IRESite_Id:481 characteristics of KMI1 IRES studied in pRKMI1F plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `481`	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 KMI1 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 ctcctccGAA TTCggaggag gaggaggagg aggGAATTCG TTGGTAAAGC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CACCATGGAA GACGCCAAAA ACATAAAGAA AGGCCCGGCG CCATTCTATC CGCTGGAAGA TGGAACCGCT GGAGAGCAAC TGCATAAGGC TATGAAGAGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TACGCCCTGG TTCCTGGAAC AATTGCTTTT ACAGATGCAC ATATCGAGGT GGACATCACT TACGCTGAGT ACTTCGAAAT GTCCGTTCGG TTGGCAGAAG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CTATGAAACG ATATGGGCTG AATACAAATC ACAGAATCGT CGTATGCAGT GAAAACTCTC TTCAATTCTT TATGCCGGTG TTGGGCGCGT TATTTATCGG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AGTTGCAGTT GCGCCCGCGA ACGACATTTA TAATGAACGT GAATTGCTCA ACAGTATGGG CATTTCGCAG CCTACCGTGG TGTTCGTTTC CAAAAAGGGG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTGCAAAAAA TTTTGAACGT GCAAAAAAAG CTCCCAATCA TCCAAAAAAT TATTATCATG GATTCTAAAA CGGATTACCA GGGATTTCAG TCGATGTACA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CGTTCGTCAC ATCTCATCTA CCTCCCGGTT TTAATGAATA CGATTTTGTG CCAGAGTCCT TCGATAGGGA CAAGACAATT GCACTGATCA TGAACTCCTC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGGATCTACT GGTCTGCCTA AAGGTGTCGC TCTGCCTCAT AGAACTGCCT GCGTGAGATT CTCGCATGCC AGAGATCCTA TTTTTGGCAA TCAAATCATT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CCGGATACTG CGATTTTAAG TGTTGTTCCA TTCCATCACG GTTTTGGAAT GTTTACTACA CTCGGATATT TGATATGTGG ATTTCGAGTC GTCTTAATGT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATAGATTTGA AGAAGAGCTG TTTCTGAGGA GCCTTCAGGA TTACAAGATT CAAAGTGCGC TGCTGGTGCC AACCCTATTC TCCTTCTTCG CCAAAAGCAC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TCTGATTGAC AAATACGATT TATCTAATTT ACACGAAATT GCTTCTGGTG GCGCTCCCCT CTCTAAGGAA GTCGGGGAAG CGGTTGCCAA GAGGTTCCAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTGCCAGGTA TCAGGCAAGG ATATGGGCTC ACTGAGACTA CATCAGCTAT TCTGATTACA CCCGAGGGGG ATGATAAACC GGGCGCGGTC GGTAAAGTTG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTCCATTTTT TGAAGCGAAG GTTGTGGATC TGGATACCGG GAAAACGCTG GGCGTTAATC AAAGAGGCGA ACTGTGTGTG AGAGGTCCTA TGATTATGTC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CGGTTATGTA AACAATCCGG AAGCGACCAA CGCCTTGATT GACAAGGATG GATGGCTACA TTCTGGAGAC ATAGCTTACT GGGACGAAGA CGAACACTTC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTCATCGTTG ACCGCCTGAA GTCTCTGATT AAGTACAAAG GCTATCAGGT GGCTCCCGCT GAATTGGAAT CCATCTTGCT CCAACACCCC AACATCTTCG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACGCAGGTGT CGCAGGTCTT CCCGACGATG ACGCCGGTGA ACTTCCCGCC GCCGTTGTTG TTTTGGAGCA CGGAAAGACG ATGACGGAAA AAGAGATCGT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GGATTACGTC GCCAGTCAAG TAACAACCGC GAAAAAGTTG CGCGGAGGAG TTGTGTTTGT GGACGAAGTA CCGAAAGGTC TTACCGGAAA ACTCGACGCA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AGAAAAATCA GAGAGATCCT CATAAAGGCC AAGAAGGGCG GAAAGATCGC CGTGTAATTC TAGAGTCGGG GCGGCCGGCC GCTTCGAGCA GACATGATAA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GATACATTGA TGAGTTTGGA CAAACCACAA CTAGAATGCA GTGAAAAAAA TGCTTTATTT GTGAAATTTG TGATGCTATT GCTTTATTTG TAACCATTAT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AAGCTGCAAT AAACAAGTTA ACAACAACAA TTGCATTCAT TTTATGTTTC AGGTTCAGGG GGAGGTGTGG GAGGTTTTTT AAAGCAAGTA AAACCTCTAC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AAATGTGGTA AAATCGATAA GGATCTGAAC GATGGAGCGG AGAATGGGCG GAACTGGGCG GAGTTAGGGG CGGGATGGGC GGAGTTAGGG GCGGGACTAT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGTTGCTGAC TAATTGAGAT GCATGCTTTG CATACTTCTG CCTGCTGGGG AGCCTGGGGA CTTTCCACAC CTGGTTGCTG ACTAATTGAG ATGCATGCTT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGCATACTTC TGCCTGCTGG GGAGCCTGGG GACTTTCCAC ACCCTAACTG ACACACATTC CACAGCG
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_except_3UTR

The name of the plasmid:
pRKMI1F 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 tcctccGAAT TCggaggagg aggaggagga ggGAATTCGT TGGTAAAGCC ACCATGGAAG ACGCCAAAAA CATAAAGAAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGCCCGGCGC CATTCTATCC GCTGGAAGAT GGAACCGCTG GAGAGCAACT GCATAAGGCT ATGAAGAGAT ACGCCCTGGT TCCTGGAACA ATTGCTTTTA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CAGATGCACA TATCGAGGTG GACATCACTT ACGCTGAGTA CTTCGAAATG TCCGTTCGGT TGGCAGAAGC TATGAAACGA TATGGGCTGA ATACAAATCA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CAGAATCGTC GTATGCAGTG AAAACTCTCT TCAATTCTTT ATGCCGGTGT TGGGCGCGTT ATTTATCGGA GTTGCAGTTG CGCCCGCGAA CGACATTTAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AATGAACGTG AATTGCTCAA CAGTATGGGC ATTTCGCAGC CTACCGTGGT GTTCGTTTCC AAAAAGGGGT TGCAAAAAAT TTTGAACGTG CAAAAAAAGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TCCCAATCAT CCAAAAAATT ATTATCATGG ATTCTAAAAC GGATTACCAG GGATTTCAGT CGATGTACAC GTTCGTCACA TCTCATCTAC CTCCCGGTTT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TAATGAATAC GATTTTGTGC CAGAGTCCTT CGATAGGGAC AAGACAATTG CACTGATCAT GAACTCCTCT GGATCTACTG GTCTGCCTAA AGGTGTCGCT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTGCCTCATA GAACTGCCTG CGTGAGATTC TCGCATGCCA GAGATCCTAT TTTTGGCAAT CAAATCATTC CGGATACTGC GATTTTAAGT GTTGTTCCAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TCCATCACGG TTTTGGAATG TTTACTACAC TCGGATATTT GATATGTGGA TTTCGAGTCG TCTTAATGTA TAGATTTGAA GAAGAGCTGT TTCTGAGGAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CCTTCAGGAT TACAAGATTC AAAGTGCGCT GCTGGTGCCA ACCCTATTCT CCTTCTTCGC CAAAAGCACT CTGATTGACA AATACGATTT ATCTAATTTA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CACGAAATTG CTTCTGGTGG CGCTCCCCTC TCTAAGGAAG TCGGGGAAGC GGTTGCCAAG AGGTTCCATC TGCCAGGTAT CAGGCAAGGA TATGGGCTCA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTGAGACTAC ATCAGCTATT CTGATTACAC CCGAGGGGGA TGATAAACCG GGCGCGGTCG GTAAAGTTGT TCCATTTTTT GAAGCGAAGG TTGTGGATCT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GGATACCGGG AAAACGCTGG GCGTTAATCA AAGAGGCGAA CTGTGTGTGA GAGGTCCTAT GATTATGTCC GGTTATGTAA ACAATCCGGA AGCGACCAAC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GCCTTGATTG ACAAGGATGG ATGGCTACAT TCTGGAGACA TAGCTTACTG GGACGAAGAC GAACACTTCT TCATCGTTGA CCGCCTGAAG TCTCTGATTA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AGTACAAAGG CTATCAGGTG GCTCCCGCTG AATTGGAATC CATCTTGCTC CAACACCCCA ACATCTTCGA CGCAGGTGTC GCAGGTCTTC CCGACGATGA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGCCGGTGAA CTTCCCGCCG CCGTTGTTGT TTTGGAGCAC GGAAAGACGA TGACGGAAAA AGAGATCGTG GATTACGTCG CCAGTCAAGT AACAACCGCG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAAAAGTTGC GCGGAGGAGT TGTGTTTGTG GACGAAGTAC CGAAAGGTCT TACCGGAAAA CTCGACGCAA GAAAAATCAG AGAGATCCTC ATAAAGGCCA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AGAAGGGCGG AAAGATCGCC GTGTAATTCT AGAGTCGGGG CGGCCGGCCG CTTCGAGCAG ACATGATAAG ATACATTGAT GAGTTTGGAC AAACCACAAC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TAGAATGCAG TGAAAAAAAT GCTTTATTTG TGAAATTTGT GATGCTATTG CTTTATTTGT AACCATTATA AGCTGCAATA AACAAGTTAA CAACAACAAT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGCATTCATT TTATGTTTCA GGTTCAGGGG GAGGTGTGGG AGGTTTTTTA AAGCAAGTAA AACCTCTACA AATGTGGTAA AATCGATAAG GATCTGAACG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATGGAGCGGA GAATGGGCGG AACTGGGCGG AGTTAGGGGC GGGATGGGCG GAGTTAGGGG CGGGACTATG GTTGCTGACT AATTGAGATG CATGCTTTGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ATACTTCTGC CTGCTGGGGA GCCTGGGGAC TTTCCACACC TGGTTGCTGA CTAATTGAGA TGCATGCTTT GCATACTTCT GCCTGCTGGG GAGCCTGGGG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ACTTTCCACA CCCTAACTGA CACACATTCC ACAGCGGATC CGTCGACCGA TGCCCTTGAG AGCCTTCAAC CCAGTCAGCT CCTTCCGGTG GGCGCGGGGC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ATGACTATCG TCGCCGCACT TATGACTGTC TTCTTTATCA TGCAACTCGT AGGACAGGTG CCGGCAGCGC TCTTCCGCTT CCTCGCTCAC TGACTCGCTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CGCTCGGTCG TTCGGCTGCG GCGAGCGGTA TCAGCTCACT CAAAGGCGGT AATACGGTTA TCCACAGAAT CAGGGGATAA CGCAGGAAAG AACATGTGAG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CAAAAGGCCA GCAAAAGGCC AGGAACCGTA AAAAGGCCGC GTTGCTGGCG TTTTTCCATA GGCTCCGCCC CCCTGACGAG CATCACAAAA ATCGACGCTC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AAGTCAGAGG TGGCGAAACC CGACAGGACT ATAAAGATAC CAGGCGTTTC CCCCTGGAAG CTCCCTCGTG CGCTCTCCTG TTCCGACCCT GCCGCTTACC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GGATACCTGT CCGCCTTTCT CCCTTCGGGA AGCGTGGCGC TTTCTCAATG CTCACGCTGT AGGTATCTCA GTTCGGTGTA GGTCGTTCGC TCCAAGCTGG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GCTGTGTGCA CGAACCCCCC GTTCAGCCCG ACCGCTGCGC CTTATCCGGT AACTATCGTC TTGAGTCCAA CCCGGTAAGA CACGACTTAT CGCCACTGGC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AGCAGCCACT GGTAACAGGA TTAGCAGAGC GAGGTATGTA GGCGGTGCTA CAGAGTTCTT GAAGTGGTGG CCTAACTACG GCTACACTAG AAGGACAGTA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TTTGGTATCT GCGCTCTGCT GAAGCCAGTT ACCTTCGGAA AAAGAGTTGG TAGCTCTTGA TCCGGCAAAC AAACCACCGC TGGTAGCGGT GGTTTTTTTG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TTTGCAAGCA GCAGATTACG CGCAGAAAAA AAGGATCTCA AGAAGATCCT TTGATCTTTT CTACGGGGTC TGACGCTCAG TGGAACGAAA ACTCACGTTA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AGGGATTTTG GTCATGAGAT TATCAAAAAG GATCTTCACC TAGATCCTTT TAAATTAAAA ATGAAGTTTT AAATCAATCT AAAGTATATA TGAGTAAACT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TGGTCTGACA GTTACCAATG CTTAATCAGT GAGGCACCTA TCTCAGCGAT CTGTCTATTT CGTTCATCCA TAGTTGCCTG ACTCCCCGTC GTGTAGATAA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CTACGATACG GGAGGGCTTA CCATCTGGCC CCAGTGCTGC AATGATACCG CGAGACCCAC GCTCACCGGC TCCAGATTTA TCAGCAATAA ACCAGCCAGC 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CGGAAGGGCC GAGCGCAGAA GTGGTCCTGC AACTTTATCC GCCTCCATCC AGTCTATTAA TTGTTGCCGG GAAGCTAGAG TAAGTAGTTC GCCAGTTAAT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

AGTTTGCGCA ACGTTGTTGC CATTGCTACA GGCATCGTGG TGTCACGCTC GTCGTTTGGT ATGGCTTCAT TCAGCTCCGG TTCCCAACGA TCAAGGCGAG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TTACATGATC CCCCATGTTG TGCAAAAAAG CGGTTAGCTC CTTCGGTCCT CCGATCGTTG TCAGAAGTAA GTTGGCCGCA GTGTTATCAC TCATGGTTAT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

GGCAGCACTG CATAATTCTC TTACTGTCAT GCCATCCGTA AGATGCTTTT CTGTGACTGG TGAGTACTCA ACCAAGTCAT TCTGAGAATA GTGTATGCGG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CGACCGAGTT GCTCTTGCCC GGCGTCAATA CGGGATAATA CCGCGCCACA TAGCAGAACT TTAAAAGTGC TCATCATTGG AAAACGTTCT TCGGGGCGAA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AACTCTCAAG GATCTTACCG CTGTTGAGAT CCAGTTCGAT GTAACCCACT CGTGCACCCA ACTGATCTTC AGCATCTTTT ACTTTCACCA GCGTTTCTGG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

GTGAGCAAAA ACAGGAAGGC AAAATGCCGC AAAAAAGGGA ATAAGGGCGA CACGGAAATG TTGAATACTC ATACTCTTCC TTTTTCAATA TTATTGAAGC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ATTTATCAGG GTTATTGTCT CATGAGCGGA TACATATTTG AATGTATTTA GAAAAATAAA CAAATAGGGG TTCCGCGCAC ATTTCCCCGA AAAGTGCCAC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CTGACGCGCC CTGTAGCGGC GCATTAAGCG CGGCGGGTGT GGTGGTTACG CGCAGCGTGA CCGCTACACT TGCCAGCGCC CTAGCGCCCG CTCCTTTCGC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TTTCTTCCCT TCCTTTCTCG CCACGTTCGC CGGCTTTCCC CGTCAAGCTC TAAATCGGGG GCTCCCTTTA GGGTTCCGAT TTAGTGCTTT ACGGCACCTC 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GACCCCAAAA AACTTGATTA GGGTGATGGT TCACGTAGTG GGCCATCGCC CTGATAGACG GTTTTTCGCC CTTTGACGTT GGAGTCCACG TTCTTTAATA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

GTGGACTCTT GTTCCAAACT GGAACAACAC TCAACCCTAT CTCGGTCTAT TCTTTTGATT TATAAGGGAT TTTGCCGATT TCGGCCTATT GGTTAAAAAA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TGAGCTGATT TAACAAAAAT TTAACGCGAA TTTTAACAAA ATATTAACGT TTACAATTTC CCATTCGCCA TTCAGGCTGC GCAACTGTTG GGAAGGGCGA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TCGGTGCGGG CCTCTTCGCT ATTACGCCAG CCCAAGCTAC CATGATAAGT AAGTAATATT AAGGTACGGG AGGTACTTGG AGCGGCCGCA ATAAAATATC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

TTTATTTTCA TTACATCTGT GTGTTGGTTT TTTGTGTGAA TCGATAGTAC TAACATACGC TCTCCATCAA AACAAAACGA AACAAAACAA ACTAGCAAAA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TAGGCTGTCC CCAGTGCAAG TGCAGGTGCC AGAACATTTC TCTATCGATA
^6501      ^6511      ^6521      ^6531      ^6541

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):

1105-2757

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: `KMI1`	The functional status of IRES: `functional`

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

1032-1089

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: `104`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-73`	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 tcctccGAAT TCggaggagg aggaggagga ggGAATTC
(((((((((( (((((((((( ((((((.... ..)))))))) )))))))))) ))))))))
^1032      ^1042      ^1052      ^1062      ^1072      ^1082

Rendering structure of Synthetic/engineered IRES in an artificial transcript 58 nt long with energy of -57.20 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: 533

Version: `1`	Last change: `2008-07-12 14:03:17`
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: `13.800`
	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):
1033-1056

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 2A.

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):
1033-1056

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 2A.

Citations:

IRES trans-acting factor (ITAF):

Version: `1`	Last change: `2008-07-12 14:23:08`
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 2A.

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):
1033-1056

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 2A.

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 2A.

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 2A.

Citations:

Regions with experimentally determined secondary structures:

A region with the experimentally determined secondary structure:

IRESite 2D Struct Id: 19

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):
1032-1107

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

GAATTCcctc ctcctcctcc tcctccGAAT TCggaggagg aggaggagga ggGAATTCGT TGGTAAAGCC ACCATG
(((((((((( (((((((((( ((((((.... ..)))))))) )))))))))) )))))))).. .......... ......
^1032      ^1042      ^1052      ^1062      ^1072      ^1082      ^1092      ^1102

Rendering structure of Synthetic/engineered IRES in an artificial transcript 76 nt long with energy of -58.50 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(i). The transcript actually mapped was probably derived from pSKUTRL although it was not
clearly stated neither in the article nor Supplementary material A. Moreover, the sequence of pSKUTRL plasmid
is not described.

Citations:

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