The nucleic acid data:
IRESite Id: 372 Version: 2
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš Last change: 2008-09-02 17:05:33
IRESite record type:
  promoter-less_plasmid_with_putative_IRES
The name of the plasmid:
pRG(-P)IRES
Description of the plasmid (facultative for promoter-less plasmid records):
Promoter-less variant of pRG-HCV1 vector (IRESite ID:) was prepared by excising the VspI/NheI fragment containing the CMV IE promoter, filling-in the recessed 3'-termini by Klenow fragment of the DNA polymerase I and by subsequent re-ligation of blunt ended vector.
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 origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Hepatitis C virus type 1a
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
HCV1a
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:


Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks):
  plasmid sequence confirmed by IRESite curators by restriction analysis
GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
pRG(-P)IRES.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: Václav Vopálenský Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
DsRED2
The description of the protein encoded in this ORF:
red fluorescent protein (DsRed2 version, Clontech)
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):
  782-1477
ORF
ORF position:   2
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
EGFP
The description of the protein encoded in this ORF:
red-shifted variant of wild-type GFP optimized for brighter fluorescence and higher expression in mammalian cells (Clontech)
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):
  1917-2636
Remarks:
The plasmid was used as the negative control for experiments in article Firefly luciferase gene contains a
cryptic promoter (Vopalensky et al., 2008; PMID:).
Citations:
Vopalensky V., Masek T., Horvath O., Vicenova B., Mokrejs M., Pospisek M. (2008) Firefly luciferase gene contains a cryptic promoter. RNA. 14(9):1720-1729
IRESs:
IRES:
Version: 2 Last change: 2008-09-02 17:05:33
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  HCV_type_1a
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1513-1897
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  36
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  420
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -404
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -20
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Vopalensky V., Masek T., Horvath O., Vicenova B., Mokrejs M., Pospisek M. (2008) Firefly luciferase gene contains a cryptic promoter. RNA. 14(9):1720-1729
Last change to the database: 2015-04-16 16:45:23 GMT+1