The nucleic acid data:
IRESite Id: 238 Version: 2
Originaly submitted by: Václav Vopálenský
Reviewed by: Václav Vopálenský Last change: 2009-09-02 23:43:01
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:
  hopefully_full-length_mRNA
The mRNA/+RNA description: 
Putative in vivo CMV promoter-derived transcript produced from bicistronic plasmid pbetaGAL/UtrA/CAT which
comprises beta galactosidase and chloramphenicol acetyltransferase as the first and the second cistron
respectively and the whole part of mouse Utrn 5' UTR (from nt -506 to nt -1 of the original sequence) mRNA
cloned between them.
The sequence ends at its 3'-end right after the poly(A) signal from BGH mRNA and thus the 3'-UTR might be
slightly wrong.
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:
pbetaGAL/UtrA/CAT
The name of the promoter used to express this mRNA:
  CMV
Description of the plasmid (facultative for promoter-less plasmid records):
Plasmid containing the whole part of human Utrn 5' UTR (nt from -506 to nt -1 of the original sequence) inserted between beta galactosidase and chloramphenicol acetyltransferase reporter genes.
The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):
  no
The in vivo produced heterogeneous transcripts occur due to alternative splicing:
  no
A promoter reported in cDNA corresponding to IRES sequence:
  no
Summary of possible issues when IRES cDNA is experimentally transcribed in vivo:
Summary of experiments studying integrity of the in vivo transcripts in a particular host:
Integrity (uniformity) of mRNA tested using Northern-blot:
homogeneous_population_of_molecules_confirmed
Integrity (uniformity) of mRNA tested using RNase protection:
not_tested
Integrity (uniformity) of mRNA tested using 5'-RACE:
not_tested
Integrity (uniformity) of mRNA tested using primer extension :
not_tested
Integrity (uniformity) of mRNA tested using RT-PCR:
homogeneous_population_of_molecules_confirmed
Integrity (uniformity) of mRNA tested using real-time quantitative polymerase chain reaction (rtqPCR):
not_tested
Integrity (uniformity) of mRNA tested using RNAi:
not_tested
Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested
Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
no_promoter_confirmed
Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
not_tested
Integrity (uniformity) of mRNA molecules or possible promoter presence expressed in vivo was tested using another method, please specify in Remarks:
not_tested
The organism used:
Mus musculus C2C12
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
Utrn
The origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
Mus musculus C2C12
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:
pbetaGAL/UtrA/CAT.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: Václav Vopálenský Reviewed by: Václav Vopálenský
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  189-3332
ORF
ORF position:   2
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The abbreviated name of this ORF/gene:
CAT
The description of the protein encoded in this ORF:
chloramphenicol acetyl transferase
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):
  4133-4792
Citations:
Miura P., Thompson J., Chakkalakal J. V., Holcik M., Jasmin B. J. (2005) The utrophin A 5'-untranslated region confers internal ribosome entry site-mediated translational control during regeneration of skeletal muscle fibers. J. Biol. Chem. 280(38):32997-33005
IRESs:
IRES:
Version: 2 Last change: 2009-09-02 23:43:01
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The IRES name:
  UtrA
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  3621-4126
How IRES boundaries were determined:
guessed
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  289
3'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  794
5'-end of IRES relative to first base of the START codon of the downstream ORF:
  -512
3'-end of IRES relative to first base of the START codon of the downstream ORF:
  -7
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Whole 5'-UTR region of Utrn mRNA (from nt -506 to nt -1 of the original sequence).
Citations:
Miura P., Thompson J., Chakkalakal J. V., Holcik M., Jasmin B. J. (2005) The utrophin A 5'-untranslated region confers internal ribosome entry site-mediated translational control during regeneration of skeletal muscle fibers. J. Biol. Chem. 280(38):32997-33005
The translation experiments:
Translation results:
IRESite Translation Id: 296
Version: 4 Last change: 2008-05-19 14:30:12
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The translation method used to study IRES function:
in vivo
The organism used for translation:
Mus musculus C2C12
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  14.900
Name of IRES used as the positive control:
  XIAP
Name of the plasmid used as the positive control.
pbetaGAL/XIAP/CAT
Name of the plasmid used as the negative control.
pbetaGAL/CAT
IRESite Id of the plasmid used as positive control.
  244
IRESite Id of the plasmid used as negative control.
  237
The relative translation efficiency in % of the positive control:
  100.000
The relative translation efficiency in % of the negative control:
  0.019
The size (length) of intercistronic region in the positive control:
1335
The size (length) of intercistronic region in the negative control:
336
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  exogenous_RNA_with_GpppG_cap_with_polyA_tail
Remarks:
Throughout the whole study Miura et al. used as a negative control vector pbetaGAL/CAT plasmid with 336 bp
spacer between LacZ and CAT reporter genes instead of 100 bp spacer plasmid variant listed in this article.
Citations:
Miura P., Thompson J., Chakkalakal J. V., Holcik M., Jasmin B. J. (2005) The utrophin A 5'-untranslated region confers internal ribosome entry site-mediated translational control during regeneration of skeletal muscle fibers. J. Biol. Chem. 280(38):32997-33005
Translation results:
IRESite Translation Id: 297
Version: 2 Last change: 2006-10-26 00:00:00
Originaly submitted by: Václav Vopálenský Reviewed by: Václav Vopálenský
The translation method used to study IRES function:
in vivo
The organism used for translation:
Mus musculus C57BL/10
The temperature (in degrees of Celsia):
37
The relative translation efficiency in % of this IRES:
  100.000
Name of the plasmid used as the negative control.
pbetaGAL/UtrA/CAT
IRESite Id of the plasmid used as negative control.
  238
The relative translation efficiency in % of the negative control:
  0.100
The size (length) of intercistronic region in the negative control:
800
The effect of 5'-cap analogs on translation:
not tested
Rapamycin affects translation:
not tested
Type of RNA subject to translation:
  exogenous_RNA_with_GpppG_cap_with_polyA_tail
Remarks:
To examine the expression of the reporter constructs during muscle regeneration, plasmid was directly injected
in both regenerating and control TA muscles 3 days after cardiotoxin treatment.
Negative control - same plasmid (pbetaGAL/UtrA/CAT) in cardiotoxin-untreated C57BL/10 mice.
Citations:
Miura P., Thompson J., Chakkalakal J. V., Holcik M., Jasmin B. J. (2005) The utrophin A 5'-untranslated region confers internal ribosome entry site-mediated translational control during regeneration of skeletal muscle fibers. J. Biol. Chem. 280(38):32997-33005
Last change to the database: 2015-04-16 16:45:23 GMT+1