaag ttgcaggacc acttctgcgc tcggcccttc cggctggctg gtttattgct gataaatctg gagccggtga gcgtgggtct 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

cgcggtatca ttgcagcact ggggccagat ggtaagccct cccgtatcgt agttatctac acgacgggga gtcaggcaac tatggatgaa cgaaatagac 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

agatcgctga gataggtgcc tcactgatta agcattggta agtttaaaca gaccacaacg gtttccctct agcgggatca attccgcccc tctccctccc 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ccccccctaa cgttactggc cgaagccgct tggaataagg ccggtgtgcg tttgtctata tgttattttc caccatattg ccgtcttttg gcaatgtgag 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ggcccggaaa cctggccctg tcttcttgac gagcattcct aggggtcttt cccctctcgc caaaggaatg caaggtctgt tgaatgtcgt gaaggaagca 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

gttcctctgg aagcttcttg aagacaaaca acgtctgtag cgaccctttg caggcagcgg aaccccccac ctggcgacag gtgcctctgc ggccaaaagc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

cacgtgtata agatacacct gcaaaggcgg cacaacccca gtgccacgtt gtgagttgga tagttgtgga aagagtcaaa tggctctcct caagcgtatt 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

caacaagggg ctgaaggatg cccagaaggt accccattgt atgggatctg atctggggcc tcggtgcaca tgctttacat gtgtttagtc gaggttaaaa 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

aacgtctagg ccccccgaac cacggggacg tggttttcct ttgaaaaaca cgataatacc atggcacctt ttacgctgca gtgtctctct gaacgtggca 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

cgctgtcagc gatggcagtg gtcatgactg gtatagaccc ccgaacttgg actggaacta tcttcagatt aggatctctg gccactagct acatgggatt 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

tgtttgtgac aacgtgttgt atactgctca ccatggcagc aaggggcgcc ggttggctca tcccacaggc tccatacacc caataaccgt tgacgcggct 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

aatgaccagg acatctatca accaccatgt ggagctgggt cccttactcg gtgctcttgc ggggagacca aggggtatct ggtaacacga ctggggtcat 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

tggttgaggt caataaatcc gatgaccctt attggtgtgt gtgcggggcc cttcccatgg ctgttgccaa gggttcttca ggtgccccga ttctgtgctc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ctccgggcat gttattggga tgttcaccgc tgctagaaat tctggcggtt cagtcagcca gattagggtt aggccgttgg tgtgtgctgg ataccatccc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

cagtacacag cacatgccac tcttgataca aaacctactg tgcctaacga gtattcagtg caaattttaa ttgcccccac tggcagcggc aagtcaacca 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

aattaccact ttcttacatg caggagaagt atgaggtctt ggtcctaaat cccagtgtgg ctacaacagc atcaatgcca aagtacatgc acgcgacgta 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

cggcgtgaat ccaaattgct attttaatgg caaatgtacc aacacagggg cttcacttac gtacagcaca tatggcatgt acctgaccgg agcatgttcc 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

cggaactatg atgtaatcat ttgtgacgaa tgccatgcta ccgatgcaac caccgtgttg ggcattggaa aggtcctaac cgaagctcca tccaaaaatg 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ttaggctagt ggttcttgcc acggctaccc cccctggagt aatccctaca ccacatgcca acataactga gattcaatta accgatgaag gcactatccc 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ctttcatgga aaaaagatta aggaggaaaa tctgaagaaa gggagacacc ttatctttga ggctaccaaa aaacactgtg atgagcttgc taacgagtta 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

gctcgaaagg gaataacagc tgtctcttac tataggggat gtgacatctc aaaaatccct gagggcgact gtgtagtagt tgccactgat gccttgtgta 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

cagggtacac tggtgacttt gattccgtgt atgactgcag cctcatggta gaaggcacat gccatgttga ccttgaccct actttcacca tgggtgttcg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

tgtgtgcggg gtttcagcaa tagttaaagg ccagcgtagg ggccgcacag gccgtgggag agctggcata tactactatg tagacgggag ttgtacccct 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

tcgggtatgg ttcctgaatg caacattgtt gaagccttcg acgcagccaa ggcatggtat ggtttgtcat caacagaagc tcaaactatt ctggacacct 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

atcgcaccca acctgggtta cctgcgatag gagcaaattt ggacgagtgg gctgatctct tttcaatggt caaccccgaa ccttcatttg tcaatactgc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

aaaaagaact gctgacaatt atgttttgtt gactgcagcc caactacaac tgtgtcatca gtatggctat gctgctccca atgacgcacc acggtggcag 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ggagcccggc ttgggaaaaa accttgtggg gttctgtggc gcttggacgg cgctgacgcc tgtcctggcc cagagcccag cgaggtgacc agataccaaa 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

tgtgcttcac tgaagtcaat acttctggga cagccgcact cgctgttggc gttggagtgg ctatggctta tctagccatt gacacttttg gcgccacttg 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

tgtgcggcgt tgctggtcta ttacatcagt ccctaccggt gctactgtcg ccccagtggt tgacgaagaa gaaatcgtgg aggagtgtgc atcattcatt 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

cccttggagg ccatggttgc tgcaattgac aagctgaaga gtacaatcac cacaactagt cctttcacat tggaaaccgc ccttgaaaaa cttaacacct 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ttcttgggcc tcatgcagct acaatccttg ctatcataga gtattgctgt ggcttagtca ctttacctga caatcccttt gcatcatgcg tgtttgcttt 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

cattgcgggt attactaccc cactacctca caagatcaaa atgttcctgt cattatttgg aggcgcaatt gcgtccaagc ttacagacgc tagaggcgca 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ctggcgttca tgatggccgg ggctgcggga acagctcttg gtacatggac atcggtgggt tttgtctttg acatgctagg cggctatgct gccgcctcat 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ccactgcttg cttgacattt aaatgcttga tgggtgagtg gcccactatg gatcagcttg ctggtttagt ctactccgcg ttcaacccgg ccgcaggagt 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

tgtgggcgtt ttgtcagctt gtgcaatgtt tgctttgaca acagcagggc cagatcactg gcccaacaga cttcttacta tgcttgctag gagcaacact 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

gtatgtaatg agtactttat tgccactcgt gacatccgca ggaagatact gggcattctg gaggcatcta ccccctggag tgtcatatca gcttgcatcc 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

gttggctcca caccccgacg gaggatgatt gcggcctcat tgcttggggt ctagagattt ggcagtacgt gtgcaatttc tttgtgattt gctttaatgt 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ccttaaagct ggagttcaga gcatggttaa cattcctggt tgtcctttct acagctgcca gaaggggtac aagggcccct ggattggatc aggtatgctc 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

caagcacgct gtccatgcgg tgctgaactc atcttttctg ttgagaatgg ttttgcaaaa ctttacaaag gacccagaac ttgttcaaat tactggagag 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

gggctgttcc agtcaacgct aggctgtgtg ggtcggctag accggaccca actgattgga ctagtcttgt cgtcaattat ggcgttaggg actactgtaa 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

atatgagaaa ttgggagatc acatctttgt tacagcagta tcctctccaa atgtctgttt cacccaggtg cccccaacct tgagagctgc agtggccgtg 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

gacggcgtac aggttcagtg ttatctaggt gagcccaaaa ctccttggac gacatctgct tgctgttacg gtcctgacgg taagggtaaa actgttaagc 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

ttcccttccg cgttgacggt cacacacctg gtgtgcgcat gcaacttaat ttgcgtgatg cacttgagac aaatgactgt aattccacaa acaacactcc 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

tagtgatgaa gccgcagtgt ccgctcttgt tttcaaacag gagttgcggc gtacaaacca attgcttgag gcaatttcag ctggcgttga caccaccaaa 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ctgccagccc cctccatcga agaggtagtg gtaagaaagc gccagttccg ggcaagaact ggttcgctta ccttgccccc ccctccgaga tccgtcccag 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

gagtgtcatg tcctgaaagc ctgcaacgaa gtgacccgtt agaaggtcct tcaaacctcc ctccttcacc acctgttcta cagttggcca tgccgatgcc 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

cctgttggga gcgggtgagt gtaacccttt cactgcaatt ggatgtgcaa tgaccgaaac aggcggaggc cctgatgatt tacccagtta ccctcccaaa 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

aaggaggtct ctgaatggtc agacgaaagt tggtcaacgg ctacaaccgc ttccagctac gttactggcc ccccgtaccc taagatacgg ggaaaggatt 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ccactcagtc agcccccgcc aaacggccta caaaaaagaa gttgggaaag agtgagtttt cgtgcagcat gagctacact tggaccgacg tgattagctt 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

caaaactgct tctaaagttc tgtctgcaac tcgggccatc actagtggtt tcctcaaaca aagatcattg gtgtatgtga ctgagccgcg ggatgcggag 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

cttagaaaac aaaaagtcac tattaataga caacctctgt tccccccatc ataccacaag caagtgagat tggctaagga gaaagcttca aaagttgtcg 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

gtgtcatgtg ggactatgat gaagtagcag ctcacacgcc ctctaagtct gctaagtccc acatcactgg ccttcggggc actgatgttc gttctggagc 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

agcccgcaag gctgttctgg acttgcagaa gtgtgtcgag gcaggtgaga taccgagtca ttatcggcaa acagtgatag ttccaaagga ggaggtcttc 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

gtgaagaccc cccagaaacc aacaaagaaa cccccaaggc tcatctcgta cccccacctt gaaatgagat gtgttgagaa gatgtactac ggtcaggttg 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

ctcctgacgt agttaaagct gtcatgggag atgcgtacgg gtttgtagat ccacgtaccc gtgtcaagcg tctgttgtcg atgtggtcac ccgatgcagt 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

cggagccaca tgcgatacag tgtgttttga cagtaccatc acacccgagg atatcatggt ggagacagac atctactcag cagctaaact cagtgaccaa 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

caccgagctg gcattcacac cattgcgagg cagttatacg ctggaggacc gatgatcgct tatgatggcc gagagatcgg atatcgtagg tgtaggtctt 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ccggcgtcta tactacctca agttccaaca gtttgacctg ctggctgaag gtaaatgctg cagccgaaca ggctggcatg aagaaccctc gcttccttat 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

ttgcggcgat gattgcaccg taatttggaa aagcgccgga gcagatgcag acaaacaagc aatgcgtgtc tttgctagct ggatgaaggt gatgggtgca 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

ccacaagatt gtgtgcctca acccaaatac agtttggaag aattaacatc atgctcatca aatgttacct ctggaattac caaaagtggc aagccttact 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

actttcttac aagagatcct cgtatccccc ttggcaggtg ctctgccgag ggtctgggat acaaccccag tgctgcgtgg attgggtatc taatacatca 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

ctacccatgt ttgtgggtta gccgtgtgtt ggctgtccat ttcatggagc agatgctctt tgaggacaaa cttcccgaga ctgtgacctt tgactggtat 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

gggaaaaatt atacggtgcc tgtagaagat ctgcccagca tcattgctgg tgtgcacggt attgaggctt tctcggtggt gcgctacacc aacgctgaga 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

tcctcagagt ttcccaatca ctaacagaca tgaccatgcc ccccctgcga gcctggcgaa agaaagccag ggcggtcctc gccagcgcca agaggcgtgg 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

cggagcacac gcaaaattgg ctcgcttcct tctctggcat gctacatcta gacctctacc agatttggat aagacgagcg tggctcggta caccactttc 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

aattattgtg atgtttactc cccggagggg gatgtgtttg ttacaccaca gagaagattg cagaagtttc ttgtgaagta tttggctgtc attgtttttg 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

ccctagggct cattgctgtt ggattagcca tcagctgaac ccccaaattc aaaattaact aacagttttt tttttttttt ttttttaggg cagcggcaac 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

aggggagacc ccgggcttaa cgaccccgcc gatgtgagtt tggcgaccat ggtggatcag aaccgtttcg ggtgaagcca tggtctgaag gggatgacgt 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

cccttctggc tcatccacaa aaaccgtctc gggtgggtga ggagtcctgg ctgtgtggga agcagtcagt ataattcccg tcgtgtgtgg tgacgcctca 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

cgacgtactt gtccgctgtg cagagcgtag taccaagggc tgcaccccgg tttttgttcc aagcggaggg caacccccgc ttggaattaa aaacttgaag 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

agcctcgagg aaaaatcagt agaaatagct gttccagtct ttctagcctt gattccactt ctgtcagatg tgccctagtc agcggagacc ttttggtttt 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

gggagagtag cgacactccc agttgttctt cagacacttg gcgcacttcg gtttttcttt ggagcacttg agctttttaa gtcggcaaat atcgcatgct 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

tgttcgatag aagacagtag cttcatcttt caggaggctt gcttcaagct tggagttgat tgtatgcttg gtatagcttg aaatattgtg cagaaaaaga 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

aacaaggaag aaagggaacg agaacaatga cgaggaaaca aaagattaat aattgcaggt ctatttatac ttgatagcaa agcggcaaac tttttttatt 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

tcaaattcaa gtaactggaa ggaaggccgt ataccgttgc tcattagaga gtagtgtgcg tgaatgaagg aaggaaaaag tttcgtgtgt tcgaagatac 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

ccctcatcag ctctggaaca acgacatctg ttggtgctgt ctttgtcgtt aattttttcc tttagtgtct tccatcattt tttttgtcat tgcggatatg 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

gtgagacaac aacgggggag agagaaaaga aaaaaaaaga aaagaagttg catgcaagca acgaagcatc tgtgcttcat tttgtagaac aaaaatgcaa 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

cgcgagagcg ctaatttttc aaacaaagaa tctgagctgc atttttacag aacagaaatg caacgcgaaa gcgctatttt accaacgaag aatctgtgct 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

tcatttttgt aaaacaaaaa tgcaacgcga gagcgctaat ttttcaaaca aagaatctga gctgcatttt tacagaacag aaatgcaacg cgagagcgct 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

attttaccaa caaagaatct atacttcttt tttgttctac aaaaatgcat cccgagagcg ctatttttct aacaaagcat cttagattac tttttttctc 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

ctttgtgcgc tctataatgc agtctcttga taactttttg cactgtaggt ccgttaaggt tagaagaagg ctactttggt gtctattttc tcttccataa 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

aaaaagcctg actccacttc ccgcgtttac tgattactag cgaagctgcg ggtgcatttt ttcaagataa aggcatcccc gattatattc tataccgatg 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

tggattgcgc atactttgtg aacagaaagt gatagcgttg atgattcttc attggtcaga aaattatgaa cggtttcttc tattttgtct ctatatacta 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

cgtataggaa atgtttacat tttcgtattg ttttcgattc actctatgaa tagttcttac tacaattttt ttgtctaaag agtaatacta gagataaaca 
^9401      ^9411      ^9421      ^9431      ^9441      ^9451      ^9461      ^9471      ^9481      ^9491      

taaaaaatgt agaggtcgag tttagatgca agttcaagga gcgaaaggtg gatgggtagg ttatataggg atatagcaca gagatatata gcaaagagat 
^9501      ^9511      ^9521      ^9531      ^9541      ^9551      ^9561      ^9571      ^9581      ^9591      

acttttgagc aatgtttgtg gaagcggtat tcgcaatatt ttagtagctc gttacagtcc ggtgcgtttt tggttttttg aaagtgcgtc ttcagagcgc 
^9601      ^9611      ^9621      ^9631      ^9641      ^9651      ^9661      ^9671      ^9681      ^9691      

ttttggtttt caaaagcgct ctgaagttcc tatactttct agctagagaa taggaacttc ggaataggaa cttcaaagcg tttccgaaaa cgagcgcttc 
^9701      ^9711      ^9721      ^9731      ^9741      ^9751      ^9761      ^9771      ^9781      ^9791      

cgaaaatgca acgcgagctg cgcacataca gctcactgtt cacgtcgcac ctatatctgc gtgttgcctg tatatatata tacatgagaa gaacggcata 
^9801      ^9811      ^9821      ^9831      ^9841      ^9851      ^9861      ^9871      ^9881      ^9891      

gtgcgtgttt atgcttaaat gcgttatggt gcactctcag tacaatctgc tctgatgccg catagttaag ccagccccga cacccgccaa cacccgctga 
^9901      ^9911      ^9921      ^9931      ^9941      ^9951      ^9961      ^9971      ^9981      ^9991      

cgcgccctga cgggcttgtc tgctcccggc atccgcttac agacaagctg tgaccgtctc cgggagctgc atgtgtcaga ggttttcacc gtcatcaccg 
^10001     ^10011     ^10021     ^10031     ^10041     ^10051     ^10061     ^10071     ^10081     ^10091     

aaacgcgcga gacgaaaggg cctcgtgata cgcctatttt tataggttaa tgtcatgata ataatggttt cttagacgtc aggtggcact tttcggggaa 
^10101     ^10111     ^10121     ^10131     ^10141     ^10151     ^10161     ^10171     ^10181     ^10191     

atgtgcgcgg aacccctatt tgtttatttt tctaaataca ttcaaatatg tatccgctca tgagacaata accctgataa atgcttcaat aatattgaaa 
^10201     ^10211     ^10221     ^10231     ^10241     ^10251     ^10261     ^10271     ^10281     ^10291     

aaggaagagt atgagtattc aacatttccg tgtcgccctt attccctttt ttgcggcatt ttgccttcct gtttttgctc acccagaaac gctggtgaaa 
^10301     ^10311     ^10321     ^10331     ^10341     ^10351     ^10361     ^10371     ^10381     ^10391     

gtaaaagatg ctgaagatca gttgggtgca cgagtgggtt acatcgaact ggatctcaac agcggtaaga tccttgagag ttttcgcccc gaagaacgtt 
^10401     ^10411     ^10421     ^10431     ^10441     ^10451     ^10461     ^10471     ^10481     ^10491     

ttccaatgat gagcactttt aaagttctgc tatgtggcgc ggtattatcc cgtattgacg ccgggcaaga gcaactcggt cgccgcatac actattctca 
^10501     ^10511     ^10521     ^10531     ^10541     ^10551     ^10561     ^10571     ^10581     ^10591     

gaatgacttg gttgagtact caccagtcac agaaaagcat cttacggatg gcatgacagt aagagaatta tgcagtgctg ccataaccat gagtgataac 
^10601     ^10611     ^10621     ^10631     ^10641     ^10651     ^10661     ^10671     ^10681     ^10691     

actgcggcca acttacttct gacaacgatc ggaggaccga aggagctaac cgcttttttg cacaacatgg gggatcatgt aactcgcctt gatcgttggg 
^10701     ^10711     ^10721     ^10731     ^10741     ^10751     ^10761     ^10771     ^10781     ^10791     

aaccggagct gaatgaagcc ataccaaacg acgagcgtga caccacgatg cctgtagcaa tggcaacaac gttgcgcaaa ctattaactg gcgaactact 
^10801     ^10811     ^10821     ^10831     ^10841     ^10851     ^10861     ^10871     ^10881     ^10891     

tactctagct tcccggcaac aattaataga ctggatggag gcggataaag ttgcaggacc acttctgcgc tcggcccttc cggctggctg gtttattgct 
^10901     ^10911     ^10921     ^10931     ^10941     ^10951     ^10961     ^10971     ^10981     ^10991     

gataaatctg gagccggtga gcgtgggtct cgcggtatca ttgcagcact ggggccagat ggtaagccct cccgtatcgt agttatctac acgacgggga 
^11001     ^11011     ^11021     ^11031     ^11041     ^11051     ^11061     ^11071     ^11081     ^11091     

gtcaggcaac tatggatgaa cgaaatagac agatcgctga gataggtgcc tcactgatta agcattggta actgtcagac caagtttact catatatact 
^11101     ^11111     ^11121     ^11131     ^11141     ^11151     ^11161     ^11171     ^11181     ^11191     

ttagattgat ttaaaacttc atttttaatt taaaaggatc taggtgaaga tcctttttga taatctcatg accaaaatcc cttaacgtga gttttcgttc 
^11201     ^11211     ^11221     ^11231     ^11241     ^11251     ^11261     ^11271     ^11281     ^11291     

cactgagcgt cagaccccgt agaaaagatc aaaggatctt cttgagatcc tttttttctg cgcgtaatct gctgcttgca aacaaaaaaa ccaccgctac 
^11301     ^11311     ^11321     ^11331     ^11341     ^11351     ^11361     ^11371     ^11381     ^11391     

cagcggtggt ttgtttgccg gatcaagagc taccaactct ttttccgaag gtaactggct tcagcagagc gcagatacca aatactgtcc ttctagtgta 
^11401     ^11411     ^11421     ^11431     ^11441     ^11451     ^11461     ^11471     ^11481     ^11491     

gccgtagtta ggccaccact tcaagaactc tgtagcaccg cctacatacc tcgctctgct aatcctgtta ccagtggctg ctgccagtgg cgataagtcg 
^11501     ^11511     ^11521     ^11531     ^11541     ^11551     ^11561     ^11571     ^11581     ^11591     

tgtcttaccg ggttggactc aagacgatag ttaccggata aggcgcagcg gtcgggctga acggggggtt cgtgcacaca gcccagcttg gagcgaacga 
^11601     ^11611     ^11621     ^11631     ^11641     ^11651     ^11661     ^11671     ^11681     ^11691     

cctacaccga actgagatac ctacagcgtg agctatgaga aagcgccacg cttcccgaag ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg 
^11701     ^11711     ^11721     ^11731     ^11741     ^11751     ^11761     ^11771     ^11781     ^11791     

aacaggagag cgcacgaggg agcttccagg gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc cacctctgac ttgagcgtcg atttttgtga 
^11801     ^11811     ^11821     ^11831     ^11841     ^11851     ^11861     ^11871     ^11881     ^11891     

tgctcgtcag gggggcggag cctatggaaa aacgccagca acgcggcctt tttacggttc ctggcctttt gctggccttt tgctcacatg ttctttcctg 
^11901     ^11911     ^11921     ^11931     ^11941     ^11951     ^11961     ^11971     ^11981     ^11991     

cgttatcccc tgattctgtg gataaccgta ttaccgcctt tgagtgagct gataccgctc gccgcagccg aacgaccgag cgcagcgagt cagtgagcga 
^12001     ^12011     ^12021     ^12031     ^12041     ^12051     ^12061     ^12071     ^12081     ^12091     

ggaagcggaa gagcgcccaa tacgcaaacc gcctctcccc gcgcgttggc cgattcatta atccagctgg cacgacaggt ttcccgactg gaaagcgggc 
^12101     ^12111     ^12121     ^12131     ^12141     ^12151     ^12161     ^12171     ^12181     ^12191     

agtgagcgca acgcaattaa tgtgagttac ctcactcatt aggcacccca ggctttacac tttatgcttc cggctcgtat gttgtgtgga attgtgagcg 
^12201     ^12211     ^12221     ^12231     ^12241     ^12251     ^12261     ^12271     ^12281     ^12291     

gataacaatt tcacacagga aacagctatg accatgatta cgaattaatt cggtcgaaaa aagaaaagga gagggccaag agggagggca ttggtgacta 
^12301     ^12311     ^12321     ^12331     ^12341     ^12351     ^12361     ^12371     ^12381     ^12391     

ttgagcacgt gagtatacgt gattaagcac acaaaggcag cttggagtat gtctgttatt aatttcacag gtagttctgg tccattggtg aaagtttgcg 
^12401     ^12411     ^12421     ^12431     ^12441     ^12451     ^12461     ^12471     ^12481     ^12491     

gcttgcagag cacagaggcc gcagaatgtg ctctagattc cgatgctgac ttgctgggta ttatatgtgt gcccaataga aagagaacaa ttgacccggt 
^12501     ^12511     ^12521     ^12531     ^12541     ^12551     ^12561     ^12571     ^12581     ^12591     

tattgcaagg aaaatttcaa gtcttgtaaa agcatataaa aatagttcag gcactccgaa atacttggtt ggcgtgtttc gtaatcaacc taaggaggat 
^12601     ^12611     ^12621     ^12631     ^12641     ^12651     ^12661     ^12671     ^12681     ^12691     

gttttggctc tggtcaatga ttacggcatt gatatcgtcc aactgcatgg agatgagtcg tggcaagaat accaagagtt cctcggtttg ccagttatta 
^12701     ^12711     ^12721     ^12731     ^12741     ^12751     ^12761     ^12771     ^12781     ^12791     

aaagactcgt atttccaaaa gactgcaaca tactactcag tgcagcttca cagaaacctc attcgtttat tcccttgttt gattcagaag caggtgggac 
^12801     ^12811     ^12821     ^12831     ^12841     ^12851     ^12861     ^12871     ^12881     ^12891     

aggtgaactt ttggattgga actcgatttc tgactgggtt ggaaggcaag agagccccga aagcttacat tttatgttag ctggtggact gacgccagaa 
^12901     ^12911     ^12921     ^12931     ^12941     ^12951     ^12961     ^12971     ^12981     ^12991     

aatgttggtg atgcgcttag attaaatggc gttattggtg ttgatgtaag cggaggtgtg gagacaaatg gtgtaaaaga ctctaacaaa atagcaaatt 
^13001     ^13011     ^13021     ^13031     ^13041     ^13051     ^13061     ^13071     ^13081     ^13091     

tcgtcaaaaa tgctaagaaa taggttatta ctgagtagta tttatttaag tattgtttgt gcacttgccg gcatgccggt agaggtgtgg tcaataagag 
^13101     ^13111     ^13121     ^13131     ^13141     ^13151     ^13161     ^13171     ^13181     ^13191     

cgacctcatg ctatacctga gaaagcaacc tgacctacag gaaagagtta ctcaagaaca agaattttcg ttttaaaacc taagagtcac tttaaaattt 
^13201     ^13211     ^13221     ^13231     ^13241     ^13251     ^13261     ^13271     ^13281     ^13291     

gtatacactt atttttttta taacttattt aataataaaa atcataaatc ataagaaatt cgcccggaat tagcttggct gcaggtcgac
^13301     ^13311     ^13321     ^13331     ^13341     ^13351     ^13361     ^13371     ^13381

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

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:
bla

The description of the protein encoded in this ORF:
beta-lactamase fusion 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):

447-1316

ORF

ORF position:

2

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:
NS3-4A, NS4B, NS5A, NS5B 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):

1936-7713

Citations:

Pizzuti M., De Tomassi A., Traboni C. (2003) Replication and IRES-dependent translation are both affected by core coding sequences in subgenomic GB virus B replicons. J. Virol. 77(13):7502-7509

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `GBV-B`	The functional status of IRES: `functional`

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

2-446

How IRES boundaries were determined:
experimentally_determined

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

accacaaaca ctccagtttg ttacactccg ctaggaatgc tcctggagca ccccccctag cagggcgtgg gggatttccc ctgcccgtct gcagaagggt 
^2         ^12        ^22        ^32        ^42        ^52        ^62        ^72        ^82        ^92        

ggagccaacc accttagtat gtaggcggcg ggactcatga cgctcgcgtg atgacaagcg ccaagcttga cttggatggc cctgatgggc gttcatgggt 
^102       ^112       ^122       ^132       ^142       ^152       ^162       ^172       ^182       ^192       

tcggtggtgg tggcgcttta ggcagcctcc acgcccacca cctcccagat agagcggcgg cactgtaggg aagaccgggg accggtcact accaaggacg 
^202       ^212       ^222       ^232       ^242       ^252       ^262       ^272       ^282       ^292       

cagacctctt tttgagtatc acgcctccgg aagtagttgg gcaagcccac ctatatgtgt tgggatggtt ggggttagcc atccataccg tactgcctga 
^302       ^312       ^322       ^332       ^342       ^352       ^362       ^372       ^382       ^392       

tagggtcctt gcgaggggat ctgggagtct cgtagaccgt agcac
^402       ^412       ^422       ^432       ^442

Remarks:

This RNA transcript is the most efficiently translated message in RRL and possibly also in cB76.1/Huh7
cells of the RepABla, RepBBla, RepCBla which differ only in the length of the included core protein
sequence at the very beginning of 1st reporter cistron which is placed right after the GBV-B IRES.

Citations:

Pizzuti M., De Tomassi A., Traboni C. (2003) Replication and IRES-dependent translation are both affected by core coding sequences in subgenomic GB virus B replicons. J. Virol. 77(13):7502-7509

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