IRESite_Id:439 characteristics of gypsy IRES studied in pDC-WT plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `439`	Version: `3`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-07-07 12:30:40`

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:
hopefully_full-length_mRNA

The mRNA/+RNA description:

In vitro T7 run-off transcript produced from bicistronic plasmid pDC-WT which comprises neomycin
phosphotransferase and truncated version of the beta-galactosidase (linearized at the AflIII site at position
4083 within pDC-WT; see 1414.gb below) as the first and the second cistron respectively and full-length
(except very 5'-most Adenosine) gypsy 5' UTR (nt from -841 to +5 of the original sequence) mRNA inserted in
between reporters.

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

GGGAGACCCA AGCTTGATAT CGAATTCCGA TCTGATCAAG AGACAGGATG AGGATCGTTT CGCATGATTG AACAAGATGG ATTGCACGCA GGTTCTCCGG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CCGCTTGGGT GGAGAGGCTA TTCGGCTATG ACTGGGCACA ACAGACAATC GGCTGCTCTG ATGCCGCCGT GTTCCGGCTG TCAGCGCAGG GGCGCCCGGT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TCTTTTTGTC AAGACCGACC TGTCCGGTGC CCTGAATGAA CTGCAGGACG AGGCAGCGCG GCTATCGTGG CTGGCCACGA CGGGCGTTCC TTGCGCAGCT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

GTGCTCGACG TTGTCACTGA AGCGGGAAGG GACTGGCTGC TATTGGGCGA AGTGCCGGGG CAGGATCTCC TGTCATCTCA CCTTGCTCCT GCCGAGAAAG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

TATCCATCAT GGCTGATGCA ATGCGGCGGC TGCATACGCT TGATCCGGCT ACCTGCCCAT TCGACCACCA AGCGAAACAT CGCATCGAGC GAGCACGTAC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCGGATGGAA GCCGGTCTTG TCGATCAGGA TGATCTGGAC GAAGAGCATC AGGGGCTCGC GCCAGCCGAA CTGTTCGCCA GGCTCAAGGC GCGCATGCCC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GACGGCGAGG ATCTCGTCGT GACCCATGGC GATGCCTGCT TGCCGAATAT CATGGTGGAA AATGGCCGCT TTTCTGGATT CATCGACTGT GGCCGGCTGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GTGTGGCGGA CCGCTATCAG GACATAGCGT TGGCTACCCG TGATATTGCT GAAGAGCTTG GCGGCGAATG GGCTGACCGC TTCCTCGTGC TTTACGGTAT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

CGCCGCTCCC GATTCGCAGC GCATCGCCTT CTATCGCCTT CTTGACGAGT TCTTCTGAGC GGGACTCTGG GGTTCGAAAT GACCGACCAA GCGACGCCCA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ACCTGCCATC ACGAGATTTC GATTCCACCG CCGCCTTCTA TGAAAGGTTG GGCTTCGGAA TCGTTTTCCG GGACGCCGGC TGGATGATCC TCCAGCGCGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GGATCTCATG CTGGAGTTCT TCGCCCACCC CGGGCTCGAT CCCCTCGAGC TAGCGTTCAA ATCTTGTGTC GAAATAAACC ACAGCTTGCT CCGGCTCATT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

GCCGTTAAAC ATCATTGTTC TTATTTACAA TCAAATCGCT ATCGCCACAA GGCTAGTGAT AATAACTAAG GGGGCGAAGT CAAGCCCTCC AACCTAATCT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCATAAACAG TGTCTAAGAC GAACCTCAGC GAAAGAAGGA AGATCTCTAG ACCTACTGGA AATAACATAA CTCTGGACCT ATTGGAACTT ATATAATTGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGCCCAACCA ACAATCTGAA CCCACCAATC TAATTTAACA CACTTTGTCA GGCGACAAAC AGGGTAGTTA AGTTAGAAAA GCATGTAAGT TTTACAAGAC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ACTTCTTTGA CGCAATCAAG AAATTTACGA GTGAAAAAAA AAAAAAAAAA AAGTTGTGTA TCTGGCCACG TAATAAGTGT GCGTTGAATT TATTCGCAAA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AACATTGCAT ATTTTCGGCA AAGTAAAATT TTGTTGCATA CCTTATCAAA AAATAAGTGC TGCATACTTT TTAGAGAAAC CAAATAATTT TTTATTGCAT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACCCGTTTTT AATAAAATAC ATTGCATACC CTCTTTTAAT AAAAAATATT GCATACTTTG ACGAAACAAA TTTTCGTTGC ATACCCAATA AAAGATTATT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATATTGCATA CCCGTTTTTA ATAAAATACA TTGCATACCC TCTTTTAATA AAAAATATTG CATACGTTGA CGAAACAAAT TTTCGTTGCA TACCCAATAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

AAGATTATTA TATTGCATAC CTTTTCTTGC CATACCATTT AGCCGATCAA TTGTGCTCGG CAACAGTATA TTTGTGGTGT GCCAACCAAC AACCAATGAG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GCTAGCGGAT CCCGTCGTTT TACAACGTCG TGACTGGGAA AACCCTGGCG TTACCCAACT TAATCGCCTT GCAGCACATC CCCCTTTCGC CAGCTGGCGT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AATAGCGAAG AGGCCCGCAC CGATCGCCCT TCCCAACAGT TGCGCAGCCT GAATGGCGAA TGGCGCTTTG CCTGGTTTCC GGCACCAGAA GCGGTGCCGG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAAGCTGGCT GGAGTGCGAT CTTCCTGAGG CCGATACTGT CGTCGTCCCC TCAAACTGGC AGATGCACGG TTACGATGCG CCCATCTACA CCAACGTAAC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTATCCCATT ACGGTCAATC CGCCGTTTGT TCCCACGGAG AATCCGACGG GTTGTTACTC GCTCACATTT AATGTTGATG AAAGCTGGCT ACAGGAAGGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CAGACGCGAA TTATTTTTGA TGGCGTTAAC TCGGCGTTTC ATCTGTGGTG CAACGGGCGC TGGGTCGGTT ACGGCCAGGA CAGTCGTTTG CCGTCTGAAT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTGACCTGAG CGCATTTTTA CGCGCCGGAG AAAACCGCCT CGCGGTGATG GTGCTGCGTT GGAGTGACGG CAGTTATCTG GAAGATCAGG ATATGTGGCG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GATGAGCGGC ATTTTCCGTG ACGTCTCGTT GCTGCATAAA CCGACTACAC AAATCAGCGA TTTCCATGTT GCCACTCGCT TTAATGATGA TTTCAGCCGC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GCTGTACTGG AGGCTGAAGT TCAGATGTGC GGCGAGTTGC GTGACTACCT ACGGGTAACA GTTTCTTTAT GGCAGGGTGA AACGCAGGTC GCCAGCGGCA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CCGCGCCTTT CGGCGGTGAA ATTATCGATG AGCGTGGTGG TTATGCCGAT CGCGTCACAC TACGTCTGAA CGTCGAAAAC CCGAAACTGT GGAGCGCCGA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

AATCCCGAAT CTCTATCGTG CGGTGGTTGA ACTGCACACC GCCGACGGCA CGCTGATTGA AGCAGAAGCC TGCGATGTCG GTTTCCGCGA GGTGCGGATT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAAAATGGTC TGCTGCTGCT GAACGGCAAG CCGTTGCTGA TTCGAGGCGT TAACCGTCAC GAGCATCATC CTCTGCATGG TCAGGTCATG GATGAGCAGA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGATGGTGCA GGATATCCTG CTGATGAAGC AGAACAACTT TAACGCCGTG CGCTGTTCGC ATTATCCGAA CCATCCGCTG TGGTACACGC TGTGCGACCG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CTACGGCCTG TATGTGGTGG ATGAAGCCAA TATTGAAACC CACGGCATGG TGCCAATGAA TCGTCTGACC GATGATCCGC GCTGGCTACC GGCGATGAGC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GAA
^3201

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pDC-WT The name of the promoter used to express this mRNA:
T7

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing gypsy 5' UTR (nt from -841 to +5 of the original sequence) inserted between neomycin phosphotransferase and beta-galactosidase reporter genes.

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:
gypsy

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Drosophila melanogaster

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

GACGGATCGG GAGATCTCCC GATCCCCTAT GGTCGACTCT CAGTACAATC TGCTCTGATG CCGCATAGTT AAGCCAGTAT CTGCTCCCTG CTTGTGTGTT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GGAGGTCGCT GAGTAGTGCG CGAGCAAAAT TTAAGCTACA ACAAGGCAAG GCTTGACCGA CAATTGCATG AAGAATCTGC TTAGGGTTAG GCGTTTTGCG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CTGCTTCGCG ATGTACGGGC CAGATATACG CGTTGACATT GATTATTGAC TAGTTATTAA TAGTAATCAA TTACGGGGTC ATTAGTTCAT AGCCCATATA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TGGAGTTCCG CGTTACATAA CTTACGGTAA ATGGCCCGCC TGGCTGACCG CCCAACGACC CCCGCCCATT GACGTCAATA ATGACGTATG TTCCCATAGT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AACGCCAATA GGGACTTTCC ATTGACGTCA ATGGGTGGAC TATTTACGGT AAACTGCCCA CTTGGCAGTA CATCAAGTGT ATCATATGCC AAGTACGCCC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCTATTGACG TCAATGACGG TAAATGGCCC GCCTGGCATT ATGCCCAGTA CATGACCTTA TGGGACTTTC CTACTTGGCA GTACATCTAC GTATTAGTCA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

TCGCTATTAC CATGGTGATG CGGTTTTGGC AGTACATCAA TGGGCGTGGA TAGCGGTTTG ACTCACGGGG ATTTCCAAGT CTCCACCCCA TTGACGTCAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGGGAGTTTG TTTTGGCACC AAAATCAACG GGACTTTCCA AAATGTCGTA ACAACTCCGC CCCATTGACG CAAATGGGCG GTAGGCGTGT ACGGTGGGAG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GTCTATATAA GCAGAGCTCT CTGGCTAACT AGAGAACCCA CTGCTTAACT GGCTTATCGA AATTAATACG ACTCACTATA GGGAGACCCA AGCTTGATAT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CGAATTCCGA TCTGATCAAG AGACAGGATG AGGATCGTTT CGCATGATTG AACAAGATGG ATTGCACGCA GGTTCTCCGG CCGCTTGGGT GGAGAGGCTA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

TTCGGCTATG ACTGGGCACA ACAGACAATC GGCTGCTCTG ATGCCGCCGT GTTCCGGCTG TCAGCGCAGG GGCGCCCGGT TCTTTTTGTC AAGACCGACC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TGTCCGGTGC CCTGAATGAA CTGCAGGACG AGGCAGCGCG GCTATCGTGG CTGGCCACGA CGGGCGTTCC TTGCGCAGCT GTGCTCGACG TTGTCACTGA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

AGCGGGAAGG GACTGGCTGC TATTGGGCGA AGTGCCGGGG CAGGATCTCC TGTCATCTCA CCTTGCTCCT GCCGAGAAAG TATCCATCAT GGCTGATGCA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ATGCGGCGGC TGCATACGCT TGATCCGGCT ACCTGCCCAT TCGACCACCA AGCGAAACAT CGCATCGAGC GAGCACGTAC TCGGATGGAA GCCGGTCTTG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TCGATCAGGA TGATCTGGAC GAAGAGCATC AGGGGCTCGC GCCAGCCGAA CTGTTCGCCA GGCTCAAGGC GCGCATGCCC GACGGCGAGG ATCTCGTCGT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GACCCATGGC GATGCCTGCT TGCCGAATAT CATGGTGGAA AATGGCCGCT TTTCTGGATT CATCGACTGT GGCCGGCTGG GTGTGGCGGA CCGCTATCAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GACATAGCGT TGGCTACCCG TGATATTGCT GAAGAGCTTG GCGGCGAATG GGCTGACCGC TTCCTCGTGC TTTACGGTAT CGCCGCTCCC GATTCGCAGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GCATCGCCTT CTATCGCCTT CTTGACGAGT TCTTCTGAGC GGGACTCTGG GGTTCGAAAT GACCGACCAA GCGACGCCCA ACCTGCCATC ACGAGATTTC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GATTCCACCG CCGCCTTCTA TGAAAGGTTG GGCTTCGGAA TCGTTTTCCG GGACGCCGGC TGGATGATCC TCCAGCGCGG GGATCTCATG CTGGAGTTCT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

TCGCCCACCC CGGGCTCGAT CCCCTCGAGC TAGCGTTCAA ATCTTGTGTC GAAATAAACC ACAGCTTGCT CCGGCTCATT GCCGTTAAAC ATCATTGTTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TTATTTACAA TCAAATCGCT ATCGCCACAA GGCTAGTGAT AATAACTAAG GGGGCGAAGT CAAGCCCTCC AACCTAATCT CCATAAACAG TGTCTAAGAC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GAACCTCAGC GAAAGAAGGA AGATCTCTAG ACCTACTGGA AATAACATAA CTCTGGACCT ATTGGAACTT ATATAATTGG CGCCCAACCA ACAATCTGAA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CCCACCAATC TAATTTAACA CACTTTGTCA GGCGACAAAC AGGGTAGTTA AGTTAGAAAA GCATGTAAGT TTTACAAGAC ACTTCTTTGA CGCAATCAAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAATTTACGA GTGAAAAAAA AAAAAAAAAA AAGTTGTGTA TCTGGCCACG TAATAAGTGT GCGTTGAATT TATTCGCAAA AACATTGCAT ATTTTCGGCA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AAGTAAAATT TTGTTGCATA CCTTATCAAA AAATAAGTGC TGCATACTTT TTAGAGAAAC CAAATAATTT TTTATTGCAT ACCCGTTTTT AATAAAATAC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ATTGCATACC CTCTTTTAAT AAAAAATATT GCATACTTTG ACGAAACAAA TTTTCGTTGC ATACCCAATA AAAGATTATT ATATTGCATA CCCGTTTTTA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATAAAATACA TTGCATACCC TCTTTTAATA AAAAATATTG CATACGTTGA CGAAACAAAT TTTCGTTGCA TACCCAATAA AAGATTATTA TATTGCATAC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CTTTTCTTGC CATACCATTT AGCCGATCAA TTGTGCTCGG CAACAGTATA TTTGTGGTGT GCCAACCAAC AACCAATGAG GCTAGCGGAT CCCGTCGTTT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TACAACGTCG TGACTGGGAA AACCCTGGCG TTACCCAACT TAATCGCCTT GCAGCACATC CCCCTTTCGC CAGCTGGCGT AATAGCGAAG AGGCCCGCAC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CGATCGCCCT TCCCAACAGT TGCGCAGCCT GAATGGCGAA TGGCGCTTTG CCTGGTTTCC GGCACCAGAA GCGGTGCCGG AAAGCTGGCT GGAGTGCGAT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CTTCCTGAGG CCGATACTGT CGTCGTCCCC TCAAACTGGC AGATGCACGG TTACGATGCG CCCATCTACA CCAACGTAAC CTATCCCATT ACGGTCAATC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CGCCGTTTGT TCCCACGGAG AATCCGACGG GTTGTTACTC GCTCACATTT AATGTTGATG AAAGCTGGCT ACAGGAAGGC CAGACGCGAA TTATTTTTGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGGCGTTAAC TCGGCGTTTC ATCTGTGGTG CAACGGGCGC TGGGTCGGTT ACGGCCAGGA CAGTCGTTTG CCGTCTGAAT TTGACCTGAG CGCATTTTTA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CGCGCCGGAG AAAACCGCCT CGCGGTGATG GTGCTGCGTT GGAGTGACGG CAGTTATCTG GAAGATCAGG ATATGTGGCG GATGAGCGGC ATTTTCCGTG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ACGTCTCGTT GCTGCATAAA CCGACTACAC AAATCAGCGA TTTCCATGTT GCCACTCGCT TTAATGATGA TTTCAGCCGC GCTGTACTGG AGGCTGAAGT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

TCAGATGTGC GGCGAGTTGC GTGACTACCT ACGGGTAACA GTTTCTTTAT GGCAGGGTGA AACGCAGGTC GCCAGCGGCA CCGCGCCTTT CGGCGGTGAA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ATTATCGATG AGCGTGGTGG TTATGCCGAT CGCGTCACAC TACGTCTGAA CGTCGAAAAC CCGAAACTGT GGAGCGCCGA AATCCCGAAT CTCTATCGTG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CGGTGGTTGA ACTGCACACC GCCGACGGCA CGCTGATTGA AGCAGAAGCC TGCGATGTCG GTTTCCGCGA GGTGCGGATT GAAAATGGTC TGCTGCTGCT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GAACGGCAAG CCGTTGCTGA TTCGAGGCGT TAACCGTCAC GAGCATCATC CTCTGCATGG TCAGGTCATG GATGAGCAGA CGATGGTGCA GGATATCCTG 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CTGATGAAGC AGAACAACTT TAACGCCGTG CGCTGTTCGC ATTATCCGAA CCATCCGCTG TGGTACACGC TGTGCGACCG CTACGGCCTG TATGTGGTGG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

ATGAAGCCAA TATTGAAACC CACGGCATGG TGCCAATGAA TCGTCTGACC GATGATCCGC GCTGGCTACC GGCGATGAGC GAACGCGTAA CGCGAATGGT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GCAGCGCGAT CGTAATCACC CGAGTGTGAT CATCTGGTCG CTGGGGAATG AATCAGGCCA CGGCGCTAAT CACGACGCGC TGTATCGCTG GATCAAATCT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GTCGATCCTT CCCGCCCGGT GCAGTATGAA GGCGGCGGAG CCGACACCAC GGCCACCGAT ATTATTTGCC CGATGTACGC GCGCGTGGAT GAAGACCAGC 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CCTTCCCGGC TGTGCCGAAA TGGTCCATCA AAAAATGGCT TTCGCTACCT GGAGAGACGC GCCCGCTGAT CCTTTGCGAA TACGCCCACG CGATGGGTAA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CAGTCTTGGC GGTTTCGCTA AATACTGGCA GGCGTTTCGT CAGTATCCCC GTTTACAGGG CGGCTTCGTC TGGGACTGGG TGGATCAGTC GCTGATTAAA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TATGATGAAA ACGGCAACCC GTGGTCGGCT TACGGCGGTG ATTTTGGCGA TACGCCGAAC GATCGCCAGT TCTGTATGAA CGGTCTGGTC TTTGCCGACC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

GCACGCCGCA TCCAGCGCTG ACGGAAGCAA AACACCAGCA GCAGTTTTTC CAGTTCCGTT TATCCGGGCA AACCATCGAA GTGACCAGCG AATACCTGTT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CCGTCAATGC GATAACGAGC TCCTGCACTG GATGGTGGCG CTGGATGGTA AGCCGCTGGC AAGCGGTGAA GTGCCTCTGG ATGTCGCTCC ACAAGGTAAA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CAGTTGATTG AACTGCCTGA ACTACCGCAG CCGGAGAGCG CCGGGCAACT CTGGCTCACA GTACGCGTAG TGCAACCGAA CGCGACCGCA TGGTCAGAAG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CCGGGCACAT CAGCGCCTGG CAGCAGTGGC GTCTGGCGGA AAACCTCAGT GTGACGCTCC CCGCCGCGTC CCACGCCATC CCGCATCTGA CCACCAGCGA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

AATGGATTTT TGCATCGAGC TGGGTAATAA GCGTTGGCAA TTTAACCGCC AGTCAGGCTT TCTTTCACAG ATGTGGATTG GCGATAAAAA ACAACTGCTG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ACGCCGCTGC GCGATCAGTT CACCCGTGCA CCGCTGGATA ACGACATTGG CGTAAGTGAA GCGACCCGCA TTGACCCTAA CGCCTGGGTC GAACGCTGGA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

AGGCGGCGGG CCATTACCAG GCCGAAGCAG CGTTGTTGCA GTGCACGGCA GATACACTTG CTGATGCGGT GCTGATTACG ACCGCTACCG CGTGGCAGCA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TCAGGGGAAA ACCTTATTTA TCAGCCGGAA AACCTACCGG ATTGATGGTA GTGGTCAAAT GGCGATTACC GTTGATGTTG AAGTGGCGAG CGATACACCG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

CATCCGGCGC GGATTGGCCT GAACTGCCAG CTGGCGCAGG TAGCAGAGCG GGTAAACTGG CTCGGATTAG GGCCGCAAGA AAACTATCCC GACCGCCTTA 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

CTGCCGCCTG TTTTGACCGC TGGGATCTGC CATTGTCAGA CATGTATACC CCGTACGTCT TCCCGAGCGA AAACGGTCTG CGCTGCGGGA CGCGCGAATT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

GAATTATGGC CCACACCAGT GGCGCGGCGA CTTCCAGTTC AACATCAGCC GCTACAGTCA ACAGCAACTG ATGGAAACCA GCCATCGCCA TCTGCTGGAC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

GCGGAAGAAG GCACATGGCT GAATATCGAC GGTTTCCATA TGGGGATTGG TGGCGACGAC TCCTGGAGCC CGTCAGTATC GGCGGAATTC CAGCTGAGCG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CCGGTCGCTC AAATTACCAG TTGGTCTGGT GTCAAAAATA ATAATAACCG GGCAGGGGGG ATCCGTCGAA GATCAGGTTA TCGATAAAAT AAAAGATTTT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ATTTAGTCTC CAGAAAAAGG GGGGAATGAA AGACCCCACC TGTAGGTTTG GCAAGCTAGT TCTAGAGGGC CCTATTCTAT AGTGTCACCT AAATGCTAGA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GCTCGCTGAT CAGCCTCGAC TGTGCCTTCT AGTTGCCAGC CATCTGTTGT TTGCCCCTCC CCCGTGCCTT CCTTGACCCT GGAAGGTGCC ACTCCCACTG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

TCCTTTCCTA ATAAAATGAG GAAATTGCAT CGCATTGTCT GAGTAGGTGT CATTCTATTC TGGGGGGTGG GGTGGGGCAG GACAGCAAGG GGGAGGATTG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

GGAAGACAAT AGCAGGCATG CTGGGGATGC GGTGGGCTCT ATGGCTTCTG AGGCGGAAAG AACCAGCTGG GGCTCGAGGG GGATCCCGTC GACCTCGAGA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

GCTTGGCGTA ATCATGGTCA TAGCTGTTTC CTGTGTGAAA TTGTTATCCG CTCACAATTC CACACAACAT ACGAGCCGGA AGCATAAAGT GTAAAGCCTG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

GGGTGCCTAA TGAGTGAGCT AACTCACATT AATTGCGTTG CGCTCACTGC CCGCTTTCCA GTCGGGAAAC CTGTCGTGCC AGCTGCATTA ATGAATCGGC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CAACGCGCGG GGAGAGGCGG TTTGCGTATT GGGCGCTCTT CCGCTTCCTC GCTCACTGAC TCGCTGCGCT CGGTCGTTCG GCTGCGGCGA GCGGTATCAG 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

CTCACTCAAA GGCGGTAATA CGGTTATCCA CAGAATCAGG GGATAACGCA GGAAAGAACA TGTGAGCAAA AGGCCAGCAA AAGGCCAGGA ACCGTAAAAA 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GGCCGCGTTG CTGGCGTTTT TCCATAGGCT CCGCCCCCCT GACGAGCATC ACAAAAATCG ACGCTCAAGT CAGAGGTGGC GAAACCCGAC AGGACTATAA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

AGATACCAGG CGTTTCCCCC TGGAAGCTCC CTCGTGCGCT CTCCTGTTCC GACCCTGCCG CTTACCGGAT ACCTGTCCGC CTTTCTCCCT TCGGGAAGCG 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

TGGCGCTTTC TCAATGCTCA CGCTGTAGGT ATCTCAGTTC GGTGTAGGTC GTTCGCTCCA AGCTGGGCTG TGTGCACGAA CCCCCCGTTC AGCCCGACCG 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

CTGCGCCTTA TCCGGTAACT ATCGTCTTGA GTCCAACCCG GTAAGACACG ACTTATCGCC ACTGGCAGCA GCCACTGGTA ACAGGATTAG CAGAGCGAGG 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

TATGTAGGCG GTGCTACAGA GTTCTTGAAG TGGTGGCCTA ACTACGGCTA CACTAGAAGG ACAGTATTTG GTATCTGCGC TCTGCTGAAG CCAGTTACCT 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TCGGAAAAAG AGTTGGTAGC TCTTGATCCG GCAAACAAAC CACCGCTGGT AGCGGTGGTT TTTTTGTTTG CAAGCAGCAG ATTACGCGCA GAAAAAAAGG 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

ATCTCAAGAA GATCCTTTGA TCTTTTCTAC GGGGTCTGAC GCTCAGTGGA ACGAAAACTC ACGTTAAGGG ATTTTGGTCA TGAGATTATC AAAAAGGATC 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

TTCACCTAGA TCCTTTTAAA TTAAAAATGA AGTTTTAAAT CAATCTAAAG TATATATGAG TAAACTTGGT CTGACAGTTA CCAATGCTTA ATCAGTGAGG 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

CACCTATCTC AGCGATCTGT CTATTTCGTT CATCCATAGT TGCCTGACTC CCCGTCGTGT AGATAACTAC GATACGGGAG GGCTTACCAT CTGGCCCCAG 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

TGCTGCAATG ATACCGCGAG ACCCACGCTC ACCGGCTCCA GATTTATCAG CAATAAACCA GCCAGCCGGA AGGGCCGAGC GCAGAAGTGG TCCTGCAACT 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

TTATCCGCCT CCATCCAGTC TATTAATTGT TGCCGGGAAG CTAGAGTAAG TAGTTCGCCA GTTAATAGTT TGCGCAACGT TGTTGCCATT GCTACAGGCA 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

TCGTGGTGTC ACGCTCGTCG TTTGGTATGG CTTCATTCAG CTCCGGTTCC CAACGATCAA GGCGAGTTAC ATGATCCCCC ATGTTGTGCA AAAAAGCGGT 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

TAGCTCCTTC GGTCCTCCGA TCGTTGTCAG AAGTAAGTTG GCCGCAGTGT TATCACTCAT GGTTATGGCA GCACTGCATA ATTCTCTTAC TGTCATGCCA 
^7901      ^7911      ^7921      ^7931      ^7941      ^7951      ^7961      ^7971      ^7981      ^7991      

TCCGTAAGAT GCTTTTCTGT GACTGGTGAG TACTCAACCA AGTCATTCTG AGAATAGTGT ATGCGGCGAC CGAGTTGCTC TTGCCCGGCG TCAATACGGG 
^8001      ^8011      ^8021      ^8031      ^8041      ^8051      ^8061      ^8071      ^8081      ^8091      

ATAATACCGC GCCACATAGC AGAACTTTAA AAGTGCTCAT CATTGGAAAA CGTTCTTCGG GGCGAAAACT CTCAAGGATC TTACCGCTGT TGAGATCCAG 
^8101      ^8111      ^8121      ^8131      ^8141      ^8151      ^8161      ^8171      ^8181      ^8191      

TTCGATGTAA CCCACTCGTG CACCCAACTG ATCTTCAGCA TCTTTTACTT TCACCAGCGT TTCTGGGTGA GCAAAAACAG GAAGGCAAAA TGCCGCAAAA 
^8201      ^8211      ^8221      ^8231      ^8241      ^8251      ^8261      ^8271      ^8281      ^8291      

AAGGGAATAA GGGCGACACG GAAATGTTGA ATACTCATAC TCTTCCTTTT TCAATATTAT TGAAGCATTT ATCAGGGTTA TTGTCTCATG AGCGGATACA 
^8301      ^8311      ^8321      ^8331      ^8341      ^8351      ^8361      ^8371      ^8381      ^8391      

TATTTGAATG TATTTAGAAA AATAAACAAA TAGGGGTTCC GCGCACATTT CCCCGAAAAG TGCCACCTGA CGTC
^8401      ^8411      ^8421      ^8431      ^8441      ^8451      ^8461      ^8471

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: Václav Vopálenský	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
aph

The description of the protein encoded in this ORF:
aminoglycoside-3'-O-phosphotransferase

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):

64-858

OPTIONAL: The function of the encoded protein

neomycin and kanamycin resistance

ORF

ORF position:

2

Version: `1`	Last change: `2008-07-08 08:54:04`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
LacZ

The description of the protein encoded in this ORF:
beta-galactosidase

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):

1896-3203

Citations:

Ronfort C., De Breyne S., Sandrin V., Darlix J. L., Ohlmann T. (2004) Characterization of two distinct RNA domains that regulate translation of the Drosophila gypsy retroelement. RNA. 10(3):504-515

IRESs:

IRES:

Version: `3`	Last change: `2008-07-07 19:17:02`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `gypsy`	The functional status of IRES: `functional`

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

1055-1900

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `197`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `1042`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-841`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `4`

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

GTTCAAATCT TGTGTCGAAA TAAACCACAG CTTGCTCCGG CTCATTGCCG TTAAACATCA TTGTTCTTAT TTACAATCAA ATCGCTATCG CCACAAGGCT 
^1055      ^1065      ^1075      ^1085      ^1095      ^1105      ^1115      ^1125      ^1135      ^1145      

AGTGATAATA ACTAAGGGGG CGAAGTCAAG CCCTCCAACC TAATCTCCAT AAACAGTGTC TAAGACGAAC CTCAGCGAAA GAAGGAAGAT CTCTAGACCT 
^1155      ^1165      ^1175      ^1185      ^1195      ^1205      ^1215      ^1225      ^1235      ^1245      

ACTGGAAATA ACATAACTCT GGACCTATTG GAACTTATAT AATTGGCGCC CAACCAACAA TCTGAACCCA CCAATCTAAT TTAACACACT TTGTCAGGCG 
^1255      ^1265      ^1275      ^1285      ^1295      ^1305      ^1315      ^1325      ^1335      ^1345      

ACAAACAGGG TAGTTAAGTT AGAAAAGCAT GTAAGTTTTA CAAGACACTT CTTTGACGCA ATCAAGAAAT TTACGAGTGA AAAAAAAAAA AAAAAAAAGT 
^1355      ^1365      ^1375      ^1385      ^1395      ^1405      ^1415      ^1425      ^1435      ^1445      

TGTGTATCTG GCCACGTAAT AAGTGTGCGT TGAATTTATT CGCAAAAACA TTGCATATTT TCGGCAAAGT AAAATTTTGT TGCATACCTT ATCAAAAAAT 
^1455      ^1465      ^1475      ^1485      ^1495      ^1505      ^1515      ^1525      ^1535      ^1545      

AAGTGCTGCA TACTTTTTAG AGAAACCAAA TAATTTTTTA TTGCATACCC GTTTTTAATA AAATACATTG CATACCCTCT TTTAATAAAA AATATTGCAT 
^1555      ^1565      ^1575      ^1585      ^1595      ^1605      ^1615      ^1625      ^1635      ^1645      

ACTTTGACGA AACAAATTTT CGTTGCATAC CCAATAAAAG ATTATTATAT TGCATACCCG TTTTTAATAA AATACATTGC ATACCCTCTT TTAATAAAAA 
^1655      ^1665      ^1675      ^1685      ^1695      ^1705      ^1715      ^1725      ^1735      ^1745      

ATATTGCATA CGTTGACGAA ACAAATTTTC GTTGCATACC CAATAAAAGA TTATTATATT GCATACCTTT TCTTGCCATA CCATTTAGCC GATCAATTGT 
^1755      ^1765      ^1775      ^1785      ^1795      ^1805      ^1815      ^1825      ^1835      ^1845      

GCTCGGCAAC AGTATATTTG TGGTGTGCCA ACCAACAACC AATGAG
^1855      ^1865      ^1875      ^1885      ^1895

Remarks:

Gypsy IRES represents the full-length (except very 5'-most Adenosine) of gypsy 5'-UTR (841 nucleotides) plus
first 5 nucleotides from the viral polyprotein.

The translation experiments:

Translation results:

IRESite Translation Id: 482

Version: `2`	Last change: `2008-07-07 19:17:02`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

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

The organism used for translation:

The temperature (in degrees of Celsia):
30

The relative translation efficiency in % of this IRES:

153.000

Name of IRES used as the positive control:

EMCV

Name of the plasmid used as the positive control. `pEMCV-D260-837`
`IRESite Id` of the plasmid used as positive control. `428`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `769`

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:

Translational data are derived from Fig. 2B using ImageJ software (http://rsbweb.nih.gov/ij/).

Citations:

Ronfort C., De Breyne S., Sandrin V., Darlix J. L., Ohlmann T. (2004) Characterization of two distinct RNA domains that regulate translation of the Drosophila gypsy retroelement. RNA. 10(3):504-515

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