The nucleic acid data:
IRESite Id: 73 Version: 8
Originaly submitted by: Barbora Škaloudová Submission date: 2005-12-21 00:00:00
Reviewed by: Martin Mokrejš Last change: 2007-01-23 00:00:00
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:
  HIV-1
The genetic origin of this natural mRNA/+RNA:
  viral
The GenBankId GI:# number of exactly this mRNA/+RNA sequence:
9629357
The mRNA/+RNA description: 
Human immunodeficiency virus 1, complete genome. The unspliced genomic RNA codes for gag and gag-pol. The
spliced version codes for env and other minor proteins. As the encapsidation signal is spliced out the
sub-genomic mRNA cannot be encapsidated.
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:
Human Immunodeficiency Virus type 1 NY5/BRU (LAV-1)
A promoter reported in cDNA corresponding to IRES sequence:
  not tested
The total number of notable open-reading frames (ORFs):
  2
Notable Open-Reading Frames (ORFs; protein coding regions) in the mRNA/+RNA sequence:
ORF
ORF position:   1
Version: 2
Originaly submitted by: Barbora Škaloudová Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
gag
The description of the protein encoded in this ORF:
Pr55 is further cleaved by a protease into final mature peptides
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):
  336-1838
ORF
ORF position:   2
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The abbreviated name of this ORF/gene:
gag-pol
The description of the protein encoded in this ORF:
Gag-Pol is further cleaved by a protease into final mature peptides
The translational frameshift (ribosome slippage) involved:
  -1
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):
  336-4642
OPTIONAL: The function of the encoded protein
viral structural protein, important for virus infectivity, protein processing, and genomic RNA dimer
stability, important for incorporation of Vpr into assembling HIV-1 virions; helps mediate efficient virus
particle release from infected cells
Citations:
Brasey A., Lopez-Lastra M., Ohlmann T., Beerens N., Berkhout B., Darlix J. L., Sonenberg N. (2003) The leader of human immunodeficiency virus type 1 genomic RNA harbors an internal ribosome entry segment that is active during the G2/M phase of the cell cycle. J. Virol. 77(7):3939-3949
Berkhout B. (1996) Structure and function of the human immunodeficiency virus leader RNA. Prog. Nucleic. Acid Res. Mol. Biol. 54:1-34
IRESs:
IRES:
Version: 7 Last change: 2009-08-18 17:28:34
Originaly submitted by: Barbora Škaloudová Reviewed by: Martin Mokrejš
The IRES name:
  HIV-1
The IRES absolute position (the range includes START and STOP codons or their equivalents):
  104-336
Conclusion:
  putative_IRES
How IRES boundaries were determined:
experimentally_determined
The sequence of IRES region aligned to its secondary structure (if available):



Remarks:
Mono- and bicistronic (capped and uncapped) T7 transcripts were tested in rabbit reticulocyte lysates. Also
transiently transfected cells were used to show IRES activity. The intercistronic region contained impaired
EMCV IRES followed by the tested HIV-1 fragment. The impaired EMCV IRES should inhibit the potential ribosome
read-through.

With further deletions of the HIV-1 UTR, region 243-336 has very low IRES activity in in vitro
bicistronic assay using capped/uncapped mRNAs. Highest IRES activity was observed with 1-336 region.
RNA:protein interactions:
The RNA:protein interaction:
Version: 1
Originaly submitted by: Barbora Škaloudová Reviewed by: Martin Mokrejš
The description of the protein interacting with the RNA:
tat protein, the trans-activator protein
The interacting RNA base range: 22-24,29-33
The function of the protein interaction:
essential for viral replication
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
protein binds TAR hairpin of HIV 5' untranslated region, the functional TAR hairpin must maintain a
base-paired stem although the actual sequence of 29-CUGGG-33 pentanucleotide is not important for Tat
responsiveness
Citations:
Dingwall C., Ernberg I., Gait M. J., Green S. M., Heaphy S., Karn J., Lowe A. D., Singh M., Skinner M. A., Valerio R. (1989) Human immunodeficiency virus 1 tat protein binds trans-activation-responsive region (TAR) RNA in vitro. Proc. Natl. Acad. Sci. U. S. A. 86(18):6925-6929
Berkhout B., Jeang K. T. (1989) trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: a quantitative analysis. J. Virol. 63(12):5501-5504
The RNA:protein interaction:
Version: 5 Last change: 2006-04-28 00:00:00
Originaly submitted by: Barbora Škaloudová Reviewed by: Martin Mokrejš
The description of the protein interacting with the RNA:
nucleocapsid protein (NC protein)
The function of the protein interaction:
virus replication (increase the efficiency of strand transfer by HIV-1 reverse transcriptase), packaging of
genomic RNA
The organism where this RNA:protein interaction occurs:
Homo sapiens
Remarks:
binding is not sequence-specific, the NC protein binds 5 untranslated region, TAR stem-loop
Citations:
Rein A., Henderson L. E., Levin J. G. (1998) Nucleic-acid-chaperone activity of retroviral nucleocapsid proteins: significance for viral replication. Trends. Biochem. Sci. 23(8):297-301
Regions with experimentally determined secondary structures:
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 34
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The function of the 2D structure:
encapsidation signal
The 2D structure causes frameshift:
unknown
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
232-369
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
The reaction mixtures were treated with
0.02 to 0.1 U of RNase T1 (Pharmacia) at 08C for 20 min,
0.15 to 0.7 U of RNase CV or V1 (Pharmacia) at 08C for 20 min,
0.5 to 1.0% dimethylsulfate (Aldrich) at 08C for 20 min,
1.5 to 3.0% diethylpyrocarbonate (Sigma) at 08C for 30 min,
20 mg of carbodiimide (Sigma) per ml at 258C for 30 min
   or 4 to 8 mg of kethoxal (U.S. Biochemical) per ml at 08C for 1 h.
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: 66
The temperature (in degrees of Celsia):
0
The enzymatic method used to determine the 2D structure:
ribonuclease T1/V1 mix
Enzyme or a combination of enzymes used in a single experiment with respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
50.00
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
50.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
30.00
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Other buffer components and their relative concentrations:
10 mM ZnCl2
2 mM dithiothreitol
4.1.2. Chemicals used to characterize at least partially the 2D structure.
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 26
The temperature (in degrees of Celsia):
0
The chemical reagent used to determine the 2D structure:
DMS/kethoxal mix
Chemical reagent used with its respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
50.00
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
50.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
30.00
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Other buffer components and their relative concentrations:
10 mM ZnCl2
2 mM dithiothreitol
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 27
The temperature (in degrees of Celsia):
0
The chemical reagent used to determine the 2D structure:
DEPC (diethylpyrocarbonate)
Chemical reagent used with its respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
50.00
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
50.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
30.00
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Other buffer components and their relative concentrations:
10 mM ZnCl2
2 mM dithiothreitol
Chemical reagent used with its respective buffer:
ss_experiment_with_chemical_id: 28
The temperature (in degrees of Celsia):
25
The chemical reagent used to determine the 2D structure:
carbodiimide
Chemical reagent used with its respective buffer:
Version: 0
pH
7.50
Li+ [mM]
0
Na+ [mM]
0
K+ [mM]
50.00
Mg2+ [mM]
0
Ca2+ [mM]
0
Cl- [mM]
50.00
Tris [mM]
0
BSA [mM]
0
HEPES [mM]
30.00
EGTA [mM]
0
EDTA [mM]
0
cacodylate [mM]
0
Other buffer components and their relative concentrations:
10 mM ZnCl2
2 mM dithiothreitol
Citations:
Clever J., Sassetti C., Parslow T. G. (1995) RNA secondary structure and binding sites for gag gene products in the 5' packaging signal of human immunodeficiency virus type 1. J. Virol. 69(4):2101-2109
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 35
Version: 1 Last change: 2009-08-18 17:58:49
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The function of the 2D structure:
other
The 2D structure causes frameshift:
unknown
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1-368
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
The HIV1 5'-UTR contains the following features:
TAR, binding site for the transcriptional activator Tat
Poly(A), polyadenylation site in the 3'-LTR
PBS, primer binding site
DIS, dimer initiation site
SD, major splice donor
PSI, encapsidation signal
AUG codon of Gag CDS
Citations:
Damgaard CK, Dyhr-Mikkelsen H, Kjems J (1998) Mapping the RNA binding sites for human immunodeficiency virus type-1 gag and NC proteins within the complete HIV-1 and -2 untranslated leader regions. Nucleic Acids Res. 16(26):3667-3676
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 36
Version: 1 Last change: 2009-08-18 17:58:49
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The function of the 2D structure:
other
The 2D structure causes frameshift:
unknown
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1-281
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
Authors have described that actually two secondary structures alternate between each other.

DEPC and DMS were used for structure probing in TEN buffer at 20 oC.

The probed region spans the following features:
TAR, binding site for the transcriptional activator Tat
Poly(A), polyadenylation site in the 3'-LTR
PBS, primer binding site
DIS, dimer initiation site
Citations:
Huthoff H, Berkhout B (2001) Two alternating structures of the HIV-1 leader RNA. RNA. 1(7):143-157
A region with the experimentally determined secondary structure:
IRESite 2D Struct Id: 38
Version: 0
Originaly submitted by: Martin Mokrejš Reviewed by: Martin Mokrejš
The function of the 2D structure:
other
The 2D structure causes frameshift:
unknown
The absolute position of the experimentally mapped region (the range includes START and STOP codons or their equivalents):
1-342
The underlying nucleic acid sequence and structure of the mapped region:



Remarks:
Authors used methylsulfate for structure probing.
Citations:
Paillart JC, Dettenhofer M, Yu XF, Ehresmann C, Ehresmann B, Marquet R (2004) First snapshots of the HIV-1 RNA structure in infected cells and in virions. J. Biol. Chem. 46(279):48397-48403
Last change to the database: 2015-04-16 16:45:23 GMT+1