The description of the protein encoded in this ORF: vascular endothelial growth factor A (initiated from AUG codon)
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: yes
The ORF absolute position (the base range includes START and STOP codons or their equivalents): 1022-1462
It is not clear how this VEGF-A region corresponds to the region used by A.-C. Prats and O. Elroy-Stein.
However, Baranick et al. picked the SP163 variant because it was reported to be more efficient than the
"native" 5'-UTR IRES in the past.
Bert et al. (2006) tested VEGF IRES in HeLa cells using promoter-less plasmids with or without the enhancer
left in (Figure 2). They showed there is a cryptic promoter activatable when the enhancer is left in.
Young et al. (2008) in Figure 2C show cryptic promoter activity in the "IRES".
It could Baranick et al. (2008) failed to catch the promoter in HeLa cells because of their PCR-primer
combination designed to reveal splicing issues (Supplementary Figure 7).
The IRES absolute position (the range includes START and STOP codons or their equivalents): 889-1021
How IRES boundaries were determined: experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):
Bert et al. (2006) reported that in direct RNA transfection the VEGF IRES is only 5.4x above the negative
control while EMCV IRES was 221x above (Figure 4).
The "IRES" was found to be not functional in vivo (Figures 1 and 2) while no issues with aberrant splicing
were reported (Baranick et al., 2008, Figure 3D).
The "IRES" is not functional in direct RNA transfection assay nor in (Young et al., 2008, Figure 3). From
Figure 2B one can gather that there in NIH3T3 plasmid transfected cells there is some "IRES" activity or the
VEGF "IRES" is well leaky-scanned so that some additional FLuc is synthesized from bicistronic messages.