The nucleic acid data:
IRESite Id: 576 Version: 9
Originaly submitted by: Martin Mokrejš Submission date: 2009-03-22 20:38:21
Reviewed by: Martin Mokrejš Last change: 2009-10-13 11:13:20
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:
  eIF4GI
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
156523974
Synonyms of the gene name:
Synonym: eIF4G1
The mRNA/+RNA description: 
Homo sapiens eukaryotic translation initiation factor 4 gamma (eIF4GI-ext), transcript variant 1, as
derived from the beta promoter. Poly(A)-tail sequence was dropped.
The mRNA/+RNA sequence represented in the +DNA notation:


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:
  unclear
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:
heterogeneous_population_of_molecules_found
Integrity (uniformity) of mRNA tested using S1 nuclease mapping:
not_tested
Cryptic promoter presence was confirmed by expression from a promoter-less plasmid:
unclear_result
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 HEK 293T/17 (ATCC CRL-11268)
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:
eIF4GI
The description of the protein encoded in this ORF:
eukaryotic translation initiation factor 4 gamma, 1 isoform 1
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):
  398-5197
Remarks:
Initially, Gradi et al. (1998) reported partial eIF4GI transcript which sequence was later extended at its
5'-end by 180nt by Johannes and Sarnow (1998) and named eIF4GI-ext (this transcript, NM_182917.3,
GI:156523974) which is derived from the beta promoter located in exons 3 and 4 of some other mRNAs.
Specifically, these exons appear also in NM_198241 (not covered by IRESite) which is derived from the alpha
promoter and therefore it is not possible to judge which transcript was partially cloned.

Byrd et al. (2005) reported promoter activity of the region between exons 1 and 2 and spanning partly into the
exon 2, cDNA obtained from human BAC clone RP 11-125E8 (Figure 1A, white bar). IRESite curator found sequence
of the clone under accession AC078797. Further to note, the region spanning exons 1-8 (the alpha-promoter
driven variant) when tested in promoter-less plasmids displayed detectable reporter protein level and siRNA
approach resulted in incomplete reduction of reporter protein levels. Authors concluded that either a weak
promoter is present in the region or a splicing issue exists in human 293T cells (Figure 4). The beta-promoter
driven messages eIF4GI and eIF4GI-ext are shorter but still share exons 2-8 and so this might still apply.

This is the longest transcript bearing the eIF4GI CDS described and is the only splice variant derived from
the beta promoter (currently accessible in RefSeq under NM_182917.3). Nowadays the RefSeq record NM_182917.3
is slightly longer by 123 bp on the very 5'-end than the original AY082886 submitted by Byrd et al. (2005) which
they termed SP4GI. In contrast, SP4GI is slightly longer than the clone called pAD-4GI, studied earlier (R.
Rhoads), see Figure 3A in Byrd et al. (2002).
Citations:
Johannes G., Sarnow P. (1998) Cap-independent polysomal association of natural mRNAs encoding c-myc, BiP, and eIF4G conferred by internal ribosome entry sites. RNA. 4(12):1500-1513
Gradi A., Imataka H., Svitkin Y. V., Rom E., Raught B., Morino S., Sonenberg N. (1998) A novel functional human eukaryotic translation initiation factor 4G. Mol. Cell. Biol. 18(1):334-342
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
IRESs:
IRES:
Version: 4 Last change: 2009-10-13 11:13:20
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  eIF4GI-ext
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  464-659
Conclusion:
  probably_not_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
The 5'-UTR (nucleotides 1-196 of their partial transcript) studied by Johannes and Sarnow was shown in Figure
6B and 8A and align to the sequence of this IRESite record exactly since the 5'-end. This region is actually
within the protein coding region of the longest protein but in front of the following protein coding sequence
and roughly maps to exons 3 and 4:

MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTAS
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTAST
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTP
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPT
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPT.
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPT..
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPT..
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPT..
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPT..
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPT..
MIPSQISYPASQGAYYIPGQGRSTYVVPTQQYPVQPGAPGFYPGASPTEFGTYAGAYYPAQGVQQFPTGVAPAPVLMNQPPQIAPKRERKTIRIRDPNQGGKDITEEIMSGARTASTPT...
In Figure 8 is was shown that eIG4GI-ext (this IRESite entry) relatively well in comparison with PV IRES in CAT/LUC
vector. Byrd et al. (2005) in agreement confined IRES activity to exon 4.
Citations:
Johannes G., Sarnow P. (1998) Cap-independent polysomal association of natural mRNAs encoding c-myc, BiP, and eIF4G conferred by internal ribosome entry sites. RNA. 4(12):1500-1513
Last change to the database: 2015-04-16 16:45:23 GMT+1