IRESite_Id:115 summary record describing characteristics of Ure2 IRES

IRESite: The database of experimentally verified IRES structures

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:

AGAAAAGCAA CTATACAAAG ACGAAAGCTT CCTTACTCGA GGTTGAAAAG AATAGCAAAA ATCTTTCCTT TTCAAACAGC TCATTTGGAA TTGTTTATAG 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

CACTGAATTG AATCGAAGAG GAATAAAGAT CCCCCGTACG AACTTCTTTA TTTTTAGTTT TTCATTTTTT GTTATTAGTC ATATTGTTTT AAGCTGCAAA 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

TTAAGTTGTA CACCAAATGA TGAATAACAA CGGCAACCAA GTGTCGAATC TCTCCAATGC GCTCCGTCAA GTAAACATAG GAAACAGGAA CAGTAATACA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

ACCACCGATC AAAGTAATAT AAATTTTGAA TTTTCAACAG GTGTAAATAA TAATAATAAT AACAATAGCA GTAGTAATAA CAATAATGTT CAAAACAATA 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ACAGCGGCCG CAATGGTAGC CAAAATAATG ATAACGAGAA TAATATCAAG AATACCTTAG AACAACATCG ACAACAACAA CAGGCATTTT CGGATATGAG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

TCACGTGGAG TATTCCAGAA TTACAAAATT TTTTCAAGAA CAACCACTGG AGGGATATAC CCTTTTCTCT CACAGGTCTG CGCCTAATGG ATTCAAAGTT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

GCTATAGTAC TAAGTGAACT TGGATTTCAT TATAACACAA TCTTCCTAGA TTTCAATCTT GGCGAACATA GGGCCCCCGA ATTTGTGTCT GTGAACCCTA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ATGCAAGAGT TCCAGCTTTA ATCGATCATG GTATGGACAA CTTGTCTATT TGGGAATCAG GGGCGATTTT ATTACATTTG GTAAATAAAT ATTACAAAGA 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

GACTGGTAAT CCATTACTCT GGTCCGATGA TTTAGCTGAC CAATCACAAA TCAACGCATG GTTGTTCTTC CAAACGTCAG GGCATGCGCC AATGATTGGA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CAAGCTTTAC ATTTCAGATA CTTCCATTCA CAAAAGATAG CAAGTGCTGT AGAAAGATAT ACGGATGAGG TTAGAAGAGT TTACGGTGTA GTGGAGATGG 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCTTGGCTGA ACGTAGAGAA GCGCTGGTGA TGGAATTAGA CACGGAAAAT GCGGCTGCAT ACTCAGCTGG TACAACACCA ATGTCACAAA GTCGTTTCTT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TGATTATCCC GTATGGCTTG TAGGAGATAA ATTAACTATA GCAGATTTGG CCTTTGTCCC ATGGAATAAT GTCGTGGATA GAATTGGCAT TAATATCAAA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

ATTGAATTTC CAGAAGTTTA CAAATGGACG AAGCATATGA TGAGAAGACC CGCGGTCATC AAGGCATTGC GTGGTGAATG A
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281

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):

AGCCAAAATA ATGATAACGA GAATAATATC AAGAATACCT TAGAACAACA TCGACAACAA CAACAGGCAT TTTCGGATAT GAGTCACGTG GAGTATTCCA 
^418       ^428       ^438       ^448       ^458       ^468       ^478       ^488       ^498       ^508       

GAATTACAAA ATTTTTTCAA GAACAACCAC TGGAGGGATA TACCCTTTTC TCTCACAGGT CTGCGCC
^518       ^528       ^538       ^548       ^558       ^568       ^578

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