The nucleic acid data:
IRESite Id: 149 Version: 4
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2006-07-26 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+3nt-CAT_with_hairpin. The hairpin is placed immediately
after the KpnI site (ggtacc) which is right after the initiator ATG codon of CSFV N-pro/CAT. The construct is
is refferred in the text of the article as pRLuc-CSFV+4-hpCAT (which would mean that the first G from KpnI
site is counted as belonging to CSFV N-pro) but named in Fig. 8b as CSFV+3-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+3-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+3-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: 2006-07-16 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: 2 Last change: 2006-07-16 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 24nt hairpin stem loop coding additional 8 aminoacid residues separated from the initiator ATG by one base on the left and by 2 bases from the CAT ORF on the right.
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):
  1372-2064
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: 1 Last change: 2006-07-16 00:00:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  CSFV+3
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  999-1374
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:
  406
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:
  2
The sequence of IRES region aligned to its secondary structure (if available):


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: 103
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:
  0
Name of IRES used as the positive control:
  CSFV+55
Name of the plasmid used as the positive control.
pRLuc-CSFV+55-CAT
IRESite Id of the plasmid used as positive control.
  144
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive 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