IRESite_Id:607 negative control plasmid H-CP-alphabeta-GUS

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `607`	Version: `1`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-23 19:19:45`
Reviewed by: Martin Mokrejš	Last change: `2009-08-25 15:15:12`

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 Potato virus X (PVX, M72416)
virus (bp 2-84) which has translational enhancer activity.

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

TCATTGTTTG CCTCCCTGCT GCGGTTTTTC ACCGAAGTTC ATGCCAGTCC AGCGTTTTTG CAGCAGAAAA GCCGCCGACT TCGGTTTGCG GTCGCGAGTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAGATCCCTT TCTTGTTACC GCCAACGCGC AATATGCCTT GCGAGGTCGC AAAATCGGCG AAATTCCATA CCTGTTCACC GACGACGGCG CTGACGCGAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CAAAGACGCG GTGATACATA TCCAGCCATG CACACTGATA CTCTTCACTC CACATGTCGG TGTACATTGA GTGCAGCCCG GCTAACGTAT CCACGCCGTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTCGGTGATG ATAATCGGCT GATGCAGTTT CTCCTGCCAG GCCAGAAGTT CTTTTTCCAG TACCTTCTCT GCCGTTTCCA AATCGCCGCT TTGGACATAC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CATCCGTAAT AACGGTTCAG GCACAGCACA TCAAAGAGAT CGCTGATGGT ATCGGTGTGA GCGTCGCAGA ACATTACATT GACGCAGGTG ATCGGACGCG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCGGGTCGAG TTTACGCGTT GCTTCCGCCA GTGGCGCGAA ATATTCCCGT GCACCTTGCG GACGGGTATC CGGTTCGTTG GCAATACTCC ACATCACCAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GCTTGGGTGG TTTTTGTCAC GCGCTATCAG CTCTTTAATC GCCTGTAAGT GCGCTTGCTG AGTTTCCCCG TTGACTGCCT CTTCGCTGTA CAGTTCTTTC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GGCTTGTTGC CCGCTTCGAA ACCAATGCCT AAAGAGAGGT TAAAGCCGAC AGCAGCAGTT TCATCAATCA CCACGATGCC ATGTTCATCT GCCCAGTCGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GCATCTCTTC AGCGTAAGGG TAATGCGAGG TACGGTAGGA GTTGGCCCCA ATCCAGTCCA TTAATGCGTG GTCGTGCACC ATCAGCACGT TATCGAATCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTTGCCACGT AAGTCCGCAT CTTCATGACG ACCAAAGCCA GTAAAGTAGA ACGGTTTGTG GTTAATCAGG AACTGTTCGC CCTTCACTGC CACTGACCGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ATGCCGACGC GAAGCGGGTA GATATCACAC TCTGTCTGGC TTTTGGCTGT GACGCACAGT TCATAGAGAT AACCTTCACC CGGTTGCCAG AGGTGCGGAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCACCACTTG CAAAGTCCCG CTAGTGCCTT GTCCAGTTGC AACCACCTGT TGATCCGCAT CACGCAGTTC AACGCTGACA TCACCATTGG CCACCACCTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCAGTCAACA GACGCGTGGT TACAGTCTTG CGCGACATGC GTCACCACGG TGATATCGTC CACCCAGGTG TTCGGCGTGG TGTAGAGCAT TACGCTGCGA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TGGATTCCGG CATAGTTAAA GAAATCATGG AAGTAAGACT GCTTTTTCTT GCCGTTTTCG TCGGTAATCA CCATTCCCGG CGGGATAGTC TGCCAGTTCA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GTTCGTTGTT CACACAAACG GTGATACGTA CACTTTTCCC GGCAATAACA TACGGCGTGA CATCGGCTTC AAATGGCGTA TAGCCGCCCT GATGCTCCAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CACTTCCTGA TTATTGACCC ACACTTTGCC GTAATGAGTG ACCGCATCGA AACGCAGCAC GATACGCTGG CCTGCCCAAC CTTTCGGTAT AAAGACTTCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CGCTGATACC AGACGTTGCC CGCATAATTA CGAATATCTG CATCGGCGAA CTGATCGTTA AAACTGCCTG GCACAGCAAT TGCCCGGCTT TCTTGTAACG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CGCTTTCCCA CCAACGCTGA TCAATTCCAC AGTTTTCGCG ATCCAGACTG AATGCCCACA GGCCGTCGAG TTTTTTGATT TCACGGGTTG GGGTTTCTAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGGACGGACC ATggtcgaca aaactaaacc atacaccaac aacacaacca aacccaccac gcccaattgt tacacacccg cttggaaaag taagtctaac 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

aaaagcttCT AAGTAGCAGC AGCAGTAGTC CATGGCACCA AAGCCTCGAA CTCTGCCCTG TTCATATAAC CATGTCCACT GGAAAGCTCG CTCAGCAACA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GCTGAATTTG ACTTCTAATG GAAACGGTCG CATCATCAAC ACGTTGTGTC GCGTTACGTA CTTCGGAAGC TGACGGGCGT GACTCCTCTT CCGTCTCTAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GATCCTATTT CTAGTATCAA AGGACTTCAT AAGAGCCTCG TACAACGGCT TTATAACAGC CGAGTTAACA TACACCCGGG ACCCTGTTTC TGGGAACCGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGGCTCGGAG CCACAACCGC ACTCAACAAG TTTGAGAATT GCTGTCTAAC AGTGTCTCTC GCAGCTTGTG TTTGGTACGA TTGTGACAAT GCCGATATGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACTGGTTAAG CATCGGAATG GGCTCTGCCC ACACCGCTGC GAAATACTGG TACTGATTCG GGTTTGTAAT GTTGTAAGAC ATggtaccgg gccccccctc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gaggtcgacg gtatcgatac cgtcgacctc gagggggggc ccggtaccca attcgccc
^2401      ^2411      ^2421      ^2431      ^2441      ^2451

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-alphabeta-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:

TCATTGTTTG CCTCCCTGCT GCGGTTTTTC ACCGAAGTTC ATGCCAGTCC AGCGTTTTTG CAGCAGAAAA GCCGCCGACT TCGGTTTGCG GTCGCGAGTG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAGATCCCTT TCTTGTTACC GCCAACGCGC AATATGCCTT GCGAGGTCGC AAAATCGGCG AAATTCCATA CCTGTTCACC GACGACGGCG CTGACGCGAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CAAAGACGCG GTGATACATA TCCAGCCATG CACACTGATA CTCTTCACTC CACATGTCGG TGTACATTGA GTGCAGCCCG GCTAACGTAT CCACGCCGTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTCGGTGATG ATAATCGGCT GATGCAGTTT CTCCTGCCAG GCCAGAAGTT CTTTTTCCAG TACCTTCTCT GCCGTTTCCA AATCGCCGCT TTGGACATAC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CATCCGTAAT AACGGTTCAG GCACAGCACA TCAAAGAGAT CGCTGATGGT ATCGGTGTGA GCGTCGCAGA ACATTACATT GACGCAGGTG ATCGGACGCG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCGGGTCGAG TTTACGCGTT GCTTCCGCCA GTGGCGCGAA ATATTCCCGT GCACCTTGCG GACGGGTATC CGGTTCGTTG GCAATACTCC ACATCACCAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GCTTGGGTGG TTTTTGTCAC GCGCTATCAG CTCTTTAATC GCCTGTAAGT GCGCTTGCTG AGTTTCCCCG TTGACTGCCT CTTCGCTGTA CAGTTCTTTC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GGCTTGTTGC CCGCTTCGAA ACCAATGCCT AAAGAGAGGT TAAAGCCGAC AGCAGCAGTT TCATCAATCA CCACGATGCC ATGTTCATCT GCCCAGTCGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GCATCTCTTC AGCGTAAGGG TAATGCGAGG TACGGTAGGA GTTGGCCCCA ATCCAGTCCA TTAATGCGTG GTCGTGCACC ATCAGCACGT TATCGAATCC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTTGCCACGT AAGTCCGCAT CTTCATGACG ACCAAAGCCA GTAAAGTAGA ACGGTTTGTG GTTAATCAGG AACTGTTCGC CCTTCACTGC CACTGACCGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ATGCCGACGC GAAGCGGGTA GATATCACAC TCTGTCTGGC TTTTGGCTGT GACGCACAGT TCATAGAGAT AACCTTCACC CGGTTGCCAG AGGTGCGGAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TCACCACTTG CAAAGTCCCG CTAGTGCCTT GTCCAGTTGC AACCACCTGT TGATCCGCAT CACGCAGTTC AACGCTGACA TCACCATTGG CCACCACCTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCAGTCAACA GACGCGTGGT TACAGTCTTG CGCGACATGC GTCACCACGG TGATATCGTC CACCCAGGTG TTCGGCGTGG TGTAGAGCAT TACGCTGCGA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TGGATTCCGG CATAGTTAAA GAAATCATGG AAGTAAGACT GCTTTTTCTT GCCGTTTTCG TCGGTAATCA CCATTCCCGG CGGGATAGTC TGCCAGTTCA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GTTCGTTGTT CACACAAACG GTGATACGTA CACTTTTCCC GGCAATAACA TACGGCGTGA CATCGGCTTC AAATGGCGTA TAGCCGCCCT GATGCTCCAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CACTTCCTGA TTATTGACCC ACACTTTGCC GTAATGAGTG ACCGCATCGA AACGCAGCAC GATACGCTGG CCTGCCCAAC CTTTCGGTAT AAAGACTTCG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CGCTGATACC AGACGTTGCC CGCATAATTA CGAATATCTG CATCGGCGAA CTGATCGTTA AAACTGCCTG GCACAGCAAT TGCCCGGCTT TCTTGTAACG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CGCTTTCCCA CCAACGCTGA TCAATTCCAC AGTTTTCGCG ATCCAGACTG AATGCCCACA GGCCGTCGAG TTTTTTGATT TCACGGGTTG GGGTTTCTAC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AGGACGGACC ATggtcgaca aaactaaacc atacaccaac aacacaacca aacccaccac gcccaattgt tacacacccg cttggaaaag taagtctaac 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

aaaagcttCT AAGTAGCAGC AGCAGTAGTC CATGGCACCA AAGCCTCGAA CTCTGCCCTG TTCATATAAC CATGTCCACT GGAAAGCTCG CTCAGCAACA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GCTGAATTTG ACTTCTAATG GAAACGGTCG CATCATCAAC ACGTTGTGTC GCGTTACGTA CTTCGGAAGC TGACGGGCGT GACTCCTCTT CCGTCTCTAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GATCCTATTT CTAGTATCAA AGGACTTCAT AAGAGCCTCG TACAACGGCT TTATAACAGC CGAGTTAACA TACACCCGGG ACCCTGTTTC TGGGAACCGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TGGCTCGGAG CCACAACCGC ACTCAACAAG TTTGAGAATT GCTGTCTAAC AGTGTCTCTC GCAGCTTGTG TTTGGTACGA TTGTGACAAT GCCGATATGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACTGGTTAAG CATCGGAATG GGCTCTGCCC ACACCGCTGC GAAATACTGG TACTGATTCG GGTTTGTAAT GTTGTAAGAC ATggtaccgg gccccccctc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gaggtcgacg gtatcgatac cgtcgacctc gagggggggc ccggtaccca attcgccc
^2401      ^2411      ^2421      ^2431      ^2441      ^2451

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:
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):

647-2458

Remarks:

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

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