IRESite_Id:629 summary record describing characteristics of TFIID IRES

IRESite: The database of experimentally verified IRES structures

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:

AGGGACGTGA AAATTACAGT AGTTACTGTT TTTTTTGGAC TATAAGATCG GGGGAAAGAT AACACATAAG AAATAAAACG ACTACTAGTT AGACTGCTCT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGGAAGAAG CAAGGAAGTA AAGGCTGCAT TTTATTTTTC TTTTCTAGTC CAACATAAAC AGGTGTATCA AGAGAAACTT TTTTAATTAT GGCCGATGAG 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

GAACGTTTAA AGGAGTTTAA AGAGGCAAAC AAGATAGTGT TTGATCCAAA TACCAGACAA GTATGGGAAA ACCAGAATCG AGATGGTACA AAACCAGCAA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CTACTTTCCA GAGTGAAGAG GACATAAAAA GAGCTACCCC AGAATCTGAA AAAGACACCT CCGCCACATC AGGTATTGTT CCAACACTAC AAAACATTGT 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

GGCAACTGTG ACTTTGGGGT GCAGGTTAGA TCTGAAAACA GTTGCGCTAC ATGCCCGTAA TGCAGAATAT AACCCCAAGC GTTTTGCTGC TGTCATCATG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

CGTATTAGAG AGCCAAAAAC TACAGCTTTG ATTTTTGCAT CAGGGAAAAT GGTTGTTACC GGTGCAAAAA GTGAGGATGA CTCAAAGCTG GCCAGTAGAA 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AATATGCAAG AATTATCCAA AAAATCGGAT TTGCTGCTAA ATTCACAGAC TTCAAAATAC AAAATATTGT CGGTTCGTGT GACGTTAAAT TCCCTATACG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TCTAGAAGGG TTAGCATTCA GTCATGGTAC TTTCTCCTCC TATGAGCCAG AATTGTTTCC TGGTTTGATC TATAGAATGG TGAAGCCGAA AATTGTGTTG 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TTAATTTTTG TTTCAGGGAA GATTGTTCTT ACTGGTGCAA AGCAAAGGGA AGAAATTTAC CAAGCTTTTG AAGCTATATA CCCTGTGCTA AGTGAATTTA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

GAAAAATGTG ATGGGGAAGG AGTAGACGAA AAGAAAAAAA GGTTTTCTAT TTGTTCCATT TTCTCAATTA TTAATGGTCC TCAAAGAAAT AAAAGAAAAG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

GAAGAAGAAG TAATTGTAAT ATCAAACGGT TTTTTATAGT ATATTCTTCT TATTCTATAT TTATATATCA ATG
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071

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):

AGGGACGTGA AAATTACAGT AGTTACTGTT TTTTTTGGAC TATAAGATCG GGGGAAAGAT AACACATAAG AAATAAAACG ACTACTAGTT AGACTGCTCT 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

GCGGAAGAAG CAAGGAAGTA AAGGCTGCAT TTTATTTTTC TTTTCTAGTC CAACATAAAC AGGTGTATCA AGAGAAACTT TTTTAATT
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181

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: 2019-03-18 09:32:49 GMT+1