The nucleic acid data:
IRESite Id: 293 Version: 2
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2008-06-04 21:55:15
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_1-920_eGFP-3'.
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(1-920)
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(1-920).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):
  2251-3054
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_1-920
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1290-2237
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:
  963
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -961
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: 363
Version: 2 Last change: 2007-05-10 00:00:00
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:
  123.000
Name of IRES used as the positive control:
  EMCV_type_R
Name of the plasmid used as the positive control.
pEMCV
IRESite Id of the plasmid used as positive control.
  292
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
567
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. 5E.
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: 364
Version: 2 Last change: 2007-05-10 00:00:00
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:
  247.000
Name of IRES used as the positive control:
  EMCV_type_R
Name of the plasmid used as the positive control.
pEMCV
IRESite Id of the plasmid used as positive control.
  292
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
567
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. 5F.
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: 367
Version: 1 Last change: 2007-05-11 00:00:00
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:
  100.000
Name of the plasmid used as the negative control.
pT7CG
IRESite Id of the plasmid used as negative control.
  270
The relative translation efficiency in % of the negative control:
  3.500
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. 3B.
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: 368
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:
  100.000
Name of the plasmid used as the negative control.
pT7CG
IRESite Id of the plasmid used as negative control.
  270
The relative translation efficiency in % of the negative control:
  5.800
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:
Fig. 3C.
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: 2015-04-16 16:45:23 GMT+1