IRESite_Id:628 summary record describing characteristics of YAP1 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `628`	Version: `0`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-08-30 21:21:18`
Reviewed by: Martin Mokrejš

IRESite record type:

natural_transcript

The shape of the nucleic acid molecule translated: `linear`	The quality of the mRNA/+RNA sequence: `possibly_wrong`
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule: `YAP1`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
4505

Synonyms of the gene name:

Synonym: SNQ3

Synonym: PAR1

The mRNA/+RNA description:

In silico reconstructed transcript studied having 164bp long 5'-UTR. This spans TATA-box at position -132 to
-137 relative to the initiator AUG codon.

The mRNA/+RNA sequence represented in the +DNA notation:

ccgattaagc acagtacctt tacgttatat ataggattgg tgtttagctt tttttcctga gcccctggtt gacttgtgca tgaacacgag ccatttttag 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tttgtttaag ggaagttttt tgccacccaa aacgtttaaa gaaggaaaag ttgtttctta aaccatgagt gtgtctaccg ccaagaggtc gctggatgtc 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

gtttctccgg gttcattagc ggagtttgag ggttcaaaat ctcgtcacga tgaaatagaa aatgaacata gacgtactgg tacacgtgat ggcgaggata 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

gcgagcaacc gaagaagaag ggtagcaaaa ctagcaaaaa gcaagatttg gatcctgaaa ctaagcagaa gaggactgcc caaaatcggg ccgctcaaag 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

agcttttagg gaacgtaagg agaggaagat gaaggaattg gagaagaagg tacaaagttt agagagtatt cagcagcaaa atgaagtgga agctactttt 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ttgagggacc agttaatcac tctggtgaat gagttaaaaa aatatagacc agagacaaga aatgactcaa aagtgctgga atatttagca aggcgagatc 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

ctaatttgca tttttcaaaa aataacgtta accacagcaa tagcgagcca attgacacac ccaatgatga catacaagaa aatgttaaac aaaagatgaa 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

tttcacgttt caatatccgc ttgataacga caacgacaac gacaacagta aaaatgtggg gaaacaatta ccttcaccaa atgatccaag tcattcggct 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

cctatgccta taaatcagac acaaaagaaa ttaagtgacg ctacagattc ctccagcgct actttggatt ccctttcaaa tagtaacgat gttcttaata 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

acacaccaaa ctcctccact tcgatggatt ggttagataa tgtaatatat actaacaggt ttgtgtcagg tgatgatggc agcaatagta aaactaagaa 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

tttagacagt aatatgtttt ctaatgactt taattttgaa aaccaatttg atgaacaagt ttcggagttt tgttcgaaaa tgaaccaggt atgtggaaca 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

aggcaatgtc ccattcccaa gaaacccatc tcggctcttg ataaagaagt tttcgcgtca tcttctatac taagttcaaa ttctcctgct ttaacaaata 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

cttgggaatc acattctaat attacagata atactcctgc taatgtcatt gctactgatg ctactaaata tgaaaattcc ttctccggtt ttggccgact 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

tggtttcgat atgagtgcca atcattacgt cgtgaatgat aatagcactg gtagcactga tagcactggt agcactggca ataagaacaa aaagaacaat 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

aataatagcg atgatgtact cccattcata tccgagtcac cgtttgatat gaaccaagtt actaattttt ttagtccggg atctaccggc atcggcaata 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

atgctgcctc taacaccaat cccagcctac tgcaaagcag caaagaggat atacctttta tcaacgcaaa tctggctttc ccagacgaca attcaactaa 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

tattcaatta caacctttct ctgaatctca atctcaaaat aagtttgact acgacatgtt ttttagagat tcatcgaagg aaggtaacaa tttatttgga 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

gagtttttag aggatgacga tgatgacaaa aaagccgcta atatgtcaga cgatgagtca agtttaatca agaaccagtt aattaacgaa gaaccagagc 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ttccgaaaca atatctacaa tcggtaccag gaaatgaaag cgaaatctca caaaaaaatg gcagtagttt acagaatgct gacaaaatca ataatggcaa 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

tgataacgat aatgataatg atgtcgttcc atctaaggaa ggctctttac taaggtgttc ggaaatttgg gatagaataa caacacatcc gaaatactca 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

gatattgatg tcgatggttt atgttccgag ctaatggcaa aggcaaaatg ttcagaaaga ggggttgtca tcaatgcaga agacgttcaa ttagctttga 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

ataagcatat gaactaaagc gggaacttta tggaaaactg ggtaaccgaa agaacttttt ctataatgtt acaattaaac ttttttaact taccttgctt 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

cgccttttcg ccgaaag
^2201      ^2211

Credibility of mRNA sequence:

only_fragment_published_or_from_author_and_the_rest_is_a_guess

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:
unclear_result

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:
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

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:
YAP1

The description of the protein encoded in this ORF:
Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium

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):

165-2117

Citations:

Hertle K, Haase E, Brendel M (1991) The SNQ3 gene of Saccharomyces cerevisiae confers hyper-resistance to several functionally unrelated chemicals. Curr. Genet. 19(6):429-433

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

IRESs:

IRES:

Version: `0`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `YAP1`

The IRES absolute position (the range includes START and STOP codons or their equivalents):

1-164

Conclusion:
disproved_IRES

How IRES boundaries were determined:
experimentally_determined

The sequence of IRES region aligned to its secondary structure (if available):

ccgattaagc acagtacctt tacgttatat ataggattgg tgtttagctt tttttcctga gcccctggtt gacttgtgca tgaacacgag ccatttttag 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

tttgtttaag ggaagttttt tgccacccaa aacgtttaaa gaaggaaaag ttgtttctta aacc
^101       ^111       ^121       ^131       ^141       ^151       ^161

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