IRESite_Id:343 characteristics of Apaf-1 IRES studied in pRMmAF plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `343`	Version: `2`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-05-22 17:32:23`

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 pRMmAF plasmid containing mouse version of
putative Apaf-1 IRES except the very last 2 bases of 5'-UTR. However, the 5'-end of the UTR is maybe
incomplete as well (by 39 bp).

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 TGATATCAAG CTCTAGCCAC CATGACTTCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AAAGTTTATG ATCCAGAACA AAGGAAACGG ATGATAACTG GTCCGCAGTG GTGGGCCAGA TGTAAACAAA TGAATGTTCT TGATTCATTT ATTAATTATT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATGATTCAGA AAAACATGCA GAAAATGCTG TTATTTTTTT ACATGGTAAC GCGGCCTCTT CTTATTTATG GCGACATGTT GTGCCACATA TTGAGCCAGT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AGCGCGGTGT ATTATACCAG ACCTTATTGG TATGGGCAAA TCAGGCAAAT CTGGTAATGG TTCTTATAGG TTACTTGATC ATTACAAATA TCTTACTGCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TGGTTTGAAC TTCTTAATTT ACCAAAGAAG ATCATTTTTG TCGGCCATGA TTGGGGTGCT TGTTTGGCAT TTCATTATAG CTATGAGCAT CAAGATAAGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCAAAGCAAT AGTTCACGCT GAAAGTGTAG TAGATGTGAT TGAATCATGG GATGAATGGC CTGATATTGA AGAAGATATT GCGTTGATCA AATCTGAAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGGAGAAAAA ATGGTTTTGG AGAATAACTT CTTCGTGGAA ACCATGTTGC CATCAAAAAT CATGAGAAAG TTAGAACCAG AAGAATTTGC AGCATATCTT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GAACCATTCA AAGAGAAAGG TGAAGTTCGT CGTCCAACAT TATCATGGCC TCGTGAAATC CCGTTAGTAA AAGGTGGTAA ACCTGACGTT GTACAAATTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTAGGAATTA TAATGCTTAT CTACGTGCAA GTGATGATTT ACCAAAAATG TTTATTGAAT CGGACCCAGG ATTCTTTTCC AATGCTATTG TTGAAGGTGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CAAGAAGTTT CCTAATACTG AATTTGTCAA AGTAAAAGGT CTTCATTTTT CGCAAGAAGA TGCACCTGAT GAAATGGGAA AATATATCAA ATCGTTCGTT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAGCGAGTTC TCAAAAATGA ACAATAATTC TAGAGCTTAT CGATACCGTC GACCTCGAAT CACTAGTCAG CTGgaattcC GGCTTGAGGC AGAGACCAGG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGGCAGCTAG AGGAGCAGAC GTCTCACTCC GCTCGCGGAA GGGTGTGAGA GGGGTGTGTG GGGGTCGGCA GCGAGGGGTG TGTGCCATCA GCCACCGGCG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ACGATCTGAG ACAGTCGCAG CGGCTTTCCG AGCGGCGTCC GCTTCCCGCC CGGGCAGCTC CCGCCAGAGG GGTGAAGCGG CGACTGGAGT GGCCGTGCTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TTGTGCCCTG GGTCCCGGTA CCCTCCCCTG GTGCGGCCCG AGGCAAGCCC ACCGAGGTGA CCACCCCTCG ACGCCGCTTG GAGATCCCGG GCATCCACCC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGCGCCCCGA GCAGCTGATA CCCAGGGAGG TGTCAGGACC TGCCCGGGGC GCGGGGTCGC CGGAAGCCAG GCGGGAGCCC CGGCTGCTTT CTGGCAATCT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGTCTCATAA GTGACCCTCC CTGGGCTGCT TTCTTTCGAT TATCATCAGT GACCCTACCC CGGCTGCTCT TCCCAGCACA ACTCCGGTGC AAAGGCTTGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCATCCTGGT GCTTTGCCTC TAGCCCATGC TCCACAGCGA GGAGAGAGAA AACCCTGAGG CACCATGGAA GACGCCAAAA ACATAAAGAA AGGCCCGGCG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCATTCTATC CGCTGGAAGA TGGAACCGCT GGAGAGCAAC TGCATAAGGC TATGAAGAGA TACGCCCTGG TTCCTGGAAC AATTGCTTTT ACAGATGCAC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATATCGAGGT GGACATCACT TACGCTGAGT ACTTCGAAAT GTCCGTTCGG TTGGCAGAAG CTATGAAACG ATATGGGCTG AATACAAATC ACAGAATCGT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CGTATGCAGT GAAAACTCTC TTCAATTCTT TATGCCGGTG TTGGGCGCGT TATTTATCGG AGTTGCAGTT GCGCCCGCGA ACGACATTTA TAATGAACGT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GAATTGCTCA ACAGTATGGG CATTTCGCAG CCTACCGTGG TGTTCGTTTC CAAAAAGGGG TTGCAAAAAA TTTTGAACGT GCAAAAAAAG CTCCCAATCA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCCAAAAAAT TATTATCATG GATTCTAAAA CGGATTACCA GGGATTTCAG TCGATGTACA CGTTCGTCAC ATCTCATCTA CCTCCCGGTT TTAATGAATA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CGATTTTGTG CCAGAGTCCT TCGATAGGGA CAAGACAATT GCACTGATCA TGAACTCCTC TGGATCTACT GGTCTGCCTA AAGGTGTCGC TCTGCCTCAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AGAACTGCCT GCGTGAGATT CTCGCATGCC AGAGATCCTA TTTTTGGCAA TCAAATCATT CCGGATACTG CGATTTTAAG TGTTGTTCCA TTCCATCACG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTTTTGGAAT GTTTACTACA CTCGGATATT TGATATGTGG ATTTCGAGTC GTCTTAATGT ATAGATTTGA AGAAGAGCTG TTTCTGAGGA GCCTTCAGGA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTACAAGATT CAAAGTGCGC TGCTGGTGCC AACCCTATTC TCCTTCTTCG CCAAAAGCAC TCTGATTGAC AAATACGATT TATCTAATTT ACACGAAATT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCTTCTGGTG GCGCTCCCCT CTCTAAGGAA GTCGGGGAAG CGGTTGCCAA GAGGTTCCAT CTGCCAGGTA TCAGGCAAGG ATATGGGCTC ACTGAGACTA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CATCAGCTAT TCTGATTACA CCCGAGGGGG ATGATAAACC GGGCGCGGTC GGTAAAGTTG TTCCATTTTT TGAAGCGAAG GTTGTGGATC TGGATACCGG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAAAACGCTG GGCGTTAATC AAAGAGGCGA ACTGTGTGTG AGAGGTCCTA TGATTATGTC CGGTTATGTA AACAATCCGG AAGCGACCAA CGCCTTGATT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GACAAGGATG GATGGCTACA TTCTGGAGAC ATAGCTTACT GGGACGAAGA CGAACACTTC TTCATCGTTG ACCGCCTGAA GTCTCTGATT AAGTACAAAG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GCTATCAGGT GGCTCCCGCT GAATTGGAAT CCATCTTGCT CCAACACCCC AACATCTTCG ACGCAGGTGT CGCAGGTCTT CCCGACGATG ACGCCGGTGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ACTTCCCGCC GCCGTTGTTG TTTTGGAGCA CGGAAAGACG ATGACGGAAA AAGAGATCGT GGATTACGTC GCCAGTCAAG TAACAACCGC GAAAAAGTTG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CGCGGAGGAG TTGTGTTTGT GGACGAAGTA CCGAAAGGTC TTACCGGAAA ACTCGACGCA AGAAAAATCA GAGAGATCCT CATAAAGGCC AAGAAGGGCG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GAAAGATCGC CGTGTAATTC TAGAGTCGGG GCGGCCGGCC GCTTCGAGCA GACATGATAA GATACATTGA TGAGTTTGGA CAAACCACAA CTAGAATGCA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GTGAAAAAAA TGCTTTATTT GTGAAATTTG TGATGCTATT GCTTTATTTG TAACCATTAT AAGCTGCAAT AAACAAGTTA ACAACAACAA TTGCATTCAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTTATGTTTC AGGTTCAGGG GGAGGTGTGG GAGGTTTTTT AAAGCAAGTA AAACCTCTAC AAATGTGGTA
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661

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:
pRMmAF 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       

TATCAAGCTC TAGCCACCAT GACTTCGAAA GTTTATGATC CAGAACAAAG GAAACGGATG ATAACTGGTC CGCAGTGGTG GGCCAGATGT AAACAAATGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATGTTCTTGA TTCATTTATT AATTATTATG ATTCAGAAAA ACATGCAGAA AATGCTGTTA TTTTTTTACA TGGTAACGCG GCCTCTTCTT ATTTATGGCG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACATGTTGTG CCACATATTG AGCCAGTAGC GCGGTGTATT ATACCAGACC TTATTGGTAT GGGCAAATCA GGCAAATCTG GTAATGGTTC TTATAGGTTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTTGATCATT ACAAATATCT TACTGCATGG TTTGAACTTC TTAATTTACC AAAGAAGATC ATTTTTGTCG GCCATGATTG GGGTGCTTGT TTGGCATTTC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATTATAGCTA TGAGCATCAA GATAAGATCA AAGCAATAGT TCACGCTGAA AGTGTAGTAG ATGTGATTGA ATCATGGGAT GAATGGCCTG ATATTGAAGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGATATTGCG TTGATCAAAT CTGAAGAAGG AGAAAAAATG GTTTTGGAGA ATAACTTCTT CGTGGAAACC ATGTTGCCAT CAAAAATCAT GAGAAAGTTA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAACCAGAAG AATTTGCAGC ATATCTTGAA CCATTCAAAG AGAAAGGTGA AGTTCGTCGT CCAACATTAT CATGGCCTCG TGAAATCCCG TTAGTAAAAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTGGTAAACC TGACGTTGTA CAAATTGTTA GGAATTATAA TGCTTATCTA CGTGCAAGTG ATGATTTACC AAAAATGTTT ATTGAATCGG ACCCAGGATT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CTTTTCCAAT GCTATTGTTG AAGGTGCCAA GAAGTTTCCT AATACTGAAT TTGTCAAAGT AAAAGGTCTT CATTTTTCGC AAGAAGATGC ACCTGATGAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ATGGGAAAAT ATATCAAATC GTTCGTTGAG CGAGTTCTCA AAAATGAACA ATAATTCTAG AGCTTATCGA TACCGTCGAC CTCGAATCAC TAGTCAGCTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

gaattcCGGC TTGAGGCAGA GACCAGGAGG CAGCTAGAGG AGCAGACGTC TCACTCCGCT CGCGGAAGGG TGTGAGAGGG GTGTGTGGGG GTCGGCAGCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGGGGTGTGT GCCATCAGCC ACCGGCGACG ATCTGAGACA GTCGCAGCGG CTTTCCGAGC GGCGTCCGCT TCCCGCCCGG GCAGCTCCCG CCAGAGGGGT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAAGCGGCGA CTGGAGTGGC CGTGCTTTTG TGCCCTGGGT CCCGGTACCC TCCCCTGGTG CGGCCCGAGG CAAGCCCACC GAGGTGACCA CCCCTCGACG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCGCTTGGAG ATCCCGGGCA TCCACCCTGC GCCCCGAGCA GCTGATACCC AGGGAGGTGT CAGGACCTGC CCGGGGCGCG GGGTCGCCGG AAGCCAGGCG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGAGCCCCGG CTGCTTTCTG GCAATCTAGT CTCATAAGTG ACCCTCCCTG GGCTGCTTTC TTTCGATTAT CATCAGTGAC CCTACCCCGG CTGCTCTTCC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CAGCACAACT CCGGTGCAAA GGCTTGGGCA TCCTGGTGCT TTGCCTCTAG CCCATGCTCC ACAGCGAGGA GAGAGAAAAC CCTGAGGCAC CATGGAAGAC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCCAAAAACA TAAAGAAAGG CCCGGCGCCA TTCTATCCGC TGGAAGATGG AACCGCTGGA GAGCAACTGC ATAAGGCTAT GAAGAGATAC GCCCTGGTTC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTGGAACAAT TGCTTTTACA GATGCACATA TCGAGGTGGA CATCACTTAC GCTGAGTACT TCGAAATGTC CGTTCGGTTG GCAGAAGCTA TGAAACGATA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TGGGCTGAAT ACAAATCACA GAATCGTCGT ATGCAGTGAA AACTCTCTTC AATTCTTTAT GCCGGTGTTG GGCGCGTTAT TTATCGGAGT TGCAGTTGCG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCCGCGAACG ACATTTATAA TGAACGTGAA TTGCTCAACA GTATGGGCAT TTCGCAGCCT ACCGTGGTGT TCGTTTCCAA AAAGGGGTTG CAAAAAATTT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TGAACGTGCA AAAAAAGCTC CCAATCATCC AAAAAATTAT TATCATGGAT TCTAAAACGG ATTACCAGGG ATTTCAGTCG ATGTACACGT TCGTCACATC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TCATCTACCT CCCGGTTTTA ATGAATACGA TTTTGTGCCA GAGTCCTTCG ATAGGGACAA GACAATTGCA CTGATCATGA ACTCCTCTGG ATCTACTGGT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CTGCCTAAAG GTGTCGCTCT GCCTCATAGA ACTGCCTGCG TGAGATTCTC GCATGCCAGA GATCCTATTT TTGGCAATCA AATCATTCCG GATACTGCGA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TTTTAAGTGT TGTTCCATTC CATCACGGTT TTGGAATGTT TACTACACTC GGATATTTGA TATGTGGATT TCGAGTCGTC TTAATGTATA GATTTGAAGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AGAGCTGTTT CTGAGGAGCC TTCAGGATTA CAAGATTCAA AGTGCGCTGC TGGTGCCAAC CCTATTCTCC TTCTTCGCCA AAAGCACTCT GATTGACAAA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TACGATTTAT CTAATTTACA CGAAATTGCT TCTGGTGGCG CTCCCCTCTC TAAGGAAGTC GGGGAAGCGG TTGCCAAGAG GTTCCATCTG CCAGGTATCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGCAAGGATA TGGGCTCACT GAGACTACAT CAGCTATTCT GATTACACCC GAGGGGGATG ATAAACCGGG CGCGGTCGGT AAAGTTGTTC CATTTTTTGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AGCGAAGGTT GTGGATCTGG ATACCGGGAA AACGCTGGGC GTTAATCAAA GAGGCGAACT GTGTGTGAGA GGTCCTATGA TTATGTCCGG TTATGTAAAC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AATCCGGAAG CGACCAACGC CTTGATTGAC AAGGATGGAT GGCTACATTC TGGAGACATA GCTTACTGGG ACGAAGACGA ACACTTCTTC ATCGTTGACC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GCCTGAAGTC TCTGATTAAG TACAAAGGCT ATCAGGTGGC TCCCGCTGAA TTGGAATCCA TCTTGCTCCA ACACCCCAAC ATCTTCGACG CAGGTGTCGC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGGTCTTCCC GACGATGACG CCGGTGAACT TCCCGCCGCC GTTGTTGTTT TGGAGCACGG AAAGACGATG ACGGAAAAAG AGATCGTGGA TTACGTCGCC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AGTCAAGTAA CAACCGCGAA AAAGTTGCGC GGAGGAGTTG TGTTTGTGGA CGAAGTACCG AAAGGTCTTA CCGGAAAACT CGACGCAAGA AAAATCAGAG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AGATCCTCAT AAAGGCCAAG AAGGGCGGAA AGATCGCCGT GTAATTCTAG AGTCGGGGCG GCCGGCCGCT TCGAGCAGAC ATGATAAGAT ACATTGATGA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GTTTGGACAA ACCACAACTA GAATGCAGTG AAAAAAATGC TTTATTTGTG AAATTTGTGA TGCTATTGCT TTATTTGTAA CCATTATAAG CTGCAATAAA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CAAGTTAACA ACAACAATTG CATTCATTTT ATGTTTCAGG TTCAGGGGGA GGTGTGGGAG GTTTTTTAAA GCAAGTAAAA CCTCTACAAA TGTGGTAAAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TCGATAAGGA TCTGAACGAT GGAGCGGAGA ATGGGCGGAA CTGGGCGGAG TTAGGGGCGG GATGGGCGGA GTTAGGGGCG GGACTATGGT TGCTGACTAA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TTGAGATGCA TGCTTTGCAT ACTTCTGCCT GCTGGGGAGC CTGGGGACTT TCCACACCTG GTTGCTGACT AATTGAGATG CATGCTTTGC ATACTTCTGC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CTGCTGGGGA GCCTGGGGAC TTTCCACACC CTAACTGACA CACATTCCAC AGCGGATCCG TCGACCGATG CCCTTGAGAG CCTTCAACCC AGTCAGCTCC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TTCCGGTGGG CGCGGGGCAT GACTATCGTC GCCGCACTTA TGACTGTCTT CTTTATCATG CAACTCGTAG GACAGGTGCC GGCAGCGCTC TTCCGCTTCC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TCGCTCACTG ACTCGCTGCG CTCGGTCGTT CGGCTGCGGC GAGCGGTATC AGCTCACTCA AAGGCGGTAA TACGGTTATC CACAGAATCA GGGGATAACG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CAGGAAAGAA CATGTGAGCA AAAGGCCAGC AAAAGGCCAG GAACCGTAAA AAGGCCGCGT TGCTGGCGTT TTTCCATAGG CTCCGCCCCC CTGACGAGCA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TCACAAAAAT CGACGCTCAA GTCAGAGGTG GCGAAACCCG ACAGGACTAT AAAGATACCA GGCGTTTCCC CCTGGAAGCT CCCTCGTGCG CTCTCCTGTT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CCGACCCTGC CGCTTACCGG ATACCTGTCC GCCTTTCTCC CTTCGGGAAG CGTGGCGCTT TCTCAATGCT CACGCTGTAG GTATCTCAGT TCGGTGTAGG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TCGTTCGCTC CAAGCTGGGC TGTGTGCACG AACCCCCCGT TCAGCCCGAC CGCTGCGCCT TATCCGGTAA CTATCGTCTT GAGTCCAACC CGGTAAGACA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CGACTTATCG CCACTGGCAG CAGCCACTGG TAACAGGATT AGCAGAGCGA GGTATGTAGG CGGTGCTACA GAGTTCTTGA AGTGGTGGCC TAACTACGGC 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TACACTAGAA GGACAGTATT TGGTATCTGC GCTCTGCTGA AGCCAGTTAC CTTCGGAAAA AGAGTTGGTA GCTCTTGATC CGGCAAACAA ACCACCGCTG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GTAGCGGTGG TTTTTTTGTT TGCAAGCAGC AGATTACGCG CAGAAAAAAA GGATCTCAAG AAGATCCTTT GATCTTTTCT ACGGGGTCTG ACGCTCAGTG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GAACGAAAAC TCACGTTAAG GGATTTTGGT CATGAGATTA TCAAAAAGGA TCTTCACCTA GATCCTTTTA AATTAAAAAT GAAGTTTTAA ATCAATCTAA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

AGTATATATG AGTAAACTTG GTCTGACAGT TACCAATGCT TAATCAGTGA GGCACCTATC TCAGCGATCT GTCTATTTCG TTCATCCATA GTTGCCTGAC 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TCCCCGTCGT GTAGATAACT ACGATACGGG AGGGCTTACC ATCTGGCCCC AGTGCTGCAA TGATACCGCG AGACCCACGC TCACCGGCTC CAGATTTATC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AGCAATAAAC CAGCCAGCCG GAAGGGCCGA GCGCAGAAGT GGTCCTGCAA CTTTATCCGC CTCCATCCAG TCTATTAATT GTTGCCGGGA AGCTAGAGTA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

AGTAGTTCGC CAGTTAATAG TTTGCGCAAC GTTGTTGCCA TTGCTACAGG CATCGTGGTG TCACGCTCGT CGTTTGGTAT GGCTTCATTC AGCTCCGGTT 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CCCAACGATC AAGGCGAGTT ACATGATCCC CCATGTTGTG CAAAAAAGCG GTTAGCTCCT TCGGTCCTCC GATCGTTGTC AGAAGTAAGT TGGCCGCAGT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GTTATCACTC ATGGTTATGG CAGCACTGCA TAATTCTCTT ACTGTCATGC CATCCGTAAG ATGCTTTTCT GTGACTGGTG AGTACTCAAC CAAGTCATTC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TGAGAATAGT GTATGCGGCG ACCGAGTTGC TCTTGCCCGG CGTCAATACG GGATAATACC GCGCCACATA GCAGAACTTT AAAAGTGCTC ATCATTGGAA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

AACGTTCTTC GGGGCGAAAA CTCTCAAGGA TCTTACCGCT GTTGAGATCC AGTTCGATGT AACCCACTCG TGCACCCAAC TGATCTTCAG CATCTTTTAC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

TTTCACCAGC GTTTCTGGGT GAGCAAAAAC AGGAAGGCAA AATGCCGCAA AAAAGGGAAT AAGGGCGACA CGGAAATGTT GAATACTCAT ACTCTTCCTT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TTTCAATATT ATTGAAGCAT TTATCAGGGT TATTGTCTCA TGAGCGGATA CATATTTGAA TGTATTTAGA AAAATAAACA AATAGGGGTT CCGCGCACAT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TTCCCCGAAA AGTGCCACCT GACGCGCCCT GTAGCGGCGC ATTAAGCGCG GCGGGTGTGG TGGTTACGCG CAGCGTGACC GCTACACTTG CCAGCGCCCT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AGCGCCCGCT CCTTTCGCTT TCTTCCCTTC CTTTCTCGCC ACGTTCGCCG GCTTTCCCCG TCAAGCTCTA AATCGGGGGC TCCCTTTAGG GTTCCGATTT 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

AGTGCTTTAC GGCACCTCGA CCCCAAAAAA CTTGATTAGG GTGATGGTTC ACGTAGTGGG CCATCGCCCT GATAGACGGT TTTTCGCCCT TTGACGTTGG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

AGTCCACGTT CTTTAATAGT GGACTCTTGT TCCAAACTGG AACAACACTC AACCCTATCT CGGTCTATTC TTTTGATTTA TAAGGGATTT TGCCGATTTC 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GGCCTATTGG TTAAAAAATG AGCTGATTTA ACAAAAATTT AACGCGAATT TTAACAAAAT ATTAACGTTT ACAATTTCCC ATTCGCCATT CAGGCTGCGC 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

AACTGTTGGG AAGGGCGATC GGTGCGGGCC TCTTCGCTAT TACGCCAGCC CAAGCTACCA TGATAAGTAA GTAATATTAA GGTACGGGAG GTACTTGGAG 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

CGGCCGCAAT AAAATATCTT TATTTTCATT ACATCTGTGT GTTGGTTTTT TGTGTGAATC GATAGTACTA ACATACGCTC TCCATCAAAA CAAAACGAAA 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CAAAACAAAC TAGCAAAATA GGCTGTCCCC AGTGCAAGTG CAGGTGCCAG AACATTTCTC TATCGATA
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061

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: `1`	Last change: `2008-05-22 17:32:23`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

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):

192-1127

ORF

ORF position:

2

Version: `2`	Last change: `2008-05-22 17:32:23`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

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):

1765-3417

Remarks:

The cloned 5'-UTR is probably not the complete 5'-UTR of Apaf-1. From the note on page 899 in the article that
the UTR is 585 bases long one can gather that GI:3694812 possibly contains the sequence cloned by authors.
Below is shown the 5'-end of mRNAs annotated in GenBank at the moment.

110347464       gtgtggactgggcgggcccagcggtgtttgagtgctccgcggtcctgaggcagagaccag
3694812         ---------------------------------------cgg-cttgaggcagagaccag
110347470       gtgtggactgggcgggcccagcggtgtttgagtgctccgcggtcctgaggcagagaccag
                                                       *** * ***************

We suppose that similarly to the case of pRAF the very last two bases 'ca' of the wild-type 5'-UTR was not
cloned to retain position of the putative IRES 'in frame' with the initiator ATG codon ('CC' bases from
cloning NcoI CCATGG site got into the place instead). This would have been clear if a sequence of the primer
used for cloning would have been published.

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: `2`	Last change: `2008-05-22 17:32:23`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
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):

1180-1762

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 
^1180      ^1190      ^1200      ^1210      ^1220      ^1230      ^1240      ^1250      ^1260      ^1270      

GTGTGCCATC AGCCACCGGC GACGATCTGA GACAGTCGCA GCGGCTTTCC GAGCGGCGTC CGCTTCCCGC CCGGGCAGCT CCCGCCAGAG GGGTGAAGCG 
^1280      ^1290      ^1300      ^1310      ^1320      ^1330      ^1340      ^1350      ^1360      ^1370      

GCGACTGGAG TGGCCGTGCT TTTGTGCCCT GGGTCCCGGT ACCCTCCCCT GGTGCGGCCC GAGGCAAGCC CACCGAGGTG ACCACCCCTC GACGCCGCTT 
^1380      ^1390      ^1400      ^1410      ^1420      ^1430      ^1440      ^1450      ^1460      ^1470      

GGAGATCCCG GGCATCCACC CTGCGCCCCG AGCAGCTGAT ACCCAGGGAG GTGTCAGGAC CTGCCCGGGG CGCGGGGTCG CCGGAAGCCA GGCGGGAGCC 
^1480      ^1490      ^1500      ^1510      ^1520      ^1530      ^1540      ^1550      ^1560      ^1570      

CCGGCTGCTT TCTGGCAATC TAGTCTCATA AGTGACCCTC CCTGGGCTGC TTTCTTTCGA TTATCATCAG TGACCCTACC CCGGCTGCTC TTCCCAGCAC 
^1580      ^1590      ^1600      ^1610      ^1620      ^1630      ^1640      ^1650      ^1660      ^1670      

AACTCCGGTG CAAAGGCTTG GGCATCCTGG TGCTTTGCCT CTAGCCCATG CTCCACAGCG AGGAGAGAGA AAACCCTGAG GCA
^1680      ^1690      ^1700      ^1710      ^1720      ^1730      ^1740      ^1750      ^1760

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: 415

Version: `2`	Last change: `2008-07-09 09:00:29`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

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:

371.000

Name of IRES used as the positive control:

Apaf-1

Name of the plasmid used as the positive control. `pRHRVF`	Name of the plasmid used as the negative control. `pRF`
`IRESite Id` of the plasmid used as positive control. `467`	`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: `10.000`
The size (length) of intercistronic region in the positive control: `637`	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. 3b

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