IRESite_Id:68 summary record describing characteristics of idefix IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `68`	Version: `18`
Originaly submitted by: Petra Sekyrová	Submission date: `2005-08-18 00:00:00`
Reviewed by: Martin Mokrejš	Last change: `2009-03-11 21:36:26`

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `our_best_guess`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `Idefix`	The genetic origin of this natural mRNA/+RNA: `viral`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
4165192

The mRNA/+RNA description:

Genomic mRNA transcript of Drosophila melanogaster Idefix retroelement containing gag and gag-pol genes. The
env gene is translated from subgenomic mRNA which is a spliced variant of genomic RNA (thus not annotated in
IRESite). We stripped U3 on its 5'-end and U5 on its 3'-end to make it resemble genomic +RNA transcript and
annotated only gag and gag-pol ORFs.

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

CAGAGTTCAG TTTGAGACCT AATTGTAAAA GGTTCGGTGT TCTTCTCAAA TAAAAAGATT GTAATCATTT AGTGAAATAA AAATTATATT TTTTTCACTT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATAAATATTG CAAGTATTTA ATTGGCGCAG TCGGTTAGGA TCCAATAAAA TAAAAGAGTC CTTTTAGTAC GGTACTGATC AACTGAAGGA TATGCTATAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GACTAGCTAT CCAAGATCAG CGAATTAAAA TAGTGATTCA AAAATATTTT TTAATCCGCA AAAGAATCTA CGTGAAAGTA GTATTCAAAA TAAAATCCCG 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TGCGGTCGGA AACAAAAATT AATTTAAATT TTTTAATTCC GAAACTTAAA ACCAAGTTTA AAGAAAACTT AAAATCAAGA AAACTTAAAA CCAAGTTTAA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

AGAAAACTTA AAATCAAGAA AACTTAAAAC CAAGTTTAAA GAAAACTTAA AATCAAGAAA ACTTAAAACC AAGTTTAAAG AAAACTCAAA ATCAAGAAAA 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CTTAAAGCCA AAATAAGCTA GAAAACTAAA AGACATCATG GCAGTCCCAC AACTCTCAGA AACACACCTA AACCAACTGC TAAACCAAAT CAAAGAATTA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AACTACTACG ATGGCGCACC TGGCAAATTA TCTGGATTCG TCAACCAAGT GGAACAACTG CTCAGTTTAT ACCCAACACA GGAAGCAAGA CAGGCACACG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TCATATATGG AGCAGTGAAG CGGTTATTAG TGGATTCAGC CTTAGAAGTC GTAACCCAGG AAAGAGCTAA CACATGGCTG GACATGAAGA AAGCACTGGC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AATGGCATTC AAAGACCATA GACCTTATGT AACTCTCATC AGACAATTAG AAGACATATC ATACCCAGGA AGTATCTGTA AGTTTATAGA AAAATTAGAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ACAATACTGG ATTATGTTCG ATAAGTTAGA ATTAGAAAGT GACCATGTTG ATAAATCGAA TTATACCGAA ATGTTAAACA AAACTGTTAA ATCAGTAATA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GATCGAAAAC TGCCGGATAG AATTTATATG TCTTTGGCAC GTAAAGATAT TGATACAATT TATAAATTAA AACAAGCATC AATGGAATTA GGCCTTTATG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATGCTATTCC AGAAAATCAC CGTTCTAATA GAACAGAAAT GAATAAACGT AGGAACAGGG GAAACTATAA TCAAAATAAT AATCAAAAAT ATTACAATAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TAGAAATCAC AACTACAGTA ATTATTATCC TAGCATGAAT CAGAATCATA ATACACAACC ACCTCAGAAT CCGACTCAAC CTATGACAAA TCAAAACCAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

TATTCACCGC GTTTCATACC GAATAATCAA AGAGGGAATT ATTATGCATT TAGACGAGAC TTAACACAAG CTCAGCAGAA CAACCCACTT AATAACACCC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

TTAACTTCCA ACCTTCGACA TCGAATAATA TTAACAGACA AGGGCCAGTA AAAAGACAAC GCGAGAGTCA GAGTGACCAA AGCAGGATGG ATGTAAATTT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TCATCAAGCT GCCTCGGACA CTCAAATGAT AGAGAAGGAC ATACAAGTCC CTATGTAAAA ATAATTCATC ATAATAAAAA TTATAAGGGA ATGATCGATA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CAGGATCATC AATTAACATC ATAAGAGAAA ATTTTGAGAA CTTAGAAGAA AAGGAAGAAA ACCTAATAGT ATACACTATT AAAGGACCAA TAACACTAAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

GAGAAGTATA ATAATAAAAC CTACTTCAGT ATGTCCGTCT GCTCAAAAAT TCTACATTCA CAAATTTTCT GATAACTATG ATTTCTTGTT AGGTCGAAAG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

TATTTAGAAG ATACAAAAGC TAAAATAGAT TATGCTAACG AAACAGTAAC ACTAGGCTCA AAAGTATTTA AGTTTCTCTA TGAAGAAAAG AAGGGCGAGA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CCGCATCCAA ATGCCTTGAC CCACAAGAAA AGAATGATTC CGCTCTAGTG GACAGAACCA AACCAAAAAT GCAAAAGGTT AAGACCGCAC CTAAGTGCCT 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TAAACCAAAG CATCAACAGC AGAAGAAAGA GACCGCATTA CCCAAATGCC TCATTTCAAA TGTTGTTAAA GACACAGTGG ACAATGATGT AACACATCTC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GATCCCATGT CCGTTGACAA CGATATAGTC AACTTCGCGA TTAACAATGA GTTACGCGAA TGTAACGAGT ATAGACTCGA ACACTTAAAT GCAGAGGAAG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TTGAATGTTT AAAGAAGTTC CTATACGAAT ATAGAGACAT TCAGTACAAA GAGGGCGAAA ATTTGACCTT CACCAGTACT ATTAAACATG TCATCCAGAC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

TCAACACGAA GACCCAGTAT ACCGTAAACC CTACAAGTAC CCTCAAAGCG TTGACCAAGA AGTTAACAAA CAAATTAAAG AAATGATAGA ACAAGGGATT 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

GTTCGCAAAT CGAAGTCCCC TTATTGTTCT CCTATTTGGG TGGTCCCCAA GAAGGCAGAC GCCTCTGGGA AACAAAAATT CAGGTTGGTA GTCGATTACA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GGAACCTAAA TGAGATAACT GTTAACGACA AATTTCCCAT TCCCCGAATG GATGAGATAT TGGACAAACT AGGTAGATGC CAATACTTTA CCACTATAGA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TCTAGCCAAG GGTTTTCACC AAATCCAAAT GGATGAAAAT TCTATTGCAA AAACAGCTTT TTCAACTAAG CATGGGCATT ATGAATATAC TCGTATGCCC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

TTTGGTTTAA AAAACGCTCC AGCTACTTTT CAGAGATGCA TGAATAATCT TCTGGAAGAT TTAATCTACA AAGACTGTTT AGTCTATTTA GACGATATTA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TTGTTTATTC CACTCCATTG GAAGAACACA TTTTATCCCT AAAGAAAGTC TTTGAAAAAC TGAGAGACGC TAATTTAAAG TTGCAACTAG ATAAATGTGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ATTCATGAAG AAAGAAACTG AATTCCTAGG ACACATCGTC ACAACAAATG GCATCAAACC AAATCCAAAT AAAACTAAAG CAATTACAAA TTTTCCATTA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CCCAAGACAC CTAAGCAAAT AAAATCATTT TTGGGATTAT GTGGATTCTA TCGCAAGTTT ATTCCTAACT TTGCCAAAAT AGTTAAACCC ATGACCCTCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

AATTAAAGAA AGGTGCTATA ATAGACACCA AATGTAAAGA ATACATCGAA TCATTTGAAA AATTAAAAGT TTTGATAACT TCAGACCCGA TATTAATCTA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

TCCTGATTTT TCAAAACCTT TTTCTTTGAC AACTGATGCT AGCAACGTAG CTATTGGTGC AGTGTTATCA CAAAATCACA AGCCAGTTTG TTATGCCAGT 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

AGAACGCTAA ACGAACATGA AATCAACTAT GCTACGATTG AAAAAGAATT GTTAGCTATA GTTTGGGCTA CAAAATATTT CAGGTCATAC TTATTCGGCA 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

GACCATTTGA AGTATTAAGT GATCACAAGC CACTGGTATG GCTCAACAAC ATTAAAGAAC CAAACATGAA ATTGCAAAGA TGGAAAATAA AACTTAATGA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

ATTCGATTAT AAAATCAAAT ATCTTCCAGG CAAAGAAAAC CATGTCGCGG ATGCTCTTTC CCGCACGAAA ATAGAAGTTA TGGTTGGCGA GGTCGCAAAT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

AGCGCAGACG CAACTATACA CAGTGCCATT GAAGATAATC TAAATTACAT ACCCATAACA GAAAGACCAA TAAATTACTT CTCTAGACAA ATAGAGATAG 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AAAAAGGCGA TAACGATACA ACAAGTGTAC AACATTTGTT TCAAAAATTA AAGATTAAGA TAGTCTATAA AGAAATGACA CCTGAACTCG CCAAAAACCT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CATTAAGGAA TATGTGTGCA CCAAAAAGAG TGCAATTTAT TTCCCTAATG ACGAAGATTT TCTGATCTTC CAGAGAGCGT TTACCGAAAT TATAAGCCCT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

AACAATTTCA CAAAACTCTT GAGATGTACC ACAAAGTTAA TTGATATACT AACGTATGCA GAATTCAAAG ATTTAATCTT AAAGAAACAT AAGGAACTTT 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

TACATCCGGG TATAGAAAAA ACAATCAATT TATTTAAAGA AGAATATTAC TATCCTGATA GTCAAAAGCT TATTCAAACC ATTATCAATG AATGTCAAAT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

TTGTTATCTA GCAAAAACGG AACATCAAAC ACAAATGACA TATGAGACTA CACCAGAAAT ATTTAACACA AGAGAAAAAT ACATGATAGA TTTTTATCTC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

ACAGGAAACC AGATCTTCTT ATCTTGCATT GATATCTATT CGAAATTTGC ATCACTAGTT GAATTAAAAA GTAGAGATTG GCTAGAAGCA AAAAGAGCCA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

TTACTAAAAT ATTCAATGAC ATGGGAAAAC CGCAAGAAAT TAAAGCAGAC AAAGACTCAG CTTTTATGTG TTTAGCCTTA CAAAATTGGT TAAGATCTGA 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

AGGTGTACAA ATTTCTATAA GCACTAGCAA AAATGGTATA TCTGATATAG AAAGATTCCA CAAGACCGTA AACGAAAAGC TAAGAATCAT TGGTAGCCAA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CAAAATGTTG AAGATAGGTG CACAAAATTC GAAAGAATTC TATACATATA CAATCACAAA ACTAAACATA ATAGTACTAA AAGATTTCCA GCAGACATTT 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TCCTATATGC AGGCAGTCCA GATTTTAATG TACAACAAAA CAAAATCGAT AGGATAGAAT ACCTCAATAA GAATAGACAC GATTTTGAAG TTGATATAAA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

ATATAGACAA GCCCCACTTG TAAAAAGTAA AATAACCAAT CCATTTAAAA AGACAGGAAG AATTGGACAA GTAGATGATA AACATTTCGA AGAAACAAAT 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

CGTGGCAGGA AGATCGTTCA CTATAAGTCA AAATTTAAGA AACAGAAAAA GTTTAATAAG AGCAAATATG ATAATTCCAG ACCAACCAAA GAAGCACAAA 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

GTACACAACA TACTTCTAAT AATGCTTAGT TGCATACTAT CACTTATCAT CACGGTCAAG TGCAACAATA TAGAAGTAAA TCCAGTAAAC GCGAAAAATG 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

GATACCTTAT ATTCCAAACA GGAACAATGG AAATTCCAAC CAGCTATGAA TACCATTATT TAAGCATAAA CATAACAAAG ACAATGCTCA TGTTCGAAGA 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

TATAGTAAGT GAAGCAAACA ACTATCCTAA TGTACCACAA ATACAATATT TAGTCGACAA ATTAAAACGA GAAATAAATG GGTTAAGAAT TATTAGTCGA 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

AGTAAAAGAG GTCTTTTAAA CGTAGTAGGA AAAGCATACA AATACTTATT CGGCACATTA GATGAGGATG ACAGAGAAGA GTTAGAAGAA AAAATAAACA 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

ACATGTCAGA AGACTCTGTA AAAACCCATG ACCTAAACAC GATTCTAGAT GTAATCAATA GTGGTATAGA TATAATTAAT AAGCTCAAAG TAGATAAAGA 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

ACAACACCAA CAAATTGCGG TACTAATATT TAACCTAGAG CAATTTACAG AATATATAGA AGACATAGAA TTGGGTCTGC AATTAACCAG ACTAGGAATT 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

TTCAATCCAA GATTACTAAA GCATGACTAT TTAAAACATG TAAATTCAGA AAAAATGCTA AAGATAAAAA CGTCAACCTG GCTTAAAACA GACACGAACG 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

AAATTTTGAT TATTTCCCAT ATTCCTAGCG AAGTTACTAA AGTTCCAATA TTCCAAATTG TTCCGTACCC AGATGAACAT AATTATATTC TAACCGAGCA 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

AATATTCGAT AAATTCTACA TATTTGATAA CCAAGTATTC CATAAAGATA CCAATAGGGA TATATTCGAC AAATGTATTA TTGGAATCAT CAAACAAGAG 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

CAAACTCAAT GCAAATATAT TAAAACACAT AAAAATTACC AAATAAATTA TATAGAACCA AATATACTAT TAACATGGAA TATTCCTGAA ACAGCTGTTA 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

ACCAAGACTG TACACACAAT AAAATATTAA TTTCAGGAAA CAACATCATT AAAATTAAAA ATTGTACCAT ACAAATAGAT GAATTCTTAA TCTCTAATAA 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

TCTAGCAGAC TTTACACAAA CAATTTATAT CACCAACAAT GTAACACGTC TAGAACCAAT AAATCACTTA CAAACGAGAG AAATGATAGA AACCCATGTA 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

AAACACTATA ACTTTTTTCA AATTATATGC ATTACAACGT TCGTCATAAT GATAATTAGT TTGACTCTGT ATGTAGCATA TAAGTTTAAA AATATACCTA 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

AGAAAATTAT TGTCAATATC GTAAGCAAAA AGAACACACG CACCTTGAAA ATAATGTCAA TGAAAATATT CAACAAGGAA ATAATATTAC CTTATACCCA 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

AATTTAACGA CCTGAGGACA GGCCAAATTC AAAGGTTGGG GGAGTGACAT ATCCATAAGT CCCTAAGACT TAAGCATATG CCTACATACT AATACACTTA 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

CAACACATAC ACCCCAATAC AACATACACT ACTCCGGATG TACCCAACAG ATACCAGATA AGAATAAGAT TGTTATATGA TCCTCGAGAA TGGAAAAAAC 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

CCCAATTCTA GATAAGTCAC CCACTGGTAG ACTAAACATC CGTTCCCCTA ATTTAAACAA TTCCTTGCTT AAGCCTCACC CCATCGTCAC ATTCCCACGT 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

TCAAAGCTCG GAGCCGCAAT CCCGAAAAAC AAAAGTATCG ATTTCAATAA ACAAATTATA AGAATCTAAG AGCACTTGTA TCCAAGAGCA AATGCACTTG 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

AATCCAAGAG AAACGCAAAG CTTTTTCTCT TTACGATCAG AATCCTAAAG TCTAAAGTCC ATATTAGAAA AGCTCGATAC CGAGGCTTGA ACGTCAACCA 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

AATCAGAATA ATTATCAGAG TTCAGTTTGA GACCTAATTG TAAAAGGTTC GGTGTTCTTC TCAAATAAAA AGATTGTAAT CATTTAGTG
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881

Credibility of mRNA sequence:

guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail

The organism containing this mRNA with IRES segment in its genome:

Drosophila melanogaster

A promoter reported in cDNA corresponding to IRES sequence:
no The total number of notable open-reading frames (ORFs):
2

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:
not_tested

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:
no_promoter_confirmed

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:

Drosophila melanogaster

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

ORF

ORF position:

1

Version: `3`	Last change: `2006-10-20 00:00:00`
Originaly submitted by: Petra Sekyrová	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
Gag

The description of the protein encoded in this ORF:
Gag protein

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:

no

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

538-1476

ORF

ORF position:

2

Version: `2`	Last change: `2006-10-20 00:00:00`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
gag-pol

The description of the protein encoded in this ORF:
gag-pol protein

The translational frameshift (ribosome slippage) involved:
0 The ribosome read-through involved:
yes

The alternative forms of this protein occur by the alternative initiation of translation:

no

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

538-4929

Remarks:

Authors studied region between bases 32 and 552 of the putative full-length viral +RNA transcript, spanning
right half of the R segment, further covering U5 region and complete UTR region (414b long 5'-UTR, immediately
downstream from LTR) with first 15b of gag (bases 1009-1023 of GI:4165192, including the initiator AUG).
Please note the encapsidation signal is within the gag region. Data about the position of LTR and CDS from
GenBank (GI:4165192) are different to those used by authors. The exact positions of U3-R-U5-UTR regions were
communicated with C. Vaury. The env protein is translated from a subgenomic mRNA which is a spliced variant of
the transcript lacking the IRES region and thus it is not annotated here (not in our scope). Possibility for a
cryptic promoter presence in the tested sequence was ruled out in transgenic Drosophila using UAS-GFP-Id-LacZ
plasmid. Actin-Gal4 was introduced into Drosophila flies by crossing and activated the expression from
UAS-GFP-Id-LacZ plasmid. But, IRES was not active in embryonic tissues and other cases. In any case, splicing
was not studied. From the mRNA sequence in GenBank we have manually removed 'CA' bases as the size of gag ORF
could not be divided by 3. The bases 'CA' were determined by alignment to GI:56411837 as returned by BLAST
search:



>gi|56411837|ref|NT_037436.2|Download subject sequence spanning the HSP Drosophila melanogaster chromosome 3L
Length=23771897  Score = 1661 bits (838), Expect = 0.0 Identities = 916/941 (97%), Gaps = 2/941 (0%)
Strand=Plus/Minus [...]

Query        361 GAAACACAATACTGGATTATGTTCGATAAGTTAGAATTAGAAAGTGACCATGTTGATAAA 420
                 ||||||  ||||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct  20274316  GAAACA--ATACTGGATTATGTTTGATAAGTTAGAATTAGAAAGTGACCCTGTTGATAAA 20274259

Citations:

Meignin C., Bailly J. L., Arnaud F., Dastugue B., Vaury C. (2003) The 5' untranslated region and Gag product of Idefix, a long terminal repeat-retrotransposon from Drosophila melanogaster, act together to initiate a switch between translated and untranslated states of the genomic mRNA. Mol. Cell. Biol. 23(22):8246-8254

Conte C., Dastugue B., Vaury C. (2002) Coupling of enhancer and insulator properties identified in two retrotransposons modulates their mutagenic impact on nearby genes. Mol. Cell. Biol. 22(6):1767-1777

IRESs:

IRES:

Version: `14`	Last change: `2008-06-26 01:00:51`
Originaly submitted by: Petra Sekyrová	Reviewed by: Martin Mokrejš
The IRES name: `idefix`

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

33-553

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

TTCGGTGTTC TTCTCAAATA AAAAGATTGT AATCATTTAG TGAAATAAAA ATTATATTTT TTTCACTTAT AAATATTGCA AGTATTTAAT TGGCGCAGTC 
^33        ^43        ^53        ^63        ^73        ^83        ^93        ^103       ^113       ^123       

GGTTAGGATC CAATAAAATA AAAGAGTCCT TTTAGTACGG TACTGATCAA CTGAAGGATA TGCTATACGA CTAGCTATCC AAGATCAGCG AATTAAAATA 
^133       ^143       ^153       ^163       ^173       ^183       ^193       ^203       ^213       ^223       

GTGATTCAAA AATATTTTTT AATCCGCAAA AGAATCTACG TGAAAGTAGT ATTCAAAATA AAATCCCGTG CGGTCGGAAA CAAAAATTAA TTTAAATTTT 
^233       ^243       ^253       ^263       ^273       ^283       ^293       ^303       ^313       ^323       

TTAATTCCGA AACTTAAAAC CAAGTTTAAA GAAAACTTAA AATCAAGAAA ACTTAAAACC AAGTTTAAAG AAAACTTAAA ATCAAGAAAA CTTAAAACCA 
^333       ^343       ^353       ^363       ^373       ^383       ^393       ^403       ^413       ^423       

AGTTTAAAGA AAACTTAAAA TCAAGAAAAC TTAAAACCAA GTTTAAAGAA AACTCAAAAT CAAGAAAACT TAAAGCCAAA ATAAGCTAGA AAACTAAAAG 
^433       ^443       ^453       ^463       ^473       ^483       ^493       ^503       ^513       ^523       

ACATCATGGC AGTCCCACAA C
^533       ^543       ^553

Remarks:

Authors conclude that the 5'UTR and the Gag product of an endogenous retrovirus Idefix from an insect may act
together to initiate the switch between translated and untranslated stage of the genomic +RNA, which will
ultimately be encapsidated.

According to the article the function of 414b long 5'UTR of Idefix IRES (actually 552nt cloned covering partly
R and U5 as well) was experimentally studied using bicistronic constructs both in vitro (rabbit reticulocyte
lysate, wheat germ lysate, translation of T7 synthesized capped transcripts at 30 oC, 90 min) and in
vivo in transgenic Drosophila.

Please refer also to sequences 1 and 2 from Patent WO0222839.

Citations:

RNA:protein interactions:

The RNA:protein interaction:

Version: `4`	Last change: `2007-01-12 00:00:00`
Originaly submitted by: Petra Sekyrová	Reviewed by: Martin Mokrejš

The description of the protein interacting with the RNA:
Gag protein encoded by Idefix LTR retroelement

The function of the protein interaction:

Gag blocks IRES function

The organism where this RNA:protein interaction occurs:

Drosophila melanogaster

Remarks:

Gag-GST fusion protein was used in a TnT (TnT Qauick coupled kit, Promega) experiment performed on plasmids
bearing EMCV (encephalomyocarditis virus) IRES and Idefix IRES respectively. Addition of 280 ng of Gag-GST
decreased translation from Idefix IRES to 42% of the control (Idefix IRES without Gag-GST supplement). No
inhibition of translation was observed with EMCV IRES + Gag-GST. Thus, Gag encoded by Idefix acts as a
trans-regulating factor that is able to repress translation initiation from the 5'UTR of Idefix.

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