IRESite_Id:52 characteristics of MYT2_1089-1152 IRES studied in pSL50 plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `52`	Version: `8`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-08-18 00:00:00`
Reviewed by: Václav Vopálenský	Last change: `2008-07-01 11:57:24`

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 1089 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 AACGGCCGAA TGACACAAAA AAACACAACC TCGACGACAC AAAAAAACAC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AACCTCGACA ATTTAGGAGT TAGAGAGGTC GTGTTTTGAG ATTAGTGAGG AGGTCGTGTT TTGAGATTAG TGAGCGGCCG CAAAATGGAA GACGCCAAAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ACATAAAGAA AGGCCCGGCG CCATTCTATC CTCTAGAGGA TGGAACCGCT GGAGAGCAAC TGCATAAGGC TATGAAGAGA TACGCCCTGG TTCCTGGAAC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AATTGCTTTT ACAGATGCAC ATATCGAGGT GAACATCACG TACGCGGAAT ACTTCGAAAT GTCCGTTCGG TTGGCAGAAG CTATGAAACG ATATGGGCTG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

AATACAAATC ACAGAATCGT CGTATGCAGT GAAAACTCTC TTCAATTCTT TATGCCGGTG TTGGGCGCGT TATTTATCGG AGTTGCAGTT GCGCCCGCGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ACGACATTTA TAATGAACGT GAATTGCTCA ACAGTATGAA CATTTCGCAG CCTACCGTAG TGTTTGTTTC CAAAAAGGGG TTGCAAAAAA TTTTGAACGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GCAAAAAAAA TTACCAATAA TCCAGAAAAT TATTATCATG GATTCTAAAA CGGATTACCA GGGATTTCAG TCGATGTACA CGTTCGTCAC ATCTCATCTA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CCTCCCGGTT TTAATGAATA CGATTTTGTA CCAGAGTCCT TTGATCGTGA CAAAACAATT GCACTGATAA TGAATTCCTC TGGATCTACT GGGTTACCTA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGGGTGTGGC CCTTCCGCAT AGAACTGCCT GCGTCAGATT CTCGCATGCC AGAGATCCTA TTTTTGGCAA TCAAATCATT CCGGATACTG CGATTTTAAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

TGTTGTTCCA TTCCATCACG GTTTTGGAAT GTTTACTACA CTCGGATATT TGATATGTGG ATTTCGAGTC GTCTTAATGT ATAGATTTGA AGAAGAGCTG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TTTTTACGAT CCCTTCAGGA TTACAAAATT CAAAGTGCGT TGCTAGTACC AACCCTATTT TCATTCTTCG CCAAAAGCAC TCTGATTGAC AAATACGATT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TATCTAATTT ACACGAAATT GCTTCTGGGG GCGCACCTCT TTCGAAAGAA GTCGGGGAAG CGGTTGCAAA ACGCTTCCAT CTTCCAGGGA TACGACAAGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATATGGGCTC ACTGAGACTA CATCAGCTAT TCTGATTACA CCCGAGGGGG ATGATAAACC GGGCGCGGTC GGTAAAGTTG TTCCATTTTT TGAAGCGAAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GTTGTGGATC TGGATACCGG GAAAACGCTG GGCGTTAATC AGAGAGGCGA ATTATGTGTC AGAGGACCTA TGATTATGTC CGGTTATGTA AACAATCCGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAGCGACCAA CGCCTTGATT GACAAGGATG GATGGCTACA TTCTGGAGAC ATAGCTTACT GGGACGAAGA CGAACACTTC TTCATAGTTG ACCGCTTGAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GTCTTTAATT AAATACAAAG GATATCAGGT GGCCCCCGCT GAATTGGAAT CGATATTGTT ACAACACCCC AACATCTTCG ACGCGGGCGT GGCAGGTCTT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CCCGACGATG ACGCCGGTGA ACTTCCCGCC GCCGTTGTTG TTTTGGAGCA CGGAAAGACG ATGACGGAAA AAGAGATCGT GGATTACGTC GCCAGTCAAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TAACAACCGC GAAAAAGTTG CGCGGAGGAG TTGTGTTTGT GGACGAAGTA CCGAAAGGTC TTACCGGAAA ACTCGACGCA AGAAAAATCA GAGAGATCCT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CATAAAGGCC AAGAAGGGCG GAAAGTCCAA ATTGTAACTC GAGCATGCAT CTAGAGGGCC CTATTCTATA GTGTCACCTA AATGCTAGAG GATCTTTGTG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

AAGGAACCTT ACTTCTGTGG TGTGACATAA TTGGACAAAC TACCTACAGA GATTTAAAGC TCTAATCCAA CCTATGGAAC TGATGAATGG GAGCAGTGGT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GGAATGCCTT TAATGAGGAA AACCTGTTTT GCTCAGAAGA AATGCCATCT AGTGATGATG AGGCTACTGC TGACTCTCAA CATTCTACTC CTCCAAAAAA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GAAGAGAAAG GTAGAAGACC CCAAGGACTT TCCTTCAGAA TTGCTAAGTT TTTTGAGTCA TGCTGTGTTT AGTAATAGAA CTCTTGCTTG CTTTGCTATT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TACACCACAA AGGAAAAAGC TGCACTGCTA TACAAGAAAA TTATGGAAAA ATATTTGATG TATAGTGCCT TGACTAGAGA TCATAATCAG CCATACCACA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TTTGTAGAGG TTTTACTTGC TTTAAAAAAC CTCCCACACC TCCCCCTGAA CCTGAAACAT AAAATGAATG CAATTGTTGT TGTTAACTTG TTTATTGCAG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CTTATAATGG TTACAAATAA A
^3101      ^3111      ^3121

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:
pSL50 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:

GAGCTTCCAG GGGGAAACGC CTGGTATCTT TATAGTCCTG TCGGGTTTCG CCACCTCTGA CTTGAGCGTC GATTTTTGTG ATGCTCGTCA GGGGGGCGGA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCCTATGGAA AAACGCCAGC AACGCAAGCT AGCTTCTAGC TAGAAATTGT AAACGTTAAT ATTTTGTTAA AATTCGCGTT AAATTTTTGT TAAATCAGCT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CATTTTTTAA CCAATAGGCC GAAATCGGCA AAATCCCTTA TAAATCAAAA GAATAGCCCG AGATAGGGTT GAGTGTTGTT CCAGTTTGGA ACAAGAGTCC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ACTATTAAAG AACGTGGACT CCAACGTCAA AGGGCGAAAA ACCGTCTATC AGGGCGATGG CCGCCCACTA CGTGAACCAT CACCCAAATC AAGTTTTTTG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GGGTCGAGGT GCCGTAAAGC ACTAAATCGG AACCCTAAAG GGAGCCCCCG ATTTAGAGCT TGACGGGGAA AGCCGGCGAA CGTGGCGAGA AAGGAAGGGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

AGAAAGCGAA AGGAGCGGGC GCTAGGGCGC TGGCAAGTGT AGCGGTCACG CTGCGCGTAA CCACCACACC CGCCGCGCTT AATGCGCCGC TACAGGGCGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GTACTATGGT TGCTTTGACG AGACCGTATA ACGTGCTTTC CTCGTTGGAA TCAGAGCGGG AGCTAAACAG GAGGCCGATT AAAGGGATTT TAGACAGGAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CGGTACGCCA GCTGGATTAC CGCGGTCTTT CTCAACGTAA CACTTTACAG CGGCGCGTCA TTTGATATGA TGCGCCCCGC TTCCCGATAA GGGAGCAGGC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CAGTAAAAGC ATTACCCGTG GTGGGGTTCC CGAGCGGCCA AAGGGAGCAG ACTCTAAATC TGCCGTCATC GACTTCGAAG GTTCGAATCC TTCCCCCACC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ACCATCACTT TCAAAAGTCC GAAAGAATCT GCTCCCTGCT TGTGTGTTGG AGGTCGCTGA GTAGTGCGCG AGTAAAATTT AAGCTACAAC AAGGCAAGGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTGACCGACA ATTGCATGAA GAATCTGCTT AGGGTTAGGC GTTTTGCGCT GCTTCGCGAT GTACGGGCCA GATATACGCG TTGACATTGA TTATTGACTA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GTTATTAATA GTAATCAATT ACGGGGTCAT TAGTTCATAG CCCATATATG GAGTTCCGCG TTACATAACT TACGGTAAAT GGCCCGCCTG GCTGACCGCC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CAACGACCCC CGCCCATTGA CGTCAATAAT GACGTATGTT CCCATAGTAA CGCCAATAGG GACTTTCCAT TGACGTCAAT GGGTGGACTA TTTACGGTAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ACTGCCCACT TGGCAGTACA TCAAGTGTAT CATATGCCAA GTACGCCCCC TATTGACGTC AATGACGGTA AATGGCCCGC CTGGCATTAT GCCCAGTACA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGACCTTATG GGACTTTCCT ACTTGGCAGT ACATCTACGT ATTAGTCATC GCTATTACCA TGGTGATGCG GTTTTGGCAG TACATCAATG GGCGTGGATA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GCGGTTTGAC TCACGGGGAT TTCCAAGTCT CCACCCCATT GACGTCAATG GGAGTTTGTT TTGGCACCAA AATCAACGGG ACTTTCCAAA ATGTCGTAAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AACTCCGCCC CATTGACGCA AATGGGCGGT AGGCGTGTAC GGTGGGAGGT CTATATAAGC AGAGCTCTCT GGCTAACTAG AGAACCCACT GCTTACTGGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TTATCGAAAT TAATACGACT CACTATAGGG AGACCCAAGC TTGCCACCAT GGAGAAAAAA ATCACTGGAT ATACCACCGT TGATATATCC CAATGGCATC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTAAAGAACA TTTTGAGGCA TTTCAGTCAG TTGCTCAATG TACCTATAAC CAGACCGTTC AGCTGGATAT TACGGCCTTT TTAAAGACCG TAAAGAAAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TAAGCACAAG TTTTATCCGG CCTTTATTCA CATTCTTGCC CGCCTGATGA ATGCTCATCC GGAATTCCGT ATGGCAATGA AAGACGGTGA GCTGGTGATA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGGGATAGTG TTCACCCTTG TTACACCGTT TTCCATGAGC AAACTGAAAC GTTTTCATCG CTCTGGAGTG AATACCACGA CGATTTCCGG CAGTTTCTAC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ACATATATTC GCAAGATGTG GCGTGTTACG GTGAAAACCT GGCCTATTTC CCTAAAGGGT TTATTGAGAA TATGTTTTTC GTCTCAGCCA ATCCCTGGGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAGTTTCACC AGTTTTGATT TAAACGTGGC CAATATGGAC AACTTCTTCG CCCCCGTTTT CACCATGGGC AAATATTATA CGCAAGGCGA CAAGGTGCTG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATGCCGCTGG CGATTCAGGT TCATCATGCC GTCTGTGATG GCTTCCATGT CGGCAGAATG CTTAATGAAT TACAACAGTA CTGCGATGAG TGGCAGGGCG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GGGCGTAATT AGATGAGGAT CCACTAGTAA CGGCCGAATG ACACAAAAAA ACACAACCTC GACGACACAA AAAAACACAA CCTCGACAAT TTAGGAGTTA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GAGAGGTCGT GTTTTGAGAT TAGTGAGGAG GTCGTGTTTT GAGATTAGTG AGCGGCCGCA AAATGGAAGA CGCCAAAAAC ATAAAGAAAG GCCCGGCGCC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATTCTATCCT CTAGAGGATG GAACCGCTGG AGAGCAACTG CATAAGGCTA TGAAGAGATA CGCCCTGGTT CCTGGAACAA TTGCTTTTAC AGATGCACAT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ATCGAGGTGA ACATCACGTA CGCGGAATAC TTCGAAATGT CCGTTCGGTT GGCAGAAGCT ATGAAACGAT ATGGGCTGAA TACAAATCAC AGAATCGTCG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TATGCAGTGA AAACTCTCTT CAATTCTTTA TGCCGGTGTT GGGCGCGTTA TTTATCGGAG TTGCAGTTGC GCCCGCGAAC GACATTTATA ATGAACGTGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATTGCTCAAC AGTATGAACA TTTCGCAGCC TACCGTAGTG TTTGTTTCCA AAAAGGGGTT GCAAAAAATT TTGAACGTGC AAAAAAAATT ACCAATAATC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CAGAAAATTA TTATCATGGA TTCTAAAACG GATTACCAGG GATTTCAGTC GATGTACACG TTCGTCACAT CTCATCTACC TCCCGGTTTT AATGAATACG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ATTTTGTACC AGAGTCCTTT GATCGTGACA AAACAATTGC ACTGATAATG AATTCCTCTG GATCTACTGG GTTACCTAAG GGTGTGGCCC TTCCGCATAG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AACTGCCTGC GTCAGATTCT CGCATGCCAG AGATCCTATT TTTGGCAATC AAATCATTCC GGATACTGCG ATTTTAAGTG TTGTTCCATT CCATCACGGT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TTTGGAATGT TTACTACACT CGGATATTTG ATATGTGGAT TTCGAGTCGT CTTAATGTAT AGATTTGAAG AAGAGCTGTT TTTACGATCC CTTCAGGATT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ACAAAATTCA AAGTGCGTTG CTAGTACCAA CCCTATTTTC ATTCTTCGCC AAAAGCACTC TGATTGACAA ATACGATTTA TCTAATTTAC ACGAAATTGC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TTCTGGGGGC GCACCTCTTT CGAAAGAAGT CGGGGAAGCG GTTGCAAAAC GCTTCCATCT TCCAGGGATA CGACAAGGAT ATGGGCTCAC TGAGACTACA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TCAGCTATTC TGATTACACC CGAGGGGGAT GATAAACCGG GCGCGGTCGG TAAAGTTGTT CCATTTTTTG AAGCGAAGGT TGTGGATCTG GATACCGGGA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AAACGCTGGG CGTTAATCAG AGAGGCGAAT TATGTGTCAG AGGACCTATG ATTATGTCCG GTTATGTAAA CAATCCGGAA GCGACCAACG CCTTGATTGA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CAAGGATGGA TGGCTACATT CTGGAGACAT AGCTTACTGG GACGAAGACG AACACTTCTT CATAGTTGAC CGCTTGAAGT CTTTAATTAA ATACAAAGGA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TATCAGGTGG CCCCCGCTGA ATTGGAATCG ATATTGTTAC AACACCCCAA CATCTTCGAC GCGGGCGTGG CAGGTCTTCC CGACGATGAC GCCGGTGAAC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TTCCCGCCGC CGTTGTTGTT TTGGAGCACG GAAAGACGAT GACGGAAAAA GAGATCGTGG ATTACGTCGC CAGTCAAGTA ACAACCGCGA AAAAGTTGCG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CGGAGGAGTT GTGTTTGTGG ACGAAGTACC GAAAGGTCTT ACCGGAAAAC TCGACGCAAG AAAAATCAGA GAGATCCTCA TAAAGGCCAA GAAGGGCGGA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

AAGTCCAAAT TGTAACTCGA GCATGCATCT AGAGGGCCCT ATTCTATAGT GTCACCTAAA TGCTAGAGGA TCTTTGTGAA GGAACCTTAC TTCTGTGGTG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TGACATAATT GGACAAACTA CCTACAGAGA TTTAAAGCTC TAAGGTAAAT ATAAAATTTT TAAGTGTATA ATGTGTTAAA CTACTGATTC TAATTGTTTG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TGTATTTTAG ATTCCAACCT ATGGAACTGA TGAATGGGAG CAGTGGTGGA ATGCCTTTAA TGAGGAAAAC CTGTTTTGCT CAGAAGAAAT GCCATCTAGT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GATGATGAGG CTACTGCTGA CTCTCAACAT TCTACTCCTC CAAAAAAGAA GAGAAAGGTA GAAGACCCCA AGGACTTTCC TTCAGAATTG CTAAGTTTTT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TGAGTCATGC TGTGTTTAGT AATAGAACTC TTGCTTGCTT TGCTATTTAC ACCACAAAGG AAAAAGCTGC ACTGCTATAC AAGAAAATTA TGGAAAAATA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TTTGATGTAT AGTGCCTTGA CTAGAGATCA TAATCAGCCA TACCACATTT GTAGAGGTTT TACTTGCTTT AAAAAACCTC CCACACCTCC CCCTGAACCT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GAAACATAAA ATGAATGCAA TTGTTGTTGT TAACTTGTTT ATTGCAGCTT ATAATGGTTA CAAATAAAGC AATAGCATCA CAAATTTCAC AAATAAAGCA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TTTTTTTCAC TGCATTCTAG TTGTGGTTTG TCCAAACTCA TCAATGTATC TTATCATGTC TGGATCATCC CGCCATGGTA TCAACGCCAT ATTTCTATTT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

ACAGTAGGGA CCTCTTCGTT GTGTAGGTAC CGCTGTATTC CTAGGGAAAT AGTAGAGGCA CCTTGAACTG TCTGCATCAG CCATATAGCC CCCGCTGTTC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GACTTACAAA CACAGGCACA GTACTGACAA ACCCATACAC CTCCTCTGAA ATACCCATAG TTGCTAGGGC TGTCTCCGAA CTCATTACAC CCTCCAAAGT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CAGAGCTGTA ATTTCGCCAT CAAGGGCAGC GAGGGCTTCT CCAGATAAAA TAGCTTCTGC CGAGAGTCCC GTAAGGGTAG ACACTTCAGC TAATCCCTCG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

ATGAGGTCTA CTAGAATAGT CAGTGCGGCT CCCATTTTGA AAATTCACTT ACTTGATCAG CTTCAGAAGA TGGCGGAGGG CCTCCAACAC AGTAATTTTC 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CTCCCGACTC TTAAAATAGA AAATGTCAAG TCAGTTAAGC AGGAAGTGGA CTAACTGACG CAGCTGGCCG TGCGACATCC TCTTTTAATT AGTTGCTAGG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

CAACGCCCTC CAGAGGGCGT GTGGTTTTGC AAGAGGAAGC AAAAGCCTCT CCACCCAGGC CTAGAATGTT TCCACCCAAT CATTACTATG ACAACAGCTG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TTTTTTTTAG TATTAAGCAG AGGCCGGGGA CCCCTGGGCC CGCTTACTCT GGAGAAAAAG AAGAGAGGCA TTGTAGAGGC TTCCAGAGGC AACTTGTCAA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

AACAGGACTG CTTCTATTTC TGTCACACTG TCTGGCCCTG TCACAAGGTC CAGCACCTCC ATACCCCCTT TAATAAGCAG TTTGGGAACG GGTGCGGGTC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TTACTCCGCC CATCCCGCCC CTAACTCCGC CCAGTTCCGC CCATTCTCCG CCCCATGGCT GACTAATTTT TTTTATTTAT GCAGAGGCCG AGGCCGCCTC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

GGCCTCTGAG CTATTCCAGA AGTAGTGAGG AGGCTTTTTT GGAGGCCTAG GCTTTTGCAA AAAGCTAATT CGGCGTAATC TGCTGCTTGC AAACAAAAAA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ACCACCGCTA CCAGCGGTGG TTTGTTTGCC GGATCAAGAG CTACCAACTC TTTTTCCGAA GGTAACTGGC TTCAGCAGAG CGCAGATACC AAATACTGTC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CTTCTAGTGT AGCCGTAGTT AGGCCACCAC TTCAAGAACT CTGTAGCACC GCCTACATAC CTCGCTCTGC TAATCCTGTT ACCAGTGGCT GCTGCCAGTG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

GCGATAAGTC GTGTCTTACC GGGTTGGACT CAAGACGATA GTTACCGGAT AAGGCGCAGC GGTCGGGCTG AACGGGGGGT TCGTGCACAC AGCCCAGCTT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

GGAGCGAACG ACCTACACCG AACTGAGATA CCTACAGCGT GAGCATTGAG AAAGCGCCAC GCTTCCCGAA GGGAGAAAGG CGGACAGGTA TCCGGTAAGC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

GGCAGGGTCG GAACAGGAGA GCGCACGAGG
^6401      ^6411      ^6421

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: `0`
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):

885-2537

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: `2`	Last change: `2006-07-25 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Václav Vopálenský
The IRES name: `MYT2_1089-1152`	The functional status of IRES: `defective`

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

762-874

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `32`	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: `-123`	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):

GACACAAAAA AACACAACCT CGACGACACA AAAAAACACA ACCTCGACAA TTTAGGAGTT AGAGAGGTCG TGTTTTGAGA TTAGTGAGGA GGTCGTGTTT 
^762       ^772       ^782       ^792       ^802       ^812       ^822       ^832       ^842       ^852       

TGAGATTAGT GAG
^862       ^872

Remarks:

Fragment nt 1089 to nt 1152 of 5' UTR of human myelin transcription factor 2 (MYT2) mRNA.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 51

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:

41.000

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: 52

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:

14.000

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:

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