IRESite_Id:604 negative control plasmid H-CP-TMV_UI

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `604`	Version: `4`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-23 17:49:38`
Reviewed by: Martin Mokrejš	Last change: `2009-08-26 13:38:16`

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 in vitro assays. The 5'-UTR could have been longer but do not
know the necessary details. The intercistronic region contains 5-UTR sequence of TMV UI virus (bp 2-68) which
does not contain IRES.

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

gggcgaattg ggtaccgggc cccccctcga ggtcgacggt atcgataccg tcgacctcga gggggggccc ggtaccATGT CTTACAACAT TACAAACCCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AATCAGTACC AGTATTTCGC AGCGGTGTGG GCAGAGCCCA TTCCGATGCT TAACCAGTGC ATATCGGCAT TGTCACAATC GTACCAAACA CAAGCTGCGA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GAGACACTGT TAGACAGCAA TTCTCAAACT TGTTGAGTGC GGTTGTGGCT CCGAGCCAGC GGTTCCCAGA AACAGGGTCC CGGGTGTATG TTAACTCGGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TGTTATAAAG CCGTTGTACG AGGCTCTTAT GAAGTCCTTT GATACTAGAA ATAGGATCAT AGAGACGGAA GAGGAGTCAC GCCCGTCAGC TTCCGAAGTA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CGTAACGCGA CACAACGTGT TGATGATGCG ACCGTTTCCA TTAGAAGTCA AATTCAGCTG TTGCTGAGCG AGCTTTCCAG TGGACATGGT TATATGAACA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GGGCAGAGTT CGAGGCTTTG GTGCCATGGA CTACTGCTGC TGCTACTTAG aagctttatt tttacaacaa ttaccaacaa caacaaacaa caaacaacat 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tacaattact atttacaatt acagtcgacc ATGGTCCGTC CTGTAGAAAC CCCAACCCGT GAAATCAAAA AACTCGACGG CCTGTGGGCA TTCAGTCTGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATCGCGAAAA CTGTGGAATT GATCAGCGTT GGTGGGAAAG CGCGTTACAA GAAAGCCGGG CAATTGCTGT GCCAGGCAGT TTTAACGATC AGTTCGCCGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TGCAGATATT CGTAATTATG CGGGCAACGT CTGGTATCAG CGCGAAGTCT TTATACCGAA AGGTTGGGCA GGCCAGCGTA TCGTGCTGCG TTTCGATGCG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GTCACTCATT ACGGCAAAGT GTGGGTCAAT AATCAGGAAG TGATGGAGCA TCAGGGCGGC TATACGCCAT TTGAAGCCGA TGTCACGCCG TATGTTATTG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCGGGAAAAG TGTACGTATC ACCGTTTGTG TGAACAACGA ACTGAACTGG CAGACTATCC CGCCGGGAAT GGTGATTACC GACGAAAACG GCAAGAAAAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GCAGTCTTAC TTCCATGATT TCTTTAACTA TGCCGGAATC CATCGCAGCG TAATGCTCTA CACCACGCCG AACACCTGGG TGGACGATAT CACCGTGGTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ACGCATGTCG CGCAAGACTG TAACCACGCG TCTGTTGACT GGCAGGTGGT GGCCAATGGT GATGTCAGCG TTGAACTGCG TGATGCGGAT CAACAGGTGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TTGCAACTGG ACAAGGCACT AGCGGGACTT TGCAAGTGGT GAATCCGCAC CTCTGGCAAC CGGGTGAAGG TTATCTCTAT GAACTGTGCG TCACAGCCAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAGCCAGACA GAGTGTGATA TCTACCCGCT TCGCGTCGGC ATCCGGTCAG TGGCAGTGAA GGGCGAACAG TTCCTGATTA ACCACAAACC GTTCTACTTT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACTGGCTTTG GTCGTCATGA AGATGCGGAC TTACGTGGCA AAGGATTCGA TAACGTGCTG ATGGTGCACG ACCACGCATT AATGGACTGG ATTGGGGCCA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACTCCTACCG TACCTCGCAT TACCCTTACG CTGAAGAGAT GCTCGACTGG GCAGATGAAC ATGGCATCGT GGTGATTGAT GAAACTGCTG CTGTCGGCTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TAACCTCTCT TTAGGCATTG GTTTCGAAGC GGGCAACAAG CCGAAAGAAC TGTACAGCGA AGAGGCAGTC AACGGGGAAA CTCAGCAAGC GCACTTACAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCGATTAAAG AGCTGATAGC GCGTGACAAA AACCACCCAA GCGTGGTGAT GTGGAGTATT GCCAACGAAC CGGATACCCG TCCGCAAGGT GCACGGGAAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATTTCGCGCC ACTGGCGGAA GCAACGCGTA AACTCGACCC GACGCGTCCG ATCACCTGCG TCAATGTAAT GTTCTGCGAC GCTCACACCG ATACCATCAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CGATCTCTTT GATGTGCTGT GCCTGAACCG TTATTACGGA TGGTATGTCC AAAGCGGCGA TTTGGAAACG GCAGAGAAGG TACTGGAAAA AGAACTTCTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCCTGGCAGG AGAAACTGCA TCAGCCGATT ATCATCACCG AATACGGCGT GGATACGTTA GCCGGGCTGC ACTCAATGTA CACCGACATG TGGAGTGAAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AGTATCAGTG TGCATGGCTG GATATGTATC ACCGCGTCTT TGATCGCGTC AGCGCCGTCG TCGGTGAACA GGTATGGAAT TTCGCCGATT TTGCGACCTC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GCAAGGCATA TTGCGCGTTG GCGGTAACAA GAAAGGGATC TTCACTCGCG ACCGCAAACC GAAGTCGGCG GCTTTTCTGC TGCAAAAACG CTGGACTGGC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ATGAACTTCG GTGAAAAACC GCAGCAGGGA GGCAAACAAT GA
^2401      ^2411      ^2421      ^2431      ^2441

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-CP-TMV_UI_omega-GUS The name of the promoter used to express this mRNA:
T7

Aliases of the plasmid name:

Alias: hCP-omega-GUS

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:

gggcgaattg ggtaccgggc cccccctcga ggtcgacggt atcgataccg tcgacctcga gggggggccc ggtaccATGT CTTACAACAT TACAAACCCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AATCAGTACC AGTATTTCGC AGCGGTGTGG GCAGAGCCCA TTCCGATGCT TAACCAGTGC ATATCGGCAT TGTCACAATC GTACCAAACA CAAGCTGCGA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GAGACACTGT TAGACAGCAA TTCTCAAACT TGTTGAGTGC GGTTGTGGCT CCGAGCCAGC GGTTCCCAGA AACAGGGTCC CGGGTGTATG TTAACTCGGC 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TGTTATAAAG CCGTTGTACG AGGCTCTTAT GAAGTCCTTT GATACTAGAA ATAGGATCAT AGAGACGGAA GAGGAGTCAC GCCCGTCAGC TTCCGAAGTA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CGTAACGCGA CACAACGTGT TGATGATGCG ACCGTTTCCA TTAGAAGTCA AATTCAGCTG TTGCTGAGCG AGCTTTCCAG TGGACATGGT TATATGAACA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GGGCAGAGTT CGAGGCTTTG GTGCCATGGA CTACTGCTGC TGCTACTTAG aagctttatt tttacaacaa ttaccaacaa caacaaacaa caaacaacat 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

tacaattact atttacaatt acagtcgacc ATGGTCCGTC CTGTAGAAAC CCCAACCCGT GAAATCAAAA AACTCGACGG CCTGTGGGCA TTCAGTCTGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATCGCGAAAA CTGTGGAATT GATCAGCGTT GGTGGGAAAG CGCGTTACAA GAAAGCCGGG CAATTGCTGT GCCAGGCAGT TTTAACGATC AGTTCGCCGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TGCAGATATT CGTAATTATG CGGGCAACGT CTGGTATCAG CGCGAAGTCT TTATACCGAA AGGTTGGGCA GGCCAGCGTA TCGTGCTGCG TTTCGATGCG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GTCACTCATT ACGGCAAAGT GTGGGTCAAT AATCAGGAAG TGATGGAGCA TCAGGGCGGC TATACGCCAT TTGAAGCCGA TGTCACGCCG TATGTTATTG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCGGGAAAAG TGTACGTATC ACCGTTTGTG TGAACAACGA ACTGAACTGG CAGACTATCC CGCCGGGAAT GGTGATTACC GACGAAAACG GCAAGAAAAA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GCAGTCTTAC TTCCATGATT TCTTTAACTA TGCCGGAATC CATCGCAGCG TAATGCTCTA CACCACGCCG AACACCTGGG TGGACGATAT CACCGTGGTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ACGCATGTCG CGCAAGACTG TAACCACGCG TCTGTTGACT GGCAGGTGGT GGCCAATGGT GATGTCAGCG TTGAACTGCG TGATGCGGAT CAACAGGTGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TTGCAACTGG ACAAGGCACT AGCGGGACTT TGCAAGTGGT GAATCCGCAC CTCTGGCAAC CGGGTGAAGG TTATCTCTAT GAACTGTGCG TCACAGCCAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AAGCCAGACA GAGTGTGATA TCTACCCGCT TCGCGTCGGC ATCCGGTCAG TGGCAGTGAA GGGCGAACAG TTCCTGATTA ACCACAAACC GTTCTACTTT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACTGGCTTTG GTCGTCATGA AGATGCGGAC TTACGTGGCA AAGGATTCGA TAACGTGCTG ATGGTGCACG ACCACGCATT AATGGACTGG ATTGGGGCCA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACTCCTACCG TACCTCGCAT TACCCTTACG CTGAAGAGAT GCTCGACTGG GCAGATGAAC ATGGCATCGT GGTGATTGAT GAAACTGCTG CTGTCGGCTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TAACCTCTCT TTAGGCATTG GTTTCGAAGC GGGCAACAAG CCGAAAGAAC TGTACAGCGA AGAGGCAGTC AACGGGGAAA CTCAGCAAGC GCACTTACAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCGATTAAAG AGCTGATAGC GCGTGACAAA AACCACCCAA GCGTGGTGAT GTGGAGTATT GCCAACGAAC CGGATACCCG TCCGCAAGGT GCACGGGAAT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ATTTCGCGCC ACTGGCGGAA GCAACGCGTA AACTCGACCC GACGCGTCCG ATCACCTGCG TCAATGTAAT GTTCTGCGAC GCTCACACCG ATACCATCAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CGATCTCTTT GATGTGCTGT GCCTGAACCG TTATTACGGA TGGTATGTCC AAAGCGGCGA TTTGGAAACG GCAGAGAAGG TACTGGAAAA AGAACTTCTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCCTGGCAGG AGAAACTGCA TCAGCCGATT ATCATCACCG AATACGGCGT GGATACGTTA GCCGGGCTGC ACTCAATGTA CACCGACATG TGGAGTGAAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AGTATCAGTG TGCATGGCTG GATATGTATC ACCGCGTCTT TGATCGCGTC AGCGCCGTCG TCGGTGAACA GGTATGGAAT TTCGCCGATT TTGCGACCTC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GCAAGGCATA TTGCGCGTTG GCGGTAACAA GAAAGGGATC TTCACTCGCG ACCGCAAACC GAAGTCGGCG GCTTTTCTGC TGCAAAAACG CTGGACTGGC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ATGAACTTCG GTGAAAAACC GCAGCAGGGA GGCAAACAAT GA
^2401      ^2411      ^2421      ^2431      ^2441

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:
CP

The description of the protein encoded in this ORF:
crTMV coat 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):

77-550

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):

631-2442

Remarks:

A single-read sequencing result between CP and GUS ORFs obtained from T. Komarova.

No proteins are produced from this message (Figure 7B and C). Removal of the hairpin from the 5'-end
(CP-TMV_UI-GUS plasmid) does not help.

Citations:

Ivanov P. A., Karpova O. V., Skulachev M. V., Tomashevskaya O. L., Rodionova N. P., Dorokhov YuL, Atabekov J. G. (1997) A tobamovirus genome that contains an internal ribosome entry site functional in vitro. Virology. 232(1):32-43

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