IRESite_Id:586 characteristics of LamB1_-335_-1 IRES studied in pR-LamB1-F plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `586`	Version: `5`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-04-14 15:10:25`
Reviewed by: Martin Mokrejš	Last change: `2009-04-30 11:36:54`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
our_best_guess

The mRNA/+RNA description:

In vivo spliced transcript derived from CMV IE promoter containing Renilla and firefly luciferases separated
by putative LamB1 IRES.

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

TCAGATCACT AGAAGCTTTA TTGCGGTAGT TTATCACAGT TAAATTGCTA ACGCAGTCAG TGCTTCTGAC ACAACAGTCT CGAACTTAAG CTGCAGTGAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TCTCTTAAGG TAGCCTTGCA GAAGTTGGTC GTGAGGCACT GGGCAGGTGT CCACTCCCAG TTCAATTACA GCTCTTAAGG CTAGAGTACT TAATACGACT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CACTATAGGC TAGCCACCAT GGCTTCGAAA GTTTATGATC CAGAACAAAG GAAACGGATG ATAACTGGTC CGCAGTGGTG GGCCAGATGT AAACAAATGA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATGTTCTTGA TTCATTTATT AATTATTATG ATTCAGAAAA ACATGCAGAA AATGCTGTTA TTTTTTTACA TGGTAACGCG GCCTCTTCTT ATTTATGGCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACATGTTGTG CCACATATTG AGCCAGTAGC GCGGTGTATT ATACCAGACC TTATTGGTAT GGGCAAATCA GGCAAATCTG GTAATGGTTC TTATAGGTTA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CTTGATCATT ACAAATATCT TACTGCATGG TTTGAACTTC TTAATTTACC AAAGAAGATC ATTTTTGTCG GCCATGATTG GGGTGCTTGT TTGGCATTTC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATTATAGCTA TGAGCATCAA GATAAGATCA AAGCAATAGT TCACGCTGAA AGTGTAGTAG ATGTGATTGA ATCATGGGAT GAATGGCCTG ATATTGAAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGATATTGCG TTGATCAAAT CTGAAGAAGG AGAAAAAATG GTTTTGGAGA ATAACTTCTT CGTGGAAACC ATGTTGCCAT CAAAAATCAT GAGAAAGTTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GAACCAGAAG AATTTGCAGC ATATCTTGAA CCATTCAAAG AGAAAGGTGA AGTTCGTCGT CCAACATTAT CATGGCCTCG TGAAATCCCG TTAGTAAAAG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GTGGTAAACC TGACGTTGTA CAAATTGTTA GGAATTATAA TGCTTATCTA CGTGCAAGTG ATGATTTACC AAAAATGTTT ATTGAATCGG ACCCAGGATT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CTTTTCCAAT GCTATTGTTG AAGGTGCCAA GAAGTTTCCT AATACTGAAT TTGTCAAAGT AAAAGGTCTT CATTTTTCGC AAGAAGATGC ACCTGATGAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATGGGAAAAT ATATCAAATC GTTCGTTGAG CGAGTTCTCA AAAATGAACA ATAATTCTAG AGCGGCCAAT TCACGCGCAT GGCGGCCGCG GGAATTCGAT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TCTAGCTAGC GGGACCTGGA AGCGCCCCAG CCCCGCAGCG ATCGCAGATT CGGCTTTCAA ACAAAAGAGG CGCCCCGGGG GGTGGGACCG GGACCTCACC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGGTCCTCGC AGAGTTGCGG CCGCCCGCCC CTTCAGCCCC GGCTCTCCGT ATGCGCATGA GCAGAGGCGC CTCCCTCTGT TCCTCCCAAG GCTAAACTTT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTAATTCCCT TCTTTGGGCT CGGGGGCTCC CGGAGCAGGG CGAGAGCTCG CGTCGCCGGA AAGGAAGACG GGAAGAAAGG GCAGGCGGCT CGGCGGGCGT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CTTCTCCACT CCTCTGCCGC GTCCCCGTGG CTGCAGGGAG CCGGCCTCGA GATCTGCGAT CTAAGTAAGC TTGGCATTCC GGTACTGTTG GTAAAGCCAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CATGGAAGAC GCCAAAAACA TAAAGAAAGG CCCGGCGCCA TTCTATCCGC TGGAAGATGG AACCGCTGGA GAGCAACTGC ATAAGGCTAT GAAGAGATAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCCCTGGTTC CTGGAACAAT TGCTTTTACA GATGCACATA TCGAGGTGGA CATCACTTAC GCTGAGTACT TCGAAATGTC CGTTCGGTTG GCAGAAGCTA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGAAACGATA TGGGCTGAAT ACAAATCACA GAATCGTCGT ATGCAGTGAA AACTCTCTTC AATTCTTTAT GCCGGTGTTG GGCGCGTTAT TTATCGGAGT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGCAGTTGCG CCCGCGAACG ACATTTATAA TGAACGTGAA TTGCTCAACA GTATGGGCAT TTCGCAGCCT ACCGTGGTGT TCGTTTCCAA AAAGGGGTTG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CAAAAAATTT TGAACGTGCA AAAAAAGCTC CCAATCATCC AAAAAATTAT TATCATGGAT TCTAAAACGG ATTACCAGGG ATTTCAGTCG ATGTACACGT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TCGTCACATC TCATCTACCT CCCGGTTTTA ATGAATACGA TTTTGTGCCA GAGTCCTTCG ATAGGGACAA GACAATTGCA CTGATCATGA ACTCCTCTGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATCTACTGGT CTGCCTAAAG GTGTCGCTCT GCCTCATAGA ACTGCCTGCG TGAGATTCTC GCATGCCAGA GATCCTATTT TTGGCAATCA AATCATTCCG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GATACTGCGA TTTTAAGTGT TGTTCCATTC CATCACGGTT TTGGAATGTT TACTACACTC GGATATTTGA TATGTGGATT TCGAGTCGTC TTAATGTATA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GATTTGAAGA AGAGCTGTTT CTGAGGAGCC TTCAGGATTA CAAGATTCAA AGTGCGCTGC TGGTGCCAAC CCTATTCTCC TTCTTCGCCA AAAGCACTCT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GATTGACAAA TACGATTTAT CTAATTTACA CGAAATTGCT TCTGGTGGCG CTCCCCTCTC TAAGGAAGTC GGGGAAGCGG TTGCCAAGAG GTTCCATCTG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CCAGGTATCA GGCAAGGATA TGGGCTCACT GAGACTACAT CAGCTATTCT GATTACACCC GAGGGGGATG ATAAACCGGG CGCGGTCGGT AAAGTTGTTC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CATTTTTTGA AGCGAAGGTT GTGGATCTGG ATACCGGGAA AACGCTGGGC GTTAATCAAA GAGGCGAACT GTGTGTGAGA GGTCCTATGA TTATGTCCGG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TTATGTAAAC AATCCGGAAG CGACCAACGC CTTGATTGAC AAGGATGGAT GGCTACATTC TGGAGACATA GCTTACTGGG ACGAAGACGA ACACTTCTTC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATCGTTGACC GCCTGAAGTC TCTGATTAAG TACAAAGGCT ATCAGGTGGC TCCCGCTGAA TTGGAATCCA TCTTGCTCCA ACACCCCAAC ATCTTCGACG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CAGGTGTCGC AGGTCTTCCC GACGATGACG CCGGTGAACT TCCCGCCGCC GTTGTTGTTT TGGAGCACGG AAAGACGATG ACGGAAAAAG AGATCGTGGA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TTACGTCGCC AGTCAAGTAA CAACCGCGAA AAAGTTGCGC GGAGGAGTTG TGTTTGTGGA CGAAGTACCG AAAGGTCTTA CCGGAAAACT CGACGCAAGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AAAATCAGAG AGATCCTCAT AAAGGCCAAG AAGGGCGGAA AGATCGCCGT GTAATTCTAG AGTCGACCCG GGCGGCCGGC CGCTTCCCTT TAGTGAGGGT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TAATGCTTCG AGCAGACATG ATAAGATACA TTGATGAGTT TGGACAAACC ACAACTAGAA TGCAGTGAAA AAAATGCTTT ATTTGTGAAA TTTGTGATGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TATTGCTTTA TTTGTAACCA TTATAAGCTG CAATAAACAA GTTAACAACA ACAATTGCAT TCATTTTATG TTTCAGGTTC AGGGGGAGAT GTGGGAGGTT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TTTTAAAGCA AGTAAAACCT CTACAAATGT GGTAAA
^3501      ^3511      ^3521      ^3531

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-LamB1-F The name of the promoter used to express this mRNA:
CMV_IE

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

no (not convincing)

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

no (not convincing)

A promoter reported in cDNA corresponding to IRES sequence:

unclear

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:
unclear_result

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

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:
unclear_result

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 MIM-R

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
LamB1

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens HeLa (ATCC CCL-2)

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

TCAATATTGG CCATTAGCCA TATTATTCAT TGGTTATATA GCATAAATCA ATATTGGCTA TTGGCCATTG CATACGTTGT ATCTATATCA TAATATGTAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATTTATATTG GCTCATGTCC AATATGACCG CCATGTTGGC ATTGATTATT GACTAGTTAT TAATAGTAAT CAATTACGGG GTCATTAGTT CATAGCCCAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATATGGAGTT CCGCGTTACA TAACTTACGG TAAATGGCCC GCCTGGCTGA CCGCCCAACG ACCCCCGCCC ATTGACGTCA ATAATGACGT ATGTTCCCAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGTAACGCCA ATAGGGACTT TCCATTGACG TCAATGGGTG GAGTATTTAC GGTAAACTGC CCACTTGGCA GTACATCAAG TGTATCATAT GCCAAGTCCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCCCCTATTG ACGTCAATGA CGGTAAATGG CCCGCCTGGC ATTATGCCCA GTACATGACC TTACGGGACT TTCCTACTTG GCAGTACATC TACGTATTAG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCATCGCTAT TACCATGGTG ATGCGGTTTT GGCAGTACAC CAATGGGCGT GGATAGCGGT TTGACTCACG GGGATTTCCA AGTCTCCACC CCATTGACGT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CAATGGGAGT TTGTTTTGGC ACCAAAATCA ACGGGACTTT CCAAAATGTC GTAACAACTG CGATCGCCCG CCCCGTTGAC GCAAATGGGC GGTAGGCGTG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TACGGTGGGA GGTCTATATA AGCAGAGCTC GTTTAGTGAA CCGTCAGATC ACTAGAAGCT TTATTGCGGT AGTTTATCAC AGTTAAATTG CTAACGCAGT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CAGTGCTTCT GACACAACAG TCTCGAACTT AAGCTGCAGT GACTCTCTTA AGGTAGCCTT GCAGAAGTTG GTCGTGAGGC ACTGGGCAGG TAAGTATCAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GGTTACAAGA CAGGTTTAAG GAGACCAATA GAAACTGGGC TTGTCGAGAC AGAGAAGACT CTTGCGTTTC TGATAGGCAC CTATTGGTCT TACTGACATC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CACTTTGCCT TTCTCTCCAC AGGTGTCCAC TCCCAGTTCA ATTACAGCTC TTAAGGCTAG AGTACTTAAT ACGACTCACT ATAGGCTAGC CACCATGGCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCGAAAGTTT ATGATCCAGA ACAAAGGAAA CGGATGATAA CTGGTCCGCA GTGGTGGGCC AGATGTAAAC AAATGAATGT TCTTGATTCA TTTATTAATT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ATTATGATTC AGAAAAACAT GCAGAAAATG CTGTTATTTT TTTACATGGT AACGCGGCCT CTTCTTATTT ATGGCGACAT GTTGTGCCAC ATATTGAGCC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AGTAGCGCGG TGTATTATAC CAGACCTTAT TGGTATGGGC AAATCAGGCA AATCTGGTAA TGGTTCTTAT AGGTTACTTG ATCATTACAA ATATCTTACT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GCATGGTTTG AACTTCTTAA TTTACCAAAG AAGATCATTT TTGTCGGCCA TGATTGGGGT GCTTGTTTGG CATTTCATTA TAGCTATGAG CATCAAGATA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGATCAAAGC AATAGTTCAC GCTGAAAGTG TAGTAGATGT GATTGAATCA TGGGATGAAT GGCCTGATAT TGAAGAAGAT ATTGCGTTGA TCAAATCTGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AGAAGGAGAA AAAATGGTTT TGGAGAATAA CTTCTTCGTG GAAACCATGT TGCCATCAAA AATCATGAGA AAGTTAGAAC CAGAAGAATT TGCAGCATAT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CTTGAACCAT TCAAAGAGAA AGGTGAAGTT CGTCGTCCAA CATTATCATG GCCTCGTGAA ATCCCGTTAG TAAAAGGTGG TAAACCTGAC GTTGTACAAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TTGTTAGGAA TTATAATGCT TATCTACGTG CAAGTGATGA TTTACCAAAA ATGTTTATTG AATCGGACCC AGGATTCTTT TCCAATGCTA TTGTTGAAGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGCCAAGAAG TTTCCTAATA CTGAATTTGT CAAAGTAAAA GGTCTTCATT TTTCGCAAGA AGATGCACCT GATGAAATGG GAAAATATAT CAAATCGTTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GTTGAGCGAG TTCTCAAAAA TGAACAATAA TTCTAGAGCG GCCAATTCAC GCGCATGGCG GCCGCGGGAA TTCGATTCTA GCTAGCGGGA CCTGGAAGCG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCCCAGCCCC GCAGCGATCG CAGATTCGGC TTTCAAACAA AAGAGGCGCC CCGGGGGGTG GGACCGGGAC CTCACCCGGT CCTCGCAGAG TTGCGGCCGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCGCCCCTTC AGCCCCGGCT CTCCGTATGC GCATGAGCAG AGGCGCCTCC CTCTGTTCCT CCCAAGGCTA AACTTTCTAA TTCCCTTCTT TGGGCTCGGG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GGCTCCCGGA GCAGGGCGAG AGCTCGCGTC GCCGGAAAGG AAGACGGGAA GAAAGGGCAG GCGGCTCGGC GGGCGTCTTC TCCACTCCTC TGCCGCGTCC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCGTGGCTGC AGGGAGCCGG CCTCGAGATC TGCGATCTAA GTAAGCTTGG CATTCCGGTA CTGTTGGTAA AGCCACCATG GAAGACGCCA AAAACATAAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GAAAGGCCCG GCGCCATTCT ATCCGCTGGA AGATGGAACC GCTGGAGAGC AACTGCATAA GGCTATGAAG AGATACGCCC TGGTTCCTGG AACAATTGCT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTTACAGATG CACATATCGA GGTGGACATC ACTTACGCTG AGTACTTCGA AATGTCCGTT CGGTTGGCAG AAGCTATGAA ACGATATGGG CTGAATACAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ATCACAGAAT CGTCGTATGC AGTGAAAACT CTCTTCAATT CTTTATGCCG GTGTTGGGCG CGTTATTTAT CGGAGTTGCA GTTGCGCCCG CGAACGACAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TTATAATGAA CGTGAATTGC TCAACAGTAT GGGCATTTCG CAGCCTACCG TGGTGTTCGT TTCCAAAAAG GGGTTGCAAA AAATTTTGAA CGTGCAAAAA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AAGCTCCCAA TCATCCAAAA AATTATTATC ATGGATTCTA AAACGGATTA CCAGGGATTT CAGTCGATGT ACACGTTCGT CACATCTCAT CTACCTCCCG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GTTTTAATGA ATACGATTTT GTGCCAGAGT CCTTCGATAG GGACAAGACA ATTGCACTGA TCATGAACTC CTCTGGATCT ACTGGTCTGC CTAAAGGTGT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CGCTCTGCCT CATAGAACTG CCTGCGTGAG ATTCTCGCAT GCCAGAGATC CTATTTTTGG CAATCAAATC ATTCCGGATA CTGCGATTTT AAGTGTTGTT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CCATTCCATC ACGGTTTTGG AATGTTTACT ACACTCGGAT ATTTGATATG TGGATTTCGA GTCGTCTTAA TGTATAGATT TGAAGAAGAG CTGTTTCTGA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GGAGCCTTCA GGATTACAAG ATTCAAAGTG CGCTGCTGGT GCCAACCCTA TTCTCCTTCT TCGCCAAAAG CACTCTGATT GACAAATACG ATTTATCTAA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TTTACACGAA ATTGCTTCTG GTGGCGCTCC CCTCTCTAAG GAAGTCGGGG AAGCGGTTGC CAAGAGGTTC CATCTGCCAG GTATCAGGCA AGGATATGGG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CTCACTGAGA CTACATCAGC TATTCTGATT ACACCCGAGG GGGATGATAA ACCGGGCGCG GTCGGTAAAG TTGTTCCATT TTTTGAAGCG AAGGTTGTGG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ATCTGGATAC CGGGAAAACG CTGGGCGTTA ATCAAAGAGG CGAACTGTGT GTGAGAGGTC CTATGATTAT GTCCGGTTAT GTAAACAATC CGGAAGCGAC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CAACGCCTTG ATTGACAAGG ATGGATGGCT ACATTCTGGA GACATAGCTT ACTGGGACGA AGACGAACAC TTCTTCATCG TTGACCGCCT GAAGTCTCTG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ATTAAGTACA AAGGCTATCA GGTGGCTCCC GCTGAATTGG AATCCATCTT GCTCCAACAC CCCAACATCT TCGACGCAGG TGTCGCAGGT CTTCCCGACG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ATGACGCCGG TGAACTTCCC GCCGCCGTTG TTGTTTTGGA GCACGGAAAG ACGATGACGG AAAAAGAGAT CGTGGATTAC GTCGCCAGTC AAGTAACAAC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CGCGAAAAAG TTGCGCGGAG GAGTTGTGTT TGTGGACGAA GTACCGAAAG GTCTTACCGG AAAACTCGAC GCAAGAAAAA TCAGAGAGAT CCTCATAAAG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GCCAAGAAGG GCGGAAAGAT CGCCGTGTAA TTCTAGAGTC GACCCGGGCG GCCGGCCGCT TCCCTTTAGT GAGGGTTAAT GCTTCGAGCA GACATGATAA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GATACATTGA TGAGTTTGGA CAAACCACAA CTAGAATGCA GTGAAAAAAA TGCTTTATTT GTGAAATTTG TGATGCTATT GCTTTATTTG TAACCATTAT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AAGCTGCAAT AAACAAGTTA ACAACAACAA TTGCATTCAT TTTATGTTTC AGGTTCAGGG GGAGATGTGG GAGGTTTTTT AAAGCAAGTA AAACCTCTAC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AAATGTGGTA AAATCCGATA AGGATCGATC CGGGCTGGCG TAATAGCGAA GAGGCCCGCA CCGATCGCCC TTCCCAACAG TTGCGCAGCC TGAATGGCGA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ATGGACGCGC CCTGTAGCGG CGCATTAAGC GCGGCGGGTG TGGTGGTTAC GCGCAGCGTG ACCGCTACAC TTGCCAGCGC CCTAGCGCCC GCTCCTTTCG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CTTTCTTCCC TTCCTTTCTC GCCACGTTCG CCGGCTTTCC CCGTCAAGCT CTAAATCGGG GGCTCCCTTT AGGGTTCCGA TTTAGAGCTT TACGGCACCT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CGACCGCAAA AAACTTGATT TGGGTGATGG TTCACGTAGT GGGCCATCGC CCTGATAGAC GGTTTTTCGC CCTTTGACGT TGGAGTCCAC GTTCTTTAAT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AGTGGACTCT TGTTCCAAAC TGGAACAACA CTCAACCCTA TCTCGGTCTA TTCTTTTGAT TTATAAGGGA TTTTGCCGAT TTCGGCCTAT TGGTTAAAAA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

ATGAGCTGAT TTAACAAATA TTTAACGCGA ATTTTAACAA AATATTAACG TTTACAATTT CGCCTGATGC GGTATTTTCT CCTTACGCAT CTGTGCGGTA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTTCACACCG CATACGCGGA TCTGCGCAGC ACCATGGCCT GAAATAACCT CTGAAAGAGG AACTTGGTTA GGTACCTTCT GAGGCGGAAA GAACCAGCTG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TGGAATGTGT GTCAGTTAGG GTGTGGAAAG TCCCCAGGCT CCCCAGCAGG CAGAAGTATG CAAAGCATGC ATCTCAATTA GTCAGCAACC AGGTGTGGAA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

AGTCCCCAGG CTCCCCAGCA GGCAGAAGTA TGCAAAGCAT GCATCTCAAT TAGTCAGCAA CCATAGTCCC GCCCCTAACT CCGCCCATCC CGCCCCTAAC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TCCGCCCAGT TCCGCCCATT CTCCGCCCCA TGGCTGACTA ATTTTTTTTA TTTATGCAGA GGCCGAGGCC GCCTCGGCCT CTGAGCTATT CCAGAAGTAG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TGAGGAGGCT TTTTTGGAGG CCTAGGCTTT TGCAAAAAGC TTGATTCTTC TGACACAACA GTCTCGAACT TAAGGCTAGA GCCACCATGA TTGAACAAGA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TGGATTGCAC GCAGGTTCTC CGGCCGCTTG GGTGGAGAGG CTATTCGGCT ATGACTGGGC ACAACAGACA ATCGGCTGCT CTGATGCCGC CGTGTTCCGG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CTGTCAGCGC AGGGGCGCCC GGTTCTTTTT GTCAAGACCG ACCTGTCCGG TGCCCTGAAT GAACTGCAGG ACGAGGCAGC GCGGCTATCG TGGCTGGCCA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CGACGGGCGT TCCTTGCGCA GCTGTGCTCG ACGTTGTCAC TGAAGCGGGA AGGGACTGGC TGCTATTGGG CGAAGTGCCG GGGCAGGATC TCCTGTCATC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TCACCTTGCT CCTGCCGAGA AAGTATCCAT CATGGCTGAT GCAATGCGGC GGCTGCATAC GCTTGATCCG GCTACCTGCC CATTCGACCA CCAAGCGAAA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CATCGCATCG AGCGAGCACG TACTCGGATG GAAGCCGGTC TTGTCGATCA GGATGATCTG GACGAAGAGC ATCAGGGGCT CGCGCCAGCC GAACTGTTCG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CCAGGCTCAA GGCGCGCATG CCCGACGGCG AGGATCTCGT CGTGACCCAT GGCGATGCCT GCTTGCCGAA TATCATGGTG GAAAATGGCC GCTTTTCTGG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ATTCATCGAC TGTGGCCGGC TGGGTGTGGC GGACCGCTAT CAGGACATAG CGTTGGCTAC CCGTGATATT GCTGAAGAGC TTGGCGGCGA ATGGGCTGAC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

CGCTTCCTCG TGCTTTACGG TATCGCCGCT CCCGATTCGC AGCGCATCGC CTTCTATCGC CTTCTTGACG AGTTCTTCTG AGCGGGACTC TGGGGTTCGA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

AATGACCGAC CAAGCGACGC CCAACCTGCC ATCACGATGG CCGCAATAAA ATATCTTTAT TTTCATTACA TCTGTGTGTT GGTTTTTTGT GTGAATCGAT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AGCGATAAGG ATCCGCGTAT GGTGCACTCT CAGTACAATC TGCTCTGATG CCGCATAGTT AAGCCAGCCC CGACACCCGC CAACACCCGC TGACGCGCCC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TGACGGGCTT GTCTGCTCCC GGCATCCGCT TACAGACAAG CTGTGACCGT CTCCGGGAGC TGCATGTGTC AGAGGTTTTC ACCGTCATCA CCGAAACGCG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CGAGACGAAA GGGCCTCGTG ATACGCCTAT TTTTATAGGT TAATGTCATG ATAATAATGG TTTCTTAGAC GTCAGGTGGC ACTTTTCGGG GAAATGTGCG 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CGGAACCCCT ATTTGTTTAT TTTTCTAAAT ACATTCAAAT ATGTATCCGC TCATGAGACA ATAACCCTGA TAAATGCTTC AATAATATTG AAAAAGGAAG 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

AGTATGAGTA TTCAACATTT CCGTGTCGCC CTTATTCCCT TTTTTGCGGC ATTTTGCCTT CCTGTTTTTG CTCACCCAGA AACGCTGGTG AAAGTAAAAG 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

ATGCTGAAGA TCAGTTGGGT GCACGAGTGG GTTACATCGA ACTGGATCTC AACAGCGGTA AGATCCTTGA GAGTTTTCGC CCCGAAGAAC GTTTTCCAAT 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

GATGAGCACT TTTAAAGTTC TGCTATGTGG CGCGGTATTA TCCCGTATTG ACGCCGGGCA AGAGCAACTC GGTCGCCGCA TACACTATTC TCAGAATGAC 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

TTGGTTGAGT ACTCACCAGT CACAGAAAAG CATCTTACGG ATGGCATGAC AGTAAGAGAA TTATGCAGTG CTGCCATAAC CATGAGTGAT AACACTGCGG 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

CCAACTTACT TCTGACAACG ATCGGAGGAC CGAAGGAGCT AACCGCTTTT TTGCACAACA TGGGGGATCA TGTAACTCGC CTTGATCGTT GGGAACCGGA 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

GCTGAATGAA GCCATACCAA ACGACGAGCG TGACACCACG ATGCCTGTAG CAATGGCAAC AACGTTGCGC AAACTATTAA CTGGCGAACT ACTTACTCTA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

GCTTCCCGGC AACAATTAAT AGACTGGATG GAGGCGGATA AAGTTGCAGG ACCACTTCTG CGCTCGGCCC TTCCGGCTGG CTGGTTTATT GCTGATAAAT 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

CTGGAGCCGG TGAGCGTGGG TCTCGCGGTA TCATTGCAGC ACTGGGGCCA GATGGTAAGC CCTCCCGTAT CGTAGTTATC TACACGACGG GGAGTCAGGC 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

AACTATGGAT GAACGAAATA GACAGATCGC TGAGATAGGT GCCTCACTGA TTAAGCATTG GTAACTGTCA GACCAAGTTT ACTCATATAT ACTTTAGATT 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

GATTTAAAAC TTCATTTTTA ATTTAAAAGG ATCTAGGTGA AGATCCTTTT TGATAATCTC ATGACCAAAA TCCCTTAACG TGAGTTTTCG TTCCACTGAG 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

CGTCAGACCC CGTAGAAAAG ATCAAAGGAT CTTCTTGAGA TCCTTTTTTT CTGCGCGTAA TCTGCTGCTT GCAAACAAAA AAACCACCGC TACCAGCGGT 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

GGTTTGTTTG CCGGATCAAG AGCTACCAAC TCTTTTTCCG AAGGTAACTG GCTTCAGCAG AGCGCAGATA CCAAATACTG TCCTTCTAGT GTAGCCGTAG 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

TTAGGCCACC ACTTCAAGAA CTCTGTAGCA CCGCCTACAT ACCTCGCTCT GCTAATCCTG TTACCAGTGG CTGCTGCCAG TGGCGATAAG TCGTGTCTTA 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

CCGGGTTGGA CTCAAGACGA TAGTTACCGG ATAAGGCGCA GCGGTCGGGC TGAACGGGGG GTTCGTGCAC ACAGCCCAGC TTGGAGCGAA CGACCTACAC 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

CGAACTGAGA TACCTACAGC GTGAGCTATG AGAAAGCGCC ACGCTTCCCG AAGGGAGAAA GGCGGACAGG TATCCGGTAA GCGGCAGGGT CGGAACAGGA 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

GAGCGCACGA GGGAGCTTCC AGGGGGAAAC GCCTGGTATC TTTATAGTCC TGTCGGGTTT CGCCACCTCT GACTTGAGCG TCGATTTTTG TGATGCTCGT 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

CAGGGGGGCG GAGCCTATGG AAAAACGCCA GCAACGCGGC CTTTTTACGG TTCCTGGCCT TTTGCTGGCC TTTTGCTCAC ATGGCTCGAC AGATCT
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471      ^8481      ^8491

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):

219-1154

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):

1602-3254

Remarks:

Based on the Figure 4B it seems that almost 20% of RLuc:FLuc activity decreased due to the LamB1 insert. That
should be related to the length of the intercistronic region: 112bp for pR-F vs. 447bp for pR-LamB1-F.

The experiments utilizing pGem-based vectors aimed to rule out presence of a cryptic promoter. The pGem
plasmid contains only T7 (in sense with FLuc) and SP6 promoters (in antisense). However, there is no
eukaryotic transcription terminator (the poly(A) signal). One can just hypothesize based on the genome
replication of SV40 and polioma viruses that concatenated transcripts encompassing (e.g. 6-8 full-length
genomic chunks would be produced) could have been detected in case there was a cryptic promoter in front of
the FLuc CDS (Petz et al. (2007), Figure 4A). The sequence of both pGem-based vector was provided directly by
M. Petz (pGem-F IRESite_ID:587, pGem-LamB1-F IRESite_Id:588).

Citations:

Petz M., Kozina D., Huber H., Siwiec T., Seipelt J., Sommergruber W., Mikulits W. (2007) The leader region of Laminin B1 mRNA confers cap-independent translation. Nucleic Acids Res. 35(8):2473-2482

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `LamB1_-335_-1`	The functional status of IRES: `functional`

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

1211-1545

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `57`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `391`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-391`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-57`

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

GGGACCTGGA AGCGCCCCAG CCCCGCAGCG ATCGCAGATT CGGCTTTCAA ACAAAAGAGG CGCCCCGGGG GGTGGGACCG GGACCTCACC CGGTCCTCGC 
^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      ^1301      

AGAGTTGCGG CCGCCCGCCC CTTCAGCCCC GGCTCTCCGT ATGCGCATGA GCAGAGGCGC CTCCCTCTGT TCCTCCCAAG GCTAAACTTT CTAATTCCCT 
^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      ^1401      

TCTTTGGGCT CGGGGGCTCC CGGAGCAGGG CGAGAGCTCG CGTCGCCGGA AAGGAAGACG GGAAGAAAGG GCAGGCGGCT CGGCGGGCGT CTTCTCCACT 
^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      ^1501      

CCTCTGCCGC GTCCCCGTGG CTGCAGGGAG CCGGC
^1511      ^1521      ^1531      ^1541

Citations:

Petz M., Kozina D., Huber H., Siwiec T., Seipelt J., Sommergruber W., Mikulits W. (2007) The leader region of Laminin B1 mRNA confers cap-independent translation. Nucleic Acids Res. 35(8):2473-2482

The translation experiments:

Translation results:

IRESite Translation Id: 621

Version: `2`	Last change: `2009-04-30 11:36:54`
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 MIM-R

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

142.000

Name of IRES used as the positive control:

EMCV-R

Name of the plasmid used as the positive control. `pR-EMCV-F`	Name of the plasmid used as the negative control. `pR-F`
`IRESite Id` of the plasmid used as positive control. `585`	`IRESite Id` of the plasmid used as negative control. `584`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `25.000`
The size (length) of intercistronic region in the positive control: `769`	The size (length) of intercistronic region in the negative control: `112`

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:

Measured luciferase activity values were provided by M. Petz for Figure 3C.

Additional notes from M Petz:

Concerning Fig. 3A, I have checked the data again. The experiment was repeated several times and the ß-Gal
activities of the cotransfected plamid were always quite equal. The normalisation to the ß-gal values did
not affect the ratio of the firefly activities in any significant way.

Citations:

Petz M., Kozina D., Huber H., Siwiec T., Seipelt J., Sommergruber W., Mikulits W. (2007) The leader region of Laminin B1 mRNA confers cap-independent translation. Nucleic Acids Res. 35(8):2473-2482

Translation results:

IRESite Translation Id: 622

Version: `1`	Last change: `2009-04-30 11:36:54`
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 SW480

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

208.000

Name of IRES used as the positive control:

EMCV-R

Name of the plasmid used as the positive control. `pR-EMCV-F`	Name of the plasmid used as the negative control. `pR-F`
`IRESite Id` of the plasmid used as positive control. `585`	`IRESite Id` of the plasmid used as negative control. `584`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `18.000`
The size (length) of intercistronic region in the positive control: `769`	The size (length) of intercistronic region in the negative control: `112`

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:

Measured luciferase activity values were provided by M. Petz for Figure 3D.

Additional notes from M Petz:

Concerning Fig. 3A, I have checked the data again. The experiment was repeated several times and the ß-Gal
activities of the cotransfected plamid were always quite equal. The normalisation to the ß-gal values did
not affect the ratio of the firefly activities in any significant way.

Citations:

Petz M., Kozina D., Huber H., Siwiec T., Seipelt J., Sommergruber W., Mikulits W. (2007) The leader region of Laminin B1 mRNA confers cap-independent translation. Nucleic Acids Res. 35(8):2473-2482

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