The nucleic acid data:
IRESite Id: 115 Version: 5
Originaly submitted by: Tomáš Mašek
Reviewed by: Tomáš Mašek Last change: 2007-09-06 00:00:00
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  3UTR_incomplete
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  Ure2
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
22135406 
Synonyms of the gene name:
Synonym: YNL229C
The mRNA/+RNA description: 
RNA encoding nitrogen catabolite repression regulator that acts by inhibition of GLN3 transcription in good
nitrogen source; altered form of Ure2p creates [URE3] prion
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  reverse_engineered_fragment_and_the_rest_is_a_guess
The organism containing this mRNA with IRES segment in its genome:
Saccharomyces cerevisiae CWO4
A promoter reported in cDNA corresponding to IRES sequence:
  no
The total number of notable open-reading frames (ORFs):
  2
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:
not_tested
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:
not_tested
Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
no_promoter_confirmed
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:
Saccharomyces cerevisiae CWO4
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 4 Last change: 2007-09-06 00:00:00
Originaly submitted by: Tomáš Mašek Reviewed by: Tomáš Mašek
The abbreviated name of this ORF/gene:
Ure2p
The description of the protein encoded in this ORF:
Nitrogen catabolite repression regulator that acts by inhibition of GLN3 transcription in good nitrogen source; altered form of full-length protein creates [URE3] prion
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:
  yes
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  217-1281
ORF
ORF position:   2
Version: 1 Last change: 2007-09-06 00:00:00
Originaly submitted by: Tomáš Mašek Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
Ure2p-truncated
The description of the protein encoded in this ORF:
Nitrogen catabolite repression regulator that acts by inhibition of GLN3 transcription in good nitrogen source; N-terminally truncated form of Ure2p (lacking amino acids 1-93) lacks the prion-forming domain.
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):
  496-1281
OPTIONAL: The function of the encoded protein
Molecular Function: phosphoprotein binding, transcription corepressor activity
Biological Process: cytoplasmic sequestering of transcription factor,regulation of nitrogen
utilization, response to aluminum ion, telomere maintenance Cellular Component: cytosol-soluble fraction
Remarks:
42 kDa and 30 kDa forms of Ure2p are detected in yeast cells. The 42 kDa isoform stems from translation
initiation on the first AUG (position 1), while N-terminally truncated 30 kDa isoform results from translation
initiation on AUG at position 94 of amino acids sequence.

To yield full-length 5'-UTR the mRNA sequence was extended by the sequence of full-length cDNA S03052-29_D08
from SGD database (http://db.yeastgenome.org/cgi-bin/locus.pl?locus=URE2 and go for GBrowse).
Citations:
Komar A. A., Lesnik T., Cullin C., Merrick W. C., Trachsel H., Altmann M. (2003) Internal initiation drives the synthesis of Ure2 protein lacking the prion domain and affects [URE3] propagation in yeast cells. EMBO J. 22(5):1199-1209
IRESs:
IRES:
Version: 5 Last change: 2007-09-06 00:00:00
Originaly submitted by: Tomáš Mašek Reviewed by: Tomáš Mašek
The IRES name:
  Ure2
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  418-584
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Internal initiation mediated by Ure2 IRES leads to the synthesis of N-terminally truncated form of the
protein (amino acids 94-354) lacking prion-forming domain. It is supposed that balance between
cap-dependently translated full-length and truncated Ure2p forms plays an important role in yeast cell
physiology and differentiation. The yeast initiation factor eIF2A functions as a suppressor of Ure2
IRES-mediated translation.
Citations:
Komar A. A., Lesnik T., Cullin C., Merrick W. C., Trachsel H., Altmann M. (2003) Internal initiation drives the synthesis of Ure2 protein lacking the prion domain and affects [URE3] propagation in yeast cells. EMBO J. 22(5):1199-1209
Komar A. A., Gross S. R., Barth-Baus D., Strachan R., Hensold J. O., Goss Kinzy T., Merrick W. C. (2005) Novel characteristics of the biological properties of the yeast Saccharomyces cerevisiae eukaryotic initiation factor 2A. J. Biol. Chem. 280(16):15601-15611
Last change to the database: 2015-04-16 16:45:23 GMT+1