The nucleic acid data:
IRESite Id: 1 Version: 9
Originaly submitted by: Martin Pospíšek Submission date: 2005-06-26 00:00:00
Reviewed by: Martin Pospíšek Last change: 2009-09-03 13:38:32
IRESite record type:
  natural_transcript
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  our_best_guess
The abbreviated name of the virus/gene coding for this mRNA/+RNA molecule:
  Hif1a
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
7363432
The mRNA/+RNA description: 
Mus musculus hypoxia inducible factor 1, alpha subunit (Hif1a), mRNA. Poly(A) tail dropped.
The mRNA/+RNA sequence represented in the +DNA notation:


Credibility of mRNA sequence:
  guessed_as_the_sequence_was_never_published_by_authors_nor_described_in_sufficient_detail
The organism containing this mRNA with IRES segment in its genome:
Mus musculus
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
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 1
Originaly submitted by: Martin Pospíšek Reviewed by: Martin Pospíšek
The abbreviated name of this ORF/gene:
Hif1a
The description of the protein encoded in this ORF:
Mus musculus hypoxia inducible factor 1, alpha subunit (Hif1a).
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:
  no
The ORF absolute position (the base range includes START and STOP codons or their equivalents):
  258-2768
Remarks:
Transiently transfected cells with pRF based vector. Integrity of the bicistronic transcripts verified by
RNase protection assay and Northern blot (Lang et al., 2002).

Bert et al. (2006) tested Hif1a IRES in HeLa cells using promoter-less plasmids with or without the enhancer
left in (Figure 2). They showed there is a cryptic promoter activatable when the enhancer is left in.

Also Young et al. (2008) report in Figure 2 a cryptic promoter in NIH3T3 cells.
Citations:
Luo G., Gu Y. Z., Jain S., Chan W. K., Carr K. M., Hogenesch J. B., Bradfield C. A. (1997) Molecular characterization of the murine Hif-1 alpha locus. Gene Expr. 6(5):287-299
Bert AG, Grépin R, Vadas MA, Goodall GJ (2006) Assessing IRES activity in the HIF-1alpha and other cellular 5' UTRs. RNA. 12(6):1074-1083
IRESs:
IRES:
Version: 9 Last change: 2009-09-03 13:33:06
Originaly submitted by: Martin Pospíšek Reviewed by: Martin Pospíšek
The IRES name:
  HIF1a
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  1-257
Conclusion:
  disproved_IRES
How IRES boundaries were determined:
guessed
The sequence of IRES region aligned to its secondary structure (if available):


Remarks:
This mRNA remains bound to polysomes both in normoxia and hypoxia. Exact IRES region was not determined.
Values represent length of the 5' UTR.

Bert et al. (2006) reported that despite the contribution of the cryptic promoter in in vivo-based
assays Hif1a IRES has "some" activity.

Young et al. (2008 reported that Hif1a IRES is not functional in directly transfected RNAs (Figure 3) nor in
NIH3T3 cells transfected by a plasmid encoding a bicistronic mRNA when subtracted the IRES-like activity
contributed by the promoter (Figure 2B vs. 2C).
Citations:
Lang K. J. D., Kappel A., Goodall G. J. (2002) Hypoxia-inducible factor-1alpha mRNA contains an internal ribosome entry site that allows efficient translation during normoxia and hypoxia. Mol. Biol. Cell. 13(5):1792-1801
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
Bert AG, Grépin R, Vadas MA, Goodall GJ (2006) Assessing IRES activity in the HIF-1alpha and other cellular 5' UTRs. RNA. 12(6):1074-1083
Last change to the database: 2015-04-16 16:45:23 GMT+1