The abbreviated name of this ORF/gene: polyprotein
The description of the protein encoded in this ORF: genome polyprotein
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): 611-7063
The sequence of the HRV2 IRES was inferred from pR-HRV-F plasmid sequence provided by N. S. Magnuson which was
actually provided from the lab of A. Willis (who copied the sequence from R. Jacksons plasmid pXLJ(10-605)).
However, A. Willis utilized PvuII/NcoI sites of the plasmid whereas N. S. Magnuson utilized SpeI/NcoI sites
(it is unclear which HRV-2 sequence used was thus shorter).
Cammas et al. (2007) excluded both splicing and cryptic promoter issues with the pR-HRV-F plasmid in DNA
transfections (Supplemental Figure S2).
The IRES name: HRV-2 Warning: please make ires_name same as the gene_name and optionally append to it coordinates. E.g. when gene/virus name is EMCV-R use EMCV-R_-222_to_-1 or EMCV-R_1-456, etc. but not Emcv-R-... or EMCV-222_to_-1. Please keep case of letters as well. This rewards when searching through the database.
The IRES absolute position (the range includes START and STOP codons or their equivalents): 11-614
How IRES boundaries were determined: experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):
The 5'-UTR tested was confirmed to be functional as IRES and without cryptic promoter activity. No integrity
of the transcripts was studied in case of in vivo DNA plasmid transfections. But, direct RNA
transfections have confirmed IRES activity (Stoneley et al. (2000), Figure 6C). The IRES sequence is
terminated here after the naturally occurring NcoI site (ccATGg).
ITAF fullname: poly(rC)-binding protein 2 (39 kDa)
ITAF description (long): Required for poliovirus IRES activity (Blyn et al. 1996 and 1997) and replication (Toyoda et al., 2007). Its
amount is not limiting in rabbit reticulocyte lysates (RRL) (Hunt and Jackson 1999).
3.2.2. 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: required_but_available_internally
Method used to demonstrate ITAF effect: in_vivo
The organism where action of this ITAF was studied:
The interaction was confirmed by several methods using HeLa cell nuclear extracts (NE) with 32P-labeled RNAs.
Data in Figure 1. In Supplemental Figure S1 are describe HRV-2 mutant IRESs lacking the binding activity.