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: end-to-end_full-length_mRNA
The mRNA/+RNA description:
mRNA produced by bicistronic plasmid pRG-HCV1 which comprises DsRED2 and EGFP genes as the first and the
second cistron, respectively. The full-length 5'-UTR of HCV genomic RNA together with the first 45 nt of a
viral polyprotein gene was inserted in frame into the intercistronic region of the reporter pRG vector, thus
making the N-terminal fusion of the first 15 amino acids residues from the HCV polyprotein with the EGFP
protein.
The sequence 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:
Credibility of mRNA sequence: end-to-end_sequence_completely_same_as_in_the_experiment
The name of the promoter used to express this mRNA: CMV_IE
Aliases of the plasmid name:
Alias: pRGIRES
Description of the plasmid (facultative for promoter-less plasmid records): Plasmid containing the full-length 5'-UTR of HCV genomic RNA together with the first 45 nt of a viral
polyprotein gene inserted between DsRED2 and EGFP 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: not tested
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid: HCV1a
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:
Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks): plasmid sequence confirmed by IRESite curators by restriction analysis + parts by PCR + sequencing
GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
The total number of notable open-reading frames (ORFs): 2
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
The description of the protein encoded in this ORF: red-shifted variant of wild-type GFP optimized for brighter fluorescence and higher expression in mammalian
cells (Clontech)
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): 1166-1885
Remarks:
IRESite notes about verification of plasmid sequence:
The complete sequence of HCV IRES region was determined by sequencing using DsRed1-C Sequencing Primer
(Clontech; #6483-1; 5'-AGCTGGACATCACCTCCCACAACG-3').