IRESite_Id:54 summary record describing characteristics of GBV-B IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `54`	Version: `10`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-09-21 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2007-05-15 00:00:00`

IRESite record type:

natural_transcript

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

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
13162187

The mRNA/+RNA description:

Hepatitis GB virus B genomic RNA.

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

ACCACAAACA CTCCAGTTTG TTACACTCCG CTAGGAATGC TCCTGGAGCA CCCCCCCTAG CAGGGCGTGG GGGATTTCCC CTGCCCGTCT GCAGAAGGGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GGAGCCAACC ACCTTAGTAT GTAGGCGGCG GGACTCATGA CGCTCGCGTG ATGACAAGCG CCAAGCTTGA CTTGGATGGC CCTGATGGGC GTTCATGGGT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCGGTGGTGG TGGCGCTTTA GGCAGCCTCC ACGCCCACCA CCTCCCAGAT AGAGCGGCGG CACTGTAGGG AAGACCGGGG ACCGGTCACT ACCAAGGACG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CAGACCTCTT TTTGAGTATC ACGCCTCCGG AAGTAGTTGG GCAAGCCCAC CTATATGTGT TGGGATGGTT GGGGTTAGCC ATCCATACCG TACTGCCTGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TAGGGTCCTT GCGAGGGGAT CTGGGAGTCT CGTAGACCGT AGCACATGCC TGTTATTTCT ACTCAAACAA GTCCTGTACC TGCGCCCAGA ACGCGCAAGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACAAGCAGAC GCAGGCTTCA TATCCTGTGT CCATTAAAAC ATCTGTTGAA AGGGGACAAC GAGCAAAGCG CAAAGTCCAG CGCGATGCTC GGCCTCGTAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTACAAAATT GCTGGTATCC ATGATGGCTT GCAGACATTG GCTCAGGCTG CTTTGCCAGC TCATGGTTGG GGACGCCAAG ACCCTCGCCA TAAGTCTCGC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AATCTTGGAA TCCTTCTGGA TTACCCTTTG GGGTGGATTG GTGATGTTAC AACTCACACA CCTCTAGTAG GCCCGCTGGT GGCAGGAGCG GTCGTTCGAC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CAGTCTGCCA GATAGTACGC TTGCTGGAGG ATGGAGTCAA CTGGGCTACT GGTTGGTTCG GTGTCCACCT TTTTGTGGTA TGTCTGCTAT CTTTGGCCTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCCCTGTAGT GGGGCGCGGG TCACTGACCC AGACACAAAT ACCACAATCC TGACCAATTG CTGCCAGCGT AATCAGGTTA TCTATTGTTC TCCTTCCACT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGTCTACACG AGCCTGGTTG TGTGATCTGT GCGGACGAGT GCTGGGTTCC CGCCAATCCG TACATCTCAC ACCCTTCCAA TTGGACTGGC ACGGACTCCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCTTGGCTGA CCACATTGAT TTTGTTATGG GCGCTCTTGT GACCTGTGAC GCCCTTGACA TTGGTGAGTT GTGTGGTGCG TGTGTATTAG TCGGTGACTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GCTTGTCAGG CACTGGCTTA TTCACATAGA CCTCAATGAA ACTGGTACTT GTTACCTGGA AGTGCCCACT GGAATAGATC CTGGGTTCCT AGGGTTTATC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGGTGGATGG CCGGCAAGGT CGAGGCTGTC ATCTTCTTGA CCAAACTGGC TTCACAAGTA CCATACGCTA TTGCGACTAT GTTTAGCAGT GTACACTACC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGGCGGTTGG CGCTCTGATC TACTATGCCT CTCGGGGCAA GTGGTATCAG TTGCTCCTAG CGCTTATGCT TTACATAGAA GCGACCTCTG GAAACCCCAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CAGGGTGCCC ACTGGATGCT CAATAGCTGA GTTTTGCTCG CCTTTGATGA TACCATGTCC TTGCCACTCT TATTTGAGTG AGAATGTGTC AGAAGTCATT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TGTTACAGTC CAAAGTGGAC CAGGCCTGTC ACTCTAGAGT ATAACAACTC CATATCTTGG TACCCCTATA CAATCCCTGG TGCGAGGGGA TGTATGGTTA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AATTCAAAAA TAACACATGG GGTTGTTGCC GTATTCGCAA TGTGCCATCG TACTGCACTA TGGGCACTGA TGCAGTGTGG AACGACACTC GCAACACTTA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CGAAGCATGC GGTGTAACAC CATGGCTAAC AACCGCATGG CACAACGGCT CAGCCCTGAA ATTGGCTATA TTACAATACC CTGGGTCTAA AGAAATGTTT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AAACCTCATA ATTGGATGTC AGGCCATTTG TATTTTGAGG GATCAGATAC CCCTATAGTT TACTTTTATG ACCCTGTGAA TTCCACTCTC CTACCACCGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGAGGTGGGC TAGGTTGCCC GGTACCCCAC CTGTGGTACG TGGTTCTTGG TTACAGGTTC CGCAAGGGTT TTACAGTGAT GTGAAAGACC TAGCCACAGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ATTGATCACC AAAGACAAAG CCTGGAAAAA TTATCAGGTC TTATATTCCG CCACGGGTGC TTTGTCTCTT ACGGGAGTTA CCACCAAGGC CGTGGTGCTA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATTCTGTTGG GGTTGTGTGG CAGCAAGTAT CTTATTTTAG CCTACCTCTG TTACTTGTCC CTTTGTTTTG GGCGCGCTTC TGGTTACCCT TTGCGTCCTG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TGCTCCCATC CCAGTCGTAT CTCCAAGCTG GCTGGGATGT TTTGTCTAAA GCTCAAGTAG CTCCTTTTGC TTTGATTTTC TTCATCTGTT GCTATCTCCG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CTGCAGGCTA CGTTATGCTG CCCTTTTAGG GTTTGTGCCC ATGGCTGCGG GCTTGCCCCT AACTTTCTTT GTTGCAGCAG CTGCTGCCCA ACCAGATTAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GACTGGTGGG TGCGACTGCT AGTGGCAGGG TTAGTTTTGT GGGCCGGCCG TGACCGTGGT CACCGCATAG CTCTGCTTGT AGGTCCTTGG CCTCTGGTAG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGCTTTTAAC CCTCTTGCAT TTGGTTACGC CTGCTTCAGC TTTTGACACC GAGATAATTG GAGGGCTGAC AATACCACCT GTAGTAGCAT TAGTTGTCAT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GTCTCGTTTT GGCTTCTTTG CTCACTTGTT ACCTCGCTGT GCTTTAGTTA ACTCCTATCT TTGGCAACGT TGGGAGAATT GGTTTTGGAA CGTTACACTA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AGACCGGAGA GGTTTTTTCT TGTGCTGGTT TGTTTCCCCG GTGCGACATA TGACGCGCTG GTGACTTTCT GTGTGTGTCA CGTAGCTCTC CTATGTTTAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CATCCAGTGC AGCATCGTTC TTTGGGACTG ACTCTAGGGT TAGGGCCCAT AGAATGTTGG TGCGTCTCGG AAAGTGCCAT GCTTGGTATT CTCATTATGT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TCTTAAGTTT TTCCTCTTAG TGTTTGGTGA GAATGGTGTG TTTTTCTATA AGCACTTGCA TGGTGATGTC TTGCCTAATG ATTTTGCCTC GAAACTACCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TTGCAAGAGC CATTTTTCCC TTTTGAAGGC AAGGCAAGGG TCTATAGGAA TGAAGGAAGA CGCTTGGCGT GTGGGGACAC GGTTGATGGT TTGCCCGTTG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTGCGCGTCT CGGCGACCTT GTTTTCGCAG GGTTAGCTAT GCCGCCAGAT GGGTGGGCCA TTACCGCACC TTTTACGCTG CAGTGTCTCT CTGAACGTGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CACGCTGTCA GCGATGGCAG TGGTCATGAC TGGTATAGAC CCCCGAACTT GGACTGGAAC TATCTTCAGA TTAGGATCTC TGGCCACTAG CTACATGGGA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TTTGTTTGTG ACAACGTGTT GTATACTGCT CACCATGGCA GCAAGGGGCG CCGGTTGGCT CATCCCACAG GCTCCATACA CCCAATAACC GTTGACGCGG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CTAATGACCA GGACATCTAT CAACCACCAT GTGGAGCTGG GTCCCTTACT CGGTGCTCTT GCGGGGAGAC CAAGGGGTAT CTGGTAACAC GACTGGGGTC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ATTGGTTGAG GTCAATAAAT CCGATGACCC TTATTGGTGT GTGTGCGGGG CCCTTCCCAT GGCTGTTGCC AAGGGTTCTT CAGGTGCCCC GATTCTGTGC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TCCTCCGGGC ATGTTATTGG GATGTTCACC GCTGCTAGAA ATTCTGGCGG TTCAGTCAGC CAGATTAGGG TTAGGCCGTT GGTGTGTGCT GGATACCATC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CCCAGTACAC AGCACATGCC ACTCTTGATA CAAAACCTAC TGTGCCTAAC GAGTATTCAG TGCAAATTTT AATTGCCCCC ACTGGCAGCG GCAAGTCAAC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CAAATTACCA CTTTCTTACA TGCAGGAGAA GTATGAGGTC TTGGTCCTAA ATCCCAGTGT GGCTACAACA GCATCAATGC CAAAGTACAT GCACGCGACG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TACGGCGTGA ATCCAAATTG CTATTTTAAT GGCAAATGTA CCAACACAGG GGCTTCACTT ACGTACAGCA CATATGGCAT GTACCTGACC GGAGCATGTT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CCCGGAACTA TGATGTAATC ATTTGTGACG AATGCCATGC TACCGATGCA ACCACCGTGT TGGGCATTGG AAAGGTCCTA ACCGAAGCTC CATCCAAAAA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TGTTAGGCTA GTGGTTCTTG CCACGGCTAC CCCCCCTGGA GTAATCCCTA CACCACATGC CAACATAACT GAGATTCAAT TAACCGATGA AGGCACTATC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CCCTTTCATG GAAAAAAGAT TAAGGAGGAA AATCTGAAGA AAGGGAGACA CCTTATCTTT GAGGCTACCA AAAAACACTG TGATGAGCTT GCTAACGAGT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TAGCTCGAAA GGGAATAACA GCTGTCTCTT ACTATAGGGG ATGTGACATC TCAAAAATCC CTGAGGGCGA CTGTGTAGTA GTTGCCACTG ATGCCTTGTG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TACAGGGTAC ACTGGTGACT TTGATTCCGT GTATGACTGC AGCCTCATGG TAGAAGGCAC ATGCCATGTT GACCTTGACC CTACTTTCAC CATGGGTGTT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CGTGTGTGCG GGGTTTCAGC AATAGTTAAA GGCCAGCGTA GGGGCCGCAC AGGCCGTGGG AGAGCTGGCA TATACTACTA TGTAGACGGG AGTTGTACCC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTTCGGGTAT GGTTCCTGAA TGCAACATTG TTGAAGCCTT CGACGCAGCC AAGGCATGGT ATGGTTTGTC ATCAACAGAA GCTCAAACTA TTCTGGACAC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CTATCGCACC CAACCTGGGT TACCTGCGAT AGGAGCAAAT TTGGACGAGT GGGCTGATCT CTTTTCAATG GTCAACCCCG AACCTTCATT TGTCAATACT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GCAAAAAGAA CTGCTGACAA TTATGTTTTG TTGACTGCAG CCCAACTACA ACTGTGTCAT CAGTATGGCT ATGCTGCTCC CAATGACGCA CCACGGTGGC 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AGGGAGCCCG GCTTGGGAAA AAACCTTGTG GGGTTCTGTG GCGCTTGGAC GGCGCTGACG CCTGTCCTGG CCCAGAGCCC AGCGAGGTGA CCAGATACCA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

AATGTGCTTC ACTGAAGTCA ATACTTCTGG GACAGCCGCA CTCGCTGTTG GCGTTGGAGT GGCTATGGCT TATCTAGCCA TTGACACTTT TGGCGCCACT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TGTGTGCGGC GTTGCTGGTC TATTACATCA GTCCCTACCG GTGCTACTGT CGCCCCAGTG GTTGACGAAG AAGAAATCGT GGAGGAGTGT GCATCATTCA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TTCCCTTGGA GGCCATGGTT GCTGCAATTG ACAAGCTGAA GAGTACAATC ACCACAACTA GTCCTTTCAC ATTGGAAACC GCCCTTGAAA AACTTAACAC 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CTTTCTTGGG CCTCATGCAG CTACAATCCT TGCTATCATA GAGTATTGCT GTGGCTTAGT CACTTTACCT GACAATCCCT TTGCATCATG CGTGTTTGCT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TTCATTGCGG GTATTACTAC CCCACTACCT CACAAGATCA AAATGTTCCT GTCATTATTT GGAGGCGCAA TTGCGTCCAA GCTTACAGAC GCTAGAGGCG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CACTGGCGTT CATGATGGCC GGGGCTGCGG GAACAGCTCT TGGTACATGG ACATCGGTGG GTTTTGTCTT TGACATGCTA GGCGGCTATG CTGCCGCCTC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ATCCACTGCT TGCTTGACAT TTAAATGCTT GATGGGTGAG TGGCCCACTA TGGATCAGCT TGCTGGTTTA GTCTACTCCG CGTTCAACCC GGCCGCAGGA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GTTGTGGGCG TTTTGTCAGC TTGTGCAATG TTTGCTTTGA CAACAGCAGG GCCAGATCAC TGGCCCAACA GACTTCTTAC TATGCTTGCT AGGAGCAACA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CTGTATGTAA TGAGTACTTT ATTGCCACTC GTGACATCCG CAGGAAGATA CTGGGCATTC TGGAGGCATC TACCCCCTGG AGTGTCATAT CAGCTTGCAT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CCGTTGGCTC CACACCCCGA CGGAGGATGA TTGCGGCCTC ATTGCTTGGG GTCTAGAGAT TTGGCAGTAC GTGTGCAATT TCTTTGTGAT TTGCTTTAAT 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GTCCTTAAAG CTGGAGTTCA GAGCATGGTT AACATTCCTG GTTGTCCTTT CTACAGCTGC CAGAAGGGGT ACAAGGGCCC CTGGATTGGA TCAGGTATGC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TCCAAGCACG CTGTCCATGC GGTGCTGAAC TCATCTTTTC TGTTGAGAAT GGTTTTGCAA AACTTTACAA AGGACCCAGA ACTTGTTCAA ATTACTGGAG 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

AGGGGCTGTT CCAGTCAACG CTAGGCTGTG TGGGTCGGCT AGACCGGACC CAACTGATTG GACTAGTCTT GTCGTCAATT ATGGCGTTAG GGACTACTGT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AAATATGAGA AATTGGGAGA TCACATCTTT GTTACAGCAG TATCCTCTCC AAATGTCTGT TTCACCCAGG TGCCCCCAAC CTTGAGAGCT GCAGTGGCCG 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TGGACGGCGT ACAGGTTCAG TGTTATCTAG GTGAGCCCAA AACTCCTTGG ACGACATCTG CTTGCTGTTA CGGTCCTGAC GGTAAGGGTA AAACTGTTAA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GCTTCCCTTC CGCGTTGACG GTCACACACC TGGTGTGCGC ATGCAACTTA ATTTGCGTGA TGCACTTGAG ACAAATGACT GTAATTCCAC AAACAACACT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CCTAGTGATG AAGCCGCAGT GTCCGCTCTT GTTTTCAAAC AGGAGTTGCG GCGTACAAAC CAATTGCTTG AGGCAATTTC AGCTGGCGTT GACACCACCA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

AACTGCCAGC CCCCTCCATC GAAGAGGTAG TGGTAAGAAA GCGCCAGTTC CGGGCAAGAA CTGGTTCGCT TACCTTGCCC CCCCCTCCGA GATCCGTCCC 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

AGGAGTGTCA TGTCCTGAAA GCCTGCAACG AAGTGACCCG TTAGAAGGTC CTTCAAACCT CCCTCCTTCA CCACCTGTTC TACAGTTGGC CATGCCGATG 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CCCCTGTTGG GAGCGGGTGA GTGTAACCCT TTCACTGCAA TTGGATGTGC AATGACCGAA ACAGGCGGAG GCCCTGATGA TTTACCCAGT TACCCTCCCA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

AAAAGGAGGT CTCTGAATGG TCAGACGAAA GTTGGTCAAC GGCTACAACC GCTTCCAGCT ACGTTACTGG CCCCCCGTAC CCTAAGATAC GGGGAAAGGA 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TTCCACTCAG TCAGCCCCCG CCAAACGGCC TACAAAAAAG AAGTTGGGAA AGAGTGAGTT TTCGTGCAGC ATGAGCTACA CTTGGACCGA CGTGATTAGC 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

TTCAAAACTG CTTCTAAAGT TCTGTCTGCA ACTCGGGCCA TCACTAGTGG TTTCCTCAAA CAAAGATCAT TGGTGTATGT GACTGAGCCG CGGGATGCGG 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

AGCTTAGAAA ACAAAAAGTC ACTATTAATA GACAACCTCT GTTCCCCCCA TCATACCACA AGCAAGTGAG ATTGGCTAAG GAGAAAGCTT CAAAAGTTGT 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

CGGTGTCATG TGGGACTATG ATGAAGTAGC AGCTCACACG CCCTCTAAGT CTGCTAAGTC CCACATCACT GGCCTTCGGG GCACTGATGT TCGTTCTGGA 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

GCAGCCCGCA AGGCTGTTCT GGACTTGCAG AAGTGTGTCG AGGCAGGTGA GATACCGAGT CATTATCGGC AAACAGTGAT AGTTCCAAAG GAGGAGGTCT 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

TCGTGAAGAC CCCCCAGAAA CCAACAAAGA AACCCCCAAG GCTCATCTCG TACCCCCACC TTGAAATGAG ATGTGTTGAG AAGATGTACT ACGGTCAGGT 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TGCTCCTGAC GTAGTTAAAG CTGTCATGGG AGATGCGTAC GGGTTTGTAG ATCCACGTAC CCGTGTCAAG CGTCTGTTGT CGATGTGGTC ACCCGATGCA 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

GTCGGAGCCA CATGCGATAC AGTGTGTTTT GACAGTACCA TCACACCCGA GGATATCATG GTGGAGACAG ACATCTACTC AGCAGCTAAA CTCAGTGACC 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

AACACCGAGC TGGCATTCAC ACCATTGCGA GGCAGTTATA CGCTGGAGGA CCGATGATCG CTTATGATGG CCGAGAGATC GGATATCGTA GGTGTAGGTC 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

TTCCGGCGTC TATACTACCT CAAGTTCCAA CAGTTTGACC TGCTGGCTGA AGGTAAATGC TGCAGCCGAA CAGGCTGGCA TGAAGAACCC TCGCTTCCTT 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

ATTTGCGGCG ATGATTGCAC CGTAATTTGG AAAAGCGCCG GAGCAGATGC AGACAAACAA GCAATGCGTG TCTTTGCTAG CTGGATGAAG GTGATGGGTG 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

CACCACAAGA TTGTGTGCCT CAACCCAAAT ACAGTTTGGA AGAATTAACA TCATGCTCAT CAAATGTTAC CTCTGGAATT ACCAAAAGTG GCAAGCCTTA 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

CTACTTTCTT ACAAGAGATC CTCGTATCCC CCTTGGCAGG TGCTCTGCCG AGGGTCTGGG ATACAACCCC AGTGCTGCGT GGATTGGGTA TCTAATACAT 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

CACTACCCAT GTTTGTGGGT TAGCCGTGTG TTGGCTGTCC ATTTCATGGA GCAGATGCTC TTTGAGGACA AACTTCCCGA GACTGTGACC TTTGACTGGT 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

ATGGGAAAAA TTATACGGTG CCTGTAGAAG ATCTGCCCAG CATCATTGCT GGTGTGCACG GTATTGAGGC TTTCTCGGTG GTGCGCTACA CCAACGCTGA 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

GATCCTCAGA GTTTCCCAAT CACTAACAGA CATGACCATG CCCCCCCTGC GAGCCTGGCG AAAGAAAGCC AGGGCGGTCC TCGCCAGCGC CAAGAGGCGT 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

GGCGGAGCAC ACGCAAAATT GGCTCGCTTC CTTCTCTGGC ATGCTACATC TAGACCTCTA CCAGATTTGG ATAAGACGAG CGTGGCTCGG TACACCACTT 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

TCAATTATTG TGATGTTTAC TCCCCGGAGG GGGATGTGTT TGTTACACCA CAGAGAAGAT TGCAGAAGTT TCTTGTGAAG TATTTGGCTG TCATTGTTTT 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

TGCCCTAGGG CTCATTGCTG TTGGATTAGC CATCAGCTGA ACCCCCAAAT TCAAAATTAA CTAACAGTTT TTTTTTTTTT TTTTTTTTAG GGCAGCGGCA 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

ACAGGGGAGA CCCCGGGCTT AACGACCCCG CCGATGTGAG TTTGGCGACC ATGGTGGATC AGAACCGTTT CGGGTGAAGC CATGGTCTGA AGGGGATGAC 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

GTCCCTTCTG GCTCATCCAC AAAAACCGTC TCGGGTGGGT GAGGAGTCCT GGCTGTGTGG GAAGCAGTCA GTATAATTCC CGTCGTGTGT GGTGACGCCT 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

CACGACGTAC TTGTCCGCTG TGCAGAGCGT AGTACCAAGG GCTGCACCCC GGTTTTTGTT CCAAGCGGAG GGCAACCCCC GCTTGGAATT AAAAACT
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391

Credibility of mRNA sequence:

reverse_engineered_fragment_and_the_rest_is_a_guess

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

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

A promoter reported in cDNA corresponding to IRES sequence:
not tested The total number of notable open-reading frames (ORFs):
1

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `2`	Last change: `2007-05-15 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
GBV-B

The description of the protein encoded in this ORF:
Hepatitis GB virus B 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):

446-9040

Remarks:

T7 transcripts were tested in rabbit reticulocyte lysates (RRL) and also in recombinant vaccinia infected
cells. Increasing KCl concentration in RRL decreased translation from first cistron but did not affect
translation from the second. [Grace et al., 1999]

Bicistronic T7 transcripts were tested for their integrity by electrophoresis in agarose gel and translated in
RRL. Also transiently transfected cells were used for the test of bicistronic constructs. Labourious site
directed mutagenesis was performed to disrupt some basepairs in putative stem loop structures or delete
certain loops and the resulting IRES activity was quantified. [Rijnbrand et al., 2000]

Citations:

Grace K., Gartland M., Karayiannis P., McGarvey M. J., Clarke B. (1999) The 5' untranslated region of GB virus B shows functional similarity to the internal ribosome entry site of hepatitis C virus. J. Gen. Virol. 80(Pt 9):2337-2341

Rijnbrand R., Abell G., Lemon S. M. (2000) Mutational analysis of the GB virus B internal ribosome entry site. J. Virol. 74(2):773-783

IRESs:

IRES:

Version: `10`	Last change: `2007-05-15 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `GBV-B`

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

30-445

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

GCTAGGAATG CTCCTGGAGC ACCCCCCCTA GCAGGGCGTG GGGGATTTCC CCTGCCCGTC TGCAGAAGGG TGGAGCCAAC CACCTTAGTA TGTAGGCGGC 
^30        ^40        ^50        ^60        ^70        ^80        ^90        ^100       ^110       ^120       

GGGACTCATG ACGCTCGCGT GATGACAAGC GCCAAGCTTG ACTTGGATGG CCCTGATGGG CGTTCATGGG TTCGGTGGTG GTGGCGCTTT AGGCAGCCTC 
^130       ^140       ^150       ^160       ^170       ^180       ^190       ^200       ^210       ^220       

CACGCCCACC ACCTCCCAGA TAGAGCGGCG GCACTGTAGG GAAGACCGGG GACCGGTCAC TACCAAGGAC GCAGACCTCT TTTTGAGTAT CACGCCTCCG 
^230       ^240       ^250       ^260       ^270       ^280       ^290       ^300       ^310       ^320       

GAAGTAGTTG GGCAAGCCCA CCTATATGTG TTGGGATGGT TGGGGTTAGC CATCCATACC GTACTGCCTG ATAGGGTCCT TGCGAGGGGA TCTGGGAGTC 
^330       ^340       ^350       ^360       ^370       ^380       ^390       ^400       ^410       ^420       

TCGTAGACCG TAGCAC
^430       ^440

Remarks:

Deletion of the 5' end to nt 21 had a positive effect on the IRES activity (caused increase to 140 % activity
compared with the full length UTR sequence). A further 5' truncation to nt 61 or to nt 88 caused substantial
decrease in the IRES activity (decrease to 63 % or 8 % respectively; compared with the full lenght UTR
sequence). An influence of downstream coding sequence on IRES activity has been described. [Grace et al.,
1999]
In results shown in De Tomassi et al. (2003) in Fig. 4 in vitro (RRL) translation of non-capped
non-poly(A)-tailed transcriptof NPT gene is GBV-B IRES driven (1st cistron) whereas NS3 is EMCV IRES
driven (2nd cistron). It was found that bases 4-29 of the 5'-UTR do not contribute significantly
to the IRES activity and are not necessary for replication of the virus either (a predicted stem-loop
is located between bases 5-20, shown in Fig. 3). It might be that bases 1-3 are necessary for
replication, though.

In Pizzuti et al. (2003) in Fig. 4 cB76.1/Huh7 cells were transiently transfected by non-capped and
non-poly(A) tailed RNA. It turned out if there is a longer sequence of GBV-B core protein left in
the construct right after the GBV-B IRES the immediately downstream reporter gene (1st cistron) is
translated more effectively. The RNA transcript contained mutation in the RGDD motif or RNA-dependent
RNA polymerase and therefore the presence of beta-lactamase protein could be solely attributed to the
translation (and is not affected by altered replication ability of the subgenomic replicon contained
in the RNA). From in vitro translation experiment in RRL shown in Fig. 5 it can be confirmed that
with longer sequence of the GBV-B core protein left in the efficiency of translation increases as well.

Citations:

Rijnbrand R., Abell G., Lemon S. M. (2000) Mutational analysis of the GB virus B internal ribosome entry site. J. Virol. 74(2):773-783

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

De Tomassi A., Pizzuti M., Traboni C. (2003) Hep3B human hepatoma cells support replication of the wild-type and a 5'-end deletion mutant GB virus B replicon. J. Virol. 77(22):11875-11881

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

De Tomassi A., Pizzuti M., Graziani R., Sbardellati A., Altamura S., Paonessa G., Traboni C. (2002) Cell clones selected from the Huh7 human hepatoma cell line support efficient replication of a subgenomic GB virus B replicon. J. Virol. 76(15):7736-7746

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