The nucleic acid data:
IRESite Id: 491 Version: 5
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš Last change: 2009-10-10 02:09:04
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:
  AQP4
The genetic origin of this natural mRNA/+RNA:
  nuclear
The GenBankId GI:# number of the most similar mRNA/+RNA sequence to this one.
1072052 
Synonyms of the gene name:
Synonym: MIWC
Synonym: HMIWC2
Synonym: MGC22454
The mRNA/+RNA description: 
Human mercurial-insensitive water channel mRNA, form 1, complete cds.
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 HEK 293T/17 (ATCC CRL-11268)
A promoter reported in cDNA corresponding to IRES sequence:
  no
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):
homogeneous_population_of_molecules_confirmed
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:
no_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 HEK293 (ATCC CRL-1573)
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 2 Last change: 2008-07-16 23:11:53
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
AQP4
The description of the protein encoded in this ORF:
mercurial-insensitive water channel
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):
  287-1192
Remarks:
For creation of this IRESite record we have used AQP4 5'-UTR used through experiments (as kindly provided by
Dr. Martin Holcik) and merged it on its right with ORF and 3'-UTR from mRNA sequence of AQP4 (GI:1072052).
Holcik et al. (2007) actually amplified the AQP4 5'-UTR sequence from HEK 293T/17 (ATCC CRL-11268) cells.
There are few single nucleotide insertions/deletions between the two sequences. Other variants of AQP4
messages lack the leftmost cca 251 bp while first exon is within first 669bp.
Citations:
Baird S. D., Lewis S. M., Turcotte M., Holcik M. (2007) A search for structurally similar cellular internal ribosome entry sites. Nucleic. Acids. Res. 35(14):4664-4677
IRESs:
IRES:
Version: 1 Last change: 2008-07-16 23:11:53
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  AQP4
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  10-293
Conclusion:
  weakly_supported_IRES
How IRES boundaries were determined:
guessed
The sequence of IRES region aligned to its secondary structure (if available):



Remarks:
AQP4 IRES represents almost the full length 5' UTR from human AQP4 mRNA (from nt -275 to nt -1 of the original
GenBank sequence) and the first 7 nts (+1 to +7) from AQP4 ORF.
Citations:
Baird S. D., Lewis S. M., Turcotte M., Holcik M. (2007) A search for structurally similar cellular internal ribosome entry sites. Nucleic. Acids. Res. 35(14):4664-4677
IRES trans-acting factor (ITAFS):
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 2 Last change: 2009-08-29 12:19:15
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
ITAF abbreviated name:
La
ITAF fullname:
La autoantigen
ITAF description (long):
La autoantigen (p52), 52 kDa RNA binding protein, predominantly localized to nucleus, unwinds the dsRNA in ATP-dependent manner, forms a dimer
3.1.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
in_vitro
In vitro system used to demonstrate ITAF effect:
other
Remarks:
HEK 293T cell extracts were used to demonstrate in vitro binding to AQP4 RNA. Data from Figure 8A.
Citations:
Baird S. D., Lewis S. M., Turcotte M., Holcik M. (2007) A search for structurally similar cellular internal ribosome entry sites. Nucleic. Acids. Res. 35(14):4664-4677
IRES trans-acting factor (ITAF):
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
Type of the interaction between ITAF and the RNA subject to translation:
direct_interaction_with_rna
ITAF protein characteristics:
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Václav Vopálenský
ITAF abbreviated name:
PTB-1
ITAF fullname:
polypyrimidine tract-binding protein isoform 1
ITAF description (long):
polypyrimidine tract-binding protein isoform 1 binds dsRNA with (CCU)n motif where n is at least 3. By SELEX approach it was found it binds to 5'-CAGCCUGGUGCCUCUCUUUCGG-3' (Singh et al. (1995) Science 268:1173-1176) but also UCUU or UCUUC within pyrimidine-rich sequence (Perez et al. (1997) RNA3:1334-1347).
3.2.2. Organisms or in vitro systems where this ITAF was functionally studied:
Organism or in vitro system where ITAF was shown:
Necessity of ITAF for translation in this particular organism or system:
required_but_available_internally
Method used to demonstrate ITAF effect:
both
In vitro system used to demonstrate ITAF effect:
other
The organism where action of this ITAF was studied:
Homo sapiens HEK 293T/17 (ATCC CRL-11268)
Remarks:
Deletion of the AQP4 5' UTR polypyrimidine tract causes a loss of PTB binding and a complete loss of IRES
activity, but does not disrupt the binding of other ITAFs.
Overexpression of PTB enhances AQP4 IRES activity approximately 2-fold.

HEK 293T cell extracts were used to demonstrate in vitro binding to AQP4 RNA. Data from Figure 8A/B/C.
Citations:
Baird S. D., Lewis S. M., Turcotte M., Holcik M. (2007) A search for structurally similar cellular internal ribosome entry sites. Nucleic. Acids. Res. 35(14):4664-4677
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 24
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The function of the 2D structure:
IRES
The 2D structure causes frameshift:
unknown
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
10-295
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
2D structure of AQP4 from Fig 5B.
4.1.1. Enzymes used to characterize at least partially the 2D structure.
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 40
The temperature (in degrees of Celsia):
22
The enzymatic method used to determine the 2D structure:
ribonuclease T1
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
100.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
120.00
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 41
The temperature (in degrees of Celsia):
22
The enzymatic method used to determine the 2D structure:
ribonuclease A
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
100.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
120.00
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 42
The temperature (in degrees of Celsia):
22
The enzymatic method used to determine the 2D structure:
ribonuclease V1
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
100.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
120.00
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
ss_experiment_with_enzyme_id: 43
The temperature (in degrees of Celsia):
22
The enzymatic method used to determine the 2D structure:
ribonuclease T2
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.00
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
100.00
Mg2+ [mM]
10.00
Ca2+ [mM]
0
Cl- [mM]
120.00
Tris [mM]
10.00
BSA [mM]
0
HEPES [mM]
0
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Citations:
Baird S. D., Lewis S. M., Turcotte M., Holcik M. (2007) A search for structurally similar cellular internal ribosome entry sites. Nucleic. Acids. Res. 35(14):4664-4677
Last change to the database: 2015-04-16 16:45:23 GMT+1