IRESite_Id:222 summary record describing characteristics of HCV_type

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `222`	Version: `6`
Originaly submitted by: Martin Mokrejš
Reviewed by: Václav Vopálenský	Last change: `2009-08-30 02:23:00`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `end-to-end_full-length_mRNA`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `HCV_type_1a`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
329737

The mRNA/+RNA description:

Hepatitis C virus subtype 1a, strain H, complete genome.

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

GCCAGCCCCC TGATGGGGGC GACACTCCAC CATGAATCAC TCCCCTGTGA GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGTCGTGCAG CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG CGGAACCGGT GAGTACACCG GAATTGCCAG GACGACCGGG TCCTTTCTTG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GATAAACCCG CTCAATGCCT GGAGATTTGG GCGTGCCCCC GCAAGACTGC TAGCCGAGTA GTGTTGGGTC GCGAAAGGCC TTGTGGTACT GCCTGATAGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTGCTTGCGA GTGCCCCGGG AGGTCTCGTA GACCGTGCAC CATGAGCACG AATCCTAAAC CTCAAAGAAA AACCAAACGT AACACCAACC GTCGCCCACA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GGACGTCAAG TTCCCGGGTG GCGGTCAGAT CGTTGGTGGA GTTTACTTGT TGCCGCGCAG GGGCCCTAGA TTGGGTGTGC GCGCGACGAG GAAGACTTCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GAGCGGTCGC AACCTCGAGG TAGACGTCAG CCTATCCCCA AGGCACGTCG GCCCGAGGGC AGGACCTGGG CTCAGCCCGG GTACCCTTGG CCCCTCTATG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GCAATGAGGG TTGCGGGTGG GCGGGATGGC TCCTGTCTCC CCGTGGCTCT CGGCCTAGCT GGGGCCCCAC AGACCCCCGG CGTAGGTCGC GCAATTTGGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TAAGGTCATC GATACCCTTA CGTGCGGCTT CGCCGACCTC ATGGGGTACA TACCGCTCGT CGGCGCCCCT CTTGGAGGCG CTGCCAGGGC CCTGGCGCAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GGCGTCCGGG TTCTGGAAGA CGGCGTGAAC TATGCAACAG GGAACCTTCC TGGTTGCTCT TTCTCTATCT TCCTTCTGGC CCTGCTCTCT TGCCTGACTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGCCCGCTTC AGCCTACCAA GTGCGCAATT CCTCGGGGCT TTACCATGTC ACCAATGATT GCCCTAACTC GAGTGTTGTG TACGAGGCGG CCGATGCCAT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCTGCACACT CCGGGGTGTG TCCCTTGCGT TCGCGAGGGT AACGCCTCGA GGTGTTGGGT GGCGGTGACC CCCACGGTGG CCACCAGGGA CGGCAAACTC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCCACAACGC AGCTTCGACG TCATATCGAT CTGCTTGTCG GGAGCGCCAC CCTCTGCTCG GCCCTCTACG TGGGGGACCT GTGCGGGTCT GTCTTTCTTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTGGTCAACT GTTTACCTTC TCTCCCAGGC ACCACTGGAC GACGCAAGAC TGCAATTGTT CTATCTATCC CGGCCATATA ACGGGTCATC GCATGGCATG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GAATATGATG ATGAACTGGT CCCCTACGGC AGCGTTGGTG GTAGCTCAGC TGCTCCGAAT CCCACAAGCC ATCATGGACA TGATCGCTGG CGCCCACTGG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GGAGTCCTGG CGGGCATAAA GTATTTCTCC ATGGTGGGGA ACTGGGCGAA GGTCCTGGTA GTGCTGCTGC TATTTGCCGG CGTCGACGCG GAAACCCACG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCACCGGGGG AAATGCCGGC CGCACCACGG CTGGGCTTGT TGGTCTCCTT ACACCAGGCG CCAAGCAGAA CATCCAACTG ATCAACACCA ACGGCAGTTG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCACATCAAT AGCACGGCCT TGAACTGCAA TGAAAGCCTT AACACCGGCT GGTTAGCAGG GCTCTTCTAT CAGCACAAAT TCAACTCTTC AGGCTGTCCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAGAGGTTGG CCAGCTGCCG ACGCCTTACC GATTTTGCCC AGGGCTGGGG TCCTATCAGT TATGCCAACG GAAGCGGCCT CGACGAACGC CCCTACTGCT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GGCACTACCC TCCAAGACCT TGTGGCATTG TGCCCGCAAA GAGCGTGTGT GGCCCGGTAT ATTGCTTCAC TCCCAGCCCC GTGGTGGTGG GAACGACCGA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CAGGTCGGGC GCGCCTACCT ACAGCTGGGG TGCAAATGAT ACGGATGTCT TCGTCCTTAA CAACACCAGG CCACCGCTGG GCAATTGGTT CGGTTGTACC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGGATGAACT CAACTGGATT CACCAAAGTG TGCGGAGCGC CCCCTTGTGT CATCGGAGGG GTGGGCAACA ACACCTTGCT CTGCCCCACT GATTGCTTCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCAAATATCC GGAAGCCACA TACTCTCGGT GCGGCTCCGG TCCCAGGATT ACACCCAGGT GCATGGTCGA CTACCCGTAT AGGCTTTGGC ACTATCCTTG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TACCATCAAT TACACCATAT TCAAAGTCAG GATGTACGTG GGAGGGGTCG AGCACAGGCT GGAAGCGGCC TGCAACTGGA CGCGGGGCGA ACGCTGTGAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CTGGAAGACA GGGACAGGTC CGAGCTCAGC CCGTTGCTGC TGTCCACCAC ACAGTGGCAG GTCCTTCCGT GTTCTTTCAC GACCCTGCCA GCCTTGTCCA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCGGCCTCAT CCACCTCCAC CAGAACATTG TGGACGTGCA GTACTTGTAC GGGGTAGGGT CAAGCATCGC GTCCTGGGCC ATTAAGTGGG AGTACGTCGT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TCTCCTGTTC CTTCTGCTTG CAGACGCGCG CGTCTGTTCC TGCTTGTGGA TGATGTTACT CATATCCCAA GCGGAGGCGG CTTTGGAGAA CCTCGTAATA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTCAATGCAG CATCCCTGGC CGGGACGCAT GGTCTTGTGT CCTTCCTCGT GTTCTTCTGC TTTGCGTGGT ATCTGAAGGG TAGGTGGGTG CCCGGAGCGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TCTACGCCCT CTACGGGATG TGGCCTCTCC TCCTGCTCCT GCTGGCGTTG CCTCAGCGGG CATACGCACT GGACACGGAG GTGGCCGCGT CGTGTGGCGG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CGTTGTTCTT GTCGGGTTAA TGGCGCTGAC TCTGTCGCCA TATTACAAGC GCTATATCAG CTGGTGCATG TGGTGGCTTC AGTATTTTCT GACCAGAGTA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAAGCGCAAC TGCACGTGTG GGTTCCCCCC CTCAACGTCC GGGGGGGGCG CGATGCCGTC ATCTTACTCA CGTGTGTAGT ACACCCGGCC CTGGTATTTG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ACATCACCAA ACTACTCCTG GCCATCTTCG GACCCCTTTG GATTCTTCAA GCCAGTTTGC TTAAAGTCCC CTACTTCGTG CGCGTTCAAG GCCTTCTCCG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GATCTGCGCG CTAGCGCGGA AGATAGCCGG AGGTCATTAC GTGCAAATGG CCATCATCAA GTTAGGGGCG CTTACTGGCA CCTGTGTGTA TAACCATCTC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GCTCCTCTTC GAGACTGGGC GCACAACGGC CTGCGAGATC TGGCCGTGGC TGTGGAACCA GTCGTCTTCT CCCGAATGGA GACCAAGCTC ATCACGTGGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GGGCAGATAC CGCCGCGTGC GGTGACATCA TCAACGGCTT GCCCGTCTCT GCCCGTAGGG GCCAGGAGAT ACTGCTTGGG CCAGCCGACG GAATGGTCTC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CAAGGGGTGG AGGTTGCTGG CGCCCATCAC GGCGTACGCC CAGCAGACGA GAGGCCTCCT AGGGTGTATA ATCACCAGCC TGACTGGCCG GGACAAAAAC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CAAGTGGAGG GTGAGGTCCA GATCGTGTCA ACTGCTACCC AGACCTTCCT GGCAACGTGC ATCAATGGGG TATGCTGGAC TGTCTACCAC GGGGCCGGAA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CGAGGACCAT CGCATCACCC AAGGGTCCTG TCATCCAGAC GTATACCAAT GTGGATCAAG ACCTCGTGGG CTGGCCCGCT CCTCAAGGTT CCCGCTCATT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GACACCCTGC ACCTGCGGCT CCTCGGACCT TTACCTGGTC ACGAGGCACG CCGATGTCAT TCCCGTGCGC CGGCGAGGTG ATAGCAGGGG TAGCCTGCTT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TCGCCCCGGC CCATTTCCTA CTTGAAAGGC TCCTCGGGGG GTCCGCTGTT GTGCCCCACG GGACACGCCG TGGGCCTATT CAGGGCCGCG GTGTGCACCC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GTGGAGTGGC TAAGGCGGTG GACTTTATCC CTGTGGAGAA CCTAGAGACA ACCATGAGAT CCCCGGTGTT CACGGACAAC TCCTCTCCAC CAGCAGTGCC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CCAGAGCTTC CAGGTGGCCC ACCTGCATGC TCCCACCGGC AGCGGTAAGA GCACCAAGGT CCCGGCTGCG TACGCAGCCA AGGGCTACAA GGTGTTGGTG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CTCAACCCCT CTGTTGCTGC AACACTGGGC TTTGGTGCTT ACATGTCCAA GGCCCATGGG GTTGATCCTA ATATCAGGAC CGGGGTGAGA ACAATTACCA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CTGGCAGCCC CATCACGTAC TCCACCTACG GCAAGTTCCT TGCCGACGCC GGGTGCTCAG GAGGTGCTTA TGACATAATA ATTTGTGACG AGTGCCACTC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CACGGATGCC ACATCCATCT CGGGCATCGG CACTGTCCTT GACCAAGCAG AGACTGCGGG GGCGAGACTG GTTGTGCTCG CCACTGCTAC CCCTCCGGGC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TCCGTCACTG TGTCCCATCC TAACATCGAG GAGGTTGCTC TGTCCACCAC CGGAGAGATC CCCTTTTACG GCAAGGCTAT CCCCCTCGAG GTGATCAAGG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GGGGAAGACA TCTCATCTTC TGCCACTCAA AGAAGAAGTG CGACGAGCTC GCCGCGAAGC TGGTCGCATT GGGCATCAAT GCCGTGGCCT ACTACCGCGG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TCTTGACGTG TCTGTCATCC CGACCAGCGG CGATGTTGTC GTCGTGTCGA CCGATGCTCT CATGACTGGC TTTACCGGCG ACTTCGACTC TGTGATAGAC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TGCAACACGT GTGTCACTCA GACAGTCGAT TTTAGCCTTG ACCCTACCTT TACCATTGAG ACAACCACGC TCCCCCAGGA TGCTGTCTCC AGGACTCAAC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GCCGGGGCAG GACTGGCAGG GGGAAGCCAG GCATCTATAG ATTTGTGGCA CCGGGGGAGC GCCCCTCCGG CATGTTCGAC TCGTCCGTCC TCTGTGAGTG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CTATGACGCG GGCTGTGCTT GGTATGAGCT CACGCCCGCC GAGACTACAG TTAGGCTACG AGCGTACATG AACACCCCGG GGCTTCCCGT GTGCCAGGAC 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CATCTTGGAT TTTGGGAGGG CGTCTTTACG GGCCTCACTC ATATAGATGC CCACTTTCTA TCCCAGACAA AGCAGAGTGG GGAGAACTTT CCTTACCTGG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TAGCGTACCA AGCCACCGTG TGCGCTAGGG CTCAAGCCCC TCCCCCATCG TGGGACCAGA TGCGGAAGTG TTTGATCCGC CTTAAACCCA CCCTCCATGG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GCCAACACCC CTGCTATACA GACTGGGCGC TGTTCAGAAT GAAGTCACCC TGACGCACCC AATCACCAAA TACATCATGA CATGCATGTC GGCCGACCTG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GAGGTCGTCA CGAGCACCTG GGTGCTCGTT GGCGGCGTCC TGGCTGCTCT GGCCGCGTAT TGCCTGTCAA CAGGCTGCGT GGTCATAGTG GGCAGGATCG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TCTTGTCCGG GAAGCCGGCA ATTATACCTG ACAGGGAGGT TCTCTACCAG GAGTTCGATG AGATGGAAGA GTGCTCTCAG CACTTACCGT ACATCGAGCA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AGGGATGATG CTCGCTGAGC AGTTCAAGCA GAAGGCCCTC GGCCTCCTGC AGACCGCGTC CCGCCATGCA GAGGTTATCA CCCCTGCTGT CCAGACCAAC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TGGCAGAAAC TCGAGGTCTT TTGGGCGAAG CACATGTGGA ATTTCATCAG TGGGATACAA TACTTGGCGG GCCTGTCAAC GCTGCCTGGT AACCCCGCCA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TTGCTTCATT GATGGCTTTT ACAGCTGCCG TCACCAGCCC ACTAACCACT GGCCAAACCC TCCTCTTCAA CATATTGGGG GGGTGGGTGG CTGCCCAGCT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CGCCGCCCCC GGTGCCGCTA CCGCCTTTGT GGGCGCTGGC TTAGCTGGCG CCGCACTCGA CAGCGTTGGA CTGGGGAAGG TCCTCGTGGA CATTCTTGCA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

GGCTATGGCG CGGGCGTGGC GGGAGCTCTT GTGGCATTCA AGATCATGAG CGGTGAGGTC CCCTCCACGG AGGACCTGGT CAATCTGCTG CCCGCCATCC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

TCTCACCTGG AGCCCTTGCA GTCGGTGTGG TCTTTGCATC AATACTGCGC CGGCGTGTTG GCCCGGGCGA GGGGGCAGTG CAATGGATGA ACCGGCTAAT 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

AGCCTTCGCC TCCCGGGGGA ACCATGTTTC CCCCACACAC TACGTGCCGG AGAGCGATGC AGCCGCCCGC GTCACTGCCA TACTCAGCAG CCTCACTGTA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

ACCCAGCTCC TGAGGCGACT GCATCAGTGG ATAAGCTCGG AGTGTACCAC TCCATGCTCC GGTTCCTGGC TAAGGGACAT CTGGGACTGG ATATGCGAGG 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TGCTGAGCGA CTTTAAGACC TGGCTGAAAG CCAAGCTCAT GCCACAACTG CCTGGGATTC CCTTTGTGTC CTGCCAGCGC GGGTATAGGG GGGTCTGGCG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AGGAGACGGC ATTATGCACA CTCGCTGCCA CTGTGGAGCT GAGATCACTG GACATGTCAA AAACGGGACG ATGAGGATCG TCGGTCCTAG GACCTGCAAG 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

AACATGTGGA GTGGGACGTT CTTCATTAAT GCCTACACCA CGGGCCCCTG TACTCCCCTT CCTGCGCCGA ACTATAAGTT CGCGCTGTGG AGGGTGTCTG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CAGAGGAATA CGTGGAGATA AGGCGGGTGG GGGACTTCCA CTACGTATCG GGCATGACTA CTGACAATCT CAAATGCCCG TGCCAGATCC CATCGCCCGA 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

ATTTTTCACA GAATTGGACG GGGTGCGCCT ACATAGGTTT GCGCCCCCTT GCAAGCCCTT GCTGCGGGAG GAGGTATCAT TCAGAGTAGG ACTCCACGAG 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

TACCCGGTGG GGTCGCAATT ACCTTGCGAG CCCGAACCGG ACGTAGCCGT GTTGACGTCC ATGCTCACTG ATCCCTCCCA TATAACAGCA GAGGCGGCCG 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

GGAGAAGGTT GGCGAGAGGG TCACCCCCTT CTATGGCCAG CTCCTCGGCT AGCCAGCTGT CCGCTCCATC TCTCAAGGCA ACTTGCACCG CCAACCATGA 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CTCCCCTGAC GCCGAGCTCA TAGAGGCTAA CCTCCTGTGG AGGCAGGAGA TGGGCGGCAA CATCACCAGG GTTGAGTCAG AGAACAAAGT GGTGATTCTG 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

GACTCCTTCG ATCCGCTTGT GGCAGAGGAG GATGAGCGGG AGGTCTCCGT ACCCGCAGAA ATTCTGCGGA AGTCTCGGAG ATTCGCCCCA GCCCTGCCCG 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TCTGGGCGCG GCCGGACTAC AACCCCCTGC TAGTAGAGAC GTGGAAAAAG CCTGACTACG AACCACCTGT GGTCCATGGC TGCCCGCTAC CACCTCCACG 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

GTCCCCTCCT GTGCCTCCGC CTCGGAAAAA GCGTACGGTG GTCCTCACCG AATCAACCCT ACCTACTGCC TTGGCCGAGC TTGCCACCAA AAGTTTTGGC 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

AGCTCCTCAA CTTCCGGCAT TACGGGCGAC AATACGACAA CATCCTCTGA GCCCGCCCCT TCTGGCTGCC CCCCCGACTC CGACGTTGAG TCCTATTCTT 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

CCATGCCCCC CCTGGAGGGG GAGCCTGGGG ATCCGGATCT CAGCGACGGG TCATGGTCGA CGGTCAGTAG TGGGGCCGAC ACGGAAGATG TCGTGTGCTG 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

CTCAATGTCT TATTCCTGGA CAGGCGCACT CGTCACCCCG TGCGCTGCGG AGGAACAAAA ACTGCCCATC AACGCACTGA GCAACTCGTT GCTACGCCAT 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

CACAATCTGG TGTATTCCAC CACTTCACGC AGTGCTTGCC AAAGGAAGAA GAAAGTCACA TTTGACAGAC TGCAAGTTCT GGACAGCCAT TACCAGGACG 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TGCTCAAGGA GGTCAAAGCA GCGGCGTCAA AAGTGAAGGC TAACTTGCTA TCCGTAGAGG AAGCTTGCAG CCTGGCGCCC CCACATTCAG CCAAATCCAA 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

GTTTGGCTAT GGGGCAAAAG ACGTCCGTTG CCATGCCAGA AAGGCCGTAG CCCACATCAA CTCCGTGTGG AAAGACCTTC TGGAAGACAG TGTAACACCA 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

ATAGACACTA CCATCATGGC CAAGAACGAG GTTTTCTGCG TTCAGCCTGA GAAGGGGGGT CGTAAGCCAG CTCGTCTCAT CGTGTTCCCC GACCTGGGCG 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

TGCGCGTGTG CGAGAAGATG GCCCTGTACG ACGTGGTTAG CAAGCTCCCC TTGGCCGTGA TGGGAAGCTC CTACGGATTC CAATACTCAC CAGGACAGCG 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

GGTTGAATTC CTCGTGCAAG CGTGGAAGTC CAAGAAGACC CCGATGGGGC TCTCGTATGA TACCCGCTGT TTTGACTCCA CAGTCACTGA GAGCGACATC 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

CGTACGGAGG AGGCAATTTA CCAATGTTGT GACCTGGACC CCCAAGCCCG CGTGGCCATC AAGTCCCTCA CTGAGAGGCT TTATGTTGGG GGCCCTCTTA 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

CTAATTCAAG GGGGGAAAAC TGCGGCTACC GCAGGTGCCG CGCGAGCAGA GTACTGACAA CTAGCTGTGG TAACACCCTC ACTCGCTACA TCAAGGCCCG 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

GGCAGCCTGT CGAGCCGCAG GGCTCCAGGA CTGCACCATG CTCGTGTGTG GCGACGACTT AGTCGTTATC TGTGAAAGTG CGGGGGTCCA GGAGGACGCG 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

GCGAGCCTGA GAGCCTTCAC GGAGGCTATG ACCAGGTACT CCGCCCCCCC CGGGGACCCC CCACAACCAG AATACGACTT GGAGCTTATA ACATCATGCT 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

CCTCCAACGT GTCAGTCGCC CACGACGGCG CTGGAAAGAG GGTCTACTAC CTTACCCGTG ACCCTACAAC CCCCCTCGCG AGAGCCGCGT GGGAGACAGC 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

AAGACACACT CCAGTCAATT CCTGGCTAGG CAACATAATC ATGTTTGCCC CCACACTGTG GGCGAGGATG ATACTGATGA CCCACTTCTT TAGCGTCCTC 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

ATAGCCAGGG ATCAGCTTGA ACAGGCTCTC AACTGCGAGA TCTACGGAGC CTGCTACTCC ATAGAACCAC TGGATCTACC TCCAATCATT CAAAGACTCC 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

ATGGCCTCAG CGCATTTTCA CTCCACAGTT ACTCTCCAGG TGAAATTAAT AGGGTGGCCG CATGCCTCAG AAAACTTGGG GTCCCGCCCT TGCGAGCTTG 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

GAGACACCGG GCCTGGAGCG TCCGCGCTAG GCTTCTGGCC AGAGGAGGCA AGGCTGCCAT ATGTGGCAAG TACCTCTTCA ACTGGGCAGT AAGAACAAAG 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

CTCAAACTCA CTCCGATAAC GGCCGCTGGC CGGCTGGACT TGTCCGGCTG GTTCACGGCT GGCTACAGCG GGGGAGACAT TTATCACAGC GTGTCTCATG 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

CCCGGCCCCG CTGGTTCTGG TTTTGCCTAC TCCTGCTTGC TGCAGGGGTA GGCATCTACC TCCTCCCCAA CCGATGAAGA TTGGGCTAAC CACTCCAGGC 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

CAATAGGCCA TTCCCT
^9401      ^9411

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

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

Hepatitis C virus

A promoter reported in cDNA corresponding to IRES sequence:
yes The total number of notable open-reading frames (ORFs):
1

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
heterogeneous_population_of_molecules_found

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
heterogeneous_population_of_molecules_found

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
promoter_confirmed

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Homo sapiens HuH7

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: Václav Vopálenský

The abbreviated name of this ORF/gene:
Polyprotein

The description of the protein encoded in this ORF:
HCV 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):

342-9377

Remarks:

There is another open-reading frame coding for the F protein. The F protein synthesis is initiated in the +1
reading frame at a non-AUG codon (GUG or GCG) overlapping codon 26 of the polyprotein (Baril et al., 2005).

A cryptic promoter activity of the HCV IRES was recently described (Masek et al., 2007) unlike by others using
insufficient combination of PCR primers (MacCallum et al, 2006).

Citations:

Inchauspe G., Zebedee S., Lee D. H., Sugitani M., Nasoff M., Prince A. M. (1991) Genomic structure of the human prototype strain H of hepatitis C virus: comparison with American and Japanese isolates. Proc. Natl. Acad. Sci. U. S. A. 88(22):10292-10296

Dumas E., Staedel C., Colombat M., Reigadas S., Chabas S., Astier-Gin T., Cahour A., Litvak S., Ventura M. (2003) A promoter activity is present in the DNA sequence corresponding to the hepatitis C virus 5' UTR. Nucleic. Acids. Res. 31(4):1275-1281

Baril M., Brakier-Gingras L. (2005) Translation of the F protein of hepatitis C virus is initiated at a non-AUG codon in a +1 reading frame relative to the polyprotein. Nucleic Acids Res. 33(5):1474-1486

Masek T, Vopalensky V, Horvath O, Vortelova L, Feketova Z, Pospisek M (2007) Hepatitis C virus internal ribosome entry site initiates protein synthesis at the authentic initiation codon in yeast. J. Gen. Virol. 7(88):1992-2002

MacCallum PR, Jack SC, Egan PA, McDermott BT, Elliott RM, Chan SW (2006) Cap-dependent and hepatitis C virus internal ribosome entry site-mediated translation are modulated by phosphorylation of eIF2alpha under oxidative stress. J. Gen. Virol. 87(Pt 11):3251-3262

IRESs:

IRES:

Version: `9`	Last change: `2009-08-30 02:54:25`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský
The IRES name: `HCV_type_1a`

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

1-383

Conclusion:
strongly_supported_IRES

How IRES boundaries were determined:
experimentally_determined

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

GCCAGCCCCC TGATGGGGGC GACACTCCAC CATGAATCAC TCCCCTGTGA GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG 
....(((((( ....)))))) .......... .......... ...((((..( (((....... ))))(((((( ...((((((. ......)))) ))....)))) 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGTCGTGCAG CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG CGGAACCGGT GAGTACACCG GAATTGCCAG GACGACCGGG TCCTTTCTTG 
))........ ....)))).. ....(((((( (((((.(((( (((((((((( (((..((((( (....))))) )((((((((( (..((.(((( (......... 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GATAAACCCG CTCAATGCCT GGAGATTTGG GCGTGCCCCC GCAAGACTGC TAGCCGAGTA GTGTTGGGTC GCGAAAGGCC TTGTGGTACT GCCTGATAGG 
.....))))) .))....))) ))))))).(( (....))))) )).))))))) ))((((..(( (((......) )))).)))). ...)))).)) (((......) 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTGCTTGCGA GTGCCCCGGG AGGTCTCGTA GACCGTGCAC CATGAGCACG AATCCTAAAC CTCAAAGAAA AACCAAACGT AAC
))((...... ..)))))))) )))....... ((.(((((.. .....))))) ..))...... .......... .......... ...
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

WARNING: bases 68 and 99 (GA) can't pair!
WARNING: bases 176 and 223 (GA) can't pair!
WARNING: bases 256 and 276 (GA) can't pair!
WARNING: bases 260 and 273 (AG) can't pair!

STDOUT was:

GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUCCUAAACCUCAAAGAAAAACCAAACGUAAC
....((((((....)))))).......................((((..((((.......))))((((((...((((((.......))))))....))))))............))))......(((((((((((.(((((((((((((((((..((((((....))))))((((((((((..((.(((((..............))))).))....)))))))))).(((....))))))).)))))))))((((..(((((......))))).))))....)))).))(((......)))((........))))))))))).......((.(((((.......)))))..))............................. (-119.40)

Rendering structure of HCV_type_1a mRNA 383 nt long with energy of -119.40 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Remarks:

For functionality of IRES is necessary that no strong secondary structures are present immediately downstream
the IRES segment in a synthetic plasmid construct. Same IRES segment is functional in some constructs whereas
it is not in others.

Secondary structure domains II-IV span the IRES. The domain III and IV are the key parts of the IRES and
include a pseudoknot structure. The structural features of many IRESs were summarized in Martinez-Salas et al.
(2001).

A recent survey of several mutations on IRES activity was published by Barrez et al. (2009), Masante et al.
(2008) and Jubin et al. (2000). Analysis of various HCV subtypes was also published (Collier et al., 1998)

Please refer also to sequence 1 from Patent WO0233376.

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

Martínez-Salas E, Ramos R, Lafuente E, López de Quinto S (2001) Functional interactions in internal translation initiation directed by viral and cellular IRES elements. J. Gen. Virol. 5(82):973-984

Barría MI, González A, Vera-Otarola J, León U, Vollrath V, Marsac D, Monasterio O, Pérez-Acle T, Soza A, López-Lastra M (2009) Analysis of natural variants of the hepatitis C virus internal ribosome entry site reveals that primary sequence plays a key role in cap-independent translation. Nucleic Acids Res. 37(3):957-971

Masante C, Mahias K, Lourenço S, Dumas E, Cahour A, Trimoulet P, Fleury H, Astier-Gin T, Ventura M (2008) Seven nucleotide changes characteristic of the hepatitis C virus genotype 3 5' untranslated region: correlation with reduced in vitro replication. J. Gen. Virol. 89(Pt 1):212-221

Collier AJ, Tang S, Elliott RM (1998) Translation efficiencies of the 5' untranslated region from representatives of the six major genotypes of hepatitis C virus using a novel bicistronic reporter assay system. J. Gen. Virol. 79(10):2359-2366

Jubin R, Vantuno NE, Kieft JS, Murray MG, Doudna JA, Lau JY, Baroudy BM (2000) Hepatitis C virus internal ribosome entry site (IRES) stem loop IIId contains a phylogenetically conserved GGG triplet essential for translation and IRES folding. J. Virol. 74(22):10430-10437

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `3`	Last change: `2009-08-30 03:21:01`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

ITAF protein characteristics:

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

ITAF abbreviated name:
PTB-1

ITAF fullname:
polypyrimidine tract-binding protein isoform 1

ITAF description (long):
polypyrimidine tract-binding protein isoform 1 binds dsRNA with (CCU)n motif where n is at least 3. By SELEX approach it was found it binds to 5'-CAGCCUGGUGCCUCUCUUUCGG-3' (Singh et al. (1995) Science 268:1173-1176) but also UCUU or UCUUC within pyrimidine-rich sequence (Perez et al. (1997) RNA3:1334-1347).

3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vivo

The organism where action of this ITAF was studied:

Homo sapiens HeLa (ATCC CCL-2)

Remarks:

Depletion of mRNA for PTB-1 and decrease of protein level to about 10% did not affect activity of HCV IRES.
Data from Figure 3E,F (in vivo). These results contradict those in vitro results from Anwar et al. (2000)
J. Biol. Chem. 275:34231-34235 and from Ali and Siddiqui (1995) J. Virol. 69:6367-6375.

BS-C-1 cells and Huh-7 cells expressing PTB protein from a plasmid displayed increase in HCV IRES activity 5
times (Gosert et al., 2000).

Citations:

Mitchell S. A., Spriggs K. A., Bushell M., Evans J. R., Stoneley M., Le Quesne J. P., Spriggs R. V., Willis A. E. (2005) Identification of a motif that mediates polypyrimidine tract-binding protein-dependent internal ribosome entry. Genes Dev. 19(13):1556-1571

Gosert R, Chang KH, Rijnbrand R, Yi M, Sangar DV, Lemon SM (2000) Transient expression of cellular polypyrimidine-tract binding protein stimulates cap-independent translation directed by both picornaviral and flaviviral internal ribosome entry sites In vivo. Mol. Cell. Biol. 20(5):1583-1595

IRES trans-acting factor (ITAF):

Version: `2`	Last change: `2009-08-29 13:12:35`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

ITAF protein characteristics:

Version: `2`	Last change: `2009-08-29 12:19:15`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
La

ITAF fullname:
La autoantigen

ITAF description (long):
La autoantigen (p52), 52 kDa RNA binding protein, predominantly localized to nucleus, unwinds the dsRNA in ATP-dependent manner, forms a dimer

3.2.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
HeLa cell lysate

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally_although_in_limiting_concentration

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Sequestration of the La autoantigen blocked HCV IRES-mediated translation. It binds to the region close to
initiator AUG codon of HCV core protein encompassed in the HCV IRES, it contains 3 RNA-recognition motifs
(RRM) and the one formed by aminoacid residues 112–184 was shown to have the binding capability (Mondal et
al., 2008).

Citations:

Ali N, Pruijn GJ, Kenan DJ, Keene JD, Siddiqui A (2000) Human La antigen is required for the hepatitis C virus internal ribosome entry site-mediated translation. J. Biol. Chem. 36(275):27531-27540

Mondal T, Ray U, Manna AK, Gupta R, Roy S, Das S (2008) Structural determinant of human La protein critical for internal initiation of translation of hepatitis C virus RNA. J. Virol. 23(82):11927-11938

IRES trans-acting factor (ITAF):

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

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

OPTIONAL: The interacting RNA base range (if any):
18-129

ITAF protein characteristics:

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

ITAF abbreviated name:
hnRNP_D

ITAF fullname:
heterogeneous ribonucleoprotein D

ITAF description (long):
heterogeneous ribonucleoprotein D (AUF1) AU-rich region binding protein

3.3.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
stimulatory

Method used to demonstrate ITAF effect:
in_vivo

The organism where action of this ITAF was studied:

Homo sapiens

Remarks:

Distribution of HCV IRES-containing mRNAs in polysomes isolated from Huh5-15 cells transfected with siRNA
against the hnRNP D changed (Paek et al., 2008). 293T, Huh7


hnRNP D is cofractionated and coimmunoprecipitated with NSAP1, another protein known to modulate HCV IRES
activity.

Citations:

Paek KY, Kim CS, Park SM, Kim JH, Jang SK (2008) RNA-binding protein hnRNP D modulates internal ribosome entry site-dependent translation of hepatitis C virus RNA. J. Virol. 82(24):12082-12093

IRES trans-acting factor (ITAF):

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

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

ITAF protein characteristics:

Version: `1`	Last change: `2009-08-30 01:32:33`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
NSAP1

ITAF fullname:
NS1-associated protein 1

ITAF description (long):
NS1-associated protein 1 (65 and 74 kDa) binding adenosine-rich regions, stimulates HCV IRES activity but not of EMCV, PV, c-myc

3.4.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
stimulatory

Method used to demonstrate ITAF effect:
in_vivo

The organism where action of this ITAF was studied:

Homo sapiens

Remarks:

It would be interesting to evaluate whether NSAP1 increased activity of the internal HCV IRES promoter (Figure
3) although it is probably already ruled out by results shown in Figure 5 (Kim et al., 2004).

Citations:

Kim JH, Paek KY, Ha SH, Cho S, Choi K, Kim CS, Ryu SH, Jang SK (2004) A cellular RNA-binding protein enhances internal ribosomal entry site-dependent translation through an interaction downstream of the hepatitis C virus polyprotein initiation codon. Mol. Cell. Biol. 24(18):7878-7890

IRES trans-acting factor (ITAF):

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

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

ITAF protein characteristics:

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

ITAF abbreviated name:
hnRNP_R

ITAF fullname:
heterogeneous ribonucleoprotein R

ITAF description (long):
heterogeneous ribonucleoprotein R (82 and 90 kDa) homologous to NSAP1

3.5.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
stimulatory

Method used to demonstrate ITAF effect:
in_vivo

The organism where action of this ITAF was studied:

Homo sapiens

Citations:

IRES trans-acting factor (ITAF):

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

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

ITAF protein characteristics:

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

ITAF abbreviated name:
hnRNP_L

ITAF fullname:
heterogeneous ribonucleoprotein L

ITAF description (long):
heterogeneous ribonucleoprotein L (68 kDa)

3.6.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
stimulatory

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
HeLa cell lysate

Citations:

Hahm B, Kim YK, Kim JH, Kim TY, Jang SK (1998) Heterogeneous nuclear ribonucleoprotein L interacts with the 3' border of the internal ribosomal entry site of hepatitis C virus. J. Virol. 72(11):8782-8788

RNA:protein interactions:

The RNA:protein interaction:

Version: `6`	Last change: `2009-08-30 04:04:24`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Abbreviated name of the protein interacting with the RNA:
eIF3b

Full name of the protein interacting with the RNA:
eukaryotic translation factor eIF3; subunit b

The description of the protein interacting with the RNA:
a subunit of translation factor 3 (110/116/120 kDa)

The function of the protein interaction:

Direct interaction between eIF3b and HCV IRES might bypass the function of eIF3j which is involved in a
 cap-dependent translation initiation.

The organism where this RNA:protein interaction occurs:

Homo sapiens

Remarks:

Interaction demonstrated by filter-binding-assay and NMR titration of purified protein and radio-labeled
RNA synthesized in vitro.

Regions of interactions reported: 200-206 or 193-200 (Buratti et al., 1998); 120-332 (Perard et al., 2009)

Citations:

Perard J., Rasia R., Medenbach J., Ayala I., Boisbouvier J., Drouet E., Baudin F. (2009) Human initiation factor eIF3 subunit b interacts with HCV IRES RNA through its N-terminal RNA recognition motif. FEBS. Lett. 583(1):70-74

Buratti E, Tisminetzky S, Zotti M, Baralle FE (1998) Functional analysis of the interaction between HCV 5'UTR and putative subunits of eukaryotic translation initiation factor eIF3. Nucleic Acids Res. 26(13):3179-3187

Sizova DV, Kolupaeva VG, Pestova TV, Shatsky IN, Hellen CU (1998) Specific interaction of eukaryotic translation initiation factor 3 with the 5' nontranslated regions of hepatitis C virus and classical swine fever virus RNAs. J. Virol. 72(6):4775-4782

The RNA:protein interaction:

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

Abbreviated name of the protein interacting with the RNA:
RPS5

Full name of the protein interacting with the RNA:
ribosomal protein S5

The description of the protein interacting with the RNA:
ribosomal protein S5, p25

The organism where this RNA:protein interaction occurs:

Homo sapiens HeLa (ATCC CCL-2)

Remarks:

It was postulated that not the mis-reported RPS9 but RPS5 interacts with HCV IRES (Fukushi et al., 2001).

Citations:

Fukushi S, Okada M, Stahl J, Kageyama T, Hoshino FB, Katayama K (2001) Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus. J. Biol. Chem. 24(276):20824-20826

The RNA:protein interaction:

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

Abbreviated name of the protein interacting with the RNA:
IGF2BP1

Full name of the protein interacting with the RNA:
IGF2 mRNA binding protein 1

The description of the protein interacting with the RNA:
insulin-like growth factor mRNA binding protein

The organism where this RNA:protein interaction occurs:

Homo sapiens HuH7

Citations:

Weinlich S, Hüttelmaier S, Schierhorn A, Behrens SE, Ostareck-Lederer A, Ostareck DH (2009) IGF2BP1 enhances HCV IRES-mediated translation initiation via the 3'UTR. RNA. 8(15):1528-1542

The RNA:protein interaction:

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

Abbreviated name of the protein interacting with the RNA:
eIF3_p170

Full name of the protein interacting with the RNA:
eIF3_p170

The description of the protein interacting with the RNA:
eIF3 subunit p170

The interacting RNA base range: 195

The organism where this RNA:protein interaction occurs:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

Remarks:

Similar results were also obtained with HeLa cells.

Citations:

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 33

Version: `1`	Last change: `2009-08-28 19:19:35`
Originaly submitted by: Tomáš Mašek	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `no`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1-383

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

GCCAGCCCCC TGATGGGGGC GACACTCCAC CATGAATCAC TCCCCTGTGA GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG 
....(((((( ....)))))) .......... .......... ...((((..( (((....... ))))(((((( ...((((((. ......)))) ))....)))) 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGTCGTGCAG CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG CGGAACCGGT GAGTACACCG GAATTGCCAG GACGACCGGG TCCTTTCTTG 
))........ ....)))).. ....(((((( (((((.(((( (((((((((( (((..((((( (....))))) )((((((((( (..((.(((( (......... 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GATAAACCCG CTCAATGCCT GGAGATTTGG GCGTGCCCCC GCAAGACTGC TAGCCGAGTA GTGTTGGGTC GCGAAAGGCC TTGTGGTACT GCCTGATAGG 
.....))))) .))....))) ))))))).(( (....))))) )).))))))) ))((((..(( (((......) )))).)))). ...)))).)) (((......) 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTGCTTGCGA GTGCCCCGGG AGGTCTCGTA GACCGTGCAC CATGAGCACG AATCCTAAAC CTCAAAGAAA AACCAAACGT AAC
))((...... ..)))))))) )))....... ((.(((((.. .....))))) ..))...... .......... .......... ...
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

WARNING: bases 68 and 99 (GA) can't pair!
WARNING: bases 176 and 223 (GA) can't pair!
WARNING: bases 256 and 276 (GA) can't pair!
WARNING: bases 260 and 273 (AG) can't pair!

STDOUT was:

GCCAGCCCCCUGAUGGGGGCGACACUCCACCAUGAAUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUCCUAAACCUCAAAGAAAAACCAAACGUAAC
....((((((....)))))).......................((((..((((.......))))((((((...((((((.......))))))....))))))............))))......(((((((((((.(((((((((((((((((..((((((....))))))((((((((((..((.(((((..............))))).))....)))))))))).(((....))))))).)))))))))((((..(((((......))))).))))....)))).))(((......)))((........))))))))))).......((.(((((.......)))))..))............................. (-119.40)

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Remarks:

Preliminary structure was determined by alignment of N2 and Hutchinson HCV strains coupled to GBV-B
primary sequence. In vitro transcripts of HCV region 1-399 were mapped by several ribonucleases. The structure
shown here is from Figure 1 in the article.

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

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

ss_experiment_with_enzyme_id: 62

The temperature (in degrees of Celsia):
20 The enzymatic method used to determine the 2D structure:
ribonuclease T1

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

Version: 0

pH `7.50`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `50.00`	Mg²⁺ [mM] `10.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `70.00`	Tris [mM] `10.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

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

ss_experiment_with_enzyme_id: 63

The temperature (in degrees of Celsia):
20 The enzymatic method used to determine the 2D structure:
ribonuclease T2

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

Version: 0

pH `7.50`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `50.00`	Mg²⁺ [mM] `10.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `70.00`	Tris [mM] `10.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

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

ss_experiment_with_enzyme_id: 64

The temperature (in degrees of Celsia):
20 The enzymatic method used to determine the 2D structure:
ribonuclease V1

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

Version: 0

pH `7.50`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `50.00`	Mg²⁺ [mM] `10.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `70.00`	Tris [mM] `10.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

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

ss_experiment_with_enzyme_id: 65

The temperature (in degrees of Celsia):
20 The enzymatic method used to determine the 2D structure:
S1 nuclease

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

Version: 0

pH `7.50`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `50.00`	Mg²⁺ [mM] `10.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `70.00`	Tris [mM] `10.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Other buffer components and their relative concentrations:

1 mM ZnSO4

Citations:

Honda M., Brown E. A., Lemon S. M. (1996) Stability of a stem-loop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA. RNA. 2(10):955-968

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 47

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `no`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
36-126

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

ATCACTCCCC TGTGAGGAAC TACTGTCTTC ACGCAGAAAG CGTCTAGCCA TGGCGTTAGT ATGAGTGTCG TGCAGCCTCC AGGACCCCCC C
........(( ((..((((.. .....))))( (((((...(( ((((...... .))))))... .))))))... .........) )))....... .
^36        ^46        ^56        ^66        ^76        ^86        ^96        ^106       ^116       ^126

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

WARNING: bases 33 and 64 (GA) can't pair!

STDOUT was:

AUCACUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCC
........((((..((((.......))))((((((...((((((.......))))))....))))))............))))........ (-15.60)

Rendering structure of HCV_type_1a mRNA 91 nt long with energy of -15.60 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

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

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

ss_experiment_with_enzyme_id: 79

The temperature (in degrees of Celsia):
20 The enzymatic method used to determine the 2D structure:
ribonuclease V1

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

Version: 0

pH `7.60`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `0`	Mg²⁺ [mM] `10.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `20.00`	Tris [mM] `10.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

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

ss_experiment_with_enzyme_id: 80

The temperature (in degrees of Celsia):
20 The enzymatic method used to determine the 2D structure:
S1 nuclease

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

Version: 0

pH `7.60`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `0`	Mg²⁺ [mM] `10.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `20.00`	Tris [mM] `10.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Other buffer components and their relative concentrations:

1 mM ZnSO4

Citations:

Honda M, Beard MR, Ping LH, Lemon SM (1999) A phylogenetically conserved stem-loop structure at the 5' border of the internal ribosome entry site of hepatitis C virus is required for cap-independent viral translation. J. Virol. 2(73):1165-1174

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 48

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `no`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1-344

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

GCCAGCCCCC TGATGGGGGC GACACTCCAC CATGAATCAC TCCCCTGTGA GGAACTACTG TCTTCACGCA GAAAGCGTCT AGCCATGGCG TTAGTATGAG 
....(((((( ....)))))) ..(((((... .......... .....((((( (((....... )))))))).. ...((((((. ......)))) )).....))) 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGTCGTGCAG CCTCCAGGAC CCCCCCTCCC GGGAGAGCCA TAGTGGTCTG CGGAACCGGT GAGTACACCG GAATTGCCAG GACGACCGGG TCCTTTCTTG 
))........ .......... ....(((((( (((((.(((( ((..(((((( (((..((((( (....))))) )((((.(((( (.((..(((( (......... 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GATAAACCCG CTCAATGCCT GGAGATTTGG GCGTGCCCCC GCAAGACTGC TAGCCGAGTA GTGTTGGGTC GCGAAAGGCC TTGTGGTACT GCCTGATAGG 
.....))))) .....))))) )).)))).(( (....))))) )).))))).. .((((..... (((......) ))....)).) ))))))).)) ((((....)) 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTGCTTGCGA GTGCCCCGGG AGGTCTCGTA GACCGTGCAC CATG
))((...... ..)))))))) )))....((( .....))).. ....
^301       ^311       ^321       ^331       ^341

Rendering structure of HCV_type_1a mRNA 344 nt long with energy of -105.00 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Remarks:

Data from Figure 3. To align the structure of the AG94 strain over the underlying sequence of this IRESite
record we had to drop an unpaired base corresponding to one of the C bases. Below is an alignment of the AG94
sequence to this IRESite sequence.

>IRESite_Id:222 HCV_type_1a virus
          Length = 9416

 Score =  591 bits (338), Expect = e-169
 Identities = 343/345 (99%), Gaps = 1/345 (0%)
 Strand = Plus / Plus


Query: 1   gccagccccctgatgggggcgacactccaccatgaatcactcccctgtgaggaactactg 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   gccagccccctgatgggggcgacactccaccatgaatcactcccctgtgaggaactactg 60


Query: 61  tcttcacgcagaaagcgtctagccatggcgttagtatgagtgtcgtgcagcctccaggac 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  tcttcacgcagaaagcgtctagccatggcgttagtatgagtgtcgtgcagcctccaggac 120


Query: 121 ccccccctcccgggagagccatagtggtctgcggaaccggtgagtacaccggaattgcca 180
           ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ccc-ccctcccgggagagccatagtggtctgcggaaccggtgagtacaccggaattgcca 179


Query: 181 ggacgaccgggtcctttcttggataaacccgctcaatgcctggagatttgggcgtgcccc 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 180 ggacgaccgggtcctttcttggataaacccgctcaatgcctggagatttgggcgtgcccc 239


Query: 241 cgcaagactgctagccgagtagtgttgggtcgcgaaaggccttgtggtactgcctgatag 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 240 cgcaagactgctagccgagtagtgttgggtcgcgaaaggccttgtggtactgcctgatag 299


Query: 301 ggtgcttgcgagtgccccgggaggtctcgtagaccgtgcatcatg 345
           |||||||||||||||||||||||||||||||||||||||| ||||
Sbjct: 300 ggtgcttgcgagtgccccgggaggtctcgtagaccgtgcaccatg 344

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

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

ss_experiment_with_enzyme_id: 81

The temperature (in degrees of Celsia):
20 The enzymatic method used to determine the 2D structure:
ribonuclease T1/T2 mix

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

Version: 0

pH `7.50`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `50.00`	Mg²⁺ [mM] `10.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `70.00`	Tris [mM] `10.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

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

ss_experiment_with_enzyme_id: 82

The temperature (in degrees of Celsia):
20 The enzymatic method used to determine the 2D structure:
S1 nuclease

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

Version: 0

pH `7.50`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `50.00`	Mg²⁺ [mM] `10.00`	Ca²⁺ [mM] `0`
Cl^- [mM] `70.00`	Tris [mM] `10.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Other buffer components and their relative concentrations:

1 mM ZnSO4

Citations:

Brown EA, Zhang H, Ping LH, Lemon SM (1992) Secondary structure of the 5' nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. Nucleic Acids Res. 19(20):5041-5045

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 49

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `no`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
40-362

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

CTCCCCTGTG AGGAACTACT GTCTTCACGC AGAAAGCGTC TAGCCATGGC GTTAGTATGA GTGTCGTGCA GCCTCCAGGA CCCCCCCTCC CGGGAGAGCC 
....((((.( (((...(((. (....(((.( (...(((((( .......))) )))....)). ))).)))).. .)))))))). .....((((( ((((((.((( 
^40        ^50        ^60        ^70        ^80        ^90        ^100       ^110       ^120       ^130       

ATAGTGGTCT GCGGAACCGG TGAGTACACC GGAATTGCCA GGACGACCGG GTCCTTTCTT GGATAAACCC GCTCAATGCC TGGAGATTTG GGCGTGCCCC 
(((..((((( ((((..(((( ((....)))) ))((((.((( ((..((.((( ((........ ......)))) ).))....)) ))).)))).( ((....)))) 
^140       ^150       ^160       ^170       ^180       ^190       ^200       ^210       ^220       ^230       

CGCAAGACTG CTAGCCGAGT AGTGTTGGGT CGCGAAAGGC CTTGTGGTAC TGCCTGATAG GGTGCTTGCG AGTGCCCCGG GAGGTCTCGT AGACCGTGCA 
))).))))). ...((((..( .(((...... ))).)..))) ).)))))).) )(((...... )))....... .....))))) ))))...... .......... 
^240       ^250       ^260       ^270       ^280       ^290       ^300       ^310       ^320       ^330       

CCATGAGCAC GAATCCTAAA CCT
.......... .......... ...
^340       ^350       ^360

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

WARNING: bases 215 and 240 (CC) can't pair!
WARNING: bases 217 and 238 (GG) can't pair!

STDOUT was:

CUCCCCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGGACCCCCCCUCCCGGGAGAGCCAUAGUGGUCUGCGGAACCGGUGAGUACACCGGAAUUGCCAGGACGACCGGGUCCUUUCUUGGAUAAACCCGCUCAAUGCCUGGAGAUUUGGGCGUGCCCCCGCAAGACUGCUAGCCGAGUAGUGUUGGGUCGCGAAAGGCCUUGUGGUACUGCCUGAUAGGGUGCUUGCGAGUGCCCCGGGAGGUCUCGUAGACCGUGCACCAUGAGCACGAAUCCUAAACCU
....((((.((((...(((.(....(((.((...((((((.......))))))....)).))).))))...))))))))......(((((((((((.((((((..(((((((((..((((((....))))))((((.(((((..((.(((((..............))))).))....))))).)))).(((....))))))).)))))....((((..(.(((......))).)..)))).)))))).))(((......)))............)))))))))....................................... (-89.50)

Rendering structure of HCV_type_1a mRNA 323 nt long with energy of -89.50 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Remarks:

Data from Figure 1.

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

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

ss_experiment_with_enzyme_id: 83

The temperature (in degrees of Celsia):
37 The enzymatic method used to determine the 2D structure:
ribonuclease T1/V1 mix

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

Version: 0

pH `7.50`	Li⁺ [mM] `0`	Na⁺ [mM] `0`	K⁺ [mM] `100.00`	Mg²⁺ [mM] `2.50`	Ca²⁺ [mM] `0`
Cl^- [mM] `100.00`	Tris [mM] `20.00`	BSA [mM] `0`	HEPES [mM] `0`	EGTA [mM] `0`	EDTA [mM] `0`
cacodylate [mM] `0`

Other buffer components and their relative concentrations:

2.5 mM acetate
2 mM dithiothreitol

Citations:

Kolupaeva VG, Pestova TV, Hellen CU (2000) An enzymatic footprinting analysis of the interaction of 40S ribosomal subunits with the internal ribosomal entry site of hepatitis C virus. J. Virol. 14(74):6242-6250

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 50

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `no`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
44-118

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

CCTGTGAGGA ACTACTGTCT TCACGCAGAA AGCGTCTAGC CATGGCGTTA GTATGAGTGT CGTGCAGCCT CCAGG
((((.((((. ..(((.(... .((((((... ((((((.... ...)))))). ...)))))). ))))...))) )))))
^44        ^54        ^64        ^74        ^84        ^94        ^104       ^114

There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:

WARNING: bases 25 and 56 (GA) can't pair!

STDOUT was:

CCUGUGAGGAACUACUGUCUUCACGCAGAAAGCGUCUAGCCAUGGCGUUAGUAUGAGUGUCGUGCAGCCUCCAGG
((((.((((...(((.(....((((((...((((((.......))))))....)))))).))))...)))))))) (-22.70)

Rendering structure of HCV_type_1a mRNA 75 nt long with energy of -22.70 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Remarks:

Data from Figure 7.

Citations:

Odreman-Macchioli F, Baralle FE, Buratti E (2001) Mutational analysis of the different bulge regions of hepatitis C virus domain II and their influence on internal ribosome entry site translational ability. J. Biol. Chem. 276(45):41648-41655

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