IRESite_Id:482 characteristics of KMI2 IRES studied in pRKMI2F plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `482`	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_possibly_incomplete

The mRNA/+RNA description:

Putative in vitro BamHI run-off T7 transcript containing synthetic KMI2 IRES.

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

GGCTAGGCTT GGCATTCCGG TACTGAATTG ATATCAAGCT CTAGCCACCA TGACTTCGAA AGTTTATGAT CCAGAACAAA GGAAACGGAT GATAACTGGT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCGCAGTGGT GGGCCAGATG TAAACAAATG AATGTTCTTG ATTCATTTAT TAATTATTAT GATTCAGAAA AACATGCAGA AAATGCTGTT ATTTTTTTAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATGGTAACGC GGCCTCTTCT TATTTATGGC GACATGTTGT GCCACATATT GAGCCAGTAG CGCGGTGTAT TATACCAGAC CTTATTGGTA TGGGCAAATC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGGCAAATCT GGTAATGGTT CTTATAGGTT ACTTGATCAT TACAAATATC TTACTGCATG GTTTGAACTT CTTAATTTAC CAAAGAAGAT CATTTTTGTC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GGCCATGATT GGGGTGCTTG TTTGGCATTT CATTATAGCT ATGAGCATCA AGATAAGATC AAAGCAATAG TTCACGCTGA AAGTGTAGTA GATGTGATTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AATCATGGGA TGAATGGCCT GATATTGAAG AAGATATTGC GTTGATCAAA TCTGAAGAAG GAGAAAAAAT GGTTTTGGAG AATAACTTCT TCGTGGAAAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CATGTTGCCA TCAAAAATCA TGAGAAAGTT AGAACCAGAA GAATTTGCAG CATATCTTGA ACCATTCAAA GAGAAAGGTG AAGTTCGTCG TCCAACATTA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TCATGGCCTC GTGAAATCCC GTTAGTAAAA GGTGGTAAAC CTGACGTTGT ACAAATTGTT AGGAATTATA ATGCTTATCT ACGTGCAAGT GATGATTTAC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CAAAAATGTT TATTGAATCG GACCCAGGAT TCTTTTCCAA TGCTATTGTT GAAGGTGCCA AGAAGTTTCC TAATACTGAA TTTGTCAAAG TAAAAGGTCT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCATTTTTCG CAAGAAGATG CACCTGATGA AATGGGAAAA TATATCAAAT CGTTCGTTGA GCGAGTTCTC AAAAATGAAC AATAATTCTA GAGCTTATCG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ATACCGTCGA CCTCGAATCA CTAGTCAGCT GGAATTCcct cctcctcctc ctcctcccct cctcctcctc ctcctccGAA TTCggaggag gaggaggagg 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

aggggaggag gaggaggagg aggGAATTCG TTGGTAAAGC CACCATGGAA GACGCCAAAA ACATAAAGAA AGGCCCGGCG CCATTCTATC CGCTGGAAGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TGGAACCGCT GGAGAGCAAC TGCATAAGGC TATGAAGAGA TACGCCCTGG TTCCTGGAAC AATTGCTTTT ACAGATGCAC ATATCGAGGT GGACATCACT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TACGCTGAGT ACTTCGAAAT GTCCGTTCGG TTGGCAGAAG CTATGAAACG ATATGGGCTG AATACAAATC ACAGAATCGT CGTATGCAGT GAAAACTCTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TTCAATTCTT TATGCCGGTG TTGGGCGCGT TATTTATCGG AGTTGCAGTT GCGCCCGCGA ACGACATTTA TAATGAACGT GAATTGCTCA ACAGTATGGG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CATTTCGCAG CCTACCGTGG TGTTCGTTTC CAAAAAGGGG TTGCAAAAAA TTTTGAACGT GCAAAAAAAG CTCCCAATCA TCCAAAAAAT TATTATCATG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GATTCTAAAA CGGATTACCA GGGATTTCAG TCGATGTACA CGTTCGTCAC ATCTCATCTA CCTCCCGGTT TTAATGAATA CGATTTTGTG CCAGAGTCCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TCGATAGGGA CAAGACAATT GCACTGATCA TGAACTCCTC TGGATCTACT GGTCTGCCTA AAGGTGTCGC TCTGCCTCAT AGAACTGCCT GCGTGAGATT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTCGCATGCC AGAGATCCTA TTTTTGGCAA TCAAATCATT CCGGATACTG CGATTTTAAG TGTTGTTCCA TTCCATCACG GTTTTGGAAT GTTTACTACA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CTCGGATATT TGATATGTGG ATTTCGAGTC GTCTTAATGT ATAGATTTGA AGAAGAGCTG TTTCTGAGGA GCCTTCAGGA TTACAAGATT CAAAGTGCGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGCTGGTGCC AACCCTATTC TCCTTCTTCG CCAAAAGCAC TCTGATTGAC AAATACGATT TATCTAATTT ACACGAAATT GCTTCTGGTG GCGCTCCCCT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTCTAAGGAA GTCGGGGAAG CGGTTGCCAA GAGGTTCCAT CTGCCAGGTA TCAGGCAAGG ATATGGGCTC ACTGAGACTA CATCAGCTAT TCTGATTACA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCCGAGGGGG ATGATAAACC GGGCGCGGTC GGTAAAGTTG TTCCATTTTT TGAAGCGAAG GTTGTGGATC TGGATACCGG GAAAACGCTG GGCGTTAATC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAAGAGGCGA ACTGTGTGTG AGAGGTCCTA TGATTATGTC CGGTTATGTA AACAATCCGG AAGCGACCAA CGCCTTGATT GACAAGGATG GATGGCTACA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTCTGGAGAC ATAGCTTACT GGGACGAAGA CGAACACTTC TTCATCGTTG ACCGCCTGAA GTCTCTGATT AAGTACAAAG GCTATCAGGT GGCTCCCGCT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GAATTGGAAT CCATCTTGCT CCAACACCCC AACATCTTCG ACGCAGGTGT CGCAGGTCTT CCCGACGATG ACGCCGGTGA ACTTCCCGCC GCCGTTGTTG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTTTGGAGCA CGGAAAGACG ATGACGGAAA AAGAGATCGT GGATTACGTC GCCAGTCAAG TAACAACCGC GAAAAAGTTG CGCGGAGGAG TTGTGTTTGT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GGACGAAGTA CCGAAAGGTC TTACCGGAAA ACTCGACGCA AGAAAAATCA GAGAGATCCT CATAAAGGCC AAGAAGGGCG GAAAGATCGC CGTGTAATTC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TAGAGTCGGG GCGGCCGGCC GCTTCGAGCA GACATGATAA GATACATTGA TGAGTTTGGA CAAACCACAA CTAGAATGCA GTGAAAAAAA TGCTTTATTT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GTGAAATTTG TGATGCTATT GCTTTATTTG TAACCATTAT AAGCTGCAAT AAACAAGTTA ACAACAACAA TTGCATTCAT TTTATGTTTC AGGTTCAGGG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GGAGGTGTGG GAGGTTTTTT AAAGCAAGTA AAACCTCTAC AAATGTGGTA AAATCGATAA GGATCTGAAC GATGGAGCGG AGAATGGGCG GAACTGGGCG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GAGTTAGGGG CGGGATGGGC GGAGTTAGGG GCGGGACTAT GGTTGCTGAC TAATTGAGAT GCATGCTTTG CATACTTCTG CCTGCTGGGG AGCCTGGGGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CTTTCCACAC CTGGTTGCTG ACTAATTGAG ATGCATGCTT TGCATACTTC TGCCTGCTGG GGAGCCTGGG GACTTTCCAC ACCCTAACTG ACACACATTC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CACAGCG
^3301

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_maybe_except_3UTR

The name of the plasmid:
pRKMI2F The name of the promoter used to express this mRNA:
T7

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 origin of IRES in the plasmid:

engineered

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

GGTACCGAGC TCTTACGCGT GCTAGCCCGG GCTCGAGATC TGCGATCTGC ATCTCAATTA GTCAGCAACC ATAGTCCCGC CCCTAACTCC GCCCATCCCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCCTAACTC CGCCCAGTTC CGCCCATTCT CCGCCCCATC GCTGACTAAT TTTTTTTATT TATGCAGAGG CCGAGGCCGC CTCGGCCTCT GAGCTATTCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGAAGTAGTG AGGAGGCTTT TTTGGAGGCC TAGGCTTTTG CAAAAAGCTG AAGTTGGTCG TGAGGCACTG GGCAGGTAAG TATCAAGGTT ACAAGACAGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTTAAGGAGA CCAATAGAAA CTGGGCTTGT CGAGACAGAG AAGACTCTTG CGTTTCTGAT AGGCACCTAT TGGTCTTACT GACATCCACT TTGCCTTTCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTCCACAGGT GTCCACTCCC AGTTCAATTA CAGCTCTTAA GGCTAGAGTA CTTAATACGA CTCACTATAG GCTAGGCTTG GCATTCCGGT ACTGAATTGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TATCAAGCTC TAGCCACCAT GACTTCGAAA GTTTATGATC CAGAACAAAG GAAACGGATG ATAACTGGTC CGCAGTGGTG GGCCAGATGT AAACAAATGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATGTTCTTGA TTCATTTATT AATTATTATG ATTCAGAAAA ACATGCAGAA AATGCTGTTA TTTTTTTACA TGGTAACGCG GCCTCTTCTT ATTTATGGCG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACATGTTGTG CCACATATTG AGCCAGTAGC GCGGTGTATT ATACCAGACC TTATTGGTAT GGGCAAATCA GGCAAATCTG GTAATGGTTC TTATAGGTTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTTGATCATT ACAAATATCT TACTGCATGG TTTGAACTTC TTAATTTACC AAAGAAGATC ATTTTTGTCG GCCATGATTG GGGTGCTTGT TTGGCATTTC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATTATAGCTA TGAGCATCAA GATAAGATCA AAGCAATAGT TCACGCTGAA AGTGTAGTAG ATGTGATTGA ATCATGGGAT GAATGGCCTG ATATTGAAGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGATATTGCG TTGATCAAAT CTGAAGAAGG AGAAAAAATG GTTTTGGAGA ATAACTTCTT CGTGGAAACC ATGTTGCCAT CAAAAATCAT GAGAAAGTTA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAACCAGAAG AATTTGCAGC ATATCTTGAA CCATTCAAAG AGAAAGGTGA AGTTCGTCGT CCAACATTAT CATGGCCTCG TGAAATCCCG TTAGTAAAAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTGGTAAACC TGACGTTGTA CAAATTGTTA GGAATTATAA TGCTTATCTA CGTGCAAGTG ATGATTTACC AAAAATGTTT ATTGAATCGG ACCCAGGATT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CTTTTCCAAT GCTATTGTTG AAGGTGCCAA GAAGTTTCCT AATACTGAAT TTGTCAAAGT AAAAGGTCTT CATTTTTCGC AAGAAGATGC ACCTGATGAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ATGGGAAAAT ATATCAAATC GTTCGTTGAG CGAGTTCTCA AAAATGAACA ATAATTCTAG AGCTTATCGA TACCGTCGAC CTCGAATCAC TAGTCAGCTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GAATTCcctc ctcctcctcc tcctcccctc ctcctcctcc tcctccGAAT TCggaggagg aggaggagga ggggaggagg aggaggagga ggGAATTCGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TGGTAAAGCC ACCATGGAAG ACGCCAAAAA CATAAAGAAA GGCCCGGCGC CATTCTATCC GCTGGAAGAT GGAACCGCTG GAGAGCAACT GCATAAGGCT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATGAAGAGAT ACGCCCTGGT TCCTGGAACA ATTGCTTTTA CAGATGCACA TATCGAGGTG GACATCACTT ACGCTGAGTA CTTCGAAATG TCCGTTCGGT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGGCAGAAGC TATGAAACGA TATGGGCTGA ATACAAATCA CAGAATCGTC GTATGCAGTG AAAACTCTCT TCAATTCTTT ATGCCGGTGT TGGGCGCGTT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATTTATCGGA GTTGCAGTTG CGCCCGCGAA CGACATTTAT AATGAACGTG AATTGCTCAA CAGTATGGGC ATTTCGCAGC CTACCGTGGT GTTCGTTTCC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AAAAAGGGGT TGCAAAAAAT TTTGAACGTG CAAAAAAAGC TCCCAATCAT CCAAAAAATT ATTATCATGG ATTCTAAAAC GGATTACCAG GGATTTCAGT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGATGTACAC GTTCGTCACA TCTCATCTAC CTCCCGGTTT TAATGAATAC GATTTTGTGC CAGAGTCCTT CGATAGGGAC AAGACAATTG CACTGATCAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAACTCCTCT GGATCTACTG GTCTGCCTAA AGGTGTCGCT CTGCCTCATA GAACTGCCTG CGTGAGATTC TCGCATGCCA GAGATCCTAT TTTTGGCAAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CAAATCATTC CGGATACTGC GATTTTAAGT GTTGTTCCAT TCCATCACGG TTTTGGAATG TTTACTACAC TCGGATATTT GATATGTGGA TTTCGAGTCG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TCTTAATGTA TAGATTTGAA GAAGAGCTGT TTCTGAGGAG CCTTCAGGAT TACAAGATTC AAAGTGCGCT GCTGGTGCCA ACCCTATTCT CCTTCTTCGC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CAAAAGCACT CTGATTGACA AATACGATTT ATCTAATTTA CACGAAATTG CTTCTGGTGG CGCTCCCCTC TCTAAGGAAG TCGGGGAAGC GGTTGCCAAG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AGGTTCCATC TGCCAGGTAT CAGGCAAGGA TATGGGCTCA CTGAGACTAC ATCAGCTATT CTGATTACAC CCGAGGGGGA TGATAAACCG GGCGCGGTCG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GTAAAGTTGT TCCATTTTTT GAAGCGAAGG TTGTGGATCT GGATACCGGG AAAACGCTGG GCGTTAATCA AAGAGGCGAA CTGTGTGTGA GAGGTCCTAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GATTATGTCC GGTTATGTAA ACAATCCGGA AGCGACCAAC GCCTTGATTG ACAAGGATGG ATGGCTACAT TCTGGAGACA TAGCTTACTG GGACGAAGAC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAACACTTCT TCATCGTTGA CCGCCTGAAG TCTCTGATTA AGTACAAAGG CTATCAGGTG GCTCCCGCTG AATTGGAATC CATCTTGCTC CAACACCCCA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ACATCTTCGA CGCAGGTGTC GCAGGTCTTC CCGACGATGA CGCCGGTGAA CTTCCCGCCG CCGTTGTTGT TTTGGAGCAC GGAAAGACGA TGACGGAAAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AGAGATCGTG GATTACGTCG CCAGTCAAGT AACAACCGCG AAAAAGTTGC GCGGAGGAGT TGTGTTTGTG GACGAAGTAC CGAAAGGTCT TACCGGAAAA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

CTCGACGCAA GAAAAATCAG AGAGATCCTC ATAAAGGCCA AGAAGGGCGG AAAGATCGCC GTGTAATTCT AGAGTCGGGG CGGCCGGCCG CTTCGAGCAG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ACATGATAAG ATACATTGAT GAGTTTGGAC AAACCACAAC TAGAATGCAG TGAAAAAAAT GCTTTATTTG TGAAATTTGT GATGCTATTG CTTTATTTGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

AACCATTATA AGCTGCAATA AACAAGTTAA CAACAACAAT TGCATTCATT TTATGTTTCA GGTTCAGGGG GAGGTGTGGG AGGTTTTTTA AAGCAAGTAA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AACCTCTACA AATGTGGTAA AATCGATAAG GATCTGAACG ATGGAGCGGA GAATGGGCGG AACTGGGCGG AGTTAGGGGC GGGATGGGCG GAGTTAGGGG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CGGGACTATG GTTGCTGACT AATTGAGATG CATGCTTTGC ATACTTCTGC CTGCTGGGGA GCCTGGGGAC TTTCCACACC TGGTTGCTGA CTAATTGAGA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TGCATGCTTT GCATACTTCT GCCTGCTGGG GAGCCTGGGG ACTTTCCACA CCCTAACTGA CACACATTCC ACAGCGGATC CGTCGACCGA TGCCCTTGAG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AGCCTTCAAC CCAGTCAGCT CCTTCCGGTG GGCGCGGGGC ATGACTATCG TCGCCGCACT TATGACTGTC TTCTTTATCA TGCAACTCGT AGGACAGGTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CCGGCAGCGC TCTTCCGCTT CCTCGCTCAC TGACTCGCTG CGCTCGGTCG TTCGGCTGCG GCGAGCGGTA TCAGCTCACT CAAAGGCGGT AATACGGTTA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TCCACAGAAT CAGGGGATAA CGCAGGAAAG AACATGTGAG CAAAAGGCCA GCAAAAGGCC AGGAACCGTA AAAAGGCCGC GTTGCTGGCG TTTTTCCATA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GGCTCCGCCC CCCTGACGAG CATCACAAAA ATCGACGCTC AAGTCAGAGG TGGCGAAACC CGACAGGACT ATAAAGATAC CAGGCGTTTC CCCCTGGAAG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CTCCCTCGTG CGCTCTCCTG TTCCGACCCT GCCGCTTACC GGATACCTGT CCGCCTTTCT CCCTTCGGGA AGCGTGGCGC TTTCTCAATG CTCACGCTGT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

AGGTATCTCA GTTCGGTGTA GGTCGTTCGC TCCAAGCTGG GCTGTGTGCA CGAACCCCCC GTTCAGCCCG ACCGCTGCGC CTTATCCGGT AACTATCGTC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TTGAGTCCAA CCCGGTAAGA CACGACTTAT CGCCACTGGC AGCAGCCACT GGTAACAGGA TTAGCAGAGC GAGGTATGTA GGCGGTGCTA CAGAGTTCTT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GAAGTGGTGG CCTAACTACG GCTACACTAG AAGGACAGTA TTTGGTATCT GCGCTCTGCT GAAGCCAGTT ACCTTCGGAA AAAGAGTTGG TAGCTCTTGA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TCCGGCAAAC AAACCACCGC TGGTAGCGGT GGTTTTTTTG TTTGCAAGCA GCAGATTACG CGCAGAAAAA AAGGATCTCA AGAAGATCCT TTGATCTTTT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTACGGGGTC TGACGCTCAG TGGAACGAAA ACTCACGTTA AGGGATTTTG GTCATGAGAT TATCAAAAAG GATCTTCACC TAGATCCTTT TAAATTAAAA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ATGAAGTTTT AAATCAATCT AAAGTATATA TGAGTAAACT TGGTCTGACA GTTACCAATG CTTAATCAGT GAGGCACCTA TCTCAGCGAT CTGTCTATTT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CGTTCATCCA TAGTTGCCTG ACTCCCCGTC GTGTAGATAA CTACGATACG GGAGGGCTTA CCATCTGGCC CCAGTGCTGC AATGATACCG CGAGACCCAC 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GCTCACCGGC TCCAGATTTA TCAGCAATAA ACCAGCCAGC CGGAAGGGCC GAGCGCAGAA GTGGTCCTGC AACTTTATCC GCCTCCATCC AGTCTATTAA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TTGTTGCCGG GAAGCTAGAG TAAGTAGTTC GCCAGTTAAT AGTTTGCGCA ACGTTGTTGC CATTGCTACA GGCATCGTGG TGTCACGCTC GTCGTTTGGT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ATGGCTTCAT TCAGCTCCGG TTCCCAACGA TCAAGGCGAG TTACATGATC CCCCATGTTG TGCAAAAAAG CGGTTAGCTC CTTCGGTCCT CCGATCGTTG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TCAGAAGTAA GTTGGCCGCA GTGTTATCAC TCATGGTTAT GGCAGCACTG CATAATTCTC TTACTGTCAT GCCATCCGTA AGATGCTTTT CTGTGACTGG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TGAGTACTCA ACCAAGTCAT TCTGAGAATA GTGTATGCGG CGACCGAGTT GCTCTTGCCC GGCGTCAATA CGGGATAATA CCGCGCCACA TAGCAGAACT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TTAAAAGTGC TCATCATTGG AAAACGTTCT TCGGGGCGAA AACTCTCAAG GATCTTACCG CTGTTGAGAT CCAGTTCGAT GTAACCCACT CGTGCACCCA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

ACTGATCTTC AGCATCTTTT ACTTTCACCA GCGTTTCTGG GTGAGCAAAA ACAGGAAGGC AAAATGCCGC AAAAAAGGGA ATAAGGGCGA CACGGAAATG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TTGAATACTC ATACTCTTCC TTTTTCAATA TTATTGAAGC ATTTATCAGG GTTATTGTCT CATGAGCGGA TACATATTTG AATGTATTTA GAAAAATAAA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CAAATAGGGG TTCCGCGCAC ATTTCCCCGA AAAGTGCCAC CTGACGCGCC CTGTAGCGGC GCATTAAGCG CGGCGGGTGT GGTGGTTACG CGCAGCGTGA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CCGCTACACT TGCCAGCGCC CTAGCGCCCG CTCCTTTCGC TTTCTTCCCT TCCTTTCTCG CCACGTTCGC CGGCTTTCCC CGTCAAGCTC TAAATCGGGG 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GCTCCCTTTA GGGTTCCGAT TTAGTGCTTT ACGGCACCTC GACCCCAAAA AACTTGATTA GGGTGATGGT TCACGTAGTG GGCCATCGCC CTGATAGACG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GTTTTTCGCC CTTTGACGTT GGAGTCCACG TTCTTTAATA GTGGACTCTT GTTCCAAACT GGAACAACAC TCAACCCTAT CTCGGTCTAT TCTTTTGATT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TATAAGGGAT TTTGCCGATT TCGGCCTATT GGTTAAAAAA TGAGCTGATT TAACAAAAAT TTAACGCGAA TTTTAACAAA ATATTAACGT TTACAATTTC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

CCATTCGCCA TTCAGGCTGC GCAACTGTTG GGAAGGGCGA TCGGTGCGGG CCTCTTCGCT ATTACGCCAG CCCAAGCTAC CATGATAAGT AAGTAATATT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AAGGTACGGG AGGTACTTGG AGCGGCCGCA ATAAAATATC TTTATTTTCA TTACATCTGT GTGTTGGTTT TTTGTGTGAA TCGATAGTAC TAACATACGC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TCTCCATCAA AACAAAACGA AACAAAACAA ACTAGCAAAA TAGGCTGTCC CCAGTGCAAG TGCAGGTGCC AGAACATTTC TCTATCGATA
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581

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):

50-985

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):

1145-2797

Remarks:

Authors did not specify how they produced T7-based transcripts. It is our guess they have used BamHI
restriction site for linearization.

Citations:

Mitchell S. A., Spriggs K. A., Bushell M., Evans J. R., Stoneley M., Le Quesne J. P., Spriggs R. V., Willis A. E. (2005) Identification of a motif that mediates polypyrimidine tract-binding protein-dependent internal ribosome entry. Genes Dev. 19(13):1556-1571

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `KMI2`	The functional status of IRES: `functional`

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

1032-1129

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `47`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `144`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-113`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-16`

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

GAATTCcctc ctcctcctcc tcctcccctc ctcctcctcc tcctccGAAT TCggaggagg aggaggagga ggggaggagg aggaggagga ggGAATTC
(((((((((( (((((((((( (((((((((( (((((((((( ((((((.... ..)))))))) )))))))))) )))))))))) )))))))))) ))))))))
^1032      ^1042      ^1052      ^1062      ^1072      ^1082      ^1092      ^1102      ^1112      ^1122

Rendering structure of Synthetic/engineered IRES in an artificial transcript 98 nt long with energy of -110.60 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 534

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vitro The in vitro translation system:
rabbit reticulocytes lysate

The organism used for translation:

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

100.000

	Name of the plasmid used as the negative control. `pRF`
	`IRESite Id` of the plasmid used as negative control. `231`
	The relative translation efficiency in % of the negative control: `10.000`
	The size (length) of intercistronic region in the negative control: `67`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_with_GpppG_cap_without_polyA_tail

Remarks:

Data from Figure 2I. It is suspicious that authors used as the control pRF-based transcripts instead of
pRKMI(1/2)F based transcripts without supplemented PTB proteins. However, the data showing that unr and La
protein do not bind to pRKMI(1/2)F transcripts so results for these two supplemented proteins confirm that
they most probably wanted to write in the figure legend that they used as the control RRL with same plasmids
but without supplemented PTB.

Citations:

IRES trans-acting factor (ITAFS):

IRES trans-acting factor (ITAF):

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

OPTIONAL: The interacting RNA base range (if any):
1033-1076

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

ITAF abbreviated name:
PTB-1

ITAF fullname:
polypyrimidine tract-binding protein isoform 1

ITAF description (long):
polypyrimidine tract-binding protein isoform 1 binds dsRNA with (CCU)n motif where n is at least 3. By SELEX approach it was found it binds to 5'-CAGCCUGGUGCCUCUCUUUCGG-3' (Singh et al. (1995) Science 268:1173-1176) but also UCUU or UCUUC within pyrimidine-rich sequence (Perez et al. (1997) RNA3:1334-1347).

3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_and_must_be_supplemented

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figure 2I.

Citations:

IRES trans-acting factor (ITAF):

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

OPTIONAL: The interacting RNA base range (if any):
1033-1076

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
PTB-2

ITAF fullname:
polypyrimidine tract-binding protein isoform 2

ITAF description (long):
polypyrimidine tract-binding protein isoform 2 binds (CCU)n motif

3.2.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_and_must_be_supplemented

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figure 2I.

Citations:

IRES trans-acting factor (ITAF):

Version: `1`	Last change: `2008-07-12 14:24:06`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
no_direct_interaction_with_rna

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
PTB-4

ITAF fullname:
polypyrimidine tract-binding protein isoform 4

ITAF description (long):
polypyrimidine tract-binding protein isoform 4 binds (CCU)n motif

3.3.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figure 2I.

Citations:

IRES trans-acting factor (ITAF):

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna

OPTIONAL: The interacting RNA base range (if any):
1033-1076

ITAF protein characteristics:

Version: `1`	Last change: `2008-07-11 23:17:15`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
nPTB

ITAF fullname:
polypyrimidine tract-binding protein isoform n

ITAF description (long):
neuronal polypyrimidine tract-binding protein isoform binds (CCU)n motif

3.4.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
required_and_must_be_supplemented

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figure 2I.

Citations:

IRES trans-acting factor (ITAF):

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
unknown

ITAF protein characteristics:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Václav Vopálenský

ITAF abbreviated name:
Unr

ITAF fullname:
upstream of N-ras

ITAF description (long):
Unr protein is known to bind to gaagaaguaa

3.5.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figure 2I.

Citations:

IRES trans-acting factor (ITAF):

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

Type of the interaction between ITAF and the RNA subject to translation:
unknown

ITAF protein characteristics:

Version: `2`	Last change: `2009-08-29 12:19:15`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

ITAF abbreviated name:
La

ITAF fullname:
La autoantigen

ITAF description (long):
La autoantigen (p52), 52 kDa RNA binding protein, predominantly localized to nucleus, unwinds the dsRNA in ATP-dependent manner, forms a dimer

3.6.2. Organisms or in vitro systems where this ITAF was functionally studied:

Organism or in vitro system where ITAF was shown:

Necessity of ITAF for translation in this particular organism or system:
no_effect_on_translation

Method used to demonstrate ITAF effect:
in_vitro In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate

Remarks:

Data from Figure 2I.

Citations:

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 20

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The function of the 2D structure: `IRES`	The 2D structure causes frameshift: `unknown`

The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1032-1147

The underlying nucleic acid sequence and structure of the mapped region:

GAATTCcctc ctcctcctcc tcctcccctc ctcctcctcc tcctccGAAT TCggaggagg aggaggagga ggggaggagg aggaggagga ggGAATTCGT 
(((((((((( (((((((((( (((((((((( (((((((((( ((((((.... ..)))))))) )))))))))) )))))))))) )))))))))) )))))))).. 
^1032      ^1042      ^1052      ^1062      ^1072      ^1082      ^1092      ^1102      ^1112      ^1122      

TGGTAAAGCC ACCATG
.......... ......
^1132      ^1142

Rendering structure of Synthetic/engineered IRES in an artificial transcript 116 nt long with energy of -111.90 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.

Remarks:

Data from Figure 2A(ii).

Citations:

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