The nucleic acid data:
IRESite Id: 578 Version: 2
Originaly submitted by: Martin Mokrejš Submission date: 2009-04-09 02:49:56
Reviewed by: Martin Mokrejš Last change: 2009-07-16 15:26:40
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:
  only_IRES_fragment
The mRNA/+RNA description: 
FeLV-Notch2 IRES fragment 1-814.
The mRNA/+RNA sequence represented in the +DNA notation:


Warning: available plasmid sequence is exactly same as the mRNA sequence. It seems we never managed to reconstruct the original plasmid sequence used to express the studied mRNA.
Credibility of mRNA sequence:
  only_fragment_published_or_from_author
The name of the plasmid:
pSV-CAT/FeLV-Notch2-1_814/LUC
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:
  no (not convincing)
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:
heterogeneous_population_of_molecules_found
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:
homogeneous_population_of_molecules_confirmed
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:
heterogeneous_population_of_molecules_found
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:
Homo sapiens HeLa (ATCC CCL-2)
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
FeLV-Notch2
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Felis silvestris 9683
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:
pSV-CAT/FeLV-Notch2-1_814/LUC.jpg
The total number of notable open-reading frames (ORFs):
  0
Remarks:
The integrity of the transcripts was assessed by RT-PCR (Rohn et al., 1996), S1 nuclease protection (Lauring
et al., 2000, Figure 1B), Northern blot (Lauring et al., 2000, Supplemental Figure 1). Please note we do not
have sequence of the vector not even of the ORFs flanking the putative IRES.
Citations:
Lauring A. S., Overbaugh J. (2000) Evidence that an IRES within the Notch2 coding region can direct expression of a nuclear form of the protein. Mol. Cell. 6(4):939-945
IRESs:
IRES:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  FeLV-Notch2_1-814
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-814
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Lauring A. S., Overbaugh J. (2000) Evidence that an IRES within the Notch2 coding region can direct expression of a nuclear form of the protein. Mol. Cell. 6(4):939-945
The translation experiments:
Translation results:
IRESite Translation Id: 615
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:
  141.000
Name of IRES used as the positive control:
  PV
Name of the plasmid used as the positive control.
pSV-CAT/polio/LUC
Name of the plasmid used as the negative control.
pSV-CAT/mutEMCV/LUC
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  13.000
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:
Figure 3B.
Citations:
Lauring A. S., Overbaugh J. (2000) Evidence that an IRES within the Notch2 coding region can direct expression of a nuclear form of the protein. Mol. Cell. 6(4):939-945
Last change to the database: 2015-04-16 16:45:23 GMT+1