IRESite_Id:572 summary record describing characteristics of TIF4631 IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `572`	Version: `4`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-03-21 20:47:35`
Reviewed by: Martin Mokrejš	Last change: `2009-08-30 20:55:44`

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: `TIF4631`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
295674

The mRNA/+RNA description:

Putative mRNA derived from DNA sequence published by Goyer et al. (1993) containing TIF4631 gene (eIF4G, 150
kDa). The DNA sequence was trimmed on its left to begin at one of the two sites determined by 5'-RACE and on
the right side to end at the putative poly(A)-site to reflect closely the presumed full-length mRNA. Later it
was found that the region -112 to -36 contains promoter (Verge et al., 2004).

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

tcattttttt gaaaattaca ttaataaggc ttttttcaat atctctggaa caacagtttg tttctactta ctaatagctt taaggaccct cttggacatc 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

atgatggcag acttccatcg tagtgggatg atcatatgat gggcgctatc ctcatcgcga ctcgataacg acgtgagaaa cgattttttt ttttcttttt 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

caccgtattt ttgtgcgtcc tttttcaatt atagcttttt tttatttttt ttttttctcg tactgtttca ctgacaaaag ttttttttca agaaaaattt 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

tcgatgccgc gttctctgtg tgcaacggat ggatggtaga tggaatttca atatgttgct tgaaatttta ccaatcttga tattgtgata atttacttaa 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

ttatgattct tcctcttccc ttcaatttct taaagcttct tactttactc cttcttgctc ataaataagc aaggtaagag gacaactgta attacctatt 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

acaataATGA CAGACGAAAC TGCTCAACCG ACACAATCTG CTTCAAAGCA GGAATCTGCT GCTCTGAAAC AGACAGGCGA TGACCAGCAG GAATCTCAGC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

AACAACGTGG CTACAACAAC TACAACAATG GTAGCAACTA TACCCAAAAG AAGCCTTACA ACAGCAACAG ACCTCATCAG CAAAGAGGTG GTAAATTTGG 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

ACCAAACAGA TATAACAACC GTGGCAACTA TAATGGTGGC GGTAGTTTCA GAGGTGGACA CATGGGAGCC AACAGCTCAA ACGTGCCATG GACTGGTTAC 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TATAATAACT ACCCCGTTTA CTACCAGCCC CAGAAAATGG CGGCCGCTGG TAGTGCCCCT GCTAATCCAA TTCCTGTCGA AGAGAAGTCA CCTGTTCCAA 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

CTAAGATAGA AATCACTACC AAGTCTGGTG AACACTTAGA TTTGAAAGAA CAGCATAAAG CCAAGCTACA GTCTCAGGAA AGATCTACTG TGTCTCCGCA 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

ACCAGAGTCA AAGTTAAAAG AAACTTCTGA TTCTACTTCT ACTTCTACTC CAACTCCTAC CCCTTCCACT AATGACTCTA AGGCCAGTTC TGAAGAAAAT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ATATCTGAAG CTGAAAAGAC AAGAAAAAAT TTCATCGAGC AAGTTAAACT TCGTAAAGCT GCTTTAGAAA AGAAGAGAAA GGAGCAACTT GAAGGTTCTA 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTGGCAACAA TAATATTCCA ATGAAGACTA CCCCAGAAAA TGTGGAAGAG AAGGGATCGG ACAAACCTGA GGTAACCGAA AAAACCAAGC CTGCTGAAGA 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

AAAATCTGCT GAGCCAGAAG TTAAGCAAGA AACTCCAGCT GAAGAAGGTG AACAAGGAGA AAAGGGCCAA ATAAAGGAAG AATCCACTCC AAAGGTGTTA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

ACCTTTGCTG AACGTTTGAA GTTGAAGAAA CAACAAAAAG AACGAGAAGA AAAAACGGAG GGGAAGGAAA ACAAGGAAGT GCCAGTACAG GAAGAGACTA 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

AGAGCGCCAT CGAGTCTGCT CCTGTGCCTC CCAGTGAACA GGTTAAAGAA GAAACTGAGG TCGCCGAAAC CGAACAGTCA AACATTGAAG AATCTGCAAC 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

AACTCCGGCT ATCCCTACTA AATCTGATGA AGCTGAAGCT GAAGTTGAGG CTGAAGCAGG TGATGCTGGA ACAAAGATTG GACTTGAAGC TGAAATCGAA 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

ACTACAACTG ATGAAACTGA TGATGGTACA AACACCGTTT CTCACATATT GAATGTATTG AAAGATGCTA CACCAATTGA AGATGTCTTT TCTTTTAACT 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

ATCCAGAAGG TATTGAAGGT CCTGATATCA AATACAAGAA AGAACACGTC AAATATACAT ATGGCCCAAC TTTCTTGCTT CAATTTAAGG ACAAACTAAA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

CGTCAAAGCG GACGCCGAAT GGGTCCAAAG CACTGCTTCT AAAATTGTCA TTCCACCAGG AATGGGCAGA GGAAATAGAT CTAGAGATTC TGGCAGATTC 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

GGCAATAATT CTAGTCGTGG CCATGACTTT AGAAATACCT CAGTGAGAAA TATGGATGAC AGAGCTAATT CAAGAACTTC ATCAAAGAGA AGATCAAAGA 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

GAATGAATGA CGACAGGAGA TCTAATAGAT CTTATACATC AAGAAGAGAC CGCGAGAGAG GCTCCTACAG AAATGAAGAG AAAAGAGAGG ACGATAAACC 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

AAAGGAAGAA GTTGCTCCAC TTGTTCCAAG TGCTAATAGG TGGGTGCCAA AATTCAAGTC TAAAAAGACT GAAAAGAAGC TAGCCCCTGA CGGAAAGACC 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

GAACTATTGG ACAAGGATGA AGTTGAAAGA AAGATGAAGT CACTACTGAA TAAACTTACT TTGGAAATGT TCGATGCTAT TTCATCTGAA ATTTTGGCTA 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

TTGCAAACAT ATCAGTATGG GAAACAAATG GTGAAACGTT AAAGGCTGTG ATAGAACAGA TTTTCTTAAA GGCCTGTGAC GAACCCCATT GGTCTTCTAT 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

GTACGCGCAA TTATGTGGTA AAGTAGTTAA AGAATTAAAC CCAGATATAA CAGATGAAAC TAATGAAGGT AAGACAGGTC CAAAATTGGT TTTGCATTAC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

TTGGTTGCTA GATGTCATGC CGAATTTGAC AAGGGTTGGA CCGATAAATT ACCCACAAAC GAAGATGGTA CTCCATTAGA ACCTGAGATG ATGTCAGAAG 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

AGTACTATGC AGCTGCTTCT GCTAAGAGAA GAGGTTTAGG TTTGGTTCGT TTCATCGGTT TCCTATACCG TCTGAATCTG TTGACTGGAA AGATGATGTT 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

CGAATGTTTC CGTAGACTAA TGAAGGATTT GACGGATTCT CCATCTGAAG AAACTCTAGA GTCCGTTGTT GAATTGTTAA ATACTGTTGG TGAACAATTT 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GAGACCGATA GTTTCAGAAC GGGTCAAGCA ACATTGGAGG GTTCGCAATT GCTCGATAGT TTGTTCGGTA TTTTAGACAA TATTATTCAA ACTGCTAAGA 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

TTTCTAGTAG AATCAAGTTC AAGTTGATCG ACATTAAAGA ATTAAGGCAC GACAAGAACT GGAACAGTGA TAAGAAGGAC AACGGTCCTA AGACCATTCA 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ACAGATTCAT GAGGAAGAGG AGAGACAACG TCAATTGAAG AATAATTCAA GATCTAATTC AAGACGTACG AACAACTCCA GTAATAGACA CTCTTTCAGA 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AGGGACGCTC CTCCTGCATC AAAAGATAGC TTTATCACAA CCAGAACATA TTCTCAAAGA AATAGCCAAA GGGCTCCTCC TCCAAAGGAA GAACCAGCTG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

CACCAACTTC TACCGCAACA AATATGTTCA GTGCATTAAT GGGAGAAAGT GATGACGAAG AGTAAcatga atagatcatg ttaagtatcg aaaatgtcac 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

ttggatacaa ggatgttggt agaaagtcta ataaaataat aaattaatag tacaacacaa atttaatctt acgtttaatc ctgcgctatt aattgaaaat 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

atatgcatgg agaagaaaaa aaaagtgtcc ctaatttacc attgttatat tttctcgatt aatgggctca tttcttttca ctaaaagcta taaacaagtt 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

tgatgcattt taatgggtaa tcctcttact gtgctttttt ttcctatctt gttctatatg tcaatgcctt tctgtatttt tatttatagc ttcgccagtc 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

ttcgtttacg atatgtttta tataatagac cactcagcat atgtatagtt ttgtat
^3701      ^3711      ^3721      ^3731      ^3741      ^3751

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:
heterogeneous_population_of_molecules_found

Integrity (uniformity) of mRNA tested using RNase protection:
not_tested

Integrity (uniformity) of mRNA tested using 5'-RACE:
heterogeneous_population_of_molecules_found

Integrity (uniformity) of mRNA tested using primer extension :
not_tested

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

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:
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 CWO4

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:
TIF4631

The description of the protein encoded in this ORF:
eIF4G protein

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):

507-3365

Remarks:

There are no EST data supporting TIF4631 at all so it is not possible to predict which regions flanking the
CDS are transcribed (except the notes in the description of this mRNA). Zhou et al. (2001) mentioned that they
studied 508bp long 5'-UTR of p150 so this sequence should be correct.

A promoter region -112 to -36 in respect to initiator AUG codon was found in S. cerevisiae CWO4 strain while
no IRES activity was found in yeast extracts. A promoter-less vector was used to show functionally TIF4631
expression in a modified strain S. cerevisiae CBY19. Finally RT-PCR  and 5'-RACE were used to map
transcription start site. The 5'-UTR of TIF4631 mRNA are usually 36bp long. However, 75bp and even longer were
detected by 5'-RACE. [Verge et al., 2004]

Citations:

Goyer C., Altmann M., Lee H. S., Blanc A., Deshmukh M., Woolford JL J. r., Trachsel H., Sonenberg N. (1993) TIF4631 and TIF4632: two yeast genes encoding the high-molecular-weight subunits of the cap-binding protein complex (eukaryotic initiation factor 4F) contain an RNA recognition motif-like sequence and carry out an essential function. Mol. Cell. Biol. 13(8):4860-4874

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

Vergé V, Vonlanthen M, Masson JM, Trachsel H, Altmann M (2004) Localization of a promoter in the putative internal ribosome entry site of the Saccharomyces cerevisiae TIF4631 gene. RNA. 10(2):277-286

IRESs:

IRES:

Version: `2`	Last change: `2009-08-30 21:01:50`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `TIF4631`

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

159-506

Conclusion:
disproved_IRES

How IRES boundaries were determined:
experimentally_determined

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

gactcgataa cgacgtgaga aacgattttt ttttttcttt ttcaccgtat ttttgtgcgt cctttttcaa ttatagcttt tttttatttt ttttttttct 
^159       ^169       ^179       ^189       ^199       ^209       ^219       ^229       ^239       ^249       

cgtactgttt cactgacaaa agtttttttt caagaaaaat tttcgatgcc gcgttctctg tgtgcaacgg atggatggta gatggaattt caatatgttg 
^259       ^269       ^279       ^289       ^299       ^309       ^319       ^329       ^339       ^349       

cttgaaattt taccaatctt gatattgtga taatttactt aattatgatt cttcctcttc ccttcaattt cttaaagctt cttactttac tccttcttgc 
^359       ^369       ^379       ^389       ^399       ^409       ^419       ^429       ^439       ^449       

tcataaataa gcaaggtaag aggacaactg taattaccta ttacaata
^459       ^469       ^479       ^489       ^499

Remarks:

The region claimed for IRES activity is from Figure 5 (Zhou et al., 2001). However, Verge et al. (2004) did
not find any significant IRES activity in their assays.

Citations:

Mauro VP, Edelman GM, Zhou W (2004) Reevaluation of the conclusion that IRES-activity reported within the 5' leader of the TIF4631 gene is due to promoter activity. RNA. 10(6):895-897

Altmann M, Trachsel H, Vonlanthen M, Vergé V (2004) Answer to 'Reevaluation of the conclusion that IRES-activity reported within the 5' leader of the TIF4631 gene is due to promoter activity.'. RNA. 10(6):898

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