The nucleic acid data:
IRESite Id: 340 Version: 1
Originaly submitted by: Martin Mokrejš
Reviewed by: Martin Mokrejš Last change: 2008-05-22 17:50:00
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:
  hopefully_full-length_mRNA
The mRNA/+RNA description: 
Putative spliced in vitro SV40 promoter-derived transcript of pRBdeltaF plasmid (same as pRBF but AUG mutated
to AGG).
The mRNA/+RNA sequence represented in the +DNA notation:


Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)
Credibility of mRNA sequence:
  guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail
The name of the plasmid:
pRBF_AUG-to-AGG
The name of the promoter used to express this mRNA:
  SV40
Aliases of the plasmid name:
Alias: pRBdeltaF
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:
Bag-1
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:
pRBF_AUG-to-AGG.jpg
The total number of notable open-reading frames (ORFs):
  1
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1 Last change: 2008-05-22 17:50:00
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):
  192-1127
Remarks:
Although this construct has mutated authentic initiator AUG codon of FLuc there are many ORFs remaining
throughout the sequence of firefly luciferase while it is not clear whether any of the protein products are
functional. Below are the positions of ORFs C-co-terminal with the full-length protein form within the
putative transcript:

1548-3200 550aa (AUG to AGG mutation)
1635-3200 521aa
1722-3200 492aa
1746-3200 484aa
1815-3200 461aa
1899-3200 433aa
2001-3200 399aa
2037-3200 387aa
2133-3200 355aa
2292-3200 302aa
2340-3200 286aa
2733-3200 155aa
2739-3200 153aa
3024-3200 58aa
Citations:
Coldwell M. J., deSchoolmeester M. L., Fraser G. A., Pickering B. M., Packham G., Willis A. E. (2001) The p36 isoform of BAG-1 is translated by internal ribosome entry following heat shock. Oncogene. 20(30):4095-4100
IRESs:
IRES:
Version: 1 Last change: 2008-05-22 17:50:00
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  BAG1_p36
The functional status of IRES:
  defective
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1179-1544
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Coldwell M. J., deSchoolmeester M. L., Fraser G. A., Pickering B. M., Packham G., Willis A. E. (2001) The p36 isoform of BAG-1 is translated by internal ribosome entry following heat shock. Oncogene. 20(30):4095-4100
The translation experiments:
Translation results:
IRESite Translation Id: 412
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 HeLa (ATCC CCL-2)
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  5.000
Name of IRES used as the positive control:
  BAG1_p36
Name of the plasmid used as the positive control.
pRBF
IRESite Id of the plasmid used as positive control.
  323
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
419
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:
Values from Figure 5B. Expression of FLuc from this plasmid could be due to ribosomal re-initiation as well as
initiation at a downstream AUG codon. However, the firefly luciferase proteins produced from shorter ORFs seem
to be non-functional or not produced.
Citations:
Coldwell M. J., deSchoolmeester M. L., Fraser G. A., Pickering B. M., Packham G., Willis A. E. (2001) The p36 isoform of BAG-1 is translated by internal ribosome entry following heat shock. Oncogene. 20(30):4095-4100
Last change to the database: 2015-04-16 16:45:23 GMT+1