IRESite_Id:462 characteristics of gypsy_env IRES studied in pMC-Env plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `462`	Version: `2`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-07-08 09:17:03`

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 transcript produced from monocistronic plasmid pMC-env containing full-length (except very 5'-most
Adenosine) gypsy-env 5' UTR (nt from -841 to -511 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 Ggttcaaatc ttgtgtcgaa 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ataaaccaca gcttgctccg gctcattgcc gttaaacatc attgttctta tttacaatca aatcgctatc gccacaaggc tagtgataat aactaagggg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

gcgaagtcaa gccctccaac ctaatctcca taaacagtgt ctaagacgaa cctcagcgaa agaaggaaga tctctagacc tactggaaat aacataactc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

tggacctatt ggaacttata taattggcgc ccaaccaaca atctgaaccc accaatctaa tttaacacac tttgtcaggc gacaaacagg gtagttaagt 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

tagaaaagca tGCTAGCGGA TCCCGTCGTT TTACAACGTC GTGACTGGGA AAACCCTGGC GTTACCCAAC TTAATCGCCT TGCAGCACAT CCCCCTTTCG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CCAGCTGGCG TAATAGCGAA GAGGCCCGCA CCGATCGCCC TTCCCAACAG TTGCGCAGCC TGAATGGCGA ATGGCGCTTT GCCTGGTTTC CGGCACCAGA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AGCGGTGCCG GAAAGCTGGC TGGAGTGCGA TCTTCCTGAG GCCGATACTG TCGTCGTCCC CTCAAACTGG CAGATGCACG GTTACGATGC GCCCATCTAC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACCAACGTAA CCTATCCCAT TACGGTCAAT CCGCCGTTTG TTCCCACGGA GAATCCGACG GGTTGTTACT CGCTCACATT TAATGTTGAT GAAAGCTGGC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TACAGGAAGG CCAGACGCGA ATTATTTTTG ATGGCGTTAA CTCGGCGTTT CATCTGTGGT GCAACGGGCG CTGGGTCGGT TACGGCCAGG ACAGTCGTTT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GCCGTCTGAA TTTGACCTGA GCGCATTTTT ACGCGCCGGA GAAAACCGCC TCGCGGTGAT GGTGCTGCGT TGGAGTGACG GCAGTTATCT GGAAGATCAG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GATATGTGGC GGATGAGCGG CATTTTCCGT GACGTCTCGT TGCTGCATAA ACCGACTACA CAAATCAGCG ATTTCCATGT TGCCACTCGC TTTAATGATG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATTTCAGCCG CGCTGTACTG GAGGCTGAAG TTCAGATGTG CGGCGAGTTG CGTGACTACC TACGGGTAAC AGTTTCTTTA TGGCAGGGTG AAACGCAGGT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CGCCAGCGGC ACCGCGCCTT TCGGCGGTGA AATTATCGAT GAGCGTGGTG GTTATGCCGA TCGCGTCACA CTACGTCTGA ACGTCGAAAA CCCGAAACTG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TGGAGCGCCG AAATCCCGAA TCTCTATCGT GCGGTGGTTG AACTGCACAC CGCCGACGGC ACGCTGATTG AAGCAGAAGC CTGCGATGTC GGTTTCCGCG 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

AGGTGCGGAT TGAAAATGGT CTGCTGCTGC TGAACGGCAA GCCGTTGCTG ATTCGAGGCG TTAACCGTCA CGAGCATCAT CCTCTGCATG GTCAGGTCAT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GGATGAGCAG ACGATGGTGC AGGATATCCT GCTGATGAAG CAGAACAACT TTAACGCCGT GCGCTGTTCG CATTATCCGA ACCATCCGCT GTGGTACACG 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CTGTGCGACC GCTACGGCCT GTATGTGGTG GATGAAGCCA ATATTGAAAC CCACGGCATG GTGCCAATGA ATCGTCTGAC CGATGATCCG CGCTGGCTAC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CGGCGATGAG CGAACGCGTA ACGCGAATGG TGCAGCGCGA TCGTAATCAC CCGAGTGTGA TCATCTGGTC GCTGGGGAAT GAATCAGGCC ACGGCGCTAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TCACGACGCG CTGTATCGCT GGATCAAATC TGTCGATCCT TCCCGCCCGG TGCAGTATGA AGGCGGCGGA GCCGACACCA CGGCCACCGA TATTATTTGC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CCGATGTACG CGCGCGTGGA TGAAGACCAG CCCTTCCCGG CTGTGCCGAA ATGGTCCATC AAAAAATGGC TTTCGCTACC TGGAGAGACG CGCCCGCTGA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TCCTTTGCGA ATACGCCCAC GCGATGGGTA ACAGTCTTGG CGGTTTCGCT AAATACTGGC AGGCGTTTCG TCAGTATCCC CGTTTACAGG GCGGCTTCGT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CTGGGACTGG GTGGATCAGT CGCTGATTAA ATATGATGAA AACGGCAACC CGTGGTCGGC TTACGGCGGT GATTTTGGCG ATACGCCGAA CGATCGCCAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTCTGTATGA ACGGTCTGGT CTTTGCCGAC CGCACGCCGC ATCCAGCGCT GACGGAAGCA AAACACCAGC AGCAGTTTTT CCAGTTCCGT TTATCCGGGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAACCATCGA AGTGACCAGC GAATACCTGT TCCGTCAATG CGATAACGAG CTCCTGCACT GGATGGTGGC GCTGGATGGT AAGCCGCTGG CAAGCGGTGA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

AGTGCCTCTG GATGTCGCTC CACAAGGTAA ACAGTTGATT GAACTGCCTG AACTACCGCA GCCGGAGAGC GCCGGGCAAC TCTGGCTCAC AGTACGCGTA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTGCAACCGA ACGCGACCGC ATGGTCAGAA GCCGGGCACA TCAGCGCCTG GCAGCAGTGG CGTCTGGCGG AAAACCTCAG TGTGACGCTC CCCGCCGCGT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CCCACGCCAT CCCGCATCTG ACCACCAGCG AAATGGATTT TTGCATCGAG CTGGGTAATA AGCGTTGGCA ATTTAACCGC CAGTCAGGCT TTCTTTCACA 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GATGTGGATT GGCGATAAAA AACAACTGCT GACGCCGCTG CGCGATCAGT TCACCCGTGC ACCGCTGGAT AACGACATTG GCGTAAGTGA AGCGACCCGC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

ATTGACCCTA ACGCCTGGGT CGAACGCTGG AAGGCGGCGG GCCATTACCA GGCCGAAGCA GCGTTGTTGC AGTGCACGGC AGATACACTT GCTGATGCGG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TGCTGATTAC GACCGCTACC GCGTGGCAGC ATCAGGGGAA AACCTTATTT ATCAGCCGGA AAACCTACCG GATTGATGGT AGTGGTCAAA TGGCGATTAC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CGTTGATGTT GAAGTGGCGA GCGATACACC GCATCCGGCG CGGATTGGCC TGAACTGCCA GCTGGCGCAG GTAGCAGAGC GGGTAAACTG GCTCGGATTA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

GGGCCGCAAG AAAACTATCC CGACCGCCTT ACTGCCGCCT GTTTTGACCG CTGGGATCTG CCATTGTCAG ACATGTATAC CCCGTACGTC TTCCCGAGCG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AAAACGGTCT GCGCTGCGGG ACGCGCGAAT TGAATTATGG CCCACACCAG TGGCGCGGCG ACTTCCAGTT CAACATCAGC CGCTACAGTC AACAGCAACT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

GATGGAAACC AGCCATCGCC ATCTGCTGGA CGCGGAAGAA GGCACATGGC TGAATATCGA CGGTTTCCAT ATGGGGATTG GTGGCGACGA CTCCTGGAGC 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CCGTCAGTAT CGGCGGAATT CCAGCTGAGC GCCGGTCGCT CAAATTACCA GTTGGTCTGG TGTCAAAAAT AATAATAACC GGGCAGGGGG GATCCGTCGA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AGATCAGGTT ATCGATAAAA TAAAAGATTT TATTTAGTCT CCAGAAAAAG GGGGGAATGA AAGACCCCAC CTGTAGGTTT GGCAAGCTAG tctagaGGGC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CCTATTCTAT AGTGTCACCT AAATGCTAGA GCTCGCTGAT CAGCCTCGAC TGTGCCTTCT AGTTGCCAGC CATCTGTTGT TTGCCCCTCC CCCGTGCCTT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

CCTTGACCCT GGAAGGTGCC ACTCCCACTG TCCTTTCCTA ATAAA
^3701      ^3711      ^3721      ^3731      ^3741

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

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

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing gypsy-env IRES (nt from -841 to nt -511 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 CGgttcaaat cttgtgtcga aataaaccac agcttgctcc ggctcattgc cgttaaacat cattgttctt atttacaatc 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

aaatcgctat cgccacaagg ctagtgataa taactaaggg ggcgaagtca agccctccaa cctaatctcc ataaacagtg tctaagacga acctcagcga 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

aagaaggaag atctctagac ctactggaaa taacataact ctggacctat tggaacttat ataattggcg cccaaccaac aatctgaacc caccaatcta 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

atttaacaca ctttgtcagg cgacaaacag ggtagttaag ttagaaaagc atGCTAGCGG ATCCCGTCGT TTTACAACGT CGTGACTGGG AAAACCCTGG 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

CGTTACCCAA CTTAATCGCC TTGCAGCACA TCCCCCTTTC GCCAGCTGGC GTAATAGCGA AGAGGCCCGC ACCGATCGCC CTTCCCAACA GTTGCGCAGC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CTGAATGGCG AATGGCGCTT TGCCTGGTTT CCGGCACCAG AAGCGGTGCC GGAAAGCTGG CTGGAGTGCG ATCTTCCTGA GGCCGATACT GTCGTCGTCC 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCTCAAACTG GCAGATGCAC GGTTACGATG CGCCCATCTA CACCAACGTA ACCTATCCCA TTACGGTCAA TCCGCCGTTT GTTCCCACGG AGAATCCGAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGGTTGTTAC TCGCTCACAT TTAATGTTGA TGAAAGCTGG CTACAGGAAG GCCAGACGCG AATTATTTTT GATGGCGTTA ACTCGGCGTT TCATCTGTGG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGCAACGGGC GCTGGGTCGG TTACGGCCAG GACAGTCGTT TGCCGTCTGA ATTTGACCTG AGCGCATTTT TACGCGCCGG AGAAAACCGC CTCGCGGTGA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TGGTGCTGCG TTGGAGTGAC GGCAGTTATC TGGAAGATCA GGATATGTGG CGGATGAGCG GCATTTTCCG TGACGTCTCG TTGCTGCATA AACCGACTAC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ACAAATCAGC GATTTCCATG TTGCCACTCG CTTTAATGAT GATTTCAGCC GCGCTGTACT GGAGGCTGAA GTTCAGATGT GCGGCGAGTT GCGTGACTAC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CTACGGGTAA CAGTTTCTTT ATGGCAGGGT GAAACGCAGG TCGCCAGCGG CACCGCGCCT TTCGGCGGTG AAATTATCGA TGAGCGTGGT GGTTATGCCG 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ATCGCGTCAC ACTACGTCTG AACGTCGAAA ACCCGAAACT GTGGAGCGCC GAAATCCCGA ATCTCTATCG TGCGGTGGTT GAACTGCACA CCGCCGACGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

CACGCTGATT GAAGCAGAAG CCTGCGATGT CGGTTTCCGC GAGGTGCGGA TTGAAAATGG TCTGCTGCTG CTGAACGGCA AGCCGTTGCT GATTCGAGGC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GTTAACCGTC ACGAGCATCA TCCTCTGCAT GGTCAGGTCA TGGATGAGCA GACGATGGTG CAGGATATCC TGCTGATGAA GCAGAACAAC TTTAACGCCG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGCGCTGTTC GCATTATCCG AACCATCCGC TGTGGTACAC GCTGTGCGAC CGCTACGGCC TGTATGTGGT GGATGAAGCC AATATTGAAA CCCACGGCAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GGTGCCAATG AATCGTCTGA CCGATGATCC GCGCTGGCTA CCGGCGATGA GCGAACGCGT AACGCGAATG GTGCAGCGCG ATCGTAATCA CCCGAGTGTG 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ATCATCTGGT CGCTGGGGAA TGAATCAGGC CACGGCGCTA ATCACGACGC GCTGTATCGC TGGATCAAAT CTGTCGATCC TTCCCGCCCG GTGCAGTATG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AAGGCGGCGG AGCCGACACC ACGGCCACCG ATATTATTTG CCCGATGTAC GCGCGCGTGG ATGAAGACCA GCCCTTCCCG GCTGTGCCGA AATGGTCCAT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CAAAAAATGG CTTTCGCTAC CTGGAGAGAC GCGCCCGCTG ATCCTTTGCG AATACGCCCA CGCGATGGGT AACAGTCTTG GCGGTTTCGC TAAATACTGG 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CAGGCGTTTC GTCAGTATCC CCGTTTACAG GGCGGCTTCG TCTGGGACTG GGTGGATCAG TCGCTGATTA AATATGATGA AAACGGCAAC CCGTGGTCGG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CTTACGGCGG TGATTTTGGC GATACGCCGA ACGATCGCCA GTTCTGTATG AACGGTCTGG TCTTTGCCGA CCGCACGCCG CATCCAGCGC TGACGGAAGC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AAAACACCAG CAGCAGTTTT TCCAGTTCCG TTTATCCGGG CAAACCATCG AAGTGACCAG CGAATACCTG TTCCGTCAAT GCGATAACGA GCTCCTGCAC 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TGGATGGTGG CGCTGGATGG TAAGCCGCTG GCAAGCGGTG AAGTGCCTCT GGATGTCGCT CCACAAGGTA AACAGTTGAT TGAACTGCCT GAACTACCGC 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AGCCGGAGAG CGCCGGGCAA CTCTGGCTCA CAGTACGCGT AGTGCAACCG AACGCGACCG CATGGTCAGA AGCCGGGCAC ATCAGCGCCT GGCAGCAGTG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GCGTCTGGCG GAAAACCTCA GTGTGACGCT CCCCGCCGCG TCCCACGCCA TCCCGCATCT GACCACCAGC GAAATGGATT TTTGCATCGA GCTGGGTAAT 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AAGCGTTGGC AATTTAACCG CCAGTCAGGC TTTCTTTCAC AGATGTGGAT TGGCGATAAA AAACAACTGC TGACGCCGCT GCGCGATCAG TTCACCCGTG 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

CACCGCTGGA TAACGACATT GGCGTAAGTG AAGCGACCCG CATTGACCCT AACGCCTGGG TCGAACGCTG GAAGGCGGCG GGCCATTACC AGGCCGAAGC 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AGCGTTGTTG CAGTGCACGG CAGATACACT TGCTGATGCG GTGCTGATTA CGACCGCTAC CGCGTGGCAG CATCAGGGGA AAACCTTATT TATCAGCCGG 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

AAAACCTACC GGATTGATGG TAGTGGTCAA ATGGCGATTA CCGTTGATGT TGAAGTGGCG AGCGATACAC CGCATCCGGC GCGGATTGGC CTGAACTGCC 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AGCTGGCGCA GGTAGCAGAG CGGGTAAACT GGCTCGGATT AGGGCCGCAA GAAAACTATC CCGACCGCCT TACTGCCGCC TGTTTTGACC GCTGGGATCT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

GCCATTGTCA GACATGTATA CCCCGTACGT CTTCCCGAGC GAAAACGGTC TGCGCTGCGG GACGCGCGAA TTGAATTATG GCCCACACCA GTGGCGCGGC 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

GACTTCCAGT TCAACATCAG CCGCTACAGT CAACAGCAAC TGATGGAAAC CAGCCATCGC CATCTGCTGG ACGCGGAAGA AGGCACATGG CTGAATATCG 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ACGGTTTCCA TATGGGGATT GGTGGCGACG ACTCCTGGAG CCCGTCAGTA TCGGCGGAAT TCCAGCTGAG CGCCGGTCGC TCAAATTACC AGTTGGTCTG 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GTGTCAAAAA TAATAATAAC CGGGCAGGGG GGATCCGTCG AAGATCAGGT TATCGATAAA ATAAAAGATT TTATTTAGTC TCCAGAAAAA GGGGGGAATG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AAAGACCCCA CCTGTAGGTT TGGCAAGCTA GtctagaGGG CCCTATTCTA TAGTGTCACC TAAATGCTAG AGCTCGCTGA TCAGCCTCGA CTGTGCCTTC 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TAGTTGCCAG CCATCTGTTG TTTGCCCCTC CCCCGTGCCT TCCTTGACCC TGGAAGGTGC CACTCCCACT GTCCTTTCCT AATAAAATGA GGAAATTGCA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TCGCATTGTC TGAGTAGGTG TCATTCTATT CTGGGGGGTG GGGTGGGGCA GGACAGCAAG GGGGAGGATT GGGAAGACAA TAGCAGGCAT GCTGGGGATG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

CGGTGGGCTC TATGGCTTCT GAGGCGGAAA GAACCAGCTG GGGCTCGAGG GGGATCCCGT CGACCTCGAG AGCTTGGCGT AATCATGGTC ATAGCTGTTT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CCTGTGTGAA ATTGTTATCC GCTCACAATT CCACACAACA TACGAGCCGG AAGCATAAAG TGTAAAGCCT GGGGTGCCTA ATGAGTGAGC TAACTCACAT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

TAATTGCGTT GCGCTCACTG CCCGCTTTCC AGTCGGGAAA CCTGTCGTGC CAGCTGCATT AATGAATCGG CCAACGCGCG GGGAGAGGCG GTTTGCGTAT 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TGGGCGCTCT TCCGCTTCCT CGCTCACTGA CTCGCTGCGC TCGGTCGTTC GGCTGCGGCG AGCGGTATCA GCTCACTCAA AGGCGGTAAT ACGGTTATCC 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

ACAGAATCAG GGGATAACGC AGGAAAGAAC ATGTGAGCAA AAGGCCAGCA AAAGGCCAGG AACCGTAAAA AGGCCGCGTT GCTGGCGTTT TTCCATAGGC 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

TCCGCCCCCC TGACGAGCAT CACAAAAATC GACGCTCAAG TCAGAGGTGG CGAAACCCGA CAGGACTATA AAGATACCAG GCGTTTCCCC CTGGAAGCTC 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

CCTCGTGCGC TCTCCTGTTC CGACCCTGCC GCTTACCGGA TACCTGTCCG CCTTTCTCCC TTCGGGAAGC GTGGCGCTTT CTCAATGCTC ACGCTGTAGG 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

TATCTCAGTT CGGTGTAGGT CGTTCGCTCC AAGCTGGGCT GTGTGCACGA ACCCCCCGTT CAGCCCGACC GCTGCGCCTT ATCCGGTAAC TATCGTCTTG 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

AGTCCAACCC GGTAAGACAC GACTTATCGC CACTGGCAGC AGCCACTGGT AACAGGATTA GCAGAGCGAG GTATGTAGGC GGTGCTACAG AGTTCTTGAA 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

GTGGTGGCCT AACTACGGCT ACACTAGAAG GACAGTATTT GGTATCTGCG CTCTGCTGAA GCCAGTTACC TTCGGAAAAA GAGTTGGTAG CTCTTGATCC 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

GGCAAACAAA CCACCGCTGG TAGCGGTGGT TTTTTTGTTT GCAAGCAGCA GATTACGCGC AGAAAAAAAG GATCTCAAGA AGATCCTTTG ATCTTTTCTA 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CGGGGTCTGA CGCTCAGTGG AACGAAAACT CACGTTAAGG GATTTTGGTC ATGAGATTAT CAAAAAGGAT CTTCACCTAG ATCCTTTTAA ATTAAAAATG 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

AAGTTTTAAA TCAATCTAAA GTATATATGA GTAAACTTGG TCTGACAGTT ACCAATGCTT AATCAGTGAG GCACCTATCT CAGCGATCTG TCTATTTCGT 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

TCATCCATAG TTGCCTGACT CCCCGTCGTG TAGATAACTA CGATACGGGA GGGCTTACCA TCTGGCCCCA GTGCTGCAAT GATACCGCGA GACCCACGCT 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

CACCGGCTCC AGATTTATCA GCAATAAACC AGCCAGCCGG AAGGGCCGAG CGCAGAAGTG GTCCTGCAAC TTTATCCGCC TCCATCCAGT CTATTAATTG 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

TTGCCGGGAA GCTAGAGTAA GTAGTTCGCC AGTTAATAGT TTGCGCAACG TTGTTGCCAT TGCTACAGGC ATCGTGGTGT CACGCTCGTC GTTTGGTATG 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

GCTTCATTCA GCTCCGGTTC CCAACGATCA AGGCGAGTTA CATGATCCCC CATGTTGTGC AAAAAAGCGG TTAGCTCCTT CGGTCCTCCG ATCGTTGTCA 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

GAAGTAAGTT GGCCGCAGTG TTATCACTCA TGGTTATGGC AGCACTGCAT AATTCTCTTA CTGTCATGCC ATCCGTAAGA TGCTTTTCTG TGACTGGTGA 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

GTACTCAACC AAGTCATTCT GAGAATAGTG TATGCGGCGA CCGAGTTGCT CTTGCCCGGC GTCAATACGG GATAATACCG CGCCACATAG CAGAACTTTA 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

AAAGTGCTCA TCATTGGAAA ACGTTCTTCG GGGCGAAAAC TCTCAAGGAT CTTACCGCTG TTGAGATCCA GTTCGATGTA ACCCACTCGT GCACCCAACT 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

GATCTTCAGC ATCTTTTACT TTCACCAGCG TTTCTGGGTG AGCAAAAACA GGAAGGCAAA ATGCCGCAAA AAAGGGAATA AGGGCGACAC GGAAATGTTG 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

AATACTCATA CTCTTCCTTT TTCAATATTA TTGAAGCATT TATCAGGGTT ATTGTCTCAT GAGCGGATAC ATATTTGAAT GTATTTAGAA AAATAAACAA 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

ATAGGGGTTC CGCGCACATT TCCCCGAAAA GTGCCACCTG ACGTC
^6901      ^6911      ^6921      ^6931      ^6941

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):

410-3472

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 12:56:41`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `gypsy_env`	The functional status of IRES: `functional`

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

82-411

How IRES boundaries were determined:
experimentally_determined

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

gttcaaatct tgtgtcgaaa taaaccacag cttgctccgg ctcattgccg ttaaacatca ttgttcttat ttacaatcaa atcgctatcg ccacaaggct 
^82        ^92        ^102       ^112       ^122       ^132       ^142       ^152       ^162       ^172       

agtgataata actaaggggg cgaagtcaag ccctccaacc taatctccat aaacagtgtc taagacgaac ctcagcgaaa gaaggaagat ctctagacct 
^182       ^192       ^202       ^212       ^222       ^232       ^242       ^252       ^262       ^272       

actggaaata acataactct ggacctattg gaacttatat aattggcgcc caaccaacaa tctgaaccca ccaatctaat ttaacacact ttgtcaggcg 
^282       ^292       ^302       ^312       ^322       ^332       ^342       ^352       ^362       ^372       

acaaacaggg tagttaagtt agaaaagcat
^382       ^392       ^402

Remarks:

Gypsy-env IRES represents the full-length (except very 5'-most Adenosine) gypsy-env 5' UTR (-330 to +1 of the
original sequence).

The translation experiments:

Translation results:

IRESite Translation Id: 503

Version: `1`	Last change: `2008-07-07 12:56:41`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens 293T (ATCC CRL-1573)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

100.000

	Name of the plasmid used as the negative control. `pbeta-actin-lacZ`
	The relative translation efficiency in % of the negative control: `14.700`

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:

In the absence of P2A (poliovirus protease 2A), the enzymatic activity of both pMC-Env and pbeta-actin-lacZ
reached similar levels. Upon P2A expression, a drastic decrease of beta-Gal expression from the
pbeta-actin-lacZ RNA (over fivefold decrease) was observed, whereas translation driven by the env 5' UTR was
moderately stimulated.
Translational data are derived from Fig. 7B.

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