The nucleic acid data:
IRESite Id: 570 Version: 3
Originaly submitted by: Martin Mokrejš Submission date: 2009-03-16 17:41:34
Reviewed by: Martin Mokrejš Last change: 2009-09-03 12:47:06
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:
  BiP
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
1143491
Synonyms of the gene name:
Synonym: GRP78
The mRNA/+RNA description: 
H.sapiens mRNA for BiP protein mRNA. 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 HeLa (ATCC CCL-2)
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:
weak_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 NIH/3T3 (ATCC CRL-1658)
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1 Last change: 2009-03-16 18:29:27
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
BiP
The description of the protein encoded in this ORF:
glucose-regulated protein (78 kDa)
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):
  223-2184
Remarks:
Thoma et al. (2004) did not show activity of BiP IRES in contrast to any other IRES. The negative control
was either BiP IRES in sense orientation on an in vitro run-off transcript without poly(A) tail or BiP IRES
in anti-sense orientation.

The region -93 to -1 does not contain functional 3'-splice acceptor site in the setup used by Baranick et al.
(2008), Supplementary Images 7 and 8. These authors also report no IRES activity of this region as well
in their in vivo based experiments (Figures 1, 2, 3).

We hypothesize that if there is a problematic 3'-splice acceptor site it must be in the region -222 to -94.

Young et al. (2008) tested BiP in a promoter-less construct (Figure 2) and reported a weak promoter. They also
showed that most of the "IRES" activity is related to this cryptic promoter (compare Figure 2B vs. 2C; scale
of 2C higher).
Citations:
Thoma C., Bergamini G., Galy B., Hundsdoerfer P., Hentze M. W. (2004) Enhancement of IRES-mediated translation of the c-myc and BiP mRNAs by the poly(A) tail is independent of intact eIF4G and PABP. Mol. Cell. 15(6):925-935
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
Young RM, Wang SJ, Gordan JD, Ji X, Liebhaber SA, Simon MC (2008) Hypoxia-mediated selective mRNA translation by an internal ribosome entry site-independent mechanism. J. Biol. Chem. 283(24):16309-16319
IRESs:
IRES:
Version: 2 Last change: 2009-09-03 12:47:06
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The IRES name:
  BiP_-222_-3
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-222
Conclusion:
  disproved_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
The BiP IRES was reported by Young et al. (2008) not to be functional in direct RNA transfection (Figure 3).
In Figure 2BC they show that most of the "IRES" activity in NIH3T3 cells is related to the cryptic promoter.
Citations:
Thoma C., Bergamini G., Galy B., Hundsdoerfer P., Hentze M. W. (2004) Enhancement of IRES-mediated translation of the c-myc and BiP mRNAs by the poly(A) tail is independent of intact eIF4G and PABP. Mol. Cell. 15(6):925-935
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
Young RM, Wang SJ, Gordan JD, Ji X, Liebhaber SA, Simon MC (2008) Hypoxia-mediated selective mRNA translation by an internal ribosome entry site-independent mechanism. J. Biol. Chem. 283(24):16309-16319
Last change to the database: 2015-04-16 16:45:23 GMT+1