IRESite_Id:494 characteristics of LINE1-ORF1-101-1 IRES studied in pR-deltaEMCV-L1_ORF1

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `494`	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:
our_best_guess

The mRNA/+RNA description:

Putative spliced in vivo transcript of pR-deltaEMCV-F with 101-1 insert of putative LINE-1 IRES from SV40
promoter

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

TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTtgatt cttctgacac aacagtctcg aacttaagct gcagaagttg 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

gtcgtgaggc actgggcagg tgtccactcc cagttcaatt acagctctta aggctagagt actTAATACG ACTCACTATA GGctagccac catgacttcg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

aaagtttatg atccagaaca aaggaaacgg atgataactg gtccgcagtg gtgggccaga tgtaaacaaa tgaatgttct tgattcattt attaattatt 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

atgattcaga aaaacatgca gaaaatgctg ttattttttt acatggtaac gcggcctctt cttatttatg gcgacatgtt gtgccacata ttgagccagt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

agcgcggtgt attataccag accttattgg tatgggcaaa tcaggcaaat ctggtaatgg ttcttatagg ttacttgatc attacaaata tcttactgca 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

tggtttgaac ttcttaattt accaaagaag atcatttttg tcggccatga ttggggtgct tgtttggcat ttcattatag ctatgagcat caagataaga 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tcaaagcaat agttcacgct gaaagtgtag tagatgtgat tgaatcatgg gatgaatggc ctgatattga agaagatatt gcgttgatca aatctgaaga 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

aggagaaaaa atggttttgg agaataactt cttcgtggaa accatgttgc catcaaaaat catgagaaag ttagaaccag aagaatttgc agcatatctt 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gaaccattca aagagaaagg tgaagttcgt cgtccaacat tatcatggcc tcgtgaaatc ccgttagtaa aaggtggtaa acctgacgtt gtacaaattg 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ttaggaatta taatgcttat ctacgtgcaa gtgatgattt accaaaaatg tttattgaat cggacccagg attcttttcc aatgctattg ttgaaggtgc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

caagaagttt cctaatactg aatttgtcaa agtaaaaggt cttcattttt cgcaagaaga tgcacctgat gaaatgggaa aatatatcaa atcgttcgtt 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

gagcgagttc tcaaaaatga acaataattc taggggctcg agcgcccctc tccctccccc ccccctaacg ttactggccg aagccgcttg gaataaggcc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ggtgtgcgtt tgtctatatg ttattttcca ccatattgcc gtcttttggc aacgtgaggg cccggaaacc tggccctgtc ttcttgacga gcaatcctag 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

agcttcttga agacaaacaa cgtctgtagc gaccctttgc aggcagcgga accccccacc tggcgacagg tgcctctgcg gccaaaagcc acgtgtataa 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

gatacacctg caaaggcggc acaaccccag tgccacgttg tgagttggat agttgtggaa agagtcaaat ggctctcctc aagcgtattc aacaaggggc 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tgaaggatgc ccagaaggta cccccttgta tgggatctga tctggggcct cggtgcacat gctttacatg tgtttagtcg aggttaaaaa aacgtctagg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ccccccgaac cacggggacg tggttttcct ttgaaaaaca cgaattcAAT AACAGAAAAA AACCAATACA AGAACGGGAA CAACGCCCTA GAAAAAACAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAAGGTAATC CCTCAACAAA CCTAAAAGAA GACAGCCACA AGAACAGAcc atggaagacg ccaaaaacat aaagaaaggc ccggcgccat tctatccgct 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ggaagatgga accgctggag agcaactgca taaggctatg aagagatacg ccctggttcc tggaacaatt gcttttacag atgcacatat cgaggtggac 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

atcacttacg ctgagtactt cgaaatgtcc gttcggttgg cagaagctat gaaacgatat gggctgaata caaatcacag aatcgtcgta tgcagtgaaa 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

actctcttca attctttatg ccggtgttgg gcgcgttatt tatcggagtt gcagttgcgc ccgcgaacga catttataat gaacgtgaat tgctcaacag 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

tatgggcatt tcgcagccta ccgtggtgtt cgtttccaaa aaggggttgc aaaaaatttt gaacgtgcaa aaaaagctcc caatcatcca aaaaattatt 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

atcatggatt ctaaaacgga ttaccaggga tttcagtcga tgtacacgtt cgtcacatct catctacctc ccggttttaa tgaatacgat tttgtgccag 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

agtccttcga tagggacaag acaattgcac tgatcatgaa ctcctctgga tctactggtc tgcctaaagg tgtcgctctg cctcatagaa ctgcctgcgt 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gagattctcg catgccagag atcctatttt tggcaatcaa atcattccgg atactgcgat tttaagtgtt gttccattcc atcacggttt tggaatgttt 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

actacactcg gatatttgat atgtggattt cgagtcgtct taatgtatag atttgaagaa gagctgtttc tgaggagcct tcaggattac aagattcaaa 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

gtgcgctgct ggtgccaacc ctattctcct tcttcgccaa aagcactctg attgacaaat acgatttatc taatttacac gaaattgctt ctggtggcgc 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

tcccctctct aaggaagtcg gggaagcggt tgccaagagg ttccatctgc caggtatcag gcaaggatat gggctcactg agactacatc agctattctg 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

attacacccg agggggatga taaaccgggc gcggtcggta aagttgttcc attttttgaa gcgaaggttg tggatctgga taccgggaaa acgctgggcg 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ttaatcaaag aggcgaactg tgtgtgagag gtcctatgat tatgtccggt tatgtaaaca atccggaagc gaccaacgcc ttgattgaca aggatggatg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

gctacattct ggagacatag cttactggga cgaagacgaa cacttcttca tcgttgaccg cctgaagtct ctgattaagt acaaaggcta tcaggtggct 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

cccgctgaat tggaatccat cttgctccaa caccccaaca tcttcgacgc aggtgtcgca ggtcttcccg acgatgacgc cggtgaactt cccgccgccg 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ttgttgtttt ggagcacgga aagacgatga cggaaaaaga gatcgtggat tacgtcgcca gtcaagtaac aaccgcgaaa aagttgcgcg gaggagttgt 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

gtttgtggac gaagtaccga aaggtcttac cggaaaactc gacgcaagaa aaatcagaga gatcctcata aaggccaaga agggcggaaa gatcgccgtg 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

taattctaga gtcggggcgg ccggccgctt cgagCAGACA TGATAAGATA CATTGATGAG TTTGGACAAA CCACAACTAG AATGCAGTGA AAAAAATGCT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TTATTTGTGA AATTTGTGAT GCTATTGCTT TATTTGTAAC CATTATAAGC TGCAATAAAC AAGTTAACAA CAACAATTGC ATTCATTTTA TGTTTCAGGT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TCAGGGGGAG GTGTGGGAGG TTTTTTAAAG CAAGTAAAAC CTCTACAAAT GTGGTA
^3601      ^3611      ^3621      ^3631      ^3641      ^3651

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

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pR-deltaEMCV-L1_ORF1_-101-1-F The name of the promoter used to express this mRNA:
SV40

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

not tested

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

not tested

A promoter reported in cDNA corresponding to IRES sequence:

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:
not_tested

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:
no_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:

Mus musculus

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
L1spa

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Mus musculus

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

ggtaccgagc tcttacgcgt gctagcccga tctgcgcagc accatggcct gaaataacct ctgaaagagg aacttggtta ggtaccttct gaggcggaaa 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

gaaccagctg tggaatgtgt gtcagttagg gtgtggaaag tccccaggct ccccagcagg cagaagtatg caaagcatgc atctcaatta gtcagcaacc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

aggtgtggaa agtccccagg ctccccagca ggcagaagta tgcaaagcat gcatctcaat tagtcagcaa ccatagtccc gcccctaact ccgcccatcc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

cgcccctaac tccgcccagt tccgcccatt ctccgcccca tggctgaCTA ATTTTTTTTA TTTATGCAGA GGCCGAGGCC GCCTCGGCCT CTGAGCTATT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCAGAAGTAG TGAGGAGGCT TTTTTGGAGG CCTAGGCTTT TGCAAAAAGC Ttgattcttc tgacacaaca gtctcgaact taagctgcag aagttggtcg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

tgaggcactg ggcagGTAAG TATCAAGGTT ACAAGACAGG TTTAAGGAGA CCAATAGAAA CTGGGCTTGT CGAGACAGAG AAGACTCTTG CGTTTCTGAT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AGGCACCTAT TGGTCTTACT GACATCCACT TTGCCTTTCT CTCCACAGgt gtccactccc agttcaatta cagctcttaa ggctagagta ctTAATACGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CTCACTATAG Gctagccacc atgacttcga aagtttatga tccagaacaa aggaaacgga tgataactgg tccgcagtgg tgggccagat gtaaacaaat 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

gaatgttctt gattcattta ttaattatta tgattcagaa aaacatgcag aaaatgctgt tattttttta catggtaacg cggcctcttc ttatttatgg 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

cgacatgttg tgccacatat tgagccagta gcgcggtgta ttataccaga ccttattggt atgggcaaat caggcaaatc tggtaatggt tcttataggt 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

tacttgatca ttacaaatat cttactgcat ggtttgaact tcttaattta ccaaagaaga tcatttttgt cggccatgat tggggtgctt gtttggcatt 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

tcattatagc tatgagcatc aagataagat caaagcaata gttcacgctg aaagtgtagt agatgtgatt gaatcatggg atgaatggcc tgatattgaa 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

gaagatattg cgttgatcaa atctgaagaa ggagaaaaaa tggttttgga gaataacttc ttcgtggaaa ccatgttgcc atcaaaaatc atgagaaagt 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tagaaccaga agaatttgca gcatatcttg aaccattcaa agagaaaggt gaagttcgtc gtccaacatt atcatggcct cgtgaaatcc cgttagtaaa 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

aggtggtaaa cctgacgttg tacaaattgt taggaattat aatgcttatc tacgtgcaag tgatgattta ccaaaaatgt ttattgaatc ggacccagga 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ttcttttcca atgctattgt tgaaggtgcc aagaagtttc ctaatactga atttgtcaaa gtaaaaggtc ttcatttttc gcaagaagat gcacctgatg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

aaatgggaaa atatatcaaa tcgttcgttg agcgagttct caaaaatgaa caataattct aggggctcga gcgcccctct ccctcccccc cccctaacgt 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

tactggccga agccgcttgg aataaggccg gtgtgcgttt gtctatatgt tattttccac catattgccg tcttttggca acgtgagggc ccggaaacct 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ggccctgtct tcttgacgag caatcctaga gcttcttgaa gacaaacaac gtctgtagcg accctttgca ggcagcggaa ccccccacct ggcgacaggt 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

gcctctgcgg ccaaaagcca cgtgtataag atacacctgc aaaggcggca caaccccagt gccacgttgt gagttggata gttgtggaaa gagtcaaatg 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gctctcctca agcgtattca acaaggggct gaaggatgcc cagaaggtac ccccttgtat gggatctgat ctggggcctc ggtgcacatg ctttacatgt 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gtttagtcga ggttaaaaaa acgtctaggc cccccgaacc acggggacgt ggttttcctt tgaaaaacac gaattcAATA ACAGAAAAAA ACCAATACAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAACGGGAAC AACGCCCTAG AAAAAACAAG AAGGTAATCC CTCAACAAAC CTAAAAGAAG ACAGCCACAA GAACAGAcca tggaagacgc caaaaacata 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

aagaaaggcc cggcgccatt ctatccgctg gaagatggaa ccgctggaga gcaactgcat aaggctatga agagatacgc cctggttcct ggaacaattg 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

cttttacaga tgcacatatc gaggtggaca tcacttacgc tgagtacttc gaaatgtccg ttcggttggc agaagctatg aaacgatatg ggctgaatac 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

aaatcacaga atcgtcgtat gcagtgaaaa ctctcttcaa ttctttatgc cggtgttggg cgcgttattt atcggagttg cagttgcgcc cgcgaacgac 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

atttataatg aacgtgaatt gctcaacagt atgggcattt cgcagcctac cgtggtgttc gtttccaaaa aggggttgca aaaaattttg aacgtgcaaa 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

aaaagctccc aatcatccaa aaaattatta tcatggattc taaaacggat taccagggat ttcagtcgat gtacacgttc gtcacatctc atctacctcc 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

cggttttaat gaatacgatt ttgtgccaga gtccttcgat agggacaaga caattgcact gatcatgaac tcctctggat ctactggtct gcctaaaggt 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

gtcgctctgc ctcatagaac tgcctgcgtg agattctcgc atgccagaga tcctattttt ggcaatcaaa tcattccgga tactgcgatt ttaagtgttg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ttccattcca tcacggtttt ggaatgttta ctacactcgg atatttgata tgtggatttc gagtcgtctt aatgtataga tttgaagaag agctgtttct 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

gaggagcctt caggattaca agattcaaag tgcgctgctg gtgccaaccc tattctcctt cttcgccaaa agcactctga ttgacaaata cgatttatct 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

aatttacacg aaattgcttc tggtggcgct cccctctcta aggaagtcgg ggaagcggtt gccaagaggt tccatctgcc aggtatcagg caaggatatg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ggctcactga gactacatca gctattctga ttacacccga gggggatgat aaaccgggcg cggtcggtaa agttgttcca ttttttgaag cgaaggttgt 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ggatctggat accgggaaaa cgctgggcgt taatcaaaga ggcgaactgt gtgtgagagg tcctatgatt atgtccggtt atgtaaacaa tccggaagcg 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

accaacgcct tgattgacaa ggatggatgg ctacattctg gagacatagc ttactgggac gaagacgaac acttcttcat cgttgaccgc ctgaagtctc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

tgattaagta caaaggctat caggtggctc ccgctgaatt ggaatccatc ttgctccaac accccaacat cttcgacgca ggtgtcgcag gtcttcccga 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

cgatgacgcc ggtgaacttc ccgccgccgt tgttgttttg gagcacggaa agacgatgac ggaaaaagag atcgtggatt acgtcgccag tcaagtaaca 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

accgcgaaaa agttgcgcgg aggagttgtg tttgtggacg aagtaccgaa aggtcttacc ggaaaactcg acgcaagaaa aatcagagag atcctcataa 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

aggccaagaa gggcggaaag atcgccgtgt aattctagag tcggggcggc cggccgcttc gagCAGACAT GATAAGATAC ATTGATGAGT TTGGACAAAC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CACAACTAGA ATGCAGTGAA AAAAATGCTT TATTTGTGAA ATTTGTGATG CTATTGCTTT ATTTGTAACC ATTATAAGCT GCAATAAACA AGTTAACAAC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AACAATTGCA TTCATTTTAT GTTTCAGGTT CAGGGGGAGG TGTGGGAGGT TTTTTAAAGC AAGTAAAACC TCTACAAATG TGGTAaaatc gataaggatc 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

tgaaCGATGG AGCGGAGAAT GGGCGGAACT GGGCGGAGTT AGGGGCGGGA TGGGCGGAGT TAGGGGCGGG ACTATGGTTG CTGACTAATT GAGATGCATG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CTTTGCATAC TTCTGCCTGC TGGGGAGCCT GGGGACTTTC CACACCTGGT TGCTGACTAA TTGAGATGCA TGCTTTGCAT ACTTCTGCCT GCTGGGGAGC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CTGGGGACTT TCCACACCCT AACTGACACA CATTCCACAG Cggatccgtc gaccgatgcc cttgagagcc ttcaacccag tcagctcctt ccggtgggcg 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

cggggcatga ctatcgtcgc cgcacttatg actgtcttct ttatcatgca actcgtagga caggtgccgg cagcgctctt ccgcttcctc gctcactgac 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

tcgctgcgct cggtcgttcg gctgcggcga gcggtatcag ctcactcaaa ggcggtaata cggttatcca cagaatcagg ggataacgca ggaaagaaca 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

tgtgagcaaa aggccagcaa aaggccagga accgtaaaaa ggccgcgttg ctggcgtttt tccataggct ccgcccccct gacgagcatc acaaaaatcg 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

acgctcaagt cagaggtggc gaaacccgac aggactataa agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca cgctgtaggt atctcagttc ggtgtaggtc gttcgctcca 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

agctgggctg tgtgcacgaa ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg gtaagacacg acttatcgcc 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

actggcagca gccactggta acaggattag cagagcgagg tatgtaggcg gtgctacaga gttcttgaag tggtggccta actacggcta cactagaaga 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

acagtatttg gtatctgcgc tctgctgaag ccagttacct tcggaaaaag agttggtagc tcttgatccg gcaaacaaac caccgctggt agcggtggtt 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

tttttgtttg caagcagcag attacgcgca gaaaaaaagg atctcaagaa gatcctttga tcttttctac ggggtctgac gctcagtgga acgaaaactc 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

acgttaaggg attttggtca tgagattatc aaaaaggatc ttcacctaga tccttttaaa ttaaaaatga agttttaaat caatctaaag tatatatgag 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

taaacttggt ctgacagtta ccaatgctta atcagtgagg cacctatctc agcgatctgt ctatttcgtt catccatagt tgcctgactc cccgtcgtgt 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

agataactac gatacgggag ggcttaccat ctggccccag tgctgcaatg ataccgcgag acccacgctc accggctcca gatttatcag caataaacca 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

gccagccgga agggccgagc gcagaagtgg tcctgcaact ttatccgcct ccatccagtc tattaattgt tgccgggaag ctagagtaag tagttcgcca 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

gttaatagtt tgcgcaacgt tgttgccatt gctacaggca tcgtggtgtc acgctcgtcg tttggtatgg cttcattcag ctccggttcc caacgatcaa 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ggcgagttac atgatccccc atgttgtgca aaaaagcggt tagctccttc ggtcctccga tcgttgtcag aagtaagttg gccgcagtgt tatcactcat 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ggttatggca gcactgcata attctcttac tgtcatgcca tccgtaagat gcttttctgt gactggtgag tactcaacca agtcattctg agaatagtgt 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

atgcggcgac cgagttgctc ttgcccggcg tcaatacggg ataataccgc gccacatagc agaactttaa aagtgctcat cattggaaaa cgttcttcgg 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

ggcgaaaact ctcaaggatc ttaccgctgt tgagatccag ttcgatgtaa cccactcgtg cacccaactg atcttcagca tcttttactt tcaccagcgt 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

ttctgggtga gcaaaaacag gaaggcaaaa tgccgcaaaa aagggaataa gggcgacacg gaaatgttga atactcatac tcttcctttt tcaatattat 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

tgaagcattt atcagggtta ttgtctcatg agcggataca tatttgaatg tatttagaaa aataaacaaa taggggttcc gcgcacattt ccccgaaaag 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

tgccacctga cgcgccctgt agcggcgcat taagcgcggc gggtgtggtg gttacgcgca gcgtgaccgc tacacttgcc agcgccctag cgcccgctcc 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

tttcgctttc ttcccttcct ttctcgccac gttcgccggc tttccccgtc aagctctaaa tcgggggctc cctttagggt tccgatttag tgctttacgg 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

cacctcgacc ccaaaaaact tgattagggt gatggttcac gtagtgggcc atcgccctga tagacggttt ttcgcccttt gacgttggag tccacgttct 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ttaatagtgg actcttgttc caaactggaa caacactcaa ccctatctcg gtctattctt ttgatttata agggattttg ccgatttcgg cctattggtt 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

aaaaaatgag ctgatttaac aaaaatttaa cgcgaatttt aacaaaatat taacgcttac aatttgccat tcgccattca ggctgcgcaa ctgttgggaa 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

gggcgatcgg tgcgggcctc ttcgctatta cgccagccca agctaccatg ataagtaagt aatattaagg tacgggaggt acttggagcg gccgcaataa 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

aatatcttta ttttcattac atctgtgtgt tggttttttg tgtgaatcga tagtactaac atacgctctc catcaaaaca aaacgaaaca aaacaaacta 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

gcaaaatagg ctgtccccag tgcaagtgca ggtgccagaa catttctcta tcgata
^7201      ^7211      ^7221      ^7231      ^7241      ^7251

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):

192-1127

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):

1751-3403

Remarks:

In preparing for submission of this IRESite record, it was found that there are 3 PCR errors (A->G @ 1481,
C->T @ 1649, del @ 1784) and a nucleotide difference between the PCR template and the GenBank database (T->G @
1592).




Overview of the mutants shown in 7B:

mL1-ORF2-138-1-mut1
2804-2941

This tested sequence is identical to "mL1-ORF2-138-1" except for 3 single point mutations [2820(G->C),
2836(A->C), 2838(G->C)] introduced to disrupt a predicted stem-loop.


mL1-ORF2-138-1-mut2
2804-2941

This tested sequence is identical to "mL1-ORF2-138-1" except for 6 single point mutations [2812(C-G),
2815(T-G), 2820(G-C), 2833(C-G), 2836(A-C), 2838(G-C)] introduced to disrupt and then restore a predicted
stem-loop.


mL1-ORF2-138-1-mut32804-2941

This tested sequence is identical to "mL1-ORF2-138-1" except for 5 single point mutations [2810(A-T),
2820(G-C), 2836(A-C), 2838(G-C), 2840(T-A)] introduced to disrupt a predicted stem-loop and avoid introducing
a small ORF.


mL1-ORF2-138-1-mut4
2804-2941

This tested sequence is identical to "mL1-ORF2-138-1" except for 8 single point mutations [2810(A-T),
2812(C-G), 2815(T-G), 2820(G-C), 2833(C-G), 2836(A-C), 2838(G-C), 2840(T-A)] introduced to disrupt/restore a
predicted stem-loop and avoid introducing a small ORF.

Citations:

Li P. W., Li J., Timmerman S. L., Krushel L. A., Martin S. L. (2006) The dicistronic RNA from the mouse LINE-1 retrotransposon contains an internal ribosome entry site upstream of each ORF: implications for retrotransposition. Nucleic. Acids Res. 34(3):853-864

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `LINE1-ORF1-101-1`	The functional status of IRES: `functional`

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

1648-1758

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `521`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `631`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-103`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `7`

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

AATAACAGAA AAAAACCAAT ACAAGAACGG GAACAACGCC CTAGAAAAAA CAAGAAGGTA ATCCCTCAAC AAACCTAAAA GAAGACAGCC ACAAGAACAG 
^1648      ^1658      ^1668      ^1678      ^1688      ^1698      ^1708      ^1718      ^1728      ^1738      

Accatggaag a
^1748      ^1758

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 544

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:

Mus musculus ltk-

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

59.000

Name of IRES used as the positive control:

CrPV_IGR_IRES

Name of the plasmid used as the positive control. `pR-deltaEMCV-CrPV-F`	Name of the plasmid used as the negative control. `pR-deltaEMCV-F`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `9.000`

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:

IRES activity 8.5x above empty pRF vector (Fig. 6C).

Citations:

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