IRESite_Id:606 characteristics of crTMV_IRESmp75 IRES studied in H-CP-crTMV

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `606`	Version: `4`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-23 18:48:48`
Reviewed by: Martin Mokrejš	Last change: `2009-08-26 13:56:44`

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:
both_UTRs_incomplete

The mRNA/+RNA description:

Part of a T7-derived transcript. The 5'-UTR could have been longer but we do not know the necessary details.
The intercistronic region contains sequence preceding movement protein (MP) ORF in crTMV (bp -75 to -3).

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 aagcttcgtt tgctttttgt agtataatta aatatttgtc agataagaga 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ttggttagag atttgttctt tgtttgaccA TGGTCCGTCC TGTAGAAACC CCAACCCGTG AAATCAAAAA ACTCGACGGC CTGTGGGCAT TCAGTCTGGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TCGCGAAAAC TGTGGAATTG ATCAGCGTTG GTGGGAAAGC GCGTTACAAG AAAGCCGGGC AATTGCTGTG CCAGGCAGTT TTAACGATCA GTTCGCCGAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GCAGATATTC GTAATTATGC GGGCAACGTC TGGTATCAGC GCGAAGTCTT TATACCGAAA GGTTGGGCAG GCCAGCGTAT CGTGCTGCGT TTCGATGCGG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCACTCATTA CGGCAAAGTG TGGGTCAATA ATCAGGAAGT GATGGAGCAT CAGGGCGGCT ATACGCCATT TGAAGCCGAT GTCACGCCGT ATGTTATTGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CGGGAAAAGT GTACGTATCA CCGTTTGTGT GAACAACGAA CTGAACTGGC AGACTATCCC GCCGGGAATG GTGATTACCG ACGAAAACGG CAAGAAAAAG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CAGTCTTACT TCCATGATTT CTTTAACTAT GCCGGAATCC ATCGCAGCGT AATGCTCTAC ACCACGCCGA ACACCTGGGT GGACGATATC ACCGTGGTGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CGCATGTCGC GCAAGACTGT AACCACGCGT CTGTTGACTG GCAGGTGGTG GCCAATGGTG ATGTCAGCGT TGAACTGCGT GATGCGGATC AACAGGTGGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TGCAACTGGA CAAGGCACTA GCGGGACTTT GCAAGTGGTG AATCCGCACC TCTGGCAACC GGGTGAAGGT TATCTCTATG AACTGTGCGT CACAGCCAAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AGCCAGACAG AGTGTGATAT CTACCCGCTT CGCGTCGGCA TCCGGTCAGT GGCAGTGAAG GGCGAACAGT TCCTGATTAA CCACAAACCG TTCTACTTTA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CTGGCTTTGG TCGTCATGAA GATGCGGACT TACGTGGCAA AGGATTCGAT AACGTGCTGA TGGTGCACGA CCACGCATTA ATGGACTGGA TTGGGGCCAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CTCCTACCGT ACCTCGCATT ACCCTTACGC TGAAGAGATG CTCGACTGGG CAGATGAACA TGGCATCGTG GTGATTGATG AAACTGCTGC TGTCGGCTTT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AACCTCTCTT TAGGCATTGG TTTCGAAGCG GGCAACAAGC CGAAAGAACT GTACAGCGAA GAGGCAGTCA ACGGGGAAAC TCAGCAAGCG CACTTACAGG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CGATTAAAGA GCTGATAGCG CGTGACAAAA ACCACCCAAG CGTGGTGATG TGGAGTATTG CCAACGAACC GGATACCCGT CCGCAAGGTG CACGGGAATA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TTTCGCGCCA CTGGCGGAAG CAACGCGTAA ACTCGACCCG ACGCGTCCGA TCACCTGCGT CAATGTAATG TTCTGCGACG CTCACACCGA TACCATCAGC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GATCTCTTTG ATGTGCTGTG CCTGAACCGT TATTACGGAT GGTATGTCCA AAGCGGCGAT TTGGAAACGG CAGAGAAGGT ACTGGAAAAA GAACTTCTGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCTGGCAGGA GAAACTGCAT CAGCCGATTA TCATCACCGA ATACGGCGTG GATACGTTAG CCGGGCTGCA CTCAATGTAC ACCGACATGT GGAGTGAAGA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GTATCAGTGT GCATGGCTGG ATATGTATCA CCGCGTCTTT GATCGCGTCA GCGCCGTCGT CGGTGAACAG GTATGGAATT TCGCCGATTT TGCGACCTCG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CAAGGCATAT TGCGCGTTGG CGGTAACAAG AAAGGGATCT TCACTCGCGA CCGCAAACCG AAGTCGGCGG CTTTTCTGCT GCAAAAACGC TGGACTGGCA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGAACTTCGG TGAAAAACCG CAGCAGGGAG GCAAACAATG A
^2401      ^2411      ^2421      ^2431      ^2441

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:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

The name of the plasmid:
H-CP-crTMV_IRESmp75-GUS The name of the promoter used to express this mRNA:
T7

Aliases of the plasmid name:

Alias: HCP(deltaI-II)IRESmp75CR-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

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:
crTMV

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Crucifer tobamovirus

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 ATggtcaaac aaagaacaaa tctctaacca atctcttatc tgacaaatat ttaattatac tacaaaaagc aaacgaagct tCTAAGTAGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AGCAGCAGTA GTCCATGGCA CCAAAGCCTC GAACTCTGCC CTGTTCATAT AACCATGTCC ACTGGAAAGC TCGCTCAGCA ACAGCTGAAT TTGACTTCTA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ATGGAAACGG TCGCATCATC AACACGTTGT GTCGCGTTAC GTACTTCGGA AGCTGACGGG CGTGACTCCT CTTCCGTCTC TATGATCCTA TTTCTAGTAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CAAAGGACTT CATAAGAGCC TCGTACAACG GCTTTATAAC AGCCGAGTTA ACATACACCC GGGACCCTGT TTCTGGGAAC CGCTGGCTCG GAGCCACAAC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CGCACTCAAC AAGTTTGAGA ATTGCTGTCT AACAGTGTCT CTCGCAGCTT GTGTTTGGTA CGATTGTGAC AATGCCGATA TGCACTGGTT AAGCATCGGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATGGGCTCTG CCCACACCGC TGCGAAATAC TGGTACTGAT TCGGGTTTGT AATGTTGTAA GACATggtac cgggcccccc ctcgaggtcg acggtatcga 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

taccgtcgac ctcgaggggg ggcccggtac ccaattcgcc c
^2401      ^2411      ^2421      ^2431      ^2441

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: 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):

630-2441

Remarks:

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

The crTMV insert matches Z29370 sequence except one base. Probably the genomic sequence was published wrong as
two additional plasmid constructs from the same lab have the same base in that position.

Citations:

Skulachev MV, Ivanov PA, Karpova OV, Korpela T, Rodionova NP, Dorokhov YL, Atabekov JG (1999) Internal initiation of translation directed by the 5'-untranslated region of the tobamovirus subgenomic RNA I(2). Virology. 1(263):139-154

IRESs:

IRES:

Version: `1`	Last change: `2009-08-26 13:56:44`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `crTMV_IRESmp75`	The functional status of IRES: `functional`

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

555-627

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `5`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `77`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-75`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-3`

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

ttcgtttgct ttttgtagta taattaaata tttgtcagat aagagattgg ttagagattt gttctttgtt tga
^555       ^565       ^575       ^585       ^595       ^605       ^615       ^625

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 644

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

The translation method used to study IRES function:
in vitro The in vitro translation system:
rabbit reticulocytes lysate

The organism used for translation:

The temperature (in degrees of Celsia):
30

The relative translation efficiency in % of this IRES:

80.000

Name of IRES used as the positive control:

crTMV_IRESmp228

Name of the plasmid used as the positive control. `H-CP-crTMV_IRESmp228`	Name of the plasmid used as the negative control. `H-CP-TMVUI_noIREScp148`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

exogenous_RNA_without_cap_without_polyA_tail

Remarks:

Values without exact quantification from Figure 8B.

Citations:

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