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: 3UTR_possibly_incomplete
The mRNA/+RNA description:
Putative spliced in vivo SV40 promoter-derived transcript produced from bicistronic plasmid pRL which
comprises renilla and firefly luciferases as the first and the second cistron, respectively and the 5' UTR (nt
8 to nt 300) plus first 27 bp of CDS from human n-myc mRNA with a hairpin in front of the first cistron.
The mRNA sequence shown in this record ends at its 3'-end right after the poly(A) signal from SV40 mRNA and
thus the 3'-UTR might be slightly wrong.
The mRNA/+RNA sequence represented in the +DNA notation:
Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)
Credibility of mRNA sequence: end-to-end_sequence_reverse_engineered_and_should_match_experiment
The name of the promoter used to express this mRNA: SV40
Description of the plasmid (facultative for promoter-less plasmid records): Plasmid containing 5' UTR (nt 8 to nt 300) plus first 27 bp from CDS from human n-myc inserted between renilla
and firefly luciferase reporter genes.
The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?): no
The in vivo produced heterogeneous transcripts occur due to alternative splicing: no
A promoter reported in cDNA corresponding to IRES sequence: no
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: not_tested
Integrity (uniformity) of mRNA tested using RNase protection: homogeneous_population_of_molecules_confirmed
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: 605.000
Name of IRES used as the positive control: n-myc
Name of the plasmid used as the positive control. pRNF
IRESite Id of the plasmid used as positive control. 72
The relative translation efficiency in % of the positive control: 100.000
The size (length) of intercistronic region in the positive control: 345
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:
As a positive control was used Neuro-2a [N2a] cell line transformed by similar vector pRNF lacking the
stem-loop in front of the first cistron. The hairpin loop impairs translation (by 75%) from the first
cistron while translation from the second cistron is not affected. Thus, the relative ratio 2nd/1st citron
increases.
Translational data are derived from Fig. 2B.