The nucleic acid data:
IRESite Id: 541 Version: 1
Originaly submitted by: Václav Vopálenský
Reviewed by: Martin Mokrejš Last change: 2008-10-28 00:39:18
IRESite record type:
  plasmid_with_promoter_and_putative_IRES_without_translational_characterization
The shape of the nucleic acid molecule translated:
  linear
The quality of the mRNA/+RNA sequence:
  only_IRES_fragment
The mRNA/+RNA description: 
In vitro T7 transcript used for structure probing experiments of AQP4 IRES. Transcription was done from PCR
template, prepared from pBiCAQP4 vector using AQP4 forward primer with built-in T7 promoter sequence
(taatacgactcactatagggGGACAGTTTGGATAA) and AQP4 reverse primer (cctcgagCCACCATGATGTTCTCT).
The mRNA/+RNA sequence represented in the +DNA notation:


Warning: mRNA sequence when devoid of trailing 'A's is still not a substring of the plasmid sequence. Is it because an intron is spliced out? Stay calm then. :-)
Credibility of mRNA sequence:
  end-to-end_sequence_reverse_engineered_and_should_match_experiment
The name of the plasmid:
pBiCAQP4
The name of the promoter used to express this mRNA:
  T7
Description of the plasmid (facultative for promoter-less plasmid records):
PCR template for structure probing experiments of AQP4 IRES was prepared from pBiCAQP4 vector using AQP4 forward primer with built-in T7 promoter sequence (taatacgactcactatagggGGACAGTTTGGATAA) and AQP4 reverse primer (cctcgagCCACCATGATGTTCTCT).
The in vivo produced transcripts are heterogeneous (due to any of promoter?/splicing?/cleavage?/breakage?):
  not tested
The in vivo produced heterogeneous transcripts occur due to alternative splicing:
  not tested
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
The abbreviated name of the donor gene or virus from which this IRES was excised and inserted into the plasmid:
AQP4
The origin of IRES in the plasmid:
  nuclear
The donor organism of the IRES segment:
Homo sapiens HEK 293T/17 (ATCC CRL-11268)
The DNA sequence of the plasmid in (+) orientation annotated by its secondary structure:


GenBank formatted file with annotated plasmid sequence hyperlinked from vector image map:
pBiCAQP4.jpg
The total number of notable open-reading frames (ORFs):
  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
IRESs:
IRES:
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The IRES name:
  AQP4
The functional status of IRES:
  functional
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  4-287
How IRES boundaries were determined:
experimentally_determined
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
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
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 29
Version: 0
Originaly submitted by: Václav Vopálenský Reviewed by: Martin Mokrejš
The function of the 2D structure:
IRES
The 2D structure causes frameshift:
no
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
4-293
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
2D structure of AQP4 from Fig 5B.
3.1.1. 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: 54
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: 55
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: 56
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: 57
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