The nucleic acid data:
IRESite Id: 239 Version: 4
Originaly submitted by: Václav Vopálenský
Reviewed by: Václav Vopálenský Last change: 2007-06-05 00:00:00
IRESite record type:
  promoter-less_plasmid_with_putative_IRES
The name of the plasmid:
(deltaCMV)betaGAL/UtrA/CAT
Description of the plasmid (facultative for promoter-less plasmid records):
Whole part of the 5' UTR from mouse Utrn mRNA (from nt -506 to nt -1 of the original sequence) has been cloned between the beta galactosidase and chloramphenicol acetyl transferase.
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 origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
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 DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:


GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
(deltaCMV)betaGAL/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):
  130-3273
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):
  4074-4733
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: 3 Last change: 2008-07-07 14:48:43
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):
  3560-4067
How IRES boundaries were determined:
guessed
5'-end of IRES relative to last base of the STOP codon of the upstream ORF:
  287
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:
  -514
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
Last change to the database: 2015-04-16 16:45:23 GMT+1