IRESite_Id:318 characteristics of LEF1 IRES studied in pRSTF-LEF1

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `318`	Version: `0`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš

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 in vivo transcript from SV40 promoter with the chimeric intron spliced out and containing
renilla_luciferase - hairpin_from_multiple_cloning_site - LEF1 IRES 1.2kb - firefly_luciferase and is
terminated after the late SV40 polyA signal. An FLuc-fusion protein should be translated from the second
cistron (4 aminoacids added extra).

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

attccagaag tagtgaggag gcttttttgg aggcctaggc ttttgcaaaa agcttgattc ttctgacaca acagtctcga acttaagctg cagaagttgg 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tcgtgaggca ctgggcaggt gtccactccc agttcaatta cagctcttaa ggctagagta cTTAATACGA CTCACTATAG Gctagccacc atGacttcga 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

aagtttatga tccagaacaa aggaaacgga tgataactgg tccgcagtgg tgggccagat gtaaacaaat gaatgttctt gattcattta ttaattatta 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

tgattcagaa aaacatgcag aaaatgctgt tattttttta catggtaacg cggcctcttc ttatttatgg cgacatgttg tgccacatat tgagccagta 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

gcgcggtgta ttataccaga ccttattggt atgggcaaat caggcaaatc tggtaatggt tcttataggt tacttgatca ttacaaatat cttactgcat 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ggtttgaact tcttaattta ccaaagaaga tcatttttgt cggccatgat tggggtgctt gtttggcatt tcattatagc tatgagcatc aagataagat 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

caaagcaata gttcacgctg aaagtgtagt agatgtgatt gaatcatggg atgaatggcc tgatattgaa gaagatattg cgttgatcaa atctgaagaa 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ggagaaaaaa tggttttgga gaataacttc ttcgtggaaa ccatgttgcc atcaaaaatc atgagaaagt tagaaccaga agaatttgca gcatatcttg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

aaccattcaa agagaaaggt gaagttcgtc gtccaacatt atcatggcct cgtgaaatcc cgttagtaaa aggtggtaaa cctgacgttg tacaaattgt 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

taggaattat aatgcttatc tacgtgcaag tgatgattta ccaaaaatgt ttattgaatc ggacccagga ttcttttcca atgctattgt tgaaggtgcc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

aagaagtttc ctaatactga atttgtcaaa gtaaaaggtc ttcatttttc gcaagaagat gcacctgatg aaatgggaaa atatatcaaa tcgttcgttg 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

agcgagttct caaaaatgaa caaatGtcga TCGACggggg cccctaggAg atccAAGCTT ATCGATTTCG AACCCGGGGT ACCGAATTCC TCGAGTCTAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGGAgcatgc TCCTCTAGAC TCGAGGAATT CGGTACCCCG GGTTCGAAAT CGATAAGCTT gGATCTAGCG CGCGGGAGGA GGAGAAGCAG TGGGGAGGCG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CAGCCGCTCA cCTGCGGGGC AGGGCGCGGA GGAGGGACCC GGNTGcGcGC TCTCGGGCCG AGGAACCAGG ACGcGCCCGG AGCCTCGCAC GCGGCCAAGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCGGGCGTCC CCTCCCCTCG GCCGGGCGAA CTCAAGGGGC GCAGCTCTTT GCTTTGACAG AGCTGGCCGG CGGAGGCGTG CAGAGCGGCG AGCCGGCGAG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCAGGCTGAG AAACTCGACC CGGGAACAAA GAGGGGTCGG ACTGAGTGTG TGTGTCGGCT CGAGCTCCGG GNAGAGGCAT TTGCCCGAGG NCCCCGCTGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GACTCCCCGA GACTCCGCAG TGCCCTCCAC TGNGGAGTCC CCGCGCTTGC CGGNAAAAAC TTTATTCTTG GCAAACTTCT CTTTCTCTTC CCCTCCTCCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CGGCCCCCAT CTTCTGCTCC TCCTCCTTCT CTAGCAGATT AAATGAGCCT CGAGAAGAAA AACCGAAGCG AAAGGGAAGA AAATAAGAAG ATCTAAAACG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GACATCTCCA GCGTGGGTGG CTCCTTTTTC TTTTTCTTTT TTTCCCACCC TTCAGGAAGT GGACGTTTCG TTATCTTCTG ATCCTTGCAC CTTCTTTTGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGCAAACGGG GCCCTTCTGC CCAGATCCCC TCTCTTTTCT CGGAAAACAA ACTACTAAGT CGGCATCCGG GGTAACTACA GTGGAGAGGG TTTCCGCGGA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GACGCGCCGC CGGACCCTCC TCTGCACTTT GGGGAGGCGT GCTCCCTCCA GAACCGGCGT TCTCCGCGCG CAAATCCCGG CGACGCGGGG TCGCGGGGTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCCGCCGGGG CAGCCTCGTC TAGCGCGCGC CGCGCAGACG CCCCCGGAGT CGCCAGCTAC CGCAGCCCTC GCCGCCCAGT GCCCTTCGGC CTCGGGGCGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GCGCCTGCGT CGGTCTCCGC GAAGCGGGAA AGCGCGGCGG CCGCCGGGAT TCGGGCGCCG CGGCAGCTGC TCCGGCTGCC GGCCGGCGGC CCCGCGCTCG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CCCGCCCCGC TTCCGCCCGC TGTCCTGCTG CACGAACCCT TCCAACTCTC CTTTCCTCCC CCACCCTTGA GTTACCCCTC TGTCTTTCCT GCTGTTGCGC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GGGTGCTCCC ACAGCGGAGC GGAGATTACA GAGCCGCCGG GATGCCCGCT GGATCCATGG aagacgccaa aaacataaag aaaggcccgg cgccattcta 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

tccgctggaa gatggaaccg ctggagagca actgcataag gctatgaaga gatacgccct ggttcctgga acaattgctt ttacagatgc acatatcgag 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

gtggacatca cttacgctga gtacttcgaa atgtccgttc ggttggcaga agctatgaaa cgatatgggc tgaatacaaa tcacagaatc gtcgtatgca 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

gtgaaaactc tcttcaattc tttatgccgg tgttgggcgc gttatttatc ggagttgcag ttgcgcccgc gaacgacatt tataatgaac gtgaattgct 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

caacagtatg ggcatttcgc agcctaccgt ggtgttcgtt tccaaaaagg ggttgcaaaa aattttgaac gtgcaaaaaa agctcccaat catccaaaaa 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

attattatca tggattctaa aacggattac cagggatttc agtcgatgta cacgttcgtc acatctcatc tacctcccgg ttttaatgaa tacgattttg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

tgccagagtc cttcgatagg gacaagacaa ttgcactgat catgaactcc tctggatcta ctggtctgcc taaaggtgtc gctctgcctc atagaactgc 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ctgcgtgaga ttctcgcatg ccagagatcc tatttttggc aatcaaatca ttccggatac tgcgatttta agtgttgttc cattccatca cggttttgga 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

atgtttacta cactcggata tttgatatgt ggatttcgag tcgtcttaat gtatagattt gaagaagagc tgtttctgag gagccttcag gattacaaga 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ttcaaagtgc gctgctggtg ccaaccctat tctccttctt cgccaaaagc actctgattg acaaatacga tttatctaat ttacacgaaa ttgcttctgg 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

tggcgctccc ctctctaagg aagtcgggga agcggttgcc aagaggttcc atctgccagg tatcaggcaa ggatatgggc tcactgagac tacatcagct 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

attctgatta cacccgaggg ggatgataaa ccgggcgcgg tcggtaaagt tgttccattt tttgaagcga aggttgtgga tctggatacc gggaaaacgc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

tgggcgttaa tcaaagaggc gaactgtgtg tgagaggtcc tatgattatg tccggttatg taaacaatcc ggaagcgacc aacgccttga ttgacaagga 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

tggatggcta cattctggag acatagctta ctgggacgaa gacgaacact tcttcatcgt tgaccgcctg aagtctctga ttaagtacaa aggctatcag 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

gtggctcccg ctgaattgga atccatcttg ctccaacacc ccaacatctt cgacgcaggt gtcgcaggtc ttcccgacga tgacgccggt gaacttcccg 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ccgccgttgt tgttttggag cacggaaaga cgatgacgga aaaagagatc gtggattacg tcgccagtca agtaacaacc gcgaaaaagt tgcgcggagg 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

agttgtgttt gtggacgaag taccgaaagg tcttaccgga aaactcgacg caagaaaaat cagagagatc ctcataaagg ccaagaaggg cggaaagatc 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

gccgtgtaat TCTAGAgcgg ccgcttcgag cagacatgat aagatacatt gatgagtttg gacaaaccac aactagaatg cagtgaaaaa aatgctttat 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ttgtgaaatt tgtgatgcta ttgctttatt tgtaaccatt ataagctgca ataaacaagt taacaacaac aattgcattc attttatgtt tcaggttcag 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ggggaggtgt gggaggtttt ttaaagcaag taaaacctct acaaatgtgg ta
^4301      ^4311      ^4321      ^4331      ^4341      ^4351

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:

reverse_engineered_sequence_and_should_match_experiment_maybe_except_both_UTRs

The name of the plasmid:
pRSTF-LEF1_1.2 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?):

yes

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

yes

A promoter reported in cDNA corresponding to IRES sequence:

no

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
heterogeneous_population_of_molecules_found

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
weak_promoter_confirmed

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Cercopithecus aethiops COS-1 (ATCC CRL-1650)

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):

191-1147

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):

2457-4109

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: `1`	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):

1270-2447

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: `-1187`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-10`

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

GCGCGGGAGG AGGAGAAGCA GTGGGGAGGC GCAGCCGCTC AcCTGCGGGG CAGGGCGCGG AGGAGGGACC CGGNTGcGcG CTCTCGGGCC GAGGAACCAG 
^1270      ^1280      ^1290      ^1300      ^1310      ^1320      ^1330      ^1340      ^1350      ^1360      

GACGcGCCCG GAGCCTCGCA CGCGGCCAAG CTCGGGCGTC CCCTCCCCTC GGCCGGGCGA ACTCAAGGGG CGCAGCTCTT TGCTTTGACA GAGCTGGCCG 
^1370      ^1380      ^1390      ^1400      ^1410      ^1420      ^1430      ^1440      ^1450      ^1460      

GCGGAGGCGT GCAGAGCGGC GAGCCGGCGA GCCAGGCTGA GAAACTCGAC CCGGGAACAA AGAGGGGTCG GACTGAGTGT GTGTGTCGGC TCGAGCTCCG 
^1470      ^1480      ^1490      ^1500      ^1510      ^1520      ^1530      ^1540      ^1550      ^1560      

GGNAGAGGCA TTTGCCCGAG GNCCCCGCTG TGACTCCCCG AGACTCCGCA GTGCCCTCCA CTGNGGAGTC CCCGCGCTTG CCGGNAAAAA CTTTATTCTT 
^1570      ^1580      ^1590      ^1600      ^1610      ^1620      ^1630      ^1640      ^1650      ^1660      

GGCAAACTTC TCTTTCTCTT CCCCTCCTCC TCGGCCCCCA TCTTCTGCTC CTCCTCCTTC TCTAGCAGAT TAAATGAGCC TCGAGAAGAA AAACCGAAGC 
^1670      ^1680      ^1690      ^1700      ^1710      ^1720      ^1730      ^1740      ^1750      ^1760      

GAAAGGGAAG AAAATAAGAA GATCTAAAAC GGACATCTCC AGCGTGGGTG GCTCCTTTTT CTTTTTCTTT TTTTCCCACC CTTCAGGAAG TGGACGTTTC 
^1770      ^1780      ^1790      ^1800      ^1810      ^1820      ^1830      ^1840      ^1850      ^1860      

GTTATCTTCT GATCCTTGCA CCTTCTTTTG GGGCAAACGG GGCCCTTCTG CCCAGATCCC CTCTCTTTTC TCGGAAAACA AACTACTAAG TCGGCATCCG 
^1870      ^1880      ^1890      ^1900      ^1910      ^1920      ^1930      ^1940      ^1950      ^1960      

GGGTAACTAC AGTGGAGAGG GTTTCCGCGG AGACGCGCCG CCGGACCCTC CTCTGCACTT TGGGGAGGCG TGCTCCCTCC AGAACCGGCG TTCTCCGCGC 
^1970      ^1980      ^1990      ^2000      ^2010      ^2020      ^2030      ^2040      ^2050      ^2060      

GCAAATCCCG GCGACGCGGG GTCGCGGGGT GGCCGCCGGG GCAGCCTCGT CTAGCGCGCG CCGCGCAGAC GCCCCCGGAG TCGCCAGCTA CCGCAGCCCT 
^2070      ^2080      ^2090      ^2100      ^2110      ^2120      ^2130      ^2140      ^2150      ^2160      

CGCCGCCCAG TGCCCTTCGG CCTCGGGGCG GGCGCCTGCG TCGGTCTCCG CGAAGCGGGA AAGCGCGGCG GCCGCCGGGA TTCGGGCGCC GCGGCAGCTG 
^2170      ^2180      ^2190      ^2200      ^2210      ^2220      ^2230      ^2240      ^2250      ^2260      

CTCCGGCTGC CGGCCGGCGG CCCCGCGCTC GCCCGCCCCG CTTCCGCCCG CTGTCCTGCT GCACGAACCC TTCCAACTCT CCTTTCCTCC CCCACCCTTG 
^2270      ^2280      ^2290      ^2300      ^2310      ^2320      ^2330      ^2340      ^2350      ^2360      

AGTTACCCCT CTGTCTTTCC TGCTGTTGCG CGGGTGCTCC CACAGCGGAG CGGAGATTAC AGAGCCGCCG GGATGCCC
^2370      ^2380      ^2390      ^2400      ^2410      ^2420      ^2430      ^2440

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: 406

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:

100.000

	Name of the plasmid used as the negative control. `pRSTF`
	`IRESite Id` of the plasmid used as negative control. `213`
	The relative translation efficiency in % of the negative control: `1.600`
	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:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

As positive controls were used Kv1.4 and CVB3 IRESs (Fig. 2B). They are not considered as correct positive
controls by IRESite due to the fact the measured values were biased by aberrant splicing of Kv1.4 and CVB3
containing plasmids.

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: 407

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:

Homo sapiens HeLa (ATCC CCL-2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

100.000

	Name of the plasmid used as the negative control. `pRSTF`
	`IRESite Id` of the plasmid used as negative control. `213`
	The relative translation efficiency in % of the negative control: `3.130`
	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:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

As positive controls were used Kv1.4 and CVB3 IRESs (Fig. 2B). They are not considered as correct positive
controls by IRESite due to the fact the measured values were biased by aberrant splicing of Kv1.4 and CVB3
containing plasmids.

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