The nucleic acid data:
IRESite Id: 572 Version: 4
Originaly submitted by: Martin Mokrejš Submission date: 2009-03-21 20:47:35
Reviewed by: Martin Mokrejš Last change: 2009-08-30 20:55:44
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  hopefully_full-length_mRNA
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  TIF4631
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
295674 
The mRNA/+RNA description: 
Putative mRNA derived from DNA sequence published by Goyer et al. (1993) containing TIF4631 gene (eIF4G, 150
kDa). The DNA sequence was trimmed on its left to begin at one of the two sites determined by 5'-RACE and on
the right side to end at the putative poly(A)-site to reflect closely the presumed full-length mRNA. Later it
was found that the region -112 to -36 contains promoter (Verge et al., 2004).
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  end-to-end_sequence_reverse_engineered_and_should_match_experiment
The organism containing this mRNA with IRES segment in its genome:
Saccharomyces cerevisiae
A promoter reported in cDNA corresponding to IRES sequence:
  yes
The total number of notable open-reading frames (ORFs):
  1
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:
heterogeneous_population_of_molecules_found
Integrity (uniformity) of mRNA tested using RNase protection:
not_tested
Integrity (uniformity) of mRNA tested using 5'-RACE:
heterogeneous_population_of_molecules_found
Integrity (uniformity) of mRNA tested using primer extension :
not_tested
Integrity (uniformity) of mRNA tested using RT-PCR:
heterogeneous_population_of_molecules_found
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:
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:
Saccharomyces cerevisiae CWO4
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:
TIF4631
The description of the protein encoded in this ORF:
eIF4G 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):
  507-3365
Remarks:
There are no EST data supporting TIF4631 at all so it is not possible to predict which regions flanking the
CDS are transcribed (except the notes in the description of this mRNA). Zhou et al. (2001) mentioned that they
studied 508bp long 5'-UTR of p150 so this sequence should be correct.

A promoter region -112 to -36 in respect to initiator AUG codon was found in S. cerevisiae CWO4 strain while
no IRES activity was found in yeast extracts. A promoter-less vector was used to show functionally TIF4631
expression in a modified strain S. cerevisiae CBY19. Finally RT-PCR  and 5'-RACE were used to map
transcription start site. The 5'-UTR of TIF4631 mRNA are usually 36bp long. However, 75bp and even longer were
detected by 5'-RACE. [Verge et al., 2004]
Citations:
Goyer C., Altmann M., Lee H. S., Blanc A., Deshmukh M., Woolford JL J. r., Trachsel H., Sonenberg N. (1993) TIF4631 and TIF4632: two yeast genes encoding the high-molecular-weight subunits of the cap-binding protein complex (eukaryotic initiation factor 4F) contain an RNA recognition motif-like sequence and carry out an essential function. Mol. Cell. Biol. 13(8):4860-4874
Zhou W, Edelman GM, Mauro VP (2001) Transcript leader regions of two Saccharomyces cerevisiae mRNAs contain internal ribosome entry sites that function in living cells. Proc. Natl. Acad. Sci. U.S.A. 98(4):1531-1536
Vergé V, Vonlanthen M, Masson JM, Trachsel H, Altmann M (2004) Localization of a promoter in the putative internal ribosome entry site of the Saccharomyces cerevisiae TIF4631 gene. RNA. 10(2):277-286
IRESs:
IRES:
Version: 2 Last change: 2009-08-30 21:01:50
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  TIF4631
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  159-506
Conclusion:
  disproved_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
The region claimed for IRES activity is from Figure 5 (Zhou et al., 2001). However, Verge et al. (2004) did
not find any significant IRES activity in their assays.
Citations:
Zhou W, Edelman GM, Mauro VP (2001) Transcript leader regions of two Saccharomyces cerevisiae mRNAs contain internal ribosome entry sites that function in living cells. Proc. Natl. Acad. Sci. U.S.A. 98(4):1531-1536
Vergé V, Vonlanthen M, Masson JM, Trachsel H, Altmann M (2004) Localization of a promoter in the putative internal ribosome entry site of the Saccharomyces cerevisiae TIF4631 gene. RNA. 10(2):277-286
Mauro VP, Edelman GM, Zhou W (2004) Reevaluation of the conclusion that IRES-activity reported within the 5' leader of the TIF4631 gene is due to promoter activity. RNA. 10(6):895-897
Altmann M, Trachsel H, Vonlanthen M, Vergé V (2004) Answer to 'Reevaluation of the conclusion that IRES-activity reported within the 5' leader of the TIF4631 gene is due to promoter activity.'. RNA. 10(6):898
Last change to the database: 2015-04-16 16:45:23 GMT+1