The nucleic acid data:
IRESite Id: 573 Version: 6
Originaly submitted by: Martin Mokrejš Submission date: 2009-03-22 18:09:07
Reviewed by: Martin Mokrejš Last change: 2009-10-13 13:22:14
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:
  eIF4GII
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
9967556
Synonyms of the gene name:
Synonym: eIF4G2
The mRNA/+RNA description: 
Homo sapiens eIF4GII mRNA, complete cds. 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:
  not tested
The total number of notable open-reading frames (ORFs):
  1
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:
eIF4GII
The description of the protein encoded in this ORF:
eukaryotic translation initiation factor 4G, isoform II
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):
  257-5014
Remarks:
This is the sequence reported by Gradi et al. (1998) in GI:9967556 alias  and is different from the
eIF4GII-long variant reported later by Johannes and Sarnow (1998) and stored under IRESiteID:574. Please note
the trailing ".2" in the previously mentioned GenBank accession number which means there was a revision of the
primary sequence under that accession number in the meantime since its initial submission. There is no
well-matching sequence in RefSeq to AF012072.2, the closest match would be NM_003760.3 but the first three
exons of NM_003760.3 (1-126, 127-310, 311-386) are replaced by 60bp of some other origin in AF012072.2.


>NC_000001 Homo sapiens chromosome 1, GRCh37 primary reference assembly.; LEN=370369
>AF012072.2|IRESite_Id:573 (this entry) Homo sapiens eIF4GII mRNA, complete cds.; LEN=5880

65465-65525  (1-61)   100% -> (GT/AG) 24
and continue with shared exons (only the first listed below)
125854-125982  (62-190)   100% -> (GT/AG) 24
[cut]

>NC_000001 Homo sapiens chromosome 1, GRCh37 primary reference assembly.; LEN=370369
>NM_003760.3 Homo sapiens eukaryotic translation initiation factor 4 gamma, 3 (EIF4G3), mRNA.; LEN=6235

1-126  (31-156)   100% -> (GT/AG) 24
490-673  (157-340)   100% -> (GT/AG) 24
87635-87710  (341-416)   100% -> (GT/AG) 24
and continue with shared exons (only the first listed below)
125854-125982  (417-545)   100% -> (GT/AG) 24
[cut]

Our extended mRNA sequence using ESTs in IRESite_Id:574 spans in front of the genomic contig NC_000001:

>NC_000001 Homo sapiens chromosome 1, GRCh37 primary reference assembly.; LEN=370369
>IRESite_Id:574 eIF4GII-long (chromosome1), IRESite extension of NM_003760.3 by 30 bp; LEN=6205

1-126  (31-156)                100% -> (GT/AG) 24   (126bp exon)
490-673  (157-340)             100% -> (GT/AG) 24   (184bp exon)
87635-87710  (341-416)         100% -> (GT/AG) 24   (76bp exon)
125854-125982  (417-545)       100% -> (GT/AG) 24   (129bp exon)


Here is conformation against whole chromosome 1 assembly:

>NT_004610 Homo sapiens chromosome 1 genomic contig, GRCh37 reference primary assembly.; LEN=16558170
>IRESite_Id:574 eIF4GII-long (chromosome1); LEN=6205

(complement)

[cut]
8057447-8057575  (5661-5789)   100% <- (GT/AG) 24   (129bp exon)
8095719-8095794  (5790-5865)   100% <- (GT/AG) 24   (76 bp exon)
8182756-8182939  (5866-6049)   100% <- (GT/AG) 24   (184bp exon)
8183303-8183458  (6050-6205)   100%                 (156bp exon)



For comparison of the eIF4G (IRESiteID:548), eIF4GI, eIF4GI-ext(IRESiteID:576), this eIF4GII and
eIF4GII-long(IRESiteID:574) see Figure 6 in Johannes and Sarnow (1998).
Citations:
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
IRESs:
IRES:
Version: 7 Last change: 2009-10-13 13:40:28
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  eIF4GII
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-256
Conclusion:
  never_claimed_to_be_IRES
How IRES boundaries were determined:
guessed
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
Nobody tried. Anyway, the eIF4GII mRNA overlaps partly with the eIF4GII-long (IRESite_Id:574) studied for IRES
activity and found not to have it (see Figure 8 in Johannes and Sarnow, 1998). See Figure 6D in their article
for comparison of the 5'-UTR sequences of both chromosome 1 variants.
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