The nucleic acid data:
IRESite Id: 308 Version: 1
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2008-06-04 21:42:37
IRESite record type:
  plasmid_with_promoter_and_putative_IRES_translationally_characterized
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  hopefully_full-length_mRNA
The mRNA/+RNA description: 
In vitro bicistronic transcript (non-capped non-poly(A)-tailed) containing
5' -GBV-B_IRES - 21nt_of_GBV-B_core_gene - beta-lactamase - EMCV-R_IRES - NS3-NS5B_GBV-B_polyprotein - 3'
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:
RepBBla
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:
GBV-B
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Hepatitis GB virus B ACY/GBV-B/FL-3
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:
RepBBla.jpg
The total number of notable open-reading frames (ORFs):
  2
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:
bla
The description of the protein encoded in this ORF:
beta-lactamase fusion protein
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):
  447-1274
ORF
ORF position:   2
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:
NS3-4A, NS4B, NS5A, NS5B 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):
  1894-7671
Citations:
Pizzuti M., De Tomassi A., Traboni C. (2003) Replication and IRES-dependent translation are both affected by core coding sequences in subgenomic GB virus B replicons. J. Virol. 77(13):7502-7509
IRESs:
IRES:
Version: 1 Last change: 2007-05-15 00:00:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  GBV-B
The functional status of IRES:
  defective
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  2-446
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Pizzuti M., De Tomassi A., Traboni C. (2003) Replication and IRES-dependent translation are both affected by core coding sequences in subgenomic GB virus B replicons. J. Virol. 77(13):7502-7509
The translation experiments:
Translation results:
IRESite Translation Id: 394
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The translation method used to study IRES function:
in vitro
The in vitro translation system:
rabbit reticulocytes lysate
The organism used for translation:
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  37.000
Name of IRES used as the positive control:
  GBV-B
Name of the plasmid used as the positive control.
RepDBla
IRESite Id of the plasmid used as positive control.
  306
The relative translation efficiency in % of the positive control:
  100.000
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  exogenous_RNA_without_cap_without_polyA_tail
Remarks:
The constructs had the putative GBV-B IRES placed in front of the 1st cistron and EMCV IRES placed in the
intercistronic region and therefore it does not make sense to consider size of the intercistronic region
in respect to GBV-B IRES.
Citations:
Pizzuti M., De Tomassi A., Traboni C. (2003) Replication and IRES-dependent translation are both affected by core coding sequences in subgenomic GB virus B replicons. J. Virol. 77(13):7502-7509
Last change to the database: 2015-04-16 16:45:23 GMT+1