The nucleic acid data:
IRESite Id: 354 Version: 4
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš Last change: 2008-06-04 22:22:42
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:
  end-to-end_full-length_mRNA
The mRNA/+RNA description: 
In vitro T3 run-off transcript containing 5' region of EMCV-R containing the IRES (-574 to -1) plus the first
8 nucleotides from the viral polyprotein cloned upstream of the luciferase reporter RNA with a poly(A) tail.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_completely_same_as_in_the_experiment
The name of the plasmid:
pEMCV.IRES-luc-pA
The name of the promoter used to express this mRNA:
  T3
Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing part of EMCV-R 5' UTR (-574 to -1) plus the first 8 nucleotides from the viral polyprotein (+1 to +8) and firefly luciferase coding region (luc version of the luciferase gene) with the poly(A) tract.
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:


Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks):
  plasmid sequence confirmed by IRESite curators by restriction analysis + parts by PCR + sequencing
GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
pEMCV.IRES-luc-pA.jpg
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: 2008-06-04 11:43:22
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
FFluc
The description of the protein encoded in this ORF:
firefly 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):
  652-2304
Remarks:
IRESite notes about verification of plasmid sequence:
The complete sequence of IRES element was determined by sequencing using pEMCV - M13_reverse primer
(CAGGAAACAGCTATGAC)
Citations:
Bergamini G., Preiss T., Hentze M. W. (2000) Picornavirus IRESes and the poly(A) tail jointly promote cap-independent translation in a mammalian cell-free system. RNA. 6(12):1781-1790
IRESs:
IRES:
Version: 3 Last change: 2011-04-08 21:49:13
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  EMCV-R_260-841
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  62-644
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
DNA fragment (-574 to +8) containing the EMCV-R IRES and 8 nucleotides from the viral polyprotein.
Citations:
Bergamini G., Preiss T., Hentze M. W. (2000) Picornavirus IRESes and the poly(A) tail jointly promote cap-independent translation in a mammalian cell-free system. RNA. 6(12):1781-1790
The translation experiments:
Translation results:
IRESite Translation Id: 425
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The translation method used to study IRES function:
in vitro
The in vitro translation system:
HeLa cell lysate
The organism used for translation:
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  100.000
Name of the plasmid used as the negative control.
pT3Luc-pA
IRESite Id of the plasmid used as negative control.
  347
The relative translation efficiency in % of the negative control:
  0.050
The effect of 5'-cap analogs on translation:
no
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  exogenous_RNA_with_ApppG_cap_with_polyA_tail
Remarks:
Translation of EMCV.IRES-pA RNA is unaffected by increasing amounts of m7GpppG competitor (see Fig. 7D).
The translation of EMCV.IRES-pA RNA is about 2.5-fold higher efficient than the translation of the
polyadenylated counterpart EMCV.IRES RNA (see Fig. 6B).
Translational data are derived from Fig. 6B.
Citations:
Bergamini G., Preiss T., Hentze M. W. (2000) Picornavirus IRESes and the poly(A) tail jointly promote cap-independent translation in a mammalian cell-free system. RNA. 6(12):1781-1790
Last change to the database: 2015-04-16 16:45:23 GMT+1