IRESite_Id:545 characteristics of EMCV-R_335-834 IRES studied in pCITE-4a plasmid

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `545`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2008-12-20 16:36:29`
Reviewed by: Martin Mokrejš

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:
hopefully_full-length_mRNA

The mRNA/+RNA description:

Putative in vitro transcript from an empty vector from T7 promoter up to Tphi transcription terminator
containing 30 nt long poly(A) stretch after the ORF but not at the physical 3'-end of the transcript.

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 cacctcaagc 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 ataatatggc caccacccat atgaaagaaa ccgctgctgc taaattcgaa cgccagcaca tggacagccc agatcagggt accctggtgc 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

cacgcggttc catggctgat atcggatccg aattcgagct ccgtcgacaa gcttgcggcc gcactcgagc accaccacca ccaccactga gatctgactg 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa gtttaaacac tagtccgctg agcaataact agcataaccc cttggggcct ctaaacgggt cttgaggggt 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

tttttg
^801

Credibility of mRNA sequence:

end-to-end_sequence_reverse_engineered_and_should_match_experiment

The name of the plasmid:
pCITE-4a 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 cacctcaagc 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 ataatatggc caccacccat atgaaagaaa ccgctgctgc taaattcgaa cgccagcaca tggacagccc agatcagggt accctggtgc 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

cacgcggttc catggctgat atcggatccg aattcgagct ccgtcgacaa gcttgcggcc gcactcgagc accaccacca ccaccactga gatctgactg 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa gtttaaacac tagtccgctg agcaataact agcataaccc cttggggcct ctaaacgggt cttgaggggt 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

tttttgctga aaggaggaac tatatccggg cttcctcgct cactgactcg ctgcgctcgg tcgttcggct gcggcgagcg gtatcagctc actcaaaggc 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

ggtaatacgg ttatccacag aatcagggga taacgcagga aagaacatgt gagcaaaagg ccagcaaaag gccaggaacc gtaaaaaggc cgcgttgctg 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

gcgtttttcc ataggctccg cccccctgac gagcatcaca aaaatcgacg ctcaagtcag aggtggcgaa acccgacagg actataaaga taccaggcgt 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ttccccctgg aagctccctc gtgcgctctc ctgttccgac cctgccgctt accggatacc tgtccgcctt tctcccttcg ggaagcgtgg cgctttctca 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

tagctcacgc tgtaggtatc tcagttcggt gtaggtcgtt cgctccaagc tgggctgtgt gcacgaaccc cccgttcagc ccgaccgctg cgccttatcc 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

ggtaactatc gtcttgagtc caacccggta agacacgact tatcgccact ggcagcagcc actggtaaca ggattagcag agcgaggtat gtaggcggtg 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ctacagagtt cttgaagtgg tggcctaact acggctacac tagaaggaca gtatttggta tctgcgctct gctgaagcca gttaccttcg gaaaaagagt 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

tggtagctct tgatccggca aacaaaccac cgctggtagc ggtggttttt ttgtttgcaa gcagcagatt acgcgcagaa aaaaaggatc tcaagaagat 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

cctttgatct tttctacggg gtctgacgct cagtggaacg aaaactcacg ttaagggatt ttggtcatga gattatcaaa aaggatcttc acctagatcc 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ttttaaatta aaaatgaagt tttaaatcaa tctaaagtat atatgagtaa acttggtctg acagttacca atgcttaatc agtgaggcac ctatctcagc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

gatctgtcta tttcgttcat ccatagttgc ctgactcccc gtcgtgtaga taactacgat acgggagggc ttaccatctg gccccagtgc tgcaatgata 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ccgcgagacc cacgctcacc ggctccagat ttatcagcaa taaaccagcc agccggaagg gccgagcgca gaagtggtcc tgcaacttta tccgcctcca 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

tccagtctat taattgttgc cgggaagcta gagtaagtag ttcgccagtt aatagtttgc gcaacgttgt tgccattgct acaggcatcg tggtgtcacg 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ctcgtcgttt ggtatggctt cattcagctc cggttcccaa cgatcaaggc gagttacatg atcccccatg ttgtgcaaaa aagcggttag ctccttcggt 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

cctccgatcg ttgtcagaag taagttggcc gcagtgttat cactcatggt tatggcagca ctgcataatt ctcttactgt catgccatcc gtaagatgct 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

tttctgtgac tggtgagtac tcaaccaagt cattctgaga atagtgtatg cggcgaccga gttgctcttg cccggcgtca atacgggata ataccgcgcc 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

acatagcaga actttaaaag tgctcatcat tggaaaacgt tcttcggggc gaaaactctc aaggatctta ccgctgttga gatccagttc gatgtaaccc 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

actcgtgcac ccaactgatc ttcagcatct tttactttca ccagcgtttc tgggtgagca aaaacaggaa ggcaaaatgc cgcaaaaaag ggaataaggg 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

cgacacggaa atgttgaata ctcatactct tcctttttca atattattga agcatttatc agggttattg tctcatgagc ggatacatat ttgaatgtat 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

ttagaaaaat aaacaaatag gggttccgcg cacatttccc cgaaaagtgc cacctgacgt ctaagaaacc attattatca tgacattaac ctataaaaat 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

aggcgtatca cgaggccctt tcgtctcgcg cgtttcggtg atgacggtga aaacctctga cacatgcagc tcccggagac ggtcacagct tgtctgtaag 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

cggatgccgg gagcagacaa gcccgtcagg gcgcgtcagc gggtgttggc gggtgtcggg gctggcttaa ctatgcggca tcagagcaga ttgtactgag 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

agtgcaccat atatgcggtg tgaaataccg cacagatgcg taaggagaaa ataccgcatc aggaaattgt aaacgttaat attttgttaa aattcgcgtt 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

aaatttttgt taaatcagct cattttttaa ccaataggcc gaaatcggca aaatccctta taaatcaaaa gaatagaccg agatagggtt gagtgttgtt 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

ccagtttgga acaagagtcc actattaaag aacgtggact ccaacgtcaa agggcgaaaa accgtctatc agggcgatgg cccactacgt gaaccatcac 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

cctaatcaag ttttttgggg tcgaggtgcc gtaaagcact aaatcggaac cctaaaggga gcccccgatt tagagcttga cggggaaagc cggcgaacgt 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ggcgagaaag gaagggaaga aagcgaaagg agcgggcgct agggcgctgg caagtgtagc ggtcacgctg cgcgtaacca ccacacccgc cgcgcttaat 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

gcgccgctac agggcgcgtc gcgccattcg ccattcaggc tgcgcaactg ttgggaaggg cgatcggtgc gggcctcttc gctattacgc cagctggcga 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

aagggggatg tgctgcaagg cgattaagtt gggtaacgcc agggttttcc cagtcacgac gttgtaaaac gacggccagt gaattgtaat acgactcact 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ata
^3701

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:
S-tag N-terminal fusion 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):

516-701

Remarks:

Vendor information: http://www.emdbiosciences.com/product/69913

IRESs:

IRES:

Version: `1`	Last change: `2011-04-08 22:13:01`
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 ggctcacctc 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