IRESite_Id:260 characteristics of c-IAP1_-1178/-64 IRES studied in pRL-cIAP1-FL-polyA plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `260`	Version: `6`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-11-02 00:00:00`

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:
our_best_guess

The mRNA/+RNA description:

In vitro T7 capped bicistronic transcript with 35b long polyA tail containing RLuc and FLuc ORFs.

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

GGCTAGCCAC CATGACTTCG AAAGTTTATG ATCCAGAACA AAGGAAACGG ATGATAACTG GTCCGCAGTG GTGGGCCAGA TGTAAACAAA TGAATGTTCT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGATTCATTT ATTAATTATT ATGATTCAGA AAAACATGCA GAAAATGCTG TTATTTTTTT ACATGGTAAC GCGGCCTCTT CTTATTTATG GCGACATGTT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GTGCCACATA TTGAGCCAGT AGCGCGGTGT ATTATACCAG ACCTTATTGG TATGGGCAAA TCAGGCAAAT CTGGTAATGG TTCTTATAGG TTACTTGATC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATTACAAATA TCTTACTGCA TGGTTTGAAC TTCTTAATTT ACCAAAGAAG ATCATTTTTG TCGGCCATGA TTGGGGTGCT TGTTTGGCAT TTCATTATAG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTATGAGCAT CAAGATAAGA TCAAAGCAAT AGTTCACGCT GAAAGTGTAG TAGATGTGAT TGAATCATGG GATGAATGGC CTGATATTGA AGAAGATATT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GCGTTGATCA AATCTGAAGA AGGAGAAAAA ATGGTTTTGG AGAATAACTT CTTCGTGGAA ACCATGTTGC CATCAAAAAT CATGAGAAAG TTAGAACCAG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AAGAATTTGC AGCATATCTT GAACCATTCA AAGAGAAAGG TGAAGTTCGT CGTCCAACAT TATCATGGCC TCGTGAAATC CCGTTAGTAA AAGGTGGTAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACCTGACGTT GTACAAATTG TTAGGAATTA TAATGCTTAT CTACGTGCAA GTGATGATTT ACCAAAAATG TTTATTGAAT CGGACCCAGG ATTCTTTTCC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AATGCTATTG TTGAAGGTGC CAAGAAGTTT CCTAATACTG AATTTGTCAA AGTAAAAGGT CTTCATTTTT CGCAAGAAGA TGCACCTGAT GAAATGGGAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AATATATCAA ATCGTTCGTT GAGCGAGTTC TCAAAAATGA ACAATAATTC TAGAGCGGCC GCacattgaa gagttttcag aaagaaggct agtagagttg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

attactgata ctttatgcta agcagtactt ttttggtagt acaatatttt gttaggcgtt tctgataaca ctagaaagga caagttttat cttgtgataa 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

attgattaat gtttacaaca tgactgataa ttatagctga atagtcctta aatgatgaac aggttattta gtttttaaat gcagtgtaaa aagtgtgctg 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tggaaatttt atggctaact aagtttatgg agaaaatacc ttcagttgat caagaataat agtggtatac aaagttagga agaaagtcaa catgatgctg 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

caggaaatgg aaacaaatac aaatgatatt taacaaagat agagtttaca gtttttgaac tttaagccaa attcatttga catcaagcac tatagcaggc 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

acaggttcaa caaagcttgt gggtattgac ttcccccaaa agttgtcagc tgaagtaatt tagcccactt aagtaaatac tatgatgata agctgtgtga 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

acttagcttt taaatagtgt gaccatatga aggttttaat tacttttgtt tattggaata aaatgagatt ttttgggttg tcatgttaaa gtgcttatag 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ggaaagaagc ctgcatataa ttttttacct tgtggcataa tcagtaattg gtctgttatt caggcttcat agcttgtaac caaatataaa taaaaggcat 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

aatttaggta ttctatagtt gcttagaatt ttgttaatat aaatctctgt gaaaaatcaa ggagttttaa tattttcaga agtgcatcca cctttcaggg 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ctttaagtta gtattactca agattatgaa caaatagcac ttaggttacc tgaaagagtt actacaaccc caaagagttg tgttctaagt agtatcttgg 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

aaattcagag agatactcat cctacctgaa tataaactga gataaatcca gtaaagaaag tgtagtaaat tctacataag agtctatcat tgatttcttt 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

tggtggtaaa aatcttagtt catgtgaaga aatttcatgt gaatgtttta gctatcaaac agcactgtca cctactcCCG CGGCCCACAG GACGTCATGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAGACGCCAA AAACATAAAG AAAGGCCCGG CGCCATTCTA TCCTCTAGAG GATGGAACCG CTGGAGAGCA ACTGCATAAG GCTATGAAGA GATACGCCCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GGTTCCTGGA ACAATTGCTT TTACAGATGC ACATATCGAG GTGAACATCA CGTACGCGGA ATACTTCGAA ATGTCCGTTC GGTTGGCAGA AGCTATGAAA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CGATATGGGC TGAATACAAA TCACAGAATC GTCGTATGCA GTGAAAACTC TCTTCAATTC TTTATGCCGG TGTTGGGCGC GTTATTTATC GGAGTTGCAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTGCGCCCGC GAACGACATT TATAATGAAC GTGAATTGCT CAACAGTATG AACATTTCGC AGCCTACCGT AGTGTTTGTT TCCAAAAAGG GGTTGCAAAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AATTTTGAAC GTGCAAAAAA AATTACCAAT AATCCAGAAA ATTATTATCA TGGATTCTAA AACGGATTAC CAGGGATTTC AGTCGATGTA CACGTTCGTC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ACATCTCATC TACCTCCCGG TTTTAATGAA TACGATTTTG TACCAGAGTC CTTTGATCGT GACAAAACAA TTGCACTGAT AATGAATTCC TCTGGATCTA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CTGGGTTACC TAAGGGTGTG GCCCTTCCGC ATAGAACTGC CTGCGTCAGA TTCTCGCATG CCAGAGATCC TATTTTTGGC AATCAAATCA TTCCGGATAC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TGCGATTTTA AGTGTTGTTC CATTCCATCA CGGTTTTGGA ATGTTTACTA CACTCGGATA TTTGATATGT GGATTTCGAG TCGTCTTAAT GTATAGATTT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAAGAAGAGC TGTTTTTACG ATCCCTTCAG GATTACAAAA TTCAAAGTGC GTTGCTAGTA CCAACCCTAT TTTCATTCTT CGCCAAAAGC ACTCTGATTG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ACAAATACGA TTTATCTAAT TTACACGAAA TTGCTTCTGG GGGCGCACCT CTTTCGAAAG AAGTCGGGGA AGCGGTTGCA AAACGCTTCC ATCTTCCAGG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GATACGACAA GGATATGGGC TCACTGAGAC TACATCAGCT ATTCTGATTA CACCCGAGGG GGATGATAAA CCGGGCGCGG TCGGTAAAGT TGTTCCATTT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTTGAAGCGA AGGTTGTGGA TCTGGATACC GGGAAAACGC TGGGCGTTAA TCAGAGAGGC GAATTATGTG TCAGAGGACC TATGATTATG TCCGGTTATG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TAAACAATCC GGAAGCGACC AACGCCTTGA TTGACAAGGA TGGATGGCTA CATTCTGGAG ACATAGCTTA CTGGGACGAA GACGAACACT TCTTCATAGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGACCGCTTG AAGTCTTTAA TTAAATACAA AGGATATCAG GTGGCCCCCG CTGAATTGGA ATCGATATTG TTACAACACC CCAACATCTT CGACGCGGGC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GTGGCAGGTC TTCCCGACGA TGACGCCGGT GAACTTCCCG CCGCCGTTGT TGTTTTGGAG CACGGAAAGA CGATGACGGA AAAAGAGATC GTGGATTACG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TGGCCAGTCA AGTAACAACC GCGAAAAAGT TGCGCGGAGG AGTTGTGTTT GTGGACGAAG TACCGAAAGG TCTTACCGGA AAACTCGACG CAAGAAAAAT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CAGAGAGATC CTCATAAAGG CCAAGAAGGG CGGAAAGTCC AAATTGTAAG GATCCGGGCC CAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAA
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791

Credibility of mRNA sequence:

reverse_engineered_fragment_and_the_rest_is_a_guess

The name of the plasmid:
pRL-cIAP1-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:
c-IAP1

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 GCCACCATGA CTTCGAAAGT TTATGATCCA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAACAAAGGA AACGGATGAT AACTGGTCCG CAGTGGTGGG CCAGATGTAA ACAAATGAAT GTTCTTGATT CATTTATTAA TTATTATGAT TCAGAAAAAC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ATGCAGAAAA TGCTGTTATT TTTTTACATG GTAACGCGGC CTCTTCTTAT TTATGGCGAC ATGTTGTGCC ACATATTGAG CCAGTAGCGC GGTGTATTAT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ACCAGACCTT ATTGGTATGG GCAAATCAGG CAAATCTGGT AATGGTTCTT ATAGGTTACT TGATCATTAC AAATATCTTA CTGCATGGTT TGAACTTCTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AATTTACCAA AGAAGATCAT TTTTGTCGGC CATGATTGGG GTGCTTGTTT GGCATTTCAT TATAGCTATG AGCATCAAGA TAAGATCAAA GCAATAGTTC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACGCTGAAAG TGTAGTAGAT GTGATTGAAT CATGGGATGA ATGGCCTGAT ATTGAAGAAG ATATTGCGTT GATCAAATCT GAAGAAGGAG AAAAAATGGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTTGGAGAAT AACTTCTTCG TGGAAACCAT GTTGCCATCA AAAATCATGA GAAAGTTAGA ACCAGAAGAA TTTGCAGCAT ATCTTGAACC ATTCAAAGAG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAAGGTGAAG TTCGTCGTCC AACATTATCA TGGCCTCGTG AAATCCCGTT AGTAAAAGGT GGTAAACCTG ACGTTGTACA AATTGTTAGG AATTATAATG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTTATCTACG TGCAAGTGAT GATTTACCAA AAATGTTTAT TGAATCGGAC CCAGGATTCT TTTCCAATGC TATTGTTGAA GGTGCCAAGA AGTTTCCTAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TACTGAATTT GTCAAAGTAA AAGGTCTTCA TTTTTCGCAA GAAGATGCAC CTGATGAAAT GGGAAAATAT ATCAAATCGT TCGTTGAGCG AGTTCTCAAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AATGAACAAT AATTCTAGAG CGGCCGCaca ttgaagagtt ttcagaaaga aggctagtag agttgattac tgatacttta tgctaagcag tacttttttg 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gtagtacaat attttgttag gcgtttctga taacactaga aaggacaagt tttatcttgt gataaattga ttaatgttta caacatgact gataattata 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

gctgaatagt ccttaaatga tgaacaggtt atttagtttt taaatgcagt gtaaaaagtg tgctgtggaa attttatggc taactaagtt tatggagaaa 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ataccttcag ttgatcaaga ataatagtgg tatacaaagt taggaagaaa gtcaacatga tgctgcagga aatggaaaca aatacaaatg atatttaaca 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

aagatagagt ttacagtttt tgaactttaa gccaaattca tttgacatca agcactatag caggcacagg ttcaacaaag cttgtgggta ttgacttccc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ccaaaagttg tcagctgaag taatttagcc cacttaagta aatactatga tgataagctg tgtgaactta gcttttaaat agtgtgacca tatgaaggtt 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ttaattactt ttgtttattg gaataaaatg agattttttg ggttgtcatg ttaaagtgct tatagggaaa gaagcctgca tataattttt taccttgtgg 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

cataatcagt aattggtctg ttattcaggc ttcatagctt gtaaccaaat ataaataaaa ggcataattt aggtattcta tagttgctta gaattttgtt 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

aatataaatc tctgtgaaaa atcaaggagt tttaatattt tcagaagtgc atccaccttt cagggcttta agttagtatt actcaagatt atgaacaaat 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

agcacttagg ttacctgaaa gagttactac aaccccaaag agttgtgttc taagtagtat cttggaaatt cagagagata ctcatcctac ctgaatataa 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

actgagataa atccagtaaa gaaagtgtag taaattctac ataagagtct atcattgatt tcttttggtg gtaaaaatct tagttcatgt gaagaaattt 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

catgtgaatg ttttagctat caaacagcac tgtcacctac tcCCGCGGCC CACAGGACGT CATGGAAGAC GCCAAAAACA TAAAGAAAGG CCCGGCGCCA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTCTATCCTC TAGAGGATGG AACCGCTGGA GAGCAACTGC ATAAGGCTAT GAAGAGATAC GCCCTGGTTC CTGGAACAAT TGCTTTTACA GATGCACATA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TCGAGGTGAA CATCACGTAC GCGGAATACT TCGAAATGTC CGTTCGGTTG GCAGAAGCTA TGAAACGATA TGGGCTGAAT ACAAATCACA GAATCGTCGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ATGCAGTGAA AACTCTCTTC AATTCTTTAT GCCGGTGTTG GGCGCGTTAT TTATCGGAGT TGCAGTTGCG CCCGCGAACG ACATTTATAA TGAACGTGAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TTGCTCAACA GTATGAACAT TTCGCAGCCT ACCGTAGTGT TTGTTTCCAA AAAGGGGTTG CAAAAAATTT TGAACGTGCA AAAAAAATTA CCAATAATCC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AGAAAATTAT TATCATGGAT TCTAAAACGG ATTACCAGGG ATTTCAGTCG ATGTACACGT TCGTCACATC TCATCTACCT CCCGGTTTTA ATGAATACGA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TTTTGTACCA GAGTCCTTTG ATCGTGACAA AACAATTGCA CTGATAATGA ATTCCTCTGG ATCTACTGGG TTACCTAAGG GTGTGGCCCT TCCGCATAGA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ACTGCCTGCG TCAGATTCTC GCATGCCAGA GATCCTATTT TTGGCAATCA AATCATTCCG GATACTGCGA TTTTAAGTGT TGTTCCATTC CATCACGGTT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TTGGAATGTT TACTACACTC GGATATTTGA TATGTGGATT TCGAGTCGTC TTAATGTATA GATTTGAAGA AGAGCTGTTT TTACGATCCC TTCAGGATTA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CAAAATTCAA AGTGCGTTGC TAGTACCAAC CCTATTTTCA TTCTTCGCCA AAAGCACTCT GATTGACAAA TACGATTTAT CTAATTTACA CGAAATTGCT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TCTGGGGGCG CACCTCTTTC GAAAGAAGTC GGGGAAGCGG TTGCAAAACG CTTCCATCTT CCAGGGATAC GACAAGGATA TGGGCTCACT GAGACTACAT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CAGCTATTCT GATTACACCC GAGGGGGATG ATAAACCGGG CGCGGTCGGT AAAGTTGTTC CATTTTTTGA AGCGAAGGTT GTGGATCTGG ATACCGGGAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AACGCTGGGC GTTAATCAGA GAGGCGAATT ATGTGTCAGA GGACCTATGA TTATGTCCGG TTATGTAAAC AATCCGGAAG CGACCAACGC CTTGATTGAC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AAGGATGGAT GGCTACATTC TGGAGACATA GCTTACTGGG ACGAAGACGA ACACTTCTTC ATAGTTGACC GCTTGAAGTC TTTAATTAAA TACAAAGGAT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ATCAGGTGGC CCCCGCTGAA TTGGAATCGA TATTGTTACA ACACCCCAAC ATCTTCGACG CGGGCGTGGC AGGTCTTCCC GACGATGACG CCGGTGAACT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TCCCGCCGCC GTTGTTGTTT TGGAGCACGG AAAGACGATG ACGGAAAAAG AGATCGTGGA TTACGTGGCC AGTCAAGTAA CAACCGCGAA AAAGTTGCGC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GGAGGAGTTG TGTTTGTGGA CGAAGTACCG AAAGGTCTTA CCGGAAAACT CGACGCAAGA AAAATCAGAG AGATCCTCAT AAAGGCCAAG AAGGGCGGAA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AGTCCAAATT GTAAGGATCC GGGCCCAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA ACCGGTGGGC CCTATTCTAT AGTGTCACCT AAATGCTAGA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GCTCGCTGAT CAGCCTCGAC TGTGCCTTCT AGTTGCCAGC CATCTGTTGT TTGCCCCTCC CCCGTGCCTT CCTTGACCCT GGAAGGTGCC ACTCCCACTG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TCCTTTCCTA ATAAAATGAG GAAATTGCAT CGCATTGTCT GAGTAGGTGT CATTCTATTC TGGGGGGTGG GGTGGGGCAG GACAGCAAGG GGGAGGATTG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GGAAGACAAT AGCAGGCATG CTGGGGATGC GGTGGGCTCT ATGGCTTCTG AGGCGGAAAG AACCAGCTGG GGCTCGAGGG GGGATCCCCA CGCGCCCTGT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

AGCGGCGCAT TAAGCGCGGC GGGTGTGGTG GTTACGCGCA GCGTGACCGC TACACTTGCC AGCGCCCTAG CGCCCGCTCC TTTCGCTTTC TTCCCTTCCT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TTCTCGCCAC GTTCGCCGGC TTTCCCCGTC AAGCTCTAAA TCGGGGCATC CCTTTAGGGT TCCGATTTAG TGCTTTACGG CACCTCGACC CCAAAAAACT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TGATTAGGGT GATGGTTCAC GTAGTGGGCC ATCGCCCTGA TAGACGGTTT TTCGCCCTTT GACGTTGGAG TCCACGTTCT TTAATAGTGG ACTCTTGTTC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

CAAACTGGAA CAACACTCAA CCCTATCTCG GTCTATTCTT TTGATTTATA AGGGATTTTG GGGATTTCGG CCTATTGGTT AAAAAATGAG CTGATTTAAC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

AAAAATTTAA CGCGAATTTT AACAAAATAT TAACGTTTAC AATTTAAATA TTTGCTTATA CAATCTTCCT GTTTTTGGGG CTTTTCTGAT TATCAACCGG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

GGTGGGTACC GAGCTCGAAT TCTGTGGAAT GTGTGTCAGT TAGGGTGTGG AAAGTCCCCA GGCTCCCCAG GCAGGCAGAA GTATGCAAAG CATGCATCTC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

AATTAGTCAG CAACCAGGTG TGGAAAGTCC CCAGGCTCCC CAGCAGGCAG AAGTATGCAA AGCATGCATC TCAATTAGTC AGCAACCATA GTCCCGCCCC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TAACTCCGCC CATCCCGCCC CTAACTCCGC CCAGTTCCGC CCATTCTCCG CCCCATGGCT GACTAATTTT TTTTATTTAT GCAGAGGCCG AGGCCGCCTC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GGCCTCTGAG CTATTCCAGA AGTAGTGAGG AGGCTTTTTT GGAGGCCTAG GCTTTTGCAA AAAGCTCCCG GGAGCTTGGA TATCCATTTT CGGATCTGAT 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CAAGAGACAG GATGAGGATC GTTTCGCATG ATTGAACAAG ATGGATTGCA CGCAGGTTCT CCGGCCGCTT GGGTGGAGAG GCTATTCGGC TATGACTGGG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

CACAACAGAC AATCGGCTGC TCTGATGCCG CCGTGTTCCG GCTGTCAGCG CAGGGGCGCC CGGTTCTTTT TGTCAAGACC GACCTGTCCG GTGCCCTGAA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TGAACTGCAG GACGAGGCAG CGCGGCTATC GTGGCTGGCC ACGACGGGCG TTCCTTGCGC AGCTGTGCTC GACGTTGTCA CTGAAGCGGG AAGGGACTGG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

CTGCTATTGG GCGAAGTGCC GGGGCAGGAT CTCCTGTCAT CTCACCTTGC TCCTGCCGAG AAAGTATCCA TCATGGCTGA TGCAATGCGG CGGCTGCATA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CGCTTGATCC GGCTACCTGC CCATTCGACC ACCAAGCGAA ACATCGCATC GAGCGAGCAC GTACTCGGAT GGAAGCCGGT CTTGTCGATC AGGATGATCT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GGACGAAGAG CATCAGGGGC TCGCGCCAGC CGAACTGTTC GCCAGGCTCA AGGCGCGCAT GCCCGACGGC GAGGATCTCG TCGTGACCCA TGGCGATGCC 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

TGCTTGCCGA ATATCATGGT GGAAAATGGC CGCTTTTCTG GATTCATCGA CTGTGGCCGG CTGGGTGTGG CGGACCGCTA TCAGGACATA GCGTTGGCTA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

CCCGTGATAT TGCTGAAGAG CTTGGCGGCG AATGGGCTGA CCGCTTCCTC GTGCTTTACG GTATCGCCGC TCCCGATTCG CAGCGCATCG CCTTCTATCG 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

CCTTCTTGAC GAGTTCTTCT GAGCGGGACT CTGGGGTTCG AAATGACCGA CCAAGCGACG CCCAACCTGC CATCACGAGA TTTCGATTCC ACCGCCGCCT 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

TCTATGAAAG GTTGGGCTTC GGAATCGTTT TCCGGGACGC CGGCTGGATG ATCCTCCAGC GCGGGGATCT CATGCTGGAG TTCTTCGCCC ACCCCAACTT 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

GTTTATTGCA GCTTATAATG GTTACAAATA AAGCAATAGC ATCACAAATT TCACAAATAA AGCATTTTTT TCACTGCATT CTAGTTGTGG TTTGTCCAAA 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

CTCATCAATG TATCTTATCA TGTCTGGATC CCGTCGACCT CGAGAGCTTG GCGTAATCAT GGTCATAGCT GTTTCCTGTG TGAAATTGTT ATCCGCTCAC 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

AATTCCACAC AACATACGAG CCGGAAGCAT AAAGTGTAAA GCCTGGGGTG CCTAATGAGT GAGCTAACTC ACATTAATTG CGTTGCGCTC ACTGCCCGCT 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

TTCCAGTCGG GAAACCTGTC GTGCCAGCTG CATTAATGAA TCGGCCAACG CGCGGGGAGA GGCGGTTTGC GTATTGGGCG CTCTTCCGCT TCCTCGCTCA 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

CTGACTCGCT GCGCTCGGTC GTTCGGCTGC GGCGAGCGGT ATCAGCTCAC TCAAAGGCGG TAATACGGTT ATCCACAGAA TCAGGGGATA ACGCAGGAAA 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

GAACATGTGA GCAAAAGGCC AGCAAAAGGC CAGGAACCGT AAAAAGGCCG CGTTGCTGGC GTTTTTCCAT AGGCTCCGCC CCCCTGACGA GCATCACAAA 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

AATCGACGCT CAAGTCAGAG GTGGCGAAAC CCGACAGGAC TATAAAGATA CCAGGCGTTT CCCCCTGGAA GCTCCCTCGT GCGCTCTCCT GTTCCGACCC 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TGCCGCTTAC CGGATACCTG TCCGCCTTTC TCCCTTCGGG AAGCGTGGCG CTTTCTCAAT GCTCACGCTG TAGGTATCTC AGTTCGGTGT AGGTCGTTCG 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

CTCCAAGCTG GGCTGTGTGC ACGAACCCCC CGTTCAGCCC GACCGCTGCG CCTTATCCGG TAACTATCGT CTTGAGTCCA ACCCGGTAAG ACACGACTTA 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

TCGCCACTGG CAGCAGCCAC TGGTAACAGG ATTAGCAGAG CGAGGTATGT AGGCGGTGCT ACAGAGTTCT TGAAGTGGTG GCCTAACTAC GGCTACACTA 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

GAAGGACAGT ATTTGGTATC TGCGCTCTGC TGAAGCCAGT TACCTTCGGA AAAAGAGTTG GTAGCTCTTG ATCCGGCAAA CAAACCACCG CTGGTAGCGG 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

TGGTTTTTTT GTTTGCAAGC AGCAGATTAC GCGCAGAAAA AAAGGATCTC AAGAAGATCC TTTGATCTTT TCTACGGGGT CTGACGCTCA GTGGAACGAA 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

AACTCACGTT AAGGGATTTT GGTCATGAGA TTATCAAAAA GGATCTTCAC CTAGATCCTT TTAAATTAAA AATGAAGTTT TAAATCAATC TAAAGTATAT 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

ATGAGTAAAC TTGGTCTGAC AGTTACCAAT GCTTAATCAG TGAGGCACCT ATCTCAGCGA TCTGTCTATT TCGTTCATCC ATAGTTGCCT GACTCCCCGT 
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491      

CGTGTAGATA ACTACGATAC GGGAGGGCTT ACCATCTGGC CCCAGTGCTG CAATGATACC GCGAGACCCA CGCTCACCGG CTCCAGATTT ATCAGCAATA 
^8501      ^8511      ^8521      ^8531      ^8541      ^8551      ^8561      ^8571      ^8581      ^8591      

AACCAGCCAG CCGGAAGGGC CGAGCGCAGA AGTGGTCCTG CAACTTTATC CGCCTCCATC CAGTCTATTA ATTGTTGCCG GGAAGCTAGA GTAAGTAGTT 
^8601      ^8611      ^8621      ^8631      ^8641      ^8651      ^8661      ^8671      ^8681      ^8691      

CGCCAGTTAA TAGTTTGCGC AACGTTGTTG CCATTGCTAC AGGCATCGTG GTGTCACGCT CGTCGTTTGG TATGGCTTCA TTCAGCTCCG GTTCCCAACG 
^8701      ^8711      ^8721      ^8731      ^8741      ^8751      ^8761      ^8771      ^8781      ^8791      

ATCAAGGCGA GTTACATGAT CCCCCATGTT GTGCAAAAAA GCGGTTAGCT CCTTCGGTCC TCCGATCGTT GTCAGAAGTA AGTTGGCCGC AGTGTTATCA 
^8801      ^8811      ^8821      ^8831      ^8841      ^8851      ^8861      ^8871      ^8881      ^8891      

CTCATGGTTA TGGCAGCACT GCATAATTCT CTTACTGTCA TGCCATCCGT AAGATGCTTT TCTGTGACTG GTGAGTACTC AACCAAGTCA TTCTGAGAAT 
^8901      ^8911      ^8921      ^8931      ^8941      ^8951      ^8961      ^8971      ^8981      ^8991      

AGTGTATGCG GCGACCGAGT TGCTCTTGCC CGGCGTCAAT ACGGGATAAT ACCGCGCCAC ATAGCAGAAC TTTAAAAGTG CTCATCATTG GAAAACGTTC 
^9001      ^9011      ^9021      ^9031      ^9041      ^9051      ^9061      ^9071      ^9081      ^9091      

TTCGGGGCGA AAACTCTCAA GGATCTTACC GCTGTTGAGA TCCAGTTCGA TGTAACCCAC TCGTGCACCC AACTGATCTT CAGCATCTTT TACTTTCACC 
^9101      ^9111      ^9121      ^9131      ^9141      ^9151      ^9161      ^9171      ^9181      ^9191      

AGCGTTTCTG GGTGAGCAAA AACAGGAAGG CAAAATGCCG CAAAAAAGGG AATAAGGGCG ACACGGAAAT GTTGAATACT CATACTCTTC CTTTTTCAAT 
^9201      ^9211      ^9221      ^9231      ^9241      ^9251      ^9261      ^9271      ^9281      ^9291      

ATTATTGAAG CATTTATCAG GGTTATTGTC TCATGAGCGG ATACATATTT GAATGTATTT AGAAAAATAA ACAAATAGGG GTTCCGCGCA CATTTCCCCG 
^9301      ^9311      ^9321      ^9331      ^9341      ^9351      ^9361      ^9371      ^9381      ^9391      

AAAAGTGCCA CCTGACGTCG ACGGATCGGG A
^9401      ^9411      ^9421      ^9431

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

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

2

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
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):

12-947

ORF

ORF position:

2

Version: `0`
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):

2097-3749

Remarks:

The cloned 5'-UTR by van Eden et al. (2004) region was not a complete 5'-UTR. There are 3 mutations in
the cloned sequence provided by R. Lloyd in comparison to both German and NIH cDNA projects: GI:34367137 and
GI:22382083. -297nt from initiator ATG is A instead of G, -177nt is A instead of T, -76nt is G instead of T.
As already mentioned the sequence provided to IRESite by R. Lloyd spans -1115 to +4 (while the +4 base not
shown in van Eden et al. (2004) Fig. 1A is 'G'. van Eden showed already published 5'-UTR of NM_001166.2
(GI:10880127) GenBank record which is 1159b long whereas current GI:41349435 (NM_001166.3) contains 1.4kb
untranslated region.

The intercistronic region contains incomplete 5'-UTR of c-IAP1 (-1115 to -1) followed by some 19 b as a
remnant of HCV ORF after mutation.

Integrity of T7 in vitro transcript was verified by glyoxal/DMSO-agarose gel electrophoresis after previous
column purification and DNAse treatment followed by phenol:chloroform (1:1) extraction. Integrity of RNA 8 hrs
after direct RNA transfection was confirmed by RT-PCR in human HEK 293T/17 cells (Fig. 5D).

Citations:

Van Eden M. E., Byrd M. P., Sherrill K. W., Lloyd R. E. (2004) Translation of cellular inhibitor of apoptosis protein 1 (c-IAP1) mRNA is IRES mediated and regulated during cell stress. RNA. 10(3):469-481

IRESs:

IRES:

Version: `1`	Last change: `2008-10-23 16:25:42`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `c-IAP1_-1178/-64`	The functional status of IRES: `functional`

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

963-2077

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `16`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `1130`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-1134`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-20`

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

acattgaaga gttttcagaa agaaggctag tagagttgat tactgatact ttatgctaag cagtactttt ttggtagtac aatattttgt taggcgtttc 
^963       ^973       ^983       ^993       ^1003      ^1013      ^1023      ^1033      ^1043      ^1053      

tgataacact agaaaggaca agttttatct tgtgataaat tgattaatgt ttacaacatg actgataatt atagctgaat agtccttaaa tgatgaacag 
^1063      ^1073      ^1083      ^1093      ^1103      ^1113      ^1123      ^1133      ^1143      ^1153      

gttatttagt ttttaaatgc agtgtaaaaa gtgtgctgtg gaaattttat ggctaactaa gtttatggag aaaatacctt cagttgatca agaataatag 
^1163      ^1173      ^1183      ^1193      ^1203      ^1213      ^1223      ^1233      ^1243      ^1253      

tggtatacaa agttaggaag aaagtcaaca tgatgctgca ggaaatggaa acaaatacaa atgatattta acaaagatag agtttacagt ttttgaactt 
^1263      ^1273      ^1283      ^1293      ^1303      ^1313      ^1323      ^1333      ^1343      ^1353      

taagccaaat tcatttgaca tcaagcacta tagcaggcac aggttcaaca aagcttgtgg gtattgactt cccccaaaag ttgtcagctg aagtaattta 
^1363      ^1373      ^1383      ^1393      ^1403      ^1413      ^1423      ^1433      ^1443      ^1453      

gcccacttaa gtaaatacta tgatgataag ctgtgtgaac ttagctttta aatagtgtga ccatatgaag gttttaatta cttttgttta ttggaataaa 
^1463      ^1473      ^1483      ^1493      ^1503      ^1513      ^1523      ^1533      ^1543      ^1553      

atgagatttt ttgggttgtc atgttaaagt gcttataggg aaagaagcct gcatataatt ttttaccttg tggcataatc agtaattggt ctgttattca 
^1563      ^1573      ^1583      ^1593      ^1603      ^1613      ^1623      ^1633      ^1643      ^1653      

ggcttcatag cttgtaacca aatataaata aaaggcataa tttaggtatt ctatagttgc ttagaatttt gttaatataa atctctgtga aaaatcaagg 
^1663      ^1673      ^1683      ^1693      ^1703      ^1713      ^1723      ^1733      ^1743      ^1753      

agttttaata ttttcagaag tgcatccacc tttcagggct ttaagttagt attactcaag attatgaaca aatagcactt aggttacctg aaagagttac 
^1763      ^1773      ^1783      ^1793      ^1803      ^1813      ^1823      ^1833      ^1843      ^1853      

tacaacccca aagagttgtg ttctaagtag tatcttggaa attcagagag atactcatcc tacctgaata taaactgaga taaatccagt aaagaaagtg 
^1863      ^1873      ^1883      ^1893      ^1903      ^1913      ^1923      ^1933      ^1943      ^1953      

tagtaaattc tacataagag tctatcattg atttcttttg gtggtaaaaa tcttagttca tgtgaagaaa tttcatgtga atgttttagc tatcaaacag 
^1963      ^1973      ^1983      ^1993      ^2003      ^2013      ^2023      ^2033      ^2043      ^2053      

cactgtcacc tactc
^2063      ^2073

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 328

Version: `1`	Last change: `2007-02-15 00:00:00`
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 HepG2 (ATCC HB-8065)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

60.900

Name of IRES used as the positive control:

HCV_type_1b

Name of the plasmid used as the positive control. `pRL-HCV-FL-polyA`	Name of the plasmid used as the negative control. `pRL-FL-polyA`
`IRESite Id` of the plasmid used as positive control. `112`	`IRESite Id` of the plasmid used as negative control. `133`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `16.100`
The size (length) of intercistronic region in the positive control: `419`	The size (length) of intercistronic region in the negative control: `28`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_GpppG_cap_with_polyA_tail

Remarks:

The more appropriate negative control pRL-null-FL-polyA said to contain 590nt spacer derived from human PKR.
We conclude part of the protein coding region was cloned, unfortunately it is not clear which exactly. For
example, GenBank GI:4506102 has 1654b long ORF. This negative control had activity of 25% of the positive
control.

The best negative control was pRL-revHCV-FL-polyA (IRESite ID:130) with 0% activity of the positive control.

See Fig. 5C.

Citations:

Translation results:

IRESite Translation Id: 329

Version: `1`	Last change: `2007-02-15 00:00:00`
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 HEK 293T/17 (ATCC CRL-11268)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

88.100

Name of IRES used as the positive control:

HCV_type_1b

Name of the plasmid used as the positive control. `pRL-HCV-FL-polyA`	Name of the plasmid used as the negative control. `pRL-FL-polyA`
`IRESite Id` of the plasmid used as positive control. `112`	`IRESite Id` of the plasmid used as negative control. `133`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `22.500`
The size (length) of intercistronic region in the positive control: `419`	The size (length) of intercistronic region in the negative control: `28`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_GpppG_cap_with_polyA_tail

Remarks:

The more appropriate negative control pRL-null-FL-polyA said to contain 590nt spacer derived from human PKR.
We conclude part of the protein coding region was cloned, unfortunately it is not clear which exactly. For
example, GenBank GI:4506102 has 1654b long ORF. This negative control had activity of 54.4% of the positive
control.

The best negative control was pRL-revHCV-FL-polyA (IRESite ID:130) with 0% activity of the positive control.

See Fig. 5C.

Citations:

Translation results:

IRESite Translation Id: 330

Version: `3`	Last change: `2007-10-23 00:00:00`
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 S3 (ATCC CCL-2.2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

65.200

Name of IRES used as the positive control:

HCV_type_1b

Name of the plasmid used as the positive control. `pRL-HCV-FL-polyA`	Name of the plasmid used as the negative control. `pRL-FL-polyA`
`IRESite Id` of the plasmid used as positive control. `112`	`IRESite Id` of the plasmid used as negative control. `133`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `17.400`
The size (length) of intercistronic region in the positive control: `419`	The size (length) of intercistronic region in the negative control: `28`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_GpppG_cap_with_polyA_tail

Remarks:

The more appropriate negative control pRL-null-FL-polyA is said to contain 590nt spacer derived from human
PKR. We conclude part of the protein coding region was cloned, unfortunately it is not clear which exactly.
For example, GenBank GI:4506102 has 1654b long ORF. This negative control had activity of 0% of the positive
control.

The best negative control was pRL-revHCV-FL-polyA (IRESite ID:130) with 0% activity of the positive control.

See Fig. 5C.

Citations:

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