IRESite record type: plasmid_with_promoter_and_putative_IRES_translationally_characterized
The shape of the nucleic acid molecule translated: linear
The quality of the mRNA/+RNA sequence: our_best_guess
The mRNA/+RNA description:
In vivo CMV driven transcript produced from bicistronic plasmid pDC-env which comprises neomycin
phosphotransferase and beta-galactosidase as the first and the second cistron respectively and full-length
(except very 5'-most Adenosine) gypsy-env 5' UTR (nt from -841 to -511 of the original sequence) mRNA inserted
in between reporters.
The mRNA/+RNA sequence represented in the +DNA notation:
Credibility of mRNA sequence: end-to-end_sequence_reverse_engineered_and_should_match_experiment
The name of the promoter used to express this mRNA: CMV
Description of the plasmid (facultative for promoter-less plasmid records): Plasmid containing gypsy-env IRES (nt from -841 to -511) inserted between neomycin phosphotransferase and
beta-galactosidase reporter genes.
The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?): not tested
The in vivo produced heterogeneous transcripts occur due to alternative splicing: not tested
A promoter reported in cDNA corresponding to IRES sequence: no (not convincing)
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: not_tested
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 relative translation efficiency in % of this IRES: 108.000
Name of IRES used as the positive control: EMCV-R
Name of the plasmid used as the positive control. pEMCV-D260-837
IRESite Id of the plasmid used as positive control. 460
The relative translation efficiency in % of the positive control: 100.000
The size (length) of intercistronic region in the positive control: 769
The effect of 5'-cap analogs on translation: not tested
Rapamycin affects translation: not tested
Type of RNA subject to translation: endogenous_nuclear_RNA_Pol_II_transcript
Remarks:
pDC-Env exhibited enhancement of the beta-Gal/neo ratio in the presence of protease P2A, indicating that the
two cistrons were not equally affected by expression of the poliovirus protease and that the RNA segment
1–330 was able to direct cap-independent translation initiation in a bicistronic context (translational data
are derived from Fig. 9A).
Translation of the pDC-Env RNA is not affected by the FMDV-L protease (see Fig. 6)