The nucleic acid data:
IRESite Id: 598 Version: 1
Originaly submitted by: Martin Mokrejš Submission date: 2009-08-19 00:47:30
Reviewed by: Martin Mokrejš Last change: 2009-09-05 13:07:58
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  hopefully_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  PV
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
332895
The mRNA/+RNA description: 
Poliovirus P3/Leon/37 (type 3), complete genome.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_reverse_engineered_and_should_match_experiment
The organism containing this mRNA with IRES segment in its genome:
Human poliovirus 1 Mahoney
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
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:
polyprotein
The description of the protein encoded in this ORF:
viral polyprotein
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):
  743-7363
Citations:
Stanway G, Hughes PJ, Mountford RC, Reeve P, Minor PD, Schild GC, Almond JW (1984) Comparison of the complete nucleotide sequences of the genomes of the neurovirulent poliovirus P3/Leon/37 and its attenuated Sabin vaccine derivative P3/Leon 12a1b. Proc. Natl. Acad. Sci. U.S.A. 5(81):1539-1543
IRESs:
IRES:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  PV_type3_Leon
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-742
Conclusion:
  strongly_supported_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Skinner MA, Racaniello VR, Dunn G, Cooper J, Minor PD, Almond JW (1989) New model for the secondary structure of the 5' non-coding RNA of poliovirus is supported by biochemical and genetic data that also show that RNA secondary structure is important in neurovirulence. J. Mol. Biol. 2(207):379-392
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 43
Version: 1 Last change: 2009-08-30 03:03:50
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The function of the 2D structure:
IRES
The 2D structure causes frameshift:
no
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1-620
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
The secondary structure probing data characterize well only two regions: 292-397 and 488-509. Most of the
structure is a prediction.
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: 72
The temperature (in degrees of Celsia):
0
The enzymatic method used to determine the 2D structure:
ribonuclease T1/T2 mix
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.80
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
300.00
Mg2+ [mM]
20.00
Ca2+ [mM]
0
Cl- [mM]
340.00
Tris [mM]
30.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 73
The temperature (in degrees of Celsia):
0
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
7.80
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
300.00
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
340.00
Tris [mM]
30.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
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: 30
The temperature (in degrees of Celsia):
30
The chemical reagent used to determine the 2D structure:
DMS/kethoxal mix
Chemical reagent used with its respective buffer:
Version: 0
pH
7.40
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
270.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
290.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
70.00
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Citations:
Skinner MA, Racaniello VR, Dunn G, Cooper J, Minor PD, Almond JW (1989) New model for the secondary structure of the 5' non-coding RNA of poliovirus is supported by biochemical and genetic data that also show that RNA secondary structure is important in neurovirulence. J. Mol. Biol. 2(207):379-392
Last change to the database: 2015-04-16 16:45:23 GMT+1