The nucleic acid data:
IRESite Id: 247 Version: 1
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2007-01-11 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: 
Putative bicistronic mRNA transcript derived from pBSRLucNFluc plasmid through SV40 promoter.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  reverse_engineered_sequence_and_should_match_experiment_except_3UTR
The name of the plasmid:
pBSRLucNFluc
The name of the promoter used to express this mRNA:
  SV40
The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):
  no (not convincing)
The in vivo produced heterogeneous transcripts occur due to alternative splicing:
  not tested
A promoter reported in cDNA corresponding to IRES sequence:
  no (not convincing)
Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:
Summary of experiments studying integrity of the in vivo transcripts in a particular host:
Integrity (uniformity) of mRNA tested using Northern-blot:
homogeneous_population_of_molecules_confirmed
Integrity (uniformity) of mRNA tested using RNase protection:
not_tested
Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested
Integrity (uniformity) of mRNA tested using primer extension :
not_tested
Integrity (uniformity) of mRNA tested using RT-PCR:
not_tested
Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested
Integrity (uniformity) of mRNA tested using RNAi:
not_tested
Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested
Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
not_tested
Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested
Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested
The organism used:
Mus musculus C243
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
NRF
The origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
Homo sapiens
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:
pBSRLucNFluc.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:
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:
  not tested
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  150-1085
ORF
ORF position:   2
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
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:
  not tested
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  1865-3517
Citations:
Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759
IRESs:
IRES:
Version: 2 Last change: 2007-01-23 00:00:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  NRF
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1098-1734
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  13
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  649
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -767
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -131
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759
The translation experiments:
Translation results:
IRESite Translation Id: 301
Version: 1 Last change: 2006-12-20 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:
Mus musculus C243
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  9235.000
Name of IRES used as the positive control:
  EMCV
Name of the plasmid used as the positive control.
pBSRLucEFluc
IRESite Id of the plasmid used as positive control.
  245
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
666
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:
The "high IRES activity" shown in Fig. 2 is suspicious and the observed "IRES activity" might be an artefact.
Citations:
Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759
Translation results:
IRESite Translation Id: 302
Version: 1 Last change: 2007-01-23 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:
Mus musculus ES
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  8500.000
Name of IRES used as the positive control:
  PV
Name of the plasmid used as the positive control.
pBSRLucPFluc
IRESite Id of the plasmid used as positive control.
  246
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
785
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:
The "high IRES activity" shown in Fig. 5 is suspicious and the observed "IRES activity" might be an artefact.
Citations:
Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759
Translation results:
IRESite Translation Id: 303
Version: 1 Last change: 2007-01-23 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:
Mus musculus EF
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  4480.000
Name of IRES used as the positive control:
  PV
Name of the plasmid used as the positive control.
pBSRLucPFluc
IRESite Id of the plasmid used as positive control.
  246
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
785
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:
The "high IRES activity" shown in Fig. 5 is suspicious and the observed "IRES activity" might be an artefact.
Citations:
Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759
Translation results:
IRESite Translation Id: 304
Version: 1 Last change: 2007-01-23 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 NIH/3T3 (ATCC CRL-1658)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  4667.000
Name of IRES used as the positive control:
  PV
Name of the plasmid used as the positive control.
pBSRLucPFluc
IRESite Id of the plasmid used as positive control.
  246
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
785
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:
The "high IRES activity" shown in Fig. 5 is suspicious and the observed "IRES activity" might be an artefact.
Citations:
Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759
Translation results:
IRESite Translation Id: 305
Version: 1 Last change: 2007-01-23 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 HeLa (ATCC CCL-2)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  3250.000
Name of IRES used as the positive control:
  PV
Name of the plasmid used as the positive control.
pBSRLucPFluc
IRESite Id of the plasmid used as positive control.
  246
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
785
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:
The "high IRES activity" shown in Fig. 5 is suspicious and the observed "IRES activity" might be an artefact.
Citations:
Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759
Translation results:
IRESite Translation Id: 306
Version: 1 Last change: 2007-01-23 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:
  7667.000
Name of IRES used as the positive control:
  PV
Name of the plasmid used as the positive control.
pBSRLucPFluc
IRESite Id of the plasmid used as positive control.
  246
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
785
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:
The "high IRES activity" shown in Fig. 5 is suspicious and the observed "IRES activity" might be an artefact.
Citations:
Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759
Translation results:
IRESite Translation Id: 307
Version: 1 Last change: 2007-01-23 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:
Cricetulus griseus CHO-K1 (ATCC CCL-61)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  6432.000
Name of IRES used as the positive control:
  PV
Name of the plasmid used as the positive control.
pBSRLucPFluc
IRESite Id of the plasmid used as positive control.
  246
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
785
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:
The "high IRES activity" shown in Fig. 5 is suspicious and the observed "IRES activity" might be an artefact.
Citations:
Oumard A., Hennecke M., Hauser H., Nourbakhsh M. (2000) Translation of NRF mRNA is mediated by highly efficient internal ribosome entry. Mol. Cell. Biol. 20(8):2755-2759
Translation results:
IRESite Translation Id: 315
Version: 1 Last change: 2007-01-23 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:
Mus musculus C243
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  2714.000
Name of IRES used as the positive control:
  EMCV
Name of the plasmid used as the positive control.
pBSRLucEFLuc
IRESite Id of the plasmid used as positive control.
  245
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
666
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:
The "high IRES activity" shown in Fig. 3e is suspicious and the observed "IRES activity" might be an artefact.
Citations:
Hennecke M., Kwissa M., Metzger K., Oumard A., Kroger A., Schirmbeck R., Reimann J., Hauser H. (2001) Composition and arrangement of genes define the strength of IRES-driven translation in bicistronic mRNAs. Nucleic. Acids Res. 29(16):3327-3334
Last change to the database: 2015-04-16 16:45:23 GMT+1