IRESite_Id:369 negative control plasmid pRG

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `369`	Version: `1`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-06-10 09:28:24`

IRESite record type:

negative_control_plasmid_with_promoter_and_without_putative_IRES

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

The mRNA/+RNA description:

Bicistronic mRNA containing DsRED2 and EGFP. The sequence ends at its 3'-end right after the poly(A) signal
from SV40 mRNA and thus the 3'-UTR might be slightly wrong.

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

TCAGATCCGC TAGCGCTACC GGTCGCCACC ATGGCCTCCT CCGAGAACGT CATCACCGAG TTCATGCGCT TCAAGGTGCG CATGGAGGGC ACCGTGAACG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCCACGAGTT CGAGATCGAG GGCGAGGGCG AGGGCCGCCC CTACGAGGGC CACAACACCG TGAAGCTGAA GGTGACCAAG GGCGGCCCCC TGCCCTTCGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CTGGGACATC CTGTCCCCCC AGTTCCAGTA CGGCTCCAAG GTGTACGTGA AGCACCCCGC CGACATCCCC GACTACAAGA AGCTGTCCTT CCCCGAGGGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTCAAGTGGG AGCGCGTGAT GAACTTCGAG GACGGCGGCG TGGCGACCGT GACCCAGGAC TCCTCCCTGC AGGACGGCTG CTTCATCTAC AAGGTGAAGT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TCATCGGCGT GAACTTCCCC TCCGACGGCC CCGTGATGCA GAAGAAGACC ATGGGCTGGG AGGCCTCCAC CGAGCGCCTG TACCCCCGCG ACGGCGTGCT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GAAGGGCGAG ACCCACAAGG CCCTGAAGCT GAAGGACGGC GGCCACTACC TGGTGGAGTT CAAGTCCATC TACATGGCCA AGAAGCCCGT GCAGCTGCCC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GGCTACTACT ACGTGGACGC CAAGCTGGAC ATCACCTCCC ACAACGAGGA CTACACCATC GTGGAGCAGT ACGAGCGCAC CGAGGGCCGC CACCACCTGT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TCCTGAGATC CAGCAAGATA TCCTAAGATC TCGAGCTCAA GCTTCGAATT CTGCAGTCGA CGGTACCGCG GGCCCGGGAT CCACCGGTCG CCACCATGGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GAGCAAGGGC GAGGAGCTGT TCACCGGGGT GGTGCCCATC CTGGTCGAGC TGGACGGCGA CGTAAACGGC CACAAGTTCA GCGTGTCCGG CGAGGGCGAG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGCGATGCCA CCTACGGCAA GCTGACCCTG AAGTTCATCT GCACCACCGG CAAGCTGCCC GTGCCCTGGC CCACCCTCGT GACCACCCTG ACCTACGGCG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGCAGTGCTT CAGCCGCTAC CCCGACCACA TGAAGCAGCA CGACTTCTTC AAGTCCGCCA TGCCCGAAGG CTACGTCCAG GAGCGCACCA TCTTCTTCAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GGACGACGGC AACTACAAGA CCCGCGCCGA GGTGAAGTTC GAGGGCGACA CCCTGGTGAA CCGCATCGAG CTGAAGGGCA TCGACTTCAA GGAGGACGGC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AACATCCTGG GGCACAAGCT GGAGTACAAC TACAACAGCC ACAACGTCTA TATCATGGCC GACAAGCAGA AGAACGGCAT CAAGGTGAAC TTCAAGATCC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GCCACAACAT CGAGGACGGC AGCGTGCAGC TCGCCGACCA CTACCAGCAG AACACCCCCA TCGGCGACGG CCCCGTGCTG CTGCCCGACA ACCACTACCT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAGCACCCAG TCCGCCCTGA GCAAAGACCC CAACGAGAAG CGCGATCACA TGGTCCTGCT GGAGTTCGTG ACCGCCGCCG GGATCACTCT CGGCATGGAC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GAGCTGTACA AGTAAAGCGG CCGCGACTCT AGATCATAAT CAGCCATACC ACATTTGTAG AGGTTTTACT TGCTTTAAAA AACCTCCCAC ACCTCCCCCT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GAACCTGAAA CATAAAATGA ATGCAATTGT TGTTGTTAAC TTGTTTATTG CAGCTTATAA TGGTTACAAA TAAAGCAATA GCATCACAAA TTTCACAAAT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AA
^1701

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pRG The name of the promoter used to express this mRNA:
CMV_IE

Description of the plasmid (facultative for promoter-less plasmid records):
The mammalian bicistronic vector pRG is a derivative of the pDsRed2-C1 vector containing the enhanced green fluorescent protein (EGFP) gene from the pEGFP-N1 vector (Clontech) inserted into the HincII site. A new stop codon was introduced at the end of the DsRed2 gene by ligation of the 5'-GATCCAGCAAGATATCCTAA-3'/5'- GATCTTAGGATATCTTGCTG-3' adaptor into the BglII site. IRESite notes about verification of plasmid sequence: The complete sequence of intercistronic region was determined by sequencing using DsRed1-C Sequencing Primer (Clontech; #6483-1; 5'-AGCTGGACATCACCTCCCACAACG-3'), nt 1205–1228.

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

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

TAGTTATTAA TAGTAATCAA TTACGGGGTC ATTAGTTCAT AGCCCATATA TGGAGTTCCG CGTTACATAA CTTACGGTAA ATGGCCCGCC TGGCTGACCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCAACGACC CCCGCCCATT GACGTCAATA ATGACGTATG TTCCCATAGT AACGCCAATA GGGACTTTCC ATTGACGTCA ATGGGTGGAG TATTTACGGT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AAACTGCCCA CTTGGCAGTA CATCAAGTGT ATCATATGCC AAGTACGCCC CCTATTGACG TCAATGACGG TAAATGGCCC GCCTGGCATT ATGCCCAGTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CATGACCTTA TGGGACTTTC CTACTTGGCA GTACATCTAC GTATTAGTCA TCGCTATTAC CATGGTGATG CGGTTTTGGC AGTACATCAA TGGGCGTGGA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TAGCGGTTTG ACTCACGGGG ATTTCCAAGT CTCCACCCCA TTGACGTCAA TGGGAGTTTG TTTTGGCACC AAAATCAACG GGACTTTCCA AAATGTCGTA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACAACTCCGC CCCATTGACG CAAATGGGCG GTAGGCGTGT ACGGTGGGAG GTCTATATAA GCAGAGCTGG TTTAGTGAAC CGTCAGATCC GCTAGCGCTA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCGGTCGCCA CCATGGCCTC CTCCGAGAAC GTCATCACCG AGTTCATGCG CTTCAAGGTG CGCATGGAGG GCACCGTGAA CGGCCACGAG TTCGAGATCG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGGGCGAGGG CGAGGGCCGC CCCTACGAGG GCCACAACAC CGTGAAGCTG AAGGTGACCA AGGGCGGCCC CCTGCCCTTC GCCTGGGACA TCCTGTCCCC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CCAGTTCCAG TACGGCTCCA AGGTGTACGT GAAGCACCCC GCCGACATCC CCGACTACAA GAAGCTGTCC TTCCCCGAGG GCTTCAAGTG GGAGCGCGTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATGAACTTCG AGGACGGCGG CGTGGCGACC GTGACCCAGG ACTCCTCCCT GCAGGACGGC TGCTTCATCT ACAAGGTGAA GTTCATCGGC GTGAACTTCC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCTCCGACGG CCCCGTGATG CAGAAGAAGA CCATGGGCTG GGAGGCCTCC ACCGAGCGCC TGTACCCCCG CGACGGCGTG CTGAAGGGCG AGACCCACAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GGCCCTGAAG CTGAAGGACG GCGGCCACTA CCTGGTGGAG TTCAAGTCCA TCTACATGGC CAAGAAGCCC GTGCAGCTGC CCGGCTACTA CTACGTGGAC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GCCAAGCTGG ACATCACCTC CCACAACGAG GACTACACCA TCGTGGAGCA GTACGAGCGC ACCGAGGGCC GCCACCACCT GTTCCTGAGA TCCAGCAAGA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TATCCTAAGA TCTCGAGCTC AAGCTTCGAA TTCTGCAGTC GACGGTACCG CGGGCCCGGG ATCCACCGGT CGCCACCATG GTGAGCAAGG GCGAGGAGCT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GTTCACCGGG GTGGTGCCCA TCCTGGTCGA GCTGGACGGC GACGTAAACG GCCACAAGTT CAGCGTGTCC GGCGAGGGCG AGGGCGATGC CACCTACGGC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AAGCTGACCC TGAAGTTCAT CTGCACCACC GGCAAGCTGC CCGTGCCCTG GCCCACCCTC GTGACCACCC TGACCTACGG CGTGCAGTGC TTCAGCCGCT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACCCCGACCA CATGAAGCAG CACGACTTCT TCAAGTCCGC CATGCCCGAA GGCTACGTCC AGGAGCGCAC CATCTTCTTC AAGGACGACG GCAACTACAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GACCCGCGCC GAGGTGAAGT TCGAGGGCGA CACCCTGGTG AACCGCATCG AGCTGAAGGG CATCGACTTC AAGGAGGACG GCAACATCCT GGGGCACAAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTGGAGTACA ACTACAACAG CCACAACGTC TATATCATGG CCGACAAGCA GAAGAACGGC ATCAAGGTGA ACTTCAAGAT CCGCCACAAC ATCGAGGACG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCAGCGTGCA GCTCGCCGAC CACTACCAGC AGAACACCCC CATCGGCGAC GGCCCCGTGC TGCTGCCCGA CAACCACTAC CTGAGCACCC AGTCCGCCCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GAGCAAAGAC CCCAACGAGA AGCGCGATCA CATGGTCCTG CTGGAGTTCG TGACCGCCGC CGGGATCACT CTCGGCATGG ACGAGCTGTA CAAGTAAAGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GGCCGCGACT CTAGATCATA ATCAGCCATA CCACATTTGT AGAGGTTTTA CTTGCTTTAA AAAACCTCCC ACACCTCCCC CTGAACCTGA AACATAAAAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAATGCAATT GTTGTTGTTA ACTTGTTTAT TGCAGCTTAT AATGGTTACA AATAAAGCAA TAGCATCACA AATTTCACAA ATAAAGCATT TTTTTCACTG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CATTCTAGTT GTGGTTTGTC CAAACTCATC AATGTATCTT AACGCGTAAA TTGTAAGCGT TAATATTTTG TTAAAATTCG CGTTAAATTT TTGTTAAATC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AGCTCATTTT TTAACCAATA GGCCGAAATC GGCAAAATCC CTTATAAATC AAAAGAATAG ACCGAGATAG GGTTGAGTGT TGTTCCAGTT TGGAACAAGA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTCCACTATT AAAGAACGTG GACTCCAACG TCAAAGGGCG AAAAACCGTC TATCAGGGCG ATGGCCCACT ACGTGAACCA TCACCCTAAT CAAGTTTTTT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GGGGTCGAGG TGCCGTAAAG CACTAAATCG GAACCCTAAA GGGAGCCCCC GATTTAGAGC TTGACGGGGA AAGCCGGCGA ACGTGGCGAG AAAGGAAGGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AAGAAAGCGA AAGGAGCGGG CGCTAGGGCG CTGGCAAGTG TAGCGGTCAC GCTGCGCGTA ACCACCACAC CCGCCGCGCT TAATGCGCCG CTACAGGGCG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CGTCAGGTGG CACTTTTCGG GGAAATGTGC GCGGAACCCC TATTTGTTTA TTTTTCTAAA TACATTCAAA TATGTATCCG CTCATGAGAC AATAACCCTG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATAAATGCTT CAATAATATT GAAAAAGGAA GAGTCCTGAG GCGGAAAGAA CCAGCTGTGG AATGTGTGTC AGTTAGGGTG TGGAAAGTCC CCAGGCTCCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CAGCAGGCAG AAGTATGCAA AGCATGCATC TCAATTAGTC AGCAACCAGG TGTGGAAAGT CCCCAGGCTC CCCAGCAGGC AGAAGTATGC AAAGCATGCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TCTCAATTAG TCAGCAACCA TAGTCCCGCC CCTAACTCCG CCCATCCCGC CCCTAACTCC GCCCAGTTCC GCCCATTCTC CGCCCCATGG CTGACTAATT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTTTTTATTT ATGCAGAGGC CGAGGCCGCC TCGGCCTCTG AGCTATTCCA GAAGTAGTGA GGAGGCTTTT TTGGAGGCCT AGGCTTTTGC AAAGATCGAT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CAAGAGACAG GATGAGGATC GTTTCGCATG ATTGAACAAG ATGGATTGCA CGCAGGTTCT CCGGCCGCTT GGGTGGAGAG GCTATTCGGC TATGACTGGG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CACAACAGAC AATCGGCTGC TCTGATGCCG CCGTGTTCCG GCTGTCAGCG CAGGGGCGCC CGGTTCTTTT TGTCAAGACC GACCTGTCCG GTGCCCTGAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TGAACTGCAA GACGAGGCAG CGCGGCTATC GTGGCTGGCC ACGACGGGCG TTCCTTGCGC AGCTGTGCTC GACGTTGTCA CTGAAGCGGG AAGGGACTGG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CTGCTATTGG GCGAAGTGCC GGGGCAGGAT CTCCTGTCAT CTCACCTTGC TCCTGCCGAG AAAGTATCCA TCATGGCTGA TGCAATGCGG CGGCTGCATA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CGCTTGATCC GGCTACCTGC CCATTCGACC ACCAAGCGAA ACATCGCATC GAGCGAGCAC GTACTCGGAT GGAAGCCGGT CTTGTCGATC AGGATGATCT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GGACGAAGAG CATCAGGGGC TCGCGCCAGC CGAACTGTTC GCCAGGCTCA AGGCGAGCAT GCCCGACGGC GAGGATCTCG TCGTGACCCA TGGCGATGCC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TGCTTGCCGA ATATCATGGT GGAAAATGGC CGCTTTTCTG GATTCATCGA CTGTGGCCGG CTGGGTGTGG CGGACCGCTA TCAGGACATA GCGTTGGCTA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CCCGTGATAT TGCTGAAGAG CTTGGCGGCG AATGGGCTGA CCGCTTCCTC GTGCTTTACG GTATCGCCGC TCCCGATTCG CAGCGCATCG CCTTCTATCG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CCTTCTTGAC GAGTTCTTCT GAGCGGGACT CTGGGGTTCG AAATGACCGA CCAAGCGACG CCCAACCTGC CATCACGAGA TTTCGATTCC ACCGCCGCCT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TCTATGAAAG GTTGGGCTTC GGAATCGTTT TCCGGGACGC CGGCTGGATG ATCCTCCAGC GCGGGGATCT CATGCTGGAG TTCTTCGCCC ACCCTAGGGG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GAGGCTAACT GAAACACGGA AGGAGACAAT ACCGGAAGGA ACCCGCGCTA TGACGGCAAT AAAAAGACAG AATAAAACGC ACGGTGTTGG GTCGTTTGTT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CATAAACGCG GGGTTCGGTC CCAGGGCTGG CACTCTGTCG ATACCCCACC GAGACCCCAT TGGGGCCAAT ACGCCCGCGT TTCTTCCTTT TCCCCACCCC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ACCCCCCAAG TTCGGGTGAA GGCCCAGGGC TCGCAGCCAA CGTCGGGGCG GCAGGCCCTG CCATAGCCTC AGGTTACTCA TATATACTTT AGATTGATTT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

AAAACTTCAT TTTTAATTTA AAAGGATCTA GGTGAAGATC CTTTTTGATA ATCTCATGAC CAAAATCCCT TAACGTGAGT TTTCGTTCCA CTGAGCGTCA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GACCCCGTAG AAAAGATCAA AGGATCTTCT TGAGATCCTT TTTTTCTGCG CGTAATCTGC TGCTTGCAAA CAAAAAAACC ACCGCTACCA GCGGTGGTTT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GTTTGCCGGA TCAAGAGCTA CCAACTCTTT TTCCGAAGGT AACTGGCTTC AGCAGAGCGC AGATACCAAA TACTGTCCTT CTAGTGTAGC CGTAGTTAGG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CCACCACTTC AAGAACTCTG TAGCACCGCC TACATACCTC GCTCTGCTAA TCCTGTTACC AGTGGCTGCT GCCAGTGGCG ATAAGTCGTG TCTTACCGGG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTGGACTCAA GACGATAGTT ACCGGATAAG GCGCAGCGGT CGGGCTGAAC GGGGGGTTCG TGCACACAGC CCAGCTTGGA GCGAACGACC TACACCGAAC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TGAGATACCT ACAGCGTGAG CTATGAGAAA GCGCCACGCT TCCCGAAGGG AGAAAGGCGG ACAGGTATCC GGTAAGCGGC AGGGTCGGAA CAGGAGAGCG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CACGAGGGAG CTTCCAGGGG GAAACGCCTG GTATCTTTAT AGTCCTGTCG GGTTTCGCCA CCTCTGACTT GAGCGTCGAT TTTTGTGATG CTCGTCAGGG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GGGCGGAGCC TATGGAAAAA CGCCAGCAAC GCGGCCTTTT TACGGTTCCT GGCCTTTTGC TGGCCTTTTG CTCACATGTT CTTTCCTGCG TTATCCCCTG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ATTCTGTGGA TAACCGTATT ACCGCCATGC AT
^5401      ^5411      ^5421      ^5431

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

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

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

A promoter reported in cDNA corresponding to IRES sequence:
not tested 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: Václav Vopálenský	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
DsRED2

The description of the protein encoded in this ORF:
red fluorescent protein (DsRed2 version, Clontech)

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):

31-726

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
EGFP

The description of the protein encoded in this ORF:
Red-shifted variant of wild-type GFP optimized for brighter fluorescence and higher expression in mammalian cells (Clontech).

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):

796-1515

Remarks:

The plasmid was used as the negative control for experiments in articles:
Hepatitis C virus internal ribosome entry site initiates protein synthesis at the authentic initiation codon
in yeast. (Masek et al., 2007; PMID: 17554033)
Firefly luciferase gene contains a cryptic promoter (Vopalensky et al., 2008; PMID:).

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

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