IRESite_Id:467 characteristics of HRV-2 IRES studied in pRHRVF plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `467`	Version: `6`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-12-16 02:44:15`

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:
our_best_guess

The mRNA/+RNA description:

Putative spliced bicistronic transcript derived from SV40 promoter based pRHRVF plasmid.

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

TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTGAAGT TGGTCGTGAG GCACTGGGCA GGTGTCCACT CCCAGTTCAA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TTACAGCTCT TAAGGCTAGA GTACTTAATA CGACTCACTA TAGGCTAGGC TTGGCATTCC GGTACTGAAT TGATATCAAG CTCTAGCCAC CATGACTTCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AAAGTTTATG ATCCAGAACA AAGGAAACGG ATGATAACTG GTCCGCAGTG GTGGGCCAGA TGTAAACAAA TGAATGTTCT TGATTCATTT ATTAATTATT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ATGATTCAGA AAAACATGCA GAAAATGCTG TTATTTTTTT ACATGGTAAC GCGGCCTCTT CTTATTTATG GCGACATGTT GTGCCACATA TTGAGCCAGT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AGCGCGGTGT ATTATACCAG ACCTTATTGG TATGGGCAAA TCAGGCAAAT CTGGTAATGG TTCTTATAGG TTACTTGATC ATTACAAATA TCTTACTGCA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TGGTTTGAAC TTCTTAATTT ACCAAAGAAG ATCATTTTTG TCGGCCATGA TTGGGGTGCT TGTTTGGCAT TTCATTATAG CTATGAGCAT CAAGATAAGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCAAAGCAAT AGTTCACGCT GAAAGTGTAG TAGATGTGAT TGAATCATGG GATGAATGGC CTGATATTGA AGAAGATATT GCGTTGATCA AATCTGAAGA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGGAGAAAAA ATGGTTTTGG AGAATAACTT CTTCGTGGAA ACCATGTTGC CATCAAAAAT CATGAGAAAG TTAGAACCAG AAGAATTTGC AGCATATCTT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GAACCATTCA AAGAGAAAGG TGAAGTTCGT CGTCCAACAT TATCATGGCC TCGTGAAATC CCGTTAGTAA AAGGTGGTAA ACCTGACGTT GTACAAATTG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTAGGAATTA TAATGCTTAT CTACGTGCAA GTGATGATTT ACCAAAAATG TTTATTGAAT CGGACCCAGG ATTCTTTTCC AATGCTATTG TTGAAGGTGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CAAGAAGTTT CCTAATACTG AATTTGTCAA AGTAAAAGGT CTTCATTTTT CGCAAGAAGA TGCACCTGAT GAAATGGGAA AATATATCAA ATCGTTCGTT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAGCGAGTTC TCAAAAATGA ACAATAATTC TAGAGCTTAT CGATACCGTC GACCTCGAAT CACTAGTCAG TCGACGAGCT CCCCGATCCA GGTTGTTCCC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ACCTGGATTT CCCACAGGGA GTGGTACTCT GTTATTACGG TAACTTTGTA CGCCAGTTTT ATCTCCCTTC CCCCATGAAC TTAGAAGTTT TTCACAAAAG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ACCAATAGCC GGTAATCAGC CAGATTACTG AAGGTCAAGC ACTTCTGTTT CCCCGGTCAA TGTTGATATG CTCCAACAGG GCAAAAACAA CTGCGATCGT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TAACCGCAAA GCGCCTACGC AAAGCTTAGT AGCATCTTTG AAATCGTTTG GCTGGTCGAT CCGCCATTTC CCCTGGTAGA CCTGGCAGAT GAGGCTAGAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ATACCCCACT GGCGACAGTG TTCTAGCCTG CGTGGCTGCC TGCACACCCT ATGGGTGTGA AGCCAAACAA TGGACAAGGT GTGAAGAGCC CCGTGTGCTC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCTTTGAGTC CTCCGGCCCC TGAATGTGGC TAACCTTAAC CCTGGCAGCT AGAGCACGTA ACCCAATGTG TATCTAGTCG TAATGAGCAA TTGCGGGATG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GGACCAACTA CTTTGGGTGT CCGTGTTTCA CTTTTTCCTT TATATTTGCT TATGGTGACA GTACCATGGA AGACGCCAAA AACATAAAGA AAGGCCCGGC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCCATTCTAT CCGCTGGAAG ATGGAACCGC TGGAGAGCAA CTGCATAAGG CTATGAAGAG ATACGCCCTG GTTCCTGGAA CAATTGCTTT TACAGATGCA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CATATCGAGG TGGACATCAC TTACGCTGAG TACTTCGAAA TGTCCGTTCG GTTGGCAGAA GCTATGAAAC GATATGGGCT GAATACAAAT CACAGAATCG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TCGTATGCAG TGAAAACTCT CTTCAATTCT TTATGCCGGT GTTGGGCGCG TTATTTATCG GAGTTGCAGT TGCGCCCGCG AACGACATTT ATAATGAACG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TGAATTGCTC AACAGTATGG GCATTTCGCA GCCTACCGTG GTGTTCGTTT CCAAAAAGGG GTTGCAAAAA ATTTTGAACG TGCAAAAAAA GCTCCCAATC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATCCAAAAAA TTATTATCAT GGATTCTAAA ACGGATTACC AGGGATTTCA GTCGATGTAC ACGTTCGTCA CATCTCATCT ACCTCCCGGT TTTAATGAAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACGATTTTGT GCCAGAGTCC TTCGATAGGG ACAAGACAAT TGCACTGATC ATGAACTCCT CTGGATCTAC TGGTCTGCCT AAAGGTGTCG CTCTGCCTCA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TAGAACTGCC TGCGTGAGAT TCTCGCATGC CAGAGATCCT ATTTTTGGCA ATCAAATCAT TCCGGATACT GCGATTTTAA GTGTTGTTCC ATTCCATCAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GGTTTTGGAA TGTTTACTAC ACTCGGATAT TTGATATGTG GATTTCGAGT CGTCTTAATG TATAGATTTG AAGAAGAGCT GTTTCTGAGG AGCCTTCAGG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATTACAAGAT TCAAAGTGCG CTGCTGGTGC CAACCCTATT CTCCTTCTTC GCCAAAAGCA CTCTGATTGA CAAATACGAT TTATCTAATT TACACGAAAT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TGCTTCTGGT GGCGCTCCCC TCTCTAAGGA AGTCGGGGAA GCGGTTGCCA AGAGGTTCCA TCTGCCAGGT ATCAGGCAAG GATATGGGCT CACTGAGACT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ACATCAGCTA TTCTGATTAC ACCCGAGGGG GATGATAAAC CGGGCGCGGT CGGTAAAGTT GTTCCATTTT TTGAAGCGAA GGTTGTGGAT CTGGATACCG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GGAAAACGCT GGGCGTTAAT CAAAGAGGCG AACTGTGTGT GAGAGGTCCT ATGATTATGT CCGGTTATGT AAACAATCCG GAAGCGACCA ACGCCTTGAT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TGACAAGGAT GGATGGCTAC ATTCTGGAGA CATAGCTTAC TGGGACGAAG ACGAACACTT CTTCATCGTT GACCGCCTGA AGTCTCTGAT TAAGTACAAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGCTATCAGG TGGCTCCCGC TGAATTGGAA TCCATCTTGC TCCAACACCC CAACATCTTC GACGCAGGTG TCGCAGGTCT TCCCGACGAT GACGCCGGTG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AACTTCCCGC CGCCGTTGTT GTTTTGGAGC ACGGAAAGAC GATGACGGAA AAAGAGATCG TGGATTACGT CGCCAGTCAA GTAACAACCG CGAAAAAGTT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GCGCGGAGGA GTTGTGTTTG TGGACGAAGT ACCGAAAGGT CTTACCGGAA AACTCGACGC AAGAAAAATC AGAGAGATCC TCATAAAGGC CAAGAAGGGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GGAAAGATCG CCGTGTAATT CTAGAGTCGG GGCGGCCGGC CGCTTCGAGC AGACATGATA AGATACATTG ATGAGTTTGG ACAAACCACA ACTAGAATGC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGTGAAAAAA ATGCTTTATT TGTGAAATTT GTGATGCTAT TGCTTTATTT GTAACCATTA TAAGCTGCAA TAAACAAGTT AACAACAACA ATTGCATTCA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TTTTATGTTT CAGGTTCAGG GGGAGGTGTG GGAGGTTTTT TAAAGCAAGT AAAACCTCTA CAAATGTGGT A
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671

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:

reverse_engineered_sequence_and_should_match_experiment_maybe_except_3UTR

The name of the plasmid:
pRHRVF The name of the promoter used to express this mRNA:
SV40

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:
HRV2

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Human rhinovirus 2

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

GGTACCGAGC TCTTACGCGT GCTAGCCCGG GCTCGAGATC TGCGATCTGC ATCTCAATTA GTCAGCAACC ATAGTCCCGC CCCTAACTCC GCCCATCCCG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCCCTAACTC CGCCCAGTTC CGCCCATTCT CCGCCCCATC GCTGACTAAT TTTTTTTATT TATGCAGAGG CCGAGGCCGC CTCGGCCTCT GAGCTATTCC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AGAAGTAGTG AGGAGGCTTT TTTGGAGGCC TAGGCTTTTG CAAAAAGCTG AAGTTGGTCG TGAGGCACTG GGCAGGTAAG TATCAAGGTT ACAAGACAGG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TTTAAGGAGA CCAATAGAAA CTGGGCTTGT CGAGACAGAG AAGACTCTTG CGTTTCTGAT AGGCACCTAT TGGTCTTACT GACATCCACT TTGCCTTTCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CTCCACAGGT GTCCACTCCC AGTTCAATTA CAGCTCTTAA GGCTAGAGTA CTTAATACGA CTCACTATAG GCTAGGCTTG GCATTCCGGT ACTGAATTGA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TATCAAGCTC TAGCCACCAT GACTTCGAAA GTTTATGATC CAGAACAAAG GAAACGGATG ATAACTGGTC CGCAGTGGTG GGCCAGATGT AAACAAATGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ATGTTCTTGA TTCATTTATT AATTATTATG ATTCAGAAAA ACATGCAGAA AATGCTGTTA TTTTTTTACA TGGTAACGCG GCCTCTTCTT ATTTATGGCG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACATGTTGTG CCACATATTG AGCCAGTAGC GCGGTGTATT ATACCAGACC TTATTGGTAT GGGCAAATCA GGCAAATCTG GTAATGGTTC TTATAGGTTA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CTTGATCATT ACAAATATCT TACTGCATGG TTTGAACTTC TTAATTTACC AAAGAAGATC ATTTTTGTCG GCCATGATTG GGGTGCTTGT TTGGCATTTC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATTATAGCTA TGAGCATCAA GATAAGATCA AAGCAATAGT TCACGCTGAA AGTGTAGTAG ATGTGATTGA ATCATGGGAT GAATGGCCTG ATATTGAAGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

AGATATTGCG TTGATCAAAT CTGAAGAAGG AGAAAAAATG GTTTTGGAGA ATAACTTCTT CGTGGAAACC ATGTTGCCAT CAAAAATCAT GAGAAAGTTA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GAACCAGAAG AATTTGCAGC ATATCTTGAA CCATTCAAAG AGAAAGGTGA AGTTCGTCGT CCAACATTAT CATGGCCTCG TGAAATCCCG TTAGTAAAAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTGGTAAACC TGACGTTGTA CAAATTGTTA GGAATTATAA TGCTTATCTA CGTGCAAGTG ATGATTTACC AAAAATGTTT ATTGAATCGG ACCCAGGATT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CTTTTCCAAT GCTATTGTTG AAGGTGCCAA GAAGTTTCCT AATACTGAAT TTGTCAAAGT AAAAGGTCTT CATTTTTCGC AAGAAGATGC ACCTGATGAA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ATGGGAAAAT ATATCAAATC GTTCGTTGAG CGAGTTCTCA AAAATGAACA ATAATTCTAG AGCTTATCGA TACCGTCGAC CTCGAATCAC TAGTCAGTCG 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACGAGCTCCC CGATCCAGGT TGTTCCCACC TGGATTTCCC ACAGGGAGTG GTACTCTGTT ATTACGGTAA CTTTGTACGC CAGTTTTATC TCCCTTCCCC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CATGAACTTA GAAGTTTTTC ACAAAAGACC AATAGCCGGT AATCAGCCAG ATTACTGAAG GTCAAGCACT TCTGTTTCCC CGGTCAATGT TGATATGCTC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CAACAGGGCA AAAACAACTG CGATCGTTAA CCGCAAAGCG CCTACGCAAA GCTTAGTAGC ATCTTTGAAA TCGTTTGGCT GGTCGATCCG CCATTTCCCC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGGTAGACCT GGCAGATGAG GCTAGAAATA CCCCACTGGC GACAGTGTTC TAGCCTGCGT GGCTGCCTGC ACACCCTATG GGTGTGAAGC CAAACAATGG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ACAAGGTGTG AAGAGCCCCG TGTGCTCGCT TTGAGTCCTC CGGCCCCTGA ATGTGGCTAA CCTTAACCCT GGCAGCTAGA GCACGTAACC CAATGTGTAT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CTAGTCGTAA TGAGCAATTG CGGGATGGGA CCAACTACTT TGGGTGTCCG TGTTTCACTT TTTCCTTTAT ATTTGCTTAT GGTGACAGTA CCATGGAAGA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGCCAAAAAC ATAAAGAAAG GCCCGGCGCC ATTCTATCCG CTGGAAGATG GAACCGCTGG AGAGCAACTG CATAAGGCTA TGAAGAGATA CGCCCTGGTT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCTGGAACAA TTGCTTTTAC AGATGCACAT ATCGAGGTGG ACATCACTTA CGCTGAGTAC TTCGAAATGT CCGTTCGGTT GGCAGAAGCT ATGAAACGAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATGGGCTGAA TACAAATCAC AGAATCGTCG TATGCAGTGA AAACTCTCTT CAATTCTTTA TGCCGGTGTT GGGCGCGTTA TTTATCGGAG TTGCAGTTGC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GCCCGCGAAC GACATTTATA ATGAACGTGA ATTGCTCAAC AGTATGGGCA TTTCGCAGCC TACCGTGGTG TTCGTTTCCA AAAAGGGGTT GCAAAAAATT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTGAACGTGC AAAAAAAGCT CCCAATCATC CAAAAAATTA TTATCATGGA TTCTAAAACG GATTACCAGG GATTTCAGTC GATGTACACG TTCGTCACAT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CTCATCTACC TCCCGGTTTT AATGAATACG ATTTTGTGCC AGAGTCCTTC GATAGGGACA AGACAATTGC ACTGATCATG AACTCCTCTG GATCTACTGG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TCTGCCTAAA GGTGTCGCTC TGCCTCATAG AACTGCCTGC GTGAGATTCT CGCATGCCAG AGATCCTATT TTTGGCAATC AAATCATTCC GGATACTGCG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ATTTTAAGTG TTGTTCCATT CCATCACGGT TTTGGAATGT TTACTACACT CGGATATTTG ATATGTGGAT TTCGAGTCGT CTTAATGTAT AGATTTGAAG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AAGAGCTGTT TCTGAGGAGC CTTCAGGATT ACAAGATTCA AAGTGCGCTG CTGGTGCCAA CCCTATTCTC CTTCTTCGCC AAAAGCACTC TGATTGACAA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

ATACGATTTA TCTAATTTAC ACGAAATTGC TTCTGGTGGC GCTCCCCTCT CTAAGGAAGT CGGGGAAGCG GTTGCCAAGA GGTTCCATCT GCCAGGTATC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AGGCAAGGAT ATGGGCTCAC TGAGACTACA TCAGCTATTC TGATTACACC CGAGGGGGAT GATAAACCGG GCGCGGTCGG TAAAGTTGTT CCATTTTTTG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AAGCGAAGGT TGTGGATCTG GATACCGGGA AAACGCTGGG CGTTAATCAA AGAGGCGAAC TGTGTGTGAG AGGTCCTATG ATTATGTCCG GTTATGTAAA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CAATCCGGAA GCGACCAACG CCTTGATTGA CAAGGATGGA TGGCTACATT CTGGAGACAT AGCTTACTGG GACGAAGACG AACACTTCTT CATCGTTGAC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CGCCTGAAGT CTCTGATTAA GTACAAAGGC TATCAGGTGG CTCCCGCTGA ATTGGAATCC ATCTTGCTCC AACACCCCAA CATCTTCGAC GCAGGTGTCG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CAGGTCTTCC CGACGATGAC GCCGGTGAAC TTCCCGCCGC CGTTGTTGTT TTGGAGCACG GAAAGACGAT GACGGAAAAA GAGATCGTGG ATTACGTCGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CAGTCAAGTA ACAACCGCGA AAAAGTTGCG CGGAGGAGTT GTGTTTGTGG ACGAAGTACC GAAAGGTCTT ACCGGAAAAC TCGACGCAAG AAAAATCAGA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

GAGATCCTCA TAAAGGCCAA GAAGGGCGGA AAGATCGCCG TGTAATTCTA GAGTCGGGGC GGCCGGCCGC TTCGAGCAGA CATGATAAGA TACATTGATG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AGTTTGGACA AACCACAACT AGAATGCAGT GAAAAAAATG CTTTATTTGT GAAATTTGTG ATGCTATTGC TTTATTTGTA ACCATTATAA GCTGCAATAA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ACAAGTTAAC AACAACAATT GCATTCATTT TATGTTTCAG GTTCAGGGGG AGGTGTGGGA GGTTTTTTAA AGCAAGTAAA ACCTCTACAA ATGTGGTAAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ATCGATAAGG ATCTGAACGA TGGAGCGGAG AATGGGCGGA ACTGGGCGGA GTTAGGGGCG GGATGGGCGG AGTTAGGGGC GGGACTATGG TTGCTGACTA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ATTGAGATGC ATGCTTTGCA TACTTCTGCC TGCTGGGGAG CCTGGGGACT TTCCACACCT GGTTGCTGAC TAATTGAGAT GCATGCTTTG CATACTTCTG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CCTGCTGGGG AGCCTGGGGA CTTTCCACAC CCTAACTGAC ACACATTCCA CAGCGGATCC GTCGACCGAT GCCCTTGAGA GCCTTCAACC CAGTCAGCTC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CTTCCGGTGG GCGCGGGGCA TGACTATCGT CGCCGCACTT ATGACTGTCT TCTTTATCAT GCAACTCGTA GGACAGGTGC CGGCAGCGCT CTTCCGCTTC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CTCGCTCACT GACTCGCTGC GCTCGGTCGT TCGGCTGCGG CGAGCGGTAT CAGCTCACTC AAAGGCGGTA ATACGGTTAT CCACAGAATC AGGGGATAAC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GCAGGAAAGA ACATGTGAGC AAAAGGCCAG CAAAAGGCCA GGAACCGTAA AAAGGCCGCG TTGCTGGCGT TTTTCCATAG GCTCCGCCCC CCTGACGAGC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATCACAAAAA TCGACGCTCA AGTCAGAGGT GGCGAAACCC GACAGGACTA TAAAGATACC AGGCGTTTCC CCCTGGAAGC TCCCTCGTGC GCTCTCCTGT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TCCGACCCTG CCGCTTACCG GATACCTGTC CGCCTTTCTC CCTTCGGGAA GCGTGGCGCT TTCTCAATGC TCACGCTGTA GGTATCTCAG TTCGGTGTAG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GTCGTTCGCT CCAAGCTGGG CTGTGTGCAC GAACCCCCCG TTCAGCCCGA CCGCTGCGCC TTATCCGGTA ACTATCGTCT TGAGTCCAAC CCGGTAAGAC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

ACGACTTATC GCCACTGGCA GCAGCCACTG GTAACAGGAT TAGCAGAGCG AGGTATGTAG GCGGTGCTAC AGAGTTCTTG AAGTGGTGGC CTAACTACGG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CTACACTAGA AGGACAGTAT TTGGTATCTG CGCTCTGCTG AAGCCAGTTA CCTTCGGAAA AAGAGTTGGT AGCTCTTGAT CCGGCAAACA AACCACCGCT 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GGTAGCGGTG GTTTTTTTGT TTGCAAGCAG CAGATTACGC GCAGAAAAAA AGGATCTCAA GAAGATCCTT TGATCTTTTC TACGGGGTCT GACGCTCAGT 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GGAACGAAAA CTCACGTTAA GGGATTTTGG TCATGAGATT ATCAAAAAGG ATCTTCACCT AGATCCTTTT AAATTAAAAA TGAAGTTTTA AATCAATCTA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

AAGTATATAT GAGTAAACTT GGTCTGACAG TTACCAATGC TTAATCAGTG AGGCACCTAT CTCAGCGATC TGTCTATTTC GTTCATCCAT AGTTGCCTGA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CTCCCCGTCG TGTAGATAAC TACGATACGG GAGGGCTTAC CATCTGGCCC CAGTGCTGCA ATGATACCGC GAGACCCACG CTCACCGGCT CCAGATTTAT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

CAGCAATAAA CCAGCCAGCC GGAAGGGCCG AGCGCAGAAG TGGTCCTGCA ACTTTATCCG CCTCCATCCA GTCTATTAAT TGTTGCCGGG AAGCTAGAGT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

AAGTAGTTCG CCAGTTAATA GTTTGCGCAA CGTTGTTGCC ATTGCTACAG GCATCGTGGT GTCACGCTCG TCGTTTGGTA TGGCTTCATT CAGCTCCGGT 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

TCCCAACGAT CAAGGCGAGT TACATGATCC CCCATGTTGT GCAAAAAAGC GGTTAGCTCC TTCGGTCCTC CGATCGTTGT CAGAAGTAAG TTGGCCGCAG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TGTTATCACT CATGGTTATG GCAGCACTGC ATAATTCTCT TACTGTCATG CCATCCGTAA GATGCTTTTC TGTGACTGGT GAGTACTCAA CCAAGTCATT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CTGAGAATAG TGTATGCGGC GACCGAGTTG CTCTTGCCCG GCGTCAATAC GGGATAATAC CGCGCCACAT AGCAGAACTT TAAAAGTGCT CATCATTGGA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

AAACGTTCTT CGGGGCGAAA ACTCTCAAGG ATCTTACCGC TGTTGAGATC CAGTTCGATG TAACCCACTC GTGCACCCAA CTGATCTTCA GCATCTTTTA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CTTTCACCAG CGTTTCTGGG TGAGCAAAAA CAGGAAGGCA AAATGCCGCA AAAAAGGGAA TAAGGGCGAC ACGGAAATGT TGAATACTCA TACTCTTCCT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TTTTCAATAT TATTGAAGCA TTTATCAGGG TTATTGTCTC ATGAGCGGAT ACATATTTGA ATGTATTTAG AAAAATAAAC AAATAGGGGT TCCGCGCACA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TTTCCCCGAA AAGTGCCACC TGACGCGCCC TGTAGCGGCG CATTAAGCGC GGCGGGTGTG GTGGTTACGC GCAGCGTGAC CGCTACACTT GCCAGCGCCC 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

TAGCGCCCGC TCCTTTCGCT TTCTTCCCTT CCTTTCTCGC CACGTTCGCC GGCTTTCCCC GTCAAGCTCT AAATCGGGGG CTCCCTTTAG GGTTCCGATT 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

TAGTGCTTTA CGGCACCTCG ACCCCAAAAA ACTTGATTAG GGTGATGGTT CACGTAGTGG GCCATCGCCC TGATAGACGG TTTTTCGCCC TTTGACGTTG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GAGTCCACGT TCTTTAATAG TGGACTCTTG TTCCAAACTG GAACAACACT CAACCCTATC TCGGTCTATT CTTTTGATTT ATAAGGGATT TTGCCGATTT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CGGCCTATTG GTTAAAAAAT GAGCTGATTT AACAAAAATT TAACGCGAAT TTTAACAAAA TATTAACGTT TACAATTTCC CATTCGCCAT TCAGGCTGCG 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

CAACTGTTGG GAAGGGCGAT CGGTGCGGGC CTCTTCGCTA TTACGCCAGC CCAAGCTACC ATGATAAGTA AGTAATATTA AGGTACGGGA GGTACTTGGA 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

GCGGCCGCAA TAAAATATCT TTATTTTCAT TACATCTGTG TGTTGGTTTT TTGTGTGAAT CGATAGTACT AACATACGCT CTCCATCAAA ACAAAACGAA 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

ACAAAACAAA CTAGCAAAAT AGGCTGTCCC CAGTGCAAGT GCAGGTGCCA GAACATTTCT CTATCGATA
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061

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: `1`	Last change: `2008-07-12 17:27:16`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
RLuc

The description of the protein encoded in this ORF:
Renilla luciferase

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):

192-1127

ORF

ORF position:

2

Version: `1`	Last change: `2008-07-12 17:27:16`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
FLuc

The description of the protein encoded in this ORF:
Firefly luciferase

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):

1766-3418

Remarks:

The sequence of this plasmid was provided by K. Spriggs. Following is the alignment to the complete genome
sequence as determined originally by Skern et al. (1985). It is unclear when the mutations were acquired
and whether they are authentic at all. Definitely, the sequence of this plasmid differs from the similarly
named plasmid pR-HRV-F (IRESite_Id:228 and IRESite_Id:232 -- both records are based on the same plasmid
sequence, just SV40 and T7-based transcripts). This plasmid sequence from K. Spriggs lacks some regions
present in pR-HRV-F.

The pR-HRV-F plasmid contains the in-frame AUG codon which is found in HRV genome in position 449 whereas
the polyprotein AUG is located at position 611 so in theory the polyprotein produced could be much larger.
In contrast, this pRHRVF construct has some single nucleotide insertion since the AUG449 so there appears
UAG STOP codon (if this is not a mistake in the sequence we have received) which interrupts that reading
frame (uORF size 54bp in total) overlapping the IRES. BTW, there are several uORFs in HRV 5'-UTR anyway.
It is not clear whether this could make any difference in experiments (probably not).


>X02316.1 Human rhinovirus 2, complete sequence
Length=7102

 Score = 1046 bits (566),  Expect = 0.0
 Identities = 574/577 (99%), Gaps = 3/577 (0%)
 Strand=Plus/Plus

pRHRVF 1    GATCCAGGTTGTTCCCACCTGGATTTCCCACAGGGAGTGGTACTCTGTTATTACGGTAAC  60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
X02316 10   GATCCAGGTTGTTCCCACCTGGATTTCCCACAGGGAGTGGTACTCTGTTATTACGGTAAC  69

pRHRVF 61   TTTGTACGCCAGTTTTATCTCCCTTCCCCCATG-AACTTAGAAGTTTTTCACAAAAGACC  119
            ||||||||||||||||||||||||||||||||| |||||||||||||||||| |||||||
X02316 70   TTTGTACGCCAGTTTTATCTCCCTTCCCCCATGTAACTTAGAAGTTTTTCAC-AAAGACC  128

pRHRVF 120  AATAGCCGGTAATCAGCCAGATTACTGAAGGTCAAGCACTTCTGTTTCCCCGGTCAATGT  179
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
X02316 129  AATAGCCGGTAATCAGCCAGATTACTGAAGGTCAAGCACTTCTGTTTCCCCGGTCAATGT  188

pRHRVF 180  TGATATGCTCCAACAGGGCAAAAACAACTGCGATCGTTAACCGCAAAGCGCCTACGCAAA  239
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
X02316 189  TGATATGCTCCAACAGGGCAAAAACAACTGCGATCGTTAACCGCAAAGCGCCTACGCAAA  248

pRHRVF 240  GCTTAGTAGCATCTTTGAAATCGTTTGGCTGGTCGATCCGCCATTTCCCCTGGTAGACCT  299
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
X02316 249  GCTTAGTAGCATCTTTGAAATCGTTTGGCTGGTCGATCCGCCATTTCCCCTGGTAGACCT  308

pRHRVF 300  GGCAGATGAGGCTAGAAATACCCCACTGGCGACAGTGTTCTAGCCTGCGTGGCTGCCTGC  359
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
X02316 309  GGCAGATGAGGCTAGAAATACCCCACTGGCGACAGTGTTCTAGCCTGCGTGGCTGCCTGC  368

pRHRVF 360  ACACCCTATGGGTGTGAAGCCAAACAATGGACAAGGTGTGAAGAGCCCCGTGTGCTCGCT  419
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
X02316 369  ACACCCTATGGGTGTGAAGCCAAACAATGGACAAGGTGTGAAGAGCCCCGTGTGCTCGCT  428

pRHRVF 420  TTGAGTCCTCCGGCCCCTGAATGTGGCTAACCTTAACCCTGGCAGCTAGAGCACGTAACC  479
            ||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
X02316 429  TTGAGTCCTCCGGCCCCTGAATGTGGCTAACCTTAACCCTG-CAGCTAGAGCACGTAACC  487

pRHRVF 480  CAATGTGTATCTAGTCGTAATGAGCAATTGCGGGATGGGACCAACTACTTTGGGTGTCCG  539
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
X02316 488  CAATGTGTATCTAGTCGTAATGAGCAATTGCGGGATGGGACCAACTACTTTGGGTGTCCG  547

pRHRVF 540  TGTTTCACTTTTTCCTTTATATTTGCTTATGGTGACAGTACC---------------------ATG
            |||||||||||||||||||||||||||||||||||||
X02316 548  TGTTTCACTTTTTCCTTTATATTTGCTTATGGTGACAATATATACAATATATATATTGGCACCATG


Probably more important is the difference between both plasmids just in front of the initiator AUG (so at
the IRES 3'-end boundary):

pRHRVF        TTTCACTTTTTCCTTTATATTTGCTTATGGTGACAGTACC---------------------ATG
pR-HRV-F      TTTCACTTTCTCCTTTATATTTGCTTATGGTGACAATATATACAATATATATATTGGCACCATG

Citations:

Stoneley M., Subkhankulova T., Le Quesne J. P., Coldwell M. J., Jopling C. L., Belsham G. J., Willis A. E. (2000) Analysis of the c-myc IRES; a potential role for cell-type specific trans-acting factors and the nuclear compartment. Nucleic Acids Res. 28(3):687-694

IRESs:

IRES:

Version: `2`	Last change: `2008-07-12 17:27:16`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `HRV-2`	The functional status of IRES: `functional`

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

1185-1760

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `58`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `633`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-581`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-6`

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

GATCCAGGTT GTTCCCACCT GGATTTCCCA CAGGGAGTGG TACTCTGTTA TTACGGTAAC TTTGTACGCC AGTTTTATCT CCCTTCCCCC ATGAACTTAG 
^1185      ^1195      ^1205      ^1215      ^1225      ^1235      ^1245      ^1255      ^1265      ^1275      

AAGTTTTTCA CAAAAGACCA ATAGCCGGTA ATCAGCCAGA TTACTGAAGG TCAAGCACTT CTGTTTCCCC GGTCAATGTT GATATGCTCC AACAGGGCAA 
^1285      ^1295      ^1305      ^1315      ^1325      ^1335      ^1345      ^1355      ^1365      ^1375      

AAACAACTGC GATCGTTAAC CGCAAAGCGC CTACGCAAAG CTTAGTAGCA TCTTTGAAAT CGTTTGGCTG GTCGATCCGC CATTTCCCCT GGTAGACCTG 
^1385      ^1395      ^1405      ^1415      ^1425      ^1435      ^1445      ^1455      ^1465      ^1475      

GCAGATGAGG CTAGAAATAC CCCACTGGCG ACAGTGTTCT AGCCTGCGTG GCTGCCTGCA CACCCTATGG GTGTGAAGCC AAACAATGGA CAAGGTGTGA 
^1485      ^1495      ^1505      ^1515      ^1525      ^1535      ^1545      ^1555      ^1565      ^1575      

AGAGCCCCGT GTGCTCGCTT TGAGTCCTCC GGCCCCTGAA TGTGGCTAAC CTTAACCCTG GCAGCTAGAG CACGTAACCC AATGTGTATC TAGTCGTAAT 
^1585      ^1595      ^1605      ^1615      ^1625      ^1635      ^1645      ^1655      ^1665      ^1675      

GAGCAATTGC GGGATGGGAC CAACTACTTT GGGTGTCCGT GTTTCACTTT TTCCTTTATA TTTGCTTATG GTGACA
^1685      ^1695      ^1705      ^1715      ^1725      ^1735      ^1745      ^1755

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 511

Version: `0`
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:

51.000

Name of IRES used as the positive control:

EMCV-R

Name of the plasmid used as the positive control. `pREMCVF`	Name of the plasmid used as the negative control. `pRF`
`IRESite Id` of the plasmid used as positive control. `349`	`IRESite Id` of the plasmid used as negative control. `184`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `2.500`
The size (length) of intercistronic region in the positive control: `619`	The size (length) of intercistronic region in the negative control: `67`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

Data from Figure 2B.

Citations:

Coldwell M. J., deSchoolmeester M. L., Fraser G. A., Pickering B. M., Packham G., Willis A. E. (2001) The p36 isoform of BAG-1 is translated by internal ribosome entry following heat shock. Oncogene. 20(30):4095-4100

Translation results:

IRESite Translation Id: 517

Version: `1`	Last change: `2008-07-08 19:30:06`
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:

67.000

Name of IRES used as the positive control:

EMCV-R

Name of the plasmid used as the positive control. `pREMCVF`	Name of the plasmid used as the negative control. `pRF`
`IRESite Id` of the plasmid used as positive control. `349`	`IRESite Id` of the plasmid used as negative control. `184`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `11.000`
The size (length) of intercistronic region in the positive control: `619`	The size (length) of intercistronic region in the negative control: `67`

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

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

Data from Figure 5.

Citations:

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