The nucleic acid data:
IRESite Id: 312 Version: 1
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2008-06-04 21:40:39
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 - neomycin phosphotransferase - 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:
RepBNeo
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:
RepBNeo.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:
aph
The description of the protein encoded in this ORF:
aminoglycoside-3'-O-phosphotransferase
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: 0
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: 397
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:
  35.000
Name of IRES used as the positive control:
  GBV-B
Name of the plasmid used as the positive control.
RepDNeo
IRESite Id of the plasmid used as positive control.
  310
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
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