The nucleic acid data:
IRESite Id: 330 Version: 6
Originaly submitted by: Tomáš Mašek
Reviewed by: Tomáš Mašek Last change: 2008-05-28 18:00:12
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:
  end-to-end_full-length_mRNA
The mRNA/+RNA description: 
In vitro transcribed bicistronic mRNA containing Idefix IRES between B2 cyclin and NS protein cistrons.
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 plasmid:
pXL-Id
The name of the promoter used to express this mRNA:
  T7
Description of the plasmid (facultative for promoter-less plasmid records):
pXL-Id is derivative of pXLJCon plasmid. It contains T7 and SP6 promoter sites and is typically used in in vitro transcription/translation assays. Bicistronic RNA is transcribed by T7 polymerase after vector linearization by EcoRI. IRES sequence (ranging from 502 to 1024 bp of Idefix sequence, GI: 4165192) was inserted as EcoRI filled-in fragment into BamHI digested and blunted pXLJCon plasmid.
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:
Id
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:


Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks):
  part of the yet unknown plasmid sequence determined by IRESite curators
GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
pXL-Id.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: 0
Originaly submitted by: Tomáš Mašek Reviewed by: Tomáš Mašek
The abbreviated name of this ORF/gene:
B2
The description of the protein encoded in this ORF:
X. laevis B2 cyclin
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  39-1217
ORF
ORF position:   2
Version: 0
Originaly submitted by: Tomáš Mašek Reviewed by: Tomáš Mašek
The abbreviated name of this ORF/gene:
NS
The description of the protein encoded in this ORF:
Truncated form of influenza NS1 protein which is N-terminally fused with 9 amino acids.
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  1927-2625
Remarks:
IRESite notes about verification of plasmid sequence:
Plasmid DNA was digested by EcoRI/SalI giving fragments 4202/1237 bp. Amplification with T7 and NS gene
specific primers (T7, ATACGACTCACTATAGGG,position within plasmid sequence:2785, NS_revseq,CTGCAACTCGTTTGCGGAC,
position within plasmid sequence:4801) gave one band of expected size. The complete sequence of IRES and 5-
and 3- flanking regions was determined by sequencing (region 3800-5172 of plasmid sequence). The rest of the
sequence presented here was reverse engineered with the help of authors description and IRESite entry 329.
There is one mutation detected in the vector backbone and 5 mutation in Idefix IRES in respect to
GI:4165192. More detailed data are annotated in the GenBank formatted sequence file provided by this page
above.
Citations:
Meignin C., Bailly J. L., Arnaud F., Dastugue B., Vaury C. (2003) The 5' untranslated region and Gag product of Idefix, a long terminal repeat-retrotransposon from Drosophila melanogaster, act together to initiate a switch between translated and untranslated states of the genomic mRNA. Mol. Cell. Biol. 23(22):8246-8254
IRESs:
IRES:
Version: 3 Last change: 2007-10-23 00:00:00
Originaly submitted by: Tomáš Mašek Reviewed by: Tomáš Mašek
The IRES name:
  idefix
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1419-1942
How IRES boundaries were determined:
unknown
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  202
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  725
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -508
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  15
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Meignin C., Bailly J. L., Arnaud F., Dastugue B., Vaury C. (2003) The 5' untranslated region and Gag product of Idefix, a long terminal repeat-retrotransposon from Drosophila melanogaster, act together to initiate a switch between translated and untranslated states of the genomic mRNA. Mol. Cell. Biol. 23(22):8246-8254
Last change to the database: 2015-04-16 16:45:23 GMT+1