IRESite_Id:251 characteristics of NRF IRES studied in pBSFLucNRLuc plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `251`	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:
3UTR_incomplete

The mRNA/+RNA description:

Putative bicistronic mRNA transcript derived from pBSFLucNRluc plasmid through SV40 promoter.

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

TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTCCCTC GAGGaactgg aaaaccagaa agttaactgg taagtttagt 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ctttttgtct tttatttcag gtcCCGGAAT TGGTTTAAAC GAATTCGAGC TCGCCCGGGG ATCCTCTAGA GTCAGCTTGA ATTCCTTTGT GTTACATTCT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TGAATGTCGC TCGCAGTGAC ATTAGCATTC CGGTACTGTT GGTAAAATGG AAGACGCCAA AAACATAAAG AAAGGCCCGG CGCCATTCTA TCCTCTAGAG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GATGGAACCG CTGGAGAGCA ACTGCATAAG GCTATGAAGA GATACGCCCT GGTTCCTGGA ACAATTGCTT TTACAGATGC ACATATCGAG GTGAACATCA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CGTACGCGGA ATACTTCGAA ATGTCCGTTC GGTTGGCAGA AGCTATGAAA CGATATGGGC TGAATACAAA TCACAGAATC GTCGTATGCA GTGAAAACTC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCTTCAATTC TTTATGCCGG TGTTGGGCGC GTTATTTATC GGAGTTGCAG TTGCGCCCGC GAACGACATT TATAATGAAC GTGAATTGCT CAACAGTATG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AACATTTCGC AGCCTACCGT AGTGTTTGTT TCCAAAAAGG GGTTGCAAAA AATTTTGAAC GTGCAAAAAA AATTACCAAT AATCCAGAAA ATTATTATCA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGGATTCTAA AACGGATTAC CAGGGATTTC AGTCGATGTA CACGTTCGTC ACATCTCATC TACCTCCCGG TTTTAATGAA TACGATTTTG TACCAGAGTC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTTTGATCGT GACAAAACAA TTGCACTGAT AATGAATTCC TCTGGATCTA CTGGGTTACC TAAGGGTGTG GCCCTTCCGC ATAGAACTGC CTGCGTCAGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTCTCGCATG CCAGAGATCC TATTTTTGGC AATCAAATCA TTCCGGATAC TGCGATTTTA AGTGTTGTTC CATTCCATCA CGGTTTTGGA ATGTTTACTA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CACTCGGATA TTTGATATGT GGATTTCGAG TCGTCTTAAT GTATAGATTT GAAGAAGAGC TGTTTTTACG ATCCCTTCAG GATTACAAAA TTCAAAGTGC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GTTGCTAGTA CCAACCCTAT TTTCATTCTT CGCCAAAAGC ACTCTGATTG ACAAATACGA TTTATCTAAT TTACACGAAA TTGCTTCTGG GGGCGCACCT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CTTTCGAAAG AAGTCGGGGA AGCGGTTGCA AAACGCTTCC ATCTTCCAGG GATACGACAA GGATATGGGC TCACTGAGAC TACATCAGCT ATTCTGATTA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CACCCGAGGG GGATGATAAA CCGGGCGCGG TCGGTAAAGT TGTTCCATTT TTTGAAGCGA AGGTTGTGGA TCTGGATACC GGGAAAACGC TGGGCGTTAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCAGAGAGGC GAATTATGTG TCAGAGGACC TATGATTATG TCCGGTTATG TAAACAATCC GGAAGCGACC AACGCCTTGA TTGACAAGGA TGGATGGCTA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CATTCTGGAG ACATAGCTTA CTGGGACGAA GACGAACACT TCTTCATAGT TGACCGCTTG AAGTCTTTAA TTAAATACAA AGGATATCAG GTGGCCCCCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CTGAATTGGA ATCGATATTG TTACAACACC CCAACATCTT CGACGCGGGC GTGGCAGGTC TTCCCGACGA TGACGCCGGT GAACTTCCCG CCGCCGTTGT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGTTTTGGAG CACGGAAAGA CGATGACGGA AAAAGAGATC GTGGATTACG TCGCCAGTCA AGTAACAACC GCGAAAAAGT TGCGCGGAGG AGTTGTGTTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTGGACGAAG TACCGAAAGG TCTTACCGGA AAACTCGACG CAAGAAAAAT CAGAGAGATC CTCATAAAGG CCAAGAAGGG CGGAAAGTCC AAATTGTAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATGTAACTGT ATTCAGCGAT GACGAAATTC TTAGCTATTG TAATAGCTGC AGGCATGCAA GCTTGCGCAG ACGTCGCGCG CGGCCGTTTT AAAACAGCTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGGGGTTGTA CCCACCCCAG AGGCCCACGT GCACGAGCAG AGTAATGACA TGGTTCCTTC CATCCTCCAA AGGTGACCAA TAATAGTTTG TAAGTATCAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TATGAACTAA TGAATTTTCA ACATATTTGA TATATTTCAA TCCATTGCCA TCATTGTTCT TATCGATATT TGAGTTGGCT CACTTTGCCA GTAAGAGTCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATTCAAATTG GCTTCTGAGT CCATTTGACA CAACACCTTT GATCTTTGAC AGTTTCCTTG GTTTTAGGTG CTAGATGATT TCTCAGGCTC ACCTTAGACA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTTCCTGCCA CAGACTTAGA ATCAGCCATT TCTCTAAGGA CCCTGATTCC ATTTCATGAG AAATGATAGA GACCACAATC AAAACAAGTC ATGAATTTAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ACTGATATTT TCAATTCAAA TTAAAGATGA GGTTTTTGCT AAATTTTTTT GAGTTTATAT TTGTATGTCT TATGCTGAAA AATCTTGTTT CCTAATTAGT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AACATAATTA TTCATTTGAT GGGTAAATAT TTTAGGGCCG ATTCTTTGGT TTTATAGCCA AGATACCCTG TTGATAAAGT CTTGTGGGAG CAATTATAAG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ACTGGCTTAT TTTGAAGCTT TTTAAAAAAG ACATCCTTAC CTGTTTTAAC TGTAGATTAT ATTAACTTAA ATAGGTACAG CCCACGCTTG GGCGCGCCGA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ATTCGAAATG ACTTCGAAAG TTTATGATCC AGAACAAAGG AAACGGATGA TAACTGGTCC GCAGTGGTGG GCCAGATGTA AACAAATGAA TGTTCTTGAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TCATTTATTA ATTATTATGA TTCAGAAAAA CATGCAGAAA ATGCTGTTAT TTTTTTACAT GGTAACGCGG CCTCTTCTTA TTTATGGCGA CATGTTGTGC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CACATATTGA GCCAGTAGCG CGGTGTATTA TACCAGACCT TATTGGTATG GGCAAATCAG GCAAATCTGG TAATGGTTCT TATAGGTTAC TTGATCATTA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CAAATATCTT ACTGCATGGT TTGAACTTCT TAATTTACCA AAGAAGATCA TTTTTGTCGG CCATGATTGG GGTGCTTGTT TGGCATTTCA TTATAGCTAT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GAGCATCAAG ATAAGATCAA AGCAATAGTT CACGCTGAAA GTGTAGTAGA TGTGATTGAA TCATGGGATG AATGGCCTGA TATTGAAGAA GATATTGCGT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGATCAAATC TGAAGAAGGA GAAAAAATGG TTTTGGAGAA TAACTTCTTC GTGGAAACCA TGTTGCCATC AAAAATCATG AGAAAGTTAG AACCAGAAGA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ATTTGCAGCA TATCTTGAAC CATTCAAAGA GAAAGGTGAA GTTCGTCGTC CAACATTATC ATGGCCTCGT GAAATCCCGT TAGTAAAAGG TGGTAAACCT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GACGTTGTAC AAATTGTTAG GAATTATAAT GCTTATCTAC GTGCAAGTGA TGATTTACCA AAAATGTTTA TTGAATCGGA CCCAGGATTC TTTTCCAATG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CTATTGTTGA AGGTGCCAAG AAGTTTCCTA ATACTGAATT TGTCAAAGTA AAAGGTCTTC ATTTTTCGCA AGAAGATGCA CCTGATGAAA TGGGAAAATA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TATCAAATCG TTCGTTGAGC GAGTTCTCAA AAATGAACAA TAAGTCGACC TGCAGAAGCT TGCGCAGACG TCGCGCGCGG CCGCTTAAGC TAGCTTCGAT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CCAGACATGA TAAGATACAT TGATGAGTTT GGACAAACCA CAACTAGAAT GCAGTGAAAA AAATGCTTTA TTTGTGAAAT TTGTGATGCT ATTGCTTTAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TTGTAACCAT TATAAGCTGC AATAAACAAG TTAACAACAA CAATTGCATT CATTTTATGT TTCAGGTTCA GGGGGAGGTG TGGGAGGTTT TTTAAAGCAA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GTAAAACCTC TACAAATGTG GTA
^3901      ^3911      ^3921

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_except_3UTR

The name of the plasmid:
pBSFLucNRLuc 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:

not tested

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

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens

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

TAGCTTCTGT GGAATGTGTG TCAGTTAGGG TGTGGAAAGT CCCCAGGCTC CCCAGCAGGC AGAAGTATGC AAAGCATGCA TCTCAATTAG TCAGCAACCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GGTGTGGAAA GTCCCCAGGC TCCCCAGCAG GCAGAAGTAT GCAAAGCATG CATCTCAATT AGTCAGCAAC CATAGTCCCG CCCCTAACTC CGCCCATCCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GCCCCTAACT CCGCCCAGTT CCGCCCATTC TCCGCCCCAT GGCTGACTAA TTTTTTTTAT TTATGCAGAG GCCGAGGCCG CCTCGGCCTC TGAGCTATTC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CAGAAGTAGT GAGGAGGCTT TTTTGGAGGC CTAGGCTTTT GCAAAAAGCT CCCTCGAGGa actggaaaac cagaaagtta actggtaagt ttagtctttt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

tgtcttttat ttcaggtcCC GGAATTGGTT TAAACGAATT CGAGCTCGCC CGGGGATCCT CTAGAGTCAG CTTGAATTCC TTTGTGTTAC ATTCTTGAAT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GTCGCTCGCA GTGACATTAG CATTCCGGTA CTGTTGGTAA AATGGAAGAC GCCAAAAACA TAAAGAAAGG CCCGGCGCCA TTCTATCCTC TAGAGGATGG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AACCGCTGGA GAGCAACTGC ATAAGGCTAT GAAGAGATAC GCCCTGGTTC CTGGAACAAT TGCTTTTACA GATGCACATA TCGAGGTGAA CATCACGTAC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GCGGAATACT TCGAAATGTC CGTTCGGTTG GCAGAAGCTA TGAAACGATA TGGGCTGAAT ACAAATCACA GAATCGTCGT ATGCAGTGAA AACTCTCTTC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AATTCTTTAT GCCGGTGTTG GGCGCGTTAT TTATCGGAGT TGCAGTTGCG CCCGCGAACG ACATTTATAA TGAACGTGAA TTGCTCAACA GTATGAACAT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTCGCAGCCT ACCGTAGTGT TTGTTTCCAA AAAGGGGTTG CAAAAAATTT TGAACGTGCA AAAAAAATTA CCAATAATCC AGAAAATTAT TATCATGGAT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TCTAAAACGG ATTACCAGGG ATTTCAGTCG ATGTACACGT TCGTCACATC TCATCTACCT CCCGGTTTTA ATGAATACGA TTTTGTACCA GAGTCCTTTG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATCGTGACAA AACAATTGCA CTGATAATGA ATTCCTCTGG ATCTACTGGG TTACCTAAGG GTGTGGCCCT TCCGCATAGA ACTGCCTGCG TCAGATTCTC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GCATGCCAGA GATCCTATTT TTGGCAATCA AATCATTCCG GATACTGCGA TTTTAAGTGT TGTTCCATTC CATCACGGTT TTGGAATGTT TACTACACTC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGATATTTGA TATGTGGATT TCGAGTCGTC TTAATGTATA GATTTGAAGA AGAGCTGTTT TTACGATCCC TTCAGGATTA CAAAATTCAA AGTGCGTTGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TAGTACCAAC CCTATTTTCA TTCTTCGCCA AAAGCACTCT GATTGACAAA TACGATTTAT CTAATTTACA CGAAATTGCT TCTGGGGGCG CACCTCTTTC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GAAAGAAGTC GGGGAAGCGG TTGCAAAACG CTTCCATCTT CCAGGGATAC GACAAGGATA TGGGCTCACT GAGACTACAT CAGCTATTCT GATTACACCC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GAGGGGGATG ATAAACCGGG CGCGGTCGGT AAAGTTGTTC CATTTTTTGA AGCGAAGGTT GTGGATCTGG ATACCGGGAA AACGCTGGGC GTTAATCAGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAGGCGAATT ATGTGTCAGA GGACCTATGA TTATGTCCGG TTATGTAAAC AATCCGGAAG CGACCAACGC CTTGATTGAC AAGGATGGAT GGCTACATTC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGGAGACATA GCTTACTGGG ACGAAGACGA ACACTTCTTC ATAGTTGACC GCTTGAAGTC TTTAATTAAA TACAAAGGAT ATCAGGTGGC CCCCGCTGAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TTGGAATCGA TATTGTTACA ACACCCCAAC ATCTTCGACG CGGGCGTGGC AGGTCTTCCC GACGATGACG CCGGTGAACT TCCCGCCGCC GTTGTTGTTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGGAGCACGG AAAGACGATG ACGGAAAAAG AGATCGTGGA TTACGTCGCC AGTCAAGTAA CAACCGCGAA AAAGTTGCGC GGAGGAGTTG TGTTTGTGGA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGAAGTACCG AAAGGTCTTA CCGGAAAACT CGACGCAAGA AAAATCAGAG AGATCCTCAT AAAGGCCAAG AAGGGCGGAA AGTCCAAATT GTAAAATGTA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ACTGTATTCA GCGATGACGA AATTCTTAGC TATTGTAATA GCTGCAGGCA TGCAAGCTTG CGCAGACGTC GCGCGCGGCC GTTTTAAAAC AGCTCTGGGG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TTGTACCCAC CCCAGAGGCC CACGTGCACG AGCAGAGTAA TGACATGGTT CCTTCCATCC TCCAAAGGTG ACCAATAATA GTTTGTAAGT ATCATTATGA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ACTAATGAAT TTTCAACATA TTTGATATAT TTCAATCCAT TGCCATCATT GTTCTTATCG ATATTTGAGT TGGCTCACTT TGCCAGTAAG AGTCTATTCA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AATTGGCTTC TGAGTCCATT TGACACAACA CCTTTGATCT TTGACAGTTT CCTTGGTTTT AGGTGCTAGA TGATTTCTCA GGCTCACCTT AGACATTTCC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TGCCACAGAC TTAGAATCAG CCATTTCTCT AAGGACCCTG ATTCCATTTC ATGAGAAATG ATAGAGACCA CAATCAAAAC AAGTCATGAA TTTATACTGA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TATTTTCAAT TCAAATTAAA GATGAGGTTT TTGCTAAATT TTTTTGAGTT TATATTTGTA TGTCTTATGC TGAAAAATCT TGTTTCCTAA TTAGTAACAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AATTATTCAT TTGATGGGTA AATATTTTAG GGCCGATTCT TTGGTTTTAT AGCCAAGATA CCCTGTTGAT AAAGTCTTGT GGGAGCAATT ATAAGACTGG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CTTATTTTGA AGCTTTTTAA AAAAGACATC CTTACCTGTT TTAACTGTAG ATTATATTAA CTTAAATAGG TACAGCCCAC GCTTGGGCGC GCCGAATTCG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AAATGACTTC GAAAGTTTAT GATCCAGAAC AAAGGAAACG GATGATAACT GGTCCGCAGT GGTGGGCCAG ATGTAAACAA ATGAATGTTC TTGATTCATT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TATTAATTAT TATGATTCAG AAAAACATGC AGAAAATGCT GTTATTTTTT TACATGGTAA CGCGGCCTCT TCTTATTTAT GGCGACATGT TGTGCCACAT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ATTGAGCCAG TAGCGCGGTG TATTATACCA GACCTTATTG GTATGGGCAA ATCAGGCAAA TCTGGTAATG GTTCTTATAG GTTACTTGAT CATTACAAAT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ATCTTACTGC ATGGTTTGAA CTTCTTAATT TACCAAAGAA GATCATTTTT GTCGGCCATG ATTGGGGTGC TTGTTTGGCA TTTCATTATA GCTATGAGCA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TCAAGATAAG ATCAAAGCAA TAGTTCACGC TGAAAGTGTA GTAGATGTGA TTGAATCATG GGATGAATGG CCTGATATTG AAGAAGATAT TGCGTTGATC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AAATCTGAAG AAGGAGAAAA AATGGTTTTG GAGAATAACT TCTTCGTGGA AACCATGTTG CCATCAAAAA TCATGAGAAA GTTAGAACCA GAAGAATTTG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CAGCATATCT TGAACCATTC AAAGAGAAAG GTGAAGTTCG TCGTCCAACA TTATCATGGC CTCGTGAAAT CCCGTTAGTA AAAGGTGGTA AACCTGACGT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TGTACAAATT GTTAGGAATT ATAATGCTTA TCTACGTGCA AGTGATGATT TACCAAAAAT GTTTATTGAA TCGGACCCAG GATTCTTTTC CAATGCTATT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GTTGAAGGTG CCAAGAAGTT TCCTAATACT GAATTTGTCA AAGTAAAAGG TCTTCATTTT TCGCAAGAAG ATGCACCTGA TGAAATGGGA AAATATATCA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AATCGTTCGT TGAGCGAGTT CTCAAAAATG AACAATAAGT CGACCTGCAG AAGCTTGCGC AGACGTCGCG CGCGGCCGCT TAAGCTAGCT TCGATCCAGA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CATGATAAGA TACATTGATG AGTTTGGACA AACCACAACT AGAATGCAGT GAAAAAAATG CTTTATTTGT GAAATTTGTG ATGCTATTGC TTTATTTGTA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ACCATTATAA GCTGCAATAA ACAAGTTAAC AACAACAATT GCATTCATTT TATGTTTCAG GTTCAGGGGG AGGTGTGGGA GGTTTTTTAA AGCAAGTAAA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ACCTCTACAA ATGTGGTATG GCTGATTATG ATCCTGCCTC GCGCGTTTCG GTGATGACGG TGAAAACCTC TGACACATGC AGCTCCCGCC TTAATTAAGG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GTTTAAACCC GGTACCCAGT CACGTAGCGA TAGCGGAGTG TACTGCATTA ATGAATCGGC CAACGCGCGG GGAGAGGCGG TTTGCGTATT GGGCGCTCTT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CCGCTTCCTC GCTCACTGAC TCGCTGCGCT CGGTCGTTCG GCTGCGGCGA GCGGTATCAG CTCACTCAAA GGCGGTAATA CGGTTATCCA CAGAATCAGG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GGATAACGCA GGAAAGAACA TGTGAGCAAA AGGCCAGCAA AAGGCCAGGA ACCGTAAAAA GGCCGCGTTG CTGGCGTTtT TCCATAGGCT CCGCCCCCCT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GACGAGCATC ACAAAAATCG ACGCTCAAGT CAGAGGTGGC GAAACCCGAC AGGACTATAA AGATACCAGG CGTTTCCCCC TGGAAGCTCC CTCGTGCGCT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTCCTGTTCC GACCCTGCCG CTTACCGGAT ACCTGTCCGC CTTTCTCCCT TCGGGAAGCG TGGCGCTTTC TCATAGCTCA CGCTGTAGGT ATCTCAGTTC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GGTGTAGGTC GTTCGCTCCA AGCTGGGCTG TGTGCACGAA CCCCCCGTTC AGCCCGACCG CTGCGCCTTA TCCGGTAACT ATCGTCTTGA GTCCAACCCG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GTAAGACACG ACTTATCGCC ACTGGCAGCA GCCACTGGTA ACAGGATTAG CAGAGCGAGG TATGTAGGCG GTGCTACAGA GTTCTTGAAG TGGTGGCCTA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

ACTACGGCTA CACTAGAAGG ACAGTATTTG GTATCTGCGC TCTGCTGAAG CCAGTTACCT TCGGAAAAAG AGTTGGTAGC TCTTGATCCG GCAAACAAAC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

CACCGCTGGT AGCGGTGGTT TTTTTGTTTG CAAGCAGCAG ATTACGCGCA GAAAAAAAGG ATCTCAAGAA GATCCTTTGA TCTTTTCTAC GGGGTCTGAC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GCTCAGTGGA ACGAAAACTC ACGTTAAGGG ATTTTGGTCA TGAGATTATC AAAAAGGATC TTCACCTAGA TCCTTTTAAA TTAAAAATGA AGTTTTAAAT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CAATCTAAAG TATATATGAG TAAACTTGGT CTGACAGTTA CCAATGCTTA ATCAGTGAGG CACCTATCTC AGCGATCTGT CTATTTCGTT CATCCATAGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TGCCTGACTC CCCGTCGTGT AGATAACTAC GATACGGGAG GGCTTACCAT CTGGCCCCAG TGCTGCAATG ATACCGCGAG ACCCACGCTC ACCGGCTCCA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

GATTTATCAG CAATAAACCA GCCAGCCGGA AGGGCCGAGC GCAGAAGTGG TCCTGCAACT TTATCCGCCT CCATCCAGTC TATTAATTGT TGCCGGGAAG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CTAGAGTAAG TAGTTCGCCA GTTAATAGTT TGCGCAACGT TGTTGCCATT GCTACAGGCA TCGTGGTGTC ACGCTCGTCG TTTGGTATGG CTTCATTCAG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CTCCGGTTCC CAACGATCAA GGCGAGTTAC ATGATCCCCC ATGTTGTGCA AAAAAGCGGT TAGCTCCTTC GGTCCTCCGA TCGTTGTCAG AAGTAAGTTG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GCCGCAGTGT TATCACTCAT GGTTATGGCA GCACTGCATA ATTCTCTTAC TGTCATGCCA TCCGTAAGAT GCTTTTCTGT GACTGGTGAG TACTCAACCA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AGTCATTCTG AGAATAGTGT ATGCGGCGAC CGAGTTGCTC TTGCCCGGCG TCAATACGGG ATAATACCGC GCCACATAGC AGAACTTTAA AAGTGCTCAT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CATTGGAAAA CGTTCTTCGG GGCGAAAACT CTCAAGGATC TTACCGCTGT TGAGATCCAG TTCGATGTAA CCCACTCGTG CACCCAACTG ATCTTCAGCA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

TCTTTTACTT TCACCAGCGT TTCTGGGTGA GCAAAAACAG GAAGGCAAAA TGCCGCAAAA AAGGGAATAA GGGCGACACG GAAATGTTGA ATACTCATAC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TCTTCCTTTT TCAATATTAT TGAAGCATTT ATCAGGGTTA TTGTCTCATG AGCGGATACA TATTTGAATG TATTTAGAAA AATAAACAAA TAGGGGTTCC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

GCGCACATTT CCCCGAAAAG TGCCACCTGA CGTCGGTACC ATTTAAATAT CGATAAGC
^6301      ^6311      ^6321      ^6331      ^6341      ^6351

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:
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):

247-1899

ORF

ORF position:

2

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):

2708-3643

Citations:

Hennecke M., Kwissa M., Metzger K., Oumard A., Kroger A., Schirmbeck R., Reimann J., Hauser H. (2001) Composition and arrangement of genes define the strength of IRES-driven translation in bicistronic mRNAs. Nucleic. Acids Res. 29(16):3327-3334

IRESs:

IRES:

Version: `3`	Last change: `2007-01-23 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `NRF`	The functional status of IRES: `defective`

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

2038-2674

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `139`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `775`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-670`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-34`

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

CAGAGTAATG ACATGGTTCC TTCCATCCTC CAAAGGTGAC CAATAATAGT TTGTAAGTAT CATTATGAAC TAATGAATTT TCAACATATT TGATATATTT 
^2038      ^2048      ^2058      ^2068      ^2078      ^2088      ^2098      ^2108      ^2118      ^2128      

CAATCCATTG CCATCATTGT TCTTATCGAT ATTTGAGTTG GCTCACTTTG CCAGTAAGAG TCTATTCAAA TTGGCTTCTG AGTCCATTTG ACACAACACC 
^2138      ^2148      ^2158      ^2168      ^2178      ^2188      ^2198      ^2208      ^2218      ^2228      

TTTGATCTTT GACAGTTTCC TTGGTTTTAG GTGCTAGATG ATTTCTCAGG CTCACCTTAG ACATTTCCTG CCACAGACTT AGAATCAGCC ATTTCTCTAA 
^2238      ^2248      ^2258      ^2268      ^2278      ^2288      ^2298      ^2308      ^2318      ^2328      

GGACCCTGAT TCCATTTCAT GAGAAATGAT AGAGACCACA ATCAAAACAA GTCATGAATT TATACTGATA TTTTCAATTC AAATTAAAGA TGAGGTTTTT 
^2338      ^2348      ^2358      ^2368      ^2378      ^2388      ^2398      ^2408      ^2418      ^2428      

GCTAAATTTT TTTGAGTTTA TATTTGTATG TCTTATGCTG AAAAATCTTG TTTCCTAATT AGTAACATAA TTATTCATTT GATGGGTAAA TATTTTAGGG 
^2438      ^2448      ^2458      ^2468      ^2478      ^2488      ^2498      ^2508      ^2518      ^2528      

CCGATTCTTT GGTTTTATAG CCAAGATACC CTGTTGATAA AGTCTTGTGG GAGCAATTAT AAGACTGGCT TATTTTGAAG CTTTTTAAAA AAGACATCCT 
^2538      ^2548      ^2558      ^2568      ^2578      ^2588      ^2598      ^2608      ^2618      ^2628      

TACCTGTTTT AACTGTAGAT TATATTAACT TAAATAG
^2638      ^2648      ^2658      ^2668

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 316

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 C243

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

8.700

Name of IRES used as the positive control:

EMCV

Name of the plasmid used as the positive control. `pBSRLucEFluc`
`IRESite Id` of the plasmid used as positive control. `245`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `666`

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:

Fig. 3e

Citations:

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