IRESite_Id:496 characteristics of LINE1-ORF1-400-1 IRES studied in pR-deltaEMCV-L1_ORF1

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `496`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-07-15 14:46:43`

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:
3UTR_possibly_incomplete

The mRNA/+RNA description:

Putative spliced in vivo transcript of pR-deltaEMCV-F from SV40 promoter with -400 to -1 insert of putative
LINE-1 IRES with cryptic promoter (probably within -400 to -200 region).

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 cgaattcATA ATAATCAGAA CATCAAATGC ACTAAATAAA GATAGAATAC TAAAAGCAGT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AAGGGAAAAA GGTCAAGTAA CATATAAAGG CAAGCCTATC AGAATTACAC CAGATTTTTC ACCAGAGACT ATGAAAGCCA GAAGAGCCTG GACAGATGTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ATACAGACAC TAAGAGAACA CAAACTGCAG CCCAGGCTAC TATACCCAGC CAAACTCTCA ATTATCATAG AGGGAGAAAC CAAAGTATTC CACGACAAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CCAAATTCAC GCATTATCTC TCCACGAATC CAGCCCTTCA AAGGATAATA ACAGAAAAAA ACCAATACAA GAACGGGAAC AACGCCCTAG AAAAAACAAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAGGTAATCC CTCAACAAAC CTAAAAGAAG ACAGCCACAA GAACAGAcca tggaagacgc caaaaacata aagaaaggcc cggcgccatt ctatccgctg 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

gaagatggaa ccgctggaga gcaactgcat aaggctatga agagatacgc cctggttcct ggaacaattg cttttacaga tgcacatatc gaggtggaca 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

tcacttacgc tgagtacttc gaaatgtccg ttcggttggc agaagctatg aaacgatatg ggctgaatac aaatcacaga atcgtcgtat gcagtgaaaa 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ctctcttcaa ttctttatgc cggtgttggg cgcgttattt atcggagttg cagttgcgcc cgcgaacgac atttataatg aacgtgaatt gctcaacagt 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

atgggcattt cgcagcctac cgtggtgttc gtttccaaaa aggggttgca aaaaattttg aacgtgcaaa aaaagctccc aatcatccaa aaaattatta 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

tcatggattc taaaacggat taccagggat ttcagtcgat gtacacgttc gtcacatctc atctacctcc cggttttaat gaatacgatt ttgtgccaga 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

gtccttcgat agggacaaga caattgcact gatcatgaac tcctctggat ctactggtct gcctaaaggt gtcgctctgc ctcatagaac tgcctgcgtg 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

agattctcgc atgccagaga tcctattttt ggcaatcaaa tcattccgga tactgcgatt ttaagtgttg ttccattcca tcacggtttt ggaatgttta 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ctacactcgg atatttgata tgtggatttc gagtcgtctt aatgtataga tttgaagaag agctgtttct gaggagcctt caggattaca agattcaaag 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tgcgctgctg gtgccaaccc tattctcctt cttcgccaaa agcactctga ttgacaaata cgatttatct aatttacacg aaattgcttc tggtggcgct 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

cccctctcta aggaagtcgg ggaagcggtt gccaagaggt tccatctgcc aggtatcagg caaggatatg ggctcactga gactacatca gctattctga 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ttacacccga gggggatgat aaaccgggcg cggtcggtaa agttgttcca ttttttgaag cgaaggttgt ggatctggat accgggaaaa cgctgggcgt 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

taatcaaaga ggcgaactgt gtgtgagagg tcctatgatt atgtccggtt atgtaaacaa tccggaagcg accaacgcct tgattgacaa ggatggatgg 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ctacattctg gagacatagc ttactgggac gaagacgaac acttcttcat cgttgaccgc ctgaagtctc tgattaagta caaaggctat caggtggctc 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ccgctgaatt ggaatccatc ttgctccaac accccaacat cttcgacgca ggtgtcgcag gtcttcccga cgatgacgcc ggtgaacttc ccgccgccgt 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

tgttgttttg gagcacggaa agacgatgac ggaaaaagag atcgtggatt acgtcgccag tcaagtaaca accgcgaaaa agttgcgcgg aggagttgtg 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

tttgtggacg aagtaccgaa aggtcttacc ggaaaactcg acgcaagaaa aatcagagag atcctcataa aggccaagaa gggcggaaag atcgccgtgt 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

aattctagag tcggggcggc cggccgcttc gagCAGACAT GATAAGATAC ATTGATGAGT TTGGACAAAC CACAACTAGA ATGCAGTGAA AAAAATGCTT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TATTTGTGAA ATTTGTGATG CTATTGCTTT ATTTGTAACC ATTATAAGCT GCAATAAACA AGTTAACAAC AACAATTGCA TTCATTTTAT GTTTCAGGTT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CAGGGGGAGG TGTGGGAGGT TTTTTAAAGC AAGTAAAACC TCTACAAATG TGGTA
^3901      ^3911      ^3921      ^3931      ^3941      ^3951

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_3UTR

The name of the plasmid:
pR-deltaEMCV-L1_ORF1_-400-1-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:

yes

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:
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 gaattcATAA TAATCAGAAC ATCAAATGCA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTAAATAAAG ATAGAATACT AAAAGCAGTA AGGGAAAAAG GTCAAGTAAC ATATAAAGGC AAGCCTATCA GAATTACACC AGATTTTTCA CCAGAGACTA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TGAAAGCCAG AAGAGCCTGG ACAGATGTTA TACAGACACT AAGAGAACAC AAACTGCAGC CCAGGCTACT ATACCCAGCC AAACTCTCAA TTATCATAGA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GGGAGAAACC AAAGTATTCC ACGACAAAAC CAAATTCACG CATTATCTCT CCACGAATCC AGCCCTTCAA AGGATAATAA CAGAAAAAAA CCAATACAAG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AACGGGAACA ACGCCCTAGA AAAAACAAGA AGGTAATCCC TCAACAAACC TAAAAGAAGA CAGCCACAAG AACAGAccat ggaagacgcc aaaaacataa 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

agaaaggccc ggcgccattc tatccgctgg aagatggaac cgctggagag caactgcata aggctatgaa gagatacgcc ctggttcctg gaacaattgc 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ttttacagat gcacatatcg aggtggacat cacttacgct gagtacttcg aaatgtccgt tcggttggca gaagctatga aacgatatgg gctgaataca 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

aatcacagaa tcgtcgtatg cagtgaaaac tctcttcaat tctttatgcc ggtgttgggc gcgttattta tcggagttgc agttgcgccc gcgaacgaca 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tttataatga acgtgaattg ctcaacagta tgggcatttc gcagcctacc gtggtgttcg tttccaaaaa ggggttgcaa aaaattttga acgtgcaaaa 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

aaagctccca atcatccaaa aaattattat catggattct aaaacggatt accagggatt tcagtcgatg tacacgttcg tcacatctca tctacctccc 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ggttttaatg aatacgattt tgtgccagag tccttcgata gggacaagac aattgcactg atcatgaact cctctggatc tactggtctg cctaaaggtg 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

tcgctctgcc tcatagaact gcctgcgtga gattctcgca tgccagagat cctatttttg gcaatcaaat cattccggat actgcgattt taagtgttgt 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

tccattccat cacggttttg gaatgtttac tacactcgga tatttgatat gtggatttcg agtcgtctta atgtatagat ttgaagaaga gctgtttctg 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

aggagccttc aggattacaa gattcaaagt gcgctgctgg tgccaaccct attctccttc ttcgccaaaa gcactctgat tgacaaatac gatttatcta 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

atttacacga aattgcttct ggtggcgctc ccctctctaa ggaagtcggg gaagcggttg ccaagaggtt ccatctgcca ggtatcaggc aaggatatgg 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

gctcactgag actacatcag ctattctgat tacacccgag ggggatgata aaccgggcgc ggtcggtaaa gttgttccat tttttgaagc gaaggttgtg 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

gatctggata ccgggaaaac gctgggcgtt aatcaaagag gcgaactgtg tgtgagaggt cctatgatta tgtccggtta tgtaaacaat ccggaagcga 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ccaacgcctt gattgacaag gatggatggc tacattctgg agacatagct tactgggacg aagacgaaca cttcttcatc gttgaccgcc tgaagtctct 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

gattaagtac aaaggctatc aggtggctcc cgctgaattg gaatccatct tgctccaaca ccccaacatc ttcgacgcag gtgtcgcagg tcttcccgac 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

gatgacgccg gtgaacttcc cgccgccgtt gttgttttgg agcacggaaa gacgatgacg gaaaaagaga tcgtggatta cgtcgccagt caagtaacaa 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ccgcgaaaaa gttgcgcgga ggagttgtgt ttgtggacga agtaccgaaa ggtcttaccg gaaaactcga cgcaagaaaa atcagagaga tcctcataaa 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ggccaagaag ggcggaaaga tcgccgtgta attctagagt cggggcggcc ggccgcttcg agCAGACATG ATAAGATACA TTGATGAGTT TGGACAAACC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ACAACTAGAA TGCAGTGAAA AAAATGCTTT ATTTGTGAAA TTTGTGATGC TATTGCTTTA TTTGTAACCA TTATAAGCTG CAATAAACAA GTTAACAACA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ACAATTGCAT TCATTTTATG TTTCAGGTTC AGGGGGAGGT GTGGGAGGTT TTTTAAAGCA AGTAAAACCT CTACAAATGT GGTAaaatcg ataaggatct 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

gaaCGATGGA GCGGAGAATG GGCGGAACTG GGCGGAGTTA GGGGCGGGAT GGGCGGAGTT AGGGGCGGGA CTATGGTTGC TGACTAATTG AGATGCATGC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TTTGCATACT TCTGCCTGCT GGGGAGCCTG GGGACTTTCC ACACCTGGTT GCTGACTAAT TGAGATGCAT GCTTTGCATA CTTCTGCCTG CTGGGGAGCC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TGGGGACTTT CCACACCCTA ACTGACACAC ATTCCACAGC ggatccgtcg accgatgccc ttgagagcct tcaacccagt cagctccttc cggtgggcgc 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ggggcatgac tatcgtcgcc gcacttatga ctgtcttctt tatcatgcaa ctcgtaggac aggtgccggc agcgctcttc cgcttcctcg ctcactgact 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

cgctgcgctc ggtcgttcgg ctgcggcgag cggtatcagc tcactcaaag gcggtaatac ggttatccac agaatcaggg gataacgcag gaaagaacat 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

gtgagcaaaa ggccagcaaa aggccaggaa ccgtaaaaag gccgcgttgc tggcgttttt ccataggctc cgcccccctg acgagcatca caaaaatcga 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

cgctcaagtc agaggtggcg aaacccgaca ggactataaa gataccaggc gtttccccct ggaagctccc tcgtgcgctc tcctgttccg accctgccgc 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ttaccggata cctgtccgcc tttctccctt cgggaagcgt ggcgctttct catagctcac gctgtaggta tctcagttcg gtgtaggtcg ttcgctccaa 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

gctgggctgt gtgcacgaac cccccgttca gcccgaccgc tgcgccttat ccggtaacta tcgtcttgag tccaacccgg taagacacga cttatcgcca 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ctggcagcag ccactggtaa caggattagc agagcgaggt atgtaggcgg tgctacagag ttcttgaagt ggtggcctaa ctacggctac actagaagaa 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

cagtatttgg tatctgcgct ctgctgaagc cagttacctt cggaaaaaga gttggtagct cttgatccgg caaacaaacc accgctggta gcggtggttt 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ttttgtttgc aagcagcaga ttacgcgcag aaaaaaagga tctcaagaag atcctttgat cttttctacg gggtctgacg ctcagtggaa cgaaaactca 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

cgttaaggga ttttggtcat gagattatca aaaaggatct tcacctagat ccttttaaat taaaaatgaa gttttaaatc aatctaaagt atatatgagt 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

aaacttggtc tgacagttac caatgcttaa tcagtgaggc acctatctca gcgatctgtc tatttcgttc atccatagtt gcctgactcc ccgtcgtgta 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

gataactacg atacgggagg gcttaccatc tggccccagt gctgcaatga taccgcgaga cccacgctca ccggctccag atttatcagc aataaaccag 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ccagccggaa gggccgagcg cagaagtggt cctgcaactt tatccgcctc catccagtct attaattgtt gccgggaagc tagagtaagt agttcgccag 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ttaatagttt gcgcaacgtt gttgccattg ctacaggcat cgtggtgtca cgctcgtcgt ttggtatggc ttcattcagc tccggttccc aacgatcaag 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

gcgagttaca tgatccccca tgttgtgcaa aaaagcggtt agctccttcg gtcctccgat cgttgtcaga agtaagttgg ccgcagtgtt atcactcatg 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

gttatggcag cactgcataa ttctcttact gtcatgccat ccgtaagatg cttttctgtg actggtgagt actcaaccaa gtcattctga gaatagtgta 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

tgcggcgacc gagttgctct tgcccggcgt caatacggga taataccgcg ccacatagca gaactttaaa agtgctcatc attggaaaac gttcttcggg 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

gcgaaaactc tcaaggatct taccgctgtt gagatccagt tcgatgtaac ccactcgtgc acccaactga tcttcagcat cttttacttt caccagcgtt 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

tctgggtgag caaaaacagg aaggcaaaat gccgcaaaaa agggaataag ggcgacacgg aaatgttgaa tactcatact cttccttttt caatattatt 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

gaagcattta tcagggttat tgtctcatga gcggatacat atttgaatgt atttagaaaa ataaacaaat aggggttccg cgcacatttc cccgaaaagt 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

gccacctgac gcgccctgta gcggcgcatt aagcgcggcg ggtgtggtgg ttacgcgcag cgtgaccgct acacttgcca gcgccctagc gcccgctcct 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

ttcgctttct tcccttcctt tctcgccacg ttcgccggct ttccccgtca agctctaaat cgggggctcc ctttagggtt ccgatttagt gctttacggc 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

acctcgaccc caaaaaactt gattagggtg atggttcacg tagtgggcca tcgccctgat agacggtttt tcgccctttg acgttggagt ccacgttctt 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

taatagtgga ctcttgttcc aaactggaac aacactcaac cctatctcgg tctattcttt tgatttataa gggattttgc cgatttcggc ctattggtta 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

aaaaatgagc tgatttaaca aaaatttaac gcgaatttta acaaaatatt aacgcttaca atttgccatt cgccattcag gctgcgcaac tgttgggaag 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

ggcgatcggt gcgggcctct tcgctattac gccagcccaa gctaccatga taagtaagta atattaaggt acgggaggta cttggagcgg ccgcaataaa 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

atatctttat tttcattaca tctgtgtgtt ggttttttgt gtgaatcgat agtactaaca tacgctctcc atcaaaacaa aacgaaacaa aacaaactag 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

caaaataggc tgtccccagt gcaagtgcag gtgccagaac atttctctat cgata
^7501      ^7511      ^7521      ^7531      ^7541      ^7551

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):

2050-3702

Remarks:

The cryptic promoter is located somewhere in the region -400 to -200.

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-ORF1-400-1`	The functional status of IRES: `functional`

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

1648-2047

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: `920`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-402`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-3`

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

ATAATAATCA GAACATCAAA TGCACTAAAT AAAGATAGAA TACTAAAAGC AGTAAGGGAA AAAGGTCAAG TAACATATAA AGGCAAGCCT ATCAGAATTA 
^1648      ^1658      ^1668      ^1678      ^1688      ^1698      ^1708      ^1718      ^1728      ^1738      

CACCAGATTT TTCACCAGAG ACTATGAAAG CCAGAAGAGC CTGGACAGAT GTTATACAGA CACTAAGAGA ACACAAACTG CAGCCCAGGC TACTATACCC 
^1748      ^1758      ^1768      ^1778      ^1788      ^1798      ^1808      ^1818      ^1828      ^1838      

AGCCAAACTC TCAATTATCA TAGAGGGAGA AACCAAAGTA TTCCACGACA AAACCAAATT CACGCATTAT CTCTCCACGA ATCCAGCCCT TCAAAGGATA 
^1848      ^1858      ^1868      ^1878      ^1888      ^1898      ^1908      ^1918      ^1928      ^1938      

ATAACAGAAA AAAACCAATA CAAGAACGGG AACAACGCCC TAGAAAAAAC AAGAAGGTAA TCCCTCAACA AACCTAAAAG AAGACAGCCA CAAGAACAGA
^1948      ^1958      ^1968      ^1978      ^1988      ^1998      ^2008      ^2018      ^2028      ^2038

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 546

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):
47

The relative translation efficiency in % of this IRES:

143.000

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:

Data from Figure 6A are affected by the cryptic promoter.

Citations:

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