The nucleic acid data:
IRESite Id: 333 Version: 1
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2008-02-12 22:23:12
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:
  only_IRES_fragment
The mRNA/+RNA description: 
In vitro T7 run-off transcript used for structure probing experiments of FMDV IRES domain 3 (transcription
runs off at cleaved SmaI site, FMDV IRES domain 3 is between EcoRI and SmaI sites).
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_reverse_engineered_and_should_match_experiment
The name of the plasmid:
pGEM3-FMDV-IRES-domain3
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:
FMDV
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Foot-and-mouth disease virus C-S8c1
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:


GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
pGEM3-FMDV-IRES-domain3.jpg
The total number of notable open-reading frames (ORFs):
  0
Citations:
Martinez-Salas E., Saiz J. C., Davila M., Belsham G. J., Domingo E. (1993) A single nucleotide substitution in the internal ribosome entry site of foot-and-mouth disease virus leads to enhanced cap-independent translation in vivo. J. Virol. 67(7):3748-3755
Additional data: http://bccm.belspo.be/db/lmbp_plasmid_details.php?NM=pBIC
Ramos R., Martinez-Salas E. (1999) Long-range RNA interactions between structural domains of the aphthovirus internal ribosome entry site (IRES). RNA. 5(10):1374-1383
IRESs:
IRES:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  FMDV_domain_3
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  15-229
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Ramos R., Martinez-Salas E. (1999) Long-range RNA interactions between structural domains of the aphthovirus internal ribosome entry site (IRES). RNA. 5(10):1374-1383
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 11
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The function of the 2D structure:
IRES
The 2D structure causes frameshift:
unknown
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
33-213
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
FMDV IRES domain3 as shown in Fig. 6
3.1.1. Enzymes used to characterize at least partially the 2D structure.
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 8
The temperature (in degrees of Celsia):
37
The enzymatic method used to determine the 2D structure:
ribonuclease T1
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
50.00
K+ [mM]
300.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
320.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
50.00
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 9
The temperature (in degrees of Celsia):
20
The enzymatic method used to determine the 2D structure:
ribonuclease T1
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
8.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
0
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
0
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
1.00
cacodylate [mM]
0
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 10
The temperature (in degrees of Celsia):
37
The enzymatic method used to determine the 2D structure:
ribonuclease A
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
50.00
K+ [mM]
300.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
320.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
50.00
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 11
The temperature (in degrees of Celsia):
20
The enzymatic method used to determine the 2D structure:
ribonuclease A
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
8.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
0
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
0
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
1.00
cacodylate [mM]
0
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 12
The temperature (in degrees of Celsia):
37
The enzymatic method used to determine the 2D structure:
ribonuclease V1
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
50.00
K+ [mM]
300.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
320.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
50.00
3.1.2. Chemicals used to characterize at least partially the 2D structure.
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 13
The temperature (in degrees of Celsia):
20
The chemical reagent used to determine the 2D structure:
DMS
Chemical reagent used with its respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
50.00
K+ [mM]
300.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
320.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
50.00
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 14
The temperature (in degrees of Celsia):
20
The chemical reagent used to determine the 2D structure:
DMS
Chemical reagent used with its respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
50.00
K+ [mM]
0
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
0
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
1.00
cacodylate [mM]
50.00
Citations:
Fernandez-Miragall O., Martinez-Salas E. (2003) Structural organization of a viral IRES depends on the integrity of the GNRA motif. RNA. 9(11):1333-1344
Last change to the database: 2015-04-16 16:45:23 GMT+1