IRESite_Id:608 characteristics of EMCV-R_315-845 IRES studied in H-GFP-IRESemcv-GUS plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `608`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-25 16:04:27`
Reviewed by: Martin Mokrejš

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 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 EMCV-R virus (bp 315-843).

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 gcttatcgat ttncgaaccc gggggtaccg aattcgagct cggtacccgg ggatcctcta gagtcggtgt gcgtttgtct 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

atatgttatt ttccaccata ttgccgtctt ttggcaatgt gagggcccgg aaacctggcc ctgtcttctt gacgagcatt cctaggggtc tttcccctct 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

cgccaaagga atgcaaggtc tgttgaatgt cgtgaaggaa gcagttcctc tggaagcttc ttgaagacaa acaacgtctg tagcgaccct ttgcaggcag 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

cggaaccccc caccgggcga caggtgcctc tgcggccaaa agccacgtgt ataagataca cctgcaaagg cggcacaacc ccagtgccac gttgtgagtt 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ggatagttgt ggaaagagtc aaatggctct cctcaagcgt attcaacaag gggctgaagg atgcccagaa ggtaccccat tgtatgggat ctgatctggg 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

gcctcggtgc acatgcttta catgtgttta gtcgaggtta aaaagcgtct aggccccccg aaccacgggg acgtggtttt cctttgaaaa acacgatgat 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

aatatggcca caaccATGGT CCGTCCTGTA GAAACCCCAA CCCGTGAAAT CAAAAAACTC GACGGCCTGT GGGCATTCAG TCTGGATCGC GAAAACTGTG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAATTGATCA GCGTTGGTGG GAAAGCGCGT TACAAGAAAG CCGGGCAATT GCTGTGCCAG GCAGTTTTAA CGATCAGTTC GCCGATGCAG ATATTCGTAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTATGCGGGC AACGTCTGGT ATCAGCGCGA AGTCTTTATA CCGAAAGGTT GGGCAGGCCA GCGTATCGTG CTGCGTTTCG ATGCGGTCAC TCATTACGGC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AAAGTGTGGG TCAATAATCA GGAAGTGATG GAGCATCAGG GCGGCTATAC GCCATTTGAA GCCGATGTCA CGCCGTATGT TATTGCCGGG AAAAGTGTAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTATCACCGT TTGTGTGAAC AACGAACTGA ACTGGCAGAC TATCCCGCCG GGAATGGTGA TTACCGACGA AAACGGCAAG AAAAAGCAGT CTTACTTCCA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGATTTCTTT AACTATGCCG GAATCCATCG CAGCGTAATG CTCTACACCA CGCCGAACAC CTGGGTGGAC GATATCACCG TGGTGACGCA TGTCGCGCAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GACTGTAACC ACGCGTCTGT TGACTGGCAG GTGGTGGCCA ATGGTGATGT CAGCGTTGAA CTGCGTGATG CGGATCAACA GGTGGTTGCA ACTGGACAAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GCACTAGCGG GACTTTGCAA GTGGTGAATC CGCACCTCTG GCAACCGGGT GAAGGTTATC TCTATGAACT GTGCGTCACA GCCAAAAGCC AGACAGAGTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGATATCTAC CCGCTTCGCG TCGGCATCCG GTCAGTGGCA GTGAAGGGCG AACAGTTCCT GATTAACCAC AAACCGTTCT ACTTTACTGG CTTTGGTCGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CATGAAGATG CGGACTTACG TGGCAAAGGA TTCGATAACG TGCTGATGGT GCACGACCAC GCATTAATGG ACTGGATTGG GGCCAACTCC TACCGTACCT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CGCATTACCC TTACGCTGAA GAGATGCTCG ACTGGGCAGA TGAACATGGC ATCGTGGTGA TTGATGAAAC TGCTGCTGTC GGCTTTAACC TCTCTTTAGG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CATTGGTTTC GAAGCGGGCA ACAAGCCGAA AGAACTGTAC AGCGAAGAGG CAGTCAACGG GGAAACTCAG CAAGCGCACT TACAGGCGAT TAAAGAGCTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATAGCGCGTG ACAAAAACCA CCCAAGCGTG GTGATGTGGA GTATTGCCAA CGAACCGGAT ACCCGTCCGC AAGGTGCACG GGAATATTTC GCGCCACTGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGGAAGCAAC GCGTAAACTC GACCCGACGC GTCCGATCAC CTGCGTCAAT GTAATGTTCT GCGACGCTCA CACCGATACC ATCAGCGATC TCTTTGATGT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCTGTGCCTG AACCGTTATT ACGGATGGTA TGTCCAAAGC GGCGATTTGG AAACGGCAGA GAAGGTACTG GAAAAAGAAC TTCTGGCCTG GCAGGAGAAA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CTGCATCAGC CGATTATCAT CACCGAATAC GGCGTGGATA CGTTAGCCGG GCTGCACTCA ATGTACACCG ACATGTGGAG TGAAGAGTAT CAGTGTGCAT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGCTGGATAT GTATCACCGC GTCTTTGATC GCGTCAGCGC CGTCGTCGGT GAACAGGTAT GGAATTTCGC CGATTTTGCG ACCTCGCAAG GCATATTGCG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGTTGGCGGT AACAAGAAAG GGATCTTCAC TCGCGACCGC AAACCGAAGT CGGCGGCTTT TCTGCTGCAA AAACGCTGGA CTGGCATGAA CTTCGGTGAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAACCGCAGC AGGGAGGCAA ACAATGA
^3101      ^3111      ^3121

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:

reverse_engineered_fragment_and_the_rest_is_a_guess

The name of the plasmid:
H-GFP-IRESemcv-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

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:
EMCV-R

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Encephalomyocarditis virus Rueckert

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 gcttatcgat ttncgaaccc gggggtaccg aattcgagct cggtacccgg ggatcctcta gagtcggtgt gcgtttgtct 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

atatgttatt ttccaccata ttgccgtctt ttggcaatgt gagggcccgg aaacctggcc ctgtcttctt gacgagcatt cctaggggtc tttcccctct 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

cgccaaagga atgcaaggtc tgttgaatgt cgtgaaggaa gcagttcctc tggaagcttc ttgaagacaa acaacgtctg tagcgaccct ttgcaggcag 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

cggaaccccc caccgggcga caggtgcctc tgcggccaaa agccacgtgt ataagataca cctgcaaagg cggcacaacc ccagtgccac gttgtgagtt 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ggatagttgt ggaaagagtc aaatggctct cctcaagcgt attcaacaag gggctgaagg atgcccagaa ggtaccccat tgtatgggat ctgatctggg 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

gcctcggtgc acatgcttta catgtgttta gtcgaggtta aaaagcgtct aggccccccg aaccacgggg acgtggtttt cctttgaaaa acacgatgat 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

aatatggcca caaccATGGT CCGTCCTGTA GAAACCCCAA CCCGTGAAAT CAAAAAACTC GACGGCCTGT GGGCATTCAG TCTGGATCGC GAAAACTGTG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GAATTGATCA GCGTTGGTGG GAAAGCGCGT TACAAGAAAG CCGGGCAATT GCTGTGCCAG GCAGTTTTAA CGATCAGTTC GCCGATGCAG ATATTCGTAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTATGCGGGC AACGTCTGGT ATCAGCGCGA AGTCTTTATA CCGAAAGGTT GGGCAGGCCA GCGTATCGTG CTGCGTTTCG ATGCGGTCAC TCATTACGGC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AAAGTGTGGG TCAATAATCA GGAAGTGATG GAGCATCAGG GCGGCTATAC GCCATTTGAA GCCGATGTCA CGCCGTATGT TATTGCCGGG AAAAGTGTAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTATCACCGT TTGTGTGAAC AACGAACTGA ACTGGCAGAC TATCCCGCCG GGAATGGTGA TTACCGACGA AAACGGCAAG AAAAAGCAGT CTTACTTCCA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGATTTCTTT AACTATGCCG GAATCCATCG CAGCGTAATG CTCTACACCA CGCCGAACAC CTGGGTGGAC GATATCACCG TGGTGACGCA TGTCGCGCAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GACTGTAACC ACGCGTCTGT TGACTGGCAG GTGGTGGCCA ATGGTGATGT CAGCGTTGAA CTGCGTGATG CGGATCAACA GGTGGTTGCA ACTGGACAAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GCACTAGCGG GACTTTGCAA GTGGTGAATC CGCACCTCTG GCAACCGGGT GAAGGTTATC TCTATGAACT GTGCGTCACA GCCAAAAGCC AGACAGAGTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGATATCTAC CCGCTTCGCG TCGGCATCCG GTCAGTGGCA GTGAAGGGCG AACAGTTCCT GATTAACCAC AAACCGTTCT ACTTTACTGG CTTTGGTCGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CATGAAGATG CGGACTTACG TGGCAAAGGA TTCGATAACG TGCTGATGGT GCACGACCAC GCATTAATGG ACTGGATTGG GGCCAACTCC TACCGTACCT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CGCATTACCC TTACGCTGAA GAGATGCTCG ACTGGGCAGA TGAACATGGC ATCGTGGTGA TTGATGAAAC TGCTGCTGTC GGCTTTAACC TCTCTTTAGG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CATTGGTTTC GAAGCGGGCA ACAAGCCGAA AGAACTGTAC AGCGAAGAGG CAGTCAACGG GGAAACTCAG CAAGCGCACT TACAGGCGAT TAAAGAGCTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATAGCGCGTG ACAAAAACCA CCCAAGCGTG GTGATGTGGA GTATTGCCAA CGAACCGGAT ACCCGTCCGC AAGGTGCACG GGAATATTTC GCGCCACTGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CGGAAGCAAC GCGTAAACTC GACCCGACGC GTCCGATCAC CTGCGTCAAT GTAATGTTCT GCGACGCTCA CACCGATACC ATCAGCGATC TCTTTGATGT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCTGTGCCTG AACCGTTATT ACGGATGGTA TGTCCAAAGC GGCGATTTGG AAACGGCAGA GAAGGTACTG GAAAAAGAAC TTCTGGCCTG GCAGGAGAAA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CTGCATCAGC CGATTATCAT CACCGAATAC GGCGTGGATA CGTTAGCCGG GCTGCACTCA ATGTACACCG ACATGTGGAG TGAAGAGTAT CAGTGTGCAT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGCTGGATAT GTATCACCGC GTCTTTGATC GCGTCAGCGC CGTCGTCGGT GAACAGGTAT GGAATTTCGC CGATTTTGCG ACCTCGCAAG GCATATTGCG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGTTGGCGGT AACAAGAAAG GGATCTTCAC TCGCGACCGC AAACCGAAGT CGGCGGCTTT TCTGCTGCAA AAACGCTGGA CTGGCATGAA CTTCGGTGAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAACCGCAGC AGGGAGGCAA ACAATGA
^3101      ^3111      ^3121

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:
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: `1`	Last change: `2009-08-25 16:06:40`
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):

1316-3127

Remarks:

The intercistronic region inherited quite a long sequence from parental plasmids (64bp). The EMCV-R fragment
was inserted downstream of this spacer using EcoRI and Nco sites just in front with the GUS ORF.

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

IRESs:

IRES:

Version: `2`	Last change: `2011-04-08 21:37:11`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `EMCV-R_315-845`	The functional status of IRES: `functional`

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

785-1315

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `65`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `595`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-531`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-1`

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

cggtgtgcgt ttgtctatat gttattttcc accatattgc cgtcttttgg caatgtgagg gcccggaaac ctggccctgt cttcttgacg agcattccta 
^785       ^795       ^805       ^815       ^825       ^835       ^845       ^855       ^865       ^875       

ggggtctttc ccctctcgcc aaaggaatgc aaggtctgtt gaatgtcgtg aaggaagcag ttcctctgga agcttcttga agacaaacaa cgtctgtagc 
^885       ^895       ^905       ^915       ^925       ^935       ^945       ^955       ^965       ^975       

gaccctttgc aggcagcgga accccccacc gggcgacagg tgcctctgcg gccaaaagcc acgtgtataa gatacacctg caaaggcggc acaaccccag 
^985       ^995       ^1005      ^1015      ^1025      ^1035      ^1045      ^1055      ^1065      ^1075      

tgccacgttg tgagttggat agttgtggaa agagtcaaat ggctctcctc aagcgtattc aacaaggggc tgaaggatgc ccagaaggta ccccattgta 
^1085      ^1095      ^1105      ^1115      ^1125      ^1135      ^1145      ^1155      ^1165      ^1175      

tgggatctga tctggggcct cggtgcacat gctttacatg tgtttagtcg aggttaaaaa gcgtctaggc cccccgaacc acggggacgt ggttttcctt 
^1185      ^1195      ^1205      ^1215      ^1225      ^1235      ^1245      ^1255      ^1265      ^1275      

tgaaaaacac gatgataata tggccacaac c
^1285      ^1295      ^1305      ^1315

Remarks:

The GFP-IRES-GUS cassette was also cloned into yeast vector PyeDP1/8-2 and expression of reporters studied in
unnamed yeast of strain 2805 grown at 30 oC! The EMCV-R IRES was found active about 10x above some negative
control.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 634

Version: `2`	Last change: `2009-08-26 12:16:33`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

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:

100.000

	Name of the plasmid used as the negative control. `H-GFP-TMV_UI-GUS`
	`IRESite Id` of the plasmid used as negative control. `611`
	The relative translation efficiency in % of the negative control: `0.860`
	The size (length) of intercistronic region in the negative control: `78`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_cytoplasmic_uncapped_T7_transcript_without_polyA_tail

Remarks:

Data from Figure 2B. The cells were infected by recombinant vaccinia virus. Also GFP-TMV_UI-GUS (TMV UI 5'-UTR
omega leader) was used as a negative control (IRESiteID:611).

Citations:

Translation results:

IRESite Translation Id: 635

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):
37

The relative translation efficiency in % of this IRES:

279.000

	Name of the plasmid used as the negative control. `NO_RNA`
	The relative translation efficiency in % of the negative control: `1.000`

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:

Data from Figure 2E.

Citations:

Translation results:

IRESite Translation Id: 636

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:
wheat germ lysate

The organism used for translation:

The temperature (in degrees of Celsia):
25

The relative translation efficiency in % of this IRES:

100.000

	Name of the plasmid used as the negative control. `NO_RNA`
	The relative translation efficiency in % of the negative control: `80.000`

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:

Data from Figure 2D.

Citations:

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