IRESite_Id:442 characteristics of gypsyD2 IRES studied in pDC-delta

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `442`	Version: `3`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-07-03 14:05:48`

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_2 which comprises neomycin
phosphotransferase and truncated version of the beta-galactosidase (linearized at the AflIII site at position
3555 within pDC-delta_2; see 1423.gb below) as the first and the second cistron respectively and part of gypsy
5' UTR (nt from -312 to nt +5) 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 TAGCATAATT TTTTATTGCA TACCCGTTTT TAATAAAATA CATTGCATAC 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CCTCTTTTAA TAAAAAATAT TGCATACTTT GACGAAACAA ATTTTCGTTG CATACCCAAT AAAAGATTAT TATATTGCAT ACCCGTTTTT AATAAAATAC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ATTGCATACC CTCTTTTAAT AAAAAATATT GCATACGTTG ACGAAACAAA TTTTCGTTGC ATACCCAATA AAAGATTATT ATATTGCATA CCTTTTCTTG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CCATACCATT TAGCCGATCA ATTGTGCTCG GCAACAGTAT ATTTGTGGTG TGCCAACCAA CAACCAATGA GGCTAGCGGA TCCCGTCGTT TTACAACGTC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GTGACTGGGA AAACCCTGGC GTTACCCAAC TTAATCGCCT TGCAGCACAT CCCCCTTTCG CCAGCTGGCG TAATAGCGAA GAGGCCCGCA CCGATCGCCC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTCCCAACAG TTGCGCAGCC TGAATGGCGA ATGGCGCTTT GCCTGGTTTC CGGCACCAGA AGCGGTGCCG GAAAGCTGGC TGGAGTGCGA TCTTCCTGAG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCCGATACTG TCGTCGTCCC CTCAAACTGG CAGATGCACG GTTACGATGC GCCCATCTAC ACCAACGTAA CCTATCCCAT TACGGTCAAT CCGCCGTTTG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TTCCCACGGA GAATCCGACG GGTTGTTACT CGCTCACATT TAATGTTGAT GAAAGCTGGC TACAGGAAGG CCAGACGCGA ATTATTTTTG ATGGCGTTAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CTCGGCGTTT CATCTGTGGT GCAACGGGCG CTGGGTCGGT TACGGCCAGG ACAGTCGTTT GCCGTCTGAA TTTGACCTGA GCGCATTTTT ACGCGCCGGA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GAAAACCGCC TCGCGGTGAT GGTGCTGCGT TGGAGTGACG GCAGTTATCT GGAAGATCAG GATATGTGGC GGATGAGCGG CATTTTCCGT GACGTCTCGT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGCTGCATAA ACCGACTACA CAAATCAGCG ATTTCCATGT TGCCACTCGC TTTAATGATG ATTTCAGCCG CGCTGTACTG GAGGCTGAAG TTCAGATGTG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGGCGAGTTG CGTGACTACC TACGGGTAAC AGTTTCTTTA TGGCAGGGTG AAACGCAGGT CGCCAGCGGC ACCGCGCCTT TCGGCGGTGA AATTATCGAT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GAGCGTGGTG GTTATGCCGA TCGCGTCACA CTACGTCTGA ACGTCGAAAA CCCGAAACTG TGGAGCGCCG AAATCCCGAA TCTCTATCGT GCGGTGGTTG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AACTGCACAC CGCCGACGGC ACGCTGATTG AAGCAGAAGC CTGCGATGTC GGTTTCCGCG AGGTGCGGAT TGAAAATGGT CTGCTGCTGC TGAACGGCAA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GCCGTTGCTG ATTCGAGGCG TTAACCGTCA CGAGCATCAT CCTCTGCATG GTCAGGTCAT GGATGAGCAG ACGATGGTGC AGGATATCCT GCTGATGAAG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CAGAACAACT TTAACGCCGT GCGCTGTTCG CATTATCCGA ACCATCCGCT GTGGTACACG CTGTGCGACC GCTACGGCCT GTATGTGGTG GATGAAGCCA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATATTGAAAC CCACGGCATG GTGCCAATGA ATCGTCTGAC CGATGATCCG CGCTGGCTAC CGGCGATGAG CGAA
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pDC-delta_2 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 -312 to nt +5) 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 TAGCATAATT TTTTATTGCA TACCCGTTTT TAATAAAATA CATTGCATAC CCTCTTTTAA TAAAAAATAT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TGCATACTTT GACGAAACAA ATTTTCGTTG CATACCCAAT AAAAGATTAT TATATTGCAT ACCCGTTTTT AATAAAATAC ATTGCATACC CTCTTTTAAT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAAAAATATT GCATACGTTG ACGAAACAAA TTTTCGTTGC ATACCCAATA AAAGATTATT ATATTGCATA CCTTTTCTTG CCATACCATT TAGCCGATCA 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

ATTGTGCTCG GCAACAGTAT ATTTGTGGTG TGCCAACCAA CAACCAATGA GGCTAGCGGA TCCCGTCGTT TTACAACGTC GTGACTGGGA AAACCCTGGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GTTACCCAAC TTAATCGCCT TGCAGCACAT CCCCCTTTCG CCAGCTGGCG TAATAGCGAA GAGGCCCGCA CCGATCGCCC TTCCCAACAG TTGCGCAGCC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGAATGGCGA ATGGCGCTTT GCCTGGTTTC CGGCACCAGA AGCGGTGCCG GAAAGCTGGC TGGAGTGCGA TCTTCCTGAG GCCGATACTG TCGTCGTCCC 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

CTCAAACTGG CAGATGCACG GTTACGATGC GCCCATCTAC ACCAACGTAA CCTATCCCAT TACGGTCAAT CCGCCGTTTG TTCCCACGGA GAATCCGACG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GGTTGTTACT CGCTCACATT TAATGTTGAT GAAAGCTGGC TACAGGAAGG CCAGACGCGA ATTATTTTTG ATGGCGTTAA CTCGGCGTTT CATCTGTGGT 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCAACGGGCG CTGGGTCGGT TACGGCCAGG ACAGTCGTTT GCCGTCTGAA TTTGACCTGA GCGCATTTTT ACGCGCCGGA GAAAACCGCC TCGCGGTGAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GGTGCTGCGT TGGAGTGACG GCAGTTATCT GGAAGATCAG GATATGTGGC GGATGAGCGG CATTTTCCGT GACGTCTCGT TGCTGCATAA ACCGACTACA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CAAATCAGCG ATTTCCATGT TGCCACTCGC TTTAATGATG ATTTCAGCCG CGCTGTACTG GAGGCTGAAG TTCAGATGTG CGGCGAGTTG CGTGACTACC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TACGGGTAAC AGTTTCTTTA TGGCAGGGTG AAACGCAGGT CGCCAGCGGC ACCGCGCCTT TCGGCGGTGA AATTATCGAT GAGCGTGGTG GTTATGCCGA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

TCGCGTCACA CTACGTCTGA ACGTCGAAAA CCCGAAACTG TGGAGCGCCG AAATCCCGAA TCTCTATCGT GCGGTGGTTG AACTGCACAC CGCCGACGGC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ACGCTGATTG AAGCAGAAGC CTGCGATGTC GGTTTCCGCG AGGTGCGGAT TGAAAATGGT CTGCTGCTGC TGAACGGCAA GCCGTTGCTG ATTCGAGGCG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TTAACCGTCA CGAGCATCAT CCTCTGCATG GTCAGGTCAT GGATGAGCAG ACGATGGTGC AGGATATCCT GCTGATGAAG CAGAACAACT TTAACGCCGT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GCGCTGTTCG CATTATCCGA ACCATCCGCT GTGGTACACG CTGTGCGACC GCTACGGCCT GTATGTGGTG GATGAAGCCA ATATTGAAAC CCACGGCATG 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GTGCCAATGA ATCGTCTGAC CGATGATCCG CGCTGGCTAC CGGCGATGAG CGAACGCGTA ACGCGAATGG TGCAGCGCGA TCGTAATCAC CCGAGTGTGA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TCATCTGGTC GCTGGGGAAT GAATCAGGCC ACGGCGCTAA TCACGACGCG CTGTATCGCT GGATCAAATC TGTCGATCCT TCCCGCCCGG TGCAGTATGA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AGGCGGCGGA GCCGACACCA CGGCCACCGA TATTATTTGC CCGATGTACG CGCGCGTGGA TGAAGACCAG CCCTTCCCGG CTGTGCCGAA ATGGTCCATC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AAAAAATGGC TTTCGCTACC TGGAGAGACG CGCCCGCTGA TCCTTTGCGA ATACGCCCAC GCGATGGGTA ACAGTCTTGG CGGTTTCGCT AAATACTGGC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AGGCGTTTCG TCAGTATCCC CGTTTACAGG GCGGCTTCGT CTGGGACTGG GTGGATCAGT CGCTGATTAA ATATGATGAA AACGGCAACC CGTGGTCGGC 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TTACGGCGGT GATTTTGGCG ATACGCCGAA CGATCGCCAG TTCTGTATGA ACGGTCTGGT CTTTGCCGAC CGCACGCCGC ATCCAGCGCT GACGGAAGCA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

AAACACCAGC AGCAGTTTTT CCAGTTCCGT TTATCCGGGC AAACCATCGA AGTGACCAGC GAATACCTGT TCCGTCAATG CGATAACGAG CTCCTGCACT 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

GGATGGTGGC GCTGGATGGT AAGCCGCTGG CAAGCGGTGA AGTGCCTCTG GATGTCGCTC CACAAGGTAA ACAGTTGATT GAACTGCCTG AACTACCGCA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GCCGGAGAGC GCCGGGCAAC TCTGGCTCAC AGTACGCGTA GTGCAACCGA ACGCGACCGC ATGGTCAGAA GCCGGGCACA TCAGCGCCTG GCAGCAGTGG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CGTCTGGCGG AAAACCTCAG TGTGACGCTC CCCGCCGCGT CCCACGCCAT CCCGCATCTG ACCACCAGCG AAATGGATTT TTGCATCGAG CTGGGTAATA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AGCGTTGGCA ATTTAACCGC CAGTCAGGCT TTCTTTCACA GATGTGGATT GGCGATAAAA AACAACTGCT GACGCCGCTG CGCGATCAGT TCACCCGTGC 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

ACCGCTGGAT AACGACATTG GCGTAAGTGA AGCGACCCGC ATTGACCCTA ACGCCTGGGT CGAACGCTGG AAGGCGGCGG GCCATTACCA GGCCGAAGCA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

GCGTTGTTGC AGTGCACGGC AGATACACTT GCTGATGCGG TGCTGATTAC GACCGCTACC GCGTGGCAGC ATCAGGGGAA AACCTTATTT ATCAGCCGGA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

AAACCTACCG GATTGATGGT AGTGGTCAAA TGGCGATTAC CGTTGATGTT GAAGTGGCGA GCGATACACC GCATCCGGCG CGGATTGGCC TGAACTGCCA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GCTGGCGCAG GTAGCAGAGC GGGTAAACTG GCTCGGATTA GGGCCGCAAG AAAACTATCC CGACCGCCTT ACTGCCGCCT GTTTTGACCG CTGGGATCTG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

CCATTGTCAG ACATGTATAC CCCGTACGTC TTCCCGAGCG AAAACGGTCT GCGCTGCGGG ACGCGCGAAT TGAATTATGG CCCACACCAG TGGCGCGGCG 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ACTTCCAGTT CAACATCAGC CGCTACAGTC AACAGCAACT GATGGAAACC AGCCATCGCC ATCTGCTGGA CGCGGAAGAA GGCACATGGC TGAATATCGA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CGGTTTCCAT ATGGGGATTG GTGGCGACGA CTCCTGGAGC CCGTCAGTAT CGGCGGAATT CCAGCTGAGC GCCGGTCGCT CAAATTACCA GTTGGTCTGG 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TGTCAAAAAT AATAATAACC GGGCAGGGGG GATCCGTCGA AGATCAGGTT ATCGATAAAA TAAAAGATTT TATTTAGTCT CCAGAAAAAG GGGGGAATGA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

AAGACCCCAC CTGTAGGTTT GGCAAGCTAG TTCTAGAGGG CCCTATTCTA TAGTGTCACC TAAATGCTAG AGCTCGCTGA TCAGCCTCGA CTGTGCCTTC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TAGTTGCCAG CCATCTGTTG TTTGCCCCTC CCCCGTGCCT TCCTTGACCC TGGAAGGTGC CACTCCCACT GTCCTTTCCT AATAAAATGA GGAAATTGCA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

TCGCATTGTC TGAGTAGGTG TCATTCTATT CTGGGGGGTG GGGTGGGGCA GGACAGCAAG GGGGAGGATT GGGAAGACAA TAGCAGGCAT GCTGGGGATG 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

CGGTGGGCTC TATGGCTTCT GAGGCGGAAA GAACCAGCTG GGGCTCGAGG GGGATCCCGT CGACCTCGAG AGCTTGGCGT AATCATGGTC ATAGCTGTTT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CCTGTGTGAA ATTGTTATCC GCTCACAATT CCACACAACA TACGAGCCGG AAGCATAAAG TGTAAAGCCT GGGGTGCCTA ATGAGTGAGC TAACTCACAT 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

TAATTGCGTT GCGCTCACTG CCCGCTTTCC AGTCGGGAAA CCTGTCGTGC CAGCTGCATT AATGAATCGG CCAACGCGCG GGGAGAGGCG GTTTGCGTAT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

TGGGCGCTCT TCCGCTTCCT CGCTCACTGA CTCGCTGCGC TCGGTCGTTC GGCTGCGGCG AGCGGTATCA GCTCACTCAA AGGCGGTAAT ACGGTTATCC 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ACAGAATCAG GGGATAACGC AGGAAAGAAC ATGTGAGCAA AAGGCCAGCA AAAGGCCAGG AACCGTAAAA AGGCCGCGTT GCTGGCGTTT TTCCATAGGC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TCCGCCCCCC TGACGAGCAT CACAAAAATC GACGCTCAAG TCAGAGGTGG CGAAACCCGA CAGGACTATA AAGATACCAG GCGTTTCCCC CTGGAAGCTC 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

CCTCGTGCGC TCTCCTGTTC CGACCCTGCC GCTTACCGGA TACCTGTCCG CCTTTCTCCC TTCGGGAAGC GTGGCGCTTT CTCAATGCTC ACGCTGTAGG 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

TATCTCAGTT CGGTGTAGGT CGTTCGCTCC AAGCTGGGCT GTGTGCACGA ACCCCCCGTT CAGCCCGACC GCTGCGCCTT ATCCGGTAAC TATCGTCTTG 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

AGTCCAACCC GGTAAGACAC GACTTATCGC CACTGGCAGC AGCCACTGGT AACAGGATTA GCAGAGCGAG GTATGTAGGC GGTGCTACAG AGTTCTTGAA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GTGGTGGCCT AACTACGGCT ACACTAGAAG GACAGTATTT GGTATCTGCG CTCTGCTGAA GCCAGTTACC TTCGGAAAAA GAGTTGGTAG CTCTTGATCC 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GGCAAACAAA CCACCGCTGG TAGCGGTGGT TTTTTTGTTT GCAAGCAGCA GATTACGCGC AGAAAAAAAG GATCTCAAGA AGATCCTTTG ATCTTTTCTA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

CGGGGTCTGA CGCTCAGTGG AACGAAAACT CACGTTAAGG GATTTTGGTC ATGAGATTAT CAAAAAGGAT CTTCACCTAG ATCCTTTTAA ATTAAAAATG 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

AAGTTTTAAA TCAATCTAAA GTATATATGA GTAAACTTGG TCTGACAGTT ACCAATGCTT AATCAGTGAG GCACCTATCT CAGCGATCTG TCTATTTCGT 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

TCATCCATAG TTGCCTGACT CCCCGTCGTG TAGATAACTA CGATACGGGA GGGCTTACCA TCTGGCCCCA GTGCTGCAAT GATACCGCGA GACCCACGCT 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CACCGGCTCC AGATTTATCA GCAATAAACC AGCCAGCCGG AAGGGCCGAG CGCAGAAGTG GTCCTGCAAC TTTATCCGCC TCCATCCAGT CTATTAATTG 
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191      

TTGCCGGGAA GCTAGAGTAA GTAGTTCGCC AGTTAATAGT TTGCGCAACG TTGTTGCCAT TGCTACAGGC ATCGTGGTGT CACGCTCGTC GTTTGGTATG 
^7201      ^7211      ^7221      ^7231      ^7241      ^7251      ^7261      ^7271      ^7281      ^7291      

GCTTCATTCA GCTCCGGTTC CCAACGATCA AGGCGAGTTA CATGATCCCC CATGTTGTGC AAAAAAGCGG TTAGCTCCTT CGGTCCTCCG ATCGTTGTCA 
^7301      ^7311      ^7321      ^7331      ^7341      ^7351      ^7361      ^7371      ^7381      ^7391      

GAAGTAAGTT GGCCGCAGTG TTATCACTCA TGGTTATGGC AGCACTGCAT AATTCTCTTA CTGTCATGCC ATCCGTAAGA TGCTTTTCTG TGACTGGTGA 
^7401      ^7411      ^7421      ^7431      ^7441      ^7451      ^7461      ^7471      ^7481      ^7491      

GTACTCAACC AAGTCATTCT GAGAATAGTG TATGCGGCGA CCGAGTTGCT CTTGCCCGGC GTCAATACGG GATAATACCG CGCCACATAG CAGAACTTTA 
^7501      ^7511      ^7521      ^7531      ^7541      ^7551      ^7561      ^7571      ^7581      ^7591      

AAAGTGCTCA TCATTGGAAA ACGTTCTTCG GGGCGAAAAC TCTCAAGGAT CTTACCGCTG TTGAGATCCA GTTCGATGTA ACCCACTCGT GCACCCAACT 
^7601      ^7611      ^7621      ^7631      ^7641      ^7651      ^7661      ^7671      ^7681      ^7691      

GATCTTCAGC ATCTTTTACT TTCACCAGCG TTTCTGGGTG AGCAAAAACA GGAAGGCAAA ATGCCGCAAA AAAGGGAATA AGGGCGACAC GGAAATGTTG 
^7701      ^7711      ^7721      ^7731      ^7741      ^7751      ^7761      ^7771      ^7781      ^7791      

AATACTCATA CTCTTCCTTT TTCAATATTA TTGAAGCATT TATCAGGGTT ATTGTCTCAT GAGCGGATAC ATATTTGAAT GTATTTAGAA AAATAAACAA 
^7801      ^7811      ^7821      ^7831      ^7841      ^7851      ^7861      ^7871      ^7881      ^7891      

ATAGGGGTTC CGCGCACATT TCCCCGAAAA GTGCCACCTG ACGTC
^7901      ^7911      ^7921      ^7931      ^7941

GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:

The total number of notable open-reading frames (ORFs):

1

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `1`	Last change: `2008-07-03 14:05:48`
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

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 08:14:23`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `gypsyD2`	The functional status of IRES: `functional`

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

1055-1371

How IRES boundaries were determined:
experimentally_determined

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

ATAATTTTTT ATTGCATACC CGTTTTTAAT AAAATACATT GCATACCCTC TTTTAATAAA AAATATTGCA TACTTTGACG AAACAAATTT TCGTTGCATA 
^1055      ^1065      ^1075      ^1085      ^1095      ^1105      ^1115      ^1125      ^1135      ^1145      

CCCAATAAAA GATTATTATA TTGCATACCC GTTTTTAATA AAATACATTG CATACCCTCT TTTAATAAAA AATATTGCAT ACGTTGACGA AACAAATTTT 
^1155      ^1165      ^1175      ^1185      ^1195      ^1205      ^1215      ^1225      ^1235      ^1245      

CGTTGCATAC CCAATAAAAG ATTATTATAT TGCATACCTT TTCTTGCCAT ACCATTTAGC CGATCAATTG TGCTCGGCAA CAGTATATTT GTGGTGTGCC 
^1255      ^1265      ^1275      ^1285      ^1295      ^1305      ^1315      ^1325      ^1335      ^1345      

AACCAACAAC CAATGAG
^1355      ^1365

Remarks:

Gypsy IRES represents part of gypsy 5' UTR (nt from -312 to nt +5).

The translation experiments:

Translation results:

IRESite Translation Id: 485

Version: `2`	Last change: `2008-07-08 09:10:07`
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:

104.000

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