IRESite_Id:24 characteristics of BVDV1_in375-378 IRES studied in AUG(In375-378) plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `24`	Version: `9`
Originaly submitted by: Václav Vopálenský	Submission date: `2005-08-02 00:00:00`
Reviewed by: Martin Pospíšek	Last change: `2006-07-25 00:00:00`

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:
3UTR_incomplete

The mRNA/+RNA description:

5' region of genomic RNA (nt 1 to nt 900) with insertion of nt 375-378 cloned between chloramphenicol
acetyltransferase and firefly luciferase. The 4-nt insertion at position 375-378 caused the authentic AUG
initiation codon to be relocated to position 390 in this mutant AUG(In375-378). This insertion increased in 4
nt the distance between the pseudoknot structure and the initiator AUGorf, defined as the first methionine
codon in frame with the polyprotein ORF.

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

AGAATACTCA AGCTTATGCA TGCGGCCGCT CAGGAGCTAA GGAAGCTAAA ATGGAGAAAA AAATCACTGG ATATACCACC GTTGATATAT CCCAATGGCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TCGTAAAGAA CATTTTGAGG CATTTCAGTC AGTTGCTCAA TGTACCTATA ACCAGACCGT TCAGCTGGAT ATTACGGCCT TTTTAAAGAC CGTAAAGAAA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

AATAAGCACA AGTTTTATCC GGCCTTTATT CACATTCTTG CCCGCCTGAT GAATGCTCAT CCGGAATTCC GTATGGCAAT GAAAGACGGT GAGCTGGTGA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TATGGGATAG TGTTCACCCT TGTTACACCG TTTTCCATGA GCAAACTGAA ACGTTTTCAT CGCTCTGGAG TGAATACCAC GACGATTTCC GGCAGTTTCT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACACATATAT TCGCAAGATG TGGCGTGTTA CGGTGAAAAC CTGGCCTATT TCCCTAAAGG GTTTATTGAG AATATGTTTT TCGTCTCAGC CAATCCCTGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GTGAGTTTCA CCAGTTTTGA TTTAAACGTG GCCAATATGG ACAACTTCTT CGCCCCCGTT TTCACCATGG GCAAATATTA TACGCAAGGC GACAAGGTGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TGATGCCGCT GGCGATTCAG GTTCATCATG CCGTCTGTGA TGGCTTCCAT GTCGGCAGAA TGCTTAATGA ATTACAACAG TACTGCGATG AGTGGCAGGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CGGGGCGTAA TTTTTTTAAG GCAGTTATTG GTGCCCTTAA ACGCCTGGTT CGTACGCCTG AATAAGTGAT AATAAGCGGA TGAATGGCAG AAATTCGAGC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GGCCGCATCT AGAGGGCCCG GATCGTATAC GAGAATTAGA AAAGGCACTC GTATACGTAT TGGGCAATTA AAAATAATAA TTAGGCCTAG GGAACAAATC 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CCTCTCAGCG AAGGCCGAAA AGAGGCTAGC CATGCCCTTA GTAGGACTAG CATAATGAGG GGGGTAGCAA CAGTGGTGAG TTCGTTGGAT GGCTTAAGCC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CTGAGTACAG GGTAGTCGTC AGTGGTTCGA CGCCTTGGAA TAAAGGTCTC GAGATGCCAC GTGGACGAGG GCATGCCCAA AGCACATCTT AACCTGAGCG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GGGGTCGCCC AGGTAAAAGC AGTTTTAACC GACTGTTACG AATACAGCCT GATAGGGTGC TGCAGAGGCC CACTGTATTG CTACTAAAAA TCTCTGCTGT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ACGTACATGG CACATGGAGT TGATCACAAA TGAACTTTTA TACAAAACAT ACAAACAAAA ACCCGTCGGG GTGGAGGAAC CTGTTTATGA TCAGGCAGGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GATCCCTTAT TTGGTGAAAG GGGAGCAGTC CACCCTCAAT CGACGCTAAA GCTCCCACAC AAGAGAGGGG AACGCGATGT TCCAACCAAC TTGGCATCCT 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TACCAAAAAG AGGTGACTGC AGGTCGGGTA ATAGCAGAGG ACCTGTGAGC GGGATCTACC TGAAGCCAGG GCCACTATTT TACCAGGACT ATAAAGGTCC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CGTCTATCAC AGGGCCCCGC TGGAGCTCTT TGAGGAGGGA TCCATGTGTG AAACGACTAA ACGGATAGGG AGAGTAACTG GAAGTGACGG AAAGCTGTAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CACATTTATG TGTGTATAGA TGGATGTATA ATAATAAAAA GTGCCACGAG AAGTTACCAA AGGGTGTTCA GGTGGGTCCA TAATAGGCTT GACTGCCCTC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TATGGGTCAC AACTTGCTCA GACACGAAGA TCCAAATGGA AGACGCCAAA AACATAAAGA AAGGCCCGGC GCCATTCTAT CCTCTAGAGG ATGGAACCGC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGGAGAGCAA CTGCATAAGG CTATGAAGAG ATACGCCCTG GTTCCTGGAA CAATTGCTTT TACAGATGCA CATATCGAGG TGAACATCAC GTACGCGGAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TACTTCGAAA TGTCCGTTCG GTTGGCAGAA GCTATGAAAC GATATGGGCT GAATACAAAT CACAGAATCG TCGTATGCAG TGAAAACTCT CTTCAATTCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TTATGCCGGT GTTGGGCGCG TTATTTATCG GAGTTGCAGT TGCGCCCGCG AACGACATTT ATAATGAACG TGAATTGCTC AACAGTATGA ACATTTCGCA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GCCTACCGTA GTGTTTGTTT CCAAAAAGGG GTTGCAAAAA ATTTTGAACG TGCAAAAAAA ATTACCAATA ATCCAGAAAA TTATTATCAT GGATTCTAAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ACGGATTACC AGGGATTTCA GTCGATGTAC ACGTTCGTCA CATCTCATCT ACCTCCCGGT TTTAATGAAT ACGATTTTGT ACCAGAGTCC TTTGATCGTG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACAAAACAAT TGCACTGATA ATGAATTCCT CTGGATCTAC TGGGTTACCT AAGGGTGTGG CCCTTCCGCA TAGAACTGCC TGCGTCAGAT TCTCGCATGC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CAGAGATCCT ATTTTTGGCA ATCAAATCAT TCCGGATACT GCGATTTTAA GTGTTGTTCC ATTCCATCAC GGTTTTGGAA TGTTTACTAC ACTCGGATAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TTGATATGTG GATTTCGAGT CGTCTTAATG TATAGATTTG AAGAAGAGCT GTTTTTACGA TCCCTTCAGG ATTACAAAAT TCAAAGTGCG TTGCTAGTAC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CAACCCTATT TTCATTCTTC GCCAAAAGCA CTCTGATTGA CAAATACGAT TTATCTAATT TACACGAAAT TGCTTCTGGG GGCGCACCTC TTTCGAAAGA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AGTCGGGGAA GCGGTTGCAA AACGCTTCCA TCTTCCAGGG ATACGACAAG GATATGGGCT CACTGAGACT ACATCAGCTA TTCTGATTAC ACCCGAGGGG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GATGATAAAC CGGGCGCGGT CGGTAAAGTT GTTCCATTTT TTGAAGCGAA GGTTGTGGAT CTGGATACCG GGAAAACGCT GGGCGTTAAT CAGAGAGGCG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

AATTATGTGT CAGAGGACCT ATGATTATGT CCGGTTATGT AAACAATCCG GAAGCGACCA ACGCCTTGAT TGACAAGGAT GGATGGCTAC ATTCTGGAGA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CATAGCTTAC TGGGACGAAG ACGAACACTT CTTCATAGTT GACCGCTTGA AGTCTTTAAT TAAATACAAA GGATATCAGG TGGCCCCCGC TGAATTGGAA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TCGATATTGT TACAACACCC CAACATCTTC GACGCGGGCG TGGCAGGTCT TCCCGACGAT GACGCCGGTG AACTTCCCGC CGCCGTTGTT GTTTTGGAGC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ACGGAAAGAC GATGACGGAA AAAGAGATCG TGGATTACGT CGCCAGTCAA GTAACAACCG CGAAAAAGTT GCGCGGAGGA GTTGTGTTTG TGGACGAAGT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ACCGAAAGGT CTTACCGGAA AACTCGACGC AAGAAAAATC AGAGAGATCC TCATAAAGGC CAAGAAGGGC GGAAAGTCCA AATTGTAA
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

The name of the plasmid:
AUG(In375-378) The name of the promoter used to express this mRNA:
SP6

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:
BVDV_1

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Bovine viral diarrhea virus 1 NADL

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

TATAGTGAGT CGTATTACAA TTCACTGGCC GTCGTTTTAC AACGTCGTGA CTGGGAAAAC CCTGGCGTTA CCCAACTTAA TCGCCTTGCA GCACATCCCC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CTTTCGCCAG CTGGCGTAAT AGCGAAGAGG CCCGCACCGA TCGCCCTTCC CAACAGTTGC GCAGCCTGAA TGGCGAATGG AAATTGTAAG CGTTAATATT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TTGTTAAAAT TCGCGTTAAA TTTTTGTTAA ATCAGCTCAT TTTTTAACCA ATAGGCCGAA ATCGGCAAAA TCCCTTATAA ATCAAAAGAA TAGACCGAGA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TAGGGTTGAG TGTTGTTCCA GTTTGGAACA AGAGTCCACT ATTAAAGAAC GTGGACTCCA ACGTCAAAGG GCGAAAAACC GTCTATCAGG GCGATGGCCC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACTACGTGAA CCATCACCCT AATCAAGTTT TTTGCGGTCG AGGTGCCGTA AAGCACTAAA TCGGAACCCT AAAGGGAGCC CCCGATTTAG AGCTTGACGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GGAAAGCCGG CGAACGTGGC GAGAAAGGAA GGGAAGAAAG CGAAAGGAGC GGGCGCTAGG GCGCTGGCAA GTGTAGCGGT CACGCTGCGC GTAACCACCA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CACCCGCCGC GCTTAATGCG CCGCTACAGG GCGCGTCCTG ATGCGGTATT TTCTCCTTAC GCATCTGTGC GGTATTTCAC ACCGCATATG GTGCACTCTC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGTACAATCT GCTCTGATGC CGCATAGTTA AGCCAGCCCC GACACCCGCC AACACCCGCT GACGCGCCCT GACGGGCTTG TCTGCTCCCG GCATCCGCTT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ACAGACAAGC TGTGACCGTC TCCGGGAGCT GCATGTGTCA GAGGTTTTCA CCGTCATCAC CGAAACGCGC GAGACGAAAG GGCCTCGTGA TACGCCTATT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TTTATAGGTT AATGTCATGA TAATAATGGT TTCTTAGACG TCAGGTGGCA CTTTTCGGGG AAATGTGCGC GGAACCCCTA TTTGTTTATT TTTCTAAATA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CATTCAAATA TGTATCCGCT CATGAGACAA TAACCCTGAT AAATGCTTCA ATAATATTGA AAAAGGAAGA GTATGAGTAT TCAACATTTC CGTGTCGCCC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TTATTCCCTT TTTTGCGGCA TTTTGCCTTC CTGTTTTTGC TCACCCAGAA ACGCTGGTGA AAGTAAAAGA TGCTGAAGAT CAGTTGGGTG CACGAGTGGG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTACATCGAA CTGGATCTCA ACAGCGGTAA GATCCTTGAG AGTTTTCGCC CCGAAGAACG TTTTCCAATG ATGAGCACTT TTAAAGTTCT GCTATGTGGC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GCGGTATTAT CCCGTATTGA CGCCGGGCAA GAGCAACTCG GTCGCCGCAT ACACTATTCT CAGAATGACT TGGTTGAGTA CTCACCAGTC ACAGAAAAGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ATCTTACGGA TGGCATGACA GTAAGAGAAT TATGCAGTGC TGCCATAACC ATGAGTGATA ACACTGCGGC CAACTTACTT CTGACAACGA TCGGAGGACC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GAAGGAGCTA ACCGCTTTTT TGCACAACAT GGGGGATCAT GTAACTCGCC TTGATCGTTG GGAACCGGAG CTGAATGAAG CCATACCAAA CGACGAGCGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GACACCACGA TGCCTGTAGC AATGGCAACA ACGTTGCGCA AACTATTAAC TGGCGAACTA CTTACTCTAG CTTCCCGGCA ACAATTAATA GACTGGATGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGGCGGATAA AGTTGCAGGA CCACTTCTGC GCTCGGCCCT TCCGGCTGGC TGGTTTATTG CTGATAAATC TGGAGCCGGT GAGCGTGGGT CTCGCGGTAT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CATTGCAGCA CTGGGGCCAG ATGGTAAGCC CTCCCGTATC GTAGTTATCT ACACGACGGG GAGTCAGGCA ACTATGGATG AACGAAATAG ACAGATCGCT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GAGATAGGTG CCTCACTGAT TAAGCATTGG TAACTGTCAG ACCAAGTTTA CTCATATATA CTTTAGATTG ATTTAAAACT TCATTTTTAA TTTAAAAGGA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TCTAGGTGAA GATCCTTTTT GATAATCTCA TGACCAAAAT CCCTTAACGT GAGTTTTCGT TCCACTGAGC GTCAGACCCC GTAGAAAAGA TCAAAGGATC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TTCTTGAGAT CCTTTTTTTC TGCGCGTAAT CTGCTGCTTG CAAACAAAAA AACCACCGCT ACCAGCGGTG GTTTGTTTGC CGGATCAAGA GCTACCAACT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTTTTTCCGA AGGTAACTGG CTTCAGCAGA GCGCAGATAC CAAATACTGT TCTTCTAGTG TAGCCGTAGT TAGGCCACCA CTTCAAGAAC TCTGTAGCAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CGCCTACATA CCTCGCTCTG CTAATCCTGT TACCAGTGGC TGCTGCCAGT GGCGATAAGT CGTGTCTTAC CGGGTTGGAC TCAAGACGAT AGTTACCGGA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TAAGGCGCAG CGGTCGGGCT GAACGGGGGG TTCGTGCACA CAGCCCAGCT TGGAGCGAAC GACCTACACC GAACTGAGAT ACCTACAGCG TGAGCTATGA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GAAAGCGCCA CGCTTCCCGA AGGGAGAAAG GCGGACAGGT ATCCGGTAAG CGGCAGGGTC GGAACAGGAG AGCGCACGAG GGAGCTTCCA GGGGGAAACG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CCTGGTATCT TTATAGTCCT GTCGGGTTTC GCCACCTCTG ACTTGAGCGT CGATTTTTGT GATGCTCGTC AGGGGGGCGG AGCCTATGGA AAAACGCCAG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CAACGCGGCC TTTTTACGGT TCCTGGCCTT TTGCTGGCCT TTTGCTCACA TGTTCTTTCC TGCGTTATCC CCTGATTCTG TGGATAACCG TATTACCGCC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TTTGAGTGAG CTGATACCGC TCGCCGCAGC CGAACGACCG AGCGCAGCGA GTCAGTGAGC GAGGAAGCGG AAGAGCGCCC AATACGCAAA CCGCCTCTCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CCGCGCGTTG GCCGATTCAT TAATGCAGCT GGCACGACAG GTTTCCCGAC TGGAAAGCGG GCAGTGAGCG CAACGCAATT AATGTGAGTT AGCTCACTCA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TTAGGCACCC CAGGCTTTAC ACTTTATGCT TCCGGCTCGT ATGTTGTGTG GAATTGTGAG CGGATAACAA TTTCACACAG GAAACAGCTA TGACCATGAT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TACGCCAAGC TATTTAGGTG ACACTATAGA ATACTCAAGC TTATGCATGC GGCCGCTCAG GAGCTAAGGA AGCTAAAATG GAGAAAAAAA TCACTGGATA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TACCACCGTT GATATATCCC AATGGCATCG TAAAGAACAT TTTGAGGCAT TTCAGTCAGT TGCTCAATGT ACCTATAACC AGACCGTTCA GCTGGATATT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ACGGCCTTTT TAAAGACCGT AAAGAAAAAT AAGCACAAGT TTTATCCGGC CTTTATTCAC ATTCTTGCCC GCCTGATGAA TGCTCATCCG GAATTCCGTA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGGCAATGAA AGACGGTGAG CTGGTGATAT GGGATAGTGT TCACCCTTGT TACACCGTTT TCCATGAGCA AACTGAAACG TTTTCATCGC TCTGGAGTGA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATACCACGAC GATTTCCGGC AGTTTCTACA CATATATTCG CAAGATGTGG CGTGTTACGG TGAAAACCTG GCCTATTTCC CTAAAGGGTT TATTGAGAAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ATGTTTTTCG TCTCAGCCAA TCCCTGGGTG AGTTTCACCA GTTTTGATTT AAACGTGGCC AATATGGACA ACTTCTTCGC CCCCGTTTTC ACCATGGGCA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AATATTATAC GCAAGGCGAC AAGGTGCTGA TGCCGCTGGC GATTCAGGTT CATCATGCCG TCTGTGATGG CTTCCATGTC GGCAGAATGC TTAATGAATT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ACAACAGTAC TGCGATGAGT GGCAGGGCGG GGCGTAATTT TTTTAAGGCA GTTATTGGTG CCCTTAAACG CCTGGTTCGT ACGCCTGAAT AAGTGATAAT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AAGCGGATGA ATGGCAGAAA TTCGAGCGGC CGCATCTAGA GGGCCCGGAT CGTATACGAG AATTAGAAAA GGCACTCGTA TACGTATTGG GCAATTAAAA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ATAATAATTA GGCCTAGGGA ACAAATCCCT CTCAGCGAAG GCCGAAAAGA GGCTAGCCAT GCCCTTAGTA GGACTAGCAT AATGAGGGGG GTAGCAACAG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TGGTGAGTTC GTTGGATGGC TTAAGCCCTG AGTACAGGGT AGTCGTCAGT GGTTCGACGC CTTGGAATAA AGGTCTCGAG ATGCCACGTG GACGAGGGCA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TGCCCAAAGC ACATCTTAAC CTGAGCGGGG GTCGCCCAGG TAAAAGCAGT TTTAACCGAC TGTTACGAAT ACAGCCTGAT AGGGTGCTGC AGAGGCCCAC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TGTATTGCTA CTAAAAATCT CTGCTGTACG TACATGGCAC ATGGAGTTGA TCACAAATGA ACTTTTATAC AAAACATACA AACAAAAACC CGTCGGGGTG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GAGGAACCTG TTTATGATCA GGCAGGTGAT CCCTTATTTG GTGAAAGGGG AGCAGTCCAC CCTCAATCGA CGCTAAAGCT CCCACACAAG AGAGGGGAAC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

GCGATGTTCC AACCAACTTG GCATCCTTAC CAAAAAGAGG TGACTGCAGG TCGGGTAATA GCAGAGGACC TGTGAGCGGG ATCTACCTGA AGCCAGGGCC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ACTATTTTAC CAGGACTATA AAGGTCCCGT CTATCACAGG GCCCCGCTGG AGCTCTTTGA GGAGGGATCC ATGTGTGAAA CGACTAAACG GATAGGGAGA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GTAACTGGAA GTGACGGAAA GCTGTACCAC ATTTATGTGT GTATAGATGG ATGTATAATA ATAAAAAGTG CCACGAGAAG TTACCAAAGG GTGTTCAGGT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GGGTCCATAA TAGGCTTGAC TGCCCTCTAT GGGTCACAAC TTGCTCAGAC ACGAAGATCC AAATGGAAGA CGCCAAAAAC ATAAAGAAAG GCCCGGCGCC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

ATTCTATCCT CTAGAGGATG GAACCGCTGG AGAGCAACTG CATAAGGCTA TGAAGAGATA CGCCCTGGTT CCTGGAACAA TTGCTTTTAC AGATGCACAT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

ATCGAGGTGA ACATCACGTA CGCGGAATAC TTCGAAATGT CCGTTCGGTT GGCAGAAGCT ATGAAACGAT ATGGGCTGAA TACAAATCAC AGAATCGTCG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TATGCAGTGA AAACTCTCTT CAATTCTTTA TGCCGGTGTT GGGCGCGTTA TTTATCGGAG TTGCAGTTGC GCCCGCGAAC GACATTTATA ATGAACGTGA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ATTGCTCAAC AGTATGAACA TTTCGCAGCC TACCGTAGTG TTTGTTTCCA AAAAGGGGTT GCAAAAAATT TTGAACGTGC AAAAAAAATT ACCAATAATC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CAGAAAATTA TTATCATGGA TTCTAAAACG GATTACCAGG GATTTCAGTC GATGTACACG TTCGTCACAT CTCATCTACC TCCCGGTTTT AATGAATACG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ATTTTGTACC AGAGTCCTTT GATCGTGACA AAACAATTGC ACTGATAATG AATTCCTCTG GATCTACTGG GTTACCTAAG GGTGTGGCCC TTCCGCATAG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AACTGCCTGC GTCAGATTCT CGCATGCCAG AGATCCTATT TTTGGCAATC AAATCATTCC GGATACTGCG ATTTTAAGTG TTGTTCCATT CCATCACGGT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TTTGGAATGT TTACTACACT CGGATATTTG ATATGTGGAT TTCGAGTCGT CTTAATGTAT AGATTTGAAG AAGAGCTGTT TTTACGATCC CTTCAGGATT 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ACAAAATTCA AAGTGCGTTG CTAGTACCAA CCCTATTTTC ATTCTTCGCC AAAAGCACTC TGATTGACAA ATACGATTTA TCTAATTTAC ACGAAATTGC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TTCTGGGGGC GCACCTCTTT CGAAAGAAGT CGGGGAAGCG GTTGCAAAAC GCTTCCATCT TCCAGGGATA CGACAAGGAT ATGGGCTCAC TGAGACTACA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TCAGCTATTC TGATTACACC CGAGGGGGAT GATAAACCGG GCGCGGTCGG TAAAGTTGTT CCATTTTTTG AAGCGAAGGT TGTGGATCTG GATACCGGGA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

AAACGCTGGG CGTTAATCAG AGAGGCGAAT TATGTGTCAG AGGACCTATG ATTATGTCCG GTTATGTAAA CAATCCGGAA GCGACCAACG CCTTGATTGA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CAAGGATGGA TGGCTACATT CTGGAGACAT AGCTTACTGG GACGAAGACG AACACTTCTT CATAGTTGAC CGCTTGAAGT CTTTAATTAA ATACAAAGGA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TATCAGGTGG CCCCCGCTGA ATTGGAATCG ATATTGTTAC AACACCCCAA CATCTTCGAC GCGGGCGTGG CAGGTCTTCC CGACGATGAC GCCGGTGAAC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TTCCCGCCGC CGTTGTTGTT TTGGAGCACG GAAAGACGAT GACGGAAAAA GAGATCGTGG ATTACGTCGC CAGTCAAGTA ACAACCGCGA AAAAGTTGCG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

CGGAGGAGTT GTGTTTGTGG ACGAAGTACC GAAAGGTCTT ACCGGAAAAC TCGACGCAAG AAAAATCAGA GAGATCCTCA TAAAGGCCAA GAAGGGCGGA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

AAGTCCAAAT TGTAAAATGT AACTGTATTC AGCGATGACG AAATTCTTAG CTATTGTAAT CCTCCGAGGC CTCGAGGTCG ACGAATTCGA GCTCGGCCGA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CTTGGCCAAT TCGCCC
^6601      ^6611

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`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek

The abbreviated name of this ORF/gene:
CAT

The description of the protein encoded in this ORF:
chloramphenicol acetyl transferase

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:

no

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

51-710

ORF

ORF position:

2

Version: `1`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek

The abbreviated name of this ORF/gene:
FFluc

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:

no

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

1736-3388

Remarks:

This item is labeled as 3'UTR incomplete because the mRNA sequence deposited here ends at the stop codon of
the second cistron.

Citations:

Chon S. K., Perez D. R., Donis R. O. (1998) Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology. 251(2):370-382

IRESs:

IRES:

Version: `2`	Last change: `2006-07-25 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek
The IRES name: `BVDV1_in375-378`	The functional status of IRES: `defective`

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

825-1728

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `115`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `1018`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-911`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-8`

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

GTATACGAGA ATTAGAAAAG GCACTCGTAT ACGTATTGGG CAATTAAAAA TAATAATTAG GCCTAGGGAA CAAATCCCTC TCAGCGAAGG CCGAAAAGAG 
^825       ^835       ^845       ^855       ^865       ^875       ^885       ^895       ^905       ^915       

GCTAGCCATG CCCTTAGTAG GACTAGCATA ATGAGGGGGG TAGCAACAGT GGTGAGTTCG TTGGATGGCT TAAGCCCTGA GTACAGGGTA GTCGTCAGTG 
^925       ^935       ^945       ^955       ^965       ^975       ^985       ^995       ^1005      ^1015      

GTTCGACGCC TTGGAATAAA GGTCTCGAGA TGCCACGTGG ACGAGGGCAT GCCCAAAGCA CATCTTAACC TGAGCGGGGG TCGCCCAGGT AAAAGCAGTT 
^1025      ^1035      ^1045      ^1055      ^1065      ^1075      ^1085      ^1095      ^1105      ^1115      

TTAACCGACT GTTACGAATA CAGCCTGATA GGGTGCTGCA GAGGCCCACT GTATTGCTAC TAAAAATCTC TGCTGTACGT ACATGGCACA TGGAGTTGAT 
^1125      ^1135      ^1145      ^1155      ^1165      ^1175      ^1185      ^1195      ^1205      ^1215      

CACAAATGAA CTTTTATACA AAACATACAA ACAAAAACCC GTCGGGGTGG AGGAACCTGT TTATGATCAG GCAGGTGATC CCTTATTTGG TGAAAGGGGA 
^1225      ^1235      ^1245      ^1255      ^1265      ^1275      ^1285      ^1295      ^1305      ^1315      

GCAGTCCACC CTCAATCGAC GCTAAAGCTC CCACACAAGA GAGGGGAACG CGATGTTCCA ACCAACTTGG CATCCTTACC AAAAAGAGGT GACTGCAGGT 
^1325      ^1335      ^1345      ^1355      ^1365      ^1375      ^1385      ^1395      ^1405      ^1415      

CGGGTAATAG CAGAGGACCT GTGAGCGGGA TCTACCTGAA GCCAGGGCCA CTATTTTACC AGGACTATAA AGGTCCCGTC TATCACAGGG CCCCGCTGGA 
^1425      ^1435      ^1445      ^1455      ^1465      ^1475      ^1485      ^1495      ^1505      ^1515      

GCTCTTTGAG GAGGGATCCA TGTGTGAAAC GACTAAACGG ATAGGGAGAG TAACTGGAAG TGACGGAAAG CTGTACCACA TTTATGTGTG TATAGATGGA 
^1525      ^1535      ^1545      ^1555      ^1565      ^1575      ^1585      ^1595      ^1605      ^1615      

TGTATAATAA TAAAAAGTGC CACGAGAAGT TACCAAAGGG TGTTCAGGTG GGTCCATAAT AGGCTTGACT GCCCTCTATG GGTCACAACT TGCTCAGACA 
^1625      ^1635      ^1645      ^1655      ^1665      ^1675      ^1685      ^1695      ^1705      ^1715      

CGAA
^1725

Remarks:

BVDV 5' UTR (389 nt, incl. insertion of nt 375-378) and open reading frame (515 nt)

Citations:

Chon S. K., Perez D. R., Donis R. O. (1998) Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology. 251(2):370-382

The translation experiments:

Translation results:

IRESite Translation Id: 40

Version: `3`	Last change: `2006-07-25 00:00:00`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Pospíšek

The translation method used to study IRES function:
in vivo

The organism used for translation:

Cercopithecus aethiops CV-1 (ATCC CCL-70)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

48.000

Name of IRES used as the positive control:

BVDV_1

Name of the plasmid used as the positive control. `pBi5_BVDV`	Name of the plasmid used as the negative control. `pBi456F`
`IRESite Id` of the plasmid used as positive control. `9`	`IRESite Id` of the plasmid used as negative control. `208`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0.300`
The size (length) of intercistronic region in the positive control: `1022`	The size (length) of intercistronic region in the negative control: `578`

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:

positive control - 5' region of genomic RNA of BVDV (nt 1 to nt 900) in the same bicistronic vector
negative control - fragment of the BVDV genome (nt 2198–2654) in the same bicistronic vector

Citations:

Chon S. K., Perez D. R., Donis R. O. (1998) Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology. 251(2):370-382

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