IRESite_Id:464 characteristics of gypsyD1 IRES studied in pMC-delta

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `464`	Version: `2`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-07-08 09:16:26`

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 vivo CMV driven transcript produced from monocistronic plasmid pMC-delta_1 containing part of gypsy
5' UTR (nt from -511 to nt +5 of the original sequence) mRNA cloned upstream of the beta-galactosidase.

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

TGCTTAACTG GCTTATCGAA ATTAATACGA CTCACTATAG GGAGACCCaa gcttgatGGG CTCGATCCCC TCGAGCTAGC Ggtaagtttt acaagacact 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tctttgacgc aatcaagaaa tttacgagtg aaaaaaaaaa aaaaaaaaag ttgtgtatct ggccacgtaa taagtgtgcg ttgaatttat tcgcaaaaac 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

attgcatatt ttcggcaaag taaaattttg ttgcatacct tatcaaaaaa taagtgctgc atacttttta gagaaaccaa ataatttttt attgcatacc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

cgtttttaat aaaatacatt gcataccctc ttttaataaa aaatattgca tactttgacg aaacaaattt tcgttgcata cccaataaaa gattattata 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ttgcataccc gtttttaata aaatacattg cataccctct tttaataaaa aatattgcat acgttgacga aacaaatttt cgttgcatac ccaataaaag 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

attattatat tgcatacctt ttcttgccat accatttagc cgatcaattg tgctcggcaa cagtatattt gtggtgtgcc aaccaacaac caatgagGCT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AGCGGATCCC GTCGTTTTAC AACGTCGTGA CTGGGAAAAC CCTGGCGTTA CCCAACTTAA TCGCCTTGCA GCACATCCCC CTTTCGCCAG CTGGCGTAAT 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

AGCGAAGAGG CCCGCACCGA TCGCCCTTCC CAACAGTTGC GCAGCCTGAA TGGCGAATGG CGCTTTGCCT GGTTTCCGGC ACCAGAAGCG GTGCCGGAAA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GCTGGCTGGA GTGCGATCTT CCTGAGGCCG ATACTGTCGT CGTCCCCTCA AACTGGCAGA TGCACGGTTA CGATGCGCCC ATCTACACCA ACGTAACCTA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCCCATTACG GTCAATCCGC CGTTTGTTCC CACGGAGAAT CCGACGGGTT GTTACTCGCT CACATTTAAT GTTGATGAAA GCTGGCTACA GGAAGGCCAG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ACGCGAATTA TTTTTGATGG CGTTAACTCG GCGTTTCATC TGTGGTGCAA CGGGCGCTGG GTCGGTTACG GCCAGGACAG TCGTTTGCCG TCTGAATTTG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACCTGAGCGC ATTTTTACGC GCCGGAGAAA ACCGCCTCGC GGTGATGGTG CTGCGTTGGA GTGACGGCAG TTATCTGGAA GATCAGGATA TGTGGCGGAT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GAGCGGCATT TTCCGTGACG TCTCGTTGCT GCATAAACCG ACTACACAAA TCAGCGATTT CCATGTTGCC ACTCGCTTTA ATGATGATTT CAGCCGCGCT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GTACTGGAGG CTGAAGTTCA GATGTGCGGC GAGTTGCGTG ACTACCTACG GGTAACAGTT TCTTTATGGC AGGGTGAAAC GCAGGTCGCC AGCGGCACCG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CGCCTTTCGG CGGTGAAATT ATCGATGAGC GTGGTGGTTA TGCCGATCGC GTCACACTAC GTCTGAACGT CGAAAACCCG AAACTGTGGA GCGCCGAAAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCCGAATCTC TATCGTGCGG TGGTTGAACT GCACACCGCC GACGGCACGC TGATTGAAGC AGAAGCCTGC GATGTCGGTT TCCGCGAGGT GCGGATTGAA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AATGGTCTGC TGCTGCTGAA CGGCAAGCCG TTGCTGATTC GAGGCGTTAA CCGTCACGAG CATCATCCTC TGCATGGTCA GGTCATGGAT GAGCAGACGA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGGTGCAGGA TATCCTGCTG ATGAAGCAGA ACAACTTTAA CGCCGTGCGC TGTTCGCATT ATCCGAACCA TCCGCTGTGG TACACGCTGT GCGACCGCTA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

CGGCCTGTAT GTGGTGGATG AAGCCAATAT TGAAACCCAC GGCATGGTGC CAATGAATCG TCTGACCGAT GATCCGCGCT GGCTACCGGC GATGAGCGAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGCGTAACGC GAATGGTGCA GCGCGATCGT AATCACCCGA GTGTGATCAT CTGGTCGCTG GGGAATGAAT CAGGCCACGG CGCTAATCAC GACGCGCTGT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ATCGCTGGAT CAAATCTGTC GATCCTTCCC GCCCGGTGCA GTATGAAGGC GGCGGAGCCG ACACCACGGC CACCGATATT ATTTGCCCGA TGTACGCGCG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CGTGGATGAA GACCAGCCCT TCCCGGCTGT GCCGAAATGG TCCATCAAAA AATGGCTTTC GCTACCTGGA GAGACGCGCC CGCTGATCCT TTGCGAATAC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

GCCCACGCGA TGGGTAACAG TCTTGGCGGT TTCGCTAAAT ACTGGCAGGC GTTTCGTCAG TATCCCCGTT TACAGGGCGG CTTCGTCTGG GACTGGGTGG 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATCAGTCGCT GATTAAATAT GATGAAAACG GCAACCCGTG GTCGGCTTAC GGCGGTGATT TTGGCGATAC GCCGAACGAT CGCCAGTTCT GTATGAACGG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TCTGGTCTTT GCCGACCGCA CGCCGCATCC AGCGCTGACG GAAGCAAAAC ACCAGCAGCA GTTTTTCCAG TTCCGTTTAT CCGGGCAAAC CATCGAAGTG 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACCAGCGAAT ACCTGTTCCG TCAATGCGAT AACGAGCTCC TGCACTGGAT GGTGGCGCTG GATGGTAAGC CGCTGGCAAG CGGTGAAGTG CCTCTGGATG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TCGCTCCACA AGGTAAACAG TTGATTGAAC TGCCTGAACT ACCGCAGCCG GAGAGCGCCG GGCAACTCTG GCTCACAGTA CGCGTAGTGC AACCGAACGC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GACCGCATGG TCAGAAGCCG GGCACATCAG CGCCTGGCAG CAGTGGCGTC TGGCGGAAAA CCTCAGTGTG ACGCTCCCCG CCGCGTCCCA CGCCATCCCG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CATCTGACCA CCAGCGAAAT GGATTTTTGC ATCGAGCTGG GTAATAAGCG TTGGCAATTT AACCGCCAGT CAGGCTTTCT TTCACAGATG TGGATTGGCG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATAAAAAACA ACTGCTGACG CCGCTGCGCG ATCAGTTCAC CCGTGCACCG CTGGATAACG ACATTGGCGT AAGTGAAGCG ACCCGCATTG ACCCTAACGC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CTGGGTCGAA CGCTGGAAGG CGGCGGGCCA TTACCAGGCC GAAGCAGCGT TGTTGCAGTG CACGGCAGAT ACACTTGCTG ATGCGGTGCT GATTACGACC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GCTACCGCGT GGCAGCATCA GGGGAAAACC TTATTTATCA GCCGGAAAAC CTACCGGATT GATGGTAGTG GTCAAATGGC GATTACCGTT GATGTTGAAG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGGCGAGCGA TACACCGCAT CCGGCGCGGA TTGGCCTGAA CTGCCAGCTG GCGCAGGTAG CAGAGCGGGT AAACTGGCTC GGATTAGGGC CGCAAGAAAA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CTATCCCGAC CGCCTTACTG CCGCCTGTTT TGACCGCTGG GATCTGCCAT TGTCAGACAT GTATACCCCG TACGTCTTCC CGAGCGAAAA CGGTCTGCGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

TGCGGGACGC GCGAATTGAA TTATGGCCCA CACCAGTGGC GCGGCGACTT CCAGTTCAAC ATCAGCCGCT ACAGTCAACA GCAACTGATG GAAACCAGCC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATCGCCATCT GCTGGACGCG GAAGAAGGCA CATGGCTGAA TATCGACGGT TTCCATATGG GGATTGGTGG CGACGACTCC TGGAGCCCGT CAGTATCGGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

GGAATTCCAG CTGAGCGCCG GTCGCTCAAA TTACCAGTTG GTCTGGTGTC AAAAATAATA ATAACCGGGC AGGGGGGATC CGTCGAAGAT CAGGTTATCG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ATAAAATAAA AGATTTTATT TAGTCTCCAG AAAAAGGGGG GAATGAAAGA CCCCACCTGT AGGTTTGGCA AGCTAGtcta gaGGGCCCTA TTCTATAGTG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

TCACCTAAAT GCTAGAGCTC GCTGATCAGC CTCGACTGTG CCTTCTAGTT GCCAGCCATC TGTTGTTTGC CCCTCCCCCG TGCCTTCCTT GACCCTGGAA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GGTGCCACTC CCACTGTCCT TTCCTAATAA A
^3901      ^3911      ^3921      ^3931

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pMC-delta_1 The name of the promoter used to express this mRNA:
CMV

Aliases of the plasmid name:

Alias: pMC-D1

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing part of gypsy 5' UTR (nt from -511 to nt +5 of the original sequence) and beta-galactosidase reporter gene.

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:

no (not convincing)

Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:

Summary of experiments studying integrity of the in vivo transcripts in a particular host:

Integrity (uniformity) of mRNA tested using Northern-blot:
homogeneous_population_of_molecules_confirmed

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested

Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested

Integrity (uniformity) of mRNA tested using RNAi:
not_tested

Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested

Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
not_tested

Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested

Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested

The organism used:

Homo sapiens 293T (ATCC CRL-1573)

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 agcttgatGG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCTCGATCCC CTCGAGCTAG CGgtaagttt tacaagacac ttctttgacg caatcaagaa atttacgagt gaaaaaaaaa aaaaaaaaaa gttgtgtatc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

tggccacgta ataagtgtgc gttgaattta ttcgcaaaaa cattgcatat tttcggcaaa gtaaaatttt gttgcatacc ttatcaaaaa ataagtgctg 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

catacttttt agagaaacca aataattttt tattgcatac ccgtttttaa taaaatacat tgcataccct cttttaataa aaaatattgc atactttgac 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

gaaacaaatt ttcgttgcat acccaataaa agattattat attgcatacc cgtttttaat aaaatacatt gcataccctc ttttaataaa aaatattgca 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tacgttgacg aaacaaattt tcgttgcata cccaataaaa gattattata ttgcatacct tttcttgcca taccatttag ccgatcaatt gtgctcggca 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

acagtatatt tgtggtgtgc caaccaacaa ccaatgagGC TAGCGGATCC CGTCGTTTTA CAACGTCGTG ACTGGGAAAA CCCTGGCGTT ACCCAACTTA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

ATCGCCTTGC AGCACATCCC CCTTTCGCCA GCTGGCGTAA TAGCGAAGAG GCCCGCACCG ATCGCCCTTC CCAACAGTTG CGCAGCCTGA ATGGCGAATG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GCGCTTTGCC TGGTTTCCGG CACCAGAAGC GGTGCCGGAA AGCTGGCTGG AGTGCGATCT TCCTGAGGCC GATACTGTCG TCGTCCCCTC AAACTGGCAG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ATGCACGGTT ACGATGCGCC CATCTACACC AACGTAACCT ATCCCATTAC GGTCAATCCG CCGTTTGTTC CCACGGAGAA TCCGACGGGT TGTTACTCGC 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCACATTTAA TGTTGATGAA AGCTGGCTAC AGGAAGGCCA GACGCGAATT ATTTTTGATG GCGTTAACTC GGCGTTTCAT CTGTGGTGCA ACGGGCGCTG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGTCGGTTAC GGCCAGGACA GTCGTTTGCC GTCTGAATTT GACCTGAGCG CATTTTTACG CGCCGGAGAA AACCGCCTCG CGGTGATGGT GCTGCGTTGG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

AGTGACGGCA GTTATCTGGA AGATCAGGAT ATGTGGCGGA TGAGCGGCAT TTTCCGTGAC GTCTCGTTGC TGCATAAACC GACTACACAA ATCAGCGATT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

TCCATGTTGC CACTCGCTTT AATGATGATT TCAGCCGCGC TGTACTGGAG GCTGAAGTTC AGATGTGCGG CGAGTTGCGT GACTACCTAC GGGTAACAGT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTCTTTATGG CAGGGTGAAA CGCAGGTCGC CAGCGGCACC GCGCCTTTCG GCGGTGAAAT TATCGATGAG CGTGGTGGTT ATGCCGATCG CGTCACACTA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

CGTCTGAACG TCGAAAACCC GAAACTGTGG AGCGCCGAAA TCCCGAATCT CTATCGTGCG GTGGTTGAAC TGCACACCGC CGACGGCACG CTGATTGAAG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CAGAAGCCTG CGATGTCGGT TTCCGCGAGG TGCGGATTGA AAATGGTCTG CTGCTGCTGA ACGGCAAGCC GTTGCTGATT CGAGGCGTTA ACCGTCACGA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GCATCATCCT CTGCATGGTC AGGTCATGGA TGAGCAGACG ATGGTGCAGG ATATCCTGCT GATGAAGCAG AACAACTTTA ACGCCGTGCG CTGTTCGCAT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TATCCGAACC ATCCGCTGTG GTACACGCTG TGCGACCGCT ACGGCCTGTA TGTGGTGGAT GAAGCCAATA TTGAAACCCA CGGCATGGTG CCAATGAATC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GTCTGACCGA TGATCCGCGC TGGCTACCGG CGATGAGCGA ACGCGTAACG CGAATGGTGC AGCGCGATCG TAATCACCCG AGTGTGATCA TCTGGTCGCT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GGGGAATGAA TCAGGCCACG GCGCTAATCA CGACGCGCTG TATCGCTGGA TCAAATCTGT CGATCCTTCC CGCCCGGTGC AGTATGAAGG CGGCGGAGCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GACACCACGG CCACCGATAT TATTTGCCCG ATGTACGCGC GCGTGGATGA AGACCAGCCC TTCCCGGCTG TGCCGAAATG GTCCATCAAA AAATGGCTTT 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGCTACCTGG AGAGACGCGC CCGCTGATCC TTTGCGAATA CGCCCACGCG ATGGGTAACA GTCTTGGCGG TTTCGCTAAA TACTGGCAGG CGTTTCGTCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GTATCCCCGT TTACAGGGCG GCTTCGTCTG GGACTGGGTG GATCAGTCGC TGATTAAATA TGATGAAAAC GGCAACCCGT GGTCGGCTTA CGGCGGTGAT 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TTTGGCGATA CGCCGAACGA TCGCCAGTTC TGTATGAACG GTCTGGTCTT TGCCGACCGC ACGCCGCATC CAGCGCTGAC GGAAGCAAAA CACCAGCAGC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AGTTTTTCCA GTTCCGTTTA TCCGGGCAAA CCATCGAAGT GACCAGCGAA TACCTGTTCC GTCAATGCGA TAACGAGCTC CTGCACTGGA TGGTGGCGCT 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GGATGGTAAG CCGCTGGCAA GCGGTGAAGT GCCTCTGGAT GTCGCTCCAC AAGGTAAACA GTTGATTGAA CTGCCTGAAC TACCGCAGCC GGAGAGCGCC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GGGCAACTCT GGCTCACAGT ACGCGTAGTG CAACCGAACG CGACCGCATG GTCAGAAGCC GGGCACATCA GCGCCTGGCA GCAGTGGCGT CTGGCGGAAA 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ACCTCAGTGT GACGCTCCCC GCCGCGTCCC ACGCCATCCC GCATCTGACC ACCAGCGAAA TGGATTTTTG CATCGAGCTG GGTAATAAGC GTTGGCAATT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TAACCGCCAG TCAGGCTTTC TTTCACAGAT GTGGATTGGC GATAAAAAAC AACTGCTGAC GCCGCTGCGC GATCAGTTCA CCCGTGCACC GCTGGATAAC 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

GACATTGGCG TAAGTGAAGC GACCCGCATT GACCCTAACG CCTGGGTCGA ACGCTGGAAG GCGGCGGGCC ATTACCAGGC CGAAGCAGCG TTGTTGCAGT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

GCACGGCAGA TACACTTGCT GATGCGGTGC TGATTACGAC CGCTACCGCG TGGCAGCATC AGGGGAAAAC CTTATTTATC AGCCGGAAAA CCTACCGGAT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TGATGGTAGT GGTCAAATGG CGATTACCGT TGATGTTGAA GTGGCGAGCG ATACACCGCA TCCGGCGCGG ATTGGCCTGA ACTGCCAGCT GGCGCAGGTA 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GCAGAGCGGG TAAACTGGCT CGGATTAGGG CCGCAAGAAA ACTATCCCGA CCGCCTTACT GCCGCCTGTT TTGACCGCTG GGATCTGCCA TTGTCAGACA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TGTATACCCC GTACGTCTTC CCGAGCGAAA ACGGTCTGCG CTGCGGGACG CGCGAATTGA ATTATGGCCC ACACCAGTGG CGCGGCGACT TCCAGTTCAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

CATCAGCCGC TACAGTCAAC AGCAACTGAT GGAAACCAGC CATCGCCATC TGCTGGACGC GGAAGAAGGC ACATGGCTGA ATATCGACGG TTTCCATATG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

GGGATTGGTG GCGACGACTC CTGGAGCCCG TCAGTATCGG CGGAATTCCA GCTGAGCGCC GGTCGCTCAA ATTACCAGTT GGTCTGGTGT CAAAAATAAT 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

AATAACCGGG CAGGGGGGAT CCGTCGAAGA TCAGGTTATC GATAAAATAA AAGATTTTAT TTAGTCTCCA GAAAAAGGGG GGAATGAAAG ACCCCACCTG 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TAGGTTTGGC AAGCTAGtct agaGGGCCCT ATTCTATAGT GTCACCTAAA TGCTAGAGCT CGCTGATCAG CCTCGACTGT GCCTTCTAGT TGCCAGCCAT 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CTGTTGTTTG CCCCTCCCCC GTGCCTTCCT TGACCCTGGA AGGTGCCACT CCCACTGTCC TTTCCTAATA AAATGAGGAA ATTGCATCGC ATTGTCTGAG 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TAGGTGTCAT TCTATTCTGG GGGGTGGGGT GGGGCAGGAC AGCAAGGGGG AGGATTGGGA AGACAATAGC AGGCATGCTG GGGATGCGGT GGGCTCTATG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GCTTCTGAGG CGGAAAGAAC CAGCTGGGGC TCGAGGGGGA TCCCGTCGAC CTCGAGAGCT TGGCGTAATC ATGGTCATAG CTGTTTCCTG TGTGAAATTG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTATCCGCTC ACAATTCCAC ACAACATACG AGCCGGAAGC ATAAAGTGTA AAGCCTGGGG TGCCTAATGA GTGAGCTAAC TCACATTAAT TGCGTTGCGC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TCACTGCCCG CTTTCCAGTC GGGAAACCTG TCGTGCCAGC TGCATTAATG AATCGGCCAA CGCGCGGGGA GAGGCGGTTT GCGTATTGGG CGCTCTTCCG 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

CTTCCTCGCT CACTGACTCG CTGCGCTCGG TCGTTCGGCT GCGGCGAGCG GTATCAGCTC ACTCAAAGGC GGTAATACGG TTATCCACAG AATCAGGGGA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

TAACGCAGGA AAGAACATGT GAGCAAAAGG CCAGCAAAAG GCCAGGAACC GTAAAAAGGC CGCGTTGCTG GCGTTTTTCC ATAGGCTCCG CCCCCCTGAC 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

GAGCATCACA AAAATCGACG CTCAAGTCAG AGGTGGCGAA ACCCGACAGG ACTATAAAGA TACCAGGCGT TTCCCCCTGG AAGCTCCCTC GTGCGCTCTC 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

CTGTTCCGAC CCTGCCGCTT ACCGGATACC TGTCCGCCTT TCTCCCTTCG GGAAGCGTGG CGCTTTCTCA ATGCTCACGC TGTAGGTATC TCAGTTCGGT 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

GTAGGTCGTT CGCTCCAAGC TGGGCTGTGT GCACGAACCC CCCGTTCAGC CCGACCGCTG CGCCTTATCC GGTAACTATC GTCTTGAGTC CAACCCGGTA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

AGACACGACT TATCGCCACT GGCAGCAGCC ACTGGTAACA GGATTAGCAG AGCGAGGTAT GTAGGCGGTG CTACAGAGTT CTTGAAGTGG TGGCCTAACT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

ACGGCTACAC TAGAAGGACA GTATTTGGTA TCTGCGCTCT GCTGAAGCCA GTTACCTTCG GAAAAAGAGT TGGTAGCTCT TGATCCGGCA AACAAACCAC 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

CGCTGGTAGC GGTGGTTTTT TTGTTTGCAA GCAGCAGATT ACGCGCAGAA AAAAAGGATC TCAAGAAGAT CCTTTGATCT TTTCTACGGG GTCTGACGCT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

CAGTGGAACG AAAACTCACG TTAAGGGATT TTGGTCATGA GATTATCAAA AAGGATCTTC ACCTAGATCC TTTTAAATTA AAAATGAAGT TTTAAATCAA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

TCTAAAGTAT ATATGAGTAA ACTTGGTCTG ACAGTTACCA ATGCTTAATC AGTGAGGCAC CTATCTCAGC GATCTGTCTA TTTCGTTCAT CCATAGTTGC 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

CTGACTCCCC GTCGTGTAGA TAACTACGAT ACGGGAGGGC TTACCATCTG GCCCCAGTGC TGCAATGATA CCGCGAGACC CACGCTCACC GGCTCCAGAT 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

TTATCAGCAA TAAACCAGCC AGCCGGAAGG GCCGAGCGCA GAAGTGGTCC TGCAACTTTA TCCGCCTCCA TCCAGTCTAT TAATTGTTGC CGGGAAGCTA 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

GAGTAAGTAG TTCGCCAGTT AATAGTTTGC GCAACGTTGT TGCCATTGCT ACAGGCATCG TGGTGTCACG CTCGTCGTTT GGTATGGCTT CATTCAGCTC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CGGTTCCCAA CGATCAAGGC GAGTTACATG ATCCCCCATG TTGTGCAAAA AAGCGGTTAG CTCCTTCGGT CCTCCGATCG TTGTCAGAAG TAAGTTGGCC 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

GCAGTGTTAT CACTCATGGT TATGGCAGCA CTGCATAATT CTCTTACTGT CATGCCATCC GTAAGATGCT TTTCTGTGAC TGGTGAGTAC TCAACCAAGT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

CATTCTGAGA ATAGTGTATG CGGCGACCGA GTTGCTCTTG CCCGGCGTCA ATACGGGATA ATACCGCGCC ACATAGCAGA ACTTTAAAAG TGCTCATCAT 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

TGGAAAACGT TCTTCGGGGC GAAAACTCTC AAGGATCTTA CCGCTGTTGA GATCCAGTTC GATGTAACCC ACTCGTGCAC CCAACTGATC TTCAGCATCT 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

TTTACTTTCA CCAGCGTTTC TGGGTGAGCA AAAACAGGAA GGCAAAATGC CGCAAAAAAG GGAATAAGGG CGACACGGAA ATGTTGAATA CTCATACTCT 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

TCCTTTTTCA ATATTATTGA AGCATTTATC AGGGTTATTG TCTCATGAGC GGATACATAT TTGAATGTAT TTAGAAAAAT AAACAAATAG GGGTTCCGCG 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

CACATTTCCC CGAAAAGTGC CACCTGACGT C
^7101      ^7111      ^7121      ^7131

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: `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):

593-3658

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: `1`	Last change: `2008-07-07 12:32:32`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `gypsyD1`	The functional status of IRES: `defective`

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

82-597

How IRES boundaries were determined:
experimentally_determined

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

gtaagtttta caagacactt ctttgacgca atcaagaaat ttacgagtga aaaaaaaaaa aaaaaaaagt tgtgtatctg gccacgtaat aagtgtgcgt 
^82        ^92        ^102       ^112       ^122       ^132       ^142       ^152       ^162       ^172       

tgaatttatt cgcaaaaaca ttgcatattt tcggcaaagt aaaattttgt tgcatacctt atcaaaaaat aagtgctgca tactttttag agaaaccaaa 
^182       ^192       ^202       ^212       ^222       ^232       ^242       ^252       ^262       ^272       

taatttttta ttgcataccc gtttttaata aaatacattg cataccctct tttaataaaa aatattgcat actttgacga aacaaatttt cgttgcatac 
^282       ^292       ^302       ^312       ^322       ^332       ^342       ^352       ^362       ^372       

ccaataaaag attattatat tgcatacccg tttttaataa aatacattgc ataccctctt ttaataaaaa atattgcata cgttgacgaa acaaattttc 
^382       ^392       ^402       ^412       ^422       ^432       ^442       ^452       ^462       ^472       

gttgcatacc caataaaaga ttattatatt gcataccttt tcttgccata ccatttagcc gatcaattgt gctcggcaac agtatatttg tggtgtgcca 
^482       ^492       ^502       ^512       ^522       ^532       ^542       ^552       ^562       ^572       

accaacaacc aatgag
^582       ^592

Remarks:

Gypsy IRES represents part of gypsy 5' UTR (nt from -511 to nt +5 of the original sequence).

The translation experiments:

Translation results:

IRESite Translation Id: 505

Version: `1`	Last change: `2008-07-07 12:29:52`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Drosophila melanogaster SL2

The temperature (in degrees of Celsia):
25

The relative translation efficiency in % of this IRES:

10.300

Name of IRES used as the positive control:

gypsy_env

Name of the plasmid used as the positive control. `pMC-Env`
`IRESite Id` of the plasmid used as positive control. `462`
The relative translation efficiency in % of the positive control: `100.000`

The effect of 5'-cap analogs on translation:
not tested

Rapamycin affects translation:
not tested

Type of RNA subject to translation:

endogenous_nuclear_RNA_Pol_II_transcript

Remarks:

Translational data are derived from Fig. 8.

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