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:



There is no Vienna RNA package installed on the server or some error/warning messages were output. Due to that maybe we cannot prepare 2D structures for display. The error/warning message was:
WARNING: bases 13 and 166 (CU) can't pair!
WARNING: bases 15 and 164 (AA) can't pair!
WARNING: bases 17 and 162 (UC) can't pair!
WARNING: bases 21 and 159 (AA) can't pair!
WARNING: bases 24 and 157 (AG) can't pair!
WARNING: bases 25 and 156 (AC) can't pair!

STDOUT was:
UCGAUCCACUGGCGAGUGUUAGUAACAGCACUGUUGCUUCGUAGCGGAGCAUGACGGCCGUGGGAACUCCUCCUUGGUAACAAGGACCCACGGGGCCAAAAGCCACGCCCACACGGGCCCGUCAUGUGUGCAACCCCAGCACGGCGACUUUACUGCGAAACCCACUUUAAAGUGACAUUGA
((.((..(((((((((((.((.((((((.....(((((((......)))(((((((((((((((......((((((....)))))))))))))(((.....)))..(((......)))))))))))(...............))))).....))))))))))))))))..)))...)).)) (-38.70)

Rendering structure of FMDV mRNA 181 nt long with energy of -38.70 kcal/mol as calculated by RNAeval using VARNA Java applet with some IRESite improvements (see VARNA modified by IRESite). Hold left mouse button to move structure parts, hold right mouse button to move whole structure, use mouse wheel to zoom. Right mouse-click opens a menu to export into JPG/SVG and many other options.

You need a Java-enabled browser so that modified varsion of VARNA could be started. See http://www.iresite.org/VARNA/ for more details.
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: 2019-03-18 09:32:49 GMT+1