The nucleic acid data:
IRESite Id: 351 Version: 3
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš Last change: 2008-06-04 15:43:01
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 HAV (HM-175/7 MK-5 strain) containing the IRES (-699 to
-1) plus the region encoding the first 51 amino acids of the viral nucleocapsid cloned upstream of the
luciferase reporter RNA lacking 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:
pHAV.IRES-luc
The name of the promoter used to express this mRNA:
  T3
Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing the major part of HAV 5' UTR (-699 to -1) plus the region encoding the first 51 amino acids of the viral polyprotein (+1 to +153) and firefly luciferase coding region (luc version of the luciferase gene) without 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:
HAV
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Hepatitis A virus HM-175/7 MK-5
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:
pHAV.IRES-luc.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 11:46:27
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):
  888-2540
Remarks:
IRESite notes about verification of plasmid sequence:
The complete sequence of IRES element was determined by sequencing using 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: 2008-06-04 11:46:27
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  HAV
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  30-881
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
DNA fragment (-699 to +153) containing the HAV IRES and 51 amino acids of the capsid protein from Hepatitis A
virus strain HAV HM-175/7 MK-5.
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: 422
Version: 1 Last change: 2008-06-04 11:46:27
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
IRESite Id of the plasmid used as negative control.
  346
The relative translation efficiency in % of the negative control:
  0.300
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_without_polyA_tail
Remarks:
The translation of the nonpolyadenylated HAV.IRES RNA is sensitive to the addition of m7GpppG, but not ApppG
competitor.
The translation of HAV.IRES RNA is about 10-fold less efficient than the translation of the polyadenylated
counterpart HAV.IRES-pA RNA.
Translational data are derived from Fig. 6A
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