The nucleic acid data:
IRESite Id: 152 Version: 1
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2006-07-17 00:00:00
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:
  our_best_guess
The mRNA/+RNA description: 
Bicistronic mRNA molecule coding for RLuc-CSFV_IRES followed by 54nt from CSFV N-pro sequence followed by KpnI
site, hairpin and CAT. It should have been better named pRLuc-CSFV+54-hpCAT.
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:
pRLuc-CSFV+55-hpCAT
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:
CSFV
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Classical swine fever virus
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:
pRLuc-CSFV+55-hpCAT.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: 1 Last change: 2006-07-17 00:00:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
RLuc
The description of the protein encoded in this ORF:
Renilla luciferase
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):
  33-968
ORF
ORF position:   2
Version: 1 Last change: 2006-07-17 00:00:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
CAT
The description of the protein encoded in this ORF:
Chloramphenicol acetyltransferase with N-terminal 54nt from CSFV N-pro ORF followed by KpnI site, hairpin stem loop and followed by CAT ORF.
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):
  1372-2115
Citations:
Rijnbrand R., Bredenbeek P. J., Haasnoot P. C., Kieft J. S., Spaan W. J., Lemon S. M. (2001) The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA. 7(4):585-597
IRESs:
IRES:
Version: 4 Last change: 2006-07-26 00:00:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  CSFV+55
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  999-1426
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  31
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  458
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -373
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  54
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
The first base from the KpnI site is annotated here as belonging to IRES although this is not consistent with
other records derived from same article. really only 54nts are retained from CSFV N-pro ORF.
Citations:
Rijnbrand R., Bredenbeek P. J., Haasnoot P. C., Kieft J. S., Spaan W. J., Lemon S. M. (2001) The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA. 7(4):585-597
The translation experiments:
Translation results:
IRESite Translation Id: 106
Version: 1 Last change: 2006-06-30 00:00:00
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:
  116.000
Name of IRES used as the positive control:
  CSFV+55
Name of the plasmid used as the positive control.
pRLuc-CSFV+55-CAT
Name of the plasmid used as the negative control.
pRLuc-CSFV+3-hpCAT
IRESite Id of the plasmid used as positive control.
  144
IRESite Id of the plasmid used as negative control.
  149
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  0
The size (length) of intercistronic region in the positive control:
403
The size (length) of intercistronic region in the negative control:
403
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:
Fig. 8
Citations:
Rijnbrand R., Bredenbeek P. J., Haasnoot P. C., Kieft J. S., Spaan W. J., Lemon S. M. (2001) The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA. 7(4):585-597
Last change to the database: 2015-04-16 16:45:23 GMT+1