The nucleic acid data:
IRESite Id: 428 Version: 5
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš Last change: 2008-07-07 19:35:29
IRESite record type:
  plasmid_with_promoter_and_putative_IRES_without_translational_characterization
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  hopefully_full-length_mRNA
The mRNA/+RNA description: 
In vitro T7 run-off transcript produced from bicistronic plasmid pDC-EMCV which encodes neomycin
phosphotransferase and truncated version of the beta-galactosidase (linearized at the Ssp1 site at position
3744 within pDC-EMCV; see 1384.gb below) as the first and the second cistron respectively and the EMCV-R IRES
(nt from -575 to nt -9 of the original sequence) inserted 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 plasmid:
pEMCV-D260-837
The name of the promoter used to express this mRNA:
  T7
Aliases of the plasmid name:
Alias: pDC-EMCV
Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing EMCV IRES (nt from -575 to -9 of the original sequence; GI:396509) 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:
  not tested
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
EMCV-R
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Encephalomyocarditis virus Ruckert
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:


GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
pEMCV-D260-837.jpg
The total number of notable open-reading frames (ORFs):
  2
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1 Last change: 2008-07-03 14:10:32
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
aph
The description of the protein encoded in this ORF:
aminoglycoside-3'-O-phosphotransferase
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):
  64-858
ORF
ORF position:   2
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
LacZ
The description of the protein encoded in this ORF:
beta-galactosidase
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):
  1628-2863
Remarks:
The plasmid was used as the positive control for experiments in article Characterization of two distinct RNA
domains that regulate translation of the Drosophila gypsy retroelement (Ronfort et al., 2004; PMID: 14970395).
Citations:
Berlioz C., Torrent C., Darlix J. L. (1995) An internal ribosomal entry signal in the rat VL30 region of the Harvey murine sarcoma virus leader and its use in dicistronic retroviral vectors. J. Virol. 69(10):6400-6407
IRESs:
IRES:
Version: 1 Last change: 2011-04-08 22:15:35
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  EMCV-R_259-825
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1059-1625
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  201
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  767
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -569
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -3
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Berlioz C., Torrent C., Darlix J. L. (1995) An internal ribosomal entry signal in the rat VL30 region of the Harvey murine sarcoma virus leader and its use in dicistronic retroviral vectors. J. Virol. 69(10):6400-6407
Last change to the database: 2015-04-16 16:45:23 GMT+1