The nucleic acid data:
IRESite Id: 606 Version: 4
Originaly submitted by: Martin Mokrejš Submission date: 2009-08-23 18:48:48
Reviewed by: Martin Mokrejš Last change: 2009-08-26 13:56:44
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:
  both_UTRs_incomplete
The mRNA/+RNA description: 
Part of a T7-derived transcript. The 5'-UTR could have been longer but we do not know the necessary details.
The intercistronic region contains sequence preceding movement protein (MP) ORF in crTMV (bp -75 to -3).
The mRNA/+RNA sequence represented in the +DNA notation:


Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)
Credibility of mRNA sequence:
  only_fragment_published_or_from_author_and_the_rest_is_a_guess
The name of the plasmid:
H-CP-crTMV_IRESmp75-GUS
The name of the promoter used to express this mRNA:
  T7
Aliases of the plasmid name:
Alias: HCP(deltaI-II)IRESmp75CR-GUS
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:
crTMV
The origin of IRES in the plasmid:
  viral
The donor organism of the IRES segment:
Crucifer tobamovirus
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:
H-CP-crTMV_IRESmp75-GUS.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: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
CP
The description of the protein encoded in this ORF:
coat protein
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):
  77-550
ORF
ORF position:   2
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
GUS
The description of the protein encoded in this ORF:
beta-glucuronidase
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):
  630-2441
Remarks:
A single-read sequencing result between CP and GUS ORFs obtained from T. Komarova.

The crTMV insert matches Z29370 sequence except one base. Probably the genomic sequence was published wrong as
two additional plasmid constructs from the same lab have the same base in that position.
Citations:
Skulachev MV, Ivanov PA, Karpova OV, Korpela T, Rodionova NP, Dorokhov YL, Atabekov JG (1999) Internal initiation of translation directed by the 5'-untranslated region of the tobamovirus subgenomic RNA I(2). Virology. 1(263):139-154
IRESs:
IRES:
Version: 1 Last change: 2009-08-26 13:56:44
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  crTMV_IRESmp75
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  555-627
How IRES boundaries were determined:
experimentally_determined
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  5
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  77
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -75
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:
Skulachev MV, Ivanov PA, Karpova OV, Korpela T, Rodionova NP, Dorokhov YL, Atabekov JG (1999) Internal initiation of translation directed by the 5'-untranslated region of the tobamovirus subgenomic RNA I(2). Virology. 1(263):139-154
The translation experiments:
Translation results:
IRESite Translation Id: 644
Version: 0
Originaly submitted by: Martin Mokrejš 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:
  80.000
Name of IRES used as the positive control:
  crTMV_IRESmp228
Name of the plasmid used as the positive control.
H-CP-crTMV_IRESmp228
Name of the plasmid used as the negative control.
H-CP-TMVUI_noIREScp148
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  0
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:
Values without exact quantification from Figure 8B.
Citations:
Skulachev MV, Ivanov PA, Karpova OV, Korpela T, Rodionova NP, Dorokhov YL, Atabekov JG (1999) Internal initiation of translation directed by the 5'-untranslated region of the tobamovirus subgenomic RNA I(2). Virology. 1(263):139-154
Last change to the database: 2015-04-16 16:45:23 GMT+1