The nucleic acid data:
IRESite Id: 89 Version: 7
Originaly submitted by: Blanka Vicenová Submission date: 2006-01-09 00:00:00
Reviewed by: Martin Mokrejš Last change: 2008-06-25 10:22:50
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:
  L-myc
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
74315996
The mRNA/+RNA description: 
Human L-myc protein gene, complete cds.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  unknown
The organism containing this mRNA with IRES segment in its genome:
Homo sapiens
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
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: 0
Originaly submitted by: Blanka Vicenová Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
L-myc
The description of the protein encoded in this ORF:
L-myc 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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  218-1312
OPTIONAL: The function of the encoded protein
Short form of the L-myc protein; belongs to the myc family of proto-oncogenes; overexpression causes cellular
transformation.
Remarks:
There are two forms of L-myc that differ in their 5'UTR length (217b and 581b long) as a result of alternative
splicing (the longer form contains intron A, Fig. 1 in the article). IRES was found only in the short, spliced
form of L-myc mRNA. Integrity of bicistronic mRNA transcripts was verified by Northern blot analysis. From
Fig. 3B and 3C comes out that the L-myc IRES driven translation is more effective than cap-dependent
translation, which is highly unexpected. In contrast, dicistronic constructs containing the long form of the
5'-UTR in pRF (or derived from) plasmids resulted in heterogeneous population of mRNA -- possibly as a result
of splicing events of the intron within the L-myc long 5'-UTR.
Citations:
Jopling C. L., Spriggs K. A., Mitchell S. A., Stoneley M., Willis A. E. (2004) L-Myc protein synthesis is initiated by internal ribosome entry. RNA. 10(2):287-298
IRESs:
IRES:
Version: 4 Last change: 2008-06-25 10:22:50
Originaly submitted by: Blanka Vicenová Reviewed by: Martin Mokrejš
The IRES name:
  L-myc
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  90-141
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):



Remarks:
Concerning the absolute IRES localization no further positional data available; according to Jopling et al.,
2004, the ribosome entry site is located between positions 90 and 141.
Citations:
Jopling C. L., Spriggs K. A., Mitchell S. A., Stoneley M., Willis A. E. (2004) L-Myc protein synthesis is initiated by internal ribosome entry. RNA. 10(2):287-298
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 7
Version: 6 Last change: 2006-04-10 00:00:00
Originaly submitted by: Blanka Vicenová Reviewed by: Martin Mokrejš
The function of the 2D structure:
IRES
The 2D structure causes frameshift:
unknown
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1-217
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
L-myc IRES RNA was generated using in vitro transcription reactions, resuspended in probing buffer, and then
heated rapidly and cooled gradually to refold the molecule into its native conformation (Le Quesne et al.
2001). RNA was treated either with DMS / kethoxal / CMCT to detect unpaired bases. RNase V1 was used to detect
basepaired regions. Secondary structure was predicted using the web implementation of the Mfold algorithm
(Zuker et al., 1999) with the experimental data used as the prediction contraints. There is a potential
pseudoknot between 32-35 and 66-69. The degree of concordance of the chemical probing data with the final
secondary structure model was not specified.
3.1.1. Enzymes used to characterize at least partially the 2D structure.
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 7
The temperature (in degrees of Celsia):
0
The enzymatic method used to determine the 2D structure:
ribonuclease V1
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
0.10
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
0.12
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
3.1.2. Chemicals used to characterize at least partially the 2D structure.
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 8
The temperature (in degrees of Celsia):
0
The chemical reagent used to determine the 2D structure:
DMS
Chemical reagent used with its respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
0.10
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
0.10
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 9
The temperature (in degrees of Celsia):
0
The chemical reagent used to determine the 2D structure:
CMCT
Chemical reagent used with its respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
0.10
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
0.10
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 10
The temperature (in degrees of Celsia):
0
The chemical reagent used to determine the 2D structure:
kethoxal
Chemical reagent used with its respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
0.10
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
0.10
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Citations:
Zuker M., Mathews D.H., Turner D.H. (1999) Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide. RNA Biochem. Biotechnol. 1:1-23
Jopling C. L., Spriggs K. A., Mitchell S. A., Stoneley M., Willis A. E. (2004) L-Myc protein synthesis is initiated by internal ribosome entry. RNA. 10(2):287-298
Le Quesne J. P., Stoneley M., Fraser G. A., Willis A. E. (2001) Derivation of a structural model for the c-myc IRES. J. Mol. Biol. 310(1):111-126
Last change to the database: 2015-04-16 16:45:23 GMT+1