The nucleic acid data:
IRESite Id: 302 Version: 1
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2008-06-04 21:51:06
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:
  hopefully_full-length_mRNA
The mRNA/+RNA description: 
Putative T7 promoter-derived transcript transcribed either in vivo or in vitro in BHK-21 cells infected by
recombinant vaccinia virus vTF7-3 containing 5'-EMCV-R_IRES-CAT-ERBV_IRES_189-920_eGFP-3' with 1st and
2nd AUG codon mutated to ATA.
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:
pEB(189-920)deltaA1/2
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:
ERBV
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Equine rhinitis B virus 1 1436/71
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: pEB(189-920)deltaA1/2.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: 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
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):
  615-1274
ORF
ORF position:   2
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
eGFP
The description of the protein encoded in this ORF:
enhanced green fluorescent protein
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):
  2063-2866
Citations:
Hinton T. M., Crabb B. S. (2001) The novel picornavirus Equine rhinitis B virus contains a strong type II internal ribosomal entry site which functions similarly to that of Encephalomyocarditis virus. J. Gen. Virol. 82(Pt 9):2257-2269
IRESs:
IRES:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  ERBV_189-920_deltaAUG1/2
The functional status of IRES:
  defective
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1290-2049
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  16
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  775
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -773
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -14
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Hinton T. M., Crabb B. S. (2001) The novel picornavirus Equine rhinitis B virus contains a strong type II internal ribosomal entry site which functions similarly to that of Encephalomyocarditis virus. J. Gen. Virol. 82(Pt 9):2257-2269
The translation experiments:
Translation results:
IRESite Translation Id: 385
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
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:
  51.000
Name of IRES used as the positive control:
  ERBV_189-920
Name of the plasmid used as the positive control.
pEB(189-920)
Name of the plasmid used as the negative control.
pT7CG
IRESite Id of the plasmid used as positive control.
  294
IRESite Id of the plasmid used as negative control.
  270
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  3.000
The size (length) of intercistronic region in the positive control:
788
The size (length) of intercistronic region in the negative control:
22
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  endogenous_cytoplasmic_uncapped_T7_transcript_without_polyA_tail
Remarks:
BHK-21 cells were infected by recombinant vaccinia virus vTF7-3. Data from Fig. 4B.
Citations:
Hinton T. M., Crabb B. S. (2001) The novel picornavirus Equine rhinitis B virus contains a strong type II internal ribosomal entry site which functions similarly to that of Encephalomyocarditis virus. J. Gen. Virol. 82(Pt 9):2257-2269
Translation results:
IRESite Translation Id: 386
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:
  45.000
Name of IRES used as the positive control:
  ERBV_189-920
Name of the plasmid used as the positive control.
pEB(189-920)
IRESite Id of the plasmid used as positive control.
  294
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
788
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  endogenous_cytoplasmic_uncapped_T7_transcript_without_polyA_tail
Remarks:
Fig. 4C.
Citations:
Hinton T. M., Crabb B. S. (2001) The novel picornavirus Equine rhinitis B virus contains a strong type II internal ribosomal entry site which functions similarly to that of Encephalomyocarditis virus. J. Gen. Virol. 82(Pt 9):2257-2269
Last change to the database: 2011-04-08 22:43:22 GMT+1