The nucleic acid data:
IRESite Id: 321 Version: 0
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  end-to-end_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  FMDV
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
6318187
The mRNA/+RNA description: 
Foot-and-mouth disease virus (FMDV) strain C, isolate c-s8c1, genomic RNA.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_completely_same_as_in_the_experiment
The organism containing this mRNA with IRES segment in its genome:
Foot-and-mouth disease virus C
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):
  1039-8022
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
IRESs:
IRES:
Version: 3 Last change: 2008-12-10 00:22:05
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  FMDV_type_C
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  578-1038
Conclusion:
  strongly_supported_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
The studied region spans region -461 to -1 relative to initiator AUG. Therefore 577nt of the 5'-most end are
in front of the IRES region.

FMDV IRES does not require Unr protein for its activity (Boussadia et al., 2003).
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
Boussadia O., Niepmann M., Creancier L., Prats A. C., Dautry F., Jacquemin-Sablon H. (2003) Unr is required in vivo for efficient initiation of translation from the internal ribosome entry sites of both rhinovirus and poliovirus. J. Virol. 77(6):3353-3359
IRES trans-acting factor (ITAFS):
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
PTB
ITAF fullname:
polypyrimidine-tract binding protein (unspecified isoform)
ITAF description (long):
polypyrimidine-tract binding protein
3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate
Remarks:
The requirement for PTB was found by toeprinting in assay of 48S formation.
Citations:
Pilipenko E. V., Pestova T. V., Kolupaeva V. G., Khitrina E. V., Poperechnaya A. N., Agol V. I., Hellen C. U. (2000) A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes. Dev. 14(16):2028-2045
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
ITAF45
ITAF fullname:
ITAF45 (murine proliferation-associated protein, Mpp1)
ITAF description (long):
proliferation-dependent protein that is not expressed in murine brain cells, its human homolog is called PAG24
3.2.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate
Remarks:
The requirement for ITAF45 was found by toeprinting in assay of 48S formation.
Citations:
Pilipenko E. V., Pestova T. V., Kolupaeva V. G., Khitrina E. V., Poperechnaya A. N., Agol V. I., Hellen C. U. (2000) A cell cycle-dependent protein serves as a template-specific translation initiation factor. Genes. Dev. 14(16):2028-2045
RNA:protein interactions:
The RNA:protein interaction:
Version: 2 Last change: 2009-09-18 13:13:41
Originaly submitted by: Zuzana Feketová Reviewed by: Martin Mokrejš
Abbreviated name of the protein interacting with the RNA:
PCBP1/hnRNP_E1
Full name of the protein interacting with the RNA:
PCBP1 /poly r(C) binding protein/ (hnRNP E1)
The description of the protein interacting with the RNA:
PCBP1 /poly r(C) binding protein/
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.
The RNA:protein interaction:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Item not reviewed
Abbreviated name of the protein interacting with the RNA:
hnRNP_K
Full name of the protein interacting with the RNA:
Heterogeneous ribonucleoprotein K
The description of the protein interacting with the RNA:
Heterogeneous ribonucleoprotein K
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.
Citations:
Pacheco A, Reigadas S, Martínez-Salas E (2008) Riboproteomic analysis of polypeptides interacting with the internal ribosome-entry site element of foot-and-mouth disease viral RNA. Proteomics. 8(22):4782-4790
The RNA:protein interaction:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Item not reviewed
Abbreviated name of the protein interacting with the RNA:
PCBP2/hnRNP_E2
Full name of the protein interacting with the RNA:
PCBP1 /poly r(C) binding protein/ (hnRNP E2)
The description of the protein interacting with the RNA:
PCBP1 /poly r(C) binding protein/
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.
The RNA:protein interaction:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Item not reviewed
Abbreviated name of the protein interacting with the RNA:
PA2G4
Full name of the protein interacting with the RNA:
PA2G4
The description of the protein interacting with the RNA:
PA2G4
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.
The RNA:protein interaction:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Item not reviewed
Abbreviated name of the protein interacting with the RNA:
eIF2c
Full name of the protein interacting with the RNA:
Eukaryotic translation initiation factor 2c
The description of the protein interacting with the RNA:
Eukaryotic translation initiation factor 2c
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.
The RNA:protein interaction:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Item not reviewed
Abbreviated name of the protein interacting with the RNA:
eIF4b
Full name of the protein interacting with the RNA:
Eukaryotic translation initiation factor 4b
The description of the protein interacting with the RNA:
Eukaryotic translation initiation factor 4b
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.
The RNA:protein interaction:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Item not reviewed
Abbreviated name of the protein interacting with the RNA:
eEF2
Full name of the protein interacting with the RNA:
Eukaryotic translation elongation factor 2
The description of the protein interacting with the RNA:
Eukaryotic translation elongation factor 2
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.
The RNA:protein interaction:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Item not reviewed
Abbreviated name of the protein interacting with the RNA:
PABP2
Full name of the protein interacting with the RNA:
Poly(A)-binding protein 2
The description of the protein interacting with the RNA:
Poly(A)-binding protein 2
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
The in vitro assays was performed using S10 BHK-21 and HeLa cells lysates.
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 45
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):
678-858
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
FMDV IRES domain3 as shown in Fig. 6
5.1.1. 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: 74
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: 75
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: 76
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: 77
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: 78
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
5.1.2. Chemicals used to characterize at least partially the 2D structure.
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 31
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: 32
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