The nucleic acid data:
IRESite Id: 37 Version: 4
Originaly submitted by: Václav Vopálenský Submission date: 2006-01-12 00:00:00
Reviewed by: Václav Vopálenský Last change: 2006-08-03 00:00:00
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  our_best_guess
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  BVDV1
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
9626649
The mRNA/+RNA description: 
Bovine viral diarrhea virus 1, complete genome.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  unknown
The organism containing this mRNA with IRES segment in its genome:
Bovine viral diarrhea virus 1 NADL
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: 1
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
BVDV_1
The description of the protein encoded in this ORF:
Bovine viral diarrhea virus 1 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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  386-12352
Remarks:
T7 derived transcripts containing BVDV IRES functional also in rabbit reticulocyte lysates (CAT and LUC were
detectable). In contrast, direct mRNA transfection of uncapped T7 transcripts yielded only LUC signal (second
cistron) in vivo. A series of 11 20b long DNA oligos was used to map which oligos inhibit in vitro
translation. The inhibitory effect was observed when they annealed to bases 154-261 (numbers not recalculated
to match the sequence used herein) of BVDV genome.
Citations:
Poole T. L., Wang C., Popp R. A., Potgieter L. N., Siddiqui A., Collett M. S. (1995) Pestivirus translation initiation occurs by internal ribosome entry. Virology. 206(1):750-754
IRESs:
IRES:
Version: 8 Last change: 2007-01-11 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The IRES name:
  BVDV1_1-385
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-385
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Deletion of the 5' end to nt 31 had no effect on the IRES activity.
Citations:
Chon S. K., Perez D. R., Donis R. O. (1998) Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology. 251(2):370-382
IRES:
Version: 3 Last change: 2007-01-11 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  BVDV1_29-391
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  29-391
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
The IRES region annotated here spans 385b of BVDV 5' UTR and 6b of the open reading frame.
Citations:
Poole T. L., Wang C., Popp R. A., Potgieter L. N., Siddiqui A., Collett M. S. (1995) Pestivirus translation initiation occurs by internal ribosome entry. Virology. 206(1):750-754
RNA:protein interactions:
The RNA:protein interaction:
Version: 4
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The description of the protein interacting with the RNA:
In UV cross-link assay p72 protein from RRL (Rabbit Reticulocyte Lysate System) binds to the BVDV IRES.
The organism where this RNA:protein interaction occurs:
Oryctolagus cuniculus RRL
Remarks:
PTB binds weakly to the BVDV IRES when added to wheat germ extract that normally does not contain PTB (but the
binding of PTB to the BVDV IRES is probably nonspecifc). PTB did not bind to the BVDV IRES in RRL, although
endogenous PTB is present in this extract in sufficient amounts.
BVDV IRES binds specifically and precisely to a ribosomal 40S (at bases 361 (U), 381 (G), 388 (G), 395-397
(AUC), 400-402 (AAA), G (404)) and 48S subunits (388 (G) and 403-405 (UGA)) respectively. BVDV IRES binds
specifically eIF3 (260-261 (AC) and also 320 (A)).
Citations:
Pestova T. V., Hellen C. U. (1999) Internal initiation of translation of bovine viral diarrhea virus RNA. Virology. 258(2):249-256
Sanderbrand S. A., Tautz N., Thiel H. J., Ochs K., Beck E., Niepmann M. (2000) Translation from the internal ribosome entry site of bovine viral diarrhea virus is independent of the interaction with polypyrimidine tract-binding protein. Vet. Microbiol. 77(1-2):215-227
Myers T. M., Kolupaeva V. G., Mendez E., Baginski S. G., Frolov I., Hellen C. U., Rice C. M. (2001) Efficient translation initiation is required for replication of bovine viral diarrhea virus subgenomic replicons. J Virol. 75(9):4226-4238
The RNA:protein interaction:
Version: 1
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
The description of the protein interacting with the RNA:
In UV cross-link assay p65 protein from RRL (Rabbit Reticulocyte Lysate System) binds to the BVDV IRES.
The organism where this RNA:protein interaction occurs:
Oryctolagus cuniculus RRL
Citations:
Pestova T. V., Hellen C. U. (1999) Internal initiation of translation of bovine viral diarrhea virus RNA. Virology. 258(2):249-256
Sanderbrand S. A., Tautz N., Thiel H. J., Ochs K., Beck E., Niepmann M. (2000) Translation from the internal ribosome entry site of bovine viral diarrhea virus is independent of the interaction with polypyrimidine tract-binding protein. Vet. Microbiol. 77(1-2):215-227
Myers T. M., Kolupaeva V. G., Mendez E., Baginski S. G., Frolov I., Hellen C. U., Rice C. M. (2001) Efficient translation initiation is required for replication of bovine viral diarrhea virus subgenomic replicons. J Virol. 75(9):4226-4238
The RNA:protein interaction:
Version: 1
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
The description of the protein interacting with the RNA:
In UV cross-link assay p50 protein from RRL (Rabbit Reticulocyte Lysate System) binds to the BVDV IRES.
The organism where this RNA:protein interaction occurs:
Oryctolagus cuniculus RRL
Citations:
Pestova T. V., Hellen C. U. (1999) Internal initiation of translation of bovine viral diarrhea virus RNA. Virology. 258(2):249-256
Sanderbrand S. A., Tautz N., Thiel H. J., Ochs K., Beck E., Niepmann M. (2000) Translation from the internal ribosome entry site of bovine viral diarrhea virus is independent of the interaction with polypyrimidine tract-binding protein. Vet. Microbiol. 77(1-2):215-227
Myers T. M., Kolupaeva V. G., Mendez E., Baginski S. G., Frolov I., Hellen C. U., Rice C. M. (2001) Efficient translation initiation is required for replication of bovine viral diarrhea virus subgenomic replicons. J Virol. 75(9):4226-4238
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 2
Version: 4 Last change: 2006-04-09 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
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):
1-38
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
Chemical probing of RNA secondary structure used the following buffers:
- probing agents DMS (buffer components: 20 mM HEPES-KOH (pH 7.9), 60 mM KCl, 12 mM MgCl2; for 5 min at 30 oC)
- probing agents CMCT (buffer components: 80 mM sodium borate (pH 8.1), 60 mM KCl, 12 mM MgCl2; 10 min at 30
oC)
4.1.1. 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: 2
The temperature (in degrees of Celsia):
0
The enzymatic method used to determine the 2D structure:
other
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
30.00
Mg2+ [mM]
20.00
Ca2+ [mM]
0
Cl- [mM]
50.00
Tris [mM]
30.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Other buffer components and their relative concentrations:
1 mM dithiothreitol (DTT)
RNases T1 (0.7 U), U2 (4 U), and PhyM (4 U) and Bacillus cereus RNase (1 U)
4.1.2. Chemicals used to characterize at least partially the 2D structure.
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 3
The temperature (in degrees of Celsia):
30
The chemical reagent used to determine the 2D structure:
DMS
Chemical reagent used with its respective buffer:
Version: 0
pH
7.90
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
60.00
Mg2+ [mM]
12.00
Ca2+ [mM]
0
Cl- [mM]
84.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
20.00
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 4
The temperature (in degrees of Celsia):
30
The chemical reagent used to determine the 2D structure:
CMCT
Chemical reagent used with its respective buffer:
Version: 0
pH
8.10
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
60.00
Mg2+ [mM]
12.00
Ca2+ [mM]
0
Cl- [mM]
84.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Other buffer components and their relative concentrations:
80 mM sodium borate (pH 8.1)
Citations:
Yu H., Isken O., Grassmann C. W., Behrens S. E. (2000) A stem-loop motif formed by the immediate 5' terminus of the bovine viral diarrhea virus genome modulates translation as well as replication of the viral RNA. J. Virol. 74(13):5825-5835
Last change to the database: 2015-04-16 16:45:23 GMT+1