IRESite_Id:345 characteristics of Apaf-1 IRES studied in phpRMmAF plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `345`	Version: `3`
Originaly submitted by: Martin Mokrejš
Reviewed by: Václav Vopálenský	Last change: `2008-06-27 12:28:14`

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:
hopefully_full-length_mRNA

The mRNA/+RNA description:

Putative spliced in vitro SV40 promoter-derived transcript of phpRMmAF plasmid containing mouse version of
putative Apaf-1 IRES with a hairpin structure in front of the first cistron.

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

TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTGAAGT TGGTCGTGAG GCACTGGGCA GGTGTCCACT CCCAGTTCAA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTACAGCTCT TAAGGCTAGA GTACTTAATA CGACTCACTA TAGGCTAGGC TTGGCATTCC GGTACTGAAT TGATAGATCT GGTACCGAGC TCCCCGGGCT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCAGCCCGGG GAGCTCGGTA CCAGATCTAT CAAGCTCTAG CCACCATGAC TTCGAAAGTT TATGATCCAG AACAAAGGAA ACGGATGATA ACTGGTCCGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGTGGTGGGC CAGATGTAAA CAAATGAATG TTCTTGATTC ATTTATTAAT TATTATGATT CAGAAAAACA TGCAGAAAAT GCTGTTATTT TTTTACATGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TAACGCGGCC TCTTCTTATT TATGGCGACA TGTTGTGCCA CATATTGAGC CAGTAGCGCG GTGTATTATA CCAGACCTTA TTGGTATGGG CAAATCAGGC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AAATCTGGTA ATGGTTCTTA TAGGTTACTT GATCATTACA AATATCTTAC TGCATGGTTT GAACTTCTTA ATTTACCAAA GAAGATCATT TTTGTCGGCC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATGATTGGGG TGCTTGTTTG GCATTTCATT ATAGCTATGA GCATCAAGAT AAGATCAAAG CAATAGTTCA CGCTGAAAGT GTAGTAGATG TGATTGAATC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATGGGATGAA TGGCCTGATA TTGAAGAAGA TATTGCGTTG ATCAAATCTG AAGAAGGAGA AAAAATGGTT TTGGAGAATA ACTTCTTCGT GGAAACCATG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TTGCCATCAA AAATCATGAG AAAGTTAGAA CCAGAAGAAT TTGCAGCATA TCTTGAACCA TTCAAAGAGA AAGGTGAAGT TCGTCGTCCA ACATTATCAT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGCCTCGTGA AATCCCGTTA GTAAAAGGTG GTAAACCTGA CGTTGTACAA ATTGTTAGGA ATTATAATGC TTATCTACGT GCAAGTGATG ATTTACCAAA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AATGTTTATT GAATCGGACC CAGGATTCTT TTCCAATGCT ATTGTTGAAG GTGCCAAGAA GTTTCCTAAT ACTGAATTTG TCAAAGTAAA AGGTCTTCAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TTTTCGCAAG AAGATGCACC TGATGAAATG GGAAAATATA TCAAATCGTT CGTTGAGCGA GTTCTCAAAA ATGAACAATA ATTCTAGAGC TTATCGATAC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CGTCGACCTC GAATCACTAG TCAGCTGgaa ttcCGGCTTG AGGCAGAGAC CAGGAGGCAG CTAGAGGAGC AGACGTCTCA CTCCGCTCGC GGAAGGGTGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GAGAGGGGTG TGTGGGGGTC GGCAGCGAGG GGTGTGTGCC ATCAGCCACC GGCGACGATC TGAGACAGTC GCAGCGGCTT TCCGAGCGGC GTCCGCTTCC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CGCCCGGGCA GCTCCCGCCA GAGGGGTGAA GCGGCGACTG GAGTGGCCGT GCTTTTGTGC CCTGGGTCCC GGTACCCTCC CCTGGTGCGG CCCGAGGCAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GCCCACCGAG GTGACCACCC CTCGACGCCG CTTGGAGATC CCGGGCATCC ACCCTGCGCC CCGAGCAGCT GATACCCAGG GAGGTGTCAG GACCTGCCCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGGCGCGGGG TCGCCGGAAG CCAGGCGGGA GCCCCGGCTG CTTTCTGGCA ATCTAGTCTC ATAAGTGACC CTCCCTGGGC TGCTTTCTTT CGATTATCAT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CAGTGACCCT ACCCCGGCTG CTCTTCCCAG CACAACTCCG GTGCAAAGGC TTGGGCATCC TGGTGCTTTG CCTCTAGCCC ATGCTCCACA GCGAGGAGAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGAAAACCCT GAGGCAccAT GGAAGACGCC AAAAACATAA AGAAAGGCCC GGCGCCATTC TATCCGCTGG AAGATGGAAC CGCTGGAGAG CAACTGCATA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGGCTATGAA GAGATACGCC CTGGTTCCTG GAACAATTGC TTTTACAGAT GCACATATCG AGGTGGACAT CACTTACGCT GAGTACTTCG AAATGTCCGT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TCGGTTGGCA GAAGCTATGA AACGATATGG GCTGAATACA AATCACAGAA TCGTCGTATG CAGTGAAAAC TCTCTTCAAT TCTTTATGCC GGTGTTGGGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCGTTATTTA TCGGAGTTGC AGTTGCGCCC GCGAACGACA TTTATAATGA ACGTGAATTG CTCAACAGTA TGGGCATTTC GCAGCCTACC GTGGTGTTCG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTTCCAAAAA GGGGTTGCAA AAAATTTTGA ACGTGCAAAA AAAGCTCCCA ATCATCCAAA AAATTATTAT CATGGATTCT AAAACGGATT ACCAGGGATT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TCAGTCGATG TACACGTTCG TCACATCTCA TCTACCTCCC GGTTTTAATG AATACGATTT TGTGCCAGAG TCCTTCGATA GGGACAAGAC AATTGCACTG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ATCATGAACT CCTCTGGATC TACTGGTCTG CCTAAAGGTG TCGCTCTGCC TCATAGAACT GCCTGCGTGA GATTCTCGCA TGCCAGAGAT CCTATTTTTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GCAATCAAAT CATTCCGGAT ACTGCGATTT TAAGTGTTGT TCCATTCCAT CACGGTTTTG GAATGTTTAC TACACTCGGA TATTTGATAT GTGGATTTCG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AGTCGTCTTA ATGTATAGAT TTGAAGAAGA GCTGTTTCTG AGGAGCCTTC AGGATTACAA GATTCAAAGT GCGCTGCTGG TGCCAACCCT ATTCTCCTTC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TTCGCCAAAA GCACTCTGAT TGACAAATAC GATTTATCTA ATTTACACGA AATTGCTTCT GGTGGCGCTC CCCTCTCTAA GGAAGTCGGG GAAGCGGTTG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CCAAGAGGTT CCATCTGCCA GGTATCAGGC AAGGATATGG GCTCACTGAG ACTACATCAG CTATTCTGAT TACACCCGAG GGGGATGATA AACCGGGCGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGTCGGTAAA GTTGTTCCAT TTTTTGAAGC GAAGGTTGTG GATCTGGATA CCGGGAAAAC GCTGGGCGTT AATCAAAGAG GCGAACTGTG TGTGAGAGGT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CCTATGATTA TGTCCGGTTA TGTAAACAAT CCGGAAGCGA CCAACGCCTT GATTGACAAG GATGGATGGC TACATTCTGG AGACATAGCT TACTGGGACG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAGACGAACA CTTCTTCATC GTTGACCGCC TGAAGTCTCT GATTAAGTAC AAAGGCTATC AGGTGGCTCC CGCTGAATTG GAATCCATCT TGCTCCAACA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CCCCAACATC TTCGACGCAG GTGTCGCAGG TCTTCCCGAC GATGACGCCG GTGAACTTCC CGCCGCCGTT GTTGTTTTGG AGCACGGAAA GACGATGACG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GAAAAAGAGA TCGTGGATTA CGTCGCCAGT CAAGTAACAA CCGCGAAAAA GTTGCGCGGA GGAGTTGTGT TTGTGGACGA AGTACCGAAA GGTCTTACCG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GAAAACTCGA CGCAAGAAAA ATCAGAGAGA TCCTCATAAA GGCCAAGAAG GGCGGAAAGA TCGCCGTGTA ATTCTAGAGT CGGGGCGGCC GGCCGCTTCG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGCAGACATG ATAAGATACA TTGATGAGTT TGGACAAACC ACAACTAGAA TGCAGTGAAA AAAATGCTTT ATTTGTGAAA TTTGTGATGC TATTGCTTTA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTTGTAACCA TTATAAGCTG CAATAAACAA GTTAACAACA ACAATTGCAT TCATTTTATG TTTCAGGTTC AGGGGGAGGT GTGGGAGGTT TTTTAAAGCA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AGTAAAACCT CTACAAATGT GGTA
^3701      ^3711      ^3721

Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
phpRMmAF The name of the promoter used to express this mRNA:
SV40

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:
Apaf-1

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Mus musculus

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

GGTACCGAGC TCTTACGCGT GCTAGCCCGG GCTCGAGATC TGCGATCTGC ATCTCAATTA GTCAGCAACC ATAGTCCCGC CCCTAACTCC GCCCATCCCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCCTAACTC CGCCCAGTTC CGCCCATTCT CCGCCCCATC GCTGACTAAT TTTTTTTATT TATGCAGAGG CCGAGGCCGC CTCGGCCTCT GAGCTATTCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGAAGTAGTG AGGAGGCTTT TTTGGAGGCC TAGGCTTTTG CAAAAAGCTG AAGTTGGTCG TGAGGCACTG GGCAGGTAAG TATCAAGGTT ACAAGACAGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTTAAGGAGA CCAATAGAAA CTGGGCTTGT CGAGACAGAG AAGACTCTTG CGTTTCTGAT AGGCACCTAT TGGTCTTACT GACATCCACT TTGCCTTTCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTCCACAGGT GTCCACTCCC AGTTCAATTA CAGCTCTTAA GGCTAGAGTA CTTAATACGA CTCACTATAG GCTAGGCTTG GCATTCCGGT ACTGAATTGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCGCCGCGGG GCGCCGCCGG CCACGTGGGT ACCCACGTGG CCGGCGGCGC CCCGCGGCGG CCGATCAAGC TCTAGCCACC ATGACTTCGA AAGTTTATGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCCAGAACAA AGGAAACGGA TGATAACTGG TCCGCAGTGG TGGGCCAGAT GTAAACAAAT GAATGTTCTT GATTCATTTA TTAATTATTA TGATTCAGAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AAACATGCAG AAAATGCTGT TATTTTTTTA CATGGTAACG CGGCCTCTTC TTATTTATGG CGACATGTTG TGCCACATAT TGAGCCAGTA GCGCGGTGTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TTATACCAGA CCTTATTGGT ATGGGCAAAT CAGGCAAATC TGGTAATGGT TCTTATAGGT TACTTGATCA TTACAAATAT CTTACTGCAT GGTTTGAACT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCTTAATTTA CCAAAGAAGA TCATTTTTGT CGGCCATGAT TGGGGTGCTT GTTTGGCATT TCATTATAGC TATGAGCATC AAGATAAGAT CAAAGCAATA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GTTCACGCTG AAAGTGTAGT AGATGTGATT GAATCATGGG ATGAATGGCC TGATATTGAA GAAGATATTG CGTTGATCAA ATCTGAAGAA GGAGAAAAAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TGGTTTTGGA GAATAACTTC TTCGTGGAAA CCATGTTGCC ATCAAAAATC ATGAGAAAGT TAGAACCAGA AGAATTTGCA GCATATCTTG AACCATTCAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGAGAAAGGT GAAGTTCGTC GTCCAACATT ATCATGGCCT CGTGAAATCC CGTTAGTAAA AGGTGGTAAA CCTGACGTTG TACAAATTGT TAGGAATTAT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AATGCTTATC TACGTGCAAG TGATGATTTA CCAAAAATGT TTATTGAATC GGACCCAGGA TTCTTTTCCA ATGCTATTGT TGAAGGTGCC AAGAAGTTTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTAATACTGA ATTTGTCAAA GTAAAAGGTC TTCATTTTTC GCAAGAAGAT GCACCTGATG AAATGGGAAA ATATATCAAA TCGTTCGTTG AGCGAGTTCT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CAAAAATGAA CAATAATTCT AGAGCTTATC GATACCGTCG ACCTCGAATC ACTAGTCAGC TGgaattcCG GCTTGAGGCA GAGACCAGGA GGCAGCTAGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGAGCAGACG TCTCACTCCG CTCGCGGAAG GGTGTGAGAG GGGTGTGTGG GGGTCGGCAG CGAGGGGTGT GTGCCATCAG CCACCGGCGA CGATCTGAGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CAGTCGCAGC GGCTTTCCGA GCGGCGTCCG CTTCCCGCCC GGGCAGCTCC CGCCAGAGGG GTGAAGCGGC GACTGGAGTG GCCGTGCTTT TGTGCCCTGG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTCCCGGTAC CCTCCCCTGG TGCGGCCCGA GGCAAGCCCA CCGAGGTGAC CACCCCTCGA CGCCGCTTGG AGATCCCGGG CATCCACCCT GCGCCCCGAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CAGCTGATAC CCAGGGAGGT GTCAGGACCT GCCCGGGGCG CGGGGTCGCC GGAAGCCAGG CGGGAGCCCC GGCTGCTTTC TGGCAATCTA GTCTCATAAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGACCCTCCC TGGGCTGCTT TCTTTCGATT ATCATCAGTG ACCCTACCCC GGCTGCTCTT CCCAGCACAA CTCCGGTGCA AAGGCTTGGG CATCCTGGTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTTTGCCTCT AGCCCATGCT CCACAGCGAG GAGAGAGAAA ACCCTGAGGC AccATGGAAG ACGCCAAAAA CATAAAGAAA GGCCCGGCGC CATTCTATCC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GCTGGAAGAT GGAACCGCTG GAGAGCAACT GCATAAGGCT ATGAAGAGAT ACGCCCTGGT TCCTGGAACA ATTGCTTTTA CAGATGCACA TATCGAGGTG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GACATCACTT ACGCTGAGTA CTTCGAAATG TCCGTTCGGT TGGCAGAAGC TATGAAACGA TATGGGCTGA ATACAAATCA CAGAATCGTC GTATGCAGTG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AAAACTCTCT TCAATTCTTT ATGCCGGTGT TGGGCGCGTT ATTTATCGGA GTTGCAGTTG CGCCCGCGAA CGACATTTAT AATGAACGTG AATTGCTCAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CAGTATGGGC ATTTCGCAGC CTACCGTGGT GTTCGTTTCC AAAAAGGGGT TGCAAAAAAT TTTGAACGTG CAAAAAAAGC TCCCAATCAT CCAAAAAATT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATTATCATGG ATTCTAAAAC GGATTACCAG GGATTTCAGT CGATGTACAC GTTCGTCACA TCTCATCTAC CTCCCGGTTT TAATGAATAC GATTTTGTGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CAGAGTCCTT CGATAGGGAC AAGACAATTG CACTGATCAT GAACTCCTCT GGATCTACTG GTCTGCCTAA AGGTGTCGCT CTGCCTCATA GAACTGCCTG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CGTGAGATTC TCGCATGCCA GAGATCCTAT TTTTGGCAAT CAAATCATTC CGGATACTGC GATTTTAAGT GTTGTTCCAT TCCATCACGG TTTTGGAATG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TTTACTACAC TCGGATATTT GATATGTGGA TTTCGAGTCG TCTTAATGTA TAGATTTGAA GAAGAGCTGT TTCTGAGGAG CCTTCAGGAT TACAAGATTC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AAAGTGCGCT GCTGGTGCCA ACCCTATTCT CCTTCTTCGC CAAAAGCACT CTGATTGACA AATACGATTT ATCTAATTTA CACGAAATTG CTTCTGGTGG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CGCTCCCCTC TCTAAGGAAG TCGGGGAAGC GGTTGCCAAG AGGTTCCATC TGCCAGGTAT CAGGCAAGGA TATGGGCTCA CTGAGACTAC ATCAGCTATT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CTGATTACAC CCGAGGGGGA TGATAAACCG GGCGCGGTCG GTAAAGTTGT TCCATTTTTT GAAGCGAAGG TTGTGGATCT GGATACCGGG AAAACGCTGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GCGTTAATCA AAGAGGCGAA CTGTGTGTGA GAGGTCCTAT GATTATGTCC GGTTATGTAA ACAATCCGGA AGCGACCAAC GCCTTGATTG ACAAGGATGG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ATGGCTACAT TCTGGAGACA TAGCTTACTG GGACGAAGAC GAACACTTCT TCATCGTTGA CCGCCTGAAG TCTCTGATTA AGTACAAAGG CTATCAGGTG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GCTCCCGCTG AATTGGAATC CATCTTGCTC CAACACCCCA ACATCTTCGA CGCAGGTGTC GCAGGTCTTC CCGACGATGA CGCCGGTGAA CTTCCCGCCG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CCGTTGTTGT TTTGGAGCAC GGAAAGACGA TGACGGAAAA AGAGATCGTG GATTACGTCG CCAGTCAAGT AACAACCGCG AAAAAGTTGC GCGGAGGAGT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TGTGTTTGTG GACGAAGTAC CGAAAGGTCT TACCGGAAAA CTCGACGCAA GAAAAATCAG AGAGATCCTC ATAAAGGCCA AGAAGGGCGG AAAGATCGCC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GTGTAATTCT AGAGTCGGGG CGGCCGGCCG CTTCGAGCAG ACATGATAAG ATACATTGAT GAGTTTGGAC AAACCACAAC TAGAATGCAG TGAAAAAAAT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GCTTTATTTG TGAAATTTGT GATGCTATTG CTTTATTTGT AACCATTATA AGCTGCAATA AACAAGTTAA CAACAACAAT TGCATTCATT TTATGTTTCA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GGTTCAGGGG GAGGTGTGGG AGGTTTTTTA AAGCAAGTAA AACCTCTACA AATGTGGTAA AATCGATAAG GATCTGAACG ATGGAGCGGA GAATGGGCGG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AACTGGGCGG AGTTAGGGGC GGGATGGGCG GAGTTAGGGG CGGGACTATG GTTGCTGACT AATTGAGATG CATGCTTTGC ATACTTCTGC CTGCTGGGGA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GCCTGGGGAC TTTCCACACC TGGTTGCTGA CTAATTGAGA TGCATGCTTT GCATACTTCT GCCTGCTGGG GAGCCTGGGG ACTTTCCACA CCCTAACTGA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CACACATTCC ACAGCGGATC CGTCGACCGA TGCCCTTGAG AGCCTTCAAC CCAGTCAGCT CCTTCCGGTG GGCGCGGGGC ATGACTATCG TCGCCGCACT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TATGACTGTC TTCTTTATCA TGCAACTCGT AGGACAGGTG CCGGCAGCGC TCTTCCGCTT CCTCGCTCAC TGACTCGCTG CGCTCGGTCG TTCGGCTGCG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GCGAGCGGTA TCAGCTCACT CAAAGGCGGT AATACGGTTA TCCACAGAAT CAGGGGATAA CGCAGGAAAG AACATGTGAG CAAAAGGCCA GCAAAAGGCC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

AGGAACCGTA AAAAGGCCGC GTTGCTGGCG TTTTTCCATA GGCTCCGCCC CCCTGACGAG CATCACAAAA ATCGACGCTC AAGTCAGAGG TGGCGAAACC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CGACAGGACT ATAAAGATAC CAGGCGTTTC CCCCTGGAAG CTCCCTCGTG CGCTCTCCTG TTCCGACCCT GCCGCTTACC GGATACCTGT CCGCCTTTCT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CCCTTCGGGA AGCGTGGCGC TTTCTCAATG CTCACGCTGT AGGTATCTCA GTTCGGTGTA GGTCGTTCGC TCCAAGCTGG GCTGTGTGCA CGAACCCCCC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GTTCAGCCCG ACCGCTGCGC CTTATCCGGT AACTATCGTC TTGAGTCCAA CCCGGTAAGA CACGACTTAT CGCCACTGGC AGCAGCCACT GGTAACAGGA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTAGCAGAGC GAGGTATGTA GGCGGTGCTA CAGAGTTCTT GAAGTGGTGG CCTAACTACG GCTACACTAG AAGGACAGTA TTTGGTATCT GCGCTCTGCT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GAAGCCAGTT ACCTTCGGAA AAAGAGTTGG TAGCTCTTGA TCCGGCAAAC AAACCACCGC TGGTAGCGGT GGTTTTTTTG TTTGCAAGCA GCAGATTACG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CGCAGAAAAA AAGGATCTCA AGAAGATCCT TTGATCTTTT CTACGGGGTC TGACGCTCAG TGGAACGAAA ACTCACGTTA AGGGATTTTG GTCATGAGAT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TATCAAAAAG GATCTTCACC TAGATCCTTT TAAATTAAAA ATGAAGTTTT AAATCAATCT AAAGTATATA TGAGTAAACT TGGTCTGACA GTTACCAATG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CTTAATCAGT GAGGCACCTA TCTCAGCGAT CTGTCTATTT CGTTCATCCA TAGTTGCCTG ACTCCCCGTC GTGTAGATAA CTACGATACG GGAGGGCTTA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

CCATCTGGCC CCAGTGCTGC AATGATACCG CGAGACCCAC GCTCACCGGC TCCAGATTTA TCAGCAATAA ACCAGCCAGC CGGAAGGGCC GAGCGCAGAA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

GTGGTCCTGC AACTTTATCC GCCTCCATCC AGTCTATTAA TTGTTGCCGG GAAGCTAGAG TAAGTAGTTC GCCAGTTAAT AGTTTGCGCA ACGTTGTTGC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CATTGCTACA GGCATCGTGG TGTCACGCTC GTCGTTTGGT ATGGCTTCAT TCAGCTCCGG TTCCCAACGA TCAAGGCGAG TTACATGATC CCCCATGTTG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TGCAAAAAAG CGGTTAGCTC CTTCGGTCCT CCGATCGTTG TCAGAAGTAA GTTGGCCGCA GTGTTATCAC TCATGGTTAT GGCAGCACTG CATAATTCTC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TTACTGTCAT GCCATCCGTA AGATGCTTTT CTGTGACTGG TGAGTACTCA ACCAAGTCAT TCTGAGAATA GTGTATGCGG CGACCGAGTT GCTCTTGCCC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GGCGTCAATA CGGGATAATA CCGCGCCACA TAGCAGAACT TTAAAAGTGC TCATCATTGG AAAACGTTCT TCGGGGCGAA AACTCTCAAG GATCTTACCG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CTGTTGAGAT CCAGTTCGAT GTAACCCACT CGTGCACCCA ACTGATCTTC AGCATCTTTT ACTTTCACCA GCGTTTCTGG GTGAGCAAAA ACAGGAAGGC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

AAAATGCCGC AAAAAAGGGA ATAAGGGCGA CACGGAAATG TTGAATACTC ATACTCTTCC TTTTTCAATA TTATTGAAGC ATTTATCAGG GTTATTGTCT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

CATGAGCGGA TACATATTTG AATGTATTTA GAAAAATAAA CAAATAGGGG TTCCGCGCAC ATTTCCCCGA AAAGTGCCAC CTGACGCGCC CTGTAGCGGC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

GCATTAAGCG CGGCGGGTGT GGTGGTTACG CGCAGCGTGA CCGCTACACT TGCCAGCGCC CTAGCGCCCG CTCCTTTCGC TTTCTTCCCT TCCTTTCTCG 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CCACGTTCGC CGGCTTTCCC CGTCAAGCTC TAAATCGGGG GCTCCCTTTA GGGTTCCGAT TTAGTGCTTT ACGGCACCTC GACCCCAAAA AACTTGATTA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GGGTGATGGT TCACGTAGTG GGCCATCGCC CTGATAGACG GTTTTTCGCC CTTTGACGTT GGAGTCCACG TTCTTTAATA GTGGACTCTT GTTCCAAACT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GGAACAACAC TCAACCCTAT CTCGGTCTAT TCTTTTGATT TATAAGGGAT TTTGCCGATT TCGGCCTATT GGTTAAAAAA TGAGCTGATT TAACAAAAAT 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

TTAACGCGAA TTTTAACAAA ATATTAACGT TTACAATTTC CCATTCGCCA TTCAGGCTGC GCAACTGTTG GGAAGGGCGA TCGGTGCGGG CCTCTTCGCT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

ATTACGCCAG CCCAAGCTAC CATGATAAGT AAGTAATATT AAGGTACGGG AGGTACTTGG AGCGGCCGCA ATAAAATATC TTTATTTTCA TTACATCTGT 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

GTGTTGGTTT TTTGTGTGAA TCGATAGTAC TAACATACGC TCTCCATCAA AACAAAACGA AACAAAACAA ACTAGCAAAA TAGGCTGTCC CCAGTGCAAG 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

TGCAGGTGCC AGAACATTTC TCTATCGATA
^7101      ^7111      ^7121

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: `2`	Last change: `2008-06-27 12:28:14`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
RLuc

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

246-1181

ORF

ORF position:

2

Version: `3`	Last change: `2008-06-27 12:28:14`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

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:

not tested

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

1819-3471

Citations:

Coldwell M. J., Mitchell S. A., Stoneley M., MacFarlane M., Willis A. E. (2000) Initiation of Apaf-1 translation by internal ribosome entry. Oncogene. 19(7):899-905

IRESs:

IRES:

Version: `3`	Last change: `2008-06-27 12:28:14`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský
The IRES name: `Apaf-1`	The functional status of IRES: `functional`

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

1234-1816

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `53`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `635`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-585`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-3`

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

CGGCTTGAGG CAGAGACCAG GAGGCAGCTA GAGGAGCAGA CGTCTCACTC CGCTCGCGGA AGGGTGTGAG AGGGGTGTGT GGGGGTCGGC AGCGAGGGGT 
^1234      ^1244      ^1254      ^1264      ^1274      ^1284      ^1294      ^1304      ^1314      ^1324      

GTGTGCCATC AGCCACCGGC GACGATCTGA GACAGTCGCA GCGGCTTTCC GAGCGGCGTC CGCTTCCCGC CCGGGCAGCT CCCGCCAGAG GGGTGAAGCG 
^1334      ^1344      ^1354      ^1364      ^1374      ^1384      ^1394      ^1404      ^1414      ^1424      

GCGACTGGAG TGGCCGTGCT TTTGTGCCCT GGGTCCCGGT ACCCTCCCCT GGTGCGGCCC GAGGCAAGCC CACCGAGGTG ACCACCCCTC GACGCCGCTT 
^1434      ^1444      ^1454      ^1464      ^1474      ^1484      ^1494      ^1504      ^1514      ^1524      

GGAGATCCCG GGCATCCACC CTGCGCCCCG AGCAGCTGAT ACCCAGGGAG GTGTCAGGAC CTGCCCGGGG CGCGGGGTCG CCGGAAGCCA GGCGGGAGCC 
^1534      ^1544      ^1554      ^1564      ^1574      ^1584      ^1594      ^1604      ^1614      ^1624      

CCGGCTGCTT TCTGGCAATC TAGTCTCATA AGTGACCCTC CCTGGGCTGC TTTCTTTCGA TTATCATCAG TGACCCTACC CCGGCTGCTC TTCCCAGCAC 
^1634      ^1644      ^1654      ^1664      ^1674      ^1684      ^1694      ^1704      ^1714      ^1724      

AACTCCGGTG CAAAGGCTTG GGCATCCTGG TGCTTTGCCT CTAGCCCATG CTCCACAGCG AGGAGAGAGA AAACCCTGAG GCA
^1734      ^1744      ^1754      ^1764      ^1774      ^1784      ^1794      ^1804      ^1814

Citations:

Coldwell M. J., Mitchell S. A., Stoneley M., MacFarlane M., Willis A. E. (2000) Initiation of Apaf-1 translation by internal ribosome entry. Oncogene. 19(7):899-905

The translation experiments:

Translation results:

IRESite Translation Id: 417

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HeLa (ATCC CCL-2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

185.000

Name of IRES used as the positive control:

Apaf-1

Name of the plasmid used as the positive control. `phpRAF`	Name of the plasmid used as the negative control. `pRF`
`IRESite Id` of the plasmid used as positive control. `344`	`IRESite Id` of the plasmid used as negative control. `184`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `2.400`
The size (length) of intercistronic region in the positive control: `624`	The size (length) of intercistronic region in the negative control: `67`

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:

Fig. 4b

Citations:

Coldwell M. J., Mitchell S. A., Stoneley M., MacFarlane M., Willis A. E. (2000) Initiation of Apaf-1 translation by internal ribosome entry. Oncogene. 19(7):899-905

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