IRESite_Id:385 negative control plasmid pNBio

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `385`	Version: `1`
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš	Last change: `2008-06-12 15:26:09`

IRESite record type:

negative_control_plasmid_with_promoter_and_without_putative_IRES

The shape of the nucleic acid molecule translated:
linear The quality of the mRNA/+RNA sequence:
3UTR_incomplete

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
104744457

The mRNA/+RNA description:

One of the two putative in vivo transcripts of mammalian expression vector pNBio: this one is from SV40
promoter only to the end of CDS because the SV40 late poly(A) signal is inserted in reverse direction and
therefore is probably non-functional.

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

TATTCCAGAA GTAGTGAGGA GGCTTTTTTG GAGGCCTAGG CTTTTGCAAA AAGCTtgcat gcctgcaggt cggccgccac gaccggtgcc gccaccatcc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

cctgacccac gcccctgacc cctcacaagg agacgacctt ccatgaccga gtacaagccc acggtgcgcc tcgccacccg cgacgacgtc ccccgggccg 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

tacgcaccct cgccgccgcg ttcgccgact accccgccac gcgccacacc gtcgacccgg accgccacat cgagcgggtc accgagctgc aagaactctt 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

cctcacgcgc gtcgggctcg acatcggcaa ggtgtgggtc gcggacgacg gcgccgcggt ggcggtctgg accacgccgg agagcgtcga agcgggggcg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

gtgttcgccg agatcggccc gcgcatggcc gagttgagcg gttcccggct ggccgcgcag caacagatgg aaggcctcct ggcgccgcac cggcccaagg 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

agcccgcgtg gttcctggcc accgtcggcg tctcgcccga ccaccagggc aagggtctgg gcagcgccgt cgtgctcccc ggagtggagg cggccgagcg 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

cgccggggtg cccgccttcc tggagacctc cgcgccccgc aacctcccct tctacgagcg gctcggcttc accgtcaccg ccgacgtcga ggtgcccgaa 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ggaccgcgca cctggtgcat gacccgcaag cccggtgcct ga
^701       ^711       ^721       ^731       ^741

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_except_3UTR

The name of the plasmid:
pNBio The name of the promoter used to express this mRNA:
SV40

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

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

ctcgagttta ccactcccta tcagtgatag agaaaagtga aagtcgagtt taccactccc tatcagtgat agagaaaagt gaaagtcgag tttaccactc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

cctatcagtg atagagaaaa gtgaaagtcg agtttaccac tccctatcag tgatagagaa aagtgaaagt cgagtttacc actccctatc agtgatagag 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

aaaagtgaaa gtcgagttta ccactcccta tcagtgatag agaaaagtga aagtcgagtt taccactccc tatcagtgat agagaaaagt gaaagtcgag 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ctcggtaccc gggtcgaggt aggcgtgtac ggtgggaggc ctatataagc agagctcgtt tagtgaaccg tcagatcgcc tggagacgcc atccacgctg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ttttgacctc catagaagac accgggaccg atccagcctc cgcggccccg aattcgagct cggtacccgg ggatctgccg ccaccatggg cctgaacgac 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

atcttcgaag ctcagaaaat cgaatggcac gggatccgat atcgcggccg cttgaacgac atttttgaag cgcaaaaaat tgaatggcat taaggccgcg 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ctagcctcga gaattcacgc gtcgagcatg catctagggc ggccaattcc gcccctctcc ctcccccccc cctaacgtta ctggccgaag ccgcttggaa 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

taaggccggt gtgcgtttgt ctatatgtga ttttccacca tattgccgtc ttttggcaat gtgagggccc ggaaacctgg ccctgtcttc ttgacgagca 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ttcctagggg tctttcccct ctcgccaaag gaatgcaagg tctgttgaat gtcgtgaagg aagcagttcc tctggaagct tcttgaagac aaacaacgtc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

tgtagcgacc ctttgcaggc agcggaaccc cccacctggc gacaggtgcc tctgcggcca aaagccacgt gtataagata cacctgcaaa ggcggcacaa 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ccccagtgcc acgttgtgag ttggatagtt gtggaaagag tcaaatggct ctcctcaagc gtattcaaca aggggctgaa ggatgcccag aaggtacccc 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

attgtatggg atctgatctg gggcctcggt gcacatgctt tacatgtgtt tagtcgaggt taaaaaaacg tctaggcccc ccgaaccacg gggacgtggt 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tttcctttga aaaacacgat gataagcttg ccacaaccca aacttaagct tggtaccgag ctcggatctg ccgccaccat ggattacaag gatgacgacg 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ataagagccc gagatccatg aaggataaca ccgtgccact gaaattgatt gccctgttag cgaacggtga atttcactct ggcgagcagt tgggtgaaac 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

gctgggaatg agccgggcgg ctattaataa acacattcag acactgcgtg actggggcgt tgatgtcttt accgttccgg gtaaaggata cagcctgcct 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

gagcctatcc agttacttaa tgctaaacag atattgggtc agctggatgg cggtagtgta gccgtgctgc cagtgattga ctccacgaat cagtaccttc 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ttgatcgtat cggagagctt aaatcgggcg atgcttgcat tgcagaatac cagcaggctg gccgtggtcg ccggggtcgg aaatggtttt cgccttttgg 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

cgcaaactta tatttgtcga tgttctggcg tctggaacaa ggcccggcgg cggcgattgg tttaagtctg gttatcggta tcgtgatggc ggaagtatta 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

cgcaagctgg gtgcagataa agttcgtgtt aaatggccta atgacctcta tctgcaggat cgcaagctgg caggcattct ggtggagctg actggcaaaa 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ctggcgatgc ggcgcaaata gtcattggag ccgggatcaa catggcaatg cgccgtgttg aagagagtgt cgttaatcag gggtggatca cgctgcagga 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

agcggggatc aatctcgatc gtaatacgtt ggcggccatg ctaatacgtg aattacgtgc tgcgttggaa ctcttcgaac aagaaggatt ggcaccttat 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ctgtcgcgct gggaaaagct ggataatttt attaatcgcc cagtgaaact tatcattggt gataaagaaa tatttggcat ttcacgcgga atagacaaac 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

agggggcttt attacttgag caggatggaa taataaaacc ctggatgggc ggtgaaatat ccctgcgtag tgcagaaaaa taagaattca gatctctgca 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

gctcgagtct agagggcccg tttatctcta gagctgagaa cttcagggtg agtttgggga cccttgattg ttctttcttt ttcgctattg taaaattcat 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

gttatatgga gggggcaaag ttttcagggt gttgtttaga atgggaagat gtcccttgta tcaccatgga ccctcatgat aattttgttt ctttcacttt 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ctactctgtt gacaaccatt gtctcctctt attttctttt cattttctgt aacttttttc gttaaacttt agcttgcatt tgtaacgaat ttttaaattc 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

actttcgttt atttgtcaga ttgtaagtac tttctctaat cacttttttt tcaaggcaat cagggtaatt atattgtact tcagcacagt tttagagaac 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

aattgttata attaaatgat aaggtagaat atttctgcat ataaattctg gctggcgtgg aaatattctt attggtagaa acaactacat cctggtaatc 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

atcctgcctt tctctttatg gttacaatga tatacactgt ttgagatgag gataaaatac tctgagtcca aaccgggccc ctctgctaac catgttcatg 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

ccttcttctt tttcctacag ctcctgggca acgtgctggt tgttgtgctg tctcatcatt ttggcaaaga attcactcct caggtgcagg ctgcctatca 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

gaaggtggtg gctggtgtgg ccaatgccct ggctcacaaa taccactgag atctttttcc ctctgccaaa aattatgggg acatcatgaa gccccttgag 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

catctgactt ctgggtaata aaggaaattt attttcattg caatagtgtg tgggaatttt ttgtgtctct cactcggaag gacatatggg agggcaaatc 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

atttaaaaca tcagaatgag tatttggttt agagtttggc aacatatgcc atatgctggc tgccatgaac aaaggtggct ataaagaggt catcagtata 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

tgaaacagcc ccctgctgtc cattccttat tccatagaaa agccttgact tgaggttaga ttttttttat attttgtttt gtgttatttt tttctttaac 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

atccctaaaa ttttccttac atgttttact agccagattt ttcctcctct cctgactact cccagtcata gctgtccctc ttctcttatg aactcgactg 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

cattaatgaa tcggccaacg cgcggggaga ggcggtttgc gtattgggcg ctcttccgct tcctcgctca ctgactcgct gcgctcggtc gttcggctgc 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ggcgagcggt atcagctcac tcaaaggcgg taatacggtt atccacagaa tcaggggata acgcaggaaa gaacatgtga gcaaaaggcc agcaaaaggc 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

caggaaccgt aaaaaggccg cgttgctggc gtttttccat aggctccgcc cccctgacga gcatcacaaa aatcgacgct caagtcagag gtggcgaaac 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

ccgacaggac tataaagata ccaggcgttt ccccctggaa gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

tcccttcggg aagcgtggcg ctttctcaat gctcacgctg taggtatctc agttcggtgt aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

cgttcagccc gaccgctgcg ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta tcgccactgg cagcagccac tggtaacagg 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

attagcagag cgaggtatgt aggcggtgct acagagttct tgaagtggtg gcctaactac ggctacacta gaaggacagt atttggtatc tgcgctctgc 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

tgaagccagt taccttcgga aaaagagttg gtagctcttg atccggcaaa caaaccaccg ctggtagcgg tggttttttt gtttgcaagc agcagattac 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

gcgcagaaaa aaaggatctc aagaagatcc tttgatcttt tctacggggt ctgacgctca gtggaacgaa aactcacgtt aagggatttt ggtcatgaga 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

ttatcaaaaa ggatcttcac ctagatcctt ttaaattaaa aatgaagttt taaatcaatc taaagtatat atgagtaaac ttggtctgac agttaccaat 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

gcttaatcag tgaggcacct atctcagcga tctgtctatt tcgttcatcc atagttgcct gactccccgt cgtgtagata actacgatac gggagggctt 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

accatctggc cccagtgctg caatgatacc gcgagaccca cgctcaccgg ctccagattt atcagcaata aaccagccag ccggaagggc cgagcgcaga 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

agtggtcctg caactttatc cgcctccatc cagtctatta attgttgccg ggaagctaga gtaagtagtt cgccagttaa tagtttgcgc aacgttgttg 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

ccattgctac aggcatcgtg gtgtcacgct cgtcgtttgg tatggcttca ttcagctccg gttcccaacg atcaaggcga gttacatgat cccccatgtt 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

gtgcaaaaaa gcggttagct ccttcggtcc tccgatcgtt gtcagaagta agttggccgc agtgttatca ctcatggtta tggcagcact gcataattct 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

cttactgtca tgccatccgt aagatgcttt tctgtgactg gtgagtactc aaccaagtca ttctgagaat agtgtatgcg gcgaccgagt tgctcttgcc 
^5001      ^5011      ^5021      ^5031      ^5041      ^5051      ^5061      ^5071      ^5081      ^5091      

cggcgtcaat acgggataat accgcgccac atagcagaac tttaaaagtg ctcatcattg gaaaacgttc ttcggggcga aaactctcaa ggatcttacc 
^5101      ^5111      ^5121      ^5131      ^5141      ^5151      ^5161      ^5171      ^5181      ^5191      

gctgttgaga tccagttcga tgtaacccac tcgtgcaccc aactgatctt cagcatcttt tactttcacc agcgtttctg ggtgagcaaa aacaggaagg 
^5201      ^5211      ^5221      ^5231      ^5241      ^5251      ^5261      ^5271      ^5281      ^5291      

caaaatgccg caaaaaaggg aataagggcg acacggaaat gttgaatact catactcttc ctttttcaat attattgaag catttatcag ggttattgtc 
^5301      ^5311      ^5321      ^5331      ^5341      ^5351      ^5361      ^5371      ^5381      ^5391      

tcatgagcgg atacatattt gaatgtattt agaaaaataa acaaataggg gttccgcgca catttccccg aaaagtgcca cctgacgtct aagaaaccat 
^5401      ^5411      ^5421      ^5431      ^5441      ^5451      ^5461      ^5471      ^5481      ^5491      

tattatcatg acattaacct ataaaaatag gcgtatcacg aggccctttc gtcttcactc gagtgtgtca gttagggtgt ggaaagtccc caggctcccc 
^5501      ^5511      ^5521      ^5531      ^5541      ^5551      ^5561      ^5571      ^5581      ^5591      

agcaggcaga agtatgcaaa gcatgcatct caattagtca gcaaccaggt gtggaaagtc cccaggctcc ccagcaggca gaagtatgca aagcatgcat 
^5601      ^5611      ^5621      ^5631      ^5641      ^5651      ^5661      ^5671      ^5681      ^5691      

ctcaattagt cagcaaccat agtcccgccc ctaactccgc ccatcccgcc cctaactccg cccagttccg cccattctcc gccccatggc tgaCTAATTT 
^5701      ^5711      ^5721      ^5731      ^5741      ^5751      ^5761      ^5771      ^5781      ^5791      

TTTTTATTTA TGCAGAGGCC GAGGCCGCCT CGGCCTCTGA GCTATTCCAG AAGTAGTGAG GAGGCTTTTT TGGAGGCCTA GGCTTTTGCA AAAAGCTtgc 
^5801      ^5811      ^5821      ^5831      ^5841      ^5851      ^5861      ^5871      ^5881      ^5891      

atgcctgcag gtcggccgcc acgaccggtg ccgccaccat cccctgaccc acgcccctga cccctcacaa ggagacgacc ttccatgacc gagtacaagc 
^5901      ^5911      ^5921      ^5931      ^5941      ^5951      ^5961      ^5971      ^5981      ^5991      

ccacggtgcg cctcgccacc cgcgacgacg tcccccgggc cgtacgcacc ctcgccgccg cgttcgccga ctaccccgcc acgcgccaca ccgtcgaccc 
^6001      ^6011      ^6021      ^6031      ^6041      ^6051      ^6061      ^6071      ^6081      ^6091      

ggaccgccac atcgagcggg tcaccgagct gcaagaactc ttcctcacgc gcgtcgggct cgacatcggc aaggtgtggg tcgcggacga cggcgccgcg 
^6101      ^6111      ^6121      ^6131      ^6141      ^6151      ^6161      ^6171      ^6181      ^6191      

gtggcggtct ggaccacgcc ggagagcgtc gaagcggggg cggtgttcgc cgagatcggc ccgcgcatgg ccgagttgag cggttcccgg ctggccgcgc 
^6201      ^6211      ^6221      ^6231      ^6241      ^6251      ^6261      ^6271      ^6281      ^6291      

agcaacagat ggaaggcctc ctggcgccgc accggcccaa ggagcccgcg tggttcctgg ccaccgtcgg cgtctcgccc gaccaccagg gcaagggtct 
^6301      ^6311      ^6321      ^6331      ^6341      ^6351      ^6361      ^6371      ^6381      ^6391      

gggcagcgcc gtcgtgctcc ccggagtgga ggcggccgag cgcgccgggg tgcccgcctt cctggagacc tccgcgcccc gcaacctccc cttctacgag 
^6401      ^6411      ^6421      ^6431      ^6441      ^6451      ^6461      ^6471      ^6481      ^6491      

cggctcggct tcaccgtcac cgccgacgtc gaggtgcccg aaggaccgcg cacctggtgc atgacccgca agcccggtgc ctgacgcccg ccccacgacc 
^6501      ^6511      ^6521      ^6531      ^6541      ^6551      ^6561      ^6571      ^6581      ^6591      

cgcagcgccc gaccgaaagg agcgcacgac cccatggctc cgaccgaagc cgacccgggc ggccccgccg accccgcacc cgcccccgag gcccaccgac 
^6601      ^6611      ^6621      ^6631      ^6641      ^6651      ^6661      ^6671      ^6681      ^6691      

tctagaggat cataatcagc cataccacat ttgtagaggt tttacttgct ttaaaaaacc tcccacacct ccccctgaac ctgaaacata aaatgaatgc 
^6701      ^6711      ^6721      ^6731      ^6741      ^6751      ^6761      ^6771      ^6781      ^6791      

aattgttgtt gttaacttgt ttattgcagc ttataatggt tacaaataaa gcaatagcat cacaaatttc acaaataaag catttttttc actgc
^6801      ^6811      ^6821      ^6831      ^6841      ^6851      ^6861      ^6871      ^6881      ^6891

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

A promoter reported in cDNA corresponding to IRES sequence:
not tested 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: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
Pur

The description of the protein encoded in this ORF:
puromycin N-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):

143-742

Citations:

Kulman J. D., Satake M., Harris J. E. (2007) A versatile system for site-specific enzymatic biotinylation and regulated expression of proteins in cultured mammalian cells. Protein Expr. Purif. 52(2):320-328

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