IRESite_Id:217 characteristics of LEF1 IRES studied in pRSTF-LEF1

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `217`	Version: `4`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2007-09-09 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:
hopefully_full-length_mRNA

The mRNA/+RNA description:

In vitro bicistronic T7 transcript containing renilla and firefly luciferases separated by LEF1 IRES

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 acaaatGtcg aTCGACgggg gcccctaggA gatccAAGCT TATCGATTTC GAACCCGGGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TACCGAATTC CTCGAGTCTA GAGGAgcatg cTCCTCTAGA CTCGAGGAAT TCGGTACCCC GGGTTCGAAA TCGATAAGCT TgGATCTAGC GCGCGGGAGG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AGGAGAAGCA GTGGGGAGGC GCAGCCGCTC AcCTGCGGGG CAGGGCGCGG AGGAGGGACC CGGNTGcGcG CTCTCGGGCC GAGGAACCAG GACGcGCCCG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GAGCCTCGCA CGCGGCCAAG CTCGGGCGTC CCCTCCCCTC GGCCGGGCGA ACTCAAGGGG CGCAGCTCTT TGCTTTGACA GAGCTGGCCG GCGGAGGCGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GCAGAGCGGC GAGCCGGCGA GCCAGGCTGA GAAACTCGAC CCGGGAACAA AGAGGGGTCG GACTGAGTGT GTGTGTCGGC TCGAGCTCCG GGNAGAGGCA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TTTGCCCGAG GNCCCCGCTG TGACTCCCCG AGACTCCGCA GTGCCCTCCA CTGNGGAGTC CCCGCGCTTG CCGGNAAAAA CTTTATTCTT GGCAAACTTC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCTTTCTCTT CCCCTCCTCC TCGGCCCCCA TCTTCTGCTC CTCCTCCTTC TCTAGCAGAT TAAATGAGCC TCGAGAAGAA AAACCGAAGC GAAAGGGAAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AAAATAAGAA GATCTAAAAC GGACATCTCC AGCGTGGGTG GCTCCTTTTT CTTTTTCTTT TTTTCCCACC CTTCAGGAAG TGGACGTTTC GTTATCTTCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GATCCTTGCA CCTTCTTTTG GGGCAAACGG GGCCCTTCTG CCCAGATCCC CTCTCTTTTC TCGGAAAACA AACTACTAAG TCGGCATCCG GGGTAACTAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGTGGAGAGG GTTTCCGCGG AGACGCGCCG CCGGACCCTC CTCTGCACTT TGGGGAGGCG TGCTCCCTCC AGAACCGGCG TTCTCCGCGC GCAAATCCCG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCGACGCGGG GTCGCGGGGT GGCCGCCGGG GCAGCCTCGT CTAGCGCGCG CCGCGCAGAC GCCCCCGGAG TCGCCAGCTA CCGCAGCCCT CGCCGCCCAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGCCCTTCGG CCTCGGGGCG GGCGCCTGCG TCGGTCTCCG CGAAGCGGGA AAGCGCGGCG GCCGCCGGGA TTCGGGCGCC GCGGCAGCTG CTCCGGCTGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGGCCGGCGG CCCCGCGCTC GCCCGCCCCG CTTCCGCCCG CTGTCCTGCT GCACGAACCC TTCCAACTCT CCTTTCCTCC CCCACCCTTG AGTTACCCCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTGTCTTTCC TGCTGTTGCG CGGGTGCTCC CACAGCGGAG CGGAGATTAC AGAGCCGCCG GGATGCCCGC TGGATCCATG Gaagacgcca aaaacataaa 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gaaaggcccg gcgccattct atccgctgga agatggaacc gctggagagc aactgcataa ggctatgaag agatacgccc tggttcctgg aacaattgct 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

tttacagatg cacatatcga ggtggacatc acttacgctg agtacttcga aatgtccgtt cggttggcag aagctatgaa acgatatggg ctgaatacaa 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

atcacagaat cgtcgtatgc agtgaaaact ctcttcaatt ctttatgccg gtgttgggcg cgttatttat cggagttgca gttgcgcccg cgaacgacat 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ttataatgaa cgtgaattgc tcaacagtat gggcatttcg cagcctaccg tggtgttcgt ttccaaaaag gggttgcaaa aaattttgaa cgtgcaaaaa 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

aagctcccaa tcatccaaaa aattattatc atggattcta aaacggatta ccagggattt cagtcgatgt acacgttcgt cacatctcat ctacctcccg 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

gttttaatga atacgatttt gtgccagagt ccttcgatag ggacaagaca attgcactga tcatgaactc ctctggatct actggtctgc ctaaaggtgt 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

cgctctgcct catagaactg cctgcgtgag attctcgcat gccagagatc ctatttttgg caatcaaatc attccggata ctgcgatttt aagtgttgtt 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ccattccatc acggttttgg aatgtttact acactcggat atttgatatg tggatttcga gtcgtcttaa tgtatagatt tgaagaagag ctgtttctga 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ggagccttca ggattacaag attcaaagtg cgctgctggt gccaacccta ttctccttct tcgccaaaag cactctgatt gacaaatacg atttatctaa 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

tttacacgaa attgcttctg gtggcgctcc cctctctaag gaagtcgggg aagcggttgc caagaggttc catctgccag gtatcaggca aggatatggg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ctcactgaga ctacatcagc tattctgatt acacccgagg gggatgataa accgggcgcg gtcggtaaag ttgttccatt ttttgaagcg aaggttgtgg 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

atctggatac cgggaaaacg ctgggcgtta atcaaagagg cgaactgtgt gtgagaggtc ctatgattat gtccggttat gtaaacaatc cggaagcgac 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

caacgccttg attgacaagg atggatggct acattctgga gacatagctt actgggacga agacgaacac ttcttcatcg ttgaccgcct gaagtctctg 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

attaagtaca aaggctatca ggtggctccc gctgaattgg aatccatctt gctccaacac cccaacatct tcgacgcagg tgtcgcaggt cttcccgacg 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

atgacgccgg tgaacttccc gccgccgttg ttgttttgga gcacggaaag acgatgacgg aaaaagagat cgtggattac gtcgccagtc aagtaacaac 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

cgcgaaaaag ttgcgcggag gagttgtgtt tgtggacgaa gtaccgaaag gtcttaccgg aaaactcgac gcaagaaaaa tcagagagat cctcataaag 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

gccaagaagg gcggaaagat cgccgtgtaa tT
^3901      ^3911      ^3921      ^3931

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pRSTF-LEF1_1.2 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:
LEF1

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens

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

agatcgatct gcgcagcacc atggcctgaa ataacctctg aaagaggaac ttggttaggt accttctgag gcggaaagaa ccagctgtgg aatgtgtgtc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

agttagggtg tggaaagtcc ccaggctccc cagcaggcag aagtatgcaa agcatgcatc tcaattagtc agcaaccagg tgtggaaagt ccccaggctc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

cccagcaggc agaagtatgc aaagcatgca tctcaattag tcagcaacca tagtcccgcc cctaactccg cccatcccgc ccctaactcc gcccagttcc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gcccattctc cgccccatgg ctgactaatt ttttttattt atgcagaggc cgaggccgcc tcggcctctg agctattcca gaagtagtga ggaggctttt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ttggaggcct aggcttttgc aaaaagcttg attcttctga cacaacagtc tcgaacttaa gctgcagaag ttggtcgtga ggcactgggc aggtaagtat 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

caaggttaca agacaggttt aaggagacca atagaaactg ggcttgtcga gacagagaag actcttgcgt ttctgatagg cacctattgg tcttactgac 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

atccactttg cctttctctc cacaggtgtc cactcccagt tcaattacag ctcttaaggc tagagtacTT AATACGACTC ACTATAGGct agccaccatG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

acttcgaaag tttatgatcc agaacaaagg aaacggatga taactggtcc gcagtggtgg gccagatgta aacaaatgaa tgttcttgat tcatttatta 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

attattatga ttcagaaaaa catgcagaaa atgctgttat ttttttacat ggtaacgcgg cctcttctta tttatggcga catgttgtgc cacatattga 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

gccagtagcg cggtgtatta taccagacct tattggtatg ggcaaatcag gcaaatctgg taatggttct tataggttac ttgatcatta caaatatctt 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

actgcatggt ttgaacttct taatttacca aagaagatca tttttgtcgg ccatgattgg ggtgcttgtt tggcatttca ttatagctat gagcatcaag 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ataagatcaa agcaatagtt cacgctgaaa gtgtagtaga tgtgattgaa tcatgggatg aatggcctga tattgaagaa gatattgcgt tgatcaaatc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tgaagaagga gaaaaaatgg ttttggagaa taacttcttc gtggaaacca tgttgccatc aaaaatcatg agaaagttag aaccagaaga atttgcagca 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tatcttgaac cattcaaaga gaaaggtgaa gttcgtcgtc caacattatc atggcctcgt gaaatcccgt tagtaaaagg tggtaaacct gacgttgtac 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

aaattgttag gaattataat gcttatctac gtgcaagtga tgatttacca aaaatgttta ttgaatcgga cccaggattc ttttccaatg ctattgttga 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

aggtgccaag aagtttccta atactgaatt tgtcaaagta aaaggtcttc atttttcgca agaagatgca cctgatgaaa tgggaaaata tatcaaatcg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ttcgttgagc gagttctcaa aaatgaacaa atGtcgaTCG ACgggggccc ctaggAgatc cAAGCTTATC GATTTCGAAC CCGGGGTACC GAATTCCTCG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGTCTAGAGG AgcatgcTCC TCTAGACTCG AGGAATTCGG TACCCCGGGT TCGAAATCGA TAAGCTTgGA TCTAGCGCGC GGGAGGAGGA GAAGCAGTGG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GGAGGCGCAG CCGCTCAcCT GCGGGGCAGG GCGCGGAGGA GGGACCCGGN TGcGcGCTCT CGGGCCGAGG AACCAGGACG cGCCCGGAGC CTCGCACGCG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCCAAGCTCG GGCGTCCCCT CCCCTCGGCC GGGCGAACTC AAGGGGCGCA GCTCTTTGCT TTGACAGAGC TGGCCGGCGG AGGCGTGCAG AGCGGCGAGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CGGCGAGCCA GGCTGAGAAA CTCGACCCGG GAACAAAGAG GGGTCGGACT GAGTGTGTGT GTCGGCTCGA GCTCCGGGNA GAGGCATTTG CCCGAGGNCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCGCTGTGAC TCCCCGAGAC TCCGCAGTGC CCTCCACTGN GGAGTCCCCG CGCTTGCCGG NAAAAACTTT ATTCTTGGCA AACTTCTCTT TCTCTTCCCC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCCTCCTCGG CCCCCATCTT CTGCTCCTCC TCCTTCTCTA GCAGATTAAA TGAGCCTCGA GAAGAAAAAC CGAAGCGAAA GGGAAGAAAA TAAGAAGATC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TAAAACGGAC ATCTCCAGCG TGGGTGGCTC CTTTTTCTTT TTCTTTTTTT CCCACCCTTC AGGAAGTGGA CGTTTCGTTA TCTTCTGATC CTTGCACCTT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CTTTTGGGGC AAACGGGGCC CTTCTGCCCA GATCCCCTCT CTTTTCTCGG AAAACAAACT ACTAAGTCGG CATCCGGGGT AACTACAGTG GAGAGGGTTT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CCGCGGAGAC GCGCCGCCGG ACCCTCCTCT GCACTTTGGG GAGGCGTGCT CCCTCCAGAA CCGGCGTTCT CCGCGCGCAA ATCCCGGCGA CGCGGGGTCG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGGGGTGGCC GCCGGGGCAG CCTCGTCTAG CGCGCGCCGC GCAGACGCCC CCGGAGTCGC CAGCTACCGC AGCCCTCGCC GCCCAGTGCC CTTCGGCCTC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GGGGCGGGCG CCTGCGTCGG TCTCCGCGAA GCGGGAAAGC GCGGCGGCCG CCGGGATTCG GGCGCCGCGG CAGCTGCTCC GGCTGCCGGC CGGCGGCCCC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GCGCTCGCCC GCCCCGCTTC CGCCCGCTGT CCTGCTGCAC GAACCCTTCC AACTCTCCTT TCCTCCCCCA CCCTTGAGTT ACCCCTCTGT CTTTCCTGCT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GTTGCGCGGG TGCTCCCACA GCGGAGCGGA GATTACAGAG CCGCCGGGAT GCCCGCTGGA TCCATGGaag acgccaaaaa cataaagaaa ggcccggcgc 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

cattctatcc gctggaagat ggaaccgctg gagagcaact gcataaggct atgaagagat acgccctggt tcctggaaca attgctttta cagatgcaca 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

tatcgaggtg gacatcactt acgctgagta cttcgaaatg tccgttcggt tggcagaagc tatgaaacga tatgggctga atacaaatca cagaatcgtc 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

gtatgcagtg aaaactctct tcaattcttt atgccggtgt tgggcgcgtt atttatcgga gttgcagttg cgcccgcgaa cgacatttat aatgaacgtg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

aattgctcaa cagtatgggc atttcgcagc ctaccgtggt gttcgtttcc aaaaaggggt tgcaaaaaat tttgaacgtg caaaaaaagc tcccaatcat 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ccaaaaaatt attatcatgg attctaaaac ggattaccag ggatttcagt cgatgtacac gttcgtcaca tctcatctac ctcccggttt taatgaatac 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

gattttgtgc cagagtcctt cgatagggac aagacaattg cactgatcat gaactcctct ggatctactg gtctgcctaa aggtgtcgct ctgcctcata 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

gaactgcctg cgtgagattc tcgcatgcca gagatcctat ttttggcaat caaatcattc cggatactgc gattttaagt gttgttccat tccatcacgg 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ttttggaatg tttactacac tcggatattt gatatgtgga tttcgagtcg tcttaatgta tagatttgaa gaagagctgt ttctgaggag ccttcaggat 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

tacaagattc aaagtgcgct gctggtgcca accctattct ccttcttcgc caaaagcact ctgattgaca aatacgattt atctaattta cacgaaattg 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

cttctggtgg cgctcccctc tctaaggaag tcggggaagc ggttgccaag aggttccatc tgccaggtat caggcaagga tatgggctca ctgagactac 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

atcagctatt ctgattacac ccgaggggga tgataaaccg ggcgcggtcg gtaaagttgt tccatttttt gaagcgaagg ttgtggatct ggataccggg 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

aaaacgctgg gcgttaatca aagaggcgaa ctgtgtgtga gaggtcctat gattatgtcc ggttatgtaa acaatccgga agcgaccaac gccttgattg 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

acaaggatgg atggctacat tctggagaca tagcttactg ggacgaagac gaacacttct tcatcgttga ccgcctgaag tctctgatta agtacaaagg 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ctatcaggtg gctcccgctg aattggaatc catcttgctc caacacccca acatcttcga cgcaggtgtc gcaggtcttc ccgacgatga cgccggtgaa 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

cttcccgccg ccgttgttgt tttggagcac ggaaagacga tgacggaaaa agagatcgtg gattacgtcg ccagtcaagt aacaaccgcg aaaaagttgc 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

gcggaggagt tgtgtttgtg gacgaagtac cgaaaggtct taccggaaaa ctcgacgcaa gaaaaatcag agagatcctc ataaaggcca agaagggcgg 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

aaagatcgcc gtgtaatTCT AGAgcggccg cttcgagcag acatgataag atacattgat gagtttggac aaaccacaac tagaatgcag tgaaaaaaat 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

gctttatttg tgaaatttgt gatgctattg ctttatttgt aaccattata agctgcaata aacaagttaa caacaacaat tgcattcatt ttatgtttca 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ggttcagggg gaggtgtggg aggtttttta aagcaagtaa aacctctaca aatgtggtaa aatcgataag tttaaacaga tccaggtggc acttttcggg 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

gaaatgtgcg cggaacccct atttgtttat ttttctaaat acattcaaat atgtatccgc tcatgagaca ataaccctga taaatgcttc aataatattg 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

aaaaaggaag agtatgagta ttcaacattt ccgtgtcgcc cttattccct tttttgcggc attttgcctt cctgtttttg ctcacccaga aacgctggtg 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

aaagtaaaag atgctgaaga tcagttgggt gcacgagtgg gttacatcga actggatctc aacagcggta agatccttga gagttttcgc cccgaagaac 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

gttttccaat gatgagcact tttaaagttc tgctatgtgg cgcggtatta tcccgtattg acgccgggca agagcaactc ggtcgccgca tacactattc 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

tcagaatgac ttggttgagt actcaccagt cacagaaaag catcttacgg atggcatgac agtaagagaa ttatgcagtg ctgccataac catgagtgat 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

aacactgcgg ccaacttact tctgacaacg atcggaggac cgaaggagct aaccgctttt ttgcacaaca tgggggatca tgtaactcgc cttgatcgtt 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

gggaaccgga gctgaatgaa gccataccaa acgacgagcg tgacaccacg atgcctgtag caatggcaac aacgttgcgc aaactattaa ctggcgaact 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

acttactcta gcttcccggc aacaattaat agactggatg gaggcggata aagttgcagg accacttctg cgctcggccc ttccggctgg ctggtttatt 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

gctgataaat ctggagccgg tgagcgtggg tctcgcggta tcattgcagc actggggcca gatggtaagc cctcccgtat cgtagttatc tacacgacgg 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ggagtcaggc aactatggat gaacgaaata gacagatcgc tgagataggt gcctcactga ttaagcattg gtaactgtca gaccaagttt actcatatat 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

actttagatt gatttaaaac ttcattttta atttaaaagg atctaggtga agatcctttt tgataatctc atgaccaaaa tcccttaacg tgagttttcg 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ttccactgag cgtcagaccc cgtagaaaag atcaaaggat cttcttgaga tccttttttt ctgcgcgtaa tctgctgctt gcaaacaaaa aaaccaccgc 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

taccagcggt ggtttgtttg ccggatcaag agctaccaac tctttttccg aaggtaactg gcttcagcag agcgcagata ccaaatactg tccttctagt 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

gtagccgtag ttaggccacc acttcaagaa ctctgtagca ccgcctacat acctcgctct gctaatcctg ttaccagtgg ctgctgccag tggcgataag 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

tcgtgtctta ccgggttgga ctcaagacga tagttaccgg ataaggcgca gcggtcgggc tgaacggggg gttcgtgcac acagcccagc ttggagcgaa 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

cgacctacac cgaactgaga tacctacagc gtgagctatg agaaagcgcc acgcttcccg aagggagaaa ggcggacagg tatccggtaa gcggcagggt 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

cggaacagga gagcgcacga gggagcttcc agggggaaac gcctggtatc tttatagtcc tgtcgggttt cgccacctct gacttgagcg tcgatttttg 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

tgatgctcgt caggggggcg gagcctatgg aaaaacgcca gcaacgcggc ctttttacgg ttcctggcct tttgctggcc ttttgctcac atggctcgac
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691

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):

12-968

ORF

ORF position:

2

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

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

The description of the protein encoded in this ORF:
Firefly luciferase with 5 additional N-terminal aminoacid residues.

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):

2263-3930

Remarks:

Authentic RNA pol II promoter was confirmed between bases +280 and +640 relative to the main start site of
transcription. Comment from J. Jimenez: Our original studies of the LEF1 5'UTR were based on characterizing
a third promoter in the 5'UTR that is responsible for generating a 3.0 kb transcript. Because we had evidence
of an authentic promoter, we performed N. blot analysis. We did also attempt RT-PCR, but had technical
problems due to the high GC content of the 5'UTR.

Possibility of aberrant splicing of the plasmids with LEF-1 was therefore ruled out only by the Northern-blot
technique (Fig. 2C and 3B).

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

IRESs:

IRES:

Version: `3`	Last change: `2007-09-06 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `LEF1`	The functional status of IRES: `functional`

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

1091-2268

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `123`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `1300`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-1172`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `5`

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

GCGCGGGAGG AGGAGAAGCA GTGGGGAGGC GCAGCCGCTC AcCTGCGGGG CAGGGCGCGG AGGAGGGACC CGGNTGcGcG CTCTCGGGCC GAGGAACCAG 
^1091      ^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      

GACGcGCCCG GAGCCTCGCA CGCGGCCAAG CTCGGGCGTC CCCTCCCCTC GGCCGGGCGA ACTCAAGGGG CGCAGCTCTT TGCTTTGACA GAGCTGGCCG 
^1191      ^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      

GCGGAGGCGT GCAGAGCGGC GAGCCGGCGA GCCAGGCTGA GAAACTCGAC CCGGGAACAA AGAGGGGTCG GACTGAGTGT GTGTGTCGGC TCGAGCTCCG 
^1291      ^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      

GGNAGAGGCA TTTGCCCGAG GNCCCCGCTG TGACTCCCCG AGACTCCGCA GTGCCCTCCA CTGNGGAGTC CCCGCGCTTG CCGGNAAAAA CTTTATTCTT 
^1391      ^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      

GGCAAACTTC TCTTTCTCTT CCCCTCCTCC TCGGCCCCCA TCTTCTGCTC CTCCTCCTTC TCTAGCAGAT TAAATGAGCC TCGAGAAGAA AAACCGAAGC 
^1491      ^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      

GAAAGGGAAG AAAATAAGAA GATCTAAAAC GGACATCTCC AGCGTGGGTG GCTCCTTTTT CTTTTTCTTT TTTTCCCACC CTTCAGGAAG TGGACGTTTC 
^1591      ^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      

GTTATCTTCT GATCCTTGCA CCTTCTTTTG GGGCAAACGG GGCCCTTCTG CCCAGATCCC CTCTCTTTTC TCGGAAAACA AACTACTAAG TCGGCATCCG 
^1691      ^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      

GGGTAACTAC AGTGGAGAGG GTTTCCGCGG AGACGCGCCG CCGGACCCTC CTCTGCACTT TGGGGAGGCG TGCTCCCTCC AGAACCGGCG TTCTCCGCGC 
^1791      ^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      

GCAAATCCCG GCGACGCGGG GTCGCGGGGT GGCCGCCGGG GCAGCCTCGT CTAGCGCGCG CCGCGCAGAC GCCCCCGGAG TCGCCAGCTA CCGCAGCCCT 
^1891      ^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      

CGCCGCCCAG TGCCCTTCGG CCTCGGGGCG GGCGCCTGCG TCGGTCTCCG CGAAGCGGGA AAGCGCGGCG GCCGCCGGGA TTCGGGCGCC GCGGCAGCTG 
^1991      ^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      

CTCCGGCTGC CGGCCGGCGG CCCCGCGCTC GCCCGCCCCG CTTCCGCCCG CTGTCCTGCT GCACGAACCC TTCCAACTCT CCTTTCCTCC CCCACCCTTG 
^2091      ^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      

AGTTACCCCT CTGTCTTTCC TGCTGTTGCG CGGGTGCTCC CACAGCGGAG CGGAGATTAC AGAGCCGCCG GGATGCCC
^2191      ^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

The translation experiments:

Translation results:

IRESite Translation Id: 195

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

6.160

Name of IRES used as the positive control:

CVB3

Name of the plasmid used as the positive control. `pRSTF-CVB3`	Name of the plasmid used as the negative control. `pRSTF`
`IRESite Id` of the plasmid used as positive control. `210`	`IRESite Id` of the plasmid used as negative control. `212`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0.210`
The size (length) of intercistronic region in the positive control: `819`	The size (length) of intercistronic region in the negative control: `131`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_without_cap_without_polyA_tail

Remarks:

Fig. 4A

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

Translation results:

IRESite Translation Id: 196

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

8.490

Name of IRES used as the positive control:

CVB3

Name of the plasmid used as the positive control. `pRSTF-CVB3`	Name of the plasmid used as the negative control. `pRSTF`
`IRESite Id` of the plasmid used as positive control. `210`	`IRESite Id` of the plasmid used as negative control. `212`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0.390`
The size (length) of intercistronic region in the positive control: `819`	The size (length) of intercistronic region in the negative control: `131`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_without_cap_without_polyA_tail

Remarks:

Fig. 4B, measured values provided by J. Jimenez.

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

Translation results:

IRESite Translation Id: 197

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

6.610

Name of IRES used as the positive control:

CVB3

Name of the plasmid used as the positive control. `pRSTF-CVB3`	Name of the plasmid used as the negative control. `pRSTF`
`IRESite Id` of the plasmid used as positive control. `210`	`IRESite Id` of the plasmid used as negative control. `212`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `6.060`
The size (length) of intercistronic region in the positive control: `819`	The size (length) of intercistronic region in the negative control: `131`

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_without_polyA_tail

Remarks:

Fig. 4B, measured values provided by J. Jimenez.

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

Translation results:

IRESite Translation Id: 198

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

2.470

Name of IRES used as the positive control:

CVB3

Name of the plasmid used as the positive control. `pRSTF-CVB3`	Name of the plasmid used as the negative control. `pRSTF`
`IRESite Id` of the plasmid used as positive control. `210`	`IRESite Id` of the plasmid used as negative control. `212`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `2.810`
The size (length) of intercistronic region in the positive control: `819`	The size (length) of intercistronic region in the negative control: `131`

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_without_polyA_tail

Remarks:

Fig. 4C, measured values provided by J. Jimenez. Cells in this experiment did not co-express PV2A protease.

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

Translation results:

IRESite Translation Id: 199

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

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

0.440

Name of IRES used as the positive control:

CVB3

Name of the plasmid used as the positive control. `pRSTF-CVB3`	Name of the plasmid used as the negative control. `pRSTF`
`IRESite Id` of the plasmid used as positive control. `210`	`IRESite Id` of the plasmid used as negative control. `212`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0.090`
The size (length) of intercistronic region in the positive control: `819`	The size (length) of intercistronic region in the negative control: `131`

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_without_polyA_tail

Remarks:

Fig. 4C, measured values provided by J. Jimenez. Cells in this experiment did co-express PV2A protease.

Citations:

Jimenez J., Jang G. M., Semler B. L., Waterman M. L. (2005) An internal ribosome entry site mediates translation of lymphoid enhancer factor-1. RNA. 11(9):1385-1399

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