IRESite_Id:611 negative control plasmid H-GFP-TMV_UI

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `611`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-25 16:51:13`
Reviewed by: Martin Mokrejš

IRESite record type:

negative_control_plasmid_with_promoter_and_without_putative_IRES

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

The mRNA/+RNA description:

Part of the T7-derived transcript studied in some in vitro assays. The 5'-UTR could have been longer but we do
not know the necessary details. The intercistronic region contains 5'-UTR sequence of genomic TMV UI RNA (bp
2-68 of M24955).

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

ATGGTGAGCA AGGGCGAGGA GCTGTTCACC GGGGTGGTGC CCATCCTGGT CGAGCTGGAC GGCGACGTAA ACGGCCACAA GTTCAGCGTG TCCGGCGAGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGAGGGCGA TGCCACCTAC GGCAAGCTGA CCCTGAAGTT CATCTGCACC ACCGGCAAGC TGCCCGTGCC CTGGCCCACC CTCGTGACCA CCTTCACCTA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CGGCGTGCAG TGCTTCAGCC GCTACCCCGA CCACATGAAG CAGCACGACT TCTTCAAGTC CGCCATGCCC GAAGGCTACG TCCAGGAGCG CACCATCTTC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTCAAGGACG ACGGCAACTA CAAGACCCGC GCCGAGGTGA AGTTCGAGGG CGACACCCTG GTGAACCGCA TCGAGCTGAA GGGCATCGAC TTCAAGGAGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACGGCAACAT CCTGGGGCAC AAGCTGGAGT ACAACTACAA CAGCCACAAC GTCTATATCA TGGCCGACAA GCAGAAGAAC GGCATCAAGG TGAACTTCAA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GATCCGCCAC AACATCGAGG ACGGCAGCGT GCAGCTCGCC GACCACTACC AGCAGAACAC CCCCATCGGC GACGGCCCCG TGCTGCTGCC CGACAACCAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TACCTGAGCA CCCAGTCCGC CCTGAGCAAA GACCCCAACG AGAAGCGCGA TCACATGGTC CTGCTGGAGT TCGTGACCGC CGCCGGGATC ACTCACGGCA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGGACGAGCT GTACAAGTAA gctttatttt tacaacaatt accaacaaca acaaacaaca aacaacatta caattactat ttacaattac agtcgaccAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GGTCCGTCCT GTAGAAACCC CAACCCGTGA AATCAAAAAA CTCGACGGCC TGTGGGCATT CAGTCTGGAT CGCGAAAACT GTGGAATTGA TCAGCGTTGG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGGGAAAGCG CGTTACAAGA AAGCCGGGCA ATTGCTGTGC CAGGCAGTTT TAACGATCAG TTCGCCGATG CAGATATTCG TAATTATGCG GGCAACGTCT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GGTATCAGCG CGAAGTCTTT ATACCGAAAG GTTGGGCAGG CCAGCGTATC GTGCTGCGTT TCGATGCGGT CACTCATTAC GGCAAAGTGT GGGTCAATAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCAGGAAGTG ATGGAGCATC AGGGCGGCTA TACGCCATTT GAAGCCGATG TCACGCCGTA TGTTATTGCC GGGAAAAGTG TACGTATCAC CGTTTGTGTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AACAACGAAC TGAACTGGCA GACTATCCCG CCGGGAATGG TGATTACCGA CGAAAACGGC AAGAAAAAGC AGTCTTACTT CCATGATTTC TTTAACTATG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCGGAATCCA TCGCAGCGTA ATGCTCTACA CCACGCCGAA CACCTGGGTG GACGATATCA CCGTGGTGAC GCATGTCGCG CAAGACTGTA ACCACGCGTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGTTGACTGG CAGGTGGTGG CCAATGGTGA TGTCAGCGTT GAACTGCGTG ATGCGGATCA ACAGGTGGTT GCAACTGGAC AAGGCACTAG CGGGACTTTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CAAGTGGTGA ATCCGCACCT CTGGCAACCG GGTGAAGGTT ATCTCTATGA ACTGTGCGTC ACAGCCAAAA GCCAGACAGA GTGTGATATC TACCCGCTTC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCGTCGGCAT CCGGTCAGTG GCAGTGAAGG GCGAACAGTT CCTGATTAAC CACAAACCGT TCTACTTTAC TGGCTTTGGT CGTCATGAAG ATGCGGACTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ACGTGGCAAA GGATTCGATA ACGTGCTGAT GGTGCACGAC CACGCATTAA TGGACTGGAT TGGGGCCAAC TCCTACCGTA CCTCGCATTA CCCTTACGCT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GAAGAGATGC TCGACTGGGC AGATGAACAT GGCATCGTGG TGATTGATGA AACTGCTGCT GTCGGCTTTA ACCTCTCTTT AGGCATTGGT TTCGAAGCGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCAACAAGCC GAAAGAACTG TACAGCGAAG AGGCAGTCAA CGGGGAAACT CAGCAAGCGC ACTTACAGGC GATTAAAGAG CTGATAGCGC GTGACAAAAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCACCCAAGC GTGGTGATGT GGAGTATTGC CAACGAACCG GATACCCGTC CGCAAGGTGC ACGGGAATAT TTCGCGCCAC TGGCGGAAGC AACGCGTAAA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTCGACCCGA CGCGTCCGAT CACCTGCGTC AATGTAATGT TCTGCGACGC TCACACCGAT ACCATCAGCG ATCTCTTTGA TGTGCTGTGC CTGAACCGTT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATTACGGATG GTATGTCCAA AGCGGCGATT TGGAAACGGC AGAGAAGGTA CTGGAAAAAG AACTTCTGGC CTGGCAGGAG AAACTGCATC AGCCGATTAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CATCACCGAA TACGGCGTGG ATACGTTAGC CGGGCTGCAC TCAATGTACA CCGACATGTG GAGTGAAGAG TATCAGTGTG CATGGCTGGA TATGTATCAC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CGCGTCTTTG ATCGCGTCAG CGCCGTCGTC GGTGAACAGG TATGGAATTT CGCCGATTTT GCGACCTCGC AAGGCATATT GCGCGTTGGC GGTAACAAGA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AAGGGATCTT CACTCGCGAC CGCAAACCGA AGTCGGCGGC TTTTCTGCTG CAAAAACGCT GGACTGGCAT GAACTTCGGT GAAAAACCGC AGCAGGGAGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CAAACAATGA
^2601

Warning: available plasmid sequence is exactly same as the mRNA sequence. It seems we never managed to reconstruct the original plasmid sequence used to express the studied mRNA.

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

The name of the plasmid:
H-GFP-TMV_UI_omega-GUS 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

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

ATGGTGAGCA AGGGCGAGGA GCTGTTCACC GGGGTGGTGC CCATCCTGGT CGAGCTGGAC GGCGACGTAA ACGGCCACAA GTTCAGCGTG TCCGGCGAGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGAGGGCGA TGCCACCTAC GGCAAGCTGA CCCTGAAGTT CATCTGCACC ACCGGCAAGC TGCCCGTGCC CTGGCCCACC CTCGTGACCA CCTTCACCTA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CGGCGTGCAG TGCTTCAGCC GCTACCCCGA CCACATGAAG CAGCACGACT TCTTCAAGTC CGCCATGCCC GAAGGCTACG TCCAGGAGCG CACCATCTTC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTCAAGGACG ACGGCAACTA CAAGACCCGC GCCGAGGTGA AGTTCGAGGG CGACACCCTG GTGAACCGCA TCGAGCTGAA GGGCATCGAC TTCAAGGAGG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACGGCAACAT CCTGGGGCAC AAGCTGGAGT ACAACTACAA CAGCCACAAC GTCTATATCA TGGCCGACAA GCAGAAGAAC GGCATCAAGG TGAACTTCAA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GATCCGCCAC AACATCGAGG ACGGCAGCGT GCAGCTCGCC GACCACTACC AGCAGAACAC CCCCATCGGC GACGGCCCCG TGCTGCTGCC CGACAACCAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TACCTGAGCA CCCAGTCCGC CCTGAGCAAA GACCCCAACG AGAAGCGCGA TCACATGGTC CTGCTGGAGT TCGTGACCGC CGCCGGGATC ACTCACGGCA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGGACGAGCT GTACAAGTAA gctttatttt tacaacaatt accaacaaca acaaacaaca aacaacatta caattactat ttacaattac agtcgaccAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GGTCCGTCCT GTAGAAACCC CAACCCGTGA AATCAAAAAA CTCGACGGCC TGTGGGCATT CAGTCTGGAT CGCGAAAACT GTGGAATTGA TCAGCGTTGG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGGGAAAGCG CGTTACAAGA AAGCCGGGCA ATTGCTGTGC CAGGCAGTTT TAACGATCAG TTCGCCGATG CAGATATTCG TAATTATGCG GGCAACGTCT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GGTATCAGCG CGAAGTCTTT ATACCGAAAG GTTGGGCAGG CCAGCGTATC GTGCTGCGTT TCGATGCGGT CACTCATTAC GGCAAAGTGT GGGTCAATAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCAGGAAGTG ATGGAGCATC AGGGCGGCTA TACGCCATTT GAAGCCGATG TCACGCCGTA TGTTATTGCC GGGAAAAGTG TACGTATCAC CGTTTGTGTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AACAACGAAC TGAACTGGCA GACTATCCCG CCGGGAATGG TGATTACCGA CGAAAACGGC AAGAAAAAGC AGTCTTACTT CCATGATTTC TTTAACTATG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCGGAATCCA TCGCAGCGTA ATGCTCTACA CCACGCCGAA CACCTGGGTG GACGATATCA CCGTGGTGAC GCATGTCGCG CAAGACTGTA ACCACGCGTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TGTTGACTGG CAGGTGGTGG CCAATGGTGA TGTCAGCGTT GAACTGCGTG ATGCGGATCA ACAGGTGGTT GCAACTGGAC AAGGCACTAG CGGGACTTTG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CAAGTGGTGA ATCCGCACCT CTGGCAACCG GGTGAAGGTT ATCTCTATGA ACTGTGCGTC ACAGCCAAAA GCCAGACAGA GTGTGATATC TACCCGCTTC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCGTCGGCAT CCGGTCAGTG GCAGTGAAGG GCGAACAGTT CCTGATTAAC CACAAACCGT TCTACTTTAC TGGCTTTGGT CGTCATGAAG ATGCGGACTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ACGTGGCAAA GGATTCGATA ACGTGCTGAT GGTGCACGAC CACGCATTAA TGGACTGGAT TGGGGCCAAC TCCTACCGTA CCTCGCATTA CCCTTACGCT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GAAGAGATGC TCGACTGGGC AGATGAACAT GGCATCGTGG TGATTGATGA AACTGCTGCT GTCGGCTTTA ACCTCTCTTT AGGCATTGGT TTCGAAGCGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCAACAAGCC GAAAGAACTG TACAGCGAAG AGGCAGTCAA CGGGGAAACT CAGCAAGCGC ACTTACAGGC GATTAAAGAG CTGATAGCGC GTGACAAAAA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCACCCAAGC GTGGTGATGT GGAGTATTGC CAACGAACCG GATACCCGTC CGCAAGGTGC ACGGGAATAT TTCGCGCCAC TGGCGGAAGC AACGCGTAAA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTCGACCCGA CGCGTCCGAT CACCTGCGTC AATGTAATGT TCTGCGACGC TCACACCGAT ACCATCAGCG ATCTCTTTGA TGTGCTGTGC CTGAACCGTT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATTACGGATG GTATGTCCAA AGCGGCGATT TGGAAACGGC AGAGAAGGTA CTGGAAAAAG AACTTCTGGC CTGGCAGGAG AAACTGCATC AGCCGATTAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CATCACCGAA TACGGCGTGG ATACGTTAGC CGGGCTGCAC TCAATGTACA CCGACATGTG GAGTGAAGAG TATCAGTGTG CATGGCTGGA TATGTATCAC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CGCGTCTTTG ATCGCGTCAG CGCCGTCGTC GGTGAACAGG TATGGAATTT CGCCGATTTT GCGACCTCGC AAGGCATATT GCGCGTTGGC GGTAACAAGA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AAGGGATCTT CACTCGCGAC CGCAAACCGA AGTCGGCGGC TTTTCTGCTG CAAAAACGCT GGACTGGCAT GAACTTCGGT GAAAAACCGC AGCAGGGAGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CAAACAATGA
^2601

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

A promoter reported in cDNA corresponding to IRES sequence:
not tested 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:
GFP

The description of the protein encoded in this ORF:
green fluorescent protein

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):

1-720

ORF

ORF position:

2

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

The abbreviated name of this ORF/gene:
GUS

The description of the protein encoded in this ORF:
beta-glucuronidase

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):

799-2610

Citations:

Dorokhov YL, Skulachev MV, Ivanov PA, Zvereva SD, Tjulkina LG, Merits A, Gleba YY, Hohn T, Atabekov JG (2002) Polypurine (A)-rich sequences promote cross-kingdom conservation of internal ribosome entry. Proc. Natl. Acad. Sci. U.S.A. 8(99):5301-5306

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