The nucleic acid data:
IRESite Id: 436 Version: 2
Originaly submitted by: Martin Mokrejš
Reviewed by: Václav Vopálenský Last change: 2008-06-26 14:58:03
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  our_best_guess
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  PITSLRE
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
507159
The mRNA/+RNA description: 
Human protein kinase PITSLRE alpha 2-2 mRNA, complete cds.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_reverse_engineered_and_should_match_experiment
The organism containing this mRNA with IRES segment in its genome:
Homo sapiens
A promoter reported in cDNA corresponding to IRES sequence:
  no
The total number of notable open-reading frames (ORFs):
  1
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:
no_promoter_confirmed
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 293T (ATCC CRL-1573)
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1 Last change: 2008-06-26 04:30:09
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
p58_PITSLRE
The description of the protein encoded in this ORF:
PITSLRE alpha 2-2
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):
  1126-2445
Remarks:
The p58 protein is produced by IRES-mediated translation initiation whereas p110 is initiated by cap-dependent
manner. Survey of the ATG codons within 5'-UTR was shown in Cornelis et al. (2000), Table 1.

Promoter-less plasmid was used to show at least 20x less-active promoter could be located in 745-1125 PITSLRE
IRES as compared to SV40 early promoter (Tinton et al. (2005), Figure 1D).
Citations:
Cornelis S., Bruynooghe Y., Denecker G., Van Huffel S., Tinton S., Beyaert R. (2000) Identification and characterization of a novel cell cycle-regulated internal ribosome entry site. Mol. Cell. 5(4):597-605
IRESs:
IRES:
Version: 4 Last change: 2008-06-26 14:58:03
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
The IRES name:
  PITSLRE_p58
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  745-1125
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Sequence 6 from patent US 6764852. Originally IRES has been mapped to 121-1125 and with finer mapping
published in Tinton et al. (2005) to 745-1125 in Di-4 plasmid and 976-1125 (Di-4 mut C).
Citations:
Cornelis S., Bruynooghe Y., Denecker G., Van Huffel S., Tinton S., Beyaert R. (2000) Identification and characterization of a novel cell cycle-regulated internal ribosome entry site. Mol. Cell. 5(4):597-605
Tinton S. A., Schepens B., Bruynooghe Y., Beyaert R., Cornelis S. (2005) Regulation of the cell-cycle-dependent internal ribosome entry site of the PITSLRE protein kinase: roles of Unr (upstream of N-ras) protein and phosphorylated translation initiation factor eIF-2alpha. Biochem. J. 385(Pt 1):155-163
IRES trans-acting factor (ITAFS):
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
OPTIONAL: The interacting RNA base range (if any):
745-1125
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
ITAF abbreviated name:
Unr
ITAF fullname:
upstream of N-ras
ITAF description (long):
Unr protein is known to bind to gaagaaguaa
3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
stimulatory
Method used to demonstrate ITAF effect:
in_vivo
In vitro system used to demonstrate ITAF effect:
rabbit reticulocytes lysate
The organism where action of this ITAF was studied:
Homo sapiens HEK 293T/17 (ATCC CRL-11268)
Citations:
Tinton S. A., Schepens B., Bruynooghe Y., Beyaert R., Cornelis S. (2005) Regulation of the cell-cycle-dependent internal ribosome entry site of the PITSLRE protein kinase: roles of Unr (upstream of N-ras) protein and phosphorylated translation initiation factor eIF-2alpha. Biochem. J. 385(Pt 1):155-163
Last change to the database: 2015-04-16 16:45:23 GMT+1