The nucleic acid data:
IRESite Id: 224 Version: 4
Originaly submitted by: Václav Vopálenský
Reviewed by: Václav Vopálenský Last change: 2007-06-14 00:00:00
IRESite record type:
  plasmid_with_promoter_and_putative_IRES_without_translational_characterization
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  3UTR_incomplete
The mRNA/+RNA description: 
Bicistronic in vivo transcript mRNA with 5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein)
of Hepatitis C virus (HCV) type 1a cloned between renilla and firefly luciferase.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail
The name of the plasmid:
pRL_1a
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:
HCV_type_1a
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Hepatitis C virus type 1a
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:
pRL_1a.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: Václav Vopálenský
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  15-950
ORF
ORF position:   2
Version: 1 Last change: 2007-09-06 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
Fluc
The description of the protein encoded in this ORF:
firefly 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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  1302-2951
Remarks:
This plasmid was used as the positive control for experiments in article Translation efficiencies of the 5'
untranslated region from representatives of the six major genotypes of hepatitis C virus using a novel
bicistronic reporter assay system (Collier et al., 1998; PMID:9780040).

This item is labeled as 3'UTR incomplete because the mRNA sequence deposited here ends at the stop codon of
the second cistron.
Citations:
Collier A. J., Tang S., Elliott R. M. (1998) Translation efficiencies of the 5' untranslated region from representatives of the six major genotypes of hepatitis C virus using a novel bicistronic reporter assay system. J. Gen. Virol. 79(Pt 10):2359-2366
IRESs:
IRES:
Version: 1 Last change: 2007-09-06 00:00:00
Originaly submitted by: Martin Mokrejš 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):
  957-1295
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  7
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  345
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -345
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -7
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
HCV UTR (324 nt) and open reading frame (15 nt)

Possible typo error in the IRES sequence within first 18 nt of IRES: GGCGACACTCCACCATGA where trailing TGA
might be TAG instead.
Citations:
Collier A. J., Tang S., Elliott R. M. (1998) Translation efficiencies of the 5' untranslated region from representatives of the six major genotypes of hepatitis C virus using a novel bicistronic reporter assay system. J. Gen. Virol. 79(Pt 10):2359-2366
Last change to the database: 2015-04-16 16:45:23 GMT+1