The nucleic acid data:
IRESite Id: 7 Version: 5
Originaly submitted by: Václav Vopálenský Submission date: 2005-08-02 00:00:00
Reviewed by: Martin Pospíšek Last change: 2006-10-04 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:
  3UTR_incomplete
The mRNA/+RNA description: 
5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus (HCV) type 6a cloned
between renilla and firefly luciferase. This sequence was hand-crafted according to Figure 1 in cited article.
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_6a
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_6a
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Hepatitis C virus type 6a
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_6a.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
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Pospíšek
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
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Pospíšek
The abbreviated name of this ORF/gene:
FFluc
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):
  1304-2953
Remarks:
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: 2 Last change: 2006-01-15 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Pospíšek
The IRES name:
  HCV_type_6a
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  957-1297
How IRES boundaries were determined:
unknown
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:
  347
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -347
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 (326 nt) and open reading frame (15 nt)
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
The translation experiments:
Translation results:
IRESite Translation Id: 21
Version: 4 Last change: 2006-10-04 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Pospíšek
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens BHK-21 (ATCC CCL-10)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  60.000
Name of IRES used as the positive control:
  HCV_type_1a
Name of the plasmid used as the positive control.
pRL_1a
IRESite Id of the plasmid used as positive control.
  224
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
352
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  endogenous_nuclear_RNA_Pol_II_transcript
Remarks:
positive control: 5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus
(HCV) type 1a (gi:329737) in the same bicistronic vector
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
Translation results:
IRESite Translation Id: 22
Version: 4 Last change: 2006-10-04 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Pospíšek
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens HuH7
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  93.000
Name of IRES used as the positive control:
  HCV_type_1a
Name of the plasmid used as the positive control.
pRL_1a
IRESite Id of the plasmid used as positive control.
  224
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
352
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  endogenous_nuclear_RNA_Pol_II_transcript
Remarks:
positive control: 5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus
(HCV) type 1a (gi:329737) in the same bicistronic vector
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
Translation results:
IRESite Translation Id: 23
Version: 4 Last change: 2006-10-04 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Pospíšek
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens HepG2 (ATCC HB-8065)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  56.000
Name of IRES used as the positive control:
  HCV_type_1a
Name of the plasmid used as the positive control.
pRL_1a
IRESite Id of the plasmid used as positive control.
  224
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
352
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  endogenous_nuclear_RNA_Pol_II_transcript
Remarks:
positive control: 5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus
(HCV) type 1a (gi:329737) in the same bicistronic vector
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
Translation results:
IRESite Translation Id: 24
Version: 4 Last change: 2006-10-04 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Pospíšek
The translation method used to study IRES function:
in vivo
The organism used for translation:
Homo sapiens HeLa-T4+
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  78.000
Name of IRES used as the positive control:
  HCV_type_1a
Name of the plasmid used as the positive control.
pRL_1a
IRESite Id of the plasmid used as positive control.
  224
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
352
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  endogenous_nuclear_RNA_Pol_II_transcript
Remarks:
positive control: 5' region (nt 18 of the 5' UTR to nt 15 of the core coding protein) of Hepatitis C virus
(HCV) type 1a (gi:329737) in the same bicistronic vector
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