IRESite_Id:116 summary record describing characteristics of HAP4 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `116`	Version: `5`
Originaly submitted by: Tomáš Mašek
Reviewed by: Tomáš Mašek	Last change: `2009-08-30 21:10:19`

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: `HAP4`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
486182

Synonyms of the gene name:

Synonym: YKL109W

The mRNA/+RNA description:

mRNA encoding a transcriptional activator and global regulator of respiratory gene expression.
The mRNA sequence is inserted without 3'UTR region, the 272 bp long 5'-UTR corresponds to the shortest
identified transcript of HAP4 gene.

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

ACCTCTCTAA ACCCCAGTTT TATATCGTAT ATGCTATCTA CAGGTCCACT TTACACTTAA TAATATAAAA ATACTACTAT AAAGGAACCA GAAAAATAAA 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

AAAGGGTCAT TATTTATTTG AGCAGATCAT TATCAAACGC ATAGGAAGAG AAAAAACACA GTTTTATTTT TTTTCCACAC ATATTTATTG GTCTCCTAGT 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

ACATCAAAGA GCATTTTAAT GGGTTGCTGA TTTGTTTTAC CTACATTTTC TAGTACAAAA AAAAAACAAA AAAAGAATCA TGACCGCAAA GACTTTTCTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

CTACAGGCCT CCGCTAGTCG CCCTCGTAGT AACCATTTTA AAAATGAGCA TAATAATATT CCATTGGCGC CTGTACCGAT CGCCCCAAAT ACCAACCATC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ATAACAATAG TTCGCTGGAA TTCGAAAACG ATGGCAGTAA AAAGAAGAAG AAGTCTAGCT TGGTGGTTAG AACTTCAAAA CATTGGGTTT TGCCCCCAAG 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ACCAAGACCT GGTAGAAGAT CATCTTCTCA CAACACTCTA CCTGCCAACA ACACCAATAA TATTTTAAAT GTTGGCCCTA ACAGCAGGAA CAGTAGTAAT 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AATAATAATA ATAATAACAT CATTTCGAAT AGGAAACAAG CTTCCAAAGA AAAGAGGAAA ATACCAAGAC ATATCCAGAC AATCGATGAA AAGCTAATAA 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACGACTCGAA TTACCTCGCA TTTTTGAAGT TCGATGACTT GGAAAATGAA AAGTTTCATT CTTCTGCCTC CTCCATTTCA TCTCCATCTT ATTCATCTCC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

ATCTTTTTCA AGTTATAGAA ATAGAAAAAA ATCAGAATTC ATGGACGATG AAAGCTGCAC CGATGTGGAA ACCATTGCTG CTCACAACAG TCTGCTAACA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

AAAAACCATC ATATAGATTC TTCTTCAAAT GTTCACGCAC CACCCACGAA AAAATCAAAG TTGAACGACT TTGATTTATT GTCCTTATCT TCCACATCTT 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CATCGGCCAC TCCGGTCCCA CAGTTGACAA AAGATTTGAA CATGAACCTA AATTTTCATA AGATCCCTCA TAAGGCTTCA TTCCCTGATT CTCCAGCAGA 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

TTTCTCTCCA GCAGATTCAG TCTCGTTGAT TAGAAACCAC TCCTTGCCTA CTAATTTGCA AGTTAAGGAC AAAATTGAGG ATTTGAACGA GATTAAATTC 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

TTTAACGATT TCGAGAAACT TGAGTTTTTC AATAAGTATG CCAAAGTCAA CACGAATAAC GACGTTAACG AAAATAATGA TCTCTGGAAT TCTTACTTAC 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AGTCTATGGA CGATACAACA GGTAAGAACA GTGGCAATTA CCAACAAGTG GACAATGACG ATAATATGTC TTTATTGAAT CTGCCAATTT TGGAGGAAAC 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

CGTATCTTCA GGGCAAGATG ATAAGGTTGA GCCAGATGAA GAAGACATTT GGAATTATTT ACCAAGTTCA AGTTCACAAC AAGAAGATTC ATCACGTGCT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

TTGAAAAAAA ATACTAATTC TGAGAAGGCG AACATCCAAG CAAAGAACGA TGAAACCTAT CTGTTTCTTC AGGATCAGGA TGAAAGCGCT GATTCGCATC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

ACCATGACGA GTTAGGTTCA GAAATCACTT TGGCTGACAA TAAGTTTTCT TATTTGCCCC CAACTCTAGA AGAGTTGATG GAAGAGCAGG ACTGTAACAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

TGGCAGATCT TTTAAAAATT TCATGTTTTC CAACGATACC GGTATTGACG GTAGTGCCGG TACTGATGAC GACTACACCA AAGTTCTGAA ATCCAAAAAA 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ATTTCTACGT CGAAGTCGAA CGCTAACCTT TATGACTTAA ACGATAACAA CAATGATGCA ACTGCCACCA ATGAACTTGA TCAAAGCAGT TTCATCGACG 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

ACCTTGACGA AGATGTCGAT TTTTTAAAGG TACAAGTATT TTGAAATAGG CATGTTGCAA TAAAACGAAA ACAACTAAAA ATCACGAAAA CAAAATGATA 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

TTATACAATA AAAAATTCTT ATTATGGGTA ATGATAGTAT TCTTCGCCTG CTTAGGCGTC CTTTTCCTTC AACAACAAAA ATTCCAAAAA AAAAAAGTAA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

AAAAACAAAA CTTTGATTGT TTTTTAATGA TGTTAATGAT TTTTTTTTTC TTTCTTTATC ATAAAAAAAA AGTTAAAATG AAAAACAAAT ATGGGTCTGG 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AAGGCCATTA TTTTTTTTTT ATTTATATAC CGTTTCTGGT ACTTAGTTAT TTATTCTCAT ACATACACTA TATTCAAATT ACCTAAGAGC ATTTTCACAT 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

ATCCGTTTAC TTTCATTTTT TTTTTTTTTG CTTCCTTTTT ACATATCTTC CGTATATCAC ATCACGTTTA CGCGTATGGT GAAACACGTC AAGAGAAAAA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TGATAAAATC AAATTTTGAT TTACATCAGG CTCCACAGGA CAGGGAAATC TATCTAGTGA GGCGATAACT GTAGTTCGAT GTACTCATTT GAACTGGACA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

AATTGAAAAT TGAGCTGAAA ACATGGGAGC ATGATTTCAT TGATAAAAAT AAAAGGGAAC CCACAAGGGA TGACATCAAG AGCCTGCGGA CTGTTCGGCA 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

GATGTATAAA CAATATTCCA CACTGAAGAA GAAACAATCT TTGCAACGAC AAAAAGTTGA CACTCAAGAG TCGGTTGAAC TCCCGGCACA TAAAAAAGAC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

CACGACGAAG TCGTAGAGAT AGGCCCTACT CCCCAAGTTT ACGGTAAGGC GATTAGTATC TTTGACATGA ATTTGTCGCC TATAAAGCCT ATATACATGA 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CATTCACAAA TAATATTGAT GTTAACAATG ATAACTCCAA GACAATTTCT AATGAATCTT CTCCACGAAA AACTATTCTC CTAAAATCGT CGCCTGCAGA 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

TCGTACGTTA GTGGCGGAAC CAATATCCAG TGTGAAACGC CAAT
^2901      ^2911      ^2921      ^2931      ^2941

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

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 :
unclear_result

Integrity (uniformity) of mRNA tested using RT-PCR:
homogeneous_population_of_molecules_confirmed

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: `2`	Last change: `2009-08-30 21:10:19`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek

The abbreviated name of this ORF/gene:
Hap4p

The description of the protein encoded in this ORF:
Subunit of the heme-activated, glucose-repressed Hap2p/3p/4p/5p CCAAT-binding complex, a transcriptional activator and global regulator of respiratory gene expression; provides the principal activation function of the complex.

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):

280-1944

Remarks:

Our mRNA sequence could be extended by ACCTCTC on its 5'-end to match the shortest full-length cDNA clone
(S03052-13_H21) as shown in SGD database in region chrXI:229155..236250
(http://db.yeastgenome.org/cgi-bin/locus.pl?locus=HAP4 and go for GBrowse). The primers used by Seino et al.
(2005) to copy the 5'-UTR region amplified only 270 bases and the cDNA region ended 2 nucleotides in front of
the initiator AUG:

iresite                                   -------TAAACCCCAGTTTTATATCGTATATGCTATCTACAGGTCCACTTTACACTTAA
second_primer_without_BamHI               ------------------------------------------------------------
S03052-13_H21                             ACCTCTCTAAACCCCAGTTTTATATCGTATATGCTATCTACAGGTCCACTTTACACTTAA
first_primer_inverted_without_EcoRI_SmaI  ------------------------------------------------------------


iresite                                   TAATATAAAAATACTACTATAAAGGAACCAGAAAAATAAAAAAGGGTCATTATTTATTTG
second_primer_without_BamHI               ------------------------------------------------------------
S03052-13_H21                             TAATATAAAAATACTACTATAAAGGAACCAGAAAAATAAAAAAGGGTCATTATTTATTTG
first_primer_inverted_without_EcoRI_SmaI  ------------------------------------------------------------


iresite                                   AGCAGATCATTATCAAACGCATAGGAAGAGAAAAAACACAGTTTTATTTTTTTTCCACAC
second_primer_without_BamHI               ------------------------------------------------------------
S03052-13_H21                             AGCAGATCATTATCAAACGCATAGGAAGAGAAAAAACACAGTTTTATTTTTTTTCCACAC
first_primer_inverted_without_EcoRI_SmaI  ------------------------------------------------------------


iresite                                   ATATTTATTGGTCTCCTAGTACATCAAAGAGCATTTTAATGGGTTGCTGATTTGTTTTAC
second_primer_without_BamHI               ------------------------------------------------------------
S03052-13_H21                             ATATTTATTGGTCTCCTAGTACATCAAAGAGCATTTTAATGGGTTGCTGATTTGTTTTAC
first_primer_inverted_without_EcoRI_SmaI  ------------------------------------------------------------


iresite                                   CTACATTTTCTAGTACAAAAAAAAAACAAAAAAAGAATCATGACCGCAAAGACTTTTCTA
second_primer_without_BamHI               ------------------------------------------------------------
S03052-13_H21                             CTACATTTTCTAGTACAAAAAAAAAACAAAAAAAGAATCATGACCGCAAAGACTTTTCTA
first_primer_inverted_without_EcoRI_SmaI  ------------GTACAAAAAAAAAACAAAAAAAGAA-----------------------

Citations:

Forsburg S. L., Guarente L. (1989) Identification and characterization of HAP4: a third component of the CCAAT-bound HAP2/HAP3 heteromer. Genes Dev. 3(8):1166-1178

IRESs:

IRES:

Version: `8`	Last change: `2007-09-06 00:00:00`
Originaly submitted by: Tomáš Mašek	Reviewed by: Tomáš Mašek
The IRES name: `HAP4`

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

8-277

Conclusion:
putative_IRES

How IRES boundaries were determined:
experimentally_determined

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

TAAACCCCAG TTTTATATCG TATATGCTAT CTACAGGTCC ACTTTACACT TAATAATATA AAAATACTAC TATAAAGGAA CCAGAAAAAT AAAAAAGGGT 
^8         ^18        ^28        ^38        ^48        ^58        ^68        ^78        ^88        ^98        

CATTATTTAT TTGAGCAGAT CATTATCAAA CGCATAGGAA GAGAAAAAAC ACAGTTTTAT TTTTTTTCCA CACATATTTA TTGGTCTCCT AGTACATCAA 
^108       ^118       ^128       ^138       ^148       ^158       ^168       ^178       ^188       ^198       

AGAGCATTTT AATGGGTTGC TGATTTGTTT TACCTACATT TTCTAGTACA AAAAAAAAAC AAAAAAAGAA
^208       ^218       ^228       ^238       ^248       ^258       ^268

Remarks:

Seino (2005) confirmed observation of Iizuka et al. 1994 that hap4 5'-UTR is translated in yeast cell lysates
in the presence of cap analogs. Further, Seino proposed cap-independent translation of HAP4 mRNA in stationary
phase in living yeast cells. On the contrary, Hecht (2002) reported that 5'-UTR of HAP4 is capable to drive
expression of promoter-less GFP construct and that this expression is induced in the presence of raffinose or
galactose but not in the presence of glucose.

Citations:

Seino A., Yanagida Y., Aizawa M., Kobatake E. (2005) Translational control by internal ribosome entry site in Saccharomyces cerevisiae. Biochim. Biophys. Acta. 1681(2-3):166-174

Hecht K., Bailey J. E., Minas W. (2002) Polycistronic gene expression in yeast versus cryptic promoter elements. FEMS Yeast. Res. 2(2):215-224

Iizuka N., Najita L., Franzusoff A., Sarnow P. (1994) Cap-dependent and cap-independent translation by internal initiation of mRNAs in cell extracts prepared from Saccharomyces cerevisiae. Mol. Cell. Biol. 14(11):7322-7330

Last change to the database: 2019-03-18 09:32:49 GMT+1