IRESite_Id:96 characteristics of HCV_type_1a_rc IRES studied in pFGAL4h-HCV1rc plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `96`	Version: `3`
Originaly submitted by: Tomáš Mašek	Submission date: `2005-12-15 00:00:00`
Reviewed by: Tomáš Mašek	Last change: `2008-07-04 12:56:59`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

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

The mRNA/+RNA description:

mRNA produced by bicistronic plasmid pFGAL4h-HCV1rc which comprises luciferase and Gal4 genes as the first and
the second cistron, respectively. The reverse complement sequence of full-length 5'-UTR of HCV genomic RNA
together with the first 45 nt of a viral polyprotein gene was inserted into the intercistronic region of the
reporter pFGAL4h vector just behind the 13G:C hairpin.

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

ATGGAAGACG CCAAAAACAT AAAGAAAGGC CCGGCGCCAT TCTATCCGCT GGAAGATGGA ACCGCTGGAG AGCAACTGCA TAAGGCTATG AAGAGATACG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCTGGTTCC TGGAACAATT GCTTTTACAG ATGCACATAT CGAGGTGGAC ATCACTTACG CTGAGTACTT CGAAATGTCC GTTCGGTTGG CAGAAGCTAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GAAACGATAT GGGCTGAATA CAAATCACAG AATCGTCGTA TGCAGTGAAA ACTCTCTTCA ATTCTTTATG CCGGTGTTGG GCGCGTTATT TATCGGAGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GCAGTTGCGC CCGCGAACGA CATTTATAAT GAACGTGAAT TGCTCAACAG TATGGGCATT TCGCAGCCTA CCGTGGTGTT CGTTTCCAAA AAGGGGTTGC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AAAAAATTTT GAACGTGCAA AAAAAGCTCC CAATCATCCA AAAAATTATT ATCATGGATT CTAAAACGGA TTACCAGGGA TTTCAGTCGA TGTACACGTT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGTCACATCT CATCTACCTC CCGGTTTTAA TGAATACGAT TTTGTGCCAG AGTCCTTCGA TAGGGACAAG ACAATTGCAC TGATCATGAA CTCCTCTGGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCTACTGGTC TGCCTAAAGG TGTCGCTCTG CCTCATAGAA CTGCCTGCGT GAGATTCTCG CATGCCAGAG ATCCTATTTT TGGCAATCAA ATCATTCCGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATACTGCGAT TTTAAGTGTT GTTCCATTCC ATCACGGTTT TGGAATGTTT ACTACACTCG GATATTTGAT ATGTGGATTT CGAGTCGTCT TAATGTATAG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATTTGAAGAA GAGCTGTTTC TGAGGAGCCT TCAGGATTAC AAGATTCAAA GTGCGCTGCT GGTGCCAACC CTATTCTCCT TCTTCGCCAA AAGCACTCTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATTGACAAAT ACGATTTATC TAATTTACAC GAAATTGCTT CTGGTGGCGC TCCCCTCTCT AAGGAAGTCG GGGAAGCGGT TGCCAAGAGG TTCCATCTGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CAGGTATCAG GCAAGGATAT GGGCTCACTG AGACTACATC AGCTATTCTG ATTACACCCG AGGGGGATGA TAAACCGGGC GCGGTCGGTA AAGTTGTTCC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATTTTTTGAA GCGAAGGTTG TGGATCTGGA TACCGGGAAA ACGCTGGGCG TTAATCAAAG AGGCGAACTG TGTGTGAGAG GTCCTATGAT TATGTCCGGT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TATGTAAACA ATCCGGAAGC GACCAACGCC TTGATTGACA AGGATGGATG GCTACATTCT GGAGACATAG CTTACTGGGA CGAAGACGAA CACTTCTTCA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TCGTTGACCG CCTGAAGTCT CTGATTAAGT ACAAAGGCTA TCAGGTGGCT CCCGCTGAAT TGGAATCCAT CTTGCTCCAA CACCCCAACA TCTTCGACGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AGGTGTCGCA GGTCTTCCCG ACGATGACGC CGGTGAACTT CCCGCCGCCG TTGTTGTTTT GGAGCACGGA AAGACGATGA CGGAAAAAGA GATCGTGGAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TACGTCGCCA GTCAAGTAAC AACCGCGAAA AAGTTGCGCG GAGGAGTTGT GTTTGTGGAC GAAGTACCGA AAGGTCTTAC CGGAAAACTC GACGCAAGAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AAATCAGAGA GATCCTCATA AAGGCCAAGA AGGGCGGAAA GATCGCCGTG TAATTCTAGC CTAGGAAACC CCCCCCCCCC CAAAGGGGGG GGGGGGGAGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCCCAGGATC CGTCGACAAG CTTGAATTCG TGTTACGTTT GGTTTTTCTT TGAGGTTTAG GATTCGTGCT CATGGTGCAC GGTCTACGAG ACCTCCCGGG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCACTCGCAA GCACCCTATC AGGCAGTACC ACAAGGCCTT TCGCGACCCA ACACTACTCG GCTAGCAGTC TTGCGGGGGC ACGCCCAAAT CTCCAGGCAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGAGCGGGTT TATCCAAGAA AGGACCCGGT CGTCCTGGCA ATTCCGGTGT ACTCACCGGT TCCGCAGACC ACTATGGCTC TCCCGGGAGG GGGGGTCCTG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GAGGCTGCAC GACACTCATA CTAACGCCAT GGCTAGACGC TTTCTGCGTG AAGACAGTAG TTCCTCACAG GGGAGTGATT CATGGTGGAG TGTCGCCCCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ATCAGGGGGC TGGCGAATTC AAAAATGAAG CTACTGTCTT CTATCGAACA AGCATGCGAT ATTTGCCGAC TTAAAAAGCT CAAGTGCTCC AAAGAAAAAC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CGAAGTGCGC CAAGTGTCTG AAGAACAACT GGGAGTGTCG CTACTCTCCC AAAACCAAAA GGTCTCCGCT GACTAGGGCA CATCTGACAG AAGTGGAATC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAGGCTAGAA AGACTGGAAC AGCTATTTCT ACTGATTTTT CCTCGAGAAG ACCTTGACAT GATTTTGAAA ATGGATTCTT TACAGGATAT AAAAGCATTG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTAACAGGAT TATTTGTACA AGATAATGTG AATAAAGATG CCGTCACAGA TAGATTGGCT TCAGTGGAGA CTGATATGCC TCTAACATTG AGACAGCATA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GAATAAGTGC GACATCATCA TCGGAAGAGA GTAGTAACAA AGGTCAAAGA CAGTTGACTG TATCGATTGA CTCGGCAGCT CATCATGATA ACTCCACAAT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TCCGTTGGAT TTTATGCCCA GGGATGCTCT TCATGGATTT GATTGGTCTG AAGAGGATGA CATGTCGGAT GGCTTGCCCT TCCTGAAAAC GGACCCCAAC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AATAATGGGT TCTTTGGCGA CGGTTCTCTC TTATGTATTC TTCGATCTAT TGGCTTTAAA CCGGAAAATT ACACGAACTC TAACGTTAAC AGGCTCCCGA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCATGATTAC GGATAGATAC ACGTTGGCTT CTAGATCCAC AACATCCCGT TTACTTCAAA GTTATCTCAA TAATTTTCAC CCCTACTGCC CTATCGTGCA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CTCACCGACG CTAATGATGT TGTATAATAA CCAGATTGAA ATCGCGTCGA AGGATCAATG GCAAATCCTT TTTAACTGCA TATTAGCCAT TGGAGCCTGG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TGTATAGAGG GGGAATCTAC TGATATAGAT GTTTTTTACT ATCAAAATGC TAAATCTCAT TTGACGAGCA AGGTCTTCGA GTCAGGTTCC ATAATTTTGG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TGACAGCCCT ACATCTTCTG TCGCGATATA CACAGTGGAG GCAGAAAACA AATACTAGCT ATAATTTTCA CAGCTTTTCC ATAAGAATGG CCATATCATT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GGGCTTGAAT AGGGACCTCC CCTCGTCCTT CAGTGATAGC AGCATTCTGG AACAAAGACG CCGAATTTGG TGGTCTGTCT ACTCTTGGGA GATCCAATTG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TCCCTGCTTT ATGGTCGATC CATCCAGCTT TCTCAGAATA CAATCTCCTT CCCTTCTTCT GTCGACGATG TGCAGCGTAC CACAACAGGT CCCACCATAT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ATCATGGCAT CATTGAAACA GCAAGGCTCT TACAAGTTTT CACAAAAATC TATGAACTAG ACAAAACAGT AACTGCAGAA AAAAGTCCTA TATGTGCAAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AAAATGCTTG ATGATTTGTA ATGAGATTGA GGAGGTTTCG AGACAGGCAC CAAAGTTTTT ACAAATGGAT ATTTCCACCA CCGCTCTAAC CAATTTGTTG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AAGGAACACC CTTGGCTATC CTTTACAAGA TTCGAACTGA AGTGGAAACA GTTGTCTCTT ATCATTTATG TATTAAGAGA TTTTTTCACT AATTTTACCC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AGAAAAAGTC ACAACTAGAA CAGGATCAAA ATGATCATCA AAGTTATGAA GTTAAACGAT GCTCCATCAT GTTAAGCGAT GCAGCACAAA GAACTGTTAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GTCTGTAAGT AGCTATATGG ACAATCATAA TGTCACCCCA TATTTTGCCT GGAATTGTTC TTATTACTTG TTCAATGCAG TCCTAGTACC CATAAAGACT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CTACTCTCAA ACTCAAAATC GAATGCTGAG AATAACGAGA CCGCACAATT ATTACAACAA ATTAACACTG TTCTGATGCT ATTAAAAAAA CTGGCCACTT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TTAAAATCCA GACTTGTGAA AAATACATTC AAGTACTGGA AGAGGTATGT GCGCCGTTTC TGTTATCACA GTGTGCAATC CCATTACCGC ATATCAGTTA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TAACAATAGT AATGGTAGCG CCATTAAAAA TATTGTCGGT TCTGCAACTA TCGCCCAATA CCCTACTCTT CCGGAGGAAA ATGTCAACAA TATCAGTGTT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

AAATATGTTT CTCCTGGCTC AGTAGGGCCT TCACCTGTGC CATTGAAATC AGGAGCAAGT TTCAGTGATC TAGTCAAGCT GTTATCTAAC CGTCCACCCT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CTCGTAACTC TCCAGTGACA ATACCAAGAA GCACACCTTC GCATCGCTCA GTCACGCCTT TTCTAGGGCA ACAGCAACAG CTGCAATCAT TAGTGCCACT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GACCCCGTCT GCTTTGTTTG GTGGCGCCAA TTTTAATCAA AGTGGGAATA TTGCTGATAG CTCATTGTCC TTCACTTTCA CTAACAGTAG CAACGGTCCG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AACCTCATAA CAACTCAAAC AAATTCTCAA GCGCTTTCAC AACCAATTGC CTCCTCTAAC GTTCATGATA ACTTCATGAA TAATGAAATC ACGGCTAGTA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

AAATTGATGA TGGTAATAAT TCAAAACCAC TGTCACCTGG TTGGACGGAC CAAACTGCGT ATAACGCGTT TGGAATCACT ACAGGGATGT TTAATACCAC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TACAATGGAT GATGTATATA ACTATCTATT CGATGATGAA GATACCCCAC CAAACCCAAA AAAAGAGTAA
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pFGAL4h-HCV1rc The name of the promoter used to express this mRNA:
TPI

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

not tested

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

not tested

A promoter reported in cDNA corresponding to IRES sequence:

not tested

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:
unclear_result

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

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

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:
not_tested

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:

Saccharomyces cerevisiae pJ69a

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
HCV1a

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Hepatitis C virus type 1a

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

GAATTAATTC ACCATGGAAG ACGCCAAAAA CATAAAGAAA GGCCCGGCGC CATTCTATCC GCTGGAAGAT GGAACCGCTG GAGAGCAACT GCATAAGGCT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATGAAGAGAT ACGCCCTGGT TCCTGGAACA ATTGCTTTTA CAGATGCACA TATCGAGGTG GACATCACTT ACGCTGAGTA CTTCGAAATG TCCGTTCGGT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGGCAGAAGC TATGAAACGA TATGGGCTGA ATACAAATCA CAGAATCGTC GTATGCAGTG AAAACTCTCT TCAATTCTTT ATGCCGGTGT TGGGCGCGTT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATTTATCGGA GTTGCAGTTG CGCCCGCGAA CGACATTTAT AATGAACGTG AATTGCTCAA CAGTATGGGC ATTTCGCAGC CTACCGTGGT GTTCGTTTCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AAAAAGGGGT TGCAAAAAAT TTTGAACGTG CAAAAAAAGC TCCCAATCAT CCAAAAAATT ATTATCATGG ATTCTAAAAC GGATTACCAG GGATTTCAGT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGATGTACAC GTTCGTCACA TCTCATCTAC CTCCCGGTTT TAATGAATAC GATTTTGTGC CAGAGTCCTT CGATAGGGAC AAGACAATTG CACTGATCAT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GAACTCCTCT GGATCTACTG GTCTGCCTAA AGGTGTCGCT CTGCCTCATA GAACTGCCTG CGTGAGATTC TCGCATGCCA GAGATCCTAT TTTTGGCAAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CAAATCATTC CGGATACTGC GATTTTAAGT GTTGTTCCAT TCCATCACGG TTTTGGAATG TTTACTACAC TCGGATATTT GATATGTGGA TTTCGAGTCG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TCTTAATGTA TAGATTTGAA GAAGAGCTGT TTCTGAGGAG CCTTCAGGAT TACAAGATTC AAAGTGCGCT GCTGGTGCCA ACCCTATTCT CCTTCTTCGC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CAAAAGCACT CTGATTGACA AATACGATTT ATCTAATTTA CACGAAATTG CTTCTGGTGG CGCTCCCCTC TCTAAGGAAG TCGGGGAAGC GGTTGCCAAG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGGTTCCATC TGCCAGGTAT CAGGCAAGGA TATGGGCTCA CTGAGACTAC ATCAGCTATT CTGATTACAC CCGAGGGGGA TGATAAACCG GGCGCGGTCG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GTAAAGTTGT TCCATTTTTT GAAGCGAAGG TTGTGGATCT GGATACCGGG AAAACGCTGG GCGTTAATCA AAGAGGCGAA CTGTGTGTGA GAGGTCCTAT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GATTATGTCC GGTTATGTAA ACAATCCGGA AGCGACCAAC GCCTTGATTG ACAAGGATGG ATGGCTACAT TCTGGAGACA TAGCTTACTG GGACGAAGAC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GAACACTTCT TCATCGTTGA CCGCCTGAAG TCTCTGATTA AGTACAAAGG CTATCAGGTG GCTCCCGCTG AATTGGAATC CATCTTGCTC CAACACCCCA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ACATCTTCGA CGCAGGTGTC GCAGGTCTTC CCGACGATGA CGCCGGTGAA CTTCCCGCCG CCGTTGTTGT TTTGGAGCAC GGAAAGACGA TGACGGAAAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGAGATCGTG GATTACGTCG CCAGTCAAGT AACAACCGCG AAAAAGTTGC GCGGAGGAGT TGTGTTTGTG GACGAAGTAC CGAAAGGTCT TACCGGAAAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CTCGACGCAA GAAAAATCAG AGAGATCCTC ATAAAGGCCA AGAAGGGCGG AAAGATCGCC GTGTAATTCT AGCCTAGGAA ACCCCCCCCC CCCCAAAGGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GGGGGGGGGG AGGGCCCAGG ATCCGTCGAC AAGCTTGAAT TCGTGTTACG TTTGGTTTTT CTTTGAGGTT TAGGATTCGT GCTCATGGTG CACGGTCTAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GAGACCTCCC GGGGCACTCG CAAGCACCCT ATCAGGCAGT ACCACAAGGC CTTTCGCGAC CCAACACTAC TCGGCTAGCA GTCTTGCGGG GGCACGCCCA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AATCTCCAGG CATTGAGCGG GTTTATCCAA GAAAGGACCC GGTCGTCCTG GCAATTCCGG TGTACTCACC GGTTCCGCAG ACCACTATGG CTCTCCCGGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGGGGGGGTC CTGGAGGCTG CACGACACTC ATACTAACGC CATGGCTAGA CGCTTTCTGC GTGAAGACAG TAGTTCCTCA CAGGGGAGTG ATTCATGGTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GAGTGTCGCC CCCATCAGGG GGCTGGCGAA TTCAAAAATG AAGCTACTGT CTTCTATCGA ACAAGCATGC GATATTTGCC GACTTAAAAA GCTCAAGTGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCCAAAGAAA AACCGAAGTG CGCCAAGTGT CTGAAGAACA ACTGGGAGTG TCGCTACTCT CCCAAAACCA AAAGGTCTCC GCTGACTAGG GCACATCTGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CAGAAGTGGA ATCAAGGCTA GAAAGACTGG AACAGCTATT TCTACTGATT TTTCCTCGAG AAGACCTTGA CATGATTTTG AAAATGGATT CTTTACAGGA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TATAAAAGCA TTGTTAACAG GATTATTTGT ACAAGATAAT GTGAATAAAG ATGCCGTCAC AGATAGATTG GCTTCAGTGG AGACTGATAT GCCTCTAACA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTGAGACAGC ATAGAATAAG TGCGACATCA TCATCGGAAG AGAGTAGTAA CAAAGGTCAA AGACAGTTGA CTGTATCGAT TGACTCGGCA GCTCATCATG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATAACTCCAC AATTCCGTTG GATTTTATGC CCAGGGATGC TCTTCATGGA TTTGATTGGT CTGAAGAGGA TGACATGTCG GATGGCTTGC CCTTCCTGAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AACGGACCCC AACAATAATG GGTTCTTTGG CGACGGTTCT CTCTTATGTA TTCTTCGATC TATTGGCTTT AAACCGGAAA ATTACACGAA CTCTAACGTT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AACAGGCTCC CGACCATGAT TACGGATAGA TACACGTTGG CTTCTAGATC CACAACATCC CGTTTACTTC AAAGTTATCT CAATAATTTT CACCCCTACT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GCCCTATCGT GCACTCACCG ACGCTAATGA TGTTGTATAA TAACCAGATT GAAATCGCGT CGAAGGATCA ATGGCAAATC CTTTTTAACT GCATATTAGC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CATTGGAGCC TGGTGTATAG AGGGGGAATC TACTGATATA GATGTTTTTT ACTATCAAAA TGCTAAATCT CATTTGACGA GCAAGGTCTT CGAGTCAGGT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TCCATAATTT TGGTGACAGC CCTACATCTT CTGTCGCGAT ATACACAGTG GAGGCAGAAA ACAAATACTA GCTATAATTT TCACAGCTTT TCCATAAGAA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGGCCATATC ATTGGGCTTG AATAGGGACC TCCCCTCGTC CTTCAGTGAT AGCAGCATTC TGGAACAAAG ACGCCGAATT TGGTGGTCTG TCTACTCTTG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GGAGATCCAA TTGTCCCTGC TTTATGGTCG ATCCATCCAG CTTTCTCAGA ATACAATCTC CTTCCCTTCT TCTGTCGACG ATGTGCAGCG TACCACAACA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GGTCCCACCA TATATCATGG CATCATTGAA ACAGCAAGGC TCTTACAAGT TTTCACAAAA ATCTATGAAC TAGACAAAAC AGTAACTGCA GAAAAAAGTC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CTATATGTGC AAAAAAATGC TTGATGATTT GTAATGAGAT TGAGGAGGTT TCGAGACAGG CACCAAAGTT TTTACAAATG GATATTTCCA CCACCGCTCT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AACCAATTTG TTGAAGGAAC ACCCTTGGCT ATCCTTTACA AGATTCGAAC TGAAGTGGAA ACAGTTGTCT CTTATCATTT ATGTATTAAG AGATTTTTTC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ACTAATTTTA CCCAGAAAAA GTCACAACTA GAACAGGATC AAAATGATCA TCAAAGTTAT GAAGTTAAAC GATGCTCCAT CATGTTAAGC GATGCAGCAC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AAAGAACTGT TATGTCTGTA AGTAGCTATA TGGACAATCA TAATGTCACC CCATATTTTG CCTGGAATTG TTCTTATTAC TTGTTCAATG CAGTCCTAGT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ACCCATAAAG ACTCTACTCT CAAACTCAAA ATCGAATGCT GAGAATAACG AGACCGCACA ATTATTACAA CAAATTAACA CTGTTCTGAT GCTATTAAAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AAACTGGCCA CTTTTAAAAT CCAGACTTGT GAAAAATACA TTCAAGTACT GGAAGAGGTA TGTGCGCCGT TTCTGTTATC ACAGTGTGCA ATCCCATTAC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CGCATATCAG TTATAACAAT AGTAATGGTA GCGCCATTAA AAATATTGTC GGTTCTGCAA CTATCGCCCA ATACCCTACT CTTCCGGAGG AAAATGTCAA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CAATATCAGT GTTAAATATG TTTCTCCTGG CTCAGTAGGG CCTTCACCTG TGCCATTGAA ATCAGGAGCA AGTTTCAGTG ATCTAGTCAA GCTGTTATCT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AACCGTCCAC CCTCTCGTAA CTCTCCAGTG ACAATACCAA GAAGCACACC TTCGCATCGC TCAGTCACGC CTTTTCTAGG GCAACAGCAA CAGCTGCAAT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CATTAGTGCC ACTGACCCCG TCTGCTTTGT TTGGTGGCGC CAATTTTAAT CAAAGTGGGA ATATTGCTGA TAGCTCATTG TCCTTCACTT TCACTAACAG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TAGCAACGGT CCGAACCTCA TAACAACTCA AACAAATTCT CAAGCGCTTT CACAACCAAT TGCCTCCTCT AACGTTCATG ATAACTTCAT GAATAATGAA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATCACGGCTA GTAAAATTGA TGATGGTAAT AATTCAAAAC CACTGTCACC TGGTTGGACG GACCAAACTG CGTATAACGC GTTTGGAATC ACTACAGGGA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TGTTTAATAC CACTACAATG GATGATGTAT ATAACTATCT ATTCGATGAT GAAGATACCC CACCAAACCC AAAAAAAGAG TAAGAGCTCA GCTAGCTAAC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TGAATAAGGA ACAATGAACG TTTTTCCTTT CTCTTGTTCC TAGTATTAAT GACTGACCGA TACATCCCTT TTTTTTTTTG TCTTTGTCTA GCTCCAATTC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GCCCTATAGT GAGTCGTATT ACAATTCACT GGCCGTCGTT TTACAACGTC GTGACTGGGA AAACCCTGGC GTTACCCAAC TTAATCGCCT TGCAGCACAT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CCCCCTTTCG CCAGCTGGCG TAATAGCGAA GAGGCCCGCA CCGATCGCCC TTCCCAACAG TTGCGCAGCC TGAATGGCGA ATGGACGCGC CCTGTAGCGG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CGCATTAAGC GCGGCGGGTG TGGTGGTTAC GCGCAGCGTG ACCGCTACAC TTGCCAGCGC CCTAGCGCCC GCTCCTTTCG CTTTCTTCCC TTCCTTTCTC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GCCACGTTCG CCGGCTTTCC CCGTCAAGCT CTAAATCGGG GGCTCCCTTT AGGGTTCCGA TTTAGTGCTT TACGGCACCT CGACCCCAAA AAACTTGATT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

AGGGTGATGG TTCACGTAGT GGGCCATCGC CCTGATAGAC GGTTTTTCGC CCTTTGACGT TGGAGTCCAC GTTCTTTAAT AGTGGACTCT TGTTCCAAAC 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TGGAACAACA CTCAACCCTA TCTCGGTCTA TTCTTTTGAT TTATAAGGGA TTTTGCCGAT TTCGGCCTAT TGGTTAAAAA ATGAGCTGAT TTAACAAAAA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TTTAACGCGA ATTTTAACAA AATATTAACG CTTACAATTT CCTGATGCGG TATTTTCTCC TTACGCATCT GTGCGGTATT TCACACCGCA TAGGGTAATA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ACTGATATAA TTAAATTGAA GCTCTAATTT GTGAGTTTAG TATACATGCA TTTACTTATA ATACAGTTTT TTAGTTTTGC TGGCCGCATC TTCTCAAATA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TGCTTCCCAG CCTGCTTTTC TGTAACGTTC ACCCTCTACC TTAGCATCCC TTCCCTTTGC AAATAGTCCT CTTCCAACAA TAATAATGTC AGATCCTGTA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GAGACCACAT CATCCACGGT TCTATACTGT TGACCCAATG CGTCTCCCTT GTCATCTAAA CCCACACCGG GTGTCATAAT CAACCAATCG TAACCTTCAT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CTCTTCCACC CATGTCTCTT TGAGCAATAA AGCCGATAAC AAAATCTTTG TCGCTCTTCG CAATGTCAAC AGTACCCTTA GTATATTCTC CAGTAGATAG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GGAGCCCTTG CATGACAATT CTGCTAACAT CAAAAGGCCT CTAGGTTCCT TTGTTACTTC TTCTGCCGCC TGCTTCAAAC CGCTAACAAT ACCTGGCCCC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ACCACACCGT GTGCATTCGT AATGTCTGCC CATTCTGCTA TTCTGTATAC ACCCGCAGAG TACTGCAATT TGACTGTATT ACCAATGTCA GCAAATTTTC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TGTCTTCGAA GAGTAAAAAA TTGTACTTGG CGGATAATGC CTTTAGCGGC TTAACTGTGC CCTCCATCGA AAAATCAGTC AATATATCCA CATGTGTTTT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TAGTAAACAA ATTTTGGGAC CTAATGCTTC AACTAACTCC AGTAATTCCT TGGTGGTACG AACATCCAAT GAAGCACACA AGTTTGTTTG CTTTTCGTGC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

ATGATATTAA ATAGCTTGGC AGCAACAGGA CTAGGATGAG TAGCAGCACG TTCCTTATAT GTAGCTTTCG ACATGATTTA TCTTCGTTTC CTGCAGGTTT 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TTGTTCTGTG CAGTTGGGTT AAGAATACTG GGCAATTTCA TGTTTCTTCA ACACTACATA TGCGTATATA TACCAATCTA AGTCTGTGCT CCTTCCTTCG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

TTCTTCCTTC TGTTCGGAGA TTACCGAATC AAAAAAATTT CAAGGAAACC GAAATCAAAA AAAAGAATAA AAAAAAAATG ATGAATTGAA AAGGTGGTAT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GGTGCACTCT CAGTACAATC TGCTCTGATG CCGCATAGTT AAGCCAGCCC CGACACCCGC CAACACCCGC TGACGCGCCC TGACGGGCTT GTCTGCTCCC 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

GGCATCCGCT TACAGACAAG CTGTGACCGT CTCCGGGAGC TGCATGTGTC AGAGGTTTTC ACCGTCATCA CCGAAACGCG CGAGACGAAA GGGCCTCGTG 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

ATACGCCTAT TTTTATAGGT TAATGTCATG ATAATAATGG TTTCTTAGAC GTGCGGCCGC TCTAGAACTA GTGGATCAAT TCCACGGACT ATAGACTATA 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CTAGTATACT CCGTCTACTG TACGATACAC TTCCGCTCAG GTCCTTGTCC TTTAACGAGG CCTTACCACT CTTTTGTTAC TCTATTGATC CAGCTCAGCA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

AAGGCAGTGT GATCTAAGAT TCTATCTTCG CGATGTAGTA AAACTAGCTA GACCGAGAAA GAGACTAGAA ATGCAAAAGG CACTTCTACA ATGGCTGCCA 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TCATTATTAT CCGATGTGAC GCTGCAGCTT CTCAATGATA TTCGAATACG CTTTGAGGAG ATACAGCCTA ATATCCGACA AACTGTTTTA CAGATTTACG 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

ATCGTACTTG TTACCCATCA TTGAATTTTG AACATCCGAA CCTGGGAGTT TTCCCTGAAA CAGATAGTAT ATTTGAACCT GTATAATAAT ATATAGTCTA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

GCGCTTTACG GAAGACAATG TATGTATTTC GGTTCCTGGA GAAACTATTG CATCTATTGC ATAGGTAATC TTGCACGTCG CATCCCCGGT TCATTTTCTG 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

CGTTTCCATC TTGCACTTCA ATAGCATATC TTTGTTAACG AAGCATCTGT GCTTCATTTT GTAGAACAAA AATGCAACGC GAGAGCGCTA ATTTTTCAAA 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

CAAAGAATCT GAGCTGCATT TTTACAGAAC AGAAATGCAA CGCGAAAGCG CTATTTTACC AACGAAGAAT CTGTGCTTCA TTTTTGTAAA ACAAAAATGC 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

AACGCGAGAG CGCTAATTTT TCAAACAAAG AATCTGAGCT GCATTTTTAC AGAACAGAAA TGCAACGCGA GAGCGCTATT TTACCAACAA AGAATCTATA 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

CTTCTTTTTT GTTCTACAAA AATGCATCCC GAGAGCGCTA TTTTTCTAAC AAAGCATCTT AGATTACTTT TTTTCTCCTT TGTGCGCTCT ATAATGCAGT 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

CTCTTGATAA CTTTTTGCAC TGTAGGTCCG TTAAGGTTAG AAGAAGGCTA CTTTGGTGTC TATTTTCTCT TCCATAAAAA AAGCCTGACT CCACTTCCCG 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

CGTTTACTGA TTACTAGCGA AGCTGCGGGT GCATTTTTTC AAGATAAAGG CATCCCCGAT TATATTCTAT ACCGATGTGG ATTGCGCATA CTTTGTGAAC 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

AGAAAGTGAT AGCGTTGATG ATTCTTCATT GGTCAGAAAA TTATGAACGG TTTCTTCTAT TTTGTCTCTA TATACTACGT ATAGGAAATG TTTACATTTT 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

CGTATTGTTT TCGATTCACT CTATGAATAG TTCTTACTAC AATTTTTTTG TCTAAAGAGT AATACTAGAG ATAAACATAA AAAATGTAGA GGTCGAGTTT 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

AGATGCAAGT TCAAGGAGCG AAAGGTGGAT GGGTAGGTTA TATAGGGATA TAGCACAGAG ATATATAGCA AAGAGATACT TTTGAGCAAT GTTTGTGGAA 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

GCGGTATTCG CAATATTTTA GTAGCTCGTT ACAGTCCGGT GCGTTTTTGG TTTTTTGAAA GTGCGTCTTC AGAGCGCTTT TGGTTTTCAA AAGCGCTCTG 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

AAGTTCCTAT ACTTTCTAGA GAATAGGAAC TTCGGAATAG GAACTTCAAA GCGTTTCCGA AAACGAGCGC TTCCGAAAAT GCAACGCGAG CTGCGCACAT 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

ACAGCTCACT GTTCACGTCG CACCTATATC TGCGTGTTGC CTGTATATAT ATATACATGA GAAGAACGGC ATAGTGCGTG TTTATGCTTA AATGCGTACT 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

TATATGCGTC TATTTATGTA GGATGAAAGG TAGTCTAGTA CCTCCTGTGA TATTATCCCA TTCCATGCGG GGTATCGTAT GCTTCCTTCA GCACTACCCT 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

TTAGCTGTTC TATATGCTGC CACTCCTCAA TTGGATTAGT CTCATCCTTC AATGCTATCA TTTCCTTTGA TATTGGATCA TATGCATAGT ACCGAGAAAC 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

TAGTGCGAAG TAGTGATCAG GTATTGCTGT TATCTGATGA GTATACGTTG TCCTGGCCAC GGCAGAAGCA CGCTTATCGC TCCAATTTCC CACAACATTA 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

GTCAACTCCG TTAGGCCCTT CATTGAAAGA AATGAGGTCA TCAAATGTCT TCCAATGTGA GATTTTGGGC CATTTTTTAT AGCAAAGATT GAATAAGGCG 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

CATTTTTCTT CAAAGCTGCG GCCGCACTCT CACTAGTACG TCAGGTGGCA CTTTTCGGGG AAATGTGCGC GGAACCCCTA TTTGTTTATT TTTCTAAATA 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

CATTCAAATA TGTATCCGCT CATGAGACAA TAACCCTGAT AAATGCTTCA ATAATATTGA AAAAGGAAGA GTATGAGTAT TCAACATTTC CGTGTCGCCC 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

TTATTCCCTT TTTTGCGGCA TTTTGCCTTC CTGTTTTTGC TCACCCAGAA ACGCTGGTGA AAGTAAAAGA TGCTGAAGAT CAGTTGGGTG CACGAGTGGG 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

TTACATCGAA CTGGATCTCA ACAGCGGTAA GATCCTTGAG AGTTTTCGCC CCGAAGAACG TTTTCCAATG ATGAGCACTT TTAAAGTTCT GCTATGTGGC 
^9401      ^9411      ^9421      ^9431      ^9441      ^9451      ^9461      ^9471      ^9481      ^9491      

GCGGTATTAT CCCGTATTGA CGCCGGGCAA GAGCAACTCG GTCGCCGCAT ACACTATTCT CAGAATGACT TGGTTGAGTA CTCACCAGTC ACAGAAAAGC 
^9501      ^9511      ^9521      ^9531      ^9541      ^9551      ^9561      ^9571      ^9581      ^9591      

ATCTTACGGA TGGCATGACA GTAAGAGAAT TATGCAGTGC TGCCATAACC ATGAGTGATA ACACTGCGGC CAACTTACTT CTGACAACGA TCGGAGGACC 
^9601      ^9611      ^9621      ^9631      ^9641      ^9651      ^9661      ^9671      ^9681      ^9691      

GAAGGAGCTA ACCGCTTTTT TGCACAACAT GGGGGATCAT GTAACTCGCC TTGATCGTTG GGAACCGGAG CTGAATGAAG CCATACCAAA CGACGAGCGT 
^9701      ^9711      ^9721      ^9731      ^9741      ^9751      ^9761      ^9771      ^9781      ^9791      

GACACCACGA TGCCTGTAGC AATGGCAACA ACGTTGCGCA AACTATTAAC TGGCGAACTA CTTACTCTAG CTTCCCGGCA ACAATTAATA GACTGGATGG 
^9801      ^9811      ^9821      ^9831      ^9841      ^9851      ^9861      ^9871      ^9881      ^9891      

AGGCGGATAA AGTTGCAGGA CCACTTCTGC GCTCGGCCCT TCCGGCTGGC TGGTTTATTG CTGATAAATC TGGAGCCGGT GAGCGTGGGT CTCGCGGTAT 
^9901      ^9911      ^9921      ^9931      ^9941      ^9951      ^9961      ^9971      ^9981      ^9991      

CATTGCAGCA CTGGGGCCAG ATGGTAAGCC CTCCCGTATC GTAGTTATCT ACACGACGGG GAGTCAGGCA ACTATGGATG AACGAAATAG ACAGATCGCT 
^10001     ^10011     ^10021     ^10031     ^10041     ^10051     ^10061     ^10071     ^10081     ^10091     

GAGATAGGTG CCTCACTGAT TAAGCATTGG TAACTGTCAG ACCAAGTTTA CTCATATATA CTTTAGATTG ATTTAAAACT TCATTTTTAA TTTAAAAGGA 
^10101     ^10111     ^10121     ^10131     ^10141     ^10151     ^10161     ^10171     ^10181     ^10191     

TCTAGGTGAA GATCCTTTTT GATAATCTCA TGACCAAAAT CCCTTAACGT GAGTTTTCGT TCCACTGAGC GTCAGACCCC GTAGAAAAGA TCAAAGGATC 
^10201     ^10211     ^10221     ^10231     ^10241     ^10251     ^10261     ^10271     ^10281     ^10291     

TTCTTGAGAT CCTTTTTTTC TGCGCGTAAT CTGCTGCTTG CAAACAAAAA AACCACCGCT ACCAGCGGTG GTTTGTTTGC CGGATCAAGA GCTACCAACT 
^10301     ^10311     ^10321     ^10331     ^10341     ^10351     ^10361     ^10371     ^10381     ^10391     

CTTTTTCCGA AGGTAACTGG CTTCAGCAGA GCGCAGATAC CAAATACTGT TCTTCTAGTG TAGCCGTAGT TAGGCCACCA CTTCAAGAAC TCTGTAGCAC 
^10401     ^10411     ^10421     ^10431     ^10441     ^10451     ^10461     ^10471     ^10481     ^10491     

CGCCTACATA CCTCGCTCTG CTAATCCTGT TACCAGTGGC TGCTGCCAGT GGCGATAAGT CGTGTCTTAC CGGGTTGGAC TCAAGACGAT AGTTACCGGA 
^10501     ^10511     ^10521     ^10531     ^10541     ^10551     ^10561     ^10571     ^10581     ^10591     

TAAGGCGCAG CGGTCGGGCT GAACGGGGGG TTCGTGCACA CAGCCCAGCT TGGAGCGAAC GACCTACACC GAACTGAGAT ACCTACAGCG TGAGCTATGA 
^10601     ^10611     ^10621     ^10631     ^10641     ^10651     ^10661     ^10671     ^10681     ^10691     

GAAAGCGCCA CGCTTCCCGA AGGGAGAAAG GCGGACAGGT ATCCGGTAAG CGGCAGGGTC GGAACAGGAG AGCGCACGAG GGAGCTTCCA GGGGGAAACG 
^10701     ^10711     ^10721     ^10731     ^10741     ^10751     ^10761     ^10771     ^10781     ^10791     

CCTGGTATCT TTATAGTCCT GTCGGGTTTC GCCACCTCTG ACTTGAGCGT CGATTTTTGT GATGCTCGTC AGGGGGGCGG AGCCTATGGA AAAACGCCAG 
^10801     ^10811     ^10821     ^10831     ^10841     ^10851     ^10861     ^10871     ^10881     ^10891     

CAACGCGGCC TTTTTACGGT TCCTGGCCTT TTGCTGGCCT TTTGCTCACA TGTTCTTTCC TGCGTTATCC CCTGATTCTG TGGATAACCG TATTACCGCC 
^10901     ^10911     ^10921     ^10931     ^10941     ^10951     ^10961     ^10971     ^10981     ^10991     

TTTGAGTGAG CTGATACCGC TCGCCGCAGC CGAACGACCG AGCGCAGCGA GTCAGTGAGC GAGGAAGCGG AAGAGCGCCC AATACGCAAA CCGCCTCTCC 
^11001     ^11011     ^11021     ^11031     ^11041     ^11051     ^11061     ^11071     ^11081     ^11091     

CCGCGCGTTG GCCGATTCAT TAATGCAGCT GGCACGACAG GTTTCCCGAC TGGAAAGCGG GCAGTGAGCG CAACGCAATT AATGTGAGTT AGCTCACTCA 
^11101     ^11111     ^11121     ^11131     ^11141     ^11151     ^11161     ^11171     ^11181     ^11191     

TTAGGCACCC CAGGCTTTAC ACTTTATGCT TCCGGCTCGT ATGTTGTGTG GAATTGTGAG CGGATAACAA TTTCACACAG GAAACAGCTA TGACCATGAT 
^11201     ^11211     ^11221     ^11231     ^11241     ^11251     ^11261     ^11271     ^11281     ^11291     

TACGCCAAGC TCGAAATTAA CCCTCACTAA AGGGAACAAA AGCTGGTACC GGGCCGGCCG TCGAGCTTGA TGGCATCGTG GTGTCACGCT CGTCGTTTGG 
^11301     ^11311     ^11321     ^11331     ^11341     ^11351     ^11361     ^11371     ^11381     ^11391     

TATGGCTTCA TTCAGCTCCG GTTCCCAACG ATCAAGGCGA GTTACATGAT CCCCCATGTT GTGCAAAAAA GCGGTTAGCT CCTTCGGTCC TCCGATCGTT 
^11401     ^11411     ^11421     ^11431     ^11441     ^11451     ^11461     ^11471     ^11481     ^11491     

GTCAGAAGTA AGTTGGCCGC AGTGTTATCA CTCATGGTTA TGGCAGCACT GCATAATTCT CTTACTGTCA TGCCATCCGT AAGATGCTTT TCTGTGACTG 
^11501     ^11511     ^11521     ^11531     ^11541     ^11551     ^11561     ^11571     ^11581     ^11591     

GTGAGTACTC AACCAAGTCA TTCTGAGAAT AGTGTATGCG GCGACCGAGT TGCTCTTGCC CGGCGTCAAC ACGGGATAAT ACCGCGCCAC ATAGCAGAAC 
^11601     ^11611     ^11621     ^11631     ^11641     ^11651     ^11661     ^11671     ^11681     ^11691     

TTTAAAAGTG CTCATCATTG GAAAACGTTC TTCGGGGCGA AAACTCTCAA GGATCTTACC GCTGTTGAGA TCCAGTTCGA TGTAACCCAC TCGTGCACCC 
^11701     ^11711     ^11721     ^11731     ^11741     ^11751     ^11761     ^11771     ^11781     ^11791     

AACTGATCTT CAGCATCTTT TACTTTCACC AGCGTTTCTG GGTGAGCAAA AACAGGAAGG CAAAATGCCG CAAAAAAGGG AATAAGGGCG ACACGGAAAT 
^11801     ^11811     ^11821     ^11831     ^11841     ^11851     ^11861     ^11871     ^11881     ^11891     

GTTGAATACT CATACTCTTC CTTTTTCAAT ATTATTGAAG CATTTATCAG GGTTATTGTC TCATGAGCGG ATACATATTT GAATGTATTT AGAAAAATAA 
^11901     ^11911     ^11921     ^11931     ^11941     ^11951     ^11961     ^11971     ^11981     ^11991     

ACAAATAGGG GTTCCGCGCA CATTTCCCCG AAAAGTGCCA CCTGACGTCT AAGAAACCAT TATTATCATG ACATTAACCT ATAAAAATAG GCGTATCACG 
^12001     ^12011     ^12021     ^12031     ^12041     ^12051     ^12061     ^12071     ^12081     ^12091     

AGGCCCTTTC GTCTTCAAGA ATTGGGGATC TACGTATGGT CATTTCTTCT TCAGATTCCC TCATGGAGAA AGTGCGGCAG ATGTATATGA CAGAGTCGCC 
^12101     ^12111     ^12121     ^12131     ^12141     ^12151     ^12161     ^12171     ^12181     ^12191     

AGTTTCCAAG AGACTTTATT CAGGCACTTC CATGATAGGC AAGAGAGAAG ACCCAGAGAT GTTGTTGTCC TAGTTACACA TGGTATTTAT TCCAGAGTAT 
^12201     ^12211     ^12221     ^12231     ^12241     ^12251     ^12261     ^12271     ^12281     ^12291     

TCCTGATGAA ATGGTTTAGA TGGACATACG AAGAGTTTGA ATCGTTTACC AATGTTCCTA ACGGGAGCGT AATGGTGATG GAACTGGACG AATCCATCAA 
^12301     ^12311     ^12321     ^12331     ^12341     ^12351     ^12361     ^12371     ^12381     ^12391     

TAGATACGTC CTGAGGACCG TGCTACCCAA ATGGACTGAT TGTGAGGGAG ACCTAACTAC ATAGTGTTTA AAGATTACGG ATATTTAACT TACTTAGAAT 
^12401     ^12411     ^12421     ^12431     ^12441     ^12451     ^12461     ^12471     ^12481     ^12491     

AATGCCATTT TTTTGAGTTA TAATAATCCT ACGTTAGTGT GAGCGGGATT TAAACTGTGA GGACCTTAAT ACATTCAGAC ACTTCTGCGG TATCACCCTA 
^12501     ^12511     ^12521     ^12531     ^12541     ^12551     ^12561     ^12571     ^12581     ^12591     

CTTATTCCCT TCGAGATTAT ATCTAGGAAC CCATCAGGTT GGTGGAAGAT TACCCGTTCT AAGACTTTTC AGCTTCCTCT ATTGATGTTA CACCTGGACA 
^12601     ^12611     ^12621     ^12631     ^12641     ^12651     ^12661     ^12671     ^12681     ^12691     

CCCCTTTTCT GGCATCCAGT TTTTAATCTT CAGTGGCATG TGAGATTCTC CGAAATTAAT TAAAGCAATC ACACAATTCT CTCGGATACC ACCTCGGTTG 
^12701     ^12711     ^12721     ^12731     ^12741     ^12751     ^12761     ^12771     ^12781     ^12791     

AAACTGACAG GTGGTTTGTT ACGCATGCTA ATGCAAAGGA GCCTATATAC CTTTGGCTCG GCTGCTGTAA CAGGGAATAT AAAGGGCAGC ATAATTTAGG 
^12801     ^12811     ^12821     ^12831     ^12841     ^12851     ^12861     ^12871     ^12881     ^12891     

AGTTTAGTGA ACTTGCAACA TTTACTATTT TCCCTTCTTA CGTAAATATT TTTCTTTTTA ATTCTAAATC AATCTTTTTC AATTTTTTGT TTGTATTCTT 
^12901     ^12911     ^12921     ^12931     ^12941     ^12951     ^12961     ^12971     ^12981     ^12991     

TTCTTGCTTA AATCTATAAC TACAAAAAAC ACATACAG
^13001     ^13011     ^13021     ^13031

Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks):

plasmid sequence confirmed by IRESite curators by restriction analysis + parts by PCR + sequencing

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

The total number of notable open-reading frames (ORFs):

2

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

ORF

ORF position:

1

Version: `0`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek

The abbreviated name of this ORF/gene:
Fluc

The description of the protein encoded in this ORF:
firefly luciferase

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:

no

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

1-1653

ORF

ORF position:

2

Version: `1`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek

The abbreviated name of this ORF/gene:
GAL4

The description of the protein encoded in this ORF:
DNA-binding transcription factor required for the activation of the GAL genes in response to galactose; repressed by Gal80p and activated by Gal3p.

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:

no

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

2125-4770

OPTIONAL: The function of the encoded protein

Molecular Function: transcriptional activator activity (TAS)
Biological Process: galactose metabolism (TAS) regulation of transcription, DNA-dependent (TAS)
Cellular Component: nucleus (TAS)

Remarks:

Sc_HCV_type_1a_rc IRES was inserted into intercistronic position of pFGAL4h bicistronic plasmid that has been
designed for the use in the pFGAL4h/PJ69A reporter system. pFGAL4h vector bears genes for the firefly
luciferase and Gal4p as a first and second cistron, respectively. A stable stem-loop hairpin containing 13G:C
pairs was inserted between the two genes in order to prevent ribosome read-through from the first to the
second cistron. The yeast strain PJ69A contains besides the GAL4 and GAL80 deletions also reporter genes
coding for the yeast Ade2 and His3 proteins and for the bacterial beta-galactosidase - all of them under the
control of the Gal4-inducible Gal1 promoter. Thus pFGAL4/PJ69A represents a specialised and sensitive system,
which allows an enhancement of the measured signal by in vivo coupled transcription and enzymatic detection.
This system can be used for both measuring the ratio of the beta-gal/luc enzymatic activities and searching
for IRES activity by screening the colony growth rates on selection media lacking adenine and histidine and
containing various concentrations of the competitive inhibitor of the histidine biosynthetic pathway.

Vector was created by IRESite curator - thus whole sequence is verified by above mentioned methods.

Citations:

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. 88(Pt 7):1992-2002

IRESs:

IRES:

Version: `3`	Last change: `2008-07-04 12:56:59`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek
The IRES name: `HCV_type_1a_rc`	The functional status of IRES: `defective`

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

1730-2114

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `77`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `461`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-395`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-11`

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

GTGTTACGTT TGGTTTTTCT TTGAGGTTTA GGATTCGTGC TCATGGTGCA CGGTCTACGA GACCTCCCGG GGCACTCGCA AGCACCCTAT CAGGCAGTAC 
^1730      ^1740      ^1750      ^1760      ^1770      ^1780      ^1790      ^1800      ^1810      ^1820      

CACAAGGCCT TTCGCGACCC AACACTACTC GGCTAGCAGT CTTGCGGGGG CACGCCCAAA TCTCCAGGCA TTGAGCGGGT TTATCCAAGA AAGGACCCGG 
^1830      ^1840      ^1850      ^1860      ^1870      ^1880      ^1890      ^1900      ^1910      ^1920      

TCGTCCTGGC AATTCCGGTG TACTCACCGG TTCCGCAGAC CACTATGGCT CTCCCGGGAG GGGGGGTCCT GGAGGCTGCA CGACACTCAT ACTAACGCCA 
^1930      ^1940      ^1950      ^1960      ^1970      ^1980      ^1990      ^2000      ^2010      ^2020      

TGGCTAGACG CTTTCTGCGT GAAGACAGTA GTTCCTCACA GGGGAGTGAT TCATGGTGGA GTGTCGCCCC CATCAGGGGG CTGGC
^2030      ^2040      ^2050      ^2060      ^2070      ^2080      ^2090      ^2100      ^2110

Remarks:

Sc_HCV_type_rc IRES represents the reverse complement sequence of the full-length 5'-UTR of HCV RNA (type 1a)
and of the first 15 codons of the viral polyprotein.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 87

Version: `3`	Last change: `2008-07-04 12:56:59`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek

The translation method used to study IRES function:
in vivo

The organism used for translation:

Saccharomyces cerevisiae pJ69a

The temperature (in degrees of Celsia):
28

The relative translation efficiency in % of this IRES:

41.000

Name of IRES used as the positive control:

HCV1a

Name of the plasmid used as the positive control. `pFGAL4h-HCV1`	Name of the plasmid used as the negative control. `pFGAL4-L428`
`IRESite Id` of the plasmid used as positive control. `86`	`IRESite Id` of the plasmid used as negative control. `126`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `3.800`
The size (length) of intercistronic region in the positive control: `453`	The size (length) of intercistronic region in the negative control: `432`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

The relative translation efficiency and size of intercistronic region of negative control have been inserted
as an average values of all negative controls used (pFGAL4-L413,L-428, L456, IDs 126-128).

Citations:

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