The nucleic acid data:
IRESite Id: 629 Version: 2
Originaly submitted by: Martin Mokrejš Submission date: 2009-08-30 21:49:28
Reviewed by: Martin Mokrejš Last change: 2009-08-30 21:54:52
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:
  TBP1
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
172898 
Synonyms of the gene name:
Synonym: TBP1
Synonym: SPT15
Synonym: YER148W
Synonym: BTF1
The mRNA/+RNA description: 
mRNA transcript from chromosome 5 of transcription initiation factor TFIID TBP subunit
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:
not_tested
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:
promoter_confirmed
Cryptic promoter presence was confirmed in an experimental setup involving inducible promoter:
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
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1 Last change: 2009-08-30 21:54:52
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
TBP1
The description of the protein encoded in this ORF:
transcription initiation factor TFIID TBP subunit
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):
  189-911
Remarks:
The description in the article of Hecht et al. (2002) that the 5'-UTR of TFIID is 188bp long matches the
5'-UTR mapped +-5bp in the GenBank entry M26403 (on which this IRESite mRNA sequence is based). Hecht et al.
reported that deletion of the region -188 to -104 removed the promoter activity.
Citations:
Hecht K., Bailey J. E., Minas W. (2002) Polycistronic gene expression in yeast versus cryptic promoter elements. FEMS Yeast. Res. 2(2):215-224
IRESs:
IRES:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  TFIID
Warning: please make ires_name same as the gene_name and optionally append to it coordinates. E.g. when gene/virus name is EMCV-R use EMCV-R_-222_to_-1 or EMCV-R_1-456, etc. but not Emcv-R-... or EMCV-222_to_-1. Please keep case of letters as well. This rewards when searching through the database.
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-188
Conclusion:
  unproved_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Citations:
Hecht K., Bailey J. E., Minas W. (2002) Polycistronic gene expression in yeast versus cryptic promoter elements. FEMS Yeast. Res. 2(2):215-224
Last change to the database: 2015-04-16 16:45:23 GMT+1