IRESite_Id:152 characteristics of CSFV+55 IRES studied in pRLuc-CSFV+55-hpCAT plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `152`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2006-07-17 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:
our_best_guess

The mRNA/+RNA description:

Bicistronic mRNA molecule coding for RLuc-CSFV_IRES followed by 54nt from CSFV N-pro sequence followed by KpnI
site, hairpin and CAT. It should have been better named pRLuc-CSFV+54-hpCAT.

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

GGCGAATTGG AGCTCCAccg cggCTAGCCA CCATGACTTC GAAAGTTTAT GATCCAGAAC AAAGGAAACG GATGATAACT GGTCCGCAGT GGTGGGCCAG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATGTAAACAA ATGAATGTTC TTGATTCATT TATTAATTAT TATGATTCAG AAAAACATGC AGAAAATGCT GTTATTTTTT TACATGGTAA CGCGGCCTCT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCTTATTTAT GGCGACATGT TGTGCCACAT ATTGAGCCAG TAGCGCGGTG TATTATACCA GACCTTATTG GTATGGGCAA ATCAGGCAAA TCTGGTAATG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTTCTTATAG GTTACTTGAT CATTACAAAT ATCTTACTGC ATGGTTTGAA CTTCTTAATT TACCAAAGAA GATCATTTTT GTCGGCCATG ATTGGGGTGC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TTGTTTGGCA TTTCATTATA GCTATGAGCA TCAAGATAAG ATCAAAGCAA TAGTTCACGC TGAAAGTGTA GTAGATGTGA TTGAATCATG GGATGAATGG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCTGATATTG AAGAAGATAT TGCGTTGATC AAATCTGAAG AAGGAGAAAA AATGGTTTTG GAGAATAACT TCTTCGTGGA AACCATGTTG CCATCAAAAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCATGAGAAA GTTAGAACCA GAAGAATTTG CAGCATATCT TGAACCATTC AAAGAGAAAG GTGAAGTTCG TCGTCCAACA TTATCATGGC CTCGTGAAAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

CCCGTTAGTA AAAGGTGGTA AACCTGACGT TGTACAAATT GTTAGGAATT ATAATGCTTA TCTACGTGCA AGTGATGATT TACCAAAAAT GTTTATTGAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TCGGACCCAG GATTCTTTTC CAATGCTATT GTTGAAGGTG CCAAGAAGTT TCCTAATACT GAATTTGTCA AAGTAAAAGG TCTTCATTTT TCGCAAGAAG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ATGCACCTGA TGAAATGGGA AAATATATCA AATCGTTCGT TGAGCGAGTT CTCAAAAATG AACAATAATT CTAGAGCTCT GCAGgaattc agatctatGc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ATACGAGGTT AGTTCATTCT CGTATACACG ATTGGACAAA TCAAAATTAT AATTTGGTTC AGGGCCTCCC TCCAGCGACG GCCGAACTGG GCTAGCCATG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCCATAGTAG GACTAGCAAA ACGGAGGGAC TAGCCATAGT GGCGAGCTCC CTGGGTGGTC TAAGTCCTGA GTACAGGACA GTCGTCAGTA GTTCGACGTG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGCAGAAGCC CACCTCGAGA TGCTACGTGG ACGAGGGCAT GCCAAGACAC ACCTTAACCC TAGCGGGGGT CGCTAGGGTG AAATCACACC ACGTGATGGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AGTACGACCT GATAGGGCGC TGCAGAGGCC CACTATTAGG CTAGTATAAA AATCTCTGCT GTACATGGCA CatGgagttg aatcactttg aacttttata 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

caaaacaaac aaacaaaaac caatgggtac cgccgagctc tcggcggtac gtCGAGAAAA AAATCACTGG ATATACCACC GTTGATATAT CCCAATGGCA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCGTAAAGAA CATTTTGAGG CATTTCAGTC AGTTGCTCAA TGTACCTATA ACCAGACCGT TCAGCTGGAT ATTACGGCCT TTTTAAAGAC CGTAAAGAAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AATAAGCACA AGTTTTATCC GGCCTTTATT CACATTCTTG CCCGCCTCAT GATGAATGCT CATCCGGAgT TCCGTATGGC AATGAAAGAC GGTGAGCTGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGATATGGGA TAGTGTTCAC CCTTGTTACA CCGTTTTCCA TGAGCAAACT GAAACGTTTT CATCGCTCTG GAGTGAATAC CACGACGATT TCCGGCAGTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCTACACATA TATTCGCAAG ATGTGGCGTG TTACGGTGAA AACCTGGCCT ATTTCCCTAA AGGGTTTATT GAGAATATGT TTTTCGTCTC AGCCAATCCC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TGGGTGAGTT TCACCAGTTT TGATTTAAAC GTGGCCAATA TGGACAACTT CTTCGCCCCC GTTTTCACtA TGGGCAAATA TTATACGCAA GGCGACAAGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGCTGATGCC GCTGGCGATT CAGGTTCATC ATGCCGTCTG TGATGGCTTC CATGTCGGCA GAATGCTTAA TGAAGTACAA CAATGTACTG CGATGAGTGC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CAGGGCGGGG CGTAATTTTT TTTAAGGCAG TTATTGGTGC CCTTAAACGC CTGGTTGCGT ACGCCTGAAT AAGTGATAAT AAGCGGATGA ATGGCAGAAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTCGACTCGA CAggatccgg ctgctaacaa agcccgaaag gaagctgagt tggctgctgc caccgctgag caataactag cataacccct tggggcctct 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

aaacgggtct tgaggggttt tttg
^2301      ^2311      ^2321

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pRLuc-CSFV+55-hpCAT 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:
CSFV

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Classical swine fever virus

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

GGAAATTGTA AACGTTAATA TTTTGTTAAA ATTCGCGTTA AATTTTTGTT AAATCAGCTC ATTTTTTAAC CAATAGGCCG AAATCGGCAA AATCCCTTAT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAATCAAAAG AATAGACCGA GATAGGGTTG AGTGTTGTTC CAGTTTGGAA CAAGAGTCCA CTATTAAAGA ACGTGGACTC CAACGTCAAA GGGCGAAAAA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CCGTCTATCA GGGCGATGGC CCACTACGTG AACCATCACC CTAATCAAGT TTTTTGGGGT CGAGGTGCCG TAAAGCACTA AATCGGAACC CTAAAGGGAG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CCCCCGATTT AGAGCTTGAC GGGGAAAGCC GGCGAACGTG GCGAGAAAGG AAGGGAAGAA AGCGAAAGGA GCGGGCGCTA GGGCGCTGGC AAGTGTAGCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GTCACGCTGC GCGTAACCAC CACACCCGCC GCGCTTAATG CGCCGCTACA GGGCGCGTCG CGCCATTCGC CATTCAGGCT GCGCAACTGT TGGGAAGGGC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

GATCGGTGCG GGCCTCTTCG CTATTACGCC AGCTGGCGAA AGGGGGATGT GCTGCAAGGC GATTAAGTTG GGTAACGCCA GGGTTTTCCC AGTCACGACG 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TTGTAAAACG ACGGCCAGTG AATTGTAATA CGACTCACTA TAGGGCGAAT TGGAGCTCCA ccgcggCTAG CCACCATGAC TTCGAAAGTT TATGATCCAG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AACAAAGGAA ACGGATGATA ACTGGTCCGC AGTGGTGGGC CAGATGTAAA CAAATGAATG TTCTTGATTC ATTTATTAAT TATTATGATT CAGAAAAACA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TGCAGAAAAT GCTGTTATTT TTTTACATGG TAACGCGGCC TCTTCTTATT TATGGCGACA TGTTGTGCCA CATATTGAGC CAGTAGCGCG GTGTATTATA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CCAGACCTTA TTGGTATGGG CAAATCAGGC AAATCTGGTA ATGGTTCTTA TAGGTTACTT GATCATTACA AATATCTTAC TGCATGGTTT GAACTTCTTA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ATTTACCAAA GAAGATCATT TTTGTCGGCC ATGATTGGGG TGCTTGTTTG GCATTTCATT ATAGCTATGA GCATCAAGAT AAGATCAAAG CAATAGTTCA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CGCTGAAAGT GTAGTAGATG TGATTGAATC ATGGGATGAA TGGCCTGATA TTGAAGAAGA TATTGCGTTG ATCAAATCTG AAGAAGGAGA AAAAATGGTT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTGGAGAATA ACTTCTTCGT GGAAACCATG TTGCCATCAA AAATCATGAG AAAGTTAGAA CCAGAAGAAT TTGCAGCATA TCTTGAACCA TTCAAAGAGA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AAGGTGAAGT TCGTCGTCCA ACATTATCAT GGCCTCGTGA AATCCCGTTA GTAAAAGGTG GTAAACCTGA CGTTGTACAA ATTGTTAGGA ATTATAATGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TTATCTACGT GCAAGTGATG ATTTACCAAA AATGTTTATT GAATCGGACC CAGGATTCTT TTCCAATGCT ATTGTTGAAG GTGCCAAGAA GTTTCCTAAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ACTGAATTTG TCAAAGTAAA AGGTCTTCAT TTTTCGCAAG AAGATGCACC TGATGAAATG GGAAAATATA TCAAATCGTT CGTTGAGCGA GTTCTCAAAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ATGAACAATA ATTCTAGAGC TCTGCAGgaa ttcagatcta tGcATACGAG GTTAGTTCAT TCTCGTATAC ACGATTGGAC AAATCAAAAT TATAATTTGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TTCAGGGCCT CCCTCCAGCG ACGGCCGAAC TGGGCTAGCC ATGCCCATAG TAGGACTAGC AAAACGGAGG GACTAGCCAT AGTGGCGAGC TCCCTGGGTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTCTAAGTCC TGAGTACAGG ACAGTCGTCA GTAGTTCGAC GTGAGCAGAA GCCCACCTCG AGATGCTACG TGGACGAGGG CATGCCAAGA CACACCTTAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CCCTAGCGGG GGTCGCTAGG GTGAAATCAC ACCACGTGAT GGGAGTACGA CCTGATAGGG CGCTGCAGAG GCCCACTATT AGGCTAGTAT AAAAATCTCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GCTGTACATG GCACatGgag ttgaatcact ttgaactttt atacaaaaca aacaaacaaa aaccaatggg taccgccgag ctctcggcgg tacgtCGAGA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAAAAATCAC TGGATATACC ACCGTTGATA TATCCCAATG GCATCGTAAA GAACATTTTG AGGCATTTCA GTCAGTTGCT CAATGTACCT ATAACCAGAC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CGTTCAGCTG GATATTACGG CCTTTTTAAA GACCGTAAAG AAAAATAAGC ACAAGTTTTA TCCGGCCTTT ATTCACATTC TTGCCCGCCT CATGATGAAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GCTCATCCGG AgTTCCGTAT GGCAATGAAA GACGGTGAGC TGGTGATATG GGATAGTGTT CACCCTTGTT ACACCGTTTT CCATGAGCAA ACTGAAACGT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTTCATCGCT CTGGAGTGAA TACCACGACG ATTTCCGGCA GTTTCTACAC ATATATTCGC AAGATGTGGC GTGTTACGGT GAAAACCTGG CCTATTTCCC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TAAAGGGTTT ATTGAGAATA TGTTTTTCGT CTCAGCCAAT CCCTGGGTGA GTTTCACCAG TTTTGATTTA AACGTGGCCA ATATGGACAA CTTCTTCGCC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CCCGTTTTCA CtATGGGCAA ATATTATACG CAAGGCGACA AGGTGCTGAT GCCGCTGGCG ATTCAGGTTC ATCATGCCGT CTGTGATGGC TTCCATGTCG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCAGAATGCT TAATGAAGTA CAACAATGTA CTGCGATGAG TGCCAGGGCG GGGCGTAATT TTTTTTAAGG CAGTTATTGG TGCCCTTAAA CGCCTGGTTG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CGTACGCCTG AATAAGTGAT AATAAGCGGA TGAATGGCAG AAATTCGACT CGACAggatc cggctgctaa caaagcccga aaggaagctg agttggctgc 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tgccaccgct gagcaataac tagcataacc ccttggggcc tctaaacggg tcttgagggg ttttttgctg aaaggaggaa ctatatccgg atatcgatat 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

cccgcaagag gcccggcagt accggcataa ccaagcctat gcctacagca tccagggtga cggtgccgag gatgacgatg agcgcattgt tagatttcat 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

acacggtgcc tgactgcgtt agcaatttaa ctgtgATAAA CTACCGCATT AaagcttATC GCCAGCTTTT GTTCCCTTTA GTGAGGGTTA ATTCCGAGCT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGGCGTAATC ATGGTCATAG CTGTTTCCTG TGTGAAATTG TTATCCGCTC ACAATTCCAC ACAACATACG AGCCGGAAGC ATAAAGTGTA AAGCCTGGGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TGCCTAATGA GTGAGCTAAC TCACATTAAT TGCGTTGCGC TCACTGCCCG CTTTCCAGTC GGGAAACCTG TCGTGCCAGC TGCATTAATG AATCGGCCAA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CGCGCGGGGA GAGGCGGTTT GCGTATTGGG CGCTCTTCCG CTTCCTCGCT CACTGACTCG CTGCGCTCGG TCGTTCGGCT GCGGCGAGCG GTATCAGCTC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ACTCAAAGGC GGTAATACGG TTATCCACAG AATCAGGGGA TAACGCAGGA AAGAACATGT GAGCAAAAGG CCAGCAAAAG GCCAGGAACC GTAAAAAGGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CGCGTTGCTG GCGTTTTTCC ATAGGCTCCG CCCCCCTGAC GAGCATCACA AAAATCGACG CTCAAGTCAG AGGTGGCGAA ACCCGACAGG ACTATAAAGA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TACCAGGCGT TTCCCCCTGG AAGCTCCCTC GTGCGCTCTC CTGTTCCGAC CCTGCCGCTT ACCGGATACC TGTCCGCCTT TCTCCCTTCG GGAAGCGTGG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CGCTTTCTCA TAGCTCACGC TGTAGGTATC TCAGTTCGGT GTAGGTCGTT CGCTCCAAGC TGGGCTGTGT GCACGAACCC CCCGTTCAGC CCGACCGCTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CGCCTTATCC GGTAACTATC GTCTTGAGTC CAACCCGGTA AGACACGACT TATCGCCACT GGCAGCAGCC ACTGGTAACA GGATTAGCAG AGCGAGGTAT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GTAGGCGGTG CTACAGAGTT CTTGAAGTGG TGGCCTAACT ACGGCTACAC TAGAAGGACA GTATTTGGTA TCTGCGCTCT GCTGAAGCCA GTTACCTTCG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GAAAAAGAGT TGGTAGCTCT TGATCCGGCA AACAAACCAC CGCTGGTAGC GGTGGTTTTT TTGTTTGCAA GCAGCAGATT ACGCGCAGAA AAAAAGGATC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TCAAGAAGAT CCTTTGATCT TTTCTACGGG GTCTGACGCT CAGTGGAACG AAAACTCACG TTAAGGGATT TTGGTCATGA GATTATCAAA AAGGATCTTC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

ACCTAGATCC TTTTAAATTA AAAATGAAGT TTTAAATCAA TCTAAAGTAT ATATGAGTAA ACTTGGTCTG ACAGTTACCA ATGCTTAATC AGTGAGGCAC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CTATCTCAGC GATCTGTCTA TTTCGTTCAT CCATAGTTGC CTGACTCCCC GTCGTGTAGA TAACTACGAT ACGGGAGGGC TTACCATCTG GCCCCAGTGC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TGCAATGATA CCGCGAGACC CACGCTCACC GGCTCCAGAT TTATCAGCAA TAAACCAGCC AGCCGGAAGG GCCGAGCGCA GAAGTGGTCC TGCAACTTTA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TCCGCCTCCA TCCAGTCTAT TAATTGTTGC CGGGAAGCTA GAGTAAGTAG TTCGCCAGTT AATAGTTTGC GCAACGTTGT TGCCATTGCT ACAGGCATCG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TGGTGTCACG CTCGTCGTTT GGTATGGCTT CATTCAGCTC CGGTTCCCAA CGATCAAGGC GAGTTACATG ATCCCCCATG TTGTGCAAAA AAGCGGTTAG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CTCCTTCGGT CCTCCGATCG TTGTCAGAAG TAAGTTGGCC GCAGTGTTAT CACTCATGGT TATGGCAGCA CTGCATAATT CTCTTACTGT CATGCCATCC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GTAAGATGCT TTTCTGTGAC TGGTGAGTAC TCAACCAAGT CATTCTGAGA ATAGTGTATG CGGCGACCGA GTTGCTCTTG CCCGGCGTCA ATACGGGATA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

ATACCGCGCC ACATAGCAGA ACTTTAAAAG TGCTCATCAT TGGAAAACGT TCTTCGGGGC GAAAACTCTC AAGGATCTTA CCGCTGTTGA GATCCAGTTC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

GATGTAACCC ACTCGTGCAC CCAACTGATC TTCAGCATCT TTTACTTTCA CCAGCGTTTC TGGGTGAGCA AAAACAGGAA GGCAAAATGC CGCAAAAAAG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

GGAATAAGGG CGACACGGAA ATGTTGAATA CTCATACTCT TCCTTTTTCA ATATTATTGA AGCATTTATC AGGGTTATTG TCTCATGAGC GGATACATAT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TTGAATGTAT TTAGAAAAAT AAACAAATAG GGGTTCCGCG CACATTTCCC CGAAAAGTGC CACCTG
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361

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: `2006-07-17 00:00:00`
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):

33-968

ORF

ORF position:

2

Version: `1`	Last change: `2006-07-17 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
CAT

The description of the protein encoded in this ORF:
Chloramphenicol acetyltransferase with N-terminal 54nt from CSFV N-pro ORF followed by KpnI site, hairpin stem loop and followed by CAT ORF.

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):

1372-2115

Citations:

Rijnbrand R., Bredenbeek P. J., Haasnoot P. C., Kieft J. S., Spaan W. J., Lemon S. M. (2001) The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA. 7(4):585-597

IRESs:

IRES:

Version: `4`	Last change: `2006-07-26 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `CSFV+55`	The functional status of IRES: `functional`

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

999-1426

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `31`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `458`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-373`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `54`

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

GcATACGAGG TTAGTTCATT CTCGTATACA CGATTGGACA AATCAAAATT ATAATTTGGT TCAGGGCCTC CCTCCAGCGA CGGCCGAACT GGGCTAGCCA 
^999       ^1009      ^1019      ^1029      ^1039      ^1049      ^1059      ^1069      ^1079      ^1089      

TGCCCATAGT AGGACTAGCA AAACGGAGGG ACTAGCCATA GTGGCGAGCT CCCTGGGTGG TCTAAGTCCT GAGTACAGGA CAGTCGTCAG TAGTTCGACG 
^1099      ^1109      ^1119      ^1129      ^1139      ^1149      ^1159      ^1169      ^1179      ^1189      

TGAGCAGAAG CCCACCTCGA GATGCTACGT GGACGAGGGC ATGCCAAGAC ACACCTTAAC CCTAGCGGGG GTCGCTAGGG TGAAATCACA CCACGTGATG 
^1199      ^1209      ^1219      ^1229      ^1239      ^1249      ^1259      ^1269      ^1279      ^1289      

GGAGTACGAC CTGATAGGGC GCTGCAGAGG CCCACTATTA GGCTAGTATA AAAATCTCTG CTGTACATGG CACatGgagt tgaatcactt tgaactttta 
^1299      ^1309      ^1319      ^1329      ^1339      ^1349      ^1359      ^1369      ^1379      ^1389      

tacaaaacaa acaaacaaaa accaatgg
^1399      ^1409      ^1419

Remarks:

The first base from the KpnI site is annotated here as belonging to IRES although this is not consistent with
other records derived from same article. really only 54nts are retained from CSFV N-pro ORF.

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 106

Version: `1`	Last change: `2006-06-30 00:00:00`
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:

116.000

Name of IRES used as the positive control:

CSFV+55

Name of the plasmid used as the positive control. `pRLuc-CSFV+55-CAT`	Name of the plasmid used as the negative control. `pRLuc-CSFV+3-hpCAT`
`IRESite Id` of the plasmid used as positive control. `144`	`IRESite Id` of the plasmid used as negative control. `149`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `0`
The size (length) of intercistronic region in the positive control: `403`	The size (length) of intercistronic region in the negative control: `403`

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:

Fig. 8

Citations:

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