IRESite_Id:563 characteristics of XIAP_-277_-7 IRES studied in pGLuc-XIAP-GFP plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `563`	Version: `3`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-03-13 18:00:00`
Reviewed by: Martin Mokrejš	Last change: `2009-03-16 23:51:23`

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:

Putative in vivo transcript driven from CMV IE promoter and terminated after the SV40 late poly(A) signal
containing GLuc (Gaussia luciferase) and GFP cistrons separated by the putative XIAP IRES.

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

GTCAGATCAC TAGAAGCTTA TCAGACGACA TCACTCGAGA CTAACTCACC GGAATTCCAA GCTGGCAACT TCCGGAAGCT GCAAGCCACC ATGGGAGTCA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAGTCCTGTT CGCTCTGATC TGCATCGCTG TGGCCGAGGC CAAGCCCACC GAGAACAACG AAGACTTCAA CATCGTCGCC GTGGCCAGCA ACTTCGCAAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CACTGATCTG GACGCTGACA GAGGCAAACT GCCTGGCAAG AAGCTGCCTC TCGAAGTCCT GAAAGAGATG GAAGCCAACG CTCGGAAGGC TGGCTGCACA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGAGGCTGCC TGATCTGCCT GTCCCACATC AAATGCACAC CCAAGATGAA GAAATTCATC CCTGGACGCT GCCACACCTA CGAAGGCGAC AAAGAATCCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CACAGGGAGG CATTGGAGAA GCCATTGTCG ACATTCCCGA GATTCCTGGA TTCAAGGACC TGGAGCCTAT GGAGCAGTTC ATCGCACAAG TCGACCTCTG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGTGGACTGC ACAACTGGAT GCCTCAAAGG CCTCGCTAAT GTCCAATGCT CTGACCTGCT CAAGAAATGG CTCCCACAGC GCTGCGCTAC CTTCGCAAGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AAGATCCAGG GCCAAGTCGA TAAGATCAAG GGAGCAGGCG GAGACTAAAC CTAGTTTAAA CGCgtattag ttttattctg cctgcttaaa tattactttc 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ctcaaaaaga gaaaacaaaa atgctagatt ttactttatg acttgaatga tgtggtaatg tcgaactcta gtatttagaa ttagaatgtt tcttagcggt 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

cgtgtagtta tttttatgtc ataagtggat aatttgttag ctcctataac aaaagtctgt tgcttgtgtt tcacattttg gatttcctaa tataatgttc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

tctttttagA AAAGGTGGAC AAGTCCTATT TTCAACGTAC GATGGTGAGC AAGGGCGAGG AGCTGTTCAC CGGGGTGGTG CCCATCCTGG TCGAGCTGGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CGGCGACGTA AACGGCCACA AGTTCAGCGT GTCCGGCGAG GGCGAGGGCG ATGCCACCTA CGGCAAGCTG ACCCTGAAGT TCATCTGCAC CACCGGCAAG 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CTGCCCGTGC CCTGGCCCAC CCTCGTGACC ACCTTGACCT ACGGCGTGCA GTGCTTCGCC CGCTACCCCG ACCACATGAA GCAGCACGAC TTCTTCAAGT 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CCGCCATGCC CGAAGGCTAC GTCCAGGAGC GCACCATCTT CTTCAAGGAC GACGGCAACT ACAAGACCCG CGCCGAGGTG AAGTTCGAGG GCGACACCCT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGTGAACCGC ATCGAGCTGA AGGGCATCGA CTTCAAGGAG GACGGCAACA TCCTGGGGCA CAAGCTGGAG TACAACTACA ACAGCCACAA GGTCTATATC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ACCGCCGACA AGCAGAAGAA CGGCATCAAG GTGAACTTCA AGACCCGCCA CAACATCGAG GACGGCAGCG TGCAGCTCGC CGACCACTAC CAGCAGAACA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

CCCCCATCGG CGACGGCCCC GTGCTGCTGC CCGACAACCA CTACCTGAGC ACCCAGTCCG CCCTGAGCAA AGACCCCAAC GAGAAGCGCG ATCACATGGT 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

CCTGCTGGAG TTCGTGACCG CCGCCGGGAT CACTCTCGGC ATGGACGAGC TGTACAAGTA GCGGCCCAAT CTAGAGTCGG GGCGGCCGGC CGCTTCGAGC 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

AGACATGATA AGATACATTG ATGAGTTTGG ACAAACCACA ACTAGAATGC AGTGAAAAAA ATGCTTTATT TGTGAAATTT GTGATGCTAT TGCTTTATTT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GTAACCATTA TAAGCTGCAA TAAACAAGTT AACAACAACA ATTGCATTCA TTTTATGTTT CAGGTTCAGG GGGAGGTGTG GGAGGTTTTT TAAAGCAAGT 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

AAAACCTCTA CAAATGTGGT A
^1901      ^1911      ^1921

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pGLuc-XIAP-GFP The name of the promoter used to express this mRNA:
CMV_IE

The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):

yes

The in vivo produced heterogeneous transcripts occur due to alternative splicing:

yes

A promoter reported in cDNA corresponding to IRES sequence:

not tested

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:
heterogeneous_population_of_molecules_found

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 HeLa (ATCC CCL-2)

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
XIAP

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens

The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:

TCAATATTGG CCATTAGCCA TATTATTCAT TGGTTATATA GCATAAATCA ATATTGGCTA TTGGCCATTG CATACGTTGT ATCTATATCA TAATATGTAC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ATTTATATTG GCTCATGTCC AATATGACCG CCATGTTGGC ATTGATTATT GACTAGTTAT TAATAGTAAT CAATTACGGG GTCATTAGTT CATAGCCCAT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ATATGGAGTT CCGCGTTACA TAACTTACGG TAAATGGCCC GCCTGGCTGA CCGCCCAACG ACCCCCGCCC ATTGACGTCA ATAATGACGT ATGTTCCCAT 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

AGTAACGCCA ATAGGGACTT TCCATTGACG TCAATGGGTG GAGTATTTAC GGTAAACTGC CCACTTGGCA GTACATCAAG TGTATCATAT GCCAAGTCCG 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCCCCTATTG ACGTCAATGA CGGTAAATGG CCCGCCTGGC ATTATGCCCA GTACATGACC TTACGGGACT TTCCTACTTG GCAGTACATC TACGTATTAG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCATCGCTAT TACCATGGTG ATGCGGTTTT GGCAGTACAC CAATGGGCGT GGATAGCGGT TTGACTCACG GGGATTTCCA AGTCTCCACC CCATTGACGT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CAATGGGAGT TTGTTTTGGC ACCAAAATCA ACGGGACTTT CCAAAATGTC GTAATAACCC CGCCCCGTTG ACGCAAATGG GCGGTAGGCG TGTACGGTGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

GAGGTCTATA TAAGCAGAGC TCGTTTAGTG AACCGTCAGA TCACTAGAAG CTTATCAGAC GACATCACTC GAGACTAACT CACCGGAATT CCAAGCTGGC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

AACTTCCGGA AGCTGCAAGC CACCATGGGA GTCAAAGTCC TGTTCGCTCT GATCTGCATC GCTGTGGCCG AGGCCAAGCC CACCGAGAAC AACGAAGACT 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TCAACATCGT CGCCGTGGCC AGCAACTTCG CAACCACTGA TCTGGACGCT GACAGAGGCA AACTGCCTGG CAAGAAGCTG CCTCTCGAAG TCCTGAAAGA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GATGGAAGCC AACGCTCGGA AGGCTGGCTG CACAAGAGGC TGCCTGATCT GCCTGTCCCA CATCAAATGC ACACCCAAGA TGAAGAAATT CATCCCTGGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

CGCTGCCACA CCTACGAAGG CGACAAAGAA TCCGCACAGG GAGGCATTGG AGAAGCCATT GTCGACATTC CCGAGATTCC TGGATTCAAG GACCTGGAGC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

CTATGGAGCA GTTCATCGCA CAAGTCGACC TCTGCGTGGA CTGCACAACT GGATGCCTCA AAGGCCTCGC TAATGTCCAA TGCTCTGACC TGCTCAAGAA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ATGGCTCCCA CAGCGCTGCG CTACCTTCGC AAGCAAGATC CAGGGCCAAG TCGATAAGAT CAAGGGAGCA GGCGGAGACT AAACCTAGTT TAAACGCgta 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ttagttttat tctgcctgct taaatattac tttcctcaaa aagagaaaac aaaaatgcta gattttactt tatgacttga atgatgtggt aatgtcgaac 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tctagtattt agaattagaa tgtttcttag cggtcgtgta gttattttta tgtcataagt ggataatttg ttagctccta taacaaaagt ctgttgcttg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tgtttcacat tttggatttc ctaatataat gttctctttt tagAAAAGGT GGACAAGTCC TATTTTCAAC GTACGATGGT GAGCAAGGGC GAGGAGCTGT 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TCACCGGGGT GGTGCCCATC CTGGTCGAGC TGGACGGCGA CGTAAACGGC CACAAGTTCA GCGTGTCCGG CGAGGGCGAG GGCGATGCCA CCTACGGCAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCTGACCCTG AAGTTCATCT GCACCACCGG CAAGCTGCCC GTGCCCTGGC CCACCCTCGT GACCACCTTG ACCTACGGCG TGCAGTGCTT CGCCCGCTAC 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CCCGACCACA TGAAGCAGCA CGACTTCTTC AAGTCCGCCA TGCCCGAAGG CTACGTCCAG GAGCGCACCA TCTTCTTCAA GGACGACGGC AACTACAAGA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CCCGCGCCGA GGTGAAGTTC GAGGGCGACA CCCTGGTGAA CCGCATCGAG CTGAAGGGCA TCGACTTCAA GGAGGACGGC AACATCCTGG GGCACAAGCT 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GGAGTACAAC TACAACAGCC ACAAGGTCTA TATCACCGCC GACAAGCAGA AGAACGGCAT CAAGGTGAAC TTCAAGACCC GCCACAACAT CGAGGACGGC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AGCGTGCAGC TCGCCGACCA CTACCAGCAG AACACCCCCA TCGGCGACGG CCCCGTGCTG CTGCCCGACA ACCACTACCT GAGCACCCAG TCCGCCCTGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GCAAAGACCC CAACGAGAAG CGCGATCACA TGGTCCTGCT GGAGTTCGTG ACCGCCGCCG GGATCACTCT CGGCATGGAC GAGCTGTACA AGTAGCGGCC 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CAATCTAGAG TCGGGGCGGC CGGCCGCTTC GAGCAGACAT GATAAGATAC ATTGATGAGT TTGGACAAAC CACAACTAGA ATGCAGTGAA AAAAATGCTT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

TATTTGTGAA ATTTGTGATG CTATTGCTTT ATTTGTAACC ATTATAAGCT GCAATAAACA AGTTAACAAC AACAATTGCA TTCATTTTAT GTTTCAGGTT 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

CAGGGGGAGG TGTGGGAGGT TTTTTAAAGC AAGTAAAACC TCTACAAATG TGGTAAAATC GATAAGGATC CGTCGACCGA TGCCCTTGAG AGCCTTCAAC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CCAGTCAGCT CCTTCCGGTG GGCGCGGGGC ATGACTATCG TCGCCGCACT TATGACTGTC TTCTTTATCA TGCAACTCGT AGGACAGGTG CCGGCAGCGC 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

TCTTCCGCTT CCTCGCTCAC TGACTCGCTG CGCTCGGTCG TTCGGCTGCG GCGAGCGGTA TCAGCTCACT CAAAGGCGGT AATACGGTTA TCCACAGAAT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

CAGGGGATAA CGCAGGAAAG AACATGTGAG CAAAAGGCCA GCAAAAGGCC AGGAACCGTA AAAAGGCCGC GTTGCTGGCG TTTTTCCATA GGCTCCGCCC 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

CCCTGACGAG CATCACAAAA ATCGACGCTC AAGTCAGAGG TGGCGAAACC CGACAGGACT ATAAAGATAC CAGGCGTTTC CCCCTGGAAG CTCCCTCGTG 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

CGCTCTCCTG TTCCGACCCT GCCGCTTACC GGATACCTGT CCGCCTTTCT CCCTTCGGGA AGCGTGGCGC TTTCTCATAG CTCACGCTGT AGGTATCTCA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

GTTCGGTGTA GGTCGTTCGC TCCAAGCTGG GCTGTGTGCA CGAACCCCCC GTTCAGCCCG ACCGCTGCGC CTTATCCGGT AACTATCGTC TTGAGTCCAA 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CCCGGTAAGA CACGACTTAT CGCCACTGGC AGCAGCCACT GGTAACAGGA TTAGCAGAGC GAGGTATGTA GGCGGTGCTA CAGAGTTCTT GAAGTGGTGG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CCTAACTACG GCTACACTAG AAGAACAGTA TTTGGTATCT GCGCTCTGCT GAAGCCAGTT ACCTTCGGAA AAAGAGTTGG TAGCTCTTGA TCCGGCAAAC 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

AAACCACCGC TGGTAGCGGT GGTTTTTTTG TTTGCAAGCA GCAGATTACG CGCAGAAAAA AAGGATCTCA AGAAGATCCT TTGATCTTTT CTACGGGGTC 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TGACGCTCAG TGGAACGAAA ACTCACGTTA AGGGATTTTG GTCATGAGAT TATCAAAAAG GATCTTCACC TAGATCCTTT TAAATTAAAA ATGAAGTTTT 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

AAATCAATCT AAAGTATATA TGAGTAAACT TGGTCTGACA GCGGCCGCAA ATGCTAAACC ACTGCAGTGG TTACCAGTGC TTGATCAGTG AGGCACCGAT 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CTCAGCGATC TGCCTATTTC GTTCGTCCAT AGTGGCCTGA CTCCCCGTCG TGTAGATCAC TACGATTCGT GAGGGCTTAC CATCAGGCCC CAGCGCAGCA 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

ATGATGCCGC GAGAGCCGCG TTCACCGGCC CCCGATTTGT CAGCAATGAA CCAGCCAGCA GGGAGGGCCG AGCGAAGAAG TGGTCCTGCT ACTTTGTCCG 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

CCTCCATCCA GTCTATGAGC TGCTGTCGTG ATGCTAGAGT AAGAAGTTCG CCAGTGAGTA GTTTCCGAAG AGTTGTGGCC ATTGCTACTG GCATCGTGGT 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

ATCACGCTCG TCGTTCGGTA TGGCTTCGTT CAACTCTGGT TCCCAGCGGT CAAGCCGGGT CACATGATCA CCCATATTAT GAAGAAATGC AGTCAGCTCC 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

TTAGGGCCTC CGATCGTTGT CAGAAGTAAG TTGGCCGCGG TGTTGTCGCT CATGGTAATG GCAGCACTAC ACAATTCTCT TACCGTCATG CCATCCGTAA 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GATGCTTTTC CGTGACCGGC GAGTACTCAA CCAAGTCGTT TTGTGAGTAG TGTATACGGC GACCAAGCTG CTCTTGCCCG GCGTCTATAC GGGACAACAC 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

CGCGCCACAT AGCAGTACTT TGAAAGTGCT CATCATCGGG AATCGTTCTT CGGGGCGGAA AGACTCAAGG ATCTTGCCGC TATTGAGATC CAGTTCGATA 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

TAGCCCACTC TTGCACCCAG TTGATCTTCA GCATCTTTTA CTTTCACCAG CGTTTCGGGG TGTGCAAAAA CAGGCAAGCA AAATGCCGCA AAGAAGGGAA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TGAGTGCGAC ACGAAAATGT TGGATGCTCA TACTCGTCCT TTTTCAATAT TATTGAAGCA TTTATCAGGG TTACTAGTAC GTCTCTCAAG GATAAGTAAG 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

TAATATTAAG GTACGGGAGG TATTGGACAG GCCGCAATAA AATATCTTTA TTTTCATTAC ATCTGTGTGT TGGTTTTTTG TGTGAATCGA TAGTACTAAC 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ATACGCTCTC CATCAAAACA AAACGAAACA AAACAAACTA GCAAAATAGG CTGTCCCCAG TGCAAGTGCA GGTGCCAGAA CATTTCTCTG GCCTAACTGG 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CC
^4901

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

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

2

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

ORF

ORF position:

1

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
GLuc

The description of the protein encoded in this ORF:
Gaussia luciferase

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):

91-648

ORF

ORF position:

2

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
GFP

The description of the protein encoded in this ORF:
green fluorescent 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:

not tested

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

942-1661

Remarks:

In addition to the unspliced message 3 alternatively spliced products were reported in HeLa cells transiently
transfected by this plasmid. Although the authors intended to use a plasmid which would be depleted of
5'-splice donor sites (Supplementary Figure 6) still two 5'-splice donor sites remained in GLuc coding region
and spliced with eIF4GI insert. In case of this plasmid with XIAP insert the 5'-donor splice site was same
with one of the two found with eIF4GI insert. Please refer to the Supplementary Figure 7 in Baranick et al.
(2008).
The sequences around the 5'-splice donor were:
GAATGATGTGgtaatgtcga (in XIAP IRES itself)
GTTTAAACGCgtattagttt (located in MluI A^CGCgt site used for cloning of the cDNA immediately upstream of XIAP
IRES) ACCTTCGCAAgcaagatcca (in GLuc coding region, C-terminus)

The 3'-splice acceptor region was: atataatgttctctttttagAA


Comments from IRESite curator:

The first variant has shorter XIAP insert while both reporter ORFs are intact, having 138bp in the
intercistronic region (instead of 293 in the unspliced message).

The second splice variant lacks almost completely the XIAP insert while is still bicistronic, having 47bp in
the intercistronic region.

The third splice variant has GLuc ORF merged in-frame to the second cistron so a fusion protein could be
produced.

Citations:

Baranick B. T., Lemp N. A., Nagashima J., Hiraoka K., Kasahara N., Logg C. R. (2008) Splicing mediates the activity of four putative cellular internal ribosome entry sites. Proc. Natl. Acad. Sci. U. S. A. 105(12):4733-4738

IRESs:

IRES:

Version: `1`	Last change: `2009-03-16 22:50:35`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `XIAP_-277_-7`	The functional status of IRES: `functional`

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

665-935

How IRES boundaries were determined:
experimentally_determined

5'-end of IRES relative to last base of the STOP codon of the upstream ORF: `17`	3'-end of IRES relative to last base of the STOP codon of the upstream ORF: `287`
5'-end of IRES relative to first base of the START codon of the downstream ORF: `-277`	3'-end of IRES relative to first base of the START codon of the downstream ORF: `-7`

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

tattagtttt attctgcctg cttaaatatt actttcctca aaaagagaaa acaaaaatgc tagattttac tttatgactt gaatgatgtg gtaatgtcga 
^665       ^675       ^685       ^695       ^705       ^715       ^725       ^735       ^745       ^755       

actctagtat ttagaattag aatgtttctt agcggtcgtg tagttatttt tatgtcataa gtggataatt tgttagctcc tataacaaaa gtctgttgct 
^765       ^775       ^785       ^795       ^805       ^815       ^825       ^835       ^845       ^855       

tgtgtttcac attttggatt tcctaatata atgttctctt tttagAAAAG GTGGACAAGT CCTATTTTCA A
^865       ^875       ^885       ^895       ^905       ^915       ^925       ^935

Citations:

The translation experiments:

Translation results:

IRESite Translation Id: 607

Version: `1`	Last change: `2009-07-16 14:44:12`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens HeLa (ATCC CCL-2)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

28.100

Name of IRES used as the positive control:

EMCV-R_-541_-7

Name of the plasmid used as the positive control. `pGLuc-EMCV-GFP`	Name of the plasmid used as the negative control. `pGLuc-GFP`
`IRESite Id` of the plasmid used as positive control. `557`	`IRESite Id` of the plasmid used as negative control. `556`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `10.800`
The size (length) of intercistronic region in the positive control: `565`	The size (length) of intercistronic region in the negative control: `17`

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:

Data from Figure 1B.

Citations:

Translation results:

IRESite Translation Id: 608

Version: `1`	Last change: `2009-07-16 14:44:13`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The translation method used to study IRES function:
in vivo

The organism used for translation:

Homo sapiens NIH/3T3 (ATCC CRL-1658)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

21.400

Name of IRES used as the positive control:

EMCV-R_-541_-7

Name of the plasmid used as the positive control. `pGLuc-EMCV-GFP`	Name of the plasmid used as the negative control. `pGLuc-GFP`
`IRESite Id` of the plasmid used as positive control. `557`	`IRESite Id` of the plasmid used as negative control. `556`
The relative translation efficiency in % of the positive control: `100.000`	The relative translation efficiency in % of the negative control: `10.900`
The size (length) of intercistronic region in the positive control: `565`	The size (length) of intercistronic region in the negative control: `17`

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:

Data from Figure 1B.

Citations:

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