IRESite_Id:312 characteristics of GBV-B IRES studied in RepBNeo plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `312`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-04 21:40:39`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

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 -
21nt_of_GBV-B_core_gene - neomycin phosphotransferase - 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 gggcgcgcca tgattgaaca agatggattg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

cacgcaggtt ctccggccgc ttgggtggag aggctattcg gctatgactg ggcacaacag acaatcggct gctctgatgc cgccgtgttc cggctgtcag 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

cgcaggggcg cccggttctt tttgtcaaga ccgacctgtc cggtgccctg aatgaactgc aggacgaggc agcgcggcta tcgtggctgg ccacgacggg 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

cgttccttgc gcagctgtgc tcgacgttgt cactgaagcg ggaagggact ggctgctatt gggcgaagtg ccggggcagg atctcctgtc atctcacctt 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gctcctgccg agaaggtatc catcatggct gatgcaatgc ggcggctgca tacgcttgat ccggctacct gcccattcga ccaccaagcg aaacatcgca 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

tcgagcgagc acgtactcgg atggaagccg gtcttgtcga tcaggatgat ctggacgagg agcatcaggg gctcgcgcca gccgaactgt tcgccaggct 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

caaggcgcgc atgcccgacg gcgaggatct cgtcgtgacc catggcgatg cctgcttgcc gaatatcatg gtggaaaatg gccgcttttc tggattcatc 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

gactgtggcc ggctgggtgt ggcggaccgc tatcaggaca tagcgttggc tacccgtgat attgctgagg agcttggcgg cgaatgggct gaccgcttcc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tcgtgcttta cggtatcgcc gctcccgatt cgcagcgcat cgccttctat cgccttcttg acgagttctt ctgagtttaa acagaccaca acggtttccc 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tctagcggga tcaattccgc ccctctccct cccccccccc taacgttact ggccgaagcc gcttggaata aggccggtgt gcgtttgtct atatgttatt 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ttccaccata ttgccgtctt ttggcaatgt gagggcccgg aaacctggcc ctgtcttctt gacgagcatt cctaggggtc tttcccctct cgccaaagga 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

atgcaaggtc tgttgaatgt cgtgaaggaa gcagttcctc tggaagcttc ttgaagacaa acaacgtctg tagcgaccct ttgcaggcag cggaaccccc 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

cacctggcga caggtgcctc tgcggccaaa agccacgtgt ataagataca cctgcaaagg cggcacaacc ccagtgccac gttgtgagtt ggatagttgt 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ggaaagagtc aaatggctct cctcaagcgt attcaacaag gggctgaagg atgcccagaa ggtaccccat tgtatgggat ctgatctggg gcctcggtgc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

acatgcttta catgtgttta gtcgaggtta aaaaacgtct aggccccccg aaccacgggg acgtggtttt cctttgaaaa acacgataat accatggcac 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

cttttacgct gcagtgtctc tctgaacgtg gcacgctgtc agcgatggca gtggtcatga ctggtataga cccccgaact tggactggaa ctatcttcag 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

attaggatct ctggccacta gctacatggg atttgtttgt gacaacgtgt tgtatactgc tcaccatggc agcaaggggc gccggttggc tcatcccaca 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ggctccatac acccaataac cgttgacgcg gctaatgacc aggacatcta tcaaccacca tgtggagctg ggtcccttac tcggtgctct tgcggggaga 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ccaaggggta tctggtaaca cgactggggt cattggttga ggtcaataaa tccgatgacc cttattggtg tgtgtgcggg gcccttccca tggctgttgc 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

caagggttct tcaggtgccc cgattctgtg ctcctccggg catgttattg ggatgttcac cgctgctaga aattctggcg gttcagtcag ccagattagg 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gttaggccgt tggtgtgtgc tggataccat ccccagtaca cagcacatgc cactcttgat acaaaaccta ctgtgcctaa cgagtattca gtgcaaattt 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

taattgcccc cactggcagc ggcaagtcaa ccaaattacc actttcttac atgcaggaga agtatgaggt cttggtccta aatcccagtg tggctacaac 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

agcatcaatg ccaaagtaca tgcacgcgac gtacggcgtg aatccaaatt gctattttaa tggcaaatgt accaacacag gggcttcact tacgtacagc 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

acatatggca tgtacctgac cggagcatgt tcccggaact atgatgtaat catttgtgac gaatgccatg ctaccgatgc aaccaccgtg ttgggcattg 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

gaaaggtcct aaccgaagct ccatccaaaa atgttaggct agtggttctt gccacggcta ccccccctgg agtaatccct acaccacatg ccaacataac 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tgagattcaa ttaaccgatg aaggcactat cccctttcat ggaaaaaaga ttaaggagga aaatctgaag aaagggagac accttatctt tgaggctacc 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

aaaaaacact gtgatgagct tgctaacgag ttagctcgaa agggaataac agctgtctct tactataggg gatgtgacat ctcaaaaatc cctgagggcg 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

actgtgtagt agttgccact gatgccttgt gtacagggta cactggtgac tttgattccg tgtatgactg cagcctcatg gtagaaggca catgccatgt 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

tgaccttgac cctactttca ccatgggtgt tcgtgtgtgc ggggtttcag caatagttaa aggccagcgt aggggccgca caggccgtgg gagagctggc 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

atatactact atgtagacgg gagttgtacc ccttcgggta tggttcctga atgcaacatt gttgaagcct tcgacgcagc caaggcatgg tatggtttgt 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

catcaacaga agctcaaact attctggaca cctatcgcac ccaacctggg ttacctgcga taggagcaaa tttggacgag tgggctgatc tcttttcaat 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ggtcaacccc gaaccttcat ttgtcaatac tgcaaaaaga actgctgaca attatgtttt gttgactgca gcccaactac aactgtgtca tcagtatggc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

tatgctgctc ccaatgacgc accacggtgg cagggagccc ggcttgggaa aaaaccttgt ggggttctgt ggcgcttgga cggcgctgac gcctgtcctg 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

gcccagagcc cagcgaggtg accagatacc aaatgtgctt cactgaagtc aatacttctg ggacagccgc actcgctgtt ggcgttggag tggctatggc 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ttatctagcc attgacactt ttggcgccac ttgtgtgcgg cgttgctggt ctattacatc agtccctacc ggtgctactg tcgccccagt ggttgacgaa 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

gaagaaatcg tggaggagtg tgcatcattc attcccttgg aggccatggt tgctgcaatt gacaagctga agagtacaat caccacaact agtcctttca 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

cattggaaac cgcccttgaa aaacttaaca cctttcttgg gcctcatgca gctacaatcc ttgctatcat agagtattgc tgtggcttag tcactttacc 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

tgacaatccc tttgcatcat gcgtgtttgc tttcattgcg ggtattacta ccccactacc tcacaagatc aaaatgttcc tgtcattatt tggaggcgca 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

attgcgtcca agcttacaga cgctagaggc gcactggcgt tcatgatggc cggggctgcg ggaacagctc ttggtacatg gacatcggtg ggttttgtct 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ttgacatgct aggcggctat gctgccgcct catccactgc ttgcttgaca tttaaatgct tgatgggtga gtggcccact atggatcagc ttgctggttt 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

agtctactcc gcgttcaacc cggccgcagg agttgtgggc gttttgtcag cttgtgcaat gtttgctttg acaacagcag ggccagatca ctggcccaac 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

agacttctta ctatgcttgc taggagcaac actgtatgta atgagtactt tattgccact cgtgacatcc gcaggaagat actgggcatt ctggaggcat 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ctaccccctg gagtgtcata tcagcttgca tccgttggct ccacaccccg acggaggatg attgcggcct cattgcttgg ggtctagaga tttggcagta 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

cgtgtgcaat ttctttgtga tttgctttaa tgtccttaaa gctggagttc agagcatggt taacattcct ggttgtcctt tctacagctg ccagaagggg 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

tacaagggcc cctggattgg atcaggtatg ctccaagcac gctgtccatg cggtgctgaa ctcatctttt ctgttgagaa tggttttgca aaactttaca 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

aaggacccag aacttgttca aattactgga gaggggctgt tccagtcaac gctaggctgt gtgggtcggc tagaccggac ccaactgatt ggactagtct 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

tgtcgtcaat tatggcgtta gggactactg taaatatgag aaattgggag atcacatctt tgttacagca gtatcctctc caaatgtctg tttcacccag 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

gtgcccccaa ccttgagagc tgcagtggcc gtggacggcg tacaggttca gtgttatcta ggtgagccca aaactccttg gacgacatct gcttgctgtt 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

acggtcctga cggtaagggt aaaactgtta agcttccctt ccgcgttgac ggtcacacac ctggtgtgcg catgcaactt aatttgcgtg atgcacttga 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

gacaaatgac tgtaattcca caaacaacac tcctagtgat gaagccgcag tgtccgctct tgttttcaaa caggagttgc ggcgtacaaa ccaattgctt 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

gaggcaattt cagctggcgt tgacaccacc aaactgccag ccccctccat cgaagaggta gtggtaagaa agcgccagtt ccgggcaaga actggttcgc 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ttaccttgcc cccccctccg agatccgtcc caggagtgtc atgtcctgaa agcctgcaac gaagtgaccc gttagaaggt ccttcaaacc tccctccttc 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

accacctgtt ctacagttgg ccatgccgat gcccctgttg ggagcgggtg agtgtaaccc tttcactgca attggatgtg caatgaccga aacaggcgga 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ggccctgatg atttacccag ttaccctccc aaaaaggagg tctctgaatg gtcagacgaa agttggtcaa cggctacaac cgcttccagc tacgttactg 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

gccccccgta ccctaagata cggggaaagg attccactca gtcagccccc gccaaacggc ctacaaaaaa gaagttggga aagagtgagt tttcgtgcag 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

catgagctac acttggaccg acgtgattag cttcaaaact gcttctaaag ttctgtctgc aactcgggcc atcactagtg gtttcctcaa acaaagatca 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ttggtgtatg tgactgagcc gcgggatgcg gagcttagaa aacaaaaagt cactattaat agacaacctc tgttcccccc atcataccac aagcaagtga 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

gattggctaa ggagaaagct tcaaaagttg tcggtgtcat gtgggactat gatgaagtag cagctcacac gccctctaag tctgctaagt cccacatcac 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

tggccttcgg ggcactgatg ttcgttctgg agcagcccgc aaggctgttc tggacttgca gaagtgtgtc gaggcaggtg agataccgag tcattatcgg 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

caaacagtga tagttccaaa ggaggaggtc ttcgtgaaga ccccccagaa accaacaaag aaacccccaa ggctcatctc gtacccccac cttgaaatga 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

gatgtgttga gaagatgtac tacggtcagg ttgctcctga cgtagttaaa gctgtcatgg gagatgcgta cgggtttgta gatccacgta cccgtgtcaa 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

gcgtctgttg tcgatgtggt cacccgatgc agtcggagcc acatgcgata cagtgtgttt tgacagtacc atcacacccg aggatatcat ggtggagaca 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

gacatctact cagcagctaa actcagtgac caacaccgag ctggcattca caccattgcg aggcagttat acgctggagg accgatgatc gcttatgatg 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

gccgagagat cggatatcgt aggtgtaggt cttccggcgt ctatactacc tcaagttcca acagtttgac ctgctggctg aaggtaaatg ctgcagccga 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

acaggctggc atgaagaacc ctcgcttcct tatttgcggc gatgattgca ccgtaatttg gaaaagcgcc ggagcagatg cagacaaaca agcaatgcgt 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

gtctttgcta gctggatgaa ggtgatgggt gcaccacaag attgtgtgcc tcaacccaaa tacagtttgg aagaattaac atcatgctca tcaaatgtta 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

cctctggaat taccaaaagt ggcaagcctt actactttct tacaagagat cctcgtatcc cccttggcag gtgctctgcc gagggtctgg gatacaaccc 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

cagtgctgcg tggattgggt atctaataca tcactaccca tgtttgtggg ttagccgtgt gttggctgtc catttcatgg agcagatgct ctttgaggac 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

aaacttcccg agactgtgac ctttgactgg tatgggaaaa attatacggt gcctgtagaa gatctgccca gcatcattgc tggtgtgcac ggtattgagg 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

ctttctcggt ggtgcgctac accaacgctg agatcctcag agtttcccaa tcactaacag acatgaccat gccccccctg cgagcctggc gaaagaaagc 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

cagggcggtc ctcgccagcg ccaagaggcg tggcggagca cacgcaaaat tggctcgctt ccttctctgg catgctacat ctagacctct accagatttg 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

gataagacga gcgtggctcg gtacaccact ttcaattatt gtgatgttta ctccccggag ggggatgtgt ttgttacacc acagagaaga ttgcagaagt 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

ttcttgtgaa gtatttggct gtcattgttt ttgccctagg gctcattgct gttggattag ccatcagctg aacccccaaa ttcaaaatta actaacagtt 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

tttttttttt ttttttttta gggcagcggc aacaggggag accccgggct taacgacccc gccgatgtga gtttggcgac catggtggat cagaaccgtt 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

tcgggtgaag ccatggtctg aaggggatga cgtcccttct ggctcatcca caaaaaccgt ctcgggtggg tgaggagtcc tggctgtgtg ggaagcagtc 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

agtataattc ccgtcgtgtg tggtgacgcc tcacgacgta cttgtccgct gtgcagagcg tagtaccaag ggctgcaccc cggtttttgt tccaagcgga 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

gggcaacccc cgcttggaat taaaaact
^8001      ^8011      ^8021

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
RepBNeo 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 aaacagggcg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

cgccatgatt gaacaagatg gattgcacgc aggttctccg gccgcttggg tggagaggct attcggctat gactgggcac aacagacaat cggctgctct 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

gatgccgccg tgttccggct gtcagcgcag gggcgcccgg ttctttttgt caagaccgac ctgtccggtg ccctgaatga actgcaggac gaggcagcgc 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ggctatcgtg gctggccacg acgggcgttc cttgcgcagc tgtgctcgac gttgtcactg aagcgggaag ggactggctg ctattgggcg aagtgccggg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gcaggatctc ctgtcatctc accttgctcc tgccgagaag gtatccatca tggctgatgc aatgcggcgg ctgcatacgc ttgatccggc tacctgccca 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ttcgaccacc aagcgaaaca tcgcatcgag cgagcacgta ctcggatgga agccggtctt gtcgatcagg atgatctgga cgaggagcat caggggctcg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

cgccagccga actgttcgcc aggctcaagg cgcgcatgcc cgacggcgag gatctcgtcg tgacccatgg cgatgcctgc ttgccgaata tcatggtgga 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

aaatggccgc ttttctggat tcatcgactg tggccggctg ggtgtggcgg accgctatca ggacatagcg ttggctaccc gtgatattgc tgaggagctt 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ggcggcgaat gggctgaccg cttcctcgtg ctttacggta tcgccgctcc cgattcgcag cgcatcgcct tctatcgcct tcttgacgag ttcttctgag 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tttaaacaga ccacaacggt ttccctctag cgggatcaat tccgcccctc tccctccccc ccccctaacg ttactggccg aagccgcttg gaataaggcc 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ggtgtgcgtt tgtctatatg ttattttcca ccatattgcc gtcttttggc aatgtgaggg cccggaaacc tggccctgtc ttcttgacga gcattcctag 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

gggtctttcc cctctcgcca aaggaatgca aggtctgttg aatgtcgtga aggaagcagt tcctctggaa gcttcttgaa gacaaacaac gtctgtagcg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

accctttgca ggcagcggaa ccccccacct ggcgacaggt gcctctgcgg ccaaaagcca cgtgtataag atacacctgc aaaggcggca caaccccagt 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

gccacgttgt gagttggata gttgtggaaa gagtcaaatg gctctcctca agcgtattca acaaggggct gaaggatgcc cagaaggtac cccattgtat 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gggatctgat ctggggcctc ggtgcacatg ctttacatgt gtttagtcga ggttaaaaaa cgtctaggcc ccccgaacca cggggacgtg gttttccttt 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

gaaaaacacg ataataccat ggcacctttt acgctgcagt gtctctctga acgtggcacg ctgtcagcga tggcagtggt catgactggt atagaccccc 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gaacttggac tggaactatc ttcagattag gatctctggc cactagctac atgggatttg tttgtgacaa cgtgttgtat actgctcacc atggcagcaa 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ggggcgccgg ttggctcatc ccacaggctc catacaccca ataaccgttg acgcggctaa tgaccaggac atctatcaac caccatgtgg agctgggtcc 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

cttactcggt gctcttgcgg ggagaccaag gggtatctgg taacacgact ggggtcattg gttgaggtca ataaatccga tgacccttat tggtgtgtgt 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gcggggccct tcccatggct gttgccaagg gttcttcagg tgccccgatt ctgtgctcct ccgggcatgt tattgggatg ttcaccgctg ctagaaattc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

tggcggttca gtcagccaga ttagggttag gccgttggtg tgtgctggat accatcccca gtacacagca catgccactc ttgatacaaa acctactgtg 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

cctaacgagt attcagtgca aattttaatt gcccccactg gcagcggcaa gtcaaccaaa ttaccacttt cttacatgca ggagaagtat gaggtcttgg 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

tcctaaatcc cagtgtggct acaacagcat caatgccaaa gtacatgcac gcgacgtacg gcgtgaatcc aaattgctat tttaatggca aatgtaccaa 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

cacaggggct tcacttacgt acagcacata tggcatgtac ctgaccggag catgttcccg gaactatgat gtaatcattt gtgacgaatg ccatgctacc 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

gatgcaacca ccgtgttggg cattggaaag gtcctaaccg aagctccatc caaaaatgtt aggctagtgg ttcttgccac ggctaccccc cctggagtaa 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tccctacacc acatgccaac ataactgaga ttcaattaac cgatgaaggc actatcccct ttcatggaaa aaagattaag gaggaaaatc tgaagaaagg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

gagacacctt atctttgagg ctaccaaaaa acactgtgat gagcttgcta acgagttagc tcgaaaggga ataacagctg tctcttacta taggggatgt 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

gacatctcaa aaatccctga gggcgactgt gtagtagttg ccactgatgc cttgtgtaca gggtacactg gtgactttga ttccgtgtat gactgcagcc 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

tcatggtaga aggcacatgc catgttgacc ttgaccctac tttcaccatg ggtgttcgtg tgtgcggggt ttcagcaata gttaaaggcc agcgtagggg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ccgcacaggc cgtgggagag ctggcatata ctactatgta gacgggagtt gtaccccttc gggtatggtt cctgaatgca acattgttga agccttcgac 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

gcagccaagg catggtatgg tttgtcatca acagaagctc aaactattct ggacacctat cgcacccaac ctgggttacc tgcgatagga gcaaatttgg 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

acgagtgggc tgatctcttt tcaatggtca accccgaacc ttcatttgtc aatactgcaa aaagaactgc tgacaattat gttttgttga ctgcagccca 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

actacaactg tgtcatcagt atggctatgc tgctcccaat gacgcaccac ggtggcaggg agcccggctt gggaaaaaac cttgtggggt tctgtggcgc 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ttggacggcg ctgacgcctg tcctggccca gagcccagcg aggtgaccag ataccaaatg tgcttcactg aagtcaatac ttctgggaca gccgcactcg 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ctgttggcgt tggagtggct atggcttatc tagccattga cacttttggc gccacttgtg tgcggcgttg ctggtctatt acatcagtcc ctaccggtgc 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

tactgtcgcc ccagtggttg acgaagaaga aatcgtggag gagtgtgcat cattcattcc cttggaggcc atggttgctg caattgacaa gctgaagagt 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

acaatcacca caactagtcc tttcacattg gaaaccgccc ttgaaaaact taacaccttt cttgggcctc atgcagctac aatccttgct atcatagagt 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

attgctgtgg cttagtcact ttacctgaca atccctttgc atcatgcgtg tttgctttca ttgcgggtat tactacccca ctacctcaca agatcaaaat 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

gttcctgtca ttatttggag gcgcaattgc gtccaagctt acagacgcta gaggcgcact ggcgttcatg atggccgggg ctgcgggaac agctcttggt 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

acatggacat cggtgggttt tgtctttgac atgctaggcg gctatgctgc cgcctcatcc actgcttgct tgacatttaa atgcttgatg ggtgagtggc 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ccactatgga tcagcttgct ggtttagtct actccgcgtt caacccggcc gcaggagttg tgggcgtttt gtcagcttgt gcaatgtttg ctttgacaac 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

agcagggcca gatcactggc ccaacagact tcttactatg cttgctagga gcaacactgt atgtaatgag tactttattg ccactcgtga catccgcagg 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

aagatactgg gcattctgga ggcatctacc ccctggagtg tcatatcagc ttgcatccgt tggctccaca ccccgacgga ggatgattgc ggcctcattg 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

cttggggtct agagatttgg cagtacgtgt gcaatttctt tgtgatttgc tttaatgtcc ttaaagctgg agttcagagc atggttaaca ttcctggttg 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

tcctttctac agctgccaga aggggtacaa gggcccctgg attggatcag gtatgctcca agcacgctgt ccatgcggtg ctgaactcat cttttctgtt 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

gagaatggtt ttgcaaaact ttacaaagga cccagaactt gttcaaatta ctggagaggg gctgttccag tcaacgctag gctgtgtggg tcggctagac 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cggacccaac tgattggact agtcttgtcg tcaattatgg cgttagggac tactgtaaat atgagaaatt gggagatcac atctttgtta cagcagtatc 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ctctccaaat gtctgtttca cccaggtgcc cccaaccttg agagctgcag tggccgtgga cggcgtacag gttcagtgtt atctaggtga gcccaaaact 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ccttggacga catctgcttg ctgttacggt cctgacggta agggtaaaac tgttaagctt cccttccgcg ttgacggtca cacacctggt gtgcgcatgc 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

aacttaattt gcgtgatgca cttgagacaa atgactgtaa ttccacaaac aacactccta gtgatgaagc cgcagtgtcc gctcttgttt tcaaacagga 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

gttgcggcgt acaaaccaat tgcttgaggc aatttcagct ggcgttgaca ccaccaaact gccagccccc tccatcgaag aggtagtggt aagaaagcgc 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

cagttccggg caagaactgg ttcgcttacc ttgccccccc ctccgagatc cgtcccagga gtgtcatgtc ctgaaagcct gcaacgaagt gacccgttag 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

aaggtccttc aaacctccct ccttcaccac ctgttctaca gttggccatg ccgatgcccc tgttgggagc gggtgagtgt aaccctttca ctgcaattgg 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

atgtgcaatg accgaaacag gcggaggccc tgatgattta cccagttacc ctcccaaaaa ggaggtctct gaatggtcag acgaaagttg gtcaacggct 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

acaaccgctt ccagctacgt tactggcccc ccgtacccta agatacgggg aaaggattcc actcagtcag cccccgccaa acggcctaca aaaaagaagt 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

tgggaaagag tgagttttcg tgcagcatga gctacacttg gaccgacgtg attagcttca aaactgcttc taaagttctg tctgcaactc gggccatcac 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

tagtggtttc ctcaaacaaa gatcattggt gtatgtgact gagccgcggg atgcggagct tagaaaacaa aaagtcacta ttaatagaca acctctgttc 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

cccccatcat accacaagca agtgagattg gctaaggaga aagcttcaaa agttgtcggt gtcatgtggg actatgatga agtagcagct cacacgccct 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

ctaagtctgc taagtcccac atcactggcc ttcggggcac tgatgttcgt tctggagcag cccgcaaggc tgttctggac ttgcagaagt gtgtcgaggc 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

aggtgagata ccgagtcatt atcggcaaac agtgatagtt ccaaaggagg aggtcttcgt gaagaccccc cagaaaccaa caaagaaacc cccaaggctc 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

atctcgtacc cccaccttga aatgagatgt gttgagaaga tgtactacgg tcaggttgct cctgacgtag ttaaagctgt catgggagat gcgtacgggt 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

ttgtagatcc acgtacccgt gtcaagcgtc tgttgtcgat gtggtcaccc gatgcagtcg gagccacatg cgatacagtg tgttttgaca gtaccatcac 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

acccgaggat atcatggtgg agacagacat ctactcagca gctaaactca gtgaccaaca ccgagctggc attcacacca ttgcgaggca gttatacgct 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

ggaggaccga tgatcgctta tgatggccga gagatcggat atcgtaggtg taggtcttcc ggcgtctata ctacctcaag ttccaacagt ttgacctgct 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ggctgaaggt aaatgctgca gccgaacagg ctggcatgaa gaaccctcgc ttccttattt gcggcgatga ttgcaccgta atttggaaaa gcgccggagc 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

agatgcagac aaacaagcaa tgcgtgtctt tgctagctgg atgaaggtga tgggtgcacc acaagattgt gtgcctcaac ccaaatacag tttggaagaa 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

ttaacatcat gctcatcaaa tgttacctct ggaattacca aaagtggcaa gccttactac tttcttacaa gagatcctcg tatccccctt ggcaggtgct 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

ctgccgaggg tctgggatac aaccccagtg ctgcgtggat tgggtatcta atacatcact acccatgttt gtgggttagc cgtgtgttgg ctgtccattt 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

catggagcag atgctctttg aggacaaact tcccgagact gtgacctttg actggtatgg gaaaaattat acggtgcctg tagaagatct gcccagcatc 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

attgctggtg tgcacggtat tgaggctttc tcggtggtgc gctacaccaa cgctgagatc ctcagagttt cccaatcact aacagacatg accatgcccc 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

ccctgcgagc ctggcgaaag aaagccaggg cggtcctcgc cagcgccaag aggcgtggcg gagcacacgc aaaattggct cgcttccttc tctggcatgc 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

tacatctaga cctctaccag atttggataa gacgagcgtg gctcggtaca ccactttcaa ttattgtgat gtttactccc cggaggggga tgtgtttgtt 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

acaccacaga gaagattgca gaagtttctt gtgaagtatt tggctgtcat tgtttttgcc ctagggctca ttgctgttgg attagccatc agctgaaccc 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

ccaaattcaa aattaactaa cagttttttt tttttttttt ttttagggca gcggcaacag gggagacccc gggcttaacg accccgccga tgtgagtttg 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

gcgaccatgg tggatcagaa ccgtttcggg tgaagccatg gtctgaaggg gatgacgtcc cttctggctc atccacaaaa accgtctcgg gtgggtgagg 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

agtcctggct gtgtgggaag cagtcagtat aattcccgtc gtgtgtggtg acgcctcacg acgtacttgt ccgctgtgca gagcgtagta ccaagggctg 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

caccccggtt tttgttccaa gcggagggca acccccgctt ggaattaaaa acttgaagag cctcgaggaa aaatcagtag aaatagctgt tccagtcttt 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

ctagccttga ttccacttct gtcagatgtg ccctagtcag cggagacctt ttggttttgg gagagtagcg acactcccag ttgttcttca gacacttggc 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

gcacttcggt ttttctttgg agcacttgag ctttttaagt cggcaaatat cgcatgcttg ttcgatagaa gacagtagct tcatctttca ggaggcttgc 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

ttcaagcttg gagttgattg tatgcttggt atagcttgaa atattgtgca gaaaaagaaa caaggaagaa agggaacgag aacaatgacg aggaaacaaa 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

agattaataa ttgcaggtct atttatactt gatagcaaag cggcaaactt tttttatttc aaattcaagt aactggaagg aaggccgtat accgttgctc 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

attagagagt agtgtgcgtg aatgaaggaa ggaaaaagtt tcgtgtgttc gaagataccc ctcatcagct ctggaacaac gacatctgtt ggtgctgtct 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

ttgtcgttaa ttttttcctt tagtgtcttc catcattttt tttgtcattg cggatatggt gagacaacaa cgggggagag agaaaagaaa aaaaaagaaa 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

agaagttgca tgcaagcaac gaagcatctg tgcttcattt tgtagaacaa aaatgcaacg cgagagcgct aatttttcaa acaaagaatc tgagctgcat 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

ttttacagaa cagaaatgca acgcgaaagc gctattttac caacgaagaa tctgtgcttc atttttgtaa aacaaaaatg caacgcgaga gcgctaattt 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

ttcaaacaaa gaatctgagc tgcattttta cagaacagaa atgcaacgcg agagcgctat tttaccaaca aagaatctat acttcttttt tgttctacaa 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

aaatgcatcc cgagagcgct atttttctaa caaagcatct tagattactt tttttctcct ttgtgcgctc tataatgcag tctcttgata actttttgca 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

ctgtaggtcc gttaaggtta gaagaaggct actttggtgt ctattttctc ttccataaaa aaagcctgac tccacttccc gcgtttactg attactagcg 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

aagctgcggg tgcatttttt caagataaag gcatccccga ttatattcta taccgatgtg gattgcgcat actttgtgaa cagaaagtga tagcgttgat 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

gattcttcat tggtcagaaa attatgaacg gtttcttcta ttttgtctct atatactacg tataggaaat gtttacattt tcgtattgtt ttcgattcac 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

tctatgaata gttcttacta caattttttt gtctaaagag taatactaga gataaacata aaaaatgtag aggtcgagtt tagatgcaag ttcaaggagc 
^9401      ^9411      ^9421      ^9431      ^9441      ^9451      ^9461      ^9471      ^9481      ^9491      

gaaaggtgga tgggtaggtt atatagggat atagcacaga gatatatagc aaagagatac ttttgagcaa tgtttgtgga agcggtattc gcaatatttt 
^9501      ^9511      ^9521      ^9531      ^9541      ^9551      ^9561      ^9571      ^9581      ^9591      

agtagctcgt tacagtccgg tgcgtttttg gttttttgaa agtgcgtctt cagagcgctt ttggttttca aaagcgctct gaagttccta tactttctag 
^9601      ^9611      ^9621      ^9631      ^9641      ^9651      ^9661      ^9671      ^9681      ^9691      

ctagagaata ggaacttcgg aataggaact tcaaagcgtt tccgaaaacg agcgcttccg aaaatgcaac gcgagctgcg cacatacagc tcactgttca 
^9701      ^9711      ^9721      ^9731      ^9741      ^9751      ^9761      ^9771      ^9781      ^9791      

cgtcgcacct atatctgcgt gttgcctgta tatatatata catgagaaga acggcatagt gcgtgtttat gcttaaatgc gttatggtgc actctcagta 
^9801      ^9811      ^9821      ^9831      ^9841      ^9851      ^9861      ^9871      ^9881      ^9891      

caatctgctc tgatgccgca tagttaagcc agccccgaca cccgccaaca cccgctgacg cgccctgacg ggcttgtctg ctcccggcat ccgcttacag 
^9901      ^9911      ^9921      ^9931      ^9941      ^9951      ^9961      ^9971      ^9981      ^9991      

acaagctgtg accgtctccg ggagctgcat gtgtcagagg ttttcaccgt catcaccgaa acgcgcgaga cgaaagggcc tcgtgatacg cctattttta 
^10001     ^10011     ^10021     ^10031     ^10041     ^10051     ^10061     ^10071     ^10081     ^10091     

taggttaatg tcatgataat aatggtttct tagacgtcag gtggcacttt tcggggaaat gtgcgcggaa cccctatttg tttatttttc taaatacatt 
^10101     ^10111     ^10121     ^10131     ^10141     ^10151     ^10161     ^10171     ^10181     ^10191     

caaatatgta tccgctcatg agacaataac cctgataaat gcttcaataa tattgaaaaa ggaagagtat gagtattcaa catttccgtg tcgcccttat 
^10201     ^10211     ^10221     ^10231     ^10241     ^10251     ^10261     ^10271     ^10281     ^10291     

tccctttttt gcggcatttt gccttcctgt ttttgctcac ccagaaacgc tggtgaaagt aaaagatgct gaagatcagt tgggtgcacg agtgggttac 
^10301     ^10311     ^10321     ^10331     ^10341     ^10351     ^10361     ^10371     ^10381     ^10391     

atcgaactgg atctcaacag cggtaagatc cttgagagtt ttcgccccga agaacgtttt ccaatgatga gcacttttaa agttctgcta tgtggcgcgg 
^10401     ^10411     ^10421     ^10431     ^10441     ^10451     ^10461     ^10471     ^10481     ^10491     

tattatcccg tattgacgcc gggcaagagc aactcggtcg ccgcatacac tattctcaga atgacttggt tgagtactca ccagtcacag aaaagcatct 
^10501     ^10511     ^10521     ^10531     ^10541     ^10551     ^10561     ^10571     ^10581     ^10591     

tacggatggc atgacagtaa gagaattatg cagtgctgcc ataaccatga gtgataacac tgcggccaac ttacttctga caacgatcgg aggaccgaag 
^10601     ^10611     ^10621     ^10631     ^10641     ^10651     ^10661     ^10671     ^10681     ^10691     

gagctaaccg cttttttgca caacatgggg gatcatgtaa ctcgccttga tcgttgggaa ccggagctga atgaagccat accaaacgac gagcgtgaca 
^10701     ^10711     ^10721     ^10731     ^10741     ^10751     ^10761     ^10771     ^10781     ^10791     

ccacgatgcc tgtagcaatg gcaacaacgt tgcgcaaact attaactggc gaactactta ctctagcttc ccggcaacaa ttaatagact ggatggaggc 
^10801     ^10811     ^10821     ^10831     ^10841     ^10851     ^10861     ^10871     ^10881     ^10891     

ggataaagtt gcaggaccac ttctgcgctc ggcccttccg gctggctggt ttattgctga taaatctgga gccggtgagc gtgggtctcg cggtatcatt 
^10901     ^10911     ^10921     ^10931     ^10941     ^10951     ^10961     ^10971     ^10981     ^10991     

gcagcactgg ggccagatgg taagccctcc cgtatcgtag ttatctacac gacggggagt caggcaacta tggatgaacg aaatagacag atcgctgaga 
^11001     ^11011     ^11021     ^11031     ^11041     ^11051     ^11061     ^11071     ^11081     ^11091     

taggtgcctc actgattaag cattggtaac tgtcagacca agtttactca tatatacttt agattgattt aaaacttcat ttttaattta aaaggatcta 
^11101     ^11111     ^11121     ^11131     ^11141     ^11151     ^11161     ^11171     ^11181     ^11191     

ggtgaagatc ctttttgata atctcatgac caaaatccct taacgtgagt tttcgttcca ctgagcgtca gaccccgtag aaaagatcaa aggatcttct 
^11201     ^11211     ^11221     ^11231     ^11241     ^11251     ^11261     ^11271     ^11281     ^11291     

tgagatcctt tttttctgcg cgtaatctgc tgcttgcaaa caaaaaaacc accgctacca gcggtggttt gtttgccgga tcaagagcta ccaactcttt 
^11301     ^11311     ^11321     ^11331     ^11341     ^11351     ^11361     ^11371     ^11381     ^11391     

ttccgaaggt aactggcttc agcagagcgc agataccaaa tactgtcctt ctagtgtagc cgtagttagg ccaccacttc aagaactctg tagcaccgcc 
^11401     ^11411     ^11421     ^11431     ^11441     ^11451     ^11461     ^11471     ^11481     ^11491     

tacatacctc gctctgctaa tcctgttacc agtggctgct gccagtggcg ataagtcgtg tcttaccggg ttggactcaa gacgatagtt accggataag 
^11501     ^11511     ^11521     ^11531     ^11541     ^11551     ^11561     ^11571     ^11581     ^11591     

gcgcagcggt cgggctgaac ggggggttcg tgcacacagc ccagcttgga gcgaacgacc tacaccgaac tgagatacct acagcgtgag ctatgagaaa 
^11601     ^11611     ^11621     ^11631     ^11641     ^11651     ^11661     ^11671     ^11681     ^11691     

gcgccacgct tcccgaaggg agaaaggcgg acaggtatcc ggtaagcggc agggtcggaa caggagagcg cacgagggag cttccagggg gaaacgcctg 
^11701     ^11711     ^11721     ^11731     ^11741     ^11751     ^11761     ^11771     ^11781     ^11791     

gtatctttat agtcctgtcg ggtttcgcca cctctgactt gagcgtcgat ttttgtgatg ctcgtcaggg gggcggagcc tatggaaaaa cgccagcaac 
^11801     ^11811     ^11821     ^11831     ^11841     ^11851     ^11861     ^11871     ^11881     ^11891     

gcggcctttt tacggttcct ggccttttgc tggccttttg ctcacatgtt ctttcctgcg ttatcccctg attctgtgga taaccgtatt accgcctttg 
^11901     ^11911     ^11921     ^11931     ^11941     ^11951     ^11961     ^11971     ^11981     ^11991     

agtgagctga taccgctcgc cgcagccgaa cgaccgagcg cagcgagtca gtgagcgagg aagcggaaga gcgcccaata cgcaaaccgc ctctccccgc 
^12001     ^12011     ^12021     ^12031     ^12041     ^12051     ^12061     ^12071     ^12081     ^12091     

gcgttggccg attcattaat ccagctggca cgacaggttt cccgactgga aagcgggcag tgagcgcaac gcaattaatg tgagttacct cactcattag 
^12101     ^12111     ^12121     ^12131     ^12141     ^12151     ^12161     ^12171     ^12181     ^12191     

gcaccccagg ctttacactt tatgcttccg gctcgtatgt tgtgtggaat tgtgagcgga taacaatttc acacaggaaa cagctatgac catgattacg 
^12201     ^12211     ^12221     ^12231     ^12241     ^12251     ^12261     ^12271     ^12281     ^12291     

aattaattcg gtcgaaaaaa gaaaaggaga gggccaagag ggagggcatt ggtgactatt gagcacgtga gtatacgtga ttaagcacac aaaggcagct 
^12301     ^12311     ^12321     ^12331     ^12341     ^12351     ^12361     ^12371     ^12381     ^12391     

tggagtatgt ctgttattaa tttcacaggt agttctggtc cattggtgaa agtttgcggc ttgcagagca cagaggccgc agaatgtgct ctagattccg 
^12401     ^12411     ^12421     ^12431     ^12441     ^12451     ^12461     ^12471     ^12481     ^12491     

atgctgactt gctgggtatt atatgtgtgc ccaatagaaa gagaacaatt gacccggtta ttgcaaggaa aatttcaagt cttgtaaaag catataaaaa 
^12501     ^12511     ^12521     ^12531     ^12541     ^12551     ^12561     ^12571     ^12581     ^12591     

tagttcaggc actccgaaat acttggttgg cgtgtttcgt aatcaaccta aggaggatgt tttggctctg gtcaatgatt acggcattga tatcgtccaa 
^12601     ^12611     ^12621     ^12631     ^12641     ^12651     ^12661     ^12671     ^12681     ^12691     

ctgcatggag atgagtcgtg gcaagaatac caagagttcc tcggtttgcc agttattaaa agactcgtat ttccaaaaga ctgcaacata ctactcagtg 
^12701     ^12711     ^12721     ^12731     ^12741     ^12751     ^12761     ^12771     ^12781     ^12791     

cagcttcaca gaaacctcat tcgtttattc ccttgtttga ttcagaagca ggtgggacag gtgaactttt ggattggaac tcgatttctg actgggttgg 
^12801     ^12811     ^12821     ^12831     ^12841     ^12851     ^12861     ^12871     ^12881     ^12891     

aaggcaagag agccccgaaa gcttacattt tatgttagct ggtggactga cgccagaaaa tgttggtgat gcgcttagat taaatggcgt tattggtgtt 
^12901     ^12911     ^12921     ^12931     ^12941     ^12951     ^12961     ^12971     ^12981     ^12991     

gatgtaagcg gaggtgtgga gacaaatggt gtaaaagact ctaacaaaat agcaaatttc gtcaaaaatg ctaagaaata ggttattact gagtagtatt 
^13001     ^13011     ^13021     ^13031     ^13041     ^13051     ^13061     ^13071     ^13081     ^13091     

tatttaagta ttgtttgtgc acttgccggc atgccggtag aggtgtggtc aataagagcg acctcatgct atacctgaga aagcaacctg acctacagga 
^13101     ^13111     ^13121     ^13131     ^13141     ^13151     ^13161     ^13171     ^13181     ^13191     

aagagttact caagaacaag aattttcgtt ttaaaaccta agagtcactt taaaatttgt atacacttat tttttttata acttatttaa taataaaaat 
^13201     ^13211     ^13221     ^13231     ^13241     ^13251     ^13261     ^13271     ^13281     ^13291     

cataaatcat aagaaattcg cccggaatta gcttggctgc aggtcgac
^13301     ^13311     ^13321     ^13331     ^13341

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:
aph

The description of the protein encoded in this ORF:
aminoglycoside-3'-O-phosphotransferase

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):

447-1274

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):

1894-7671

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: `defective`

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

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

The translation experiments:

Translation results:

IRESite Translation Id: 397

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

The translation method used to study IRES function:
in vitro The in vitro translation system:
rabbit reticulocytes lysate

The organism used for translation:

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

35.000

Name of IRES used as the positive control:

GBV-B

Name of the plasmid used as the positive control. `RepDNeo`
`IRESite Id` of the plasmid used as positive control. `310`
The relative translation efficiency in % of the positive control: `100.000`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_without_cap_without_polyA_tail

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