IRESite_Id:536 characteristics of c-IAP_-150/-1 IRES studied in pHIAP2(1073-1222)/CAT plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `536`	Version: `3`
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš	Last change: `2008-10-27 23:45:50`

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:
3UTR_incomplete

The mRNA/+RNA description:

Putative in vivo CMV promoter-derived transcript produced from monocistronic plasmid pHIAP2(1073-1222)/CAT
which contains the part of human c-IAP1 5' UTR (nt from -150 to nt -1 of the original sequence) mRNA ahead of
chloramphenicol acetyltransferase reporter gene.
The sequence ends at its 3'-end right after the poly(A) signal from BGH mRNA and thus the 3'-UTR might be
slightly wrong.

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

agagaaccca ctgcttactg gcttatcgaa attaatacga ctcactatag ggagacccaa gcttggtacc gagctcggat ccactagtaa cggccgccag 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tgtgctggaa ttctgcagat atccatcaca ctggcggccg cctcgagtga tttctttttg tggtaaaaat cttagttcat gtgaagaaat ttcatgtgaa 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

tgttttagct atcaaacagt actgtcacct actcatacac aaaactgcct cccaaagact tttcccaggt ccctcgtatc aaaacattaa gagtatactc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gagatggaga aaaaaatcac tggatatacc accgttgata tatcccaatg gcatcgtaaa gaacattttg aggcatttca gtcagttgct caatgtacct 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ataaccagac cgttcagctg gatattacgg cctttttaaa gaccgtaaag aaaaataagc acaagtttta tccggccttt attcacattc ttgcccgcct 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

gatgaatgct catccggaat tccgtatggc aatgaaagac ggtgagctgg tgatatggga tagtgttcac ccttgttaca ccgttttcca tgagcaaact 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

gaaacgtttt catcgctctg gagtgaatac cacgacgatt tccggcagtt tctacacata tattcgcaag atgtggcgtg ttacggtgaa aacctggcct 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

atttccctaa agggtttatt gagaatatgt ttttcgtctc agccaatccc tgggtgagtt tcaccagttt tgatttaaac gtggccaata tggacaactt 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

cttcgccccc gttttcacca tgggcaaata ttatacgcaa ggcgacaagg tgctgatgcc gctggcgatt caggttcatc atgccgtctg tgatggcttc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

catgtcggca gaatgcttaa tgaattacaa cagtactgcg atgagtggca gggcggggcg taattttttt aaggcagtta ttggtgccct taaacgcctg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

gtgctacgcc tgaataagtg ataataagcg gatgaatggc agaaattcgc cggatctttg tgaaggaacc ttacttctgt ggtgtgacat aattggacaa 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

actacctaca gagatttaaa gctctaaggt aaatataaaa tttttaagtg tataatgtgt taaactactg attctaattg tttgtgtatt ttagattcca 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

acctatggaa ctgatgaatg ggagcagtgg tggaatgcct ttaatgagga aaacctgttt tgctcagaag aaatgccatc tagtgatgat gaggctactg 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ctgactctca acattctact cctccaaaaa agaagagaaa ggtagaagac cccaaggact ttccttcaga attgctaagt tttttgagtc atgctgtgtt 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

tagtaataga actcttgctt gctttgctat ttacaccaca aaggaaaaag ctgcactgct atacaagaaa attatggaaa aatattctgt aacctttata 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

agtaggcata acagttataa tcataacata ctgttttttc ttactccaca caggcataga gtgtctgcta ttaataacta tgctcaaaaa ttgtgtacct 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ttagcttttt aatttgtaaa ggggttaata aggaatattt gatgtatagt gccttgacta gagatcataa tcagccatac cacatttgta gaggttttac 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ttgctttaaa aaacctccca cacctccccc tgaacctgaa acataaaatg aatgcaattg ttgttgttaa cttgtttatt gcagcttata atggttacaa 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ataaagcaat agcatcacaa atttcacaaa taaagcattt ttttcactgc attctagttg tggtttgtcc aaactcatca atgtatctta tcatgtctgc 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ctagagggcc ctattctata gtgtcaccta aatgctagag ctcgctgatc agcctcgact gtgccttcta gttgccagcc atctgttgtt tgcccctccc 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ccgtgccttc cttgaccctg gaaggtgcca ctcccactgt cctttcctaa taa
^2001      ^2011      ^2021      ^2031      ^2041      ^2051

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_maybe_except_3UTR

The name of the plasmid:
pHIAP2(1073-1222)/CAT The name of the promoter used to express this mRNA:
CMV

Aliases of the plasmid name:

Alias: HIAP2(1073-1222)CAT

Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing part of human c-IAP1 5' UTR (nt from -150 to nt -1 of the original sequence) ahead of chloramphenicol acetyltransferase reporter gene.

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

no (not convincing)

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

not tested

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:
unclear_result

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 HEK 293T (ATCC 293tsA1609neo)

The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
c-IAP1

The origin of IRES in the plasmid:

nuclear

The donor organism of the IRES segment:

Homo sapiens Jurkat

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

cggatacata tttgaatgta tttagaaaaa taaacaaata ggggttccgc gcacatttcc ccgaaaagtg ccacctgacg tcgacggatc gggagatctc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

ccgatcccct atggtcgact ctcagtacaa tctgctctga tgccgcatag ttaagccagt atctgctccc tgcttgtgtg ttggaggtcg ctgagtagtg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

cgcgagcaaa atttaagcta caacaaggca aggcttgacc gacaattgca tgaagaatct gcttagggtt aggcgttttg cgctgcttcg cgatgtacgg 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gccagatata cgcgttgaca ttgattattg actagttatt aatagtaatc aattacgggg tcattagttc atagcccata tatggagttc cgcgttacat 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

aacttacggt aaatggcccg cctggctgac cgcccaacga cccccgccca ttgacgtcaa taatgacgta tgttcccata gtaacgccaa tagggacttt 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ccattgacgt caatgggtgg actatttacg gtaaactgcc cacttggcag tacatcaagt gtatcatatg ccaagtacgc cccctattga cgtcaatgac 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ggtaaatggc ccgcctggca ttatgcccag tacatgacct tatgggactt tcctacttgg cagtacatct acgtattagt catcgctatt accatggtga 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

tgcggttttg gcagtacatc aatgggcgtg gatagcggtt tgactcacgg ggatttccaa gtctccaccc cattgacgtc aatgggagtt tgttttggca 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ccaaaatcaa cgggactttc caaaatgtcg taacaactcc gccccattga cgcaaatggg cggtaggcgt gtacggtggg aggtctatat aagcagagct 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ctctggctaa ctagagaacc cactgcttac tggcttatcg aaattaatac gactcactat agggagaccc aagcttggta ccgagctcgg atccactagt 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

aacggccgcc agtgtgctgg aattctgcag atatccatca cactggcggc cgcctcgagt gatttctttt tgtggtaaaa atcttagttc atgtgaagaa 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

atttcatgtg aatgttttag ctatcaaaca gtactgtcac ctactcatac acaaaactgc ctcccaaaga cttttcccag gtccctcgta tcaaaacatt 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

aagagtatac tcgagatgga gaaaaaaatc actggatata ccaccgttga tatatcccaa tggcatcgta aagaacattt tgaggcattt cagtcagttg 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ctcaatgtac ctataaccag accgttcagc tggatattac ggccttttta aagaccgtaa agaaaaataa gcacaagttt tatccggcct ttattcacat 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

tcttgcccgc ctgatgaatg ctcatccgga attccgtatg gcaatgaaag acggtgagct ggtgatatgg gatagtgttc acccttgtta caccgttttc 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

catgagcaaa ctgaaacgtt ttcatcgctc tggagtgaat accacgacga tttccggcag tttctacaca tatattcgca agatgtggcg tgttacggtg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

aaaacctggc ctatttccct aaagggttta ttgagaatat gtttttcgtc tcagccaatc cctgggtgag tttcaccagt tttgatttaa acgtggccaa 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

tatggacaac ttcttcgccc ccgttttcac catgggcaaa tattatacgc aaggcgacaa ggtgctgatg ccgctggcga ttcaggttca tcatgccgtc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

tgtgatggct tccatgtcgg cagaatgctt aatgaattac aacagtactg cgatgagtgg cagggcgggg cgtaattttt ttaaggcagt tattggtgcc 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

cttaaacgcc tggtgctacg cctgaataag tgataataag cggatgaatg gcagaaattc gccggatctt tgtgaaggaa ccttacttct gtggtgtgac 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

ataattggac aaactaccta cagagattta aagctctaag gtaaatataa aatttttaag tgtataatgt gttaaactac tgattctaat tgtttgtgta 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ttttagattc caacctatgg aactgatgaa tgggagcagt ggtggaatgc ctttaatgag gaaaacctgt tttgctcaga agaaatgcca tctagtgatg 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

atgaggctac tgctgactct caacattcta ctcctccaaa aaagaagaga aaggtagaag accccaagga ctttccttca gaattgctaa gttttttgag 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

tcatgctgtg tttagtaata gaactcttgc ttgctttgct atttacacca caaaggaaaa agctgcactg ctatacaaga aaattatgga aaaatattct 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gtaaccttta taagtaggca taacagttat aatcataaca tactgttttt tcttactcca cacaggcata gagtgtctgc tattaataac tatgctcaaa 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

aattgtgtac ctttagcttt ttaatttgta aaggggttaa taaggaatat ttgatgtata gtgccttgac tagagatcat aatcagccat accacatttg 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

tagaggtttt acttgcttta aaaaacctcc cacacctccc cctgaacctg aaacataaaa tgaatgcaat tgttgttgtt aacttgttta ttgcagctta 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

taatggttac aaataaagca atagcatcac aaatttcaca aataaagcat ttttttcact gcattctagt tgtggtttgt ccaaactcat caatgtatct 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

tatcatgtct gcctagaggg ccctattcta tagtgtcacc taaatgctag agctcgctga tcagcctcga ctgtgccttc tagttgccag ccatctgttg 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

tttgcccctc ccccgtgcct tccttgaccc tggaaggtgc cactcccact gtcctttcct aataaaatga ggaaattgca tcgcattgtc tgagtaggtg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

tcattctatt ctggggggtg gggtggggca ggacagcaag ggggaggatt gggaagacaa tagcaggcat gctggggatg cggtgggctc tatggcttct 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

gaggcggaaa gaaccagctg gggctctagg gggtatcccc acgcgccctg tagcggcgca ttaagcgcgg cgggtgtggt ggttacgcgc agcgtgaccg 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ctacacttgc cagcgcccta gcgcccgctc ctttcgcttt cttcccttcc tttctcgcca cgttcgccgg ctttccccgt caagctctaa atcggggcat 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

ccctttaggg ttccgattta gtgctttacg gcacctcgac cccaaaaaac ttgattaggg tgatggttca cgtagtgggc catcgccctg atagacggtt 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

tttcgccctt tgacgttgga gtccacgttc tttaatagtg gactcttgtt ccaaactgga acaacactca accctatctc ggtctattct tttgatttat 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

aagggatttt ggggatttcg gcctattggt taaaaaatga gctgatttaa caaaaattta acgcgaatta attctgtgga atgtgtgtca gttagggtgt 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ggaaagtccc caggctcccc aggcaggcag aagtatgcaa agcatgcatc tcaattagtc agcaaccagg tgtggaaagt ccccaggctc cccagcaggc 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

agaagtatgc aaagcatgca tctcaattag tcagcaacca tagtcccgcc cctaactccg cccatcccgc ccctaactcc gcccagttcc gcccattctc 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

cgccccatgg ctgactaatt ttttttattt atgcagaggc cgaggccgcc tctgcctctg agctattcca gaagtagtga ggaggctttt ttggaggcct 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

aggcttttgc aaaaagctcc cgggagcttg tatatccatt ttcggatctg atcaagagac aggatgagga tcgtttcgca tgattgaaca agatggattg 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

cacgcaggtt ctccggccgc ttgggtggag aggctattcg gctatgactg ggcacaacag acaatcggct gctctgatgc cgccgtgttc cggctgtcag 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

cgcaggggcg cccggttctt tttgtcaaga ccgacctgtc cggtgccctg aatgaactgc aggacgaggc agcgcggcta tcgtggctgg ccacgacggg 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

cgttccttgc gcagctgtgc tcgacgttgt cactgaagcg ggaagggact ggctgctatt gggcgaagtg ccggggcagg atctcctgtc atctcacctt 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

gctcctgccg agaaagtatc catcatggct gatgcaatgc ggcggctgca tacgcttgat ccggctacct gcccattcga ccaccaagcg aaacatcgca 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

tcgagcgagc acgtactcgg atggaagccg gtcttgtcga tcaggatgat ctggacgaag agcatcaggg gctcgcgcca gccgaactgt tcgccaggct 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

caaggcgcgc atgcccgacg gcgaggatct cgtcgtgacc catggcgatg cctgcttgcc gaatatcatg gtggaaaatg gccgcttttc tggattcatc 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

gactgtggcc ggctgggtgt ggcggaccgc tatcaggaca tagcgttggc tacccgtgat attgctgaag agcttggcgg cgaatgggct gaccgcttcc 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

tcgtgcttta cggtatcgcc gctcccgatt cgcagcgcat cgccttctat cgccttcttg acgagttctt ctgagcggga ctctggggtt cgaaatgacc 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

gaccaagcga cgcccaacct gccatcacga gatttcgatt ccaccgccgc cttctatgaa aggttgggct tcggaatcgt tttccgggac gccggctgga 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

tgatcctcca gcgcggggat ctcatgctgg agttcttcgc ccaccccaac ttgtttattg cagcttataa tggttacaaa taaagcaata gcatcacaaa 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

tttcacaaat aaagcatttt tttcactgca ttctagttgt ggtttgtcca aactcatcaa tgtatcttat catgtctgta taccgtcgac ctctagctag 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

agcttggcgt aatcatggtc atagctgttt cctgtgtgaa attgttatcc gctcacaatt ccacacaaca tacgagccgg aagcataaag tgtaaagcct 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

ggggtgccta atgagtgagc taactcacat taattgcgtt gcgctcactg cccgctttcc agtcgggaaa cctgtcgtgc cagctgcatt aatgaatcgg 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

ccaacgcgcg gggagaggcg gtttgcgtat tgggcgctct tccgcttcct cgctcactga ctcgctgcgc tcggtcgttc ggctgcggcg agcggtatca 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

gctcactcaa aggcggtaat acggttatcc acagaatcag gggataacgc aggaaagaac atgtgagcaa aaggccagca aaaggccagg aaccgtaaaa 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

aggccgcgtt gctggcgttt ttccataggc tccgcccccc tgacgagcat cacaaaaatc gacgctcaag tcagaggtgg cgaaacccga caggactata 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

aagataccag gcgtttcccc ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga tacctgtccg cctttctccc ttcgggaagc 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

gtggcgcttt ctcaatgctc acgctgtagg tatctcagtt cggtgtaggt cgttcgctcc aagctgggct gtgtgcacga accccccgtt cagcccgacc 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

gctgcgcctt atccggtaac tatcgtcttg agtccaaccc ggtaagacac gacttatcgc cactggcagc agccactggt aacaggatta gcagagcgag 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

gtatgtaggc ggtgctacag agttcttgaa gtggtggcct aactacggct acactagaag gacagtattt ggtatctgcg ctctgctgaa gccagttacc 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ttcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

gatctcaaga agatcctttg atcttttcta cggggtctga cgctcagtgg aacgaaaact cacgttaagg gattttggtc atgagattat caaaaaggat 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

cttcacctag atccttttaa attaaaaatg aagttttaaa tcaatctaaa gtatatatga gtaaacttgg tctgacagtt accaatgctt aatcagtgag 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

gcacctatct cagcgatctg tctatttcgt tcatccatag ttgcctgact ccccgtcgtg tagataacta cgatacggga gggcttacca tctggcccca 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

gtgctgcaat gataccgcga gacccacgct caccggctcc agatttatca gcaataaacc agccagccgg aagggccgag cgcagaagtg gtcctgcaac 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

tttatccgcc tccatccagt ctattaattg ttgccgggaa gctagagtaa gtagttcgcc agttaatagt ttgcgcaacg ttgttgccat tgctacaggc 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

atcgtggtgt cacgctcgtc gtttggtatg gcttcattca gctccggttc ccaacgatca aggcgagtta catgatcccc catgttgtgc aaaaaagcgg 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

ttagctcctt cggtcctccg atcgttgtca gaagtaagtt ggccgcagtg ttatcactca tggttatggc agcactgcat aattctctta ctgtcatgcc 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

atccgtaaga tgcttttctg tgactggtga gtactcaacc aagtcattct gagaatagtg tatgcggcga ccgagttgct cttgcccggc gtcaatacgg 
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891      

gataataccg cgccacatag cagaacttta aaagtgctca tcattggaaa acgttcttcg gggcgaaaac tctcaaggat cttaccgctg ttgagatcca 
^6901      ^6911      ^6921      ^6931      ^6941      ^6951      ^6961      ^6971      ^6981      ^6991      

gttcgatgta acccactcgt gcacccaact gatcttcagc atcttttact ttcaccagcg tttctgggtg agcaaaaaca ggaaggcaaa atgccgcaaa 
^7001      ^7011      ^7021      ^7031      ^7041      ^7051      ^7061      ^7071      ^7081      ^7091      

aaagggaata agggcgacac ggaaatgttg aatactcata ctcttccttt ttcaatatta ttgaagcatt tatcagggtt attgtctcat gag
^7101      ^7111      ^7121      ^7131      ^7141      ^7151      ^7161      ^7171      ^7181      ^7191

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

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

1

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

ORF

ORF position:

1

Version: `1`	Last change: `2008-10-27 23:45:50`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
CAT

The description of the protein encoded in this ORF:
chloramphenicol acetyltransferase

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):

304-963

Citations:

Warnakulasuriyarachchi D., Ungureanu N. H., Holcik M. (2003) The translation of an antiapoptotic protein HIAP2 is regulated by an upstream open reading frame. Cell. Death. Differ. 10(8):899-904

IRESs:

IRES:

Version: `1`	Last change: `2008-10-23 12:55:50`
Originaly submitted by: Václav Vopálenský	Reviewed by: Martin Mokrejš
The IRES name: `c-IAP_-150/-1`	The functional status of IRES: `functional`

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

148-297

How IRES boundaries were determined:
experimentally_determined

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

tgatttcttt ttgtggtaaa aatcttagtt catgtgaaga aatttcatgt gaatgtttta gctatcaaac agtactgtca cctactcata cacaaaactg 
^148       ^158       ^168       ^178       ^188       ^198       ^208       ^218       ^228       ^238       

cctcccaaag acttttccca ggtccctcgt atcaaaacat taagagtata
^248       ^258       ^268       ^278       ^288

Remarks:

c-IAP1_-150/-1 IRES represents part of the human c-IAP1 5' UTR (nt from -150 to nt -1).

Citations:

Warnakulasuriyarachchi D., Ungureanu N. H., Holcik M. (2003) The translation of an antiapoptotic protein HIAP2 is regulated by an upstream open reading frame. Cell. Death. Differ. 10(8):899-904

The translation experiments:

Translation results:

IRESite Translation Id: 584

Version: `4`	Last change: `2008-10-23 12:55:50`
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 HEK 293T (ATCC 293tsA1609neo)

The temperature (in degrees of Celsia):
37

The relative translation efficiency in % of this IRES:

1.000

Name of IRES used as the positive control:

XIAP

Name of the plasmid used as the positive control. `pXIAP(1-1076)/CAT`
The relative translation efficiency in % of the positive control: `100.000`
The size (length) of intercistronic region in the positive control: `0`

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:

The c-IAP1 5' UTR contains an upstream ORF (uORF) that prevents translation of the c-IAP1 ORF under normal
conditions (Warnakulasuriyarachchi et al., 2003) (this case of translation experiment).
Subsequent investigations revealed an IRES element at position -149 to position -1 in the c-IAP1 5' UTR that
mediates c-IAP1 translation following endoplasmic reticulum (ER) stress (treatment with etoposide or with
sodium arsenate (Van Eden et al., 2004) or treatment with thapsigargin (an inhibitor of ER calcium pump) or
tunicamycin (an inhibitor of protein glycosylation) (Warnakulasuriyarachchi et al., 2004)). Thus, expression
of c-IAP1 is regulated by a cap-independent translation initiation mechanism following cell stress. ER stress
causes cleavage of the eIF-4G family member p97/DAP5/NAT1 from its p97 form to a p86 form, and the p86 form
induces the activity of the c-IAP1 IRES resulting in an increase in c-IAP1 protein levels. However, direct
binding of the p86 form of p97/DAP5/NAT1 to c-IAP1 IRES RNA has not yet been demonstrated, and therefore p86
may exert its effect on c-IAP1 IRES activity either directly or via a downstream ITAF that interacts with the
c-IAP1 IRES.

Translational data are derived from Fig. 3A.

Citations:

Warnakulasuriyarachchi D., Ungureanu N. H., Holcik M. (2003) The translation of an antiapoptotic protein HIAP2 is regulated by an upstream open reading frame. Cell. Death. Differ. 10(8):899-904

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