IRESite_Id:121 characteristics of BCL2 IRES studied in pBCL2-FL-polyA plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `121`	Version: `6`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2006-10-30 00:00:00`

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:
hopefully_full-length_mRNA

The mRNA/+RNA description:

Monocistronic mRNA containing 5'-UTR from BCL2 and firefly luciferase with 6 extra N-terminal codons from
BCL2.

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

GGCTAGGGCC GCAAAAAATA AAACCCTCCC CCACCACCTC CTTCTCCCCA CCCCTCGCCG CACCACACAC AGCGCGGGCT TCTAGCGCTC GGCACCGGCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GGCCAGGCGC GTCCTGCCTT CATTTATCCA GCAGCTTTTC GGAAAATGCA TTTGCTGTTC GGAGTTTAAT CAGAAGACGA TTCCTGCCTC CGTCCCCGGC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCCTTCATCG TCCCATCTCC CCTGTCTCTC TCCTGGGGAG GCGTGAAGCG GTCCCGTGGA TAGAGATTCA TGCCTGTGTC CGCGCGTGTG TGCGCGCGTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TAAATTGCCG AGAAGGGGAA AACATCACAG GACTTCTGCG AATACCGGAC TGAAAATTGT AATTCATCTG CCGCCGCCGC TGCCTTTTTT TTTTCTCGAG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTCTTGAGAT CTCCGGTTGG GATTCCTGCG GATTGACATT TCTGTGAAGC AGAAGTCTGG GAATCGATCT GGAAATCCTC CTAATTTTTA CTCCCTCTCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCCCGACTCC TGATTCATTG GGAAGTTTCA AATCAGCTAT AACTGGAGAG TGCTGAAGAT TGATGGGATC GTTGCCTTAT GCATTTGTTT TGGTTTTACA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AAAAGGAAAC TTGACAGAGG ATCATGCTGT ACTTAAAAAA TACAAGTAAG TCTCGCACAG GAAATTGGTT TAATGTAACT TTCAATGGAA ACCTTTGAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TTTTTTACTT AAAGTGCATT CGAGTAAATT TAATTTCCAG GCAGCTTAAT ACATTGTTTT TAGCCGTGTT ACTTGTAGTG TGTATGCCCT GCTTTCACTC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AGTGTGTACA GGGAAACGCA CCTGATTTTT TACTTATTAG TTTGTTTTTT CTTTAACCTT TCAGCATCAC AGAGGAAGTA GACTGATATT AACAATACTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ACTAATAATA ACGTGCCTCA TGAAATAAAG ATCCGAAAGG AATTGGAATA AAAATTTCCT GCGTCTCATG CCAAGAGGGA AACACCAGAA TCAAGTGTTC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CGCGTGATTG AAGACACCCC CTCGTCCAAG AATGCAAAGC ACATCCAATA AAATAGCTGG ATTATAACTC CTCTTCTTTC TCTGGGGGCC GTGGGGTGGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AGCTGGGGCG AGAGGTGCCG TTGGCCCCCG TTGCTTTTCT TCTGGGAAGC ATGGGCCCAC AGGACGTCAT GGAAGACGCC AAAAACATAA AGAAAGGCCC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GGCGCCATTC TATCCTCTAG AGGATGGAAC CGCTGGAGAG CAACTGCATA AGGCTATGAA GAGATACGCC CTGGTTCCTG GAACAATTGC TTTTACAGAT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GCACATATCG AGGTGAACAT CACGTACGCG GAATACTTCG AAATGTCCGT TCGGTTGGCA GAAGCTATGA AACGATATGG GCTGAATACA AATCACAGAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCGTCGTATG CAGTGAAAAC TCTCTTCAAT TCTTTATGCC GGTGTTGGGC GCGTTATTTA TCGGAGTTGC AGTTGCGCCC GCGAACGACA TTTATAATGA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACGTGAATTG CTCAACAGTA TGAACATTTC GCAGCCTACC GTAGTGTTTG TTTCCAAAAA GGGGTTGCAA AAAATTTTGA ACGTGCAAAA AAAATTACCA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ATAATCCAGA AAATTATTAT CATGGATTCT AAAACGGATT ACCAGGGATT TCAGTCGATG TACACGTTCG TCACATCTCA TCTACCTCCC GGTTTTAATG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AATACGATTT TGTACCAGAG TCCTTTGATC GTGACAAAAC AATTGCACTG ATAATGAATT CCTCTGGATC TACTGGGTTA CCTAAGGGTG TGGCCCTTCC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCATAGAACT GCCTGCGTCA GATTCTCGCA TGCCAGAGAT CCTATTTTTG GCAATCAAAT CATTCCGGAT ACTGCGATTT TAAGTGTTGT TCCATTCCAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CACGGTTTTG GAATGTTTAC TACACTCGGA TATTTGATAT GTGGATTTCG AGTCGTCTTA ATGTATAGAT TTGAAGAAGA GCTGTTTTTA CGATCCCTTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGGATTACAA AATTCAAAGT GCGTTGCTAG TACCAACCCT ATTTTCATTC TTCGCCAAAA GCACTCTGAT TGACAAATAC GATTTATCTA ATTTACACGA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AATTGCTTCT GGGGGCGCAC CTCTTTCGAA AGAAGTCGGG GAAGCGGTTG CAAAACGCTT CCATCTTCCA GGGATACGAC AAGGATATGG GCTCACTGAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ACTACATCAG CTATTCTGAT TACACCCGAG GGGGATGATA AACCGGGCGC GGTCGGTAAA GTTGTTCCAT TTTTTGAAGC GAAGGTTGTG GATCTGGATA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CCGGGAAAAC GCTGGGCGTT AATCAGAGAG GCGAATTATG TGTCAGAGGA CCTATGATTA TGTCCGGTTA TGTAAACAAT CCGGAAGCGA CCAACGCCTT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GATTGACAAG GATGGATGGC TACATTCTGG AGACATAGCT TACTGGGACG AAGACGAACA CTTCTTCATA GTTGACCGCT TGAAGTCTTT AATTAAATAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AAAGGATATC AGGTGGCCCC CGCTGAATTG GAATCGATAT TGTTACAACA CCCCAACATC TTCGACGCGG GCGTGGCAGG TCTTCCCGAC GATGACGCCG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GTGAACTTCC CGCCGCCGTT GTTGTTTTGG AGCACGGAAA GACGATGACG GAAAAAGAGA TCGTGGATTA CGTGGCCAGT CAAGTAACAA CCGCGAAAAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GTTGCGCGGA GGAGTTGTGT TTGTGGACGA AGTACCGAAA GGTCTTACCG GAAAACTCGA CGCAAGAAAA ATCAGAGAGA TCCTCATAAA GGCCAAGAAG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GGCGGAAAGT CCAAATTGTA AGGATCCGGG CCCAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAA
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861

Credibility of mRNA sequence:

end-to-end_sequence_completely_same_as_in_the_experiment

The name of the plasmid:
pBCL2-FL-polyA The name of the promoter used to express this mRNA:
T7

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:
BCL2

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens HeLa (ATCC CCL-2)

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

ATTAAACCTC GATCTTCAAT ATTGGCCATT AGCCATATTA TTCATTGGTT ATATAGCATA AATCAATATT GGCTATTGGC CATTGCATAC GTTGTATCTA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TATCATAATA TGTACATTTA TATTGGCTCA TGTCCAATAT GACCGCCATG TTGGCATTGA TTATTGACTA GTTATTAATA GTAATCAATT ACGGGGTCAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TAGTTCATAG CCCATATATG GAGTTCCGCG TTACATAACT TACGGTAAAT GGCCCGCCTG GCTGACCGCC CAACGACCCC CGCCCATTGA CGTCAATAAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GACGTATGTT CCCATAGTAA CGCCAATAGG GACTTTCCAT TGACGTCAAT GGGTGGAGTA TTTACGGTAA ACTGCCCACT TGGCAGTACA TCAAGTGTAT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CATATGCCAA GTCCGCCCCC TATTGACGTC AATGACGGTA AATGGCCCGC CTGGCATTAT GCCCAGTACA TGACCTTACG GGACTTTCCT ACTTGGCAGT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACATCTACGT ATTAGTCATC GCTATTACCA TGGTGATGCG GTTTTGGCAG TACACCAATG GGCGTGGATA GCGGTTTGAC TCACGGGGAT TTCCAAGTCT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCACCCCATT GACGTCAATG GGAGTTTGTT TTGGCACCAA AATCAACGGG ACTTTCCAAA ATGTCGTAAT AACCCCGCCC CGTTGACGCA AATGGGCGGT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGGCGTGTAC GGTGGGAGGT CTATATAAGC AGAGCTCGTT TAGTGAACCG TCAGATCACT AGAAGCTTTA TTGCGGTAGT TTATCACAGT TAAATTGCTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ACGCAGTCAG TGCTTCTGAC ACAACAGTCT CGAACTTAAG CTGCAGAAGT TGGTCGTGAG GCACTGGGCA GGTAAGTATC AAGGTTACAA GACAGGTTTA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AGGAGACCAA TAGAAACTGG GCTTGTCGAG ACAGAGAAGA CTCTTGCGTT TCTGATAGGC ACCTATTGGT CTTACTGACA TCCACTTTGC CTTTCTCTCC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ACAGGTGTCC ACTCCCAGTT CAATTACAGC TCTTAAGGCT AGAGTACTTA ATACGACTCA CTATAGGCTA GGGCCGCAAA AAATAAAACC CTCCCCCACC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACCTCCTTCT CCCCACCCCT CGCCGCACCA CACACAGCGC GGGCTTCTAG CGCTCGGCAC CGGCGGGCCA GGCGCGTCCT GCCTTCATTT ATCCAGCAGC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTTTCGGAAA ATGCATTTGC TGTTCGGAGT TTAATCAGAA GACGATTCCT GCCTCCGTCC CCGGCTCCTT CATCGTCCCA TCTCCCCTGT CTCTCTCCTG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGGAGGCGTG AAGCGGTCCC GTGGATAGAG ATTCATGCCT GTGTCCGCGC GTGTGTGCGC GCGTATAAAT TGCCGAGAAG GGGAAAACAT CACAGGACTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTGCGAATAC CGGACTGAAA ATTGTAATTC ATCTGCCGCC GCCGCTGCCT TTTTTTTTTC TCGAGCTCTT GAGATCTCCG GTTGGGATTC CTGCGGATTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACATTTCTGT GAAGCAGAAG TCTGGGAATC GATCTGGAAA TCCTCCTAAT TTTTACTCCC TCTCCCCCCG ACTCCTGATT CATTGGGAAG TTTCAAATCA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCTATAACTG GAGAGTGCTG AAGATTGATG GGATCGTTGC CTTATGCATT TGTTTTGGTT TTACAAAAAG GAAACTTGAC AGAGGATCAT GCTGTACTTA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAAAATACAA GTAAGTCTCG CACAGGAAAT TGGTTTAATG TAACTTTCAA TGGAAACCTT TGAGATTTTT TACTTAAAGT GCATTCGAGT AAATTTAATT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCCAGGCAGC TTAATACATT GTTTTTAGCC GTGTTACTTG TAGTGTGTAT GCCCTGCTTT CACTCAGTGT GTACAGGGAA ACGCACCTGA TTTTTTACTT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATTAGTTTGT TTTTTCTTTA ACCTTTCAGC ATCACAGAGG AAGTAGACTG ATATTAACAA TACTTACTAA TAATAACGTG CCTCATGAAA TAAAGATCCG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAAGGAATTG GAATAAAAAT TTCCTGCGTC TCATGCCAAG AGGGAAACAC CAGAATCAAG TGTTCCGCGT GATTGAAGAC ACCCCCTCGT CCAAGAATGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAAGCACATC CAATAAAATA GCTGGATTAT AACTCCTCTT CTTTCTCTGG GGGCCGTGGG GTGGGAGCTG GGGCGAGAGG TGCCGTTGGC CCCCGTTGCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTTCTTCTGG GAAGCATGGG CCCACAGGAC GTCATGGAAG ACGCCAAAAA CATAAAGAAA GGCCCGGCGC CATTCTATCC TCTAGAGGAT GGAACCGCTG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GAGAGCAACT GCATAAGGCT ATGAAGAGAT ACGCCCTGGT TCCTGGAACA ATTGCTTTTA CAGATGCACA TATCGAGGTG AACATCACGT ACGCGGAATA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CTTCGAAATG TCCGTTCGGT TGGCAGAAGC TATGAAACGA TATGGGCTGA ATACAAATCA CAGAATCGTC GTATGCAGTG AAAACTCTCT TCAATTCTTT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATGCCGGTGT TGGGCGCGTT ATTTATCGGA GTTGCAGTTG CGCCCGCGAA CGACATTTAT AATGAACGTG AATTGCTCAA CAGTATGAAC ATTTCGCAGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTACCGTAGT GTTTGTTTCC AAAAAGGGGT TGCAAAAAAT TTTGAACGTG CAAAAAAAAT TACCAATAAT CCAGAAAATT ATTATCATGG ATTCTAAAAC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GGATTACCAG GGATTTCAGT CGATGTACAC GTTCGTCACA TCTCATCTAC CTCCCGGTTT TAATGAATAC GATTTTGTAC CAGAGTCCTT TGATCGTGAC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AAAACAATTG CACTGATAAT GAATTCCTCT GGATCTACTG GGTTACCTAA GGGTGTGGCC CTTCCGCATA GAACTGCCTG CGTCAGATTC TCGCATGCCA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAGATCCTAT TTTTGGCAAT CAAATCATTC CGGATACTGC GATTTTAAGT GTTGTTCCAT TCCATCACGG TTTTGGAATG TTTACTACAC TCGGATATTT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GATATGTGGA TTTCGAGTCG TCTTAATGTA TAGATTTGAA GAAGAGCTGT TTTTACGATC CCTTCAGGAT TACAAAATTC AAAGTGCGTT GCTAGTACCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ACCCTATTTT CATTCTTCGC CAAAAGCACT CTGATTGACA AATACGATTT ATCTAATTTA CACGAAATTG CTTCTGGGGG CGCACCTCTT TCGAAAGAAG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TCGGGGAAGC GGTTGCAAAA CGCTTCCATC TTCCAGGGAT ACGACAAGGA TATGGGCTCA CTGAGACTAC ATCAGCTATT CTGATTACAC CCGAGGGGGA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TGATAAACCG GGCGCGGTCG GTAAAGTTGT TCCATTTTTT GAAGCGAAGG TTGTGGATCT GGATACCGGG AAAACGCTGG GCGTTAATCA GAGAGGCGAA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TTATGTGTCA GAGGACCTAT GATTATGTCC GGTTATGTAA ACAATCCGGA AGCGACCAAC GCCTTGATTG ACAAGGATGG ATGGCTACAT TCTGGAGACA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TAGCTTACTG GGACGAAGAC GAACACTTCT TCATAGTTGA CCGCTTGAAG TCTTTAATTA AATACAAAGG ATATCAGGTG GCCCCCGCTG AATTGGAATC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GATATTGTTA CAACACCCCA ACATCTTCGA CGCGGGCGTG GCAGGTCTTC CCGACGATGA CGCCGGTGAA CTTCCCGCCG CCGTTGTTGT TTTGGAGCAC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GGAAAGACGA TGACGGAAAA AGAGATCGTG GATTACGTGG CCAGTCAAGT AACAACCGCG AAAAAGTTGC GCGGAGGAGT TGTGTTTGTG GACGAAGTAC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CGAAAGGTCT TACCGGAAAA CTCGACGCAA GAAAAATCAG AGAGATCCTC ATAAAGGCCA AGAAGGGCGG AAAGTCCAAA TTGTAAGGAT CCGGGCCCAA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAACCGGTGG GCCCTATTCT ATAGTGTCAC CTAAATGCTA GAGCTCGCTG ATCAGCCTCG ACTGTGCCTT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CTAGTTGCCA GCCATCTGTT GTTTGCCCCT CCCCCGTGCC TTCCTTGACC CTGGAAGGTG CCACTCCCAC TGTCCTTTCC TAATAAAATG AGGAAATTGC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ATCGCATTGT CTGAGTAGGT GTCATTCTAT TCTGGGGGGT GGGGTGGGGC AGGACAGCAA GGGGGAGGAT TGGGAAGACA ATAGCAGGCA TGCTGGGGAT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCGGTGGGCT CTATGGCTTC TGAGGCGGAA AGAACCAGCT GGGGCTCGAG GGGGGATCCC CACGCGCCCT GTAGCGGCGC ATTAAGCGCG GCGGGTGTGG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TGGTTACGCG CAGCGTGACC GCTACACTTG CCAGCGCCCT AGCGCCCGCT CCTTTCGCTT TCTTCCCTTC CTTTCTCGCC ACGTTCGCCG GCTTTCCCCG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TCAAGCTCTA AATCGGGGCA TCCCTTTAGG GTTCCGATTT AGTGCTTTAC GGCACCTCGA CCCCAAAAAA CTTGATTAGG GTGATGGTTC ACGTAGTGGG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CCATCGCCCT GATAGACGGT TTTTCGCCCT TTGACGTTGG AGTCCACGTT CTTTAATAGT GGACTCTTGT TCCAAACTGG AACAACACTC AACCCTATCT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CGGTCTATTC TTTTGATTTA TAAGGGATTT TGGGGATTTC GGCCTATTGG TTAAAAAATG AGCTGATTTA ACAAAAATTT AACGCGAATT TTAACAAAAT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ATTAACGTTT ACAATTTAAA TATTTGCTTA TACAATCTTC CTGTTTTTGG GGCTTTTCTG ATTATCAACC GGGGTGGGTA CCGAGCTCGA ATTCTGTGGA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ATGTGTGTCA GTTAGGGTGT GGAAAGTCCC CAGGCTCCCC AGGCAGGCAG AAGTATGCAA AGCATGCATC TCAATTAGTC AGCAACCAGG TGTGGAAAGT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CCCCAGGCTC CCCAGCAGGC AGAAGTATGC AAAGCATGCA TCTCAATTAG TCAGCAACCA TAGTCCCGCC CCTAACTCCG CCCATCCCGC CCCTAACTCC 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GCCCAGTTCC GCCCATTCTC CGCCCCATGG CTGACTAATT TTTTTTATTT ATGCAGAGGC CGAGGCCGCC TCGGCCTCTG AGCTATTCCA GAAGTAGTGA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GGAGGCTTTT TTGGAGGCCT AGGCTTTTGC AAAAAGCTCC CGGGAGCTTG GATATCCATT TTCGGATCTG ATCAAGAGAC AGGATGAGGA TCGTTTCGCA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TGATTGAACA AGATGGATTG CACGCAGGTT CTCCGGCCGC TTGGGTGGAG AGGCTATTCG GCTATGACTG GGCACAACAG ACAATCGGCT GCTCTGATGC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CGCCGTGTTC CGGCTGTCAG CGCAGGGGCG CCCGGTTCTT TTTGTCAAGA CCGACCTGTC CGGTGCCCTG AATGAACTGC AGGACGAGGC AGCGCGGCTA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TCGTGGCTGG CCACGACGGG CGTTCCTTGC GCAGCTGTGC TCGACGTTGT CACTGAAGCG GGAAGGGACT GGCTGCTATT GGGCGAAGTG CCGGGGCAGG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

ATCTCCTGTC ATCTCACCTT GCTCCTGCCG AGAAAGTATC CATCATGGCT GATGCAATGC GGCGGCTGCA TACGCTTGAT CCGGCTACCT GCCCATTCGA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CCACCAAGCG AAACATCGCA TCGAGCGAGC ACGTACTCGG ATGGAAGCCG GTCTTGTCGA TCAGGATGAT CTGGACGAAG AGCATCAGGG GCTCGCGCCA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

GCCGAACTGT TCGCCAGGCT CAAGGCGCGC ATGCCCGACG GCGAGGATCT CGTCGTGACC CATGGCGATG CCTGCTTGCC GAATATCATG GTGGAAAATG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GCCGCTTTTC TGGATTCATC GACTGTGGCC GGCTGGGTGT GGCGGACCGC TATCAGGACA TAGCGTTGGC TACCCGTGAT ATTGCTGAAG AGCTTGGCGG 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CGAATGGGCT GACCGCTTCC TCGTGCTTTA CGGTATCGCC GCTCCCGATT CGCAGCGCAT CGCCTTCTAT CGCCTTCTTG ACGAGTTCTT CTGAGCGGGA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CTCTGGGGTT CGAAATGACC GACCAAGCGA CGCCCAACCT GCCATCACGA GATTTCGATT CCACCGCCGC CTTCTATGAA AGGTTGGGCT TCGGAATCGT 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

TTTCCGGGAC GCCGGCTGGA TGATCCTCCA GCGCGGGGAT CTCATGCTGG AGTTCTTCGC CCACCCCAAC TTGTTTATTG CAGCTTATAA TGGTTACAAA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TAAAGCAATA GCATCACAAA TTTCACAAAT AAAGCATTTT TTTCACTGCA TTCTAGTTGT GGTTTGTCCA AACTCATCAA TGTATCTTAT CATGTCTGGA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TCCCGTCGAC CTCGAGAGCT TGGCGTAATC ATGGTCATAG CTGTTTCCTG TGTGAAATTG TTATCCGCTC ACAATTCCAC ACAACATACG AGCCGGAAGC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

ATAAAGTGTA AAGCCTGGGG TGCCTAATGA GTGAGCTAAC TCACATTAAT TGCGTTGCGC TCACTGCCCG CTTTCCAGTC GGGAAACCTG TCGTGCCAGC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TGCATTAATG AATCGGCCAA CGCGCGGGGA GAGGCGGTTT GCGTATTGGG CGCTCTTCCG CTTCCTCGCT CACTGACTCG CTGCGCTCGG TCGTTCGGCT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GCGGCGAGCG GTATCAGCTC ACTCAAAGGC GGTAATACGG TTATCCACAG AATCAGGGGA TAACGCAGGA AAGAACATGT GAGCAAAAGG CCAGCAAAAG 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GCCAGGAACC GTAAAAAGGC CGCGTTGCTG GCGTTTTTCC ATAGGCTCCG CCCCCCTGAC GAGCATCACA AAAATCGACG CTCAAGTCAG AGGTGGCGAA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ACCCGACAGG ACTATAAAGA TACCAGGCGT TTCCCCCTGG AAGCTCCCTC GTGCGCTCTC CTGTTCCGAC CCTGCCGCTT ACCGGATACC TGTCCGCCTT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

TCTCCCTTCG GGAAGCGTGG CGCTTTCTCA ATGCTCACGC TGTAGGTATC TCAGTTCGGT GTAGGTCGTT CGCTCCAAGC TGGGCTGTGT GCACGAACCC 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CCCGTTCAGC CCGACCGCTG CGCCTTATCC GGTAACTATC GTCTTGAGTC CAACCCGGTA AGACACGACT TATCGCCACT GGCAGCAGCC ACTGGTAACA 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

GGATTAGCAG AGCGAGGTAT GTAGGCGGTG CTACAGAGTT CTTGAAGTGG TGGCCTAACT ACGGCTACAC TAGAAGGACA GTATTTGGTA TCTGCGCTCT 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

GCTGAAGCCA GTTACCTTCG GAAAAAGAGT TGGTAGCTCT TGATCCGGCA AACAAACCAC CGCTGGTAGC GGTGGTTTTT TTGTTTGCAA GCAGCAGATT 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

ACGCGCAGAA AAAAAGGATC TCAAGAAGAT CCTTTGATCT TTTCTACGGG GTCTGACGCT CAGTGGAACG AAAACTCACG TTAAGGGATT TTGGTCATGA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

GATTATCAAA AAGGATCTTC ACCTAGATCC TTTTAAATTA AAAATGAAGT TTTAAATCAA TCTAAAGTAT ATATGAGTAA ACTTGGTCTG ACAGTTACCA 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

ATGCTTAATC AGTGAGGCAC CTATCTCAGC GATCTGTCTA TTTCGTTCAT CCATAGTTGC CTGACTCCCC GTCGTGTAGA TAACTACGAT ACGGGAGGGC 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

TTACCATCTG GCCCCAGTGC TGCAATGATA CCGCGAGACC CACGCTCACC GGCTCCAGAT TTATCAGCAA TAAACCAGCC AGCCGGAAGG GCCGAGCGCA 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

GAAGTGGTCC TGCAACTTTA TCCGCCTCCA TCCAGTCTAT TAATTGTTGC CGGGAAGCTA GAGTAAGTAG TTCGCCAGTT AATAGTTTGC GCAACGTTGT 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TGCCATTGCT ACAGGCATCG TGGTGTCACG CTCGTCGTTT GGTATGGCTT CATTCAGCTC CGGTTCCCAA CGATCAAGGC GAGTTACATG ATCCCCCATG 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

TTGTGCAAAA AAGCGGTTAG CTCCTTCGGT CCTCCGATCG TTGTCAGAAG TAAGTTGGCC GCAGTGTTAT CACTCATGGT TATGGCAGCA CTGCATAATT 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

CTCTTACTGT CATGCCATCC GTAAGATGCT TTTCTGTGAC TGGTGAGTAC TCAACCAAGT CATTCTGAGA ATAGTGTATG CGGCGACCGA GTTGCTCTTG 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

CCCGGCGTCA ATACGGGATA ATACCGCGCC ACATAGCAGA ACTTTAAAAG TGCTCATCAT TGGAAAACGT TCTTCGGGGC GAAAACTCTC AAGGATCTTA 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

CCGCTGTTGA GATCCAGTTC GATGTAACCC ACTCGTGCAC CCAACTGATC TTCAGCATCT TTTACTTTCA CCAGCGTTTC TGGGTGAGCA AAAACAGGAA 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

GGCAAAATGC CGCAAAAAAG GGAATAAGGG CGACACGGAA ATGTTGAATA CTCATACTCT TCCTTTTTCA ATATTATTGA AGCATTTATC AGGGTTATTG 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

TCTCATGAGC GGATACATAT TTGAATGTAT TTAGAAAAAT AAACAAATAG GGGTTCCGCG CACATTTCCC CGAAAAGTGC CACCTGACGT CGACGGATCG 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

GGA
^8501

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

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

1

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

ORF

ORF position:

1

Version: `1`	Last change: `2006-06-05 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
FLuc-fusion

The description of the protein encoded in this ORF:
firefly luciferase with 6 extra N-terminal codons from BCL2

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):

1151-2821

Remarks:

Annotation of the plasmid: 16-812: CMV immediate early enhancer/promoter; 751: CMV transcription start;
869-1005: chimeric intron; 977-1001: FWD primer; 1049-1067: T7 RNA polymerase promoter (-17 - +2); 1066: T7
promoter transcription start (+1); 1078-2215: BCL2 5'-UTR; 2216-3886: FFluc-fusion protein ORF; 4794-2139:
SV40 enhancer; 4983-5118: SV40 ori; 5200-5990: Kan/Neo resistance (neomycin phosphotransferase); 8208-8232:
REV primer

In vitro transcripts from this plasmid were used in Fig. 2. Otherwise pretty much useless construct showing
only that phpBCL2-FL in contrast to this plasmid is less translated because of the "php" stem loop barrier.
Fig. 4B shows that translation of capped and polyA tailed monocistronic mRNA is about 11x higher than that of
uncapped mRNA and that "php" stem loop as the barrier decreases translation down to about 8%.

Citations:

Sherrill K. W., Byrd M. P., Van Eden M. E., Lloyd R. E. (2004) BCL-2 translation is mediated via internal ribosome entry during cell stress. J. Biol. Chem. 279(28):29066-29074

IRESs:

IRES:

Version: `2`	Last change: `2006-06-05 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `BCL2`	The functional status of IRES: `functional`

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

191-1328

How IRES boundaries were determined:
experimentally_determined

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

CGTCCCCGGC TCCTTCATCG TCCCATCTCC CCTGTCTCTC TCCTGGGGAG GCGTGAAGCG GTCCCGTGGA TAGAGATTCA TGCCTGTGTC CGCGCGTGTG 
^191       ^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       

TGCGCGCGTA TAAATTGCCG AGAAGGGGAA AACATCACAG GACTTCTGCG AATACCGGAC TGAAAATTGT AATTCATCTG CCGCCGCCGC TGCCTTTTTT 
^291       ^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       

TTTTCTCGAG CTCTTGAGAT CTCCGGTTGG GATTCCTGCG GATTGACATT TCTGTGAAGC AGAAGTCTGG GAATCGATCT GGAAATCCTC CTAATTTTTA 
^391       ^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       

CTCCCTCTCC CCCCGACTCC TGATTCATTG GGAAGTTTCA AATCAGCTAT AACTGGAGAG TGCTGAAGAT TGATGGGATC GTTGCCTTAT GCATTTGTTT 
^491       ^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       

TGGTTTTACA AAAAGGAAAC TTGACAGAGG ATCATGCTGT ACTTAAAAAA TACAAGTAAG TCTCGCACAG GAAATTGGTT TAATGTAACT TTCAATGGAA 
^591       ^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       

ACCTTTGAGA TTTTTTACTT AAAGTGCATT CGAGTAAATT TAATTTCCAG GCAGCTTAAT ACATTGTTTT TAGCCGTGTT ACTTGTAGTG TGTATGCCCT 
^691       ^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       

GCTTTCACTC AGTGTGTACA GGGAAACGCA CCTGATTTTT TACTTATTAG TTTGTTTTTT CTTTAACCTT TCAGCATCAC AGAGGAAGTA GACTGATATT 
^791       ^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       

AACAATACTT ACTAATAATA ACGTGCCTCA TGAAATAAAG ATCCGAAAGG AATTGGAATA AAAATTTCCT GCGTCTCATG CCAAGAGGGA AACACCAGAA 
^891       ^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       

TCAAGTGTTC CGCGTGATTG AAGACACCCC CTCGTCCAAG AATGCAAAGC ACATCCAATA AAATAGCTGG ATTATAACTC CTCTTCTTTC TCTGGGGGCC 
^991       ^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      

GTGGGGTGGG AGCTGGGGCG AGAGGTGCCG TTGGCCCCCG TTGCTTTTCT TCTGGGAAGC ATGGGCCCAC AGGACGTCAT GGAAGACGCC AAAAACATAA 
^1091      ^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      

AGAAAGGCCC GGCGCCATTC TATCCTCTAG AGGATGGAAC CGCTGGAGAG CAACTGCATA AGGCTATGAA GAGATACGCC CTGGTTCCTG GAACAATTGC 
^1191      ^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      

TTTTACAGAT GCACATATCG AGGTGAACAT CACGTACG
^1291      ^1301      ^1311      ^1321

Citations:

Sherrill K. W., Byrd M. P., Van Eden M. E., Lloyd R. E. (2004) BCL-2 translation is mediated via internal ribosome entry during cell stress. J. Biol. Chem. 279(28):29066-29074

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