The nucleic acid data:
IRESite Id: 441 Version: 4
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš Last change: 2008-07-07 12:31:59
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 vitro T7 run-off transcript produced from bicistronic plasmid pDC-delta_1 which comprises neomycin
phosphotransferase and truncated version of the beta-galactosidase (linearized at the AflIII site at position
3754 within pDC-delta_1; see 1420.gb below) as the first and the second cistron respectively and part of gypsy
5' UTR (nt from -511 to nt +5 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 plasmid:
pDC-delta_1
The name of the promoter used to express this mRNA:
  T7
Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing part of gypsy 5' UTR (nt from -511 to nt +5 of the original sequence) 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:
gypsy
The origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
Drosophila melanogaster
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:
pDC-delta_1.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 14:08:22
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):
  1566-2873
Citations:
Ronfort C., De Breyne S., Sandrin V., Darlix J. L., Ohlmann T. (2004) Characterization of two distinct RNA domains that regulate translation of the Drosophila gypsy retroelement. RNA. 10(3):504-515
IRESs:
IRES:
Version: 4 Last change: 2008-07-07 12:31:59
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  gypsyD1
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1055-1570
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  197
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  712
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -511
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  4
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Gypsy IRES represents part of gypsy 5' UTR (nt from -511 to nt +5 of the original sequence).
The translation experiments:
Translation results:
IRESite Translation Id: 484
Version: 2 Last change: 2008-07-07 19:20:13
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
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:
  118.000
Name of IRES used as the positive control:
  gypsy
Name of the plasmid used as the positive control.
pDC-WT
IRESite Id of the plasmid used as positive control.
  439
The relative translation efficiency in % of the positive control:
  100.000
The size (length) of intercistronic region in the positive control:
1037
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  exogenous_RNA_without_cap_without_polyA_tail
Remarks:
Translational data are derived from Fig. 4B using ImageJ software (http://rsbweb.nih.gov/ij/).
Citations:
Ronfort C., De Breyne S., Sandrin V., Darlix J. L., Ohlmann T. (2004) Characterization of two distinct RNA domains that regulate translation of the Drosophila gypsy retroelement. RNA. 10(3):504-515
Last change to the database: 2015-04-16 16:45:23 GMT+1