IRESite_Id:557 characteristics of EMCV-R_-541_-7 IRES studied in pGLuc-EMCV-GFP plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `557`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-03-13 17:02:47`
Reviewed by: Martin Mokrejš

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

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

The mRNA/+RNA description:

Putative in vivo transcript driven from CMV IE promoter and terminated after the SV40 late poly(A) signal
containing GLuc (Gaussia luciferase) and GFP cistrons separated by EMCV IRES.

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

GTCAGATCAC TAGAAGCTTA TCAGACGACA TCACTCGAGA CTAACTCACC GGAATTCCAA GCTGGCAACT TCCGGAAGCT GCAAGCCACC ATGGGAGTCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAGTCCTGTT CGCTCTGATC TGCATCGCTG TGGCCGAGGC CAAGCCCACC GAGAACAACG AAGACTTCAA CATCGTCGCC GTGGCCAGCA ACTTCGCAAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CACTGATCTG GACGCTGACA GAGGCAAACT GCCTGGCAAG AAGCTGCCTC TCGAAGTCCT GAAAGAGATG GAAGCCAACG CTCGGAAGGC TGGCTGCACA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGAGGCTGCC TGATCTGCCT GTCCCACATC AAATGCACAC CCAAGATGAA GAAATTCATC CCTGGACGCT GCCACACCTA CGAAGGCGAC AAAGAATCCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CACAGGGAGG CATTGGAGAA GCCATTGTCG ACATTCCCGA GATTCCTGGA TTCAAGGACC TGGAGCCTAT GGAGCAGTTC ATCGCACAAG TCGACCTCTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGTGGACTGC ACAACTGGAT GCCTCAAAGG CCTCGCTAAT GTCCAATGCT CTGACCTGCT CAAGAAATGG CTCCCACAGC GCTGCGCTAC CTTCGCAAGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AAGATCCAGG GCCAAGTCGA TAAGATCAAG GGAGCAGGCG GAGACTAAAC CTAGTTTAAA CGCGTTACTG GCCGAAGCCG CTTGGAATAA GGCCGGTGTG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CGTTTGTCTA TATGTTATTT TCCACCATAT TGCCGTCTTT TGGCAATGTG AGGGCCCGGA AACCTGGCCC TGTCTTCTTG ACGAGCATTC CTAGGGGTCT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TTCCCCTCTC GCCAAAGGAA TGCAAGGTCT GTTGAATGTC GTGAAGGAAG CAGTTCCTCT GGAAGCTTCT TGAAGACAAA CAACGTCTGT AGCGACCCTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGCAGGCAGC GGAACCCCCC ACCTGGCGAC AGGTGCCTCT GCGGCCAAAA GCCACGTGTA TAAGATACAC CTGCAAAGGC GGCACAACCC CAGTGCCACG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTGTGAGTTG GATAGTTGTG GAAAGAGTCA AATGGCTCTC CTCAAGCGTA TTCAACAAGG GGCTGAAGGA TGCCCAGAAG GTACCCCATT GTATGGGATC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TGATCTGGGG CCTCGGTGCA CATGCTTTAC ATGTGTTTAG TCGAGGTTAA AAAAACGTCT AGGCCCCCCG AACCACGGGG ACGTGGTTTT CCTTTGAAAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ACACGATAAT ACCATGGCCA TTCGAACAAA GGGCGAGGAG CTGTTCACCG GGGTGGTGCC CATCCTGGTC GAGCTGGACG GCGACGTAAA CGGCCACAAG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TTCAGCGTGT CCGGCGAGGG CGAGGGCGAT GCCACCTACG GCAAGCTGAC CCTGAAGTTC ATCTGCACCA CCGGCAAGCT GCCCGTGCCC TGGCCCACCC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCGTGACCAC CTTGACCTAC GGCGTGCAGT GCTTCGCCCG CTACCCCGAC CACATGAAGC AGCACGACTT CTTCAAGTCC GCCATGCCCG AAGGCTACGT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCAGGAGCGC ACCATCTTCT TCAAGGACGA CGGCAACTAC AAGACCCGCG CCGAGGTGAA GTTCGAGGGC GACACCCTGG TGAACCGCAT CGAGCTGAAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGCATCGACT TCAAGGAGGA CGGCAACATC CTGGGGCACA AGCTGGAGTA CAACTACAAC AGCCACAAGG TCTATATCAC CGCCGACAAG CAGAAGAACG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCATCAAGGT GAACTTCAAG ACCCGCCACA ACATCGAGGA CGGCAGCGTG CAGCTCGCCG ACCACTACCA GCAGAACACC CCCATCGGCG ACGGCCCCGT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCTGCTGCCC GACAACCACT ACCTGAGCAC CCAGTCCGCC CTGAGCAAAG ACCCCAACGA GAAGCGCGAT CACATGGTCC TGCTGGAGTT CGTGACCGCC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCCGGGATCA CTCTCGGCAT GGACGAGCTG TACAAGTAGC GGCCCAATCT AGAGTCGGGG CGGCCGGCCG CTTCGAGCAG ACATGATAAG ATACATTGAT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GAGTTTGGAC AAACCACAAC TAGAATGCAG TGAAAAAAAT GCTTTATTTG TGAAATTTGT GATGCTATTG CTTTATTTGT AACCATTATA AGCTGCAATA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AACAAGTTAA CAACAACAAT TGCATTCATT TTATGTTTCA GGTTCAGGGG GAGGTGTGGG AGGTTTTTTA AAGCAAGTAA AACCTCTACA AATGTGGTA
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pGLuc-EMCV-GFP The name of the promoter used to express this mRNA:
CMV_IE

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

not tested

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

not tested

A promoter reported in cDNA corresponding to IRES sequence:

not tested

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

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Encephalomyocarditis virus Ruckert

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

TCAATATTGG CCATTAGCCA TATTATTCAT TGGTTATATA GCATAAATCA ATATTGGCTA TTGGCCATTG CATACGTTGT ATCTATATCA TAATATGTAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATTTATATTG GCTCATGTCC AATATGACCG CCATGTTGGC ATTGATTATT GACTAGTTAT TAATAGTAAT CAATTACGGG GTCATTAGTT CATAGCCCAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATATGGAGTT CCGCGTTACA TAACTTACGG TAAATGGCCC GCCTGGCTGA CCGCCCAACG ACCCCCGCCC ATTGACGTCA ATAATGACGT ATGTTCCCAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGTAACGCCA ATAGGGACTT TCCATTGACG TCAATGGGTG GAGTATTTAC GGTAAACTGC CCACTTGGCA GTACATCAAG TGTATCATAT GCCAAGTCCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCCCCTATTG ACGTCAATGA CGGTAAATGG CCCGCCTGGC ATTATGCCCA GTACATGACC TTACGGGACT TTCCTACTTG GCAGTACATC TACGTATTAG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCATCGCTAT TACCATGGTG ATGCGGTTTT GGCAGTACAC CAATGGGCGT GGATAGCGGT TTGACTCACG GGGATTTCCA AGTCTCCACC CCATTGACGT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CAATGGGAGT TTGTTTTGGC ACCAAAATCA ACGGGACTTT CCAAAATGTC GTAATAACCC CGCCCCGTTG ACGCAAATGG GCGGTAGGCG TGTACGGTGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GAGGTCTATA TAAGCAGAGC TCGTTTAGTG AACCGTCAGA TCACTAGAAG CTTATCAGAC GACATCACTC GAGACTAACT CACCGGAATT CCAAGCTGGC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AACTTCCGGA AGCTGCAAGC CACCATGGGA GTCAAAGTCC TGTTCGCTCT GATCTGCATC GCTGTGGCCG AGGCCAAGCC CACCGAGAAC AACGAAGACT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCAACATCGT CGCCGTGGCC AGCAACTTCG CAACCACTGA TCTGGACGCT GACAGAGGCA AACTGCCTGG CAAGAAGCTG CCTCTCGAAG TCCTGAAAGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GATGGAAGCC AACGCTCGGA AGGCTGGCTG CACAAGAGGC TGCCTGATCT GCCTGTCCCA CATCAAATGC ACACCCAAGA TGAAGAAATT CATCCCTGGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CGCTGCCACA CCTACGAAGG CGACAAAGAA TCCGCACAGG GAGGCATTGG AGAAGCCATT GTCGACATTC CCGAGATTCC TGGATTCAAG GACCTGGAGC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CTATGGAGCA GTTCATCGCA CAAGTCGACC TCTGCGTGGA CTGCACAACT GGATGCCTCA AAGGCCTCGC TAATGTCCAA TGCTCTGACC TGCTCAAGAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ATGGCTCCCA CAGCGCTGCG CTACCTTCGC AAGCAAGATC CAGGGCCAAG TCGATAAGAT CAAGGGAGCA GGCGGAGACT AAACCTAGTT TAAACGCGTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ACTGGCCGAA GCCGCTTGGA ATAAGGCCGG TGTGCGTTTG TCTATATGTT ATTTTCCACC ATATTGCCGT CTTTTGGCAA TGTGAGGGCC CGGAAACCTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GCCCTGTCTT CTTGACGAGC ATTCCTAGGG GTCTTTCCCC TCTCGCCAAA GGAATGCAAG GTCTGTTGAA TGTCGTGAAG GAAGCAGTTC CTCTGGAAGC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTCTTGAAGA CAAACAACGT CTGTAGCGAC CCTTTGCAGG CAGCGGAACC CCCCACCTGG CGACAGGTGC CTCTGCGGCC AAAAGCCACG TGTATAAGAT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ACACCTGCAA AGGCGGCACA ACCCCAGTGC CACGTTGTGA GTTGGATAGT TGTGGAAAGA GTCAAATGGC TCTCCTCAAG CGTATTCAAC AAGGGGCTGA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGGATGCCCA GAAGGTACCC CATTGTATGG GATCTGATCT GGGGCCTCGG TGCACATGCT TTACATGTGT TTAGTCGAGG TTAAAAAAAC GTCTAGGCCC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CCCGAACCAC GGGGACGTGG TTTTCCTTTG AAAAACACGA TAATACCATG GCCATTCGAA CAAAGGGCGA GGAGCTGTTC ACCGGGGTGG TGCCCATCCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGTCGAGCTG GACGGCGACG TAAACGGCCA CAAGTTCAGC GTGTCCGGCG AGGGCGAGGG CGATGCCACC TACGGCAAGC TGACCCTGAA GTTCATCTGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACCACCGGCA AGCTGCCCGT GCCCTGGCCC ACCCTCGTGA CCACCTTGAC CTACGGCGTG CAGTGCTTCG CCCGCTACCC CGACCACATG AAGCAGCACG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ACTTCTTCAA GTCCGCCATG CCCGAAGGCT ACGTCCAGGA GCGCACCATC TTCTTCAAGG ACGACGGCAA CTACAAGACC CGCGCCGAGG TGAAGTTCGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGGCGACACC CTGGTGAACC GCATCGAGCT GAAGGGCATC GACTTCAAGG AGGACGGCAA CATCCTGGGG CACAAGCTGG AGTACAACTA CAACAGCCAC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AAGGTCTATA TCACCGCCGA CAAGCAGAAG AACGGCATCA AGGTGAACTT CAAGACCCGC CACAACATCG AGGACGGCAG CGTGCAGCTC GCCGACCACT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACCAGCAGAA CACCCCCATC GGCGACGGCC CCGTGCTGCT GCCCGACAAC CACTACCTGA GCACCCAGTC CGCCCTGAGC AAAGACCCCA ACGAGAAGCG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGATCACATG GTCCTGCTGG AGTTCGTGAC CGCCGCCGGG ATCACTCTCG GCATGGACGA GCTGTACAAG TAGCGGCCCA ATCTAGAGTC GGGGCGGCCG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCCGCTTCGA GCAGACATGA TAAGATACAT TGATGAGTTT GGACAAACCA CAACTAGAAT GCAGTGAAAA AAATGCTTTA TTTGTGAAAT TTGTGATGCT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ATTGCTTTAT TTGTAACCAT TATAAGCTGC AATAAACAAG TTAACAACAA CAATTGCATT CATTTTATGT TTCAGGTTCA GGGGGAGGTG TGGGAGGTTT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TTTAAAGCAA GTAAAACCTC TACAAATGTG GTAAAATCGA TAAGGATCCG TCGACCGATG CCCTTGAGAG CCTTCAACCC AGTCAGCTCC TTCCGGTGGG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGCGGGGCAT GACTATCGTC GCCGCACTTA TGACTGTCTT CTTTATCATG CAACTCGTAG GACAGGTGCC GGCAGCGCTC TTCCGCTTCC TCGCTCACTG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ACTCGCTGCG CTCGGTCGTT CGGCTGCGGC GAGCGGTATC AGCTCACTCA AAGGCGGTAA TACGGTTATC CACAGAATCA GGGGATAACG CAGGAAAGAA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CATGTGAGCA AAAGGCCAGC AAAAGGCCAG GAACCGTAAA AAGGCCGCGT TGCTGGCGTT TTTCCATAGG CTCCGCCCCC CTGACGAGCA TCACAAAAAT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CGACGCTCAA GTCAGAGGTG GCGAAACCCG ACAGGACTAT AAAGATACCA GGCGTTTCCC CCTGGAAGCT CCCTCGTGCG CTCTCCTGTT CCGACCCTGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CGCTTACCGG ATACCTGTCC GCCTTTCTCC CTTCGGGAAG CGTGGCGCTT TCTCATAGCT CACGCTGTAG GTATCTCAGT TCGGTGTAGG TCGTTCGCTC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CAAGCTGGGC TGTGTGCACG AACCCCCCGT TCAGCCCGAC CGCTGCGCCT TATCCGGTAA CTATCGTCTT GAGTCCAACC CGGTAAGACA CGACTTATCG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CCACTGGCAG CAGCCACTGG TAACAGGATT AGCAGAGCGA GGTATGTAGG CGGTGCTACA GAGTTCTTGA AGTGGTGGCC TAACTACGGC TACACTAGAA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GAACAGTATT TGGTATCTGC GCTCTGCTGA AGCCAGTTAC CTTCGGAAAA AGAGTTGGTA GCTCTTGATC CGGCAAACAA ACCACCGCTG GTAGCGGTGG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TTTTTTTGTT TGCAAGCAGC AGATTACGCG CAGAAAAAAA GGATCTCAAG AAGATCCTTT GATCTTTTCT ACGGGGTCTG ACGCTCAGTG GAACGAAAAC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TCACGTTAAG GGATTTTGGT CATGAGATTA TCAAAAAGGA TCTTCACCTA GATCCTTTTA AATTAAAAAT GAAGTTTTAA ATCAATCTAA AGTATATATG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AGTAAACTTG GTCTGACAGC GGCCGCAAAT GCTAAACCAC TGCAGTGGTT ACCAGTGCTT GATCAGTGAG GCACCGATCT CAGCGATCTG CCTATTTCGT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TCGTCCATAG TGGCCTGACT CCCCGTCGTG TAGATCACTA CGATTCGTGA GGGCTTACCA TCAGGCCCCA GCGCAGCAAT GATGCCGCGA GAGCCGCGTT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CACCGGCCCC CGATTTGTCA GCAATGAACC AGCCAGCAGG GAGGGCCGAG CGAAGAAGTG GTCCTGCTAC TTTGTCCGCC TCCATCCAGT CTATGAGCTG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CTGTCGTGAT GCTAGAGTAA GAAGTTCGCC AGTGAGTAGT TTCCGAAGAG TTGTGGCCAT TGCTACTGGC ATCGTGGTAT CACGCTCGTC GTTCGGTATG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GCTTCGTTCA ACTCTGGTTC CCAGCGGTCA AGCCGGGTCA CATGATCACC CATATTATGA AGAAATGCAG TCAGCTCCTT AGGGCCTCCG ATCGTTGTCA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GAAGTAAGTT GGCCGCGGTG TTGTCGCTCA TGGTAATGGC AGCACTACAC AATTCTCTTA CCGTCATGCC ATCCGTAAGA TGCTTTTCCG TGACCGGCGA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GTACTCAACC AAGTCGTTTT GTGAGTAGTG TATACGGCGA CCAAGCTGCT CTTGCCCGGC GTCTATACGG GACAACACCG CGCCACATAG CAGTACTTTG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AAAGTGCTCA TCATCGGGAA TCGTTCTTCG GGGCGGAAAG ACTCAAGGAT CTTGCCGCTA TTGAGATCCA GTTCGATATA GCCCACTCTT GCACCCAGTT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GATCTTCAGC ATCTTTTACT TTCACCAGCG TTTCGGGGTG TGCAAAAACA GGCAAGCAAA ATGCCGCAAA GAAGGGAATG AGTGCGACAC GAAAATGTTG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GATGCTCATA CTCGTCCTTT TTCAATATTA TTGAAGCATT TATCAGGGTT ACTAGTACGT CTCTCAAGGA TAAGTAAGTA ATATTAAGGT ACGGGAGGTA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTGGACAGGC CGCAATAAAA TATCTTTATT TTCATTACAT CTGTGTGTTG GTTTTTTGTG TGAATCGATA GTACTAACAT ACGCTCTCCA TCAAAACAAA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ACGAAACAAA ACAAACTAGC AAAATAGGCT GTCCCCAGTG CAAGTGCAGG TGCCAGAACA TTTCTCTGGC CTAACTGGCC
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171

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

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

2

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
GLuc

The description of the protein encoded in this ORF:
Gaussia 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:

not tested

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

91-648

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
GFP

The description of the protein encoded in this ORF:
green fluorescent protein

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):

1214-1939

Citations:

Baranick B. T., Lemp N. A., Nagashima J., Hiraoka K., Kasahara N., Logg C. R. (2008) Splicing mediates the activity of four putative cellular internal ribosome entry sites. Proc. Natl. Acad. Sci. U. S. A. 105(12):4733-4738

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `EMCV-R_-541_-7`	The functional status of IRES: `functional`

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

666-1207

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `18`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `559`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-548`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-7`

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

TACTGGCCGA AGCCGCTTGG AATAAGGCCG GTGTGCGTTT GTCTATATGT TATTTTCCAC CATATTGCCG TCTTTTGGCA ATGTGAGGGC CCGGAAACCT 
^666       ^676       ^686       ^696       ^706       ^716       ^726       ^736       ^746       ^756       

GGCCCTGTCT TCTTGACGAG CATTCCTAGG GGTCTTTCCC CTCTCGCCAA AGGAATGCAA GGTCTGTTGA ATGTCGTGAA GGAAGCAGTT CCTCTGGAAG 
^766       ^776       ^786       ^796       ^806       ^816       ^826       ^836       ^846       ^856       

CTTCTTGAAG ACAAACAACG TCTGTAGCGA CCCTTTGCAG GCAGCGGAAC CCCCCACCTG GCGACAGGTG CCTCTGCGGC CAAAAGCCAC GTGTATAAGA 
^866       ^876       ^886       ^896       ^906       ^916       ^926       ^936       ^946       ^956       

TACACCTGCA AAGGCGGCAC AACCCCAGTG CCACGTTGTG AGTTGGATAG TTGTGGAAAG AGTCAAATGG CTCTCCTCAA GCGTATTCAA CAAGGGGCTG 
^966       ^976       ^986       ^996       ^1006      ^1016      ^1026      ^1036      ^1046      ^1056      

AAGGATGCCC AGAAGGTACC CCATTGTATG GGATCTGATC TGGGGCCTCG GTGCACATGC TTTACATGTG TTTAGTCGAG GTTAAAAAAA CGTCTAGGCC 
^1066      ^1076      ^1086      ^1096      ^1106      ^1116      ^1126      ^1136      ^1146      ^1156      

CCCCGAACCA CGGGGACGTG GTTTTCCTTT GAAAAACACG AT
^1166      ^1176      ^1186      ^1196      ^1206

Remarks:

The EMCV IRES was the only one functional in HeLa and NIH3T3 cells transiently transfected by the
pGLuc-GFP-based plasmid DNA.

Citations:

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