Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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 Community
1
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3
DISCUSSION
0
null
null
17,151,076
pmid-11406596|pmid-10899131|pmid-12145212|pmid-9776761|pmid-9334319|pmid-11689695
The strong conservation of R480, W482 and W489 among species, combined with the observation that all three of these residues make extensive contributions to the Pcf11–Clp1 interface, suggests that the interactions made by these residues occur in the CFIA of other yeasts as well as in the 3′ end processing complexes of ...
null
338
5,500
0
false
null
null
The strong conservation of R480, W482 and W489 among species, combined with the observation that all three of these residues make extensive contributions to the Pcf11–Clp1 interface, suggests that the interactions made by these residues occur in the CFIA of other yeasts as well as in the 3′ end processing complexes of ...
true
true
true
true
true
919
3
DISCUSSION
0
null
null
17,151,076
pmid-11406596|pmid-10899131|pmid-12145212|pmid-9776761|pmid-9334319|pmid-11689695
In the mammalian system, there is no equivalent of CFIA.
null
56
5,501
0
false
null
null
In the mammalian system, there is no equivalent of CFIA.
true
true
true
true
true
919
3
DISCUSSION
0
null
null
17,151,076
pmid-11406596|pmid-10899131|pmid-12145212|pmid-9776761|pmid-9334319|pmid-11689695
hPcf11 and hClp are the only characterized components of the CFIIm complex and CstF77 and CstF64, the mammalian homologues of Rna14 and Rna15 are combined with a third protein CstF50 forming CstF (cleavage stimulation factor).
null
226
5,502
0
false
null
null
hPcf11 and hClp are the only characterized components of the CFIIm complex and CstF77 and CstF64, the mammalian homologues of Rna14 and Rna15 are combined with a third protein CstF50 forming CstF (cleavage stimulation factor).
false
true
true
true
false
919
3
DISCUSSION
0
null
null
17,151,076
pmid-11406596|pmid-10899131|pmid-12145212|pmid-9776761|pmid-9334319|pmid-11689695
However, our data now suggest that although the subunit composition of yeast and mammalian 3′ end processing complexes may have diverged, it is likely that many of the interactions at the Clp1–Pcf11 interface have been preserved.
null
229
5,503
0
false
null
null
However, our data now suggest that although the subunit composition of yeast and mammalian 3′ end processing complexes may have diverged, it is likely that many of the interactions at the Clp1–Pcf11 interface have been preserved.
true
true
true
true
true
919
3
DISCUSSION
0
null
null
17,151,076
pmid-11406596|pmid-10899131|pmid-12145212|pmid-9776761|pmid-9334319|pmid-11689695
Furthermore, since Pcf11 is extensively involved at the interface between the complexes involved in 3′ end processing it seems likely that this highly conserved Clp1–Pcf11 interaction is required to ensure the efficient and timely recruitment of the ATPase activity of Clp1 to the polyadenylation machinery.
null
307
5,504
0
false
null
null
Furthermore, since Pcf11 is extensively involved at the interface between the complexes involved in 3′ end processing it seems likely that this highly conserved Clp1–Pcf11 interaction is required to ensure the efficient and timely recruitment of the ATPase activity of Clp1 to the polyadenylation machinery.
true
true
true
true
true
919
4
DISCUSSION
1
12
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
The exact nature of ATP-binding and/or hydrolysis in the 3′ end processing reaction remains unclear.
[ "12", "58", "59" ]
100
5,505
0
false
The exact nature of ATP-binding and/or hydrolysis in the 3′ end processing reaction remains unclear.
[]
The exact nature of ATP-binding and/or hydrolysis in the 3′ end processing reaction remains unclear.
true
true
true
true
true
920
4
DISCUSSION
1
12
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
It has been demonstrated that in vitro reconstitution of the 3′ end cleavage and polyadenylation reaction is stimulated by ATP (12) and that the cleavage reaction alone can proceed in the presence of other nucleotides, CTP and 3′ dATP (58).
[ "12", "58", "59" ]
240
5,506
1
false
It has been demonstrated that in vitro reconstitution of the 3′ end cleavage and polyadenylation reaction is stimulated by ATP and that the cleavage reaction alone can proceed in the presence of other nucleotides, CTP and 3′ dATP.
[ "12", "58" ]
It has been demonstrated that in vitro reconstitution of the 3′ end cleavage and polyadenylation reaction is stimulated by ATP and that the cleavage reaction alone can proceed in the presence of other nucleotides, CTP and 3′ dATP.
true
true
true
true
true
920
4
DISCUSSION
1
59
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
Furthermore, it has been shown that ATP is required for CFII to bind to RNA through the Cft2 protein (59).
[ "12", "58", "59" ]
106
5,507
1
false
Furthermore, it has been shown that ATP is required for CFII to bind to RNA through the Cft2 protein.
[ "59" ]
Furthermore, it has been shown that ATP is required for CFII to bind to RNA through the Cft2 protein.
true
true
true
true
true
920
4
DISCUSSION
1
12
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
In light of these observations, it seems likely that ATP is required for several steps of the cleavage and polyadenylation reaction, but to date an ATPase enzyme has not been identified within the 3′ end processing machinery.
[ "12", "58", "59" ]
225
5,508
0
false
In light of these observations, it seems likely that ATP is required for several steps of the cleavage and polyadenylation reaction, but to date an ATPase enzyme has not been identified within the 3′ end processing machinery.
[]
In light of these observations, it seems likely that ATP is required for several steps of the cleavage and polyadenylation reaction, but to date an ATPase enzyme has not been identified within the 3′ end processing machinery.
true
true
true
true
true
920
4
DISCUSSION
1
12
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
Our data now reveal that Clp1 is an ATP-binding protein that could provide ATPase activity in this system.
[ "12", "58", "59" ]
106
5,509
0
false
Our data now reveal that Clp1 is an ATP-binding protein that could provide ATPase activity in this system.
[]
Our data now reveal that Clp1 is an ATP-binding protein that could provide ATPase activity in this system.
true
true
true
true
true
920
4
DISCUSSION
1
12
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
The structure contains ATP bound at a P-loop and the conformation of the switch regions in the nucleotide binding site together with co-ordination of the magnesium ion is similar to that observed in other SIMIBI-class catalytically competent ATPases, most notably NifH.
[ "12", "58", "59" ]
269
5,510
0
false
The structure contains ATP bound at a P-loop and the conformation of the switch regions in the nucleotide binding site together with co-ordination of the magnesium ion is similar to that observed in other SIMIBI-class catalytically competent ATPases, most notably NifH.
[]
The structure contains ATP bound at a P-loop and the conformation of the switch regions in the nucleotide binding site together with co-ordination of the magnesium ion is similar to that observed in other SIMIBI-class catalytically competent ATPases, most notably NifH.
true
true
true
true
true
920
4
DISCUSSION
1
12
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
However, although the Clp1 ATP-binding site appears capable of supporting nucleotide hydrolysis, in an in vitro assay we have been unable to detect any ATPase activity either using Clp1 alone or Clp1–Pcf11 complexes in combination with other components of CFI, with or without the addition of RNA (C. G. Noble and I.
[ "12", "58", "59" ]
316
5,511
0
false
However, although the Clp1 ATP-binding site appears capable of supporting nucleotide hydrolysis, in an in vitro assay we have been unable to detect any ATPase activity either using Clp1 alone or Clp1–Pcf11 complexes in combination with other components of CFI, with or without the addition of RNA (C. G. Noble and I.
[]
However, although the Clp1 ATP-binding site appears capable of supporting nucleotide hydrolysis, in an in vitro assay we have been unable to detect any ATPase activity either using Clp1 alone or Clp1–Pcf11 complexes in combination with other components of CFI, with or without the addition of RNA (C. G. Noble and I.
true
true
true
true
true
920
4
DISCUSSION
1
12
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
A. Taylor, unpublished data).
[ "12", "58", "59" ]
29
5,512
0
false
A. Taylor, unpublished data).
[]
A. Taylor, unpublished data).
true
true
true
true
true
920
4
DISCUSSION
1
12
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
This lack of enzymatic turnover combined with the inaccessibility of the bound ATP molecule poses the question of whether the nucleotide can be hydrolysed in vivo or whether it functions purely as a structural element of the Clp1 protein.
[ "12", "58", "59" ]
238
5,513
0
false
This lack of enzymatic turnover combined with the inaccessibility of the bound ATP molecule poses the question of whether the nucleotide can be hydrolysed in vivo or whether it functions purely as a structural element of the Clp1 protein.
[]
This lack of enzymatic turnover combined with the inaccessibility of the bound ATP molecule poses the question of whether the nucleotide can be hydrolysed in vivo or whether it functions purely as a structural element of the Clp1 protein.
true
true
true
true
true
920
4
DISCUSSION
1
12
[ "b12", "b58", "b59" ]
17,151,076
pmid-8900210|pmid-11344258|pmid-9334319|pmid-15215336|pmid-11344258|pmid-10619842|pmid-12853609|pmid-12853609|pmid-11344258|pmid-9032237|pmid-12727883|pmid-12727883|pmid-15665873|pmid-1352851|pmid-9857200|pmid-9099738
What is clear is that turnover of bound ATP would require significant conformational rearrangements in the protein in order for catalysis to occur together with ADP dissociation and ATP re-binding.
[ "12", "58", "59" ]
197
5,514
0
false
What is clear is that turnover of bound ATP would require significant conformational rearrangements in the protein in order for catalysis to occur together with ADP dissociation and ATP re-binding.
[]
What is clear is that turnover of bound ATP would require significant conformational rearrangements in the protein in order for catalysis to occur together with ADP dissociation and ATP re-binding.
true
true
true
true
true
920
5
DISCUSSION
1
56
[ "b56", "b60", "b61" ]
17,151,076
pmid-11060040|pmid-6329717|pmid-11344258|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040|pmid-11848849|pmid-15458408|pmid-15635448
In support of the idea that Clp1 does have ATPase activity it is interesting to examine the structurally related NifH protein.
[ "56", "60", "61" ]
126
5,515
0
false
In support of the idea that Clp1 does have ATPase activity it is interesting to examine the structurally related NifH protein.
[]
In support of the idea that Clp1 does have ATPase activity it is interesting to examine the structurally related NifH protein.
true
true
true
true
true
921
5
DISCUSSION
1
56
[ "b56", "b60", "b61" ]
17,151,076
pmid-11060040|pmid-6329717|pmid-11344258|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040|pmid-11848849|pmid-15458408|pmid-15635448
In this system, NifH lacks ATPase activity in isolation and in fact nucleotide hydrolysis activity only becomes strongly stimulated through the interaction of NifH with the Mo-Fe subunit of the nitrogenase (56).
[ "56", "60", "61" ]
211
5,516
1
false
In this system, NifH lacks ATPase activity in isolation and in fact nucleotide hydrolysis activity only becomes strongly stimulated through the interaction of NifH with the Mo-Fe subunit of the nitrogenase.
[ "56" ]
In this system, NifH lacks ATPase activity in isolation and in fact nucleotide hydrolysis activity only becomes strongly stimulated through the interaction of NifH with the Mo-Fe subunit of the nitrogenase.
true
true
true
true
true
921
5
DISCUSSION
1
60
[ "b56", "b60", "b61" ]
17,151,076
pmid-11060040|pmid-6329717|pmid-11344258|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040|pmid-11848849|pmid-15458408|pmid-15635448
Similarly, two other related SIMIBI ATPases, MinD and Soj also require the interaction of other components of a macromolecular complex to stimulate ATP hydrolysis; MinE in the MinCDE cell-division system (60) and SpoJ in the Soj bacterial chromosome segregation system (61).
[ "56", "60", "61" ]
274
5,517
1
false
Similarly, two other related SIMIBI ATPases, MinD and Soj also require the interaction of other components of a macromolecular complex to stimulate ATP hydrolysis; MinE in the MinCDE cell-division system and SpoJ in the Soj bacterial chromosome segregation system.
[ "60", "61" ]
Similarly, two other related SIMIBI ATPases, MinD and Soj also require the interaction of other components of a macromolecular complex to stimulate ATP hydrolysis; MinE in the MinCDE cell-division system and SpoJ in the Soj bacterial chromosome segregation system.
true
true
true
true
true
921
5
DISCUSSION
1
56
[ "b56", "b60", "b61" ]
17,151,076
pmid-11060040|pmid-6329717|pmid-11344258|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040|pmid-11848849|pmid-15458408|pmid-15635448
Another common factor in all of these complexes is that the energy of ATP hydrolysis is coupled to the transduction of conformational changes through the macromolecular complex.
[ "56", "60", "61" ]
177
5,518
0
false
Another common factor in all of these complexes is that the energy of ATP hydrolysis is coupled to the transduction of conformational changes through the macromolecular complex.
[]
Another common factor in all of these complexes is that the energy of ATP hydrolysis is coupled to the transduction of conformational changes through the macromolecular complex.
true
true
true
true
true
921
5
DISCUSSION
1
56
[ "b56", "b60", "b61" ]
17,151,076
pmid-11060040|pmid-6329717|pmid-11344258|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040|pmid-11848849|pmid-15458408|pmid-15635448
For instance in NifH the conformational changes that result from ATP hydrolysis direct the transfer of electrons from NifH to the Mo-Fe subunit of the nitrogenase.
[ "56", "60", "61" ]
163
5,519
0
false
For instance in NifH the conformational changes that result from ATP hydrolysis direct the transfer of electrons from NifH to the Mo-Fe subunit of the nitrogenase.
[]
For instance in NifH the conformational changes that result from ATP hydrolysis direct the transfer of electrons from NifH to the Mo-Fe subunit of the nitrogenase.
true
true
true
true
true
921
6
DISCUSSION
1
27
[ "b27", "b37", "b39", "b35" ]
17,151,076
pmid-11916378|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040
In light of these observations, it seems plausible that activation of Clp1 ATPase activity might require the interaction with a further 3′ end processing-factor.
[ "27", "37", "39", "35" ]
161
5,520
0
false
In light of these observations, it seems plausible that activation of Clp1 ATPase activity might require the interaction with a further 3′ end processing-factor.
[]
In light of these observations, it seems plausible that activation of Clp1 ATPase activity might require the interaction with a further 3′ end processing-factor.
true
true
true
true
true
922
6
DISCUSSION
1
27
[ "b27", "b37", "b39", "b35" ]
17,151,076
pmid-11916378|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040
As we do not observe a stimulation of Clp1 ATPase activity upon the addition of the other CFI subunits, the question arises of which other 3′ end processing-factor might be required.
[ "27", "37", "39", "35" ]
182
5,521
0
false
As we do not observe a stimulation of Clp1 ATPase activity upon the addition of the other CFI subunits, the question arises of which other 3′ end processing-factor might be required.
[]
As we do not observe a stimulation of Clp1 ATPase activity upon the addition of the other CFI subunits, the question arises of which other 3′ end processing-factor might be required.
true
true
true
true
true
922
6
DISCUSSION
1
27
[ "b27", "b37", "b39", "b35" ]
17,151,076
pmid-11916378|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040
Other than Pcf11, the only other factor demonstrated to bind to Clp1 is the Ysh1 subunit of CPF (27), proposed to be the endonuclease responsible for transcript cleavage (37–39).
[ "27", "37", "39", "35" ]
178
5,522
1
false
Other than Pcf11, the only other factor demonstrated to bind to Clp1 is the Ysh1 subunit of CPF, proposed to be the endonuclease responsible for transcript cleavage.
[ "27", "37–39" ]
Other than Pcf11, the only other factor demonstrated to bind to Clp1 is the Ysh1 subunit of CPF, proposed to be the endonuclease responsible for transcript cleavage.
true
true
true
true
true
922
6
DISCUSSION
1
27
[ "b27", "b37", "b39", "b35" ]
17,151,076
pmid-11916378|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040
Since both CFIA and CPF are required for the cleavage reaction we propose that the association of the CFIA and CPF complexes bound at polyadenylation signal sequences is required to trigger nucleotide hydrolysis, perhaps through an Ysh1–Clp1 interaction.
[ "27", "37", "39", "35" ]
254
5,523
0
false
Since both CFIA and CPF are required for the cleavage reaction we propose that the association of the CFIA and CPF complexes bound at polyadenylation signal sequences is required to trigger nucleotide hydrolysis, perhaps through an Ysh1–Clp1 interaction.
[]
Since both CFIA and CPF are required for the cleavage reaction we propose that the association of the CFIA and CPF complexes bound at polyadenylation signal sequences is required to trigger nucleotide hydrolysis, perhaps through an Ysh1–Clp1 interaction.
true
true
true
true
true
922
6
DISCUSSION
1
35
[ "b27", "b37", "b39", "b35" ]
17,151,076
pmid-11916378|pmid-12853609|pmid-12177301|pmid-16213211|pmid-11060040
This notion that Clp1 might link 3′ end processing complexes together has a precedence in the mammalian system where it has been proposed that Clp1 is involved in bridging CFIIm to the other mammalian 3′ end processing complexes CPSF and CFIm (35).
[ "27", "37", "39", "35" ]
248
5,524
1
false
This notion that Clp1 might link 3′ end processing complexes together has a precedence in the mammalian system where it has been proposed that Clp1 is involved in bridging CFIIm to the other mammalian 3′ end processing complexes CPSF and CFIm.
[ "35" ]
This notion that Clp1 might link 3′ end processing complexes together has a precedence in the mammalian system where it has been proposed that Clp1 is involved in bridging CFIIm to the other mammalian 3′ end processing complexes CPSF and CFIm.
true
true
true
true
true
922
7
DISCUSSION
0
null
null
17,151,076
null
The function of Clp1 mediated nucleotide hydrolysis in 3′-end processing remains obscure.
null
89
5,525
0
false
null
null
The function of Clp1 mediated nucleotide hydrolysis in 3′-end processing remains obscure.
true
true
true
true
true
923
7
DISCUSSION
0
null
null
17,151,076
null
However, in the other structurally related ATPases that forms part of multisubunit complexes, hydrolysis results in conformational changes that are transmitted between component subunits and actuate a variety of diverse effects.
null
228
5,526
0
false
null
null
However, in the other structurally related ATPases that forms part of multisubunit complexes, hydrolysis results in conformational changes that are transmitted between component subunits and actuate a variety of diverse effects.
true
true
true
true
true
923
7
DISCUSSION
0
null
null
17,151,076
null
Therefore, the idea that Clp1 mediated ATP hydrolysis might be used to transduce conformational effects through complexes bound at the polyadenylation site is an attractive proposition.
null
185
5,527
0
false
null
null
Therefore, the idea that Clp1 mediated ATP hydrolysis might be used to transduce conformational effects through complexes bound at the polyadenylation site is an attractive proposition.
true
true
true
true
true
923
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,517,771
pmid-12522297|pmid-14675814|pmid-15546744|pmid-20859781|NA
Chemical shift contains a wealth of structural information of DNAs.
[ "1–3", "4", "5" ]
67
5,528
0
false
Chemical shift contains a wealth of structural information of DNAs.
[]
Chemical shift contains a wealth of structural information of DNAs.
true
true
true
true
true
924
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,517,771
pmid-12522297|pmid-14675814|pmid-15546744|pmid-20859781|NA
At present, several methods have been established to predict chemical shifts of DNAs in random coil form (1–3) and double helical B-form (4,5).
[ "1–3", "4", "5" ]
143
5,529
1
false
At present, several methods have been established to predict chemical shifts of DNAs in random coil form and double helical B-form.
[ "1–3", "4,5" ]
At present, several methods have been established to predict chemical shifts of DNAs in random coil form and double helical B-form.
true
true
true
true
true
924
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,517,771
pmid-12522297|pmid-14675814|pmid-15546744|pmid-20859781|NA
These methods are based on sets of reference chemical shift values and correction factors from experimental measurements, statistical analysis or semi-empirical calculations.
[ "1–3", "4", "5" ]
174
5,530
0
false
These methods are based on sets of reference chemical shift values and correction factors from experimental measurements, statistical analysis or semi-empirical calculations.
[]
These methods are based on sets of reference chemical shift values and correction factors from experimental measurements, statistical analysis or semi-empirical calculations.
true
true
true
true
true
924
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,517,771
pmid-12522297|pmid-14675814|pmid-15546744|pmid-20859781|NA
Shielding or deshielding contributions from nearest neighbor and/or next-nearest neighbor nucleotides have been included in these prediction methods.
[ "1–3", "4", "5" ]
149
5,531
0
false
Shielding or deshielding contributions from nearest neighbor and/or next-nearest neighbor nucleotides have been included in these prediction methods.
[]
Shielding or deshielding contributions from nearest neighbor and/or next-nearest neighbor nucleotides have been included in these prediction methods.
true
true
true
true
true
924
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,517,771
pmid-12522297|pmid-14675814|pmid-15546744|pmid-20859781|NA
To automate these prediction methods, a web server called ‘DSHIFT’ has been established for predicting DNA chemical shifts in this work.
[ "1–3", "4", "5" ]
136
5,532
0
false
To automate these prediction methods, a web server called ‘DSHIFT’ has been established for predicting DNA chemical shifts in this work.
[]
To automate these prediction methods, a web server called ‘DSHIFT’ has been established for predicting DNA chemical shifts in this work.
true
true
true
true
true
924
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,517,771
pmid-12522297|pmid-14675814|pmid-15546744|pmid-20859781|NA
This web server is open access to everyone.
[ "1–3", "4", "5" ]
43
5,533
0
false
This web server is open access to everyone.
[]
This web server is open access to everyone.
true
true
true
true
true
924
0
INTRODUCTION
1
1–3
[ "B1 B2 B3", "B4", "B5" ]
17,517,771
pmid-12522297|pmid-14675814|pmid-15546744|pmid-20859781|NA
Through entering a DNA sequence, random coil or double helical B-DNA chemical shifts will be predicted.
[ "1–3", "4", "5" ]
103
5,534
0
false
Through entering a DNA sequence, random coil or double helical B-DNA chemical shifts will be predicted.
[]
Through entering a DNA sequence, random coil or double helical B-DNA chemical shifts will be predicted.
true
true
true
true
true
924
1
INTRODUCTION
0
null
null
17,517,771
null
DSHIFT results can provide a quick reference guide for resonance assignments based on conventional NOESY and COSY-type experiments, thus facilitating solution structure studies of DNAs.
null
185
5,535
0
false
null
null
DSHIFT results can provide a quick reference guide for resonance assignments based on conventional NOESY and COSY-type experiments, thus facilitating solution structure studies of DNAs.
true
true
true
true
true
925
1
INTRODUCTION
0
null
null
17,517,771
null
These results can also provide useful information for studying structure–chemical shift relationship, identifying unstructured or right-handed double helical regions, monitoring DNA–drug or DNA–protein binding, and investigating conformational details of special features in DNA structures.
null
290
5,536
0
false
null
null
These results can also provide useful information for studying structure–chemical shift relationship, identifying unstructured or right-handed double helical regions, monitoring DNA–drug or DNA–protein binding, and investigating conformational details of special features in DNA structures.
true
true
true
true
true
925
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
Viral infection often entails the hindering of the host cell's translation machinery in order that the viral genome is expressed more efficiently relative to the expression of the host's proteins.
[ "1", "2–4" ]
196
5,537
0
false
Viral infection often entails the hindering of the host cell's translation machinery in order that the viral genome is expressed more efficiently relative to the expression of the host's proteins.
[]
Viral infection often entails the hindering of the host cell's translation machinery in order that the viral genome is expressed more efficiently relative to the expression of the host's proteins.
true
true
true
true
true
926
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
In the Picornaviridae family of single-stranded RNA viruses, a viral protease cleaves the scaffolding translation initiation factors of the eIF4G family, thereby reducing the efficiency of the host cell's cap-dependent translation initiation and favouring the alternate internal ribosome entry site (IRES) mechanism used...
[ "1", "2–4" ]
338
5,538
1
false
In the Picornaviridae family of single-stranded RNA viruses, a viral protease cleaves the scaffolding translation initiation factors of the eIF4G family, thereby reducing the efficiency of the host cell's cap-dependent translation initiation and favouring the alternate internal ribosome entry site (IRES) mechanism used...
[ "1" ]
In the Picornaviridae family of single-stranded RNA viruses, a viral protease cleaves the scaffolding translation initiation factors of the eIF4G family, thereby reducing the efficiency of the host cell's cap-dependent translation initiation and favouring the alternate internal ribosome entry site (IRES) mechanism used...
true
true
true
true
true
926
0
INTRODUCTION
1
2–4
[ "B1", "B2 B3 B4" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
The importance of this mechanism for viruses has been best demonstrated in the attenuated Sabin poliovirus strains used for worldwide polio vaccination, which contains point mutations in the IRES (2–4) that allow efficient translation in the gut but not in neuronal cells.
[ "1", "2–4" ]
272
5,539
1
false
The importance of this mechanism for viruses has been best demonstrated in the attenuated Sabin poliovirus strains used for worldwide polio vaccination, which contains point mutations in the IRES that allow efficient translation in the gut but not in neuronal cells.
[ "2–4" ]
The importance of this mechanism for viruses has been best demonstrated in the attenuated Sabin poliovirus strains used for worldwide polio vaccination, which contains point mutations in the IRES that allow efficient translation in the gut but not in neuronal cells.
true
true
true
true
true
926
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
Cap-dependent translation initiation is also rendered less efficient under several cellular conditions, but specific cellular mRNAs are still translated with relative efficiency using the IRES mechanism for translation initiation.
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
230
5,540
0
false
Cap-dependent translation initiation is also rendered less efficient under several cellular conditions, but specific cellular mRNAs are still translated with relative efficiency using the IRES mechanism for translation initiation.
[]
Cap-dependent translation initiation is also rendered less efficient under several cellular conditions, but specific cellular mRNAs are still translated with relative efficiency using the IRES mechanism for translation initiation.
true
true
true
true
true
927
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
Many fine reviews have been written on IRES in cellular messages (5), viruses (6,7), stress and apoptosis (8–10).
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
113
5,541
1
false
Many fine reviews have been written on IRES in cellular messages, viruses, stress and apoptosis.
[ "5", "6,7", "8–10" ]
Many fine reviews have been written on IRES in cellular messages, viruses, stress and apoptosis.
true
true
true
true
true
927
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
Typical translation of cellular messages in eukaryotes begins with the association of translation initiation factors with the cap-binding protein factor, eIF4E, on the 5′end of the message where the ‘cap’, a methyl7GDP nucleotide resides.
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
238
5,542
0
false
Typical translation of cellular messages in eukaryotes begins with the association of translation initiation factors with the cap-binding protein factor, eIF4E, on the 5′end of the message where the ‘cap’, a methyl7GDP nucleotide resides.
[]
Typical translation of cellular messages in eukaryotes begins with the association of translation initiation factors with the cap-binding protein factor, eIF4E, on the 5′end of the message where the ‘cap’, a methyl7GDP nucleotide resides.
true
true
true
true
true
927
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
This complex, which includes eIF4E, eIF4G, eIF4A, eIF3, the 40S ribosomal small subunit and an activated start codon tRNAi, will scan along the untranslated region (UTR) of the mRNA until it finds a suitable start codon where the large ribosomal subunit will join and protein translation will begin.
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
299
5,543
0
false
This complex, which includes eIF4E, eIF4G, eIF4A, eIF3, the 40S ribosomal small subunit and an activated start codon tRNAi, will scan along the untranslated region (UTR) of the mRNA until it finds a suitable start codon where the large ribosomal subunit will join and protein translation will begin.
[]
This complex, which includes eIF4E, eIF4G, eIF4A, eIF3, the 40S ribosomal small subunit and an activated start codon tRNAi, will scan along the untranslated region (UTR) of the mRNA until it finds a suitable start codon where the large ribosomal subunit will join and protein translation will begin.
true
true
true
true
true
927
1
INTRODUCTION
1
11
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
During mitosis, cellular perturbation or stress, and apoptosis, canonical initiation factors like eIF4E, 4E-BPs, eIF2α and the eIF4G family of proteins are either modified by changes in phosphorylation state or by protein cleavage (11) and are no longer available for efficient cap-dependent translation initiation.
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
315
5,544
1
false
During mitosis, cellular perturbation or stress, and apoptosis, canonical initiation factors like eIF4E, 4E-BPs, eIF2α and the eIF4G family of proteins are either modified by changes in phosphorylation state or by protein cleavage and are no longer available for efficient cap-dependent translation initiation.
[ "11" ]
During mitosis, cellular perturbation or stress, and apoptosis, canonical initiation factors like eIF4E, 4E-BPs, eIF2α and the eIF4G family of proteins are either modified by changes in phosphorylation state or by protein cleavage and are no longer available for efficient cap-dependent translation initiation.
true
true
true
true
true
927
1
INTRODUCTION
1
12
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
The ribosome may also undergo some modifications as well (12).
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
62
5,545
1
false
The ribosome may also undergo some modifications as well.
[ "12" ]
The ribosome may also undergo some modifications as well.
true
true
true
true
true
927
1
INTRODUCTION
1
13
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
At these times, other protein factors (13), many of which are part of the ribonucleoprotein complex, are required to enhance translation initiation through the IRES mechanism.
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
175
5,546
1
false
At these times, other protein factors, many of which are part of the ribonucleoprotein complex, are required to enhance translation initiation through the IRES mechanism.
[ "13" ]
At these times, other protein factors, many of which are part of the ribonucleoprotein complex, are required to enhance translation initiation through the IRES mechanism.
true
true
true
true
true
927
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
An IRES is a stretch of sequence usually upstream of the AUG start codon in the 5′ untranslated region (UTR) of the messenger RNA that along with the IRES trans-acting protein factors (ITAFs), recruit the ribosome.
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
214
5,547
0
false
An IRES is a stretch of sequence usually upstream of the AUG start codon in the 5′ untranslated region (UTR) of the messenger RNA that along with the IRES trans-acting protein factors (ITAFs), recruit the ribosome.
[]
An IRES is a stretch of sequence usually upstream of the AUG start codon in the 5′ untranslated region (UTR) of the messenger RNA that along with the IRES trans-acting protein factors (ITAFs), recruit the ribosome.
true
true
true
true
true
927
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
It is not clear whether these factors need a sequence motif or a RNA secondary structure/sequence motif combination to bind to IRES-containing mRNAs.
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
149
5,548
0
false
It is not clear whether these factors need a sequence motif or a RNA secondary structure/sequence motif combination to bind to IRES-containing mRNAs.
[]
It is not clear whether these factors need a sequence motif or a RNA secondary structure/sequence motif combination to bind to IRES-containing mRNAs.
true
true
true
true
true
927
1
INTRODUCTION
1
14–19
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
In viral IRESes, like HCV and EMCV, RNA secondary structure has been shown to be crucial for IRES function (14–19).
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
115
5,549
1
false
In viral IRESes, like HCV and EMCV, RNA secondary structure has been shown to be crucial for IRES function.
[ "14–19" ]
In viral IRESes, like HCV and EMCV, RNA secondary structure has been shown to be crucial for IRES function.
true
true
true
true
true
927
1
INTRODUCTION
1
5
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
These structures are also conserved in other viruses that do not share primary sequence similarity.
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
99
5,550
0
false
These structures are also conserved in other viruses that do not share primary sequence similarity.
[]
These structures are also conserved in other viruses that do not share primary sequence similarity.
true
true
true
true
true
927
1
INTRODUCTION
1
22
[ "B5", "B6", "B7", "B8 B9 B10", "B11", "B12", "B13", "B14 B15 B16 B17 B18 B19", "B20", "B21", "B22" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
For example, the HCV IRES structure is similar to CSFV and BVDV (20,21), whereas the EMCV IRES structure is shared with other cardio- picornaviruses (22).
[ "5", "6", "7", "8–10", "11", "12", "13", "14–19", "20", "21", "22" ]
154
5,551
1
false
For example, the HCV IRES structure is similar to CSFV and BVDV, whereas the EMCV IRES structure is shared with other cardio- picornaviruses.
[ "20,21", "22" ]
For example, the HCV IRES structure is similar to CSFV and BVDV, whereas the EMCV IRES structure is shared with other cardio- picornaviruses.
true
true
true
true
true
927
2
INTRODUCTION
1
23
[ "B23", "B24", "B25", "B26", "B27", "B28", "B29", "B30", "B31", "B32" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
The secondary structure of the cellular IRES of c-Myc (23), L-Myc (24), Apaf-1 (25), FGF-2 (26), FGF1 (27), Kv1.4 (28), Bag-1 (29), Igf2 (30), cat-1 (31), Mnt and MTG8a (32) have been empirically determined using enzymatic and chemical probing, but no similarities between the structures of these cellular IRES were iden...
[ "23", "24", "25", "26", "27", "28", "29", "30", "31", "32" ]
327
5,552
1
false
The secondary structure of the cellular IRES of c-Myc, L-Myc, Apaf-1, FGF-2, FGF1, Kv1.4, Bag-1, Igf2, cat-1, Mnt and MTG8a have been empirically determined using enzymatic and chemical probing, but no similarities between the structures of these cellular IRES were identified.
[ "23", "24", "25", "26", "27", "28", "29", "30", "31", "32" ]
The secondary structure of the cellular IRES of c-Myc, L-Myc, Apaf-1, FGF-2, FGF1, Kv1.4, Bag-1, Igf2, cat-1, Mnt and MTG8a have been empirically determined using enzymatic and chemical probing, but no similarities between the structures of these cellular IRES were identified.
true
true
true
true
true
928
2
INTRODUCTION
1
23
[ "B23", "B24", "B25", "B26", "B27", "B28", "B29", "B30", "B31", "B32" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
This could be due to a much wider regulatory range of translation initiation that is needed in distinct cellular contexts relative to a virus's need to translate its messages more efficiently than the host's transcripts.
[ "23", "24", "25", "26", "27", "28", "29", "30", "31", "32" ]
220
5,553
0
false
This could be due to a much wider regulatory range of translation initiation that is needed in distinct cellular contexts relative to a virus's need to translate its messages more efficiently than the host's transcripts.
[]
This could be due to a much wider regulatory range of translation initiation that is needed in distinct cellular contexts relative to a virus's need to translate its messages more efficiently than the host's transcripts.
true
true
true
true
true
928
2
INTRODUCTION
1
23
[ "B23", "B24", "B25", "B26", "B27", "B28", "B29", "B30", "B31", "B32" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
Therefore, the possibility exists that there are structural motifs that are shared in co-ordinately regulated as yet undiscovered IRES.
[ "23", "24", "25", "26", "27", "28", "29", "30", "31", "32" ]
135
5,554
0
false
Therefore, the possibility exists that there are structural motifs that are shared in co-ordinately regulated as yet undiscovered IRES.
[]
Therefore, the possibility exists that there are structural motifs that are shared in co-ordinately regulated as yet undiscovered IRES.
true
true
true
true
true
928
3
INTRODUCTION
1
33
[ "B33" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
Determination of viral IRES structures can often benefit from the comparison of many sequences from the same virus, using the variation of sequence to determine which bases pair together.
[ "33" ]
187
5,555
0
false
Determination of viral IRES structures can often benefit from the comparison of many sequences from the same virus, using the variation of sequence to determine which bases pair together.
[]
Determination of viral IRES structures can often benefit from the comparison of many sequences from the same virus, using the variation of sequence to determine which bases pair together.
true
true
true
true
true
929
3
INTRODUCTION
1
33
[ "B33" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
When a structure is preserved, a mutation in a base will be coupled with a second site mutation that preserves the base pairing, and therefore the IRES structure.
[ "33" ]
162
5,556
0
false
When a structure is preserved, a mutation in a base will be coupled with a second site mutation that preserves the base pairing, and therefore the IRES structure.
[]
When a structure is preserved, a mutation in a base will be coupled with a second site mutation that preserves the base pairing, and therefore the IRES structure.
true
true
true
true
true
929
3
INTRODUCTION
1
33
[ "B33" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
This co-variation analysis is not always possible with a lower number of available mammalian sequences, and therefore secondary structure determination requires enzymatic or chemical probing to determine the secondary structure in lieu of tertiary structure analysis with NMR or X-ray crystallography.
[ "33" ]
301
5,557
0
false
This co-variation analysis is not always possible with a lower number of available mammalian sequences, and therefore secondary structure determination requires enzymatic or chemical probing to determine the secondary structure in lieu of tertiary structure analysis with NMR or X-ray crystallography.
[]
This co-variation analysis is not always possible with a lower number of available mammalian sequences, and therefore secondary structure determination requires enzymatic or chemical probing to determine the secondary structure in lieu of tertiary structure analysis with NMR or X-ray crystallography.
true
true
true
true
true
929
3
INTRODUCTION
1
33
[ "B33" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
Computational de novo secondary structure prediction has still not achieved the accuracy needed to skip empirical structure determination, but it can be used for comparative purposes when at least one structure is known (33).
[ "33" ]
225
5,558
1
false
Computational de novo secondary structure prediction has still not achieved the accuracy needed to skip empirical structure determination, but it can be used for comparative purposes when at least one structure is known.
[ "33" ]
Computational de novo secondary structure prediction has still not achieved the accuracy needed to skip empirical structure determination, but it can be used for comparative purposes when at least one structure is known.
true
true
true
true
true
929
4
INTRODUCTION
1
34
[ "B34", "B35", "B35 B36 B37 B38 B39", "B40", "B41" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
The X-linked inhibitor of apoptosis protein (XIAP) is the key inhibitor of apoptosis by virtue of binding to and inhibiting distinct caspases (34).
[ "34", "35", "35–39", "40", "41" ]
147
5,559
1
false
The X-linked inhibitor of apoptosis protein (XIAP) is the key inhibitor of apoptosis by virtue of binding to and inhibiting distinct caspases.
[ "34" ]
The X-linked inhibitor of apoptosis protein (XIAP) is the key inhibitor of apoptosis by virtue of binding to and inhibiting distinct caspases.
true
true
true
true
true
930
4
INTRODUCTION
1
35
[ "B34", "B35", "B35 B36 B37 B38 B39", "B40", "B41" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
It was shown that XIAP mRNA is translated by an IRES-dependent mechanism (35), and that this mode of XIAP translation is absolutely required for maintaining protective levels of XIAP protein in cells undergoing various forms of cellular stress (35–39).
[ "34", "35", "35–39", "40", "41" ]
252
5,560
1
false
It was shown that XIAP mRNA is translated by an IRES-dependent mechanism, and that this mode of XIAP translation is absolutely required for maintaining protective levels of XIAP protein in cells undergoing various forms of cellular stress.
[ "35", "35–39" ]
It was shown that XIAP mRNA is translated by an IRES-dependent mechanism, and that this mode of XIAP translation is absolutely required for maintaining protective levels of XIAP protein in cells undergoing various forms of cellular stress.
true
true
true
true
true
930
4
INTRODUCTION
1
34
[ "B34", "B35", "B35 B36 B37 B38 B39", "B40", "B41" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
Thus, it is likely that functionally similar IRES exist that govern the expression of cellular genes involved in the control of cellular growth, proliferation and death.
[ "34", "35", "35–39", "40", "41" ]
169
5,561
0
false
Thus, it is likely that functionally similar IRES exist that govern the expression of cellular genes involved in the control of cellular growth, proliferation and death.
[]
Thus, it is likely that functionally similar IRES exist that govern the expression of cellular genes involved in the control of cellular growth, proliferation and death.
true
true
true
true
true
930
4
INTRODUCTION
1
34
[ "B34", "B35", "B35 B36 B37 B38 B39", "B40", "B41" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
In this work, the secondary structure of the XIAP IRES was determined using enzymatic probing.
[ "34", "35", "35–39", "40", "41" ]
94
5,562
0
false
In this work, the secondary structure of the XIAP IRES was determined using enzymatic probing.
[]
In this work, the secondary structure of the XIAP IRES was determined using enzymatic probing.
true
true
true
true
true
930
4
INTRODUCTION
1
40
[ "B34", "B35", "B35 B36 B37 B38 B39", "B40", "B41" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
This structure was then used to search a 5′UTR database using the RSEARCH program (40), which predicted that several mRNAs had some similar structure features.
[ "34", "35", "35–39", "40", "41" ]
159
5,563
1
false
This structure was then used to search a 5′UTR database using the RSEARCH program, which predicted that several mRNAs had some similar structure features.
[ "40" ]
This structure was then used to search a 5′UTR database using the RSEARCH program, which predicted that several mRNAs had some similar structure features.
true
true
true
true
true
930
4
INTRODUCTION
1
41
[ "B34", "B35", "B35 B36 B37 B38 B39", "B40", "B41" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
When tested in a bicistronic reporter construct, two of these UTRs from Aquaporin4 and the uncharacterized ELG1 exhibited IRES activity, while the 5′UTR of NRF was shown previously to contain an IRES element (41).
[ "34", "35", "35–39", "40", "41" ]
213
5,564
1
false
When tested in a bicistronic reporter construct, two of these UTRs from Aquaporin4 and the uncharacterized ELG1 exhibited IRES activity, while the 5′UTR of NRF was shown previously to contain an IRES element.
[ "41" ]
When tested in a bicistronic reporter construct, two of these UTRs from Aquaporin4 and the uncharacterized ELG1 exhibited IRES activity, while the 5′UTR of NRF was shown previously to contain an IRES element.
true
true
true
true
true
930
4
INTRODUCTION
1
34
[ "B34", "B35", "B35 B36 B37 B38 B39", "B40", "B41" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
Further structural and biochemical probing showed that XIAP, AQP4 and ELG1 share only limited RNA structure similarity; however, additional biochemical analyses demonstrated that they have several IRES trans-acting factors in common.
[ "34", "35", "35–39", "40", "41" ]
233
5,565
0
false
Further structural and biochemical probing showed that XIAP, AQP4 and ELG1 share only limited RNA structure similarity; however, additional biochemical analyses demonstrated that they have several IRES trans-acting factors in common.
[]
Further structural and biochemical probing showed that XIAP, AQP4 and ELG1 share only limited RNA structure similarity; however, additional biochemical analyses demonstrated that they have several IRES trans-acting factors in common.
true
true
true
true
true
930
4
INTRODUCTION
1
34
[ "B34", "B35", "B35 B36 B37 B38 B39", "B40", "B41" ]
17,591,613
pmid-11433370|pmid-10559907|pmid-10559907|pmid-10962579|pmid-12458215|pmid-16595687|pmid-16690864|pmid-14499004|pmid-10733578|pmid-11239155|pmid-10966112|pmid-9759489
These data prompt us to propose that, unlike viral IRES elements, the cellular IRES are primarily defined not by an overall common structure but rather by common short RNA motifs and shared trans-acting factors.
[ "34", "35", "35–39", "40", "41" ]
211
5,566
0
false
These data prompt us to propose that, unlike viral IRES elements, the cellular IRES are primarily defined not by an overall common structure but rather by common short RNA motifs and shared trans-acting factors.
[]
These data prompt us to propose that, unlike viral IRES elements, the cellular IRES are primarily defined not by an overall common structure but rather by common short RNA motifs and shared trans-acting factors.
true
true
true
true
true
930
0
DISCUSSION
1
20
[ "B20", "B21", "B54" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
In this work, we empirically determined the secondary structure of the XIAP IRES and set out to identify novel cellular IRES by searching for human 5′UTR sequences that display a structural similarity to the XIAP IRES.
[ "20", "21", "54" ]
218
5,567
0
false
In this work, we empirically determined the secondary structure of the XIAP IRES and set out to identify novel cellular IRES by searching for human 5′UTR sequences that display a structural similarity to the XIAP IRES.
[]
In this work, we empirically determined the secondary structure of the XIAP IRES and set out to identify novel cellular IRES by searching for human 5′UTR sequences that display a structural similarity to the XIAP IRES.
true
true
true
true
true
931
0
DISCUSSION
1
20
[ "B20", "B21", "B54" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
We first tested the efficacy of our search protocol by using the well-characterized structure of the HCV IRES to search a database of human 5′UTRs and UTRs known to contain IRES.
[ "20", "21", "54" ]
178
5,568
0
false
We first tested the efficacy of our search protocol by using the well-characterized structure of the HCV IRES to search a database of human 5′UTRs and UTRs known to contain IRES.
[]
We first tested the efficacy of our search protocol by using the well-characterized structure of the HCV IRES to search a database of human 5′UTRs and UTRs known to contain IRES.
true
true
true
true
true
931
0
DISCUSSION
1
20
[ "B20", "B21", "B54" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
This search effectively identified IRES from GbvB, CSFV and BVDV, which have been previously shown to have structural similarity to the HCV IRES (20,21,54).
[ "20", "21", "54" ]
156
5,569
0
false
This search effectively identified IRES from GbvB, CSFV and BVDV, which have been previously shown to have structural similarity to the HCV IRES.
[ "20,21,54" ]
This search effectively identified IRES from GbvB, CSFV and BVDV, which have been previously shown to have structural similarity to the HCV IRES.
true
true
true
true
true
931
0
DISCUSSION
1
20
[ "B20", "B21", "B54" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
This exercise established that structurally similar UTRs could be found using the RSEARCH program, thus validating our approach.
[ "20", "21", "54" ]
128
5,570
0
false
This exercise established that structurally similar UTRs could be found using the RSEARCH program, thus validating our approach.
[]
This exercise established that structurally similar UTRs could be found using the RSEARCH program, thus validating our approach.
true
true
true
true
true
931
0
DISCUSSION
1
20
[ "B20", "B21", "B54" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
Our search of the human 5′UTR database using the structure of the XIAP IRES resulted in the identification of five 5′UTRs in which the region with structural similarity was in the correct position (at the 3′ end of the UTR, proximal to the AUG codon) and orientation to exhibit IRES activity.
[ "20", "21", "54" ]
292
5,571
0
false
Our search of the human 5′UTR database using the structure of the XIAP IRES resulted in the identification of five 5′UTRs in which the region with structural similarity was in the correct position (at the 3′ end of the UTR, proximal to the AUG codon) and orientation to exhibit IRES activity.
[]
Our search of the human 5′UTR database using the structure of the XIAP IRES resulted in the identification of five 5′UTRs in which the region with structural similarity was in the correct position (at the 3′ end of the UTR, proximal to the AUG codon) and orientation to exhibit IRES activity.
true
true
true
true
true
931
0
DISCUSSION
1
20
[ "B20", "B21", "B54" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
Characterization of the IRES activity of these identified sequences showed that the 5′UTRs of AQP4, ELG1 and NRF promote IRES-dependent translation.
[ "20", "21", "54" ]
148
5,572
0
false
Characterization of the IRES activity of these identified sequences showed that the 5′UTRs of AQP4, ELG1 and NRF promote IRES-dependent translation.
[]
Characterization of the IRES activity of these identified sequences showed that the 5′UTRs of AQP4, ELG1 and NRF promote IRES-dependent translation.
true
true
true
true
true
931
0
DISCUSSION
1
20
[ "B20", "B21", "B54" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
However, empirical determination of the structure of the AQP4 and ELG1 5′UTRs and subsequent comparison to the structure of the XIAP IRES revealed that the structures of these sequences share little similarity.
[ "20", "21", "54" ]
210
5,573
0
false
However, empirical determination of the structure of the AQP4 and ELG1 5′UTRs and subsequent comparison to the structure of the XIAP IRES revealed that the structures of these sequences share little similarity.
[]
However, empirical determination of the structure of the AQP4 and ELG1 5′UTRs and subsequent comparison to the structure of the XIAP IRES revealed that the structures of these sequences share little similarity.
true
true
true
true
true
931
0
DISCUSSION
1
20
[ "B20", "B21", "B54" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
We then found that a polypyrimidine tract in the XIAP IRES and AQP4 IRES is absolutely necessary for IRES activity, and that similar trans-acting factors (ITAFs) can bind to these IRES sequences.
[ "20", "21", "54" ]
195
5,574
0
false
We then found that a polypyrimidine tract in the XIAP IRES and AQP4 IRES is absolutely necessary for IRES activity, and that similar trans-acting factors (ITAFs) can bind to these IRES sequences.
[]
We then found that a polypyrimidine tract in the XIAP IRES and AQP4 IRES is absolutely necessary for IRES activity, and that similar trans-acting factors (ITAFs) can bind to these IRES sequences.
true
true
true
true
true
931
0
DISCUSSION
1
20
[ "B20", "B21", "B54" ]
17,591,613
pmid-9736694|pmid-2536835|pmid-2539491|pmid-2536836|pmid-1329037|NA|pmid-10501485
Our results lead us to propose that, unlike the viral IRES, the overall structure of cellular IRES is not necessarily an important factor in determining IRES activity, but rather small motifs and the cohort of proteins that bind them define cellular IRES activity.
[ "20", "21", "54" ]
264
5,575
0
false
Our results lead us to propose that, unlike the viral IRES, the overall structure of cellular IRES is not necessarily an important factor in determining IRES activity, but rather small motifs and the cohort of proteins that bind them define cellular IRES activity.
[]
Our results lead us to propose that, unlike the viral IRES, the overall structure of cellular IRES is not necessarily an important factor in determining IRES activity, but rather small motifs and the cohort of proteins that bind them define cellular IRES activity.
true
true
true
true
true
931
1
DISCUSSION
1
14
[ "B14", "B15", "B17", "B62" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
It has been recognized that both viral and cellular IRES do not share primary sequence homology, and therefore it is not possible to identify mRNAs that harbour IRES elements by comparison of sequence data using search programs such as BLAST.
[ "14", "15", "17", "62" ]
242
5,576
0
false
It has been recognized that both viral and cellular IRES do not share primary sequence homology, and therefore it is not possible to identify mRNAs that harbour IRES elements by comparison of sequence data using search programs such as BLAST.
[]
It has been recognized that both viral and cellular IRES do not share primary sequence homology, and therefore it is not possible to identify mRNAs that harbour IRES elements by comparison of sequence data using search programs such as BLAST.
true
true
true
true
true
932
1
DISCUSSION
1
14
[ "B14", "B15", "B17", "B62" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
This realization has presented a barrier to the genome-wide identification of IRES, resulting in the identification of mRNAs that contain IRES in a piecemeal fashion—a message is suspected to be translated under conditions that repress cap-dependent translation and the 5′UTR is subsequently tested for IRES activity.
[ "14", "15", "17", "62" ]
317
5,577
0
false
This realization has presented a barrier to the genome-wide identification of IRES, resulting in the identification of mRNAs that contain IRES in a piecemeal fashion—a message is suspected to be translated under conditions that repress cap-dependent translation and the 5′UTR is subsequently tested for IRES activity.
[]
This realization has presented a barrier to the genome-wide identification of IRES, resulting in the identification of mRNAs that contain IRES in a piecemeal fashion—a message is suspected to be translated under conditions that repress cap-dependent translation and the 5′UTR is subsequently tested for IRES activity.
true
true
true
true
true
932
1
DISCUSSION
1
62
[ "B14", "B15", "B17", "B62" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
However, several studies have highlighted the importance of secondary structure for the function of viral IRES (14,15,17) and some viral IRES share structural homology, suggesting that an underlying determinant for function of viral IRES is the presence of specific structural elements (62).
[ "14", "15", "17", "62" ]
291
5,578
1
false
However, several studies have highlighted the importance of secondary structure for the function of viral IRES and some viral IRES share structural homology, suggesting that an underlying determinant for function of viral IRES is the presence of specific structural elements.
[ "14,15,17", "62" ]
However, several studies have highlighted the importance of secondary structure for the function of viral IRES and some viral IRES share structural homology, suggesting that an underlying determinant for function of viral IRES is the presence of specific structural elements.
true
true
true
true
true
932
1
DISCUSSION
1
14
[ "B14", "B15", "B17", "B62" ]
17,591,613
pmid-11445534|pmid-8840784|pmid-12457563|pmid-11050335|pmid-15803138|pmid-15818406|pmid-15900314|pmid-15883184|pmid-15900315|pmid-10497018|pmid-11498532|pmid-10648778|pmid-1656072|pmid-8972770|pmid-7769702|pmid-1329037|NA|pmid-2548167|pmid-10497018|pmid-11498532|pmid-1656072|pmid-9926403
We therefore hypothesized that cellular IRES may also share structural homology, and that comparison of the secondary structure of 5′UTRs may be a means to identify novel IRES on a genomic scale.
[ "14", "15", "17", "62" ]
195
5,579
0
false
We therefore hypothesized that cellular IRES may also share structural homology, and that comparison of the secondary structure of 5′UTRs may be a means to identify novel IRES on a genomic scale.
[]
We therefore hypothesized that cellular IRES may also share structural homology, and that comparison of the secondary structure of 5′UTRs may be a means to identify novel IRES on a genomic scale.
true
true
true
true
true
932
2
DISCUSSION
1
35
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
Our searches of a human 5′UTR genome, supplemented with 5′UTRs known to exhibit IRES activity from all species and viruses, with the structure of the XIAP IRES did indeed result in the identification of RNA sequences that exhibit IRES activity.
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
244
5,580
0
false
Our searches of a human 5′UTR genome, supplemented with 5′UTRs known to exhibit IRES activity from all species and viruses, with the structure of the XIAP IRES did indeed result in the identification of RNA sequences that exhibit IRES activity.
[]
Our searches of a human 5′UTR genome, supplemented with 5′UTRs known to exhibit IRES activity from all species and viruses, with the structure of the XIAP IRES did indeed result in the identification of RNA sequences that exhibit IRES activity.
true
true
true
true
true
933
2
DISCUSSION
1
35
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
Of the top matches, two were the 5′UTRs of the mouse XIAP ortholog (MIAP) and the rat XIAP ortholog (RIAP) that both display IRES activity (35) (Holcik,M., unpublished data), one that has previously been shown to have IRES activity [NRF;(41)], and we have demonstrated that two others (ELG1 and AQP4) also display IRES f...
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
328
5,581
1
false
Of the top matches, two were the 5′UTRs of the mouse XIAP ortholog (MIAP) and the rat XIAP ortholog (RIAP) that both display IRES activity (Holcik,M., unpublished data), one that has previously been shown to have IRES activity, and we have demonstrated that two others (ELG1 and AQP4) also display IRES function.
[ "35", "NRF;(41)" ]
Of the top matches, two were the 5′UTRs of the mouse XIAP ortholog (MIAP) and the rat XIAP ortholog (RIAP) that both display IRES activity (Holcik,M., unpublished data), one that has previously been shown to have IRES activity, and we have demonstrated that two others (ELG1 and AQP4) also display IRES function.
true
true
true
true
true
933
2
DISCUSSION
1
35
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
The IRES activity of AQP4 and ELG1 are much less than XIAP.
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
59
5,582
0
false
The IRES activity of AQP4 and ELG1 are much less than XIAP.
[]
The IRES activity of AQP4 and ELG1 are much less than XIAP.
true
true
true
true
true
933
2
DISCUSSION
1
35
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
However, we have only tested IRES activity in one cell line and under conditions of normal cell growth.
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
103
5,583
0
false
However, we have only tested IRES activity in one cell line and under conditions of normal cell growth.
[]
However, we have only tested IRES activity in one cell line and under conditions of normal cell growth.
true
true
true
true
true
933
2
DISCUSSION
1
63
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
AQP4, a water channel-forming protein expressed in the brain, has recently been shown to have a role in edema during eclampsia, as its protein levels are elevated during pregnancy (63).
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
185
5,584
1
false
AQP4, a water channel-forming protein expressed in the brain, has recently been shown to have a role in edema during eclampsia, as its protein levels are elevated during pregnancy.
[ "63" ]
AQP4, a water channel-forming protein expressed in the brain, has recently been shown to have a role in edema during eclampsia, as its protein levels are elevated during pregnancy.
true
true
true
true
true
933
2
DISCUSSION
1
63
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
Interestingly, mRNA levels of AQP4 have not been shown to change (63), suggesting a possible IRES function.
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
107
5,585
1
false
Interestingly, mRNA levels of AQP4 have not been shown to change, suggesting a possible IRES function.
[ "63" ]
Interestingly, mRNA levels of AQP4 have not been shown to change, suggesting a possible IRES function.
true
true
true
true
true
933
2
DISCUSSION
1
35
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
ELG1 is an uncharacterized transcript that exists in the database as a fully sequenced cDNA clone, accession # AK125048 and a portion of the UTR is represented by EST DB217710.1.
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
178
5,586
0
false
ELG1 is an uncharacterized transcript that exists in the database as a fully sequenced cDNA clone, accession # AK125048 and a portion of the UTR is represented by EST DB217710.1.
[]
ELG1 is an uncharacterized transcript that exists in the database as a fully sequenced cDNA clone, accession # AK125048 and a portion of the UTR is represented by EST DB217710.1.
true
true
true
true
true
933
2
DISCUSSION
1
33
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
While the presence of numerous AUGs in its 5′UTRs is unusual, it is nevertheless not completely uncommon as around 1% of all 5′UTRs have 30 to 100 upstream AUGs (33).
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
166
5,587
1
false
While the presence of numerous AUGs in its 5′UTRs is unusual, it is nevertheless not completely uncommon as around 1% of all 5′UTRs have 30 to 100 upstream AUGs.
[ "33" ]
While the presence of numerous AUGs in its 5′UTRs is unusual, it is nevertheless not completely uncommon as around 1% of all 5′UTRs have 30 to 100 upstream AUGs.
true
true
true
true
true
933
2
DISCUSSION
1
64
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
Interestingly, we did not identify the 5′UTRs of p27(Kip1) (64) or Bcl-xL, both of which exhibit IRES activity (39), in our search (matching scores were between 16 and 17).
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
172
5,588
1
false
Interestingly, we did not identify the 5′UTRs of p27(Kip1) or Bcl-xL, both of which exhibit IRES activity, in our search (matching scores were between 16 and 17).
[ "64", "39" ]
Interestingly, we did not identify the 5′UTRs of p27(Kip1) or Bcl-xL, both of which exhibit IRES activity, in our search.
true
true
true
true
true
933
2
DISCUSSION
1
35
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
Yoon et al.
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
11
5,589
0
false
Yoon et al.
[]
Yoon et al.
true
true
true
true
true
933
2
DISCUSSION
1
39
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
(39) recently showed that the IRES activity of XIAP, p27(Kip1) and Bcl-xL is specifically and severely impaired in cells harbouring mutations in the pseudouridinase gene Dkc1.
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
175
5,590
1
false
recently showed that the IRES activity of XIAP, p27(Kip1) and Bcl-xL is specifically and severely impaired in cells harbouring mutations in the pseudouridinase gene Dkc1.
[ "39" ]
recently showed that the IRES activity of XIAP, p27(Kip1) and Bcl-xL is specifically and severely impaired in cells harbouring mutations in the pseudouridinase gene Dkc1.
false
true
true
true
false
933
2
DISCUSSION
1
39
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
This mutation was shown to prevent the proper pseudouridylation of rRNA and is thought to disrupt ribosome structure (39).
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
122
5,591
1
false
This mutation was shown to prevent the proper pseudouridylation of rRNA and is thought to disrupt ribosome structure.
[ "39" ]
This mutation was shown to prevent the proper pseudouridylation of rRNA and is thought to disrupt ribosome structure.
true
true
true
true
true
933
2
DISCUSSION
1
35
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
The IRES-dependent translation of the XIAP, p27(Kip1) and Bcl-xL messages is specifically sensitive to these changes, as global translation is not affected.
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
156
5,592
0
false
The IRES-dependent translation of the XIAP, p27(Kip1) and Bcl-xL messages is specifically sensitive to these changes, as global translation is not affected.
[]
The IRES-dependent translation of the XIAP, p27(Kip1) and Bcl-xL messages is specifically sensitive to these changes, as global translation is not affected.
true
true
true
true
true
933
2
DISCUSSION
1
39
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
It was therefore hypothesized that these IRES may share some common feature, such as secondary structure, that is sensitive to changes in ribosome architecture (39).
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
165
5,593
1
false
It was therefore hypothesized that these IRES may share some common feature, such as secondary structure, that is sensitive to changes in ribosome architecture.
[ "39" ]
It was therefore hypothesized that these IRES may share some common feature, such as secondary structure, that is sensitive to changes in ribosome architecture.
true
true
true
true
true
933
2
DISCUSSION
1
35
[ "B35", "B41", "B63", "B63", "B33", "B64", "B39", "B39", "B39", "B39" ]
17,591,613
pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-10559907|pmid-10733578|pmid-15677340|pmid-15677340|pmid-16957278|pmid-11438653|pmid-16690864|pmid-16690864|pmid-16690864|pmid-16690864
Based on our results, the secondary structures of these IRES elements may not be similar, and other factors, such as changes in the association of trans-acting factors with the modified ribosome or direct association of the IRES with the ribosome, may account for the coordinated reduction of XIAP, p27(Kip1) and Bcl-xL ...
[ "35", "41", "63", "63", "33", "64", "39", "39", "39", "39" ]
355
5,594
0
false
Based on our results, the secondary structures of these IRES elements may not be similar, and other factors, such as changes in the association of trans-acting factors with the modified ribosome or direct association of the IRES with the ribosome, may account for the coordinated reduction of XIAP, p27(Kip1) and Bcl-xL ...
[]
Based on our results, the secondary structures of these IRES elements may not be similar, and other factors, such as changes in the association of trans-acting factors with the modified ribosome or direct association of the IRES with the ribosome, may account for the coordinated reduction of XIAP, p27(Kip1) and Bcl-xL ...
true
true
true
true
true
933
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
To our surprise, comparison of the empirically determined secondary structures of the ELG1 and AQP4 5′UTRs to the secondary structure of the XIAP IRES showed only limited homology, with only small regions of AQP4 displaying some similarity within the overall structure.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
269
5,595
0
false
To our surprise, comparison of the empirically determined secondary structures of the ELG1 and AQP4 5′UTRs to the secondary structure of the XIAP IRES showed only limited homology, with only small regions of AQP4 displaying some similarity within the overall structure.
[]
To our surprise, comparison of the empirically determined secondary structures of the ELG1 and AQP4 5′UTRs to the secondary structure of the XIAP IRES showed only limited homology, with only small regions of AQP4 displaying some similarity within the overall structure.
true
true
true
true
true
934
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
From the search of HCV IRES structure we learned that the score of CSFV, which is just over 13% of a perfect match, was significant.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
132
5,596
0
false
From the search of HCV IRES structure we learned that the score of CSFV, which is just over 13% of a perfect match, was significant.
[]
From the search of HCV IRES structure we learned that the score of CSFV, which is just over 13% of a perfect match, was significant.
true
true
true
true
true
934
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
Our search for a similar IRES structure with a cut-off score of 35 had us examining matches with scores in the range of 11–14% of a perfect match.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
146
5,597
0
false
Our search for a similar IRES structure with a cut-off score of 35 had us examining matches with scores in the range of 11–14% of a perfect match.
[]
Our search for a similar IRES structure with a cut-off score of 35 had us examining matches with scores in the range of 11–14% of a perfect match.
true
true
true
true
true
934
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
In retrospect, these values may have been too low to be significant, but represent the top matches available.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
109
5,598
0
false
In retrospect, these values may have been too low to be significant, but represent the top matches available.
[]
In retrospect, these values may have been too low to be significant, but represent the top matches available.
true
true
true
true
true
934
3
DISCUSSION
1
23–32
[ "B23 B24 B25 B26 B27 B28 B29 B30 B31 B32", "B65", "B29", "B28", "B66", "B67", "B68", "B31" ]
17,591,613
pmid-16957278|pmid-11419940|pmid-14730027|pmid-12667457|pmid-12857733|pmid-15314170|pmid-15339906|pmid-15169918|pmid-11903044|pmid-12757712|pmid-15998809|pmid-14712232|pmid-15169918|pmid-15339906|pmid-10677496|pmid-2536978|pmid-15452230|pmid-12757712
As the search with the HCV structure validated this search protocol, the lack of results with the XIAP IRES structure search strongly supports the notion that there are no similar structures.
[ "23–32", "65", "29", "28", "66", "67", "68", "31" ]
191
5,599
0
false
As the search with the HCV structure validated this search protocol, the lack of results with the XIAP IRES structure search strongly supports the notion that there are no similar structures.
[]
As the search with the HCV structure validated this search protocol, the lack of results with the XIAP IRES structure search strongly supports the notion that there are no similar structures.
true
true
true
true
true
934