IRESite_Id:444 characteristics of gypsyD3 IRES studied in pDC-delta

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `444`	Version: `3`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-07-07 12:33:41`

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:

In vitro T7 run-off transcript produced from bicistronic plasmid pDC-delta_3 which comprises neomycin
phosphotransferase and truncated version of the beta-galactosidase (linearized at the AflIII site at position
3421 within pDC-delta_3; see 1431.gb below) as the first and the second cistron respectively and part of gypsy
5' UTR (nt from -178 to nt +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 TAGCTTAATA AAATACATTG CATACCCTCT TTTAATAAAA AATATTGCAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACGTTGACGA AACAAATTTT CGTTGCATAC CCAATAAAAG ATTATTATAT TGCATACCTT TTCTTGCCAT ACCATTTAGC CGATCAATTG TGCTCGGCAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CAGTATATTT GTGGTGTGCC AACCAACAAC CAATGAGGCT AGCGGATCCC GTCGTTTTAC AACGTCGTGA CTGGGAAAAC CCTGGCGTTA CCCAACTTAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TCGCCTTGCA GCACATCCCC CTTTCGCCAG CTGGCGTAAT AGCGAAGAGG CCCGCACCGA TCGCCCTTCC CAACAGTTGC GCAGCCTGAA TGGCGAATGG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CGCTTTGCCT GGTTTCCGGC ACCAGAAGCG GTGCCGGAAA GCTGGCTGGA GTGCGATCTT CCTGAGGCCG ATACTGTCGT CGTCCCCTCA AACTGGCAGA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TGCACGGTTA CGATGCGCCC ATCTACACCA ACGTAACCTA TCCCATTACG GTCAATCCGC CGTTTGTTCC CACGGAGAAT CCGACGGGTT GTTACTCGCT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CACATTTAAT GTTGATGAAA GCTGGCTACA GGAAGGCCAG ACGCGAATTA TTTTTGATGG CGTTAACTCG GCGTTTCATC TGTGGTGCAA CGGGCGCTGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GTCGGTTACG GCCAGGACAG TCGTTTGCCG TCTGAATTTG ACCTGAGCGC ATTTTTACGC GCCGGAGAAA ACCGCCTCGC GGTGATGGTG CTGCGTTGGA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTGACGGCAG TTATCTGGAA GATCAGGATA TGTGGCGGAT GAGCGGCATT TTCCGTGACG TCTCGTTGCT GCATAAACCG ACTACACAAA TCAGCGATTT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CCATGTTGCC ACTCGCTTTA ATGATGATTT CAGCCGCGCT GTACTGGAGG CTGAAGTTCA GATGTGCGGC GAGTTGCGTG ACTACCTACG GGTAACAGTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TCTTTATGGC AGGGTGAAAC GCAGGTCGCC AGCGGCACCG CGCCTTTCGG CGGTGAAATT ATCGATGAGC GTGGTGGTTA TGCCGATCGC GTCACACTAC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GTCTGAACGT CGAAAACCCG AAACTGTGGA GCGCCGAAAT CCCGAATCTC TATCGTGCGG TGGTTGAACT GCACACCGCC GACGGCACGC TGATTGAAGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AGAAGCCTGC GATGTCGGTT TCCGCGAGGT GCGGATTGAA AATGGTCTGC TGCTGCTGAA CGGCAAGCCG TTGCTGATTC GAGGCGTTAA CCGTCACGAG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CATCATCCTC TGCATGGTCA GGTCATGGAT GAGCAGACGA TGGTGCAGGA TATCCTGCTG ATGAAGCAGA ACAACTTTAA CGCCGTGCGC TGTTCGCATT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ATCCGAACCA TCCGCTGTGG TACACGCTGT GCGACCGCTA CGGCCTGTAT GTGGTGGATG AAGCCAATAT TGAAACCCAC GGCATGGTGC CAATGAATCG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TCTGACCGAT GATCCGCGCT GGCTACCGGC GATGAGCGAA
^2501      ^2511      ^2521      ^2531

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pDC-delta_3 The name of the promoter used to express this mRNA:
T7

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing part of gypsy 5' UTR (nt from -178 to nt +5 of the original sequence) mRNA 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 TAGCTTAATA AAATACATTG CATACCCTCT TTTAATAAAA AATATTGCAT ACGTTGACGA AACAAATTTT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CGTTGCATAC CCAATAAAAG ATTATTATAT TGCATACCTT TTCTTGCCAT ACCATTTAGC CGATCAATTG TGCTCGGCAA CAGTATATTT GTGGTGTGCC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AACCAACAAC CAATGAGGCT AGCGGATCCC GTCGTTTTAC AACGTCGTGA CTGGGAAAAC CCTGGCGTTA CCCAACTTAA TCGCCTTGCA GCACATCCCC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CTTTCGCCAG CTGGCGTAAT AGCGAAGAGG CCCGCACCGA TCGCCCTTCC CAACAGTTGC GCAGCCTGAA TGGCGAATGG CGCTTTGCCT GGTTTCCGGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ACCAGAAGCG GTGCCGGAAA GCTGGCTGGA GTGCGATCTT CCTGAGGCCG ATACTGTCGT CGTCCCCTCA AACTGGCAGA TGCACGGTTA CGATGCGCCC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ATCTACACCA ACGTAACCTA TCCCATTACG GTCAATCCGC CGTTTGTTCC CACGGAGAAT CCGACGGGTT GTTACTCGCT CACATTTAAT GTTGATGAAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GCTGGCTACA GGAAGGCCAG ACGCGAATTA TTTTTGATGG CGTTAACTCG GCGTTTCATC TGTGGTGCAA CGGGCGCTGG GTCGGTTACG GCCAGGACAG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TCGTTTGCCG TCTGAATTTG ACCTGAGCGC ATTTTTACGC GCCGGAGAAA ACCGCCTCGC GGTGATGGTG CTGCGTTGGA GTGACGGCAG TTATCTGGAA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GATCAGGATA TGTGGCGGAT GAGCGGCATT TTCCGTGACG TCTCGTTGCT GCATAAACCG ACTACACAAA TCAGCGATTT CCATGTTGCC ACTCGCTTTA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ATGATGATTT CAGCCGCGCT GTACTGGAGG CTGAAGTTCA GATGTGCGGC GAGTTGCGTG ACTACCTACG GGTAACAGTT TCTTTATGGC AGGGTGAAAC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GCAGGTCGCC AGCGGCACCG CGCCTTTCGG CGGTGAAATT ATCGATGAGC GTGGTGGTTA TGCCGATCGC GTCACACTAC GTCTGAACGT CGAAAACCCG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

AAACTGTGGA GCGCCGAAAT CCCGAATCTC TATCGTGCGG TGGTTGAACT GCACACCGCC GACGGCACGC TGATTGAAGC AGAAGCCTGC GATGTCGGTT 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TCCGCGAGGT GCGGATTGAA AATGGTCTGC TGCTGCTGAA CGGCAAGCCG TTGCTGATTC GAGGCGTTAA CCGTCACGAG CATCATCCTC TGCATGGTCA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GGTCATGGAT GAGCAGACGA TGGTGCAGGA TATCCTGCTG ATGAAGCAGA ACAACTTTAA CGCCGTGCGC TGTTCGCATT ATCCGAACCA TCCGCTGTGG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TACACGCTGT GCGACCGCTA CGGCCTGTAT GTGGTGGATG AAGCCAATAT TGAAACCCAC GGCATGGTGC CAATGAATCG TCTGACCGAT GATCCGCGCT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GGCTACCGGC GATGAGCGAA CGCGTAACGC GAATGGTGCA GCGCGATCGT AATCACCCGA GTGTGATCAT CTGGTCGCTG GGGAATGAAT CAGGCCACGG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

CGCTAATCAC GACGCGCTGT ATCGCTGGAT CAAATCTGTC GATCCTTCCC GCCCGGTGCA GTATGAAGGC GGCGGAGCCG ACACCACGGC CACCGATATT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ATTTGCCCGA TGTACGCGCG CGTGGATGAA GACCAGCCCT TCCCGGCTGT GCCGAAATGG TCCATCAAAA AATGGCTTTC GCTACCTGGA GAGACGCGCC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CGCTGATCCT TTGCGAATAC GCCCACGCGA TGGGTAACAG TCTTGGCGGT TTCGCTAAAT ACTGGCAGGC GTTTCGTCAG TATCCCCGTT TACAGGGCGG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CTTCGTCTGG GACTGGGTGG ATCAGTCGCT GATTAAATAT GATGAAAACG GCAACCCGTG GTCGGCTTAC GGCGGTGATT TTGGCGATAC GCCGAACGAT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

CGCCAGTTCT GTATGAACGG TCTGGTCTTT GCCGACCGCA CGCCGCATCC AGCGCTGACG GAAGCAAAAC ACCAGCAGCA GTTTTTCCAG TTCCGTTTAT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CCGGGCAAAC CATCGAAGTG ACCAGCGAAT ACCTGTTCCG TCAATGCGAT AACGAGCTCC TGCACTGGAT GGTGGCGCTG GATGGTAAGC CGCTGGCAAG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CGGTGAAGTG CCTCTGGATG TCGCTCCACA AGGTAAACAG TTGATTGAAC TGCCTGAACT ACCGCAGCCG GAGAGCGCCG GGCAACTCTG GCTCACAGTA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CGCGTAGTGC AACCGAACGC GACCGCATGG TCAGAAGCCG GGCACATCAG CGCCTGGCAG CAGTGGCGTC TGGCGGAAAA CCTCAGTGTG ACGCTCCCCG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CCGCGTCCCA CGCCATCCCG CATCTGACCA CCAGCGAAAT GGATTTTTGC ATCGAGCTGG GTAATAAGCG TTGGCAATTT AACCGCCAGT CAGGCTTTCT 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TTCACAGATG TGGATTGGCG ATAAAAAACA ACTGCTGACG CCGCTGCGCG ATCAGTTCAC CCGTGCACCG CTGGATAACG ACATTGGCGT AAGTGAAGCG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

ACCCGCATTG ACCCTAACGC CTGGGTCGAA CGCTGGAAGG CGGCGGGCCA TTACCAGGCC GAAGCAGCGT TGTTGCAGTG CACGGCAGAT ACACTTGCTG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ATGCGGTGCT GATTACGACC GCTACCGCGT GGCAGCATCA GGGGAAAACC TTATTTATCA GCCGGAAAAC CTACCGGATT GATGGTAGTG GTCAAATGGC 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GATTACCGTT GATGTTGAAG TGGCGAGCGA TACACCGCAT CCGGCGCGGA TTGGCCTGAA CTGCCAGCTG GCGCAGGTAG CAGAGCGGGT AAACTGGCTC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

GGATTAGGGC CGCAAGAAAA CTATCCCGAC CGCCTTACTG CCGCCTGTTT TGACCGCTGG GATCTGCCAT TGTCAGACAT GTATACCCCG TACGTCTTCC 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CGAGCGAAAA CGGTCTGCGC TGCGGGACGC GCGAATTGAA TTATGGCCCA CACCAGTGGC GCGGCGACTT CCAGTTCAAC ATCAGCCGCT ACAGTCAACA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GCAACTGATG GAAACCAGCC ATCGCCATCT GCTGGACGCG GAAGAAGGCA CATGGCTGAA TATCGACGGT TTCCATATGG GGATTGGTGG CGACGACTCC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TGGAGCCCGT CAGTATCGGC GGAATTCCAG CTGAGCGCCG GTCGCTCAAA TTACCAGTTG GTCTGGTGTC AAAAATAATA ATAACCGGGC AGGGGGGATC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CGTCGAAGAT CAGGTTATCG ATAAAATAAA AGATTTTATT TAGTCTCCAG AAAAAGGGGG GAATGAAAGA CCCCACCTGT AGGTTTGGCA AGCTAGTTCT 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

AGAGGGCCCT ATTCTATAGT GTCACCTAAA TGCTAGAGCT CGCTGATCAG CCTCGACTGT GCCTTCTAGT TGCCAGCCAT CTGTTGTTTG CCCCTCCCCC 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GTGCCTTCCT TGACCCTGGA AGGTGCCACT CCCACTGTCC TTTCCTAATA AAATGAGGAA ATTGCATCGC ATTGTCTGAG TAGGTGTCAT TCTATTCTGG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

GGGGTGGGGT GGGGCAGGAC AGCAAGGGGG AGGATTGGGA AGACAATAGC AGGCATGCTG GGGATGCGGT GGGCTCTATG GCTTCTGAGG CGGAAAGAAC 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

CAGCTGGGGC TCGAGGGGGA TCCCGTCGAC CTCGAGAGCT TGGCGTAATC ATGGTCATAG CTGTTTCCTG TGTGAAATTG TTATCCGCTC ACAATTCCAC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ACAACATACG AGCCGGAAGC ATAAAGTGTA AAGCCTGGGG TGCCTAATGA GTGAGCTAAC TCACATTAAT TGCGTTGCGC TCACTGCCCG CTTTCCAGTC 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

GGGAAACCTG TCGTGCCAGC TGCATTAATG AATCGGCCAA CGCGCGGGGA GAGGCGGTTT GCGTATTGGG CGCTCTTCCG CTTCCTCGCT CACTGACTCG 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CTGCGCTCGG TCGTTCGGCT GCGGCGAGCG GTATCAGCTC ACTCAAAGGC GGTAATACGG TTATCCACAG AATCAGGGGA TAACGCAGGA AAGAACATGT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

GAGCAAAAGG CCAGCAAAAG GCCAGGAACC GTAAAAAGGC CGCGTTGCTG GCGTTTTTCC ATAGGCTCCG CCCCCCTGAC GAGCATCACA AAAATCGACG 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CTCAAGTCAG AGGTGGCGAA ACCCGACAGG ACTATAAAGA TACCAGGCGT TTCCCCCTGG AAGCTCCCTC GTGCGCTCTC CTGTTCCGAC CCTGCCGCTT 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

ACCGGATACC TGTCCGCCTT TCTCCCTTCG GGAAGCGTGG CGCTTTCTCA ATGCTCACGC TGTAGGTATC TCAGTTCGGT GTAGGTCGTT CGCTCCAAGC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TGGGCTGTGT GCACGAACCC CCCGTTCAGC CCGACCGCTG CGCCTTATCC GGTAACTATC GTCTTGAGTC CAACCCGGTA AGACACGACT TATCGCCACT 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

GGCAGCAGCC ACTGGTAACA GGATTAGCAG AGCGAGGTAT GTAGGCGGTG CTACAGAGTT CTTGAAGTGG TGGCCTAACT ACGGCTACAC TAGAAGGACA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

GTATTTGGTA TCTGCGCTCT GCTGAAGCCA GTTACCTTCG GAAAAAGAGT TGGTAGCTCT TGATCCGGCA AACAAACCAC CGCTGGTAGC GGTGGTTTTT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

TTGTTTGCAA GCAGCAGATT ACGCGCAGAA AAAAAGGATC TCAAGAAGAT CCTTTGATCT TTTCTACGGG GTCTGACGCT CAGTGGAACG AAAACTCACG 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

TTAAGGGATT TTGGTCATGA GATTATCAAA AAGGATCTTC ACCTAGATCC TTTTAAATTA AAAATGAAGT TTTAAATCAA TCTAAAGTAT ATATGAGTAA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

ACTTGGTCTG ACAGTTACCA ATGCTTAATC AGTGAGGCAC CTATCTCAGC GATCTGTCTA TTTCGTTCAT CCATAGTTGC CTGACTCCCC GTCGTGTAGA 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

TAACTACGAT ACGGGAGGGC TTACCATCTG GCCCCAGTGC TGCAATGATA CCGCGAGACC CACGCTCACC GGCTCCAGAT TTATCAGCAA TAAACCAGCC 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

AGCCGGAAGG GCCGAGCGCA GAAGTGGTCC TGCAACTTTA TCCGCCTCCA TCCAGTCTAT TAATTGTTGC CGGGAAGCTA GAGTAAGTAG TTCGCCAGTT 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

AATAGTTTGC GCAACGTTGT TGCCATTGCT ACAGGCATCG TGGTGTCACG CTCGTCGTTT GGTATGGCTT CATTCAGCTC CGGTTCCCAA CGATCAAGGC 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

GAGTTACATG ATCCCCCATG TTGTGCAAAA AAGCGGTTAG CTCCTTCGGT CCTCCGATCG TTGTCAGAAG TAAGTTGGCC GCAGTGTTAT CACTCATGGT 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

TATGGCAGCA CTGCATAATT CTCTTACTGT CATGCCATCC GTAAGATGCT TTTCTGTGAC TGGTGAGTAC TCAACCAAGT CATTCTGAGA ATAGTGTATG 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

CGGCGACCGA GTTGCTCTTG CCCGGCGTCA ATACGGGATA ATACCGCGCC ACATAGCAGA ACTTTAAAAG TGCTCATCAT TGGAAAACGT TCTTCGGGGC 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

GAAAACTCTC AAGGATCTTA CCGCTGTTGA GATCCAGTTC GATGTAACCC ACTCGTGCAC CCAACTGATC TTCAGCATCT TTTACTTTCA CCAGCGTTTC 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

TGGGTGAGCA AAAACAGGAA GGCAAAATGC CGCAAAAAAG GGAATAAGGG CGACACGGAA ATGTTGAATA CTCATACTCT TCCTTTTTCA ATATTATTGA 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

AGCATTTATC AGGGTTATTG TCTCATGAGC GGATACATAT TTGAATGTAT TTAGAAAAAT AAACAAATAG GGGTTCCGCG CACATTTCCC CGAAAAGTGC 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

CACCTGACGT C
^7801      ^7811

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: `2008-07-03 14:04:53`
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

ORF

ORF position:

2

Version: `0`
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):

1233-2540

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 12:33:41`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `gypsyD3`	The functional status of IRES: `defective`

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

1055-1237

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: `379`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-178`	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):

TTAATAAAAT ACATTGCATA CCCTCTTTTA ATAAAAAATA TTGCATACGT TGACGAAACA AATTTTCGTT GCATACCCAA TAAAAGATTA TTATATTGCA 
^1055      ^1065      ^1075      ^1085      ^1095      ^1105      ^1115      ^1125      ^1135      ^1145      

TACCTTTTCT TGCCATACCA TTTAGCCGAT CAATTGTGCT CGGCAACAGT ATATTTGTGG TGTGCCAACC AACAACCAAT GAG
^1155      ^1165      ^1175      ^1185      ^1195      ^1205      ^1215      ^1225      ^1235

Remarks:

Gypsy_-178/+5 IRES represents part of gypsy 5' UTR (nt from -178 to nt +5 of the original sequence).

The translation experiments:

Translation results:

IRESite Translation Id: 487

Version: `1`	Last change: `2008-07-08 09:10:27`
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:

44.000

Name of IRES used as the positive control:

gypsy

Name of the plasmid used as the positive control. `pDC-WT`
`IRESite Id` of the plasmid used as positive control. `439`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `1037`

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. 4B 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