The description of the protein encoded in this ORF: Firefly luciferase
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): 2239-3891
The cloned 5'-UTR by van Eden et al. (2004) region was not a complete 5'-UTR. There are 3 mutations in
the cloned sequence provided by R. Lloyd in comparison to both German and NIH cDNA projects: GI:34367137 and
GI:22382083. -297nt from initiator ATG is A instead of G, -177nt is A instead of T, -76nt is G instead of T.
As already mentioned the sequence provided to IRESite by R. Lloyd spans -1115 to +4 (while the +4 base not
shown in van Eden et al. (2004) Fig. 1A is 'G'. van Eden showed already published 5'-UTR of NM_001166.2
(GI:10880127) GenBank record which is 1159b long whereas current GI:41349435 (NM_001166.3) contains 1.4kb
The intercistronic region contains incomplete 5'-UTR of c-IAP1 (-1115 to -1) followed by some 19 b as a
remnant of HCV ORF after mutation.
The translation method used to study IRES function: in vitro
The in vitro translation system: rabbit reticulocytes lysate
The organism used for translation:
The temperature (in degrees of Celsia): 30
The relative translation efficiency in % of this IRES: 3968.000
Name of IRES used as the positive control: HCV_type_1b
Name of the plasmid used as the positive control. pRL-HCV-FL
Name of the plasmid used as the negative control. pRL-null-FL
IRESite Id of the plasmid used as positive control. 131
The relative translation efficiency in % of the positive control: 100.000
The relative translation efficiency in % of the negative control: 11.950
The size (length) of intercistronic region in the positive control: 419
The effect of 5'-cap analogs on translation: not tested
Rapamycin affects translation: not tested
Type of RNA subject to translation: exogenous_RNA_with_GpppG_cap_without_polyA_tail
Sequence of the negative control is said to contain 590nt spacer derived from human PKR but is not available
from authors. We conclude part of the protein coding region was cloned, unfortunately it is not clear which
exactly. For example, GenBank GI:4506102 has 1654b long ORF. This negative control had activity of 0% of the
From Fig. 2B is clear that FLUC/RLUC ratio of phpRL-cIAP1-FL is about 30x higher than that of pRL-cIAP1-FL.
The values presented here are extrapolated from Fig 2B, 2C and seem to match the values for pRL-cIAP1-FL.
in Fig. 2D although is is hard to say what the value for RLUC really was. Authors possibly intentionally
omitted the FLUC/RLUC value for this phpRL-cIAP1-FL plasmid from Fig. 2C. From Fig. 2C we calculated
that pRL-cIAP1-FL is 132.27% of the pRL-HL (should be named actually pRL-HCV-FL not to be confused with the
plasmid from Honda S.) positive control (set by definition to 100%) and that the negative control pRL-null-FL
was about 11.95% of the positive control. The value presented by IRESite above 3968 is therefore calculated
as 30 * 132.27%.