IRESite_Id:544 characteristics of EMCV-R_335-834 IRES studied in pCITE-2a plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `544`	Version: `1`
Originaly submitted by: Martin Mokrejš	Submission date: `2008-12-20 16:26:53`
Reviewed by: Martin Mokrejš	Last change: `2011-04-08 22:11:58`

IRESite record type:

plasmid_with_promoter_and_putative_IRES_without_translational_characterization

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

The mRNA/+RNA description:

Putative in vitro T7 promoter derived transcript of the empty vector up to the linearization PstI site.

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

gggcgaatta attccggtta ttttccacca tattgccgtc ttttggcaat gtgagggccc ggaaacctgg ccctgtcttc ttgacgagca ttcctagggg 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tctttcccct ctcgccaaag gaatgcaagg tctgttgaat gtcgtgaagg aagcagttcc tctggaagct tcttgaagac aaacaacgtc tgtagcgacc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ctttgcaggc agcggaaccc cccacctggc gacaggtgcc tctgcggcca aaagccacgt gtataagata cacctgcaaa ggcggcacaa ccccagtgcc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

acgttgtgag ttggatagtt gtggaaagag tcaaatggct ctcctcaagc gtattcaaca aggggctgaa ggatgcccag aaggtacccc attgtatggg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

atctgatctg gggcctcggt gcacatgctt tacatgtgtt tagtcgaggt taaaaaacgt ctaggccccc cgaaccacgg ggacgtggtt ttcctttgaa 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

aaacacgatg ataataccat ggccaccacc catatggata tcggatccga attcgagctc cgtcgacaag cttgcggccg cactcgagca ccaccaccac 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

caccactgag atctccgatc ctctagagtc gatcgacctg ca
^601       ^611       ^621       ^631       ^641

Credibility of mRNA sequence:

reverse_engineered_sequence_and_should_match_experiment_except_3UTR

The name of the plasmid:
pCITE-2a The name of the promoter used to express this mRNA:
T7

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

not tested

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

not tested

A promoter reported in cDNA corresponding to IRES sequence:

not tested

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

The origin of IRES in the plasmid:

viral

The donor organism of the IRES segment:

Encephalomyocarditis virus Rueckert

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

gggcgaatta attccggtta ttttccacca tattgccgtc ttttggcaat gtgagggccc ggaaacctgg ccctgtcttc ttgacgagca ttcctagggg 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tctttcccct ctcgccaaag gaatgcaagg tctgttgaat gtcgtgaagg aagcagttcc tctggaagct tcttgaagac aaacaacgtc tgtagcgacc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ctttgcaggc agcggaaccc cccacctggc gacaggtgcc tctgcggcca aaagccacgt gtataagata cacctgcaaa ggcggcacaa ccccagtgcc 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

acgttgtgag ttggatagtt gtggaaagag tcaaatggct ctcctcaagc gtattcaaca aggggctgaa ggatgcccag aaggtacccc attgtatggg 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

atctgatctg gggcctcggt gcacatgctt tacatgtgtt tagtcgaggt taaaaaacgt ctaggccccc cgaaccacgg ggacgtggtt ttcctttgaa 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

aaacacgatg ataataccat ggccaccacc catatggata tcggatccga attcgagctc cgtcgacaag cttgcggccg cactcgagca ccaccaccac 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

caccactgag atctccgatc ctctagagtc gatcgacctg caggcatgca agcttttgtt ccctttagtg agggttaatt tcgagcttgg cgtaatcatg 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

gtcatagctg tttcctgtgt gaaattgtta tccgctcaca attccacaca acatacgagc cggaagcata aagtgtaaag cctggggtgc ctaatgagtg 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

agctaactca cattaattgc gttgcgctca ctgcccgctt tccagtcggg aaacctgtcg tgccagctgc attaatgaat cggccaacgc gcggggagag 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

gcggtttgcg tattgggcgc tcttccgctt cctcgctcac tgactcgctg cgctcggtcg ttcggctgcg gcgagcggta tcagctcact caaaggcggt 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

aatacggtta tccacagaat caggggataa cgcaggaaag aacatgtgag caaaaggcca gcaaaaggcc aggaaccgta aaaaggccgc gttgctggcg 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

tttttccata ggctccgccc ccctgacgag catcacaaaa atcgacgctc aagtcagagg tggcgaaacc cgacaggact ataaagatac caggcgtttc 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

cccctggaag ctccctcgtg cgctctcctg ttccgaccct gccgcttacc ggatacctgt ccgcctttct cccttcggga agcgtggcgc tttctcatag 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ctcacgctgt aggtatctca gttcggtgta ggtcgttcgc tccaagctgg gctgtgtgca cgaacccccc gttcagcccg accgctgcgc cttatccggt 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

aactatcgtc ttgagtccaa cccggtaaga cacgacttat cgccactggc agcagccact ggtaacagga ttagcagagc gaggtatgta ggcggtgcta 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

cagagttctt gaagtggtgg cctaactacg gctacactag aaggacagta tttggtatct gcgctctgct gaagccagtt accttcggaa aaagagttgg 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tagctcttga tccggcaaac aaaccaccgc tggtagcggt ggtttttttg tttgcaagca gcagattacg cgcagaaaaa aaggatctca agaagatcct 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ttgatctttt ctacggggtc tgacgctcag tggaacgaaa actcacgtta agggattttg gtcatgagat tatcaaaaag gatcttcacc tagatccttt 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

taaattaaaa atgaagtttt aaatcaatct aaagtatata tgagtaaact tggtctgaca gttaccaatg cttaatcagt gaggcaccta tctcagcgat 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ctgtctattt cgttcatcca tagttgcctg actccccgtc gtgtagataa ctacgatacg ggagggctta ccatctggcc ccagtgctgc aatgataccg 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

cgagacccac gctcaccggc tccagattta tcagcaataa accagccagc cggaagggcc gagcgcagaa gtggtcctgc aactttatcc gcctccatcc 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

agtctattaa ttgttgccgg gaagctagag taagtagttc gccagttaat agtttgcgca acgttgttgc cattgctaca ggcatcgtgg tgtcacgctc 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

gtcgtttggt atggcttcat tcagctccgg ttcccaacga tcaaggcgag ttacatgatc ccccatgttg tgcaaaaaag cggttagctc cttcggtcct 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ccgatcgttg tcagaagtaa gttggccgca gtgttatcac tcatggttat ggcagcactg cataattctc ttactgtcat gccatccgta agatgctttt 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

ctgtgactgg tgagtactca accaagtcat tctgagaata gtgtatgcgg cgaccgagtt gctcttgccc ggcgtcaata cgggataata ccgcgccaca 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

tagcagaact ttaaaagtgc tcatcattgg aaaacgttct tcggggcgaa aactctcaag gatcttaccg ctgttgagat ccagttcgat gtaacccact 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

cgtgcaccca actgatcttc agcatctttt actttcacca gcgtttctgg gtgagcaaaa acaggaaggc aaaatgccgc aaaaaaggga ataagggcga 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

cacggaaatg ttgaatactc atactcttcc tttttcaata ttattgaagc atttatcagg gttattgtct catgagcgga tacatatttg aatgtattta 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

gaaaaataaa caaatagggg ttccgcgcac atttccccga aaagtgccac ctgacgtcta agaaaccatt attatcatga cattaaccta taaaaatagg 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

cgtatcacga ggccctttcg tctcgcgcgt ttcggtgatg acggtgaaaa cctctgacac atgcagctcc cggagacggt cacagcttgt ctgtaagcgg 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

atgccgggag cagacaagcc cgtcagggcg cgtcagcggg tgttggcggg tgtcggggct ggcttaacta tgcggcatca gagcagattg tactgagagt 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

gcaccatata tgcggtgtga aataccgcac agatgcgtaa ggagaaaata ccgcatcagg aaattgtaaa cgttaatatt ttgttaaaat tcgcgttaaa 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

tttttgttaa atcagctcat tttttaacca ataggccgaa atcggcaaaa tcccttataa atcaaaagaa tagaccgaga tagggttgag tgttgttcca 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

gtttggaaca agagtccact attaaagaac gtggactcca acgtcaaagg gcgaaaaacc gtctatcagg gcgatggccc actacgtgaa ccatcaccct 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

aatcaagttt tttggggtcg aggtgccgta aagcactaaa tcggaaccct aaagggagcc cccgatttag agcttgacgg ggaaagccgg cgaacgtggc 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

gagaaaggaa gggaagaaag cgaaaggagc gggcgctagg gcgctggcaa gtgtagcggt cacgctgcgc gtaaccacca cacccgccgc gcttaatgcg 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

ccgctacagg gcgcgtcgcg ccattcgcca ttcaggctgc gcaactgttg ggaagggcga tcggtgcggg cctcttcgct attacgccag ctggcgaaag 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ggggatgtgc tgcaaggcga ttaagttggg taacgccagg gttttcccag tcacgacgtt gtaaaacgac ggccagtgaa ttgtaatacg actcactata
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791

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

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

1

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

ORF

ORF position:

1

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

The abbreviated name of this ORF/gene:
fusion_protein

The description of the protein encoded in this ORF:
fusion protein spanning the MCS site and His tag

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):

519-626

Remarks:

This is the ORF encoded by the empty vector and annotated here for completeness. However, it is always
destroyed by insertion of a reporter protein into the multiple cloning site of the vector. The initiator ATG
codon is overlapped by NcoI site.

Original information from Novagen: http://www.emdbiosciences.com/Products/ProductDisplay.asp?catno=69290

IRESs:

IRES:

Version: `1`	Last change: `2011-04-08 22:11:58`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `EMCV-R_335-834`	The functional status of IRES: `functional`

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

17-516

How IRES boundaries were determined:
experimentally_determined

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

gttattttcc accatattgc cgtcttttgg caatgtgagg gcccggaaac ctggccctgt cttcttgacg agcattccta ggggtctttc ccctctcgcc 
^17        ^27        ^37        ^47        ^57        ^67        ^77        ^87        ^97        ^107       

aaaggaatgc aaggtctgtt gaatgtcgtg aaggaagcag ttcctctgga agcttcttga agacaaacaa cgtctgtagc gaccctttgc aggcagcgga 
^117       ^127       ^137       ^147       ^157       ^167       ^177       ^187       ^197       ^207       

accccccacc tggcgacagg tgcctctgcg gccaaaagcc acgtgtataa gatacacctg caaaggcggc acaaccccag tgccacgttg tgagttggat 
^217       ^227       ^237       ^247       ^257       ^267       ^277       ^287       ^297       ^307       

agttgtggaa agagtcaaat ggctctcctc aagcgtattc aacaaggggc tgaaggatgc ccagaaggta ccccattgta tgggatctga tctggggcct 
^317       ^327       ^337       ^347       ^357       ^367       ^377       ^387       ^397       ^407       

cggtgcacat gctttacatg tgtttagtcg aggttaaaaa acgtctaggc cccccgaacc acggggacgt ggttttcctt tgaaaaacac gatgataata
^417       ^427       ^437       ^447       ^457       ^467       ^477       ^487       ^497       ^507

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