The nucleic acid data:
IRESite Id: 329 Version: 5
Originaly submitted by: Tomáš Mašek
Reviewed by: Tomáš Mašek Last change: 2008-05-28 17:59:29
IRESite record type:
  negative_control_plasmid_with_promoter_and_without_putative_IRES
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 encoding B2 cyclin and NS protein as the first and the second cistron,
respectively.
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:
pXLJCon
The name of the promoter used to express this mRNA:
  T7
Aliases of the plasmid name:
Alias: pXLJ0
Description of the plasmid (facultative for promoter-less plasmid records):
pXLJCon is derived from pGEM-2 (Promega) backbone (GI: 58197). It contains T7 and SP6 promoter sites and is typically used in in vitro transcription/translation assays. Bicistronic RNA, which contains B2 and NS cistrons (GI:214094, GI:21693177), is transcribed by T7 polymerase after vector linearization by EcoRI.
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
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:
pXLJCon.jpg
Plasmid sequence verified (partially/completely) by IRESite (more details in Remarks):
  part of the yet unknown plasmid sequence determined by IRESite curators
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
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: 2007-10-23 00:00:00
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:
Xenopus 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: 1 Last change: 2007-10-23 00:00:00
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 3 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):
  1407-2087
Remarks:
IRESite notes about verification of plasmid sequence:
Plasmid DNA was digested by EcoRI/SalI giving fragments 4202/699 bp. Amplification with T7 and NS gene
specific primers (T7, ATACGACTCACTATAGGG,position within plasmid sequence:2785, NS_revseq,
CTGCAACTCGTTTGCGGAC, position within plasmid sequence:4263) gave one band of expected size. The partial
sequence of the vector and the partial sequence encoding bicistronic RNA was determined by sequencing (regions
2050-4584 and 4830-350 of plasmid sequence respectively). The rest of the sequence presented here was
reverse engineered with the help of authors description and Genbank entries (GI:58197 and GI:21693177).
There is one mutation detected in the vector backbone. More detailed data are annotated in the GenBank
formatted plasmid sequence file provided on this page above.
Citations:
Borman A., Jackson R. J. (1992) Initiation of translation of human rhinovirus RNA: mapping the internal ribosome entry site. Virology. 188(2):685-696
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