IRESite_Id:50 characteristics of MYT2_997-1152 IRES studied in pSL100 plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `50`	Version: `9`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-08-18 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2008-07-01 11:58:09`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_translationally_characterized

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

The mRNA/+RNA description:

Putative spliced bicistronic mRNA derived from pSL based plasmid with part of the 5' UTR (nt 997 to nt 1152)
of human myelin transcription factor 2 (MYT2) mRNA cloned between chloramphenicol acetyltransferase and
firefly luciferase.

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

AGAGAACCCA CTGCTTACTG GCTTATCGAA ATTAATACGA CTCACTATAG GGAGACCCAA GCTTGCCACC ATGGAGAAAA AAATCACTGG ATATACCACC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GTTGATATAT CCCAATGGCA TCGTAAAGAA CATTTTGAGG CATTTCAGTC AGTTGCTCAA TGTACCTATA ACCAGACCGT TCAGCTGGAT ATTACGGCCT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TTTTAAAGAC CGTAAAGAAA AATAAGCACA AGTTTTATCC GGCCTTTATT CACATTCTTG CCCGCCTGAT GAATGCTCAT CCGGAATTCC GTATGGCAAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GAAAGACGGT GAGCTGGTGA TATGGGATAG TGTTCACCCT TGTTACACCG TTTTCCATGA GCAAACTGAA ACGTTTTCAT CGCTCTGGAG TGAATACCAC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GACGATTTCC GGCAGTTTCT ACACATATAT TCGCAAGATG TGGCGTGTTA CGGTGAAAAC CTGGCCTATT TCCCTAAAGG GTTTATTGAG AATATGTTTT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCGTCTCAGC CAATCCCTGG GTGAGTTTCA CCAGTTTTGA TTTAAACGTG GCCAATATGG ACAACTTCTT CGCCCCCGTT TTCACCATGG GCAAATATTA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TACGCAAGGC GACAAGGTGC TGATGCCGCT GGCGATTCAG GTTCATCATG CCGTCTGTGA TGGCTTCCAT GTCGGCAGAA TGCTTAATGA ATTACAACAG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TACTGCGATG AGTGGCAGGG CGGGGCGTAA TTAGATGAGG ATCCACTAGT AACGGCCGCG CCCGTAAAAT GGGAACGTAG AACTCGTCAT GACACTTGTG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GTAAAATAAC ATTATTCGCT TGCAAAAAAC GATGTACTTT GACAATTTAA GACACAAAAA AACACAACCT CGACAATTTA GGAGTTAGAG AGGTCGTGTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTGAGATTAG TGAGCGGCCG CAAAATGGAA GACGCCAAAA ACATAAAGAA AGGCCCGGCG CCATTCTATC CTCTAGAGGA TGGAACCGCT GGAGAGCAAC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TGCATAAGGC TATGAAGAGA TACGCCCTGG TTCCTGGAAC AATTGCTTTT ACAGATGCAC ATATCGAGGT GAACATCACG TACGCGGAAT ACTTCGAAAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GTCCGTTCGG TTGGCAGAAG CTATGAAACG ATATGGGCTG AATACAAATC ACAGAATCGT CGTATGCAGT GAAAACTCTC TTCAATTCTT TATGCCGGTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTGGGCGCGT TATTTATCGG AGTTGCAGTT GCGCCCGCGA ACGACATTTA TAATGAACGT GAATTGCTCA ACAGTATGAA CATTTCGCAG CCTACCGTAG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TGTTTGTTTC CAAAAAGGGG TTGCAAAAAA TTTTGAACGT GCAAAAAAAA TTACCAATAA TCCAGAAAAT TATTATCATG GATTCTAAAA CGGATTACCA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GGGATTTCAG TCGATGTACA CGTTCGTCAC ATCTCATCTA CCTCCCGGTT TTAATGAATA CGATTTTGTA CCAGAGTCCT TTGATCGTGA CAAAACAATT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GCACTGATAA TGAATTCCTC TGGATCTACT GGGTTACCTA AGGGTGTGGC CCTTCCGCAT AGAACTGCCT GCGTCAGATT CTCGCATGCC AGAGATCCTA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTTTTGGCAA TCAAATCATT CCGGATACTG CGATTTTAAG TGTTGTTCCA TTCCATCACG GTTTTGGAAT GTTTACTACA CTCGGATATT TGATATGTGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATTTCGAGTC GTCTTAATGT ATAGATTTGA AGAAGAGCTG TTTTTACGAT CCCTTCAGGA TTACAAAATT CAAAGTGCGT TGCTAGTACC AACCCTATTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCATTCTTCG CCAAAAGCAC TCTGATTGAC AAATACGATT TATCTAATTT ACACGAAATT GCTTCTGGGG GCGCACCTCT TTCGAAAGAA GTCGGGGAAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGGTTGCAAA ACGCTTCCAT CTTCCAGGGA TACGACAAGG ATATGGGCTC ACTGAGACTA CATCAGCTAT TCTGATTACA CCCGAGGGGG ATGATAAACC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGGCGCGGTC GGTAAAGTTG TTCCATTTTT TGAAGCGAAG GTTGTGGATC TGGATACCGG GAAAACGCTG GGCGTTAATC AGAGAGGCGA ATTATGTGTC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AGAGGACCTA TGATTATGTC CGGTTATGTA AACAATCCGG AAGCGACCAA CGCCTTGATT GACAAGGATG GATGGCTACA TTCTGGAGAC ATAGCTTACT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GGGACGAAGA CGAACACTTC TTCATAGTTG ACCGCTTGAA GTCTTTAATT AAATACAAAG GATATCAGGT GGCCCCCGCT GAATTGGAAT CGATATTGTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACAACACCCC AACATCTTCG ACGCGGGCGT GGCAGGTCTT CCCGACGATG ACGCCGGTGA ACTTCCCGCC GCCGTTGTTG TTTTGGAGCA CGGAAAGACG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ATGACGGAAA AAGAGATCGT GGATTACGTC GCCAGTCAAG TAACAACCGC GAAAAAGTTG CGCGGAGGAG TTGTGTTTGT GGACGAAGTA CCGAAAGGTC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTACCGGAAA ACTCGACGCA AGAAAAATCA GAGAGATCCT CATAAAGGCC AAGAAGGGCG GAAAGTCCAA ATTGTAACTC GAGCATGCAT CTAGAGGGCC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTATTCTATA GTGTCACCTA AATGCTAGAG GATCTTTGTG AAGGAACCTT ACTTCTGTGG TGTGACATAA TTGGACAAAC TACCTACAGA GATTTAAAGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TCTAATCCAA CCTATGGAAC TGATGAATGG GAGCAGTGGT GGAATGCCTT TAATGAGGAA AACCTGTTTT GCTCAGAAGA AATGCCATCT AGTGATGATG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AGGCTACTGC TGACTCTCAA CATTCTACTC CTCCAAAAAA GAAGAGAAAG GTAGAAGACC CCAAGGACTT TCCTTCAGAA TTGCTAAGTT TTTTGAGTCA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGCTGTGTTT AGTAATAGAA CTCTTGCTTG CTTTGCTATT TACACCACAA AGGAAAAAGC TGCACTGCTA TACAAGAAAA TTATGGAAAA ATATTTGATG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TATAGTGCCT TGACTAGAGA TCATAATCAG CCATACCACA TTTGTAGAGG TTTTACTTGC TTTAAAAAAC CTCCCACACC TCCCCCTGAA CCTGAAACAT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAAATGAATG CAATTGTTGT TGTTAACTTG TTTATTGCAG CTTATAATGG TTACAAATAA A
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161

Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

The name of the plasmid:
pSL100 The name of the promoter used to express this mRNA:
CMV

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:
MYT2

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:

TCCGGTAAGC GGCAGGGTCG GAACAGGAGA GCGCACGAGG GAGCTTCCAG GGGGAAACGC CTGGTATCTT TATAGTCCTG TCGGGTTTCG CCACCTCTGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CTTGAGCGTC GATTTTTGTG ATGCTCGTCA GGGGGGCGGA GCCTATGGAA AAACGCCAGC AACGCAAGCT AGCTTCTAGC TAGAAATTGT AAACGTTAAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATTTTGTTAA AATTCGCGTT AAATTTTTGT TAAATCAGCT CATTTTTTAA CCAATAGGCC GAAATCGGCA AAATCCCTTA TAAATCAAAA GAATAGCCCG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGATAGGGTT GAGTGTTGTT CCAGTTTGGA ACAAGAGTCC ACTATTAAAG AACGTGGACT CCAACGTCAA AGGGCGAAAA ACCGTCTATC AGGGCGATGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCGCCCACTA CGTGAACCAT CACCCAAATC AAGTTTTTTG GGGTCGAGGT GCCGTAAAGC ACTAAATCGG AACCCTAAAG GGAGCCCCCG ATTTAGAGCT 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TGACGGGGAA AGCCGGCGAA CGTGGCGAGA AAGGAAGGGA AGAAAGCGAA AGGAGCGGGC GCTAGGGCGC TGGCAAGTGT AGCGGTCACG CTGCGCGTAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CCACCACACC CGCCGCGCTT AATGCGCCGC TACAGGGCGC GTACTATGGT TGCTTTGACG AGACCGTATA ACGTGCTTTC CTCGTTGGAA TCAGAGCGGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGCTAAACAG GAGGCCGATT AAAGGGATTT TAGACAGGAA CGGTACGCCA GCTGGATTAC CGCGGTCTTT CTCAACGTAA CACTTTACAG CGGCGCGTCA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TTTGATATGA TGCGCCCCGC TTCCCGATAA GGGAGCAGGC CAGTAAAAGC ATTACCCGTG GTGGGGTTCC CGAGCGGCCA AAGGGAGCAG ACTCTAAATC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGCCGTCATC GACTTCGAAG GTTCGAATCC TTCCCCCACC ACCATCACTT TCAAAAGTCC GAAAGAATCT GCTCCCTGCT TGTGTGTTGG AGGTCGCTGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GTAGTGCGCG AGTAAAATTT AAGCTACAAC AAGGCAAGGC TTGACCGACA ATTGCATGAA GAATCTGCTT AGGGTTAGGC GTTTTGCGCT GCTTCGCGAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GTACGGGCCA GATATACGCG TTGACATTGA TTATTGACTA GTTATTAATA GTAATCAATT ACGGGGTCAT TAGTTCATAG CCCATATATG GAGTTCCGCG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTACATAACT TACGGTAAAT GGCCCGCCTG GCTGACCGCC CAACGACCCC CGCCCATTGA CGTCAATAAT GACGTATGTT CCCATAGTAA CGCCAATAGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GACTTTCCAT TGACGTCAAT GGGTGGACTA TTTACGGTAA ACTGCCCACT TGGCAGTACA TCAAGTGTAT CATATGCCAA GTACGCCCCC TATTGACGTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AATGACGGTA AATGGCCCGC CTGGCATTAT GCCCAGTACA TGACCTTATG GGACTTTCCT ACTTGGCAGT ACATCTACGT ATTAGTCATC GCTATTACCA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGGTGATGCG GTTTTGGCAG TACATCAATG GGCGTGGATA GCGGTTTGAC TCACGGGGAT TTCCAAGTCT CCACCCCATT GACGTCAATG GGAGTTTGTT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TTGGCACCAA AATCAACGGG ACTTTCCAAA ATGTCGTAAC AACTCCGCCC CATTGACGCA AATGGGCGGT AGGCGTGTAC GGTGGGAGGT CTATATAAGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGAGCTCTCT GGCTAACTAG AGAACCCACT GCTTACTGGC TTATCGAAAT TAATACGACT CACTATAGGG AGACCCAAGC TTGCCACCAT GGAGAAAAAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ATCACTGGAT ATACCACCGT TGATATATCC CAATGGCATC GTAAAGAACA TTTTGAGGCA TTTCAGTCAG TTGCTCAATG TACCTATAAC CAGACCGTTC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGCTGGATAT TACGGCCTTT TTAAAGACCG TAAAGAAAAA TAAGCACAAG TTTTATCCGG CCTTTATTCA CATTCTTGCC CGCCTGATGA ATGCTCATCC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGAATTCCGT ATGGCAATGA AAGACGGTGA GCTGGTGATA TGGGATAGTG TTCACCCTTG TTACACCGTT TTCCATGAGC AAACTGAAAC GTTTTCATCG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTCTGGAGTG AATACCACGA CGATTTCCGG CAGTTTCTAC ACATATATTC GCAAGATGTG GCGTGTTACG GTGAAAACCT GGCCTATTTC CCTAAAGGGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTATTGAGAA TATGTTTTTC GTCTCAGCCA ATCCCTGGGT GAGTTTCACC AGTTTTGATT TAAACGTGGC CAATATGGAC AACTTCTTCG CCCCCGTTTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CACCATGGGC AAATATTATA CGCAAGGCGA CAAGGTGCTG ATGCCGCTGG CGATTCAGGT TCATCATGCC GTCTGTGATG GCTTCCATGT CGGCAGAATG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CTTAATGAAT TACAACAGTA CTGCGATGAG TGGCAGGGCG GGGCGTAATT AGATGAGGAT CCACTAGTAA CGGCCGCGCC CGTAAAATGG GAACGTAGAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CTCGTCATGA CACTTGTGGT AAAATAACAT TATTCGCTTG CAAAAAACGA TGTACTTTGA CAATTTAAGA CACAAAAAAA CACAACCTCG ACAATTTAGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AGTTAGAGAG GTCGTGTTTT GAGATTAGTG AGCGGCCGCA AAATGGAAGA CGCCAAAAAC ATAAAGAAAG GCCCGGCGCC ATTCTATCCT CTAGAGGATG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GAACCGCTGG AGAGCAACTG CATAAGGCTA TGAAGAGATA CGCCCTGGTT CCTGGAACAA TTGCTTTTAC AGATGCACAT ATCGAGGTGA ACATCACGTA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CGCGGAATAC TTCGAAATGT CCGTTCGGTT GGCAGAAGCT ATGAAACGAT ATGGGCTGAA TACAAATCAC AGAATCGTCG TATGCAGTGA AAACTCTCTT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CAATTCTTTA TGCCGGTGTT GGGCGCGTTA TTTATCGGAG TTGCAGTTGC GCCCGCGAAC GACATTTATA ATGAACGTGA ATTGCTCAAC AGTATGAACA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TTTCGCAGCC TACCGTAGTG TTTGTTTCCA AAAAGGGGTT GCAAAAAATT TTGAACGTGC AAAAAAAATT ACCAATAATC CAGAAAATTA TTATCATGGA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TTCTAAAACG GATTACCAGG GATTTCAGTC GATGTACACG TTCGTCACAT CTCATCTACC TCCCGGTTTT AATGAATACG ATTTTGTACC AGAGTCCTTT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GATCGTGACA AAACAATTGC ACTGATAATG AATTCCTCTG GATCTACTGG GTTACCTAAG GGTGTGGCCC TTCCGCATAG AACTGCCTGC GTCAGATTCT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CGCATGCCAG AGATCCTATT TTTGGCAATC AAATCATTCC GGATACTGCG ATTTTAAGTG TTGTTCCATT CCATCACGGT TTTGGAATGT TTACTACACT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CGGATATTTG ATATGTGGAT TTCGAGTCGT CTTAATGTAT AGATTTGAAG AAGAGCTGTT TTTACGATCC CTTCAGGATT ACAAAATTCA AAGTGCGTTG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CTAGTACCAA CCCTATTTTC ATTCTTCGCC AAAAGCACTC TGATTGACAA ATACGATTTA TCTAATTTAC ACGAAATTGC TTCTGGGGGC GCACCTCTTT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CGAAAGAAGT CGGGGAAGCG GTTGCAAAAC GCTTCCATCT TCCAGGGATA CGACAAGGAT ATGGGCTCAC TGAGACTACA TCAGCTATTC TGATTACACC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CGAGGGGGAT GATAAACCGG GCGCGGTCGG TAAAGTTGTT CCATTTTTTG AAGCGAAGGT TGTGGATCTG GATACCGGGA AAACGCTGGG CGTTAATCAG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AGAGGCGAAT TATGTGTCAG AGGACCTATG ATTATGTCCG GTTATGTAAA CAATCCGGAA GCGACCAACG CCTTGATTGA CAAGGATGGA TGGCTACATT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CTGGAGACAT AGCTTACTGG GACGAAGACG AACACTTCTT CATAGTTGAC CGCTTGAAGT CTTTAATTAA ATACAAAGGA TATCAGGTGG CCCCCGCTGA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ATTGGAATCG ATATTGTTAC AACACCCCAA CATCTTCGAC GCGGGCGTGG CAGGTCTTCC CGACGATGAC GCCGGTGAAC TTCCCGCCGC CGTTGTTGTT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TTGGAGCACG GAAAGACGAT GACGGAAAAA GAGATCGTGG ATTACGTCGC CAGTCAAGTA ACAACCGCGA AAAAGTTGCG CGGAGGAGTT GTGTTTGTGG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ACGAAGTACC GAAAGGTCTT ACCGGAAAAC TCGACGCAAG AAAAATCAGA GAGATCCTCA TAAAGGCCAA GAAGGGCGGA AAGTCCAAAT TGTAACTCGA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GCATGCATCT AGAGGGCCCT ATTCTATAGT GTCACCTAAA TGCTAGAGGA TCTTTGTGAA GGAACCTTAC TTCTGTGGTG TGACATAATT GGACAAACTA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CCTACAGAGA TTTAAAGCTC TAAGGTAAAT ATAAAATTTT TAAGTGTATA ATGTGTTAAA CTACTGATTC TAATTGTTTG TGTATTTTAG ATTCCAACCT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ATGGAACTGA TGAATGGGAG CAGTGGTGGA ATGCCTTTAA TGAGGAAAAC CTGTTTTGCT CAGAAGAAAT GCCATCTAGT GATGATGAGG CTACTGCTGA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

CTCTCAACAT TCTACTCCTC CAAAAAAGAA GAGAAAGGTA GAAGACCCCA AGGACTTTCC TTCAGAATTG CTAAGTTTTT TGAGTCATGC TGTGTTTAGT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AATAGAACTC TTGCTTGCTT TGCTATTTAC ACCACAAAGG AAAAAGCTGC ACTGCTATAC AAGAAAATTA TGGAAAAATA TTTGATGTAT AGTGCCTTGA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CTAGAGATCA TAATCAGCCA TACCACATTT GTAGAGGTTT TACTTGCTTT AAAAAACCTC CCACACCTCC CCCTGAACCT GAAACATAAA ATGAATGCAA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TTGTTGTTGT TAACTTGTTT ATTGCAGCTT ATAATGGTTA CAAATAAAGC AATAGCATCA CAAATTTCAC AAATAAAGCA TTTTTTTCAC TGCATTCTAG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTGTGGTTTG TCCAAACTCA TCAATGTATC TTATCATGTC TGGATCATCC CGCCATGGTA TCAACGCCAT ATTTCTATTT ACAGTAGGGA CCTCTTCGTT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GTGTAGGTAC CGCTGTATTC CTAGGGAAAT AGTAGAGGCA CCTTGAACTG TCTGCATCAG CCATATAGCC CCCGCTGTTC GACTTACAAA CACAGGCACA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GTACTGACAA ACCCATACAC CTCCTCTGAA ATACCCATAG TTGCTAGGGC TGTCTCCGAA CTCATTACAC CCTCCAAAGT CAGAGCTGTA ATTTCGCCAT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CAAGGGCAGC GAGGGCTTCT CCAGATAAAA TAGCTTCTGC CGAGAGTCCC GTAAGGGTAG ACACTTCAGC TAATCCCTCG ATGAGGTCTA CTAGAATAGT 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CAGTGCGGCT CCCATTTTGA AAATTCACTT ACTTGATCAG CTTCAGAAGA TGGCGGAGGG CCTCCAACAC AGTAATTTTC CTCCCGACTC TTAAAATAGA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AAATGTCAAG TCAGTTAAGC AGGAAGTGGA CTAACTGACG CAGCTGGCCG TGCGACATCC TCTTTTAATT AGTTGCTAGG CAACGCCCTC CAGAGGGCGT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

GTGGTTTTGC AAGAGGAAGC AAAAGCCTCT CCACCCAGGC CTAGAATGTT TCCACCCAAT CATTACTATG ACAACAGCTG TTTTTTTTAG TATTAAGCAG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

AGGCCGGGGA CCCCTGGGCC CGCTTACTCT GGAGAAAAAG AAGAGAGGCA TTGTAGAGGC TTCCAGAGGC AACTTGTCAA AACAGGACTG CTTCTATTTC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TGTCACACTG TCTGGCCCTG TCACAAGGTC CAGCACCTCC ATACCCCCTT TAATAAGCAG TTTGGGAACG GGTGCGGGTC TTACTCCGCC CATCCCGCCC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CTAACTCCGC CCAGTTCCGC CCATTCTCCG CCCCATGGCT GACTAATTTT TTTTATTTAT GCAGAGGCCG AGGCCGCCTC GGCCTCTGAG CTATTCCAGA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

AGTAGTGAGG AGGCTTTTTT GGAGGCCTAG GCTTTTGCAA AAAGCTAATT CGGCGTAATC TGCTGCTTGC AAACAAAAAA ACCACCGCTA CCAGCGGTGG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

TTTGTTTGCC GGATCAAGAG CTACCAACTC TTTTTCCGAA GGTAACTGGC TTCAGCAGAG CGCAGATACC AAATACTGTC CTTCTAGTGT AGCCGTAGTT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

AGGCCACCAC TTCAAGAACT CTGTAGCACC GCCTACATAC CTCGCTCTGC TAATCCTGTT ACCAGTGGCT GCTGCCAGTG GCGATAAGTC GTGTCTTACC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

GGGTTGGACT CAAGACGATA GTTACCGGAT AAGGCGCAGC GGTCGGGCTG AACGGGGGGT TCGTGCACAC AGCCCAGCTT GGAGCGAACG ACCTACACCG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

AACTGAGATA CCTACAGCGT GAGCATTGAG AAAGCGCCAC GCTTCCCGAA GGGAGAAAGG CGGACAGGTA
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461

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: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
CAT

The description of the protein encoded in this ORF:
chloramphenicol acetyltransferase

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:

no

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

71-730

ORF

ORF position:

2

Version: `1`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The abbreviated name of this ORF/gene:
FFluc

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:

no

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

925-2577

Citations:

Kim J. G., Armstrong R. C., Berndt J. A., Kim N. W., Hudson L. D. (1998) A secreted DNA-binding protein that is translated through an internal ribosome entry site (IRES) and distributed in a discrete pattern in the central nervous system. Mol. Cell. Neurosci. 12(3):119-140

IRESs:

IRES:

Version: `4`	Last change: `2006-07-25 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `MYT2_997-1152`	The functional status of IRES: `functional`

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

759-914

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `29`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `184`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-166`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-11`

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

CGCCCGTAAA ATGGGAACGT AGAACTCGTC ATGACACTTG TGGTAAAATA ACATTATTCG CTTGCAAAAA ACGATGTACT TTGACAATTT AAGACACAAA 
^759       ^769       ^779       ^789       ^799       ^809       ^819       ^829       ^839       ^849       

AAAACACAAC CTCGACAATT TAGGAGTTAG AGAGGTCGTG TTTTGAGATT AGTGAG
^859       ^869       ^879       ^889       ^899       ^909

Remarks:

Fragment nt 997 to nt 1152 of 5' UTR of human myelin transcription factor 2 (MYT2) mRNA.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 49

Version: `4`	Last change: `2006-07-25 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HeLa (ATCC CCL-2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

141.000

Name of IRES used as the positive control:

BiP

Name of the plasmid used as the positive control. `pcBIP`	Name of the plasmid used as the negative control. `pCAT/LUC`
	`IRESite Id` of the plasmid used as negative control. `218`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `25.000`
The size (length) of intercistronic region in the positive control: `264`	The size (length) of intercistronic region in the negative control: `76`

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:

The pcBIP plasmid is currently not available. It is also not clear whether the pCAT/LUC plasmid used as
negative control was the one with 76b long intercistronic region or whether the plasmid was pCAT/LUC with 17nt
long hairpin structure. However, authors mention luciferase activities in SVG and HeLa cells was same.

Citations:

Translation results:

IRESite Translation Id: 50

Version: `4`	Last change: `2006-07-25 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens SVG

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

126.000

Name of IRES used as the positive control:

BiP

Name of the plasmid used as the positive control. `pcBIP`	Name of the plasmid used as the negative control. `pCAT/LUC`
	`IRESite Id` of the plasmid used as negative control. `218`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `24.000`
The size (length) of intercistronic region in the positive control: `264`	The size (length) of intercistronic region in the negative control: `76`

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:

The pcBIP plasmid is currently not available. It is also not clear whether the pCAT/LUC plasmid used as
negative control was the one with 76b long intercistronic region or whether the plasmid was pCAT/LUC with 17nt
long hairpin structure. However, authors mention luciferase activities in SVG and HeLa cells was same.

Citations:

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