The nucleic acid data:
IRESite Id: 19 Version: 6
Originaly submitted by: Václav Vopálenský Submission date: 2005-08-02 00:00:00
Reviewed by: Martin Pospíšek Last change: 2006-07-25 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 of genomic RNA (nt 1 to nt 900) with insertion of nt 102-105 cloned between chloramphenicol
acetyltransferase 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:
IIa-b(In102-105)
The name of the promoter used to express this mRNA:
  SP6
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:
BVDV_1
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Bovine viral diarrhea virus 1 NADL
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:
IIa-b(In102-105).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:
CAT
The description of the protein encoded in this ORF:
chloramphenicol acetyl transferase
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):
  51-710
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):
  1736-3388
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:
Chon S. K., Perez D. R., Donis R. O. (1998) Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology. 251(2):370-382
IRESs:
IRES:
Version: 2 Last change: 2006-07-25 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Pospíšek
The IRES name:
  BVDV1_in102-105
The functional status of IRES:
  defective
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  825-1728
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  115
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  1018
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -911
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -8
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
BVDV 5' UTR (389 nt, incl. insertion of nt 102-105) and open reading frame (515 nt)
Citations:
Chon S. K., Perez D. R., Donis R. O. (1998) Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology. 251(2):370-382
The translation experiments:
Translation results:
IRESite Translation Id: 35
Version: 3 Last change: 2006-07-25 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:
Cercopithecus aethiops CV-1 (ATCC CCL-70)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  12.000
Name of IRES used as the positive control:
  BVDV_1
Name of the plasmid used as the positive control.
pBi5_BVDV
Name of the plasmid used as the negative control.
pBi456F
IRESite Id of the plasmid used as positive control.
  9
IRESite Id of the plasmid used as negative control.
  208
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  0.300
The size (length) of intercistronic region in the positive control:
1022
The size (length) of intercistronic region in the negative control:
578
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 of genomic RNA of BVDV (nt 1 to nt 900) in the same bicistronic vector
negative control - fragment of the BVDV genome (nt 2198–2654) in the same bicistronic vector
Citations:
Chon S. K., Perez D. R., Donis R. O. (1998) Genetic analysis of the internal ribosome entry segment of bovine viral diarrhea virus. Virology. 251(2):370-382
Last change to the database: 2015-04-16 16:45:23 GMT+1