IRESite_Id:548 summary record describing characteristics of eIF4G IRES

IRESite: The database of experimentally verified IRES structures

The nucleic acid data:

IRESite Id: `548`	Version: `19`
Originaly submitted by: Martin Mokrejš	Submission date: `2009-03-09 19:58:21`
Reviewed by: Martin Mokrejš	Last change: `2009-10-13 11:39:08`

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: `eIF4G`	The genetic origin of this natural mRNA/+RNA: `nuclear`

The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
219612

The mRNA/+RNA description:

Homo sapiens mRNA for eukaryotic initiation factor 4 gamma (eIF4G), as derived from the gamma promoter.

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

TCTAGATGGG GGTCCTGGGC CCCAGGGTGT GCAGCCACTG ACTTGGGGAC TGCTGGTGGG GTAGGGATGA GGGAGGGAGG GGCATTGTGA TGTACAGGGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGCTCTGTGA GATCAAGGGT CTCTTAAGGG TGGGAGCTGG GGCAGGGACT ACGAGAGCAG CCAGATGGGC TGAAAGTGGA ACTCAAGGGG TTTCTGGCAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CTACCTACCT GCTTCCCGCT GGGGGGTGGG GAGTTGGCCC AGAGTCTTAA GATTGGGGCA GGGTGGAGAG GTGGGCTCTT CCTGCTTCCC ACTCATCTTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TAGCTTTCTT TCCCCAGATC CGAATTCGAG ATCCAAACCA AGGAGGAAAG GATATCACAG AGGAGATCAT GTCTGGGGCC CGCACTGCCT CCACACCCAC 
^301       ^311       ^321       ^331       ^341       ^351       ^361       ^371       ^381       ^391       

CCCTCCCCAG ACGGGAGGCA GTCTGGAGCC TCAAGCTAAT GGGGAGACGC CCCAGGTTGC TGTCATTGTC CGGCCAGATG ACCGGTCACA GGGAGCAATC 
^401       ^411       ^421       ^431       ^441       ^451       ^461       ^471       ^481       ^491       

ATTGCTGACC GGCCAGGGCT GCCTGGCCCA GAGCATAGCC CTTCAGAATC CCAGCCTTCG TCGCCTTCTC CGACCCCATC ACCATCCCCA GTCTTGGAAC 
^501       ^511       ^521       ^531       ^541       ^551       ^561       ^571       ^581       ^591       

CGGGGTCTGA GCCTAATCTC GCAGTCCTCT CTATTCCTGG GGACACTATG ACAACTATAC AAATGTCTGT AGAAGAATCA ACCCCCATCT CCCGTGAAAC 
^601       ^611       ^621       ^631       ^641       ^651       ^661       ^671       ^681       ^691       

TGGGGAGCCA TATCGCCTCT CTCCAGAACC CACTCCTCTC GCCGAACCCA TACTGGAAGT AGAAGTGACA CTTAGCAAAC CGGTTCCAGA ATCTGAGTTT 
^701       ^711       ^721       ^731       ^741       ^751       ^761       ^771       ^781       ^791       

TCTTCCAGTC CTCTCCAGGC TCCCACCCCT TTGGCATCTC ACACAGTGGA AATTCATGAG CCTAATGGCA TGGTCCCATC TGAAGATCTG GAACCAGAGG 
^801       ^811       ^821       ^831       ^841       ^851       ^861       ^871       ^881       ^891       

TGGAGTCAAG CCCAGAGCTT GCTCCTCCCC CAGCTTGCCC CTCCGAATCC CCTGTGCCCA TTGCTCCAAC TGCCCAACCT GAGGAACTGC TCAACGGAGC 
^901       ^911       ^921       ^931       ^941       ^951       ^961       ^971       ^981       ^991       

CCCCTCGCCA CCAGCTGTGG ACTTAAGCCC AGTCAGTGAG CCAGAGGAGC AGGCCAAGGA GGTGACAGCA TCAGTGGCGC CCCCCACCAT CCCCTCTGCT 
^1001      ^1011      ^1021      ^1031      ^1041      ^1051      ^1061      ^1071      ^1081      ^1091      

ACTCCAGCTA CGGCTCCTTC AGCTACTTCC CCAGCTCAGG AGGAGGAAAT GGAAGAAGAA GAAGATGAGG AAGAAGGAGA AGTAGGGGAA GCAGGGGAAG 
^1101      ^1111      ^1121      ^1131      ^1141      ^1151      ^1161      ^1171      ^1181      ^1191      

GTGAGAGTGA GAAGAGAGGA GAGGAACTGC TCCCCCCAGA GAGTACCCCT ATTCCAGCCA ACTTGTCTCA GAATTTGGAG GCAGCAGCAG CCACTCAAGT 
^1201      ^1211      ^1221      ^1231      ^1241      ^1251      ^1261      ^1271      ^1281      ^1291      

GGCAGTATCT GTGCCAAAGA GGAGACGGAA AATTAAGGAG CTAAATAAGA AGGAGGCTGT TGGAGACCTT CTGGATGCCT TCAAGGAGGC GAACCCGGCA 
^1301      ^1311      ^1321      ^1331      ^1341      ^1351      ^1361      ^1371      ^1381      ^1391      

GTACCAGAGG TGGAAAATCA GCCTCCTGCA GGCAGCAATC CAGGCCCAGA GTCTGAGGGC AGTGGTGTGC CCCCACGTCC TGAGGAAGCA GATGAGACCT 
^1401      ^1411      ^1421      ^1431      ^1441      ^1451      ^1461      ^1471      ^1481      ^1491      

GGGACTCAAA GGAAGACAAA ATTCACAATG CTGAGAACAT CCAGCCCGGG GAACAGAAGT ATGAATATAA GTCAGATCAG TGGAAGCCTC CAAACCTAGA 
^1501      ^1511      ^1521      ^1531      ^1541      ^1551      ^1561      ^1571      ^1581      ^1591      

GGAGAAAAAA CGTTACGACC GTGAGTTCCT GCTTGGTTTT CAGTTCATCT TTTGCCAGAT GCAGAAGCCA GAGGGATTGC CACATATCAG TGACGTGGTG 
^1601      ^1611      ^1621      ^1631      ^1641      ^1651      ^1661      ^1671      ^1681      ^1691      

CTGGACAAGG CCAATAAAAC ACCACTGCGG CCACTGGATC CCACTAGACT ACAAGGCATA AATTGTGGCC CAGACTTCAC TCCATCCTTT GCCAACCTTG 
^1701      ^1711      ^1721      ^1731      ^1741      ^1751      ^1761      ^1771      ^1781      ^1791      

GCCGGACAAC CCTTAGCACC CGTGGGCCCC CAAGGGGTGG GCCAGGTGGG GAGCTCGCCC GTGGCGCGCA GGCTGGCCTG GGACCCCGGC GCTCTCAGCA 
^1801      ^1811      ^1821      ^1831      ^1841      ^1851      ^1861      ^1871      ^1881      ^1891      

GGGACCCCGA AAAGAACCAC GCAAGATCAT TGCCACAGTG TTAATGACCG AAGATATAAA ACTGAACAAA GCAGAGAAAG CCTGGAAACC CAGCAGCAAG 
^1901      ^1911      ^1921      ^1931      ^1941      ^1951      ^1961      ^1971      ^1981      ^1991      

CGGACAGCGG CTGATAAGGA TCGAGGGGAA GAAGATGCTG ATGGCAGCAA AACCCAGGAC CTATTCCGCA GGTGGCGCTC CATCCTGAAT AAACTGACAC 
^2001      ^2011      ^2021      ^2031      ^2041      ^2051      ^2061      ^2071      ^2081      ^2091      

CCCAGATGTT CCAGCAGCTG ATGAAGCAAG TGACGCAGCT GGCCATCGAC ACCGAGGACG CCTCAAAGGG GTCATTGACC TCATTTTTGA GAAGGCCATT 
^2101      ^2111      ^2121      ^2131      ^2141      ^2151      ^2161      ^2171      ^2181      ^2191      

TCAGAGCCCA ACTTCTCTGT GGCCTATCCA ACATGTGCCG CTGCCTCATG GCGCTGAAAG TGCCCACTAC GGAAAGCCAA CAGTGACTGT GAACTTCCGA 
^2201      ^2211      ^2221      ^2231      ^2241      ^2251      ^2261      ^2271      ^2281      ^2291      

AAGCTGTTGT TGAATCGATG TCAGAAGGAG TTTGAGAAAG ACAAAGATGA TGATGAGGTT TTTGAGAAGA AGCAAAAAGA GATGGATGAA GCTGCTACGG 
^2301      ^2311      ^2321      ^2331      ^2341      ^2351      ^2361      ^2371      ^2381      ^2391      

CAGAGGAACG AGAACGCCTG AAGGAGGAGC TGGAAGAGGC TCGGGACATA GCCCGGCGCT GCTCTTTAGG GAATATCAAG TTTATTGGAG AGTTGTTCAA 
^2401      ^2411      ^2421      ^2431      ^2441      ^2451      ^2461      ^2471      ^2481      ^2491      

ACTGAAGATG TTAACAGAGG CAATAATGCA TGACTGTGTG GTCAAACTGC TTAAGAACCA TGATGAAGAG TCCCTTGAGT GCCTTTGTCG TCTGCTCACC 
^2501      ^2511      ^2521      ^2531      ^2541      ^2551      ^2561      ^2571      ^2581      ^2591      

ACCATTGGCA AAGACCTGGA CTTTGAAAAA GCCAAGCCCC GAATGGATCA GTATTTCAAC CAGATGGAAA AAATCATTAA AGAAAAGAAG ACGTCATCCC 
^2601      ^2611      ^2621      ^2631      ^2641      ^2651      ^2661      ^2671      ^2681      ^2691      

GCATCCGCTT TATGCTGCAG GACGTGCTGG ATCTGCGAGG GAGCAATTGG GTGCCACGCC GAGGGGATCA GGGTCCAAGA CCATTGACCA GATCCATAAG 
^2701      ^2711      ^2721      ^2731      ^2741      ^2751      ^2761      ^2771      ^2781      ^2791      

GAGGCTGAGA TGGAAGACAT CGAGAGCACA TCAAAGTGCA GCAGCTCATG CAAGGGCAGT GACAAGCGTC GGGGCGGTCC TCCAGGCCCT CCCATCAGCC 
^2801      ^2811      ^2821      ^2831      ^2841      ^2851      ^2861      ^2871      ^2881      ^2891      

GTGGACTTCC CCTTGTGGAT GATGGTGGCT GACACAGTTC CCATCAGCAA AGGTAGCCGC CCCATTGACA CCTCACGACT CACCAAGATC ACCAAGCCTG 
^2901      ^2911      ^2921      ^2931      ^2941      ^2951      ^2961      ^2971      ^2981      ^2991      

GCTCCATCGA TTCTAACAAC CAGCTCTTTG CACCTGGAGG GCGACTGAGC TGGGGCAAGG GCAGCAGCGG AGGGTCAGGA GCCCAGCCCT CAGACGCAGC 
^3001      ^3011      ^3021      ^3031      ^3041      ^3051      ^3061      ^3071      ^3081      ^3091      

ATCAGAAGCT GCTCGCCCAG CTACTAGTAC TTTGATTCGC TTCTCAGCCC TTCAACAAGC GGTACCCACA GAAAGCACAG ATAATAGACG TGTGGTGCAG 
^3101      ^3111      ^3121      ^3131      ^3141      ^3151      ^3161      ^3171      ^3181      ^3191      

AGGAGTAGCT TGAGCCGAGA ACGAGGCGAG AAAGCTGGAG ACCGAGGAGA CCGCCTAGAG CGAGTGAACG GGGAGGGGAC CGTGGGGACC GGCTTGATCG 
^3201      ^3211      ^3221      ^3231      ^3241      ^3251      ^3261      ^3271      ^3281      ^3291      

TGTCGCGGAC ACCTGCTACC AAGCGGACGT TCAGCAAGGA AGTGGAGGAG CGGAGTAGAG AACGGCCCTC CCAGCCTGAG GGGCTGCGCA AGGCAGCTAG 
^3301      ^3311      ^3321      ^3331      ^3341      ^3351      ^3361      ^3371      ^3381      ^3391      

CCTCACGGAG GATCGGGACC GTGGGCGGGA TGCCGTGAAG CGAGAAGCTG CCCTACCCCC AGTGAGCCCC CTGAAGGCGG CTCTCTCTGA GGAGGAGTTA 
^3401      ^3411      ^3421      ^3431      ^3441      ^3451      ^3461      ^3471      ^3481      ^3491      

GAGAAGAAAT CCAAGGCTAT CATTGAGGAA TATCTCCATC TCAATGACAT GAAAGAGGCA GTCCAGTGCG TGCAGGAGCT GGCCTCACCC TCCTTGCTCT 
^3501      ^3511      ^3521      ^3531      ^3541      ^3551      ^3561      ^3571      ^3581      ^3591      

TCATCTTTGT ACGGCATGGT GTCGAGTCTA CGCTGGAGCG CAGTGCCATT GCTCGTGAGC ATATGGGGCA GCTGCTGCAC CAGCTGCTCT GTGCTGGGCA 
^3601      ^3611      ^3621      ^3631      ^3641      ^3651      ^3661      ^3671      ^3681      ^3691      

TCTGTCTACT GCTCAGTACT ACCAAGGGTT GTATGAAATC TTGGAATTGG CTGAGGACAT GGAAATTGAC ATCCCCCACG TGTGGCTCTA CCTAGCGGAA 
^3701      ^3711      ^3721      ^3731      ^3741      ^3751      ^3761      ^3771      ^3781      ^3791      

CTGGTAACAC CCATTCTGCA GGAAGGTGGG GTGCCCATGG GGGAGCTGTT CAGGGAGATT ACAAAGCCTC TGAGACCGTT GGGCAAAGCT GCTTCCCTGT 
^3801      ^3811      ^3821      ^3831      ^3841      ^3851      ^3861      ^3871      ^3881      ^3891      

TGCTGGAGAT CCTGGGCCTC CTGTGCAAAA GCATGGGTCC TAAAAAGGTG GGGACGCTGT GGCGAGAAGC CGGGCTTAGC TGGAAGGAAT TTCTACCTGA 
^3901      ^3911      ^3921      ^3931      ^3941      ^3951      ^3961      ^3971      ^3981      ^3991      

AGGCCAGGAC ATTGGTGCAT TCGTCGCTGA ACAGAAGGTG GAGTATACCC TGGGAGAGGA GTCGGAAGCC CCTGGCCAGA GGGCACTCCC CTCCGAGGAG 
^4001      ^4011      ^4021      ^4031      ^4041      ^4051      ^4061      ^4071      ^4081      ^4091      

CTGAACAGGC AGCTGGAGAA GCTGCTGAAG GAGGGCAGCA GTAACCAGCG GGTGTTCGAC TGGATAGAGG CCAACCTGAG TGAGCAGATA GTATCCAACA 
^4101      ^4111      ^4121      ^4131      ^4141      ^4151      ^4161      ^4171      ^4181      ^4191      

CGTTAGTTCG AGCCCTCATG ACGGCTGTCT GCTATTCTGC AATTATTTTT GAGACTCCCC TCCGAGTGGA CGTTGCAGTG CTGAAAGGCG ACATAGTGCT 
^4201      ^4211      ^4221      ^4231      ^4241      ^4251      ^4261      ^4271      ^4281      ^4291      

GCAGAAATAC CTGTGTGACG AAGCAGAAGG AGCTACAGGC GCTCTACGCC TCCAGGCCCT TGTAGTGACC TTAGAACAGC CTCCCAACCT GCTGCGGATG 
^4301      ^4311      ^4321      ^4331      ^4341      ^4351      ^4361      ^4371      ^4381      ^4391      

TTCTTTGACG CACTGTATGA CGAGGACGTG GTGAAGGAGG ATGCCTTCTA CAGTTGGGAG AGTAGCAAGG ACCCCGCTGA GCAGCAGGGC AAGGGTGTGG 
^4401      ^4411      ^4421      ^4431      ^4441      ^4451      ^4461      ^4471      ^4481      ^4491      

CCCTTAAATC TGTCACAGCC TTCTTCAAGT GGCTCCGTGA AGTCAGAGGA GGAGTCTGAC CACAACTGAG GGCTGGTGGG GCCGGGGACC TGGAGCCCCA 
^4501      ^4511      ^4521      ^4531      ^4541      ^4551      ^4561      ^4571      ^4581      ^4591      

TGGACACACA GATGGCTCCG GCTAGCCGCC TGGACTGCAG GGGGGCGGCA GCAGCGGCGG TGGCAGTGGG TGCCTGTAGT GTGATGTGTC TGAACTAATA 
^4601      ^4611      ^4621      ^4631      ^4641      ^4651      ^4661      ^4671      ^4681      ^4691      

AAGTGGCTGA AGAGGCAGGA TGGCTTGGGG CTGCCTGGGC CCCCCTCCAG GATGCCGCCA GGTGTCCCTC TCCTCCCCTG GGGCACAGAG ATATATTATA 
^4701      ^4711      ^4721      ^4731      ^4741      ^4751      ^4761      ^4771      ^4781      ^4791      

TATAAAGTCT TGAAAATTTT GAAATTTGGT GTGTCTTGGG GTGGGGAGGG GCACCAACGC CTGCCCCTGG GGTCCTTTTT TTTATTTTCT GAAAATCACT 
^4801      ^4811      ^4821      ^4831      ^4841      ^4851      ^4861      ^4871      ^4881      ^4891      

CTCGGACTGC CGTCCTCGCT GCTGGGCATA TGCCCCAGCC CCTGTACCAC CCCTGCTGTT GCCTGGGCAG GGGGAAGGGG GGGCACGGTG CCTGTAATTA 
^4901      ^4911      ^4921      ^4931      ^4941      ^4951      ^4961      ^4971      ^4981      ^4991      

TTAAACATGA ATTCAATT
^5001      ^5011

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:

Homo sapiens

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:
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:

Homo sapiens HeLa (ATCC CCL-2)

Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:

ORF

ORF position:

1

Version: `1`	Last change: `2009-09-02 01:03:32`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš

The abbreviated name of this ORF/gene:
eIF4G

The description of the protein encoded in this ORF:
eukaryotic translation initiation factor 4 gamma

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):

369-4559

Remarks:

This is the transcript with 5'-UTR of 368bp reported by Yan et al. (1992) and reported to GenBank accession
D12686 (GI:219612) and studied later by Gan and Rhoads (1998) with IRES reported between positions 1-357 (in
other words -368 to -12 relatively to the initiator AUG). The transcript is derived from the later called
gamma promoter (nomenclature used in Byrd et al., 2005 and Baranick et al., 2008).

This is the transcript studied by Baranick et al. (2008) as well. This splice variant is incompletely covered
by RefSeq record NM_004953.3 (it lacks part of the 5'-UTR, probably because of missing EST coverage) which
gives the hint where the promoter is located in the 5'-UTR cloned in 1992 and later reported as "IRES".
Anyway, as the mRNA is derived from the most downstream gamma promoter therefore it encodes N-terminally
shortened eIF4GI while the CDS spans over the shared exons 8-33 (as defined by Byrd et al., 2005 while not by
Byrd et al. (2002)).

Our own search for ESTs supporting existence of the region -368 to -219 failed. The sequence -218 to -1 is
covered by 12 EST records in dbEST to date from human. All these ESTs have its first nucleotide within this
region. Although EST mights not be full-length cDNA copies it seems highly probably the transcription start
sites are located only in this region. In other words, the region -368 to -219 is likely a promoter. Yan et al
(1992) determined the sequence of cDNA clone from human brain lambdaDR2 (Clontech) library and confirmed the
sequence except its very first base using placental mRNA prepared by guanidium isothiocyanate-based method.
However, there are no mentions that the sample was treated by DNase and we do not know about the lambdaDR12
library either. We further support under suspicion that the promoter is located in the region upstream of -218
because a 5'-terminus of a full-length cDNA clone (AL703840 alias DKFZp686M1927_r1) originates at position
-215. Another clone (AL704011 alias DKFZp686J1628_r1) at -213. It seems the D12686 sequence published by Yan
et al. (1992) on which is based this IRESite entry contains some sequencing errors as judged by alignment
to the RefSeq variants and the genome. However, the insertions/deletions/mutations are not in the "IRES" nor
presumed promoter region of the "5'-UTR" (-368 to -219).

Notably, Byrd et al. (2005) mentioned on page 18613 that they obtained from HeLa cells this gamma
promoter-based transcript which contained completely the 5'-UTR of the clone obtained by Yan et al. (1992).
Thus, this sometimes called "intronic IRES" containing a cryptic promoter might sometimes appear in a
transcript.

Baranick et al. (2008) report that a 3'-splice acceptor site is present in the putative IRES region and
that this site is being not only used in their engineered bicistronic messages transcribed from CMV IE
promoter but also occurs in natural mRNAs as well (Supplementary Figure 12). Further, in Supplementary
Figure 7 they show also 5'-splice donor site located in the eIF4G IRES region.

Let us note that the 3'-splice acceptor site is optional as well as the two 5'-splice donor sites.

Byrd et al. (2002) mapped splice variants from alpha-, beta- and gamma-promoters. They investigated which
AUG codons act as initiator codons in translation and confirmed positions 275, 395, 536, 767, and 863
(AY082886). Mostly they studied the longest transcript bearing the eIF4GI CDS which is the only one derived
from the beta promoter (currently accessible in RefSeq under NM_182917.3). Nowadays the RefSeq record
NM_182917.3 is slightly longer than the original AY082886 which they termed SP4GI by 123 bp on the very
5'-end. In contrast, SP4GI is slightly longer than the clone called pAD-4GI (R. Rhoads), see Figure 3A in Byrd
et al. (2002). The corresponding IRESite entry of a beta promoter-derived mRNA is the longest of the three
just mentioned and accessible under IRESite_Id:576.

Byrd et al. (2005) studied mainly eIF4GI splice variants 5'-UTRs derived from alpha, beta promoter but
isolated cytoplasmic RNA without DNase treatment (probably not an issue as the amplicons spanned several exon
junctions confirming the cDNA was not contaminated). The first strand cDNA synthesis was carried using random
primers instead of oligo(dT) primers. eIF4GI specific primers were used for PCR amplification. However, they
focused on studies of 5'-UTRs of alpha-and beta- derived splice variants. They confirmed promoter activities
in both beta- and gamma-promoter regions immediately preceding the very first exon of the resp. splice variant
(Figure 1A, white thick bars).

Han and Zhang (2002) reported a promoter in the poly-pyrimidine tract (PPT) overlapping with the originally
reported "IRES" region using promoter-less based assay. The PPT region was found to bind C/EBPbeta
transcription factor. See Figures 3-5 in their article.

Citations:

Yan R., Rychlik W., Etchison D., Rhoads R. E. (1992) Amino acid sequence of the human protein synthesis initiation factor eIF-4 gamma. J. Biol. Chem. 267(32):23226-23231

Byrd M. P., Zamora M., Lloyd R. E. (2005) Translation of eukaryotic translation initiation factor 4GI (eIF4GI) proceeds from multiple mRNAs containing a novel cap-dependent internal ribosome entry site (IRES) that is active during poliovirus infection. J. Biol. Chem. 280(19):18610-18622

Byrd M. P., Zamora M., Lloyd R. E. (2002) Generation of multiple isoforms of eukaryotic translation initiation factor 4GI by use of alternate translation initiation codons. Mol. Cell. Biol. 22(13):4499-4511

Gan W., LaCelle M., Rhoads R. E. (1998) Functional characterization of the internal ribosome entry site of eIF4G mRNA. J. Biol. Chem. 273(9):5006-5012

IRESs:

IRES:

Version: `9`	Last change: `2009-09-02 01:03:32`
Originaly submitted by: Martin Mokrejš	Reviewed by: Martin Mokrejš
The IRES name: `eIF4G`

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

1-357

Conclusion:
disproved_IRES

How IRES boundaries were determined:
experimentally_determined

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

TCTAGATGGG GGTCCTGGGC CCCAGGGTGT GCAGCCACTG ACTTGGGGAC TGCTGGTGGG GTAGGGATGA GGGAGGGAGG GGCATTGTGA TGTACAGGGC 
^1         ^11        ^21        ^31        ^41        ^51        ^61        ^71        ^81        ^91        

TGCTCTGTGA GATCAAGGGT CTCTTAAGGG TGGGAGCTGG GGCAGGGACT ACGAGAGCAG CCAGATGGGC TGAAAGTGGA ACTCAAGGGG TTTCTGGCAC 
^101       ^111       ^121       ^131       ^141       ^151       ^161       ^171       ^181       ^191       

CTACCTACCT GCTTCCCGCT GGGGGGTGGG GAGTTGGCCC AGAGTCTTAA GATTGGGGCA GGGTGGAGAG GTGGGCTCTT CCTGCTTCCC ACTCATCTTA 
^201       ^211       ^221       ^231       ^241       ^251       ^261       ^271       ^281       ^291       

TAGCTTTCTT TCCCCAGATC CGAATTCGAG ATCCAAACCA AGGAGGAAAG GATATCA
^301       ^311       ^321       ^331       ^341       ^351

Remarks:

This region has been investigated recently by Baranick et al., 2008 and they postulate that most of the "IRES"
activity observed so far was due to the splice artifacts (low IRES activity in vivo when 5'-splice donor
depleted plasmid was used and low yields of reporter provirus sensitive to altered levels of splice products).
Please refer to Figures 1, 2, 3D in the article and Supplementary Figure 7.

Han and Zhang (2002) reported no IRES activity in direct RNA transfection.

Citations:

Baranick B. T., Lemp N. A., Nagashima J., Hiraoka K., Kasahara N., Logg C. R. (2008) Splicing mediates the activity of four putative cellular internal ribosome entry sites. Proc. Natl. Acad. Sci. U. S. A. 105(12):4733-4738

Han B., Zhang J. T. (2002) Regulation of gene expression by internal ribosome entry sites or cryptic promoters: the eIF4G story. Mol. Cell. Biol. 22(21):7372-7384

Gan W., LaCelle M., Rhoads R. E. (1998) Functional characterization of the internal ribosome entry site of eIF4G mRNA. J. Biol. Chem. 273(9):5006-5012

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