Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
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6
DISCUSSION
1
29
[ "B29", "B30", "B30" ]
17,567,602
pmid-12783536|pmid-14758353|pmid-14758353
A similar discussion could be extended to a DNA enzyme 7S11 that ligates RNA sequences through 2′–5′ phosphodiester linkage.
[ "29", "30", "30" ]
124
4,500
0
false
A similar discussion could be extended to a DNA enzyme 7S11 that ligates RNA sequences through 2′–5′ phosphodiester linkage.
[]
A similar discussion could be extended to a DNA enzyme 7S11 that ligates RNA sequences through 2′–5′ phosphodiester linkage.
true
true
true
true
true
762
6
DISCUSSION
1
29
[ "B29", "B30", "B30" ]
17,567,602
pmid-12783536|pmid-14758353|pmid-14758353
Unlike the ligase ribozymes discussed earlier, this DNA enzyme produces a branched or lariat RNA (29,30) using an internal unpaired nucleotide as a branch-site.
[ "29", "30", "30" ]
160
4,501
0
false
Unlike the ligase ribozymes discussed earlier, this DNA enzyme produces a branched or lariat RNA using an internal unpaired nucleotide as a branch-site.
[ "29,30" ]
Unlike the ligase ribozymes discussed earlier, this DNA enzyme produces a branched or lariat RNA using an internal unpaired nucleotide as a branch-site.
true
true
true
true
true
762
6
DISCUSSION
1
29
[ "B29", "B30", "B30" ]
17,567,602
pmid-12783536|pmid-14758353|pmid-14758353
Though 7S11 is a DNA enzyme that reacts with a RNA substrate, it shares a similarity in structure to M4 where the electrophilic 5′-ppp-end of substrate is needed to be unpaired (Figure 6F).
[ "29", "30", "30" ]
189
4,502
0
false
Though 7S11 is a DNA enzyme that reacts with a RNA substrate, it shares a similarity in structure to M4 where the electrophilic 5′-ppp-end of substrate is needed to be unpaired (Figure 6F).
[]
Though 7S11 is a DNA enzyme that reacts with a RNA substrate, it shares a similarity in structure to M4 where the electrophilic 5′-ppp-end of substrate is needed to be unpaired (Figure 6F).
true
true
true
true
true
762
6
DISCUSSION
1
30
[ "B29", "B30", "B30" ]
17,567,602
pmid-12783536|pmid-14758353|pmid-14758353
Moreover, it was shown that the branch-site nucleotide should be a purine nucleotide with 2′-hydroxyl even though adenosine was preferred to guanosine kinetically (30), which makes this reaction analogous to the M4-catalyzed purine nucleotidyl transfer.
[ "29", "30", "30" ]
253
4,503
1
false
Moreover, it was shown that the branch-site nucleotide should be a purine nucleotide with 2′-hydroxyl even though adenosine was preferred to guanosine kinetically, which makes this reaction analogous to the M4-catalyzed purine nucleotidyl transfer.
[ "30" ]
Moreover, it was shown that the branch-site nucleotide should be a purine nucleotide with 2′-hydroxyl even though adenosine was preferred to guanosine kinetically, which makes this reaction analogous to the M4-catalyzed purine nucleotidyl transfer.
true
true
true
true
true
762
7
DISCUSSION
0
null
null
17,567,602
null
The trans-acting activity of rM4 and the feasibility of designing the substrate strand guide sequence can lead us to the development of a new tool for the 5′-end modification using purine nucleotides.
null
200
4,504
0
false
null
null
The trans-acting activity of rM4 and the feasibility of designing the substrate strand guide sequence can lead us to the development of a new tool for the 5′-end modification using purine nucleotides.
true
true
true
true
true
763
7
DISCUSSION
0
null
null
17,567,602
null
Particularly, the unnatural 2′–5′ phosphodiester linkage at the 5′-end makes the oligonucleotide resistant toward 5′-exonucleases.
null
130
4,505
0
false
null
null
Particularly, the unnatural 2′–5′ phosphodiester linkage at the 5′-end makes the oligonucleotide resistant toward 5′-exonucleases.
true
true
true
true
true
763
7
DISCUSSION
0
null
null
17,567,602
null
Unfortunately, the current system is not yet sustainable for such applications due to the poor activity (using GMP-αS as a substrate, kcat and KM were 0.070 h−1 and 34 mM, respectively).
null
186
4,506
0
false
null
null
Unfortunately, the current system is not yet sustainable for such applications due to the poor activity (using GMP-αS as a substrate, kcat and KM were 0.070 h−1 and 34 mM, respectively).
true
true
true
true
true
763
7
DISCUSSION
0
null
null
17,567,602
null
However, re-evolution of M4 ribozyme with appendix domains would potentially produce M4 variants with higher activities, so that a new tool for the 5′-nucleotide modification of RNA can be devised.
null
197
4,507
0
false
null
null
However, re-evolution of M4 ribozyme with appendix domains would potentially produce M4 variants with higher activities, so that a new tool for the 5′-nucleotide modification of RNA can be devised.
true
true
true
true
true
763
0
INTRODUCTION
1
3
[ "b1", "b2", "b3", "b4", "b5", "b6", "b9" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
Mutations that affect pre-mRNA splicing have been shown to account for up to a half of disease-causing gene alterations (1,2), potentially representing the most frequent cause of hereditary disorders (3).
[ "1", "2", "3", "4", "5", "6", "9" ]
204
4,508
1
false
Mutations that affect pre-mRNA splicing have been shown to account for up to a half of disease-causing gene alterations, potentially representing the most frequent cause of hereditary disorders.
[ "1,2", "3" ]
Mutations that affect pre-mRNA splicing have been shown to account for up to a half of disease-causing gene alterations, potentially representing the most frequent cause of hereditary disorders.
true
true
true
true
true
764
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b9" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
The most common consequence of splicing mutations is skipping of one or more exons, followed by the activation of aberrant 5′ (donor) splice sites (5′ss), 3′ (acceptor) splice sites (3′ss) and retention of full introns in mRNA (4,5).
[ "1", "2", "3", "4", "5", "6", "9" ]
233
4,509
0
false
The most common consequence of splicing mutations is skipping of one or more exons, followed by the activation of aberrant 5′ (donor) splice sites, 3′ (acceptor) splice sites and retention of full introns in mRNA.
[ "5′ss", "3′ss", "4,5" ]
The most common consequence of splicing mutations is skipping of one or more exons, followed by the activation of aberrant 5′ (donor) splice sites, 3′ (acceptor) splice sites and retention of full introns in mRNA.
true
true
true
true
true
764
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b9" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
Each of these four events may have a dramatic impact on the structure or outcome of mature transcripts, function of their translation products and phenotypic manifestations.
[ "1", "2", "3", "4", "5", "6", "9" ]
173
4,510
0
false
Each of these four events may have a dramatic impact on the structure or outcome of mature transcripts, function of their translation products and phenotypic manifestations.
[]
Each of these four events may have a dramatic impact on the structure or outcome of mature transcripts, function of their translation products and phenotypic manifestations.
true
true
true
true
true
764
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b4", "b5", "b6", "b9" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
However, gene mutations or variants can also have more subtle effects at the level of splicing by altering the expression of pre-existing alternatively spliced mRNA isoforms, which can considerably modify not only phenotypic severity of both Mendelian and complex traits, but also their population prevalence (6–9).
[ "1", "2", "3", "4", "5", "6", "9" ]
315
4,511
0
false
However, gene mutations or variants can also have more subtle effects at the level of splicing by altering the expression of pre-existing alternatively spliced mRNA isoforms, which can considerably modify not only phenotypic severity of both Mendelian and complex traits, but also their population prevalence.
[ "6–9" ]
However, gene mutations or variants can also have more subtle effects at the level of splicing by altering the expression of pre-existing alternatively spliced mRNA isoforms, which can considerably modify not only phenotypic severity of both Mendelian and complex traits, but also their population prevalence.
true
true
true
true
true
764
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b17", "b18", "b19" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
Mutation-induced aberrant splice sites have been classified into two categories (10): (i) cryptic splice sites, which are only used when a mutation disrupts use of the authentic site, and (ii) de novo splice sites, which are induced by mutations elsewhere in introns or exons and increase the match to a splice site cons...
[ "10", "11", "12", "17", "18", "19" ]
326
4,512
1
false
Mutation-induced aberrant splice sites have been classified into two categories : (i) cryptic splice sites, which are only used when a mutation disrupts use of the authentic site, and (ii) de novo splice sites, which are induced by mutations elsewhere in introns or exons and increase the match to a splice site consensu...
[ "10" ]
Mutation-induced aberrant splice sites have been classified into two categories : (i) cryptic splice sites, which are only used when a mutation disrupts use of the authentic site, and (ii) de novo splice sites, which are induced by mutations elsewhere in introns or exons and increase the match to a splice site consensu...
true
true
true
true
true
765
1
INTRODUCTION
1
11
[ "b10", "b11", "b12", "b17", "b18", "b19" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
However, distinction between the two categories may be ambiguous in some cases since disruption of the authentic site may create a new splice site consensus, and is less obvious for 3′ss than 5′ss because accurate recognition of acceptor sites requires additional signal sequences in introns (11).
[ "10", "11", "12", "17", "18", "19" ]
297
4,513
1
false
However, distinction between the two categories may be ambiguous in some cases since disruption of the authentic site may create a new splice site consensus, and is less obvious for 3′ss than 5′ss because accurate recognition of acceptor sites requires additional signal sequences in introns.
[ "11" ]
However, distinction between the two categories may be ambiguous in some cases since disruption of the authentic site may create a new splice site consensus, and is less obvious for 3′ss than 5′ss because accurate recognition of acceptor sites requires additional signal sequences in introns.
true
true
true
true
true
765
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b17", "b18", "b19" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
The splicing signals of acceptor sites, namely the branch point sequence (BPS), polypyrimidine tract (PPT), and 3′AG, are recognized by RNA–protein interactions involving splicing factor 1 (SF1) and 65 and 35 kDa subunits of the U2 small nuclear RNP auxiliary factor (U2AF65 and U2AF35), respectively (12–17).
[ "10", "11", "12", "17", "18", "19" ]
309
4,514
0
false
The splicing signals of acceptor sites, namely the branch point sequence (BPS), polypyrimidine tract (PPT), and 3′AG, are recognized by RNA–protein interactions involving splicing factor 1 (SF1) and 65 and 35 kDa subunits of the U2 small nuclear RNP auxiliary factor (U2AF65 and U2AF35), respectively.
[ "12–17" ]
The splicing signals of acceptor sites, namely the branch point sequence (BPS), polypyrimidine tract (PPT), and 3′AG, are recognized by RNA–protein interactions involving splicing factor 1 and 65 and 35 kDa subunits of the U2 small nuclear RNP auxiliary factor (U2AF65 and U2AF35), respectively.
true
true
true
true
true
765
1
INTRODUCTION
1
10
[ "b10", "b11", "b12", "b17", "b18", "b19" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
The overall strength of 3′ss is defined by optimal sequences for interaction with each cognate factor as well as their distances from each other (18,19).
[ "10", "11", "12", "17", "18", "19" ]
153
4,515
0
false
The overall strength of 3′ss is defined by optimal sequences for interaction with each cognate factor as well as their distances from each other.
[ "18,19" ]
The overall strength of 3′ss is defined by optimal sequences for interaction with each cognate factor as well as their distances from each other.
true
true
true
true
true
765
2
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b18", "b21", "b22" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
Cryptic 5′ss have a similar frequency distribution in exons and introns and their number decreases with an increasing distance from authentic 5′ss (10).
[ "10", "11", "11", "18", "21", "22" ]
152
4,516
1
false
Cryptic 5′ss have a similar frequency distribution in exons and introns and their number decreases with an increasing distance from authentic 5′ss.
[ "10" ]
Cryptic 5′ss have a similar frequency distribution in exons and introns and their number decreases with an increasing distance from authentic 5′ss.
true
true
true
true
true
766
2
INTRODUCTION
1
11
[ "b10", "b11", "b11", "b18", "b21", "b22" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
In contrast, the localization of cryptic 3′ss is biased towards exons, whereas de novo 3′ss usually reside in introns, particularly within the PPT of authentic 3′ss (11).
[ "10", "11", "11", "18", "21", "22" ]
170
4,517
1
false
In contrast, the localization of cryptic 3′ss is biased towards exons, whereas de novo 3′ss usually reside in introns, particularly within the PPT of authentic 3′ss.
[ "11" ]
In contrast, the localization of cryptic 3′ss is biased towards exons, whereas de novo 3′ss usually reside in introns, particularly within the PPT of authentic 3′ss.
true
true
true
true
true
766
2
INTRODUCTION
1
11
[ "b10", "b11", "b11", "b18", "b21", "b22" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
The distribution bias and a lower prevalence of aberrant 3′ss than 5′ss in vivo is most likely due to sequence constraints near intron/exon boundaries, including depletion of AG dinucleotides and the presence of PPT and BPS upstream of 3′ss (11).
[ "10", "11", "11", "18", "21", "22" ]
246
4,518
1
false
The distribution bias and a lower prevalence of aberrant 3′ss than 5′ss in vivo is most likely due to sequence constraints near intron/exon boundaries, including depletion of AG dinucleotides and the presence of PPT and BPS upstream of 3′ss.
[ "11" ]
The distribution bias and a lower prevalence of aberrant 3′ss than 5′ss in vivo is most likely due to sequence constraints near intron/exon boundaries, including depletion of AG dinucleotides and the presence of PPT and BPS upstream of 3′ss.
true
true
true
true
true
766
2
INTRODUCTION
1
22
[ "b10", "b11", "b11", "b18", "b21", "b22" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
In addition, the multifaceted distribution of aberrant 3′ss would be predicted to reflect variable distances between the 3′ss signal sequence from intron to intron (18–21), including the presence of putative ‘distant BPS’ that are not located within an optimal distance of 18–40 nt 5′ of 3′ss, but may reside up to sever...
[ "10", "11", "11", "18", "21", "22" ]
365
4,519
1
false
In addition, the multifaceted distribution of aberrant 3′ss would be predicted to reflect variable distances between the 3′ss signal sequence from intron to intron, including the presence of putative ‘distant BPS’ that are not located within an optimal distance of 18–40 nt 5′ of 3′ss, but may reside up to several hundr...
[ "18–21", "22" ]
In addition, the multifaceted distribution of aberrant 3′ss would be predicted to reflect variable distances between the 3′ss signal sequence from intron to intron, including the presence of putative ‘distant BPS’ that are not located within an optimal distance of 18–40 nt 5′ of 3′ss, but may reside up to several hundr...
true
true
true
true
true
766
2
INTRODUCTION
1
10
[ "b10", "b11", "b11", "b18", "b21", "b22" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
Despite a growing number of reported splicing mutations and associated phenotypes, the localization of the resulting aberrant 3′ss and their effect on gene expression remain difficult to predict.
[ "10", "11", "11", "18", "21", "22" ]
195
4,520
0
false
Despite a growing number of reported splicing mutations and associated phenotypes, the localization of the resulting aberrant 3′ss and their effect on gene expression remain difficult to predict.
[]
Despite a growing number of reported splicing mutations and associated phenotypes, the localization of the resulting aberrant 3′ss and their effect on gene expression remain difficult to predict.
true
true
true
true
true
766
3
INTRODUCTION
1
25
[ "b23", "b24", "b25", "b26", "b27", "b28", "b29" ]
16,963,498
pmid-3658675|pmid-2314278|pmid-2067018|pmid-9278062|pmid-9711873|pmid-15285897|pmid-10637326|pmid-15285897|pmid-2067018|pmid-8811101|pmid-16226402
Currently available computational tools that estimate the splice site strength have been based on a variety of methods, including nucleotide frequency matrices (23,24), machine learning approaches (25), neural networks (26), information theory (27) and interdependence between adjacent (the first-order Markov model) or ...
[ "23", "24", "25", "26", "27", "28", "29" ]
412
4,521
1
false
Currently available computational tools that estimate the splice site strength have been based on a variety of methods, including nucleotide frequency matrices, machine learning approaches, neural networks, information theory and interdependence between adjacent (the first-order Markov model) or more distant (the maxim...
[ "23,24", "25", "26", "27", "28" ]
Currently available computational tools that estimate the splice site strength have been based on a variety of methods, including nucleotide frequency matrices, machine learning approaches, neural networks, information theory and interdependence between adjacent (the first-order Markov model) or more distant (the maxim...
true
true
true
true
true
767
3
INTRODUCTION
1
29
[ "b23", "b24", "b25", "b26", "b27", "b28", "b29" ]
16,963,498
pmid-3658675|pmid-2314278|pmid-2067018|pmid-9278062|pmid-9711873|pmid-15285897|pmid-10637326|pmid-15285897|pmid-2067018|pmid-8811101|pmid-16226402
Gene prediction algorithms that take into account protein coding information have been shown to perform better than those that rely only on signals present in the splice sites (29).
[ "23", "24", "25", "26", "27", "28", "29" ]
181
4,522
1
false
Gene prediction algorithms that take into account protein coding information have been shown to perform better than those that rely only on signals present in the splice sites.
[ "29" ]
Gene prediction algorithms that take into account protein coding information have been shown to perform better than those that rely only on signals present in the splice sites.
true
true
true
true
true
767
3
INTRODUCTION
1
23
[ "b23", "b24", "b25", "b26", "b27", "b28", "b29" ]
16,963,498
pmid-3658675|pmid-2314278|pmid-2067018|pmid-9278062|pmid-9711873|pmid-15285897|pmid-10637326|pmid-15285897|pmid-2067018|pmid-8811101|pmid-16226402
However, the strength of mutation-induced aberrant splice acceptor sites has not been systematically analyzed, and it is unknown at present which models best predict the localization of cryptic or de novo 3′ss activated in vivo.
[ "23", "24", "25", "26", "27", "28", "29" ]
228
4,523
0
false
However, the strength of mutation-induced aberrant splice acceptor sites has not been systematically analyzed, and it is unknown at present which models best predict the localization of cryptic or de novo 3′ss activated in vivo.
[]
However, the strength of mutation-induced aberrant splice acceptor sites has not been systematically analyzed, and it is unknown at present which models best predict the localization of cryptic or de novo 3′ss activated in vivo.
true
true
true
true
true
767
4
INTRODUCTION
0
null
null
16,963,498
NA
Here, nucleotide sequences of aberrant 3′ss that were reported previously in human disease genes have been compiled and made available to the public through an online retrieval tool.
null
182
4,524
0
false
null
null
Here, nucleotide sequences of aberrant 3′ss that were reported previously in human disease genes have been compiled and made available to the public through an online retrieval tool.
true
true
true
true
true
768
4
INTRODUCTION
0
null
null
16,963,498
NA
Comparison of the splice site strength using current prediction algorithms showed that the maximum entropy model allowed the best discrimination between authentic and mutation-induced aberrant 3′ss, validating this model as the most sensitive instrument.
null
254
4,525
0
false
null
null
Comparison of the splice site strength using current prediction algorithms showed that the maximum entropy model allowed the best discrimination between authentic and mutation-induced aberrant 3′ss, validating this model as the most sensitive instrument.
true
true
true
true
true
768
4
INTRODUCTION
0
null
null
16,963,498
NA
In addition, this study provides a detailed characterization of the underlying mutation pattern and comparison of nucleotide composition upstream of aberrant and corresponding authentic 3′ss.
null
191
4,526
0
false
null
null
In addition, this study provides a detailed characterization of the underlying mutation pattern and comparison of nucleotide composition upstream of aberrant and corresponding authentic 3′ss.
true
true
true
true
true
768
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
This study is the first to provide a detailed survey of mutations leading to aberrant 3′ss.
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
91
4,527
0
false
This study is the first to provide a detailed survey of mutations leading to aberrant 3′ss.
[]
This study is the first to provide a detailed survey of mutations leading to aberrant 3′ss.
true
true
true
true
true
769
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
It showed that the distribution of single-nucleotide substitutions roughly reflected the degree of conservation of consensus sequences that define 3′ss (Figure 1) and revealed a high proportion of mutations creating the 3′AG consensus (Table 1).
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
245
4,528
0
false
It showed that the distribution of single-nucleotide substitutions roughly reflected the degree of conservation of consensus sequences that define 3′ss (Figure 1) and revealed a high proportion of mutations creating the 3′AG consensus (Table 1).
[]
It showed that the distribution of single-nucleotide substitutions roughly reflected the degree of conservation of consensus sequences that define 3′ss (Figure 1) and revealed a high proportion of mutations creating the 3′AG consensus (Table 1).
true
true
true
true
true
769
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
The observed frequency of AG-creating mutations (42%) was considerably higher than the estimated ∼13% in the initial analysis of splicing mutations (47).
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
153
4,529
1
false
The observed frequency of AG-creating mutations (42%) was considerably higher than the estimated ∼13% in the initial analysis of splicing mutations.
[ "47" ]
The observed frequency of AG-creating mutations was considerably higher than the estimated ∼13% in the initial analysis of splicing mutations.
true
true
true
true
true
769
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
Only ∼5% (n = 11, Table 2) of these mutations failed to activate de novo 3′ss in situ and instead induced one or more aberrant 3′ss upstream (36,70,93–96) or downstream (62,97,98) of the newly introduced AGs.
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
208
4,530
0
false
Only ∼5% of these mutations failed to activate de novo 3′ss in situ and instead induced one or more aberrant 3′ss upstream or downstream of the newly introduced AGs.
[ "n = 11, Table 2", "36,70,93–96", "62,97,98" ]
Only ∼5% of these mutations failed to activate de novo 3′ss in situ and instead induced one or more aberrant 3′ss upstream or downstream of the newly introduced AGs.
true
true
true
true
true
769
0
DISCUSSION
1
70
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
These mutations were in position −3 (36,93), −9 (62,98), −10 (96), −14 (70), −15 (97), −17 (95) and −24 (94) relative to authentic 3′ss (Supplementary Table 1).
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
160
4,531
1
false
These mutations were in position −3, −9, −10, −14, −15, −17 and −24 relative to authentic 3′ss (Supplementary Table 1).
[ "36,93", "62,98", "96", "70", "97", "95", "94" ]
These mutations were in position −3, −9, −10, −14, −15, −17 and −24 relative to authentic 3′ss (Supplementary Table 1).
true
true
true
true
true
769
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
Mutations in positions −3 and −24 directly inactivated 3′YAG and BPS, respectively, but the remaining AG-creating mutations were all in ‘AG-exclusion zones’ downstream of the BPS.
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
179
4,532
0
false
Mutations in positions −3 and −24 directly inactivated 3′YAG and BPS, respectively, but the remaining AG-creating mutations were all in ‘AG-exclusion zones’ downstream of the BPS.
[]
Mutations in positions −3 and −24 directly inactivated 3′YAG and BPS, respectively, but the remaining AG-creating mutations were all in ‘AG-exclusion zones’ downstream of the BPS.
true
true
true
true
true
769
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
The distance between predicted BP adenosine and new 3′AG/ was 9–20 nt (Supplementary Table 1).
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
94
4,533
0
false
The distance between predicted BP adenosine and new 3′AG/ was 9–20 nt (Supplementary Table 1).
[]
The distance between predicted BP adenosine and new 3′AG/ was 9–20 nt (Supplementary Table 1).
true
true
true
true
true
769
0
DISCUSSION
1
99
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
Aberrant 3′ss with the ‘BP-new AG’ distances between 9 and 16 nt were either in exons or upstream of the BPS, and new AGs were never selected as 3′ss, consistent with protein complexes bound to ∼19 nt region downstream of BP (99).
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
230
4,534
1
false
Aberrant 3′ss with the ‘BP-new AG’ distances between 9 and 16 nt were either in exons or upstream of the BPS, and new AGs were never selected as 3′ss, consistent with protein complexes bound to ∼19 nt region downstream of BP.
[ "99" ]
Aberrant 3′ss with the ‘BP-new AG’ distances between 9 and 16 nt were either in exons or upstream of the BPS, and new AGs were never selected as 3′ss, consistent with protein complexes bound to ∼19 nt region downstream of BP.
true
true
true
true
true
769
0
DISCUSSION
1
70
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
In the FALDH gene (70), this distance was 20 nt and normally silent AG located 9 nt downstream of the BPS was activated by the newly created AG further 11 nt downstream.
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
169
4,535
1
false
In the FALDH gene, this distance was 20 nt and normally silent AG located 9 nt downstream of the BPS was activated by the newly created AG further 11 nt downstream.
[ "70" ]
In the FALDH gene, this distance was 20 nt and normally silent AG located 9 nt downstream of the BPS was activated by the newly created AG further 11 nt downstream.
true
true
true
true
true
769
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
However, this putative exception can be explained by inefficient recognition of new 3′AG, which was preceded by G, unlike the remaining aberrant 3′ss (Supplementary Table 1).
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
174
4,536
0
false
However, this putative exception can be explained by inefficient recognition of new 3′AG, which was preceded by G, unlike the remaining aberrant 3′ss (Supplementary Table 1).
[]
However, this putative exception can be explained by inefficient recognition of new 3′AG, which was preceded by G, unlike the remaining aberrant 3′ss (Supplementary Table 1).
true
true
true
true
true
769
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
Alternatively, selection of aberrant 3′ss in this FALDH intron can be explained by almost identical BPS sequences arranged in tandem, with the upstream BP in the optimal distance (18 nt) from aberrant 3′ss.
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
206
4,537
0
false
Alternatively, selection of aberrant 3′ss in this FALDH intron can be explained by almost identical BPS sequences arranged in tandem, with the upstream BP in the optimal distance (18 nt) from aberrant 3′ss.
[]
Alternatively, selection of aberrant 3′ss in this FALDH intron can be explained by almost identical BPS sequences arranged in tandem, with the upstream BP in the optimal distance (18 nt) from aberrant 3′ss.
true
true
true
true
true
769
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
In contrast, wild-type AGs 6 and 7 nt downstream of the predicted BP were not selected (36,98).
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
95
4,538
0
false
In contrast, wild-type AGs 6 and 7 nt downstream of the predicted BP were not selected.
[ "36,98" ]
In contrast, wild-type AGs 6 and 7 nt downstream of the predicted BP were not selected.
true
true
true
true
true
769
0
DISCUSSION
1
47
[ "b47", "b36", "b70", "b93", "b96", "b62", "b97", "b98", "b36", "b93", "b62", "b98", "b96", "b70", "b97", "b95", "b94", "b99", "b70", "b36", "b98", "b11", "b19", "b21", "b99" ]
16,963,498
pmid-10330348|pmid-10607834|pmid-15792793|pmid-1427786|pmid-8163185|pmid-9311728|pmid-16380501|NA|pmid-9326325|pmid-10577908|pmid-10190324|pmid-16075202|NA|pmid-11068191|pmid-7716548|pmid-9326325|pmid-10190324|NA|pmid-7716548|pmid-16075202|pmid-10577908|pmid-11068191|pmid-9856491|pmid-11281275|pmid-11238888|pmid-105779...
Although the location of AG exclusion zones is likely to be substrate-dependent, these data suggest that the average zone is between ∼7 and ∼19 nt downstream of the BP adenosine, consistent with previous studies of intervening AGs (11,19,21,99).
[ "47", "36", "70", "93", "96", "62", "97", "98", "36", "93", "62", "98", "96", "70", "97", "95", "94", "99", "70", "36", "98", "11", "19", "21", "99" ]
245
4,539
0
false
Although the location of AG exclusion zones is likely to be substrate-dependent, these data suggest that the average zone is between ∼7 and ∼19 nt downstream of the BP adenosine, consistent with previous studies of intervening AGs.
[ "11,19,21,99" ]
Although the location of AG exclusion zones is likely to be substrate-dependent, these data suggest that the average zone is between ∼7 and ∼19 nt downstream of the BP adenosine, consistent with previous studies of intervening AGs.
true
true
true
true
true
769
1
DISCUSSION
1
91
[ "b91", "b67", "b100", "b106", "b107", "b108", "b2", "b65", "b66", "b72", "b93", "b109", "b116", "b117", "b87", "b36", "b118", "b119" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
If 3′ss are selected by unidirectional scanning for 3′YAG downstream of the BPS (91), why are so many cryptic 3′ss upstream of the predicted BPS used in vivo?
[ "91", "67", "100", "106", "107", "108", "2", "65", "66", "72", "93", "109", "116", "117", "87", "36", "118", "119" ]
158
4,540
1
false
If 3′ss are selected by unidirectional scanning for 3′YAG downstream of the BPS, why are so many cryptic 3′ss upstream of the predicted BPS used in vivo?
[ "91" ]
If 3′ss are selected by unidirectional scanning for 3′YAG downstream of the BPS, why are so many cryptic 3′ss upstream of the predicted BPS used in vivo?
true
true
true
true
true
770
1
DISCUSSION
1
107
[ "b91", "b67", "b100", "b106", "b107", "b108", "b2", "b65", "b66", "b72", "b93", "b109", "b116", "b117", "b87", "b36", "b118", "b119" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
Inspection of downstream exonic sequences in 29 cases of intronic cryptic 3′ss (Table 2) showed that eight were in terminal introns (67,100–106) (Table 1), which was significantly more frequent (χ2 = 5.6, P = 0.018) than for the remaining categories of aberrant 3′ss (Table 1), one was activated in a downstream intron (...
[ "91", "67", "100", "106", "107", "108", "2", "65", "66", "72", "93", "109", "116", "117", "87", "36", "118", "119" ]
395
4,541
1
false
Inspection of downstream exonic sequences in 29 cases of intronic cryptic 3′ss showed that eight were in terminal introns (Table 1), which was significantly more frequent than for the remaining categories of aberrant 3′ss (Table 1), one was activated in a downstream intron and two were associated with cryptic 3′ss in t...
[ "Table 2", "67,100–106", "χ2 = 5.6, P = 0.018", "107", "108" ]
Inspection of downstream exonic sequences in 29 cases of intronic cryptic 3′ss showed that eight were in terminal introns, which was significantly more frequent than for the remaining categories of aberrant 3′ss, one was activated in a downstream intron and two were associated with cryptic 3′ss in the following exon.
true
true
true
true
true
770
1
DISCUSSION
1
91
[ "b91", "b67", "b100", "b106", "b107", "b108", "b2", "b65", "b66", "b72", "b93", "b109", "b116", "b117", "b87", "b36", "b118", "b119" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
Of the remaining sites, 13 cases either completely lacked exonic 3′YAG consensus in the context of four or more upstream pyrimidines or contained this consensus only in the last 20 nt of the exon (2,65,66,72,93,109–116)
[ "91", "67", "100", "106", "107", "108", "2", "65", "66", "72", "93", "109", "116", "117", "87", "36", "118", "119" ]
219
4,542
0
false
Of the remaining sites, 13 cases either completely lacked exonic 3′YAG consensus in the context of four or more upstream pyrimidines or contained this consensus only in the last 20 nt of the exon
[ "2,65,66,72,93,109–116" ]
Of the remaining sites, 13 cases either completely lacked exonic 3′YAG consensus in the context of four or more upstream pyrimidines or contained this consensus only in the last 20 nt of the exon
true
true
false
true
false
770
1
DISCUSSION
1
117
[ "b91", "b67", "b100", "b106", "b107", "b108", "b2", "b65", "b66", "b72", "b93", "b109", "b116", "b117", "b87", "b36", "b118", "b119" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
These 3′YAGs are unlikely to be used as 3′ss given inefficient inclusion of very small exons in mRNA (117) and a typical recognition site of RRM of ∼4–7 nt
[ "91", "67", "100", "106", "107", "108", "2", "65", "66", "72", "93", "109", "116", "117", "87", "36", "118", "119" ]
155
4,543
1
false
These 3′YAGs are unlikely to be used as 3′ss given inefficient inclusion of very small exons in mRNA and a typical recognition site of RRM of ∼4–7 nt
[ "117" ]
These 3′YAGs are unlikely to be used as 3′ss given inefficient inclusion of very small exons in mRNA and a typical recognition site of RRM of ∼4–7 nt
true
true
false
true
false
770
1
DISCUSSION
1
91
[ "b91", "b67", "b100", "b106", "b107", "b108", "b2", "b65", "b66", "b72", "b93", "b109", "b116", "b117", "b87", "b36", "b118", "b119" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
[(87) and references therein].
[ "91", "67", "100", "106", "107", "108", "2", "65", "66", "72", "93", "109", "116", "117", "87", "36", "118", "119" ]
30
4,544
0
false
.
[ "(87) and references therein" ]
.
false
false
true
true
false
770
1
DISCUSSION
1
91
[ "b91", "b67", "b100", "b106", "b107", "b108", "b2", "b65", "b66", "b72", "b93", "b109", "b116", "b117", "b87", "b36", "b118", "b119" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
This strongly suggests that the choice of upstream 3′ss is influenced by the availability of 3′YAGs in the downstream exon and their distance from the exon end, and is consistent with unidirectional scanning that is inefficient in terminal exons.
[ "91", "67", "100", "106", "107", "108", "2", "65", "66", "72", "93", "109", "116", "117", "87", "36", "118", "119" ]
246
4,545
0
false
This strongly suggests that the choice of upstream 3′ss is influenced by the availability of 3′YAGs in the downstream exon and their distance from the exon end, and is consistent with unidirectional scanning that is inefficient in terminal exons.
[]
This strongly suggests that the choice of upstream 3′ss is influenced by the availability of 3′YAGs in the downstream exon and their distance from the exon end, and is consistent with unidirectional scanning that is inefficient in terminal exons.
true
true
true
true
true
770
1
DISCUSSION
1
91
[ "b91", "b67", "b100", "b106", "b107", "b108", "b2", "b65", "b66", "b72", "b93", "b109", "b116", "b117", "b87", "b36", "b118", "b119" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
It is therefore possible that a new, competing BPS-PPT-3′AG unit is selected after the initial scanning of the downstream exon for AGs is completed.
[ "91", "67", "100", "106", "107", "108", "2", "65", "66", "72", "93", "109", "116", "117", "87", "36", "118", "119" ]
148
4,546
0
false
It is therefore possible that a new, competing BPS-PPT-3′AG unit is selected after the initial scanning of the downstream exon for AGs is completed.
[]
It is therefore possible that a new, competing BPS-PPT-3′AG unit is selected after the initial scanning of the downstream exon for AGs is completed.
true
true
true
true
true
770
1
DISCUSSION
1
91
[ "b91", "b67", "b100", "b106", "b107", "b108", "b2", "b65", "b66", "b72", "b93", "b109", "b116", "b117", "b87", "b36", "b118", "b119" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
However, there has been no obvious reason for using upstream 3′ss in at least some of the remaining introns (36,118,119).
[ "91", "67", "100", "106", "107", "108", "2", "65", "66", "72", "93", "109", "116", "117", "87", "36", "118", "119" ]
121
4,547
0
false
However, there has been no obvious reason for using upstream 3′ss in at least some of the remaining introns.
[ "36,118,119" ]
However, there has been no obvious reason for using upstream 3′ss in at least some of the remaining introns.
true
true
true
true
true
770
1
DISCUSSION
1
91
[ "b91", "b67", "b100", "b106", "b107", "b108", "b2", "b65", "b66", "b72", "b93", "b109", "b116", "b117", "b87", "b36", "b118", "b119" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-9182766|pmid-10617207|pmid-2628164|pmid-8336728|pmid-2812024|pmid-9804951|pmid-15507752|pmid-9634533|pmid-12378390|pmid-9457913|pmid-10607834|pmid-10732814|pmid-10612843|pmid-11091205|pmid-10190324|pmid-9311736|pmid-8281149|pmid-1944277|pmid-12554879|pmid-9326325|pmid-10521298|pmid-1086...
These rare cases and similar examples identified in the future might provide interesting insights into cellular mechanisms that discriminate between authentic 3′ss and pseudo-acceptors.
[ "91", "67", "100", "106", "107", "108", "2", "65", "66", "72", "93", "109", "116", "117", "87", "36", "118", "119" ]
185
4,548
0
false
These rare cases and similar examples identified in the future might provide interesting insights into cellular mechanisms that discriminate between authentic 3′ss and pseudo-acceptors.
[]
These rare cases and similar examples identified in the future might provide interesting insights into cellular mechanisms that discriminate between authentic 3′ss and pseudo-acceptors.
true
true
true
true
true
770
2
DISCUSSION
1
120
[ "b120", "b121", "b10", "b11", "b122" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
Aberrant splicing often results in transcripts containing premature termination codons (PTCs).
[ "120", "121", "10", "11", "122" ]
94
4,549
0
false
Aberrant splicing often results in transcripts containing premature termination codons (PTCs).
[]
Aberrant splicing often results in transcripts containing premature termination codons (PTCs).
true
true
true
true
true
771
2
DISCUSSION
1
120
[ "b120", "b121", "b10", "b11", "b122" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
Such transcripts are downregulated by nonsense mediated RNA decay (NMD), which degrades PTC-containing mRNAs whose translation may be deleterious for the cell (120).
[ "120", "121", "10", "11", "122" ]
165
4,550
1
false
Such transcripts are downregulated by nonsense mediated RNA decay (NMD), which degrades PTC-containing mRNAs whose translation may be deleterious for the cell.
[ "120" ]
Such transcripts are downregulated by nonsense mediated RNA decay (NMD), which degrades PTC-containing mRNAs whose translation may be deleterious for the cell.
true
true
true
true
true
771
2
DISCUSSION
1
121
[ "b120", "b121", "b10", "b11", "b122" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
Whereas EST databases over-represent alternative splicing events that maintain the reading frame (121), neither cryptic 5′ss (10) nor aberrant 3′ss (Table 1, χ2 = 8.2, 6 d.f., P = 0.2) (11) showed any bias against splice sites involving a frameshift with respect to the authentic sites, even though many mRNAs frameshift...
[ "120", "121", "10", "11", "122" ]
372
4,551
1
false
Whereas EST databases over-represent alternative splicing events that maintain the reading frame, neither cryptic 5′ss nor aberrant 3′ss (Table 1, χ2 = 8.2, 6 d.f., P = 0.2) showed any bias against splice sites involving a frameshift with respect to the authentic sites, even though many mRNAs frameshifted by +1 and +2 ...
[ "121", "10", "11" ]
Whereas EST databases over-represent alternative splicing events that maintain the reading frame, neither cryptic 5′ss nor aberrant 3′ss showed any bias against splice sites involving a frameshift with respect to the authentic sites, even though many mRNAs frameshifted by +1 and +2 nt would be expected to trigger NMD.
true
true
true
true
true
771
2
DISCUSSION
1
122
[ "b120", "b121", "b10", "b11", "b122" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
These results can be explained by a great reduction of RNA downregulation in response to a PTC in transcripts containing PPT Y-to-R mutations that reduced splicing (122).
[ "120", "121", "10", "11", "122" ]
170
4,552
1
false
These results can be explained by a great reduction of RNA downregulation in response to a PTC in transcripts containing PPT Y-to-R mutations that reduced splicing.
[ "122" ]
These results can be explained by a great reduction of RNA downregulation in response to a PTC in transcripts containing PPT Y-to-R mutations that reduced splicing.
true
true
true
true
true
771
2
DISCUSSION
1
120
[ "b120", "b121", "b10", "b11", "b122" ]
16,963,498
pmid-14576320|pmid-16141195|pmid-16141195|pmid-2628164|pmid-15857856|pmid-16507133|pmid-15860725|pmid-14982953|pmid-14576320|pmid-16141195|pmid-16116435
In addition, NMD usually does not completely eliminate RNAs with PTCs and the activated cryptic sites that result in frameshifts can still be detected with RT–PCR, a method used by the authors of most DBASS3 records.
[ "120", "121", "10", "11", "122" ]
216
4,553
0
false
In addition, NMD usually does not completely eliminate RNAs with PTCs and the activated cryptic sites that result in frameshifts can still be detected with RT–PCR, a method used by the authors of most DBASS3 records.
[]
In addition, NMD usually does not completely eliminate RNAs with PTCs and the activated cryptic sites that result in frameshifts can still be detected with RT–PCR, a method used by the authors of most DBASS3 records.
true
true
true
true
true
771
3
DISCUSSION
1
28
[ "b28", "b25", "b123", "b124" ]
16,963,498
pmid-3658675|pmid-2314278|pmid-2067018|pmid-9278062|pmid-9711873|pmid-15285897|pmid-10637326|pmid-15285897|pmid-2067018|pmid-8811101|pmid-16226402
This study demonstrated that the ability of current computational tools to predict utilization of aberrant 3′ss is influenced by their localization and the underlying mutation.
[ "28", "25", "123", "124" ]
176
4,554
0
false
This study demonstrated that the ability of current computational tools to predict utilization of aberrant 3′ss is influenced by their localization and the underlying mutation.
[]
This study demonstrated that the ability of current computational tools to predict utilization of aberrant 3′ss is influenced by their localization and the underlying mutation.
true
true
true
true
true
772
3
DISCUSSION
1
28
[ "b28", "b25", "b123", "b124" ]
16,963,498
pmid-3658675|pmid-2314278|pmid-2067018|pmid-9278062|pmid-9711873|pmid-15285897|pmid-10637326|pmid-15285897|pmid-2067018|pmid-8811101|pmid-16226402
The best overall model discriminating authentic and aberrant 3′ ss was the ME model, validating previous predictions based on comparisons of genuine 3′ss and pseudo-acceptors (28).
[ "28", "25", "123", "124" ]
180
4,555
1
false
The best overall model discriminating authentic and aberrant 3′ ss was the ME model, validating previous predictions based on comparisons of genuine 3′ss and pseudo-acceptors.
[ "28" ]
The best overall model discriminating authentic and aberrant 3′ ss was the ME model, validating previous predictions based on comparisons of genuine 3′ss and pseudo-acceptors.
true
true
true
true
true
772
3
DISCUSSION
1
28
[ "b28", "b25", "b123", "b124" ]
16,963,498
pmid-3658675|pmid-2314278|pmid-2067018|pmid-9278062|pmid-9711873|pmid-15285897|pmid-10637326|pmid-15285897|pmid-2067018|pmid-8811101|pmid-16226402
The ME model outperformed the remaining algorithms for each category of aberrant 3′ss and, together with the MM model, was the only method that could separate authentic from de novo 3′ss in introns at a significance level <0.01.
[ "28", "25", "123", "124" ]
228
4,556
0
false
The ME model outperformed the remaining algorithms for each category of aberrant 3′ss and, together with the MM model, was the only method that could separate authentic from de novo 3′ss in introns at a significance level <0.01.
[]
The ME model outperformed the remaining algorithms for each category of aberrant 3′ss and, together with the MM model, was the only method that could separate authentic from de novo 3′ss in introns at a significance level <0.01.
true
true
true
true
true
772
3
DISCUSSION
1
124
[ "b28", "b25", "b123", "b124" ]
16,963,498
pmid-3658675|pmid-2314278|pmid-2067018|pmid-9278062|pmid-9711873|pmid-15285897|pmid-10637326|pmid-15285897|pmid-2067018|pmid-8811101|pmid-16226402
Since none of the tested tools discriminated between de novo 3′ss in exons and their authentic counterparts (Table 5), these aberrant 3′ss were tested with additional algorithms, including NetGene2 (25,123) available at and ASSP (alternative splice site predictor; ) method (124).
[ "28", "25", "123", "124" ]
281
4,557
1
false
Since none of the tested tools discriminated between de novo 3′ss in exons and their authentic counterparts (Table 5), these aberrant 3′ss were tested with additional algorithms, including NetGene2 available at and ASSP (alternative splice site predictor; ) method.
[ "25,123", "124" ]
Since none of the tested tools discriminated between de novo 3′ss in exons and their authentic counterparts (Table 5), these aberrant 3′ss were tested with additional algorithms, including NetGene2 available at and ASSP (alternative splice site predictor; ) method.
true
true
true
true
true
772
3
DISCUSSION
1
28
[ "b28", "b25", "b123", "b124" ]
16,963,498
pmid-3658675|pmid-2314278|pmid-2067018|pmid-9278062|pmid-9711873|pmid-15285897|pmid-10637326|pmid-15285897|pmid-2067018|pmid-8811101|pmid-16226402
NetGene2 considers more distant features that include global coding information and distances between potential splice sites, whereas ASSP is based on two neural networks pre-processed by position specific matrix scores.
[ "28", "25", "123", "124" ]
220
4,558
0
false
NetGene2 considers more distant features that include global coding information and distances between potential splice sites, whereas ASSP is based on two neural networks pre-processed by position specific matrix scores.
[]
NetGene2 considers more distant features that include global coding information and distances between potential splice sites, whereas ASSP is based on two neural networks pre-processed by position specific matrix scores.
true
true
true
true
true
772
3
DISCUSSION
1
28
[ "b28", "b25", "b123", "b124" ]
16,963,498
pmid-3658675|pmid-2314278|pmid-2067018|pmid-9278062|pmid-9711873|pmid-15285897|pmid-10637326|pmid-15285897|pmid-2067018|pmid-8811101|pmid-16226402
However, neither method revealed a difference for this category of aberrant 3′ss.
[ "28", "25", "123", "124" ]
81
4,559
0
false
However, neither method revealed a difference for this category of aberrant 3′ss.
[]
However, neither method revealed a difference for this category of aberrant 3′ss.
true
true
true
true
true
772
4
DISCUSSION
1
75
[ "b75" ]
16,963,498
NA
Although this study is the first to focus on 3′ss utilized in vivo as opposed to previous comparisons with pseudo-sites, there are limitations of this approach.
[ "75" ]
160
4,560
0
false
Although this study is the first to focus on 3′ss utilized in vivo as opposed to previous comparisons with pseudo-sites, there are limitations of this approach.
[]
Although this study is the first to focus on 3′ss utilized in vivo as opposed to previous comparisons with pseudo-sites, there are limitations of this approach.
true
true
true
true
true
773
4
DISCUSSION
1
75
[ "b75" ]
16,963,498
NA
First, even though each aberrant 3′ss was confirmed by sequencing, aberrant splicing was reliably and accurately quantified only in a subset of case reports and was highly variable from mutation to mutation, ranging from a few to hundred per cent utilization.
[ "75" ]
259
4,561
0
false
First, even though each aberrant 3′ss was confirmed by sequencing, aberrant splicing was reliably and accurately quantified only in a subset of case reports and was highly variable from mutation to mutation, ranging from a few to hundred per cent utilization.
[]
First, even though each aberrant 3′ss was confirmed by sequencing, aberrant splicing was reliably and accurately quantified only in a subset of case reports and was highly variable from mutation to mutation, ranging from a few to hundred per cent utilization.
true
true
true
true
true
773
4
DISCUSSION
1
75
[ "b75" ]
16,963,498
NA
This could be improved in future case reports and, as DBASS3 submissions permit inclusion of this information in future database records, taken into account in subsequent analyses.
[ "75" ]
180
4,562
0
false
This could be improved in future case reports and, as DBASS3 submissions permit inclusion of this information in future database records, taken into account in subsequent analyses.
[]
This could be improved in future case reports and, as DBASS3 submissions permit inclusion of this information in future database records, taken into account in subsequent analyses.
true
true
true
true
true
773
4
DISCUSSION
1
75
[ "b75" ]
16,963,498
NA
Second, despite the cell-specific nature of alternative splicing, measurements of aberrant and authentic RNA products have been obtained largely for blood leukocytes and only rarely for other cell types.
[ "75" ]
203
4,563
0
false
Second, despite the cell-specific nature of alternative splicing, measurements of aberrant and authentic RNA products have been obtained largely for blood leukocytes and only rarely for other cell types.
[]
Second, despite the cell-specific nature of alternative splicing, measurements of aberrant and authentic RNA products have been obtained largely for blood leukocytes and only rarely for other cell types.
true
true
true
true
true
773
4
DISCUSSION
1
75
[ "b75" ]
16,963,498
NA
Even with these limitations, future updates of DBASS3 may provide valuable insights into nucleotide dependencies between individual positions and distribution of trinucleotides that were significantly favoured or avoided upstream of authentic 3′ss as compared to pseudo-sites (75), as well as other motifs.
[ "75" ]
306
4,564
1
false
Even with these limitations, future updates of DBASS3 may provide valuable insights into nucleotide dependencies between individual positions and distribution of trinucleotides that were significantly favoured or avoided upstream of authentic 3′ss as compared to pseudo-sites, as well as other motifs.
[ "75" ]
Even with these limitations, future updates of DBASS3 may provide valuable insights into nucleotide dependencies between individual positions and distribution of trinucleotides that were significantly favoured or avoided upstream of authentic 3′ss as compared to pseudo-sites, as well as other motifs.
true
true
true
true
true
773
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Guanine-rich regions abound in the human genome and they have the propensity to fold into higher order DNA structures such as quadruplexes (1,2) which result from the hydrophobic stacking of several guanine quartets (3) (Figure 1).
[ "1", "2", "3", "4–7", "8–11" ]
231
4,565
1
false
Guanine-rich regions abound in the human genome and they have the propensity to fold into higher order DNA structures such as quadruplexes which result from the hydrophobic stacking of several guanine quartets.
[ "1,2", "3", "Figure 1" ]
Guanine-rich regions abound in the human genome and they have the propensity to fold into higher order DNA structures such as quadruplexes which result from the hydrophobic stacking of several guanine quartets.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
A cation (typically Na+ or K+) located between two quartets participates in cation–dipole interactions with eight guanines, thereby reducing the repulsion of the central oxygen atoms, enhancing hydrogen bond strength and stabilizing quartet stacking.
[ "1", "2", "3", "4–7", "8–11" ]
250
4,566
0
false
A cation (typically Na+ or K+) located between two quartets participates in cation–dipole interactions with eight guanines, thereby reducing the repulsion of the central oxygen atoms, enhancing hydrogen bond strength and stabilizing quartet stacking.
[]
A cation (typically Na+ or K+) located between two quartets participates in cation–dipole interactions with eight guanines, thereby reducing the repulsion of the central oxygen atoms, enhancing hydrogen bond strength and stabilizing quartet stacking.
true
true
true
true
true
774
0
INTRODUCTION
1
4–7
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
In the past decade, the level of interest in these peculiar structures has increased due to the putative roles of quadruplexes in key biological processes and to recent demonstrations of their existence in vivo (4–7).
[ "1", "2", "3", "4–7", "8–11" ]
217
4,567
1
false
In the past decade, the level of interest in these peculiar structures has increased due to the putative roles of quadruplexes in key biological processes and to recent demonstrations of their existence in vivo.
[ "4–7" ]
In the past decade, the level of interest in these peculiar structures has increased due to the putative roles of quadruplexes in key biological processes and to recent demonstrations of their existence in vivo.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
G-quadruplexes may have applications in areas ranging from supramolecular chemistry to medicinal chemistry and nanotechnology [reviewed in (8–11)].
[ "1", "2", "3", "4–7", "8–11" ]
147
4,568
0
false
G-quadruplexes may have applications in areas ranging from supramolecular chemistry to medicinal chemistry and nanotechnology.
[ "reviewed in (8–11)" ]
G-quadruplexes may have applications in areas ranging from supramolecular chemistry to medicinal chemistry and nanotechnology.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Therefore, it is important to understand the rules that govern the formation of these complexes and to determine their stabilities and association kinetics.
[ "1", "2", "3", "4–7", "8–11" ]
156
4,569
0
false
Therefore, it is important to understand the rules that govern the formation of these complexes and to determine their stabilities and association kinetics.
[]
Therefore, it is important to understand the rules that govern the formation of these complexes and to determine their stabilities and association kinetics.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Figure 1.A G-quartet and bases tested here.
[ "1", "2", "3", "4–7", "8–11" ]
43
4,570
0
false
Figure 1.A G-quartet and bases tested here.
[]
Figure 1.A G-quartet and bases tested here.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Top: Chemical formulae of the bases tested here.
[ "1", "2", "3", "4–7", "8–11" ]
48
4,571
0
false
Top: Chemical formulae of the bases tested here.
[]
Top: Chemical formulae of the bases tested here.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
I = Inosine; 6 = 6-thioguanine; 7 = 7-deazaguanine; 8 = 8-oxoguanine; P = 6MI = 6-methylisoxanthopterin; Q = 3MI = 3-methylisoxanthopterin; M = 6-methyl guanine; X = 8-bromo-guanine.
[ "1", "2", "3", "4–7", "8–11" ]
182
4,572
0
false
I = Inosine; 6 = 6-thioguanine; 7 = 7-deazaguanine; 8 = 8-oxoguanine; P = 6MI = 6-methylisoxanthopterin; Q = 3MI = 3-methylisoxanthopterin; M = 6-methyl guanine; X = 8-bromo-guanine.
[]
I = Inosine; 6 = 6-thioguanine; 7 = 7-deazaguanine; 8 = 8-oxoguanine; P = 6MI = 6-methylisoxanthopterin; Q = 3MI = 3-methylisoxanthopterin; M = 6-methyl guanine; X = 8-bromo-guanine.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Formula of the regular DNA and RNA bases (A, C, T, U) are not shown.
[ "1", "2", "3", "4–7", "8–11" ]
68
4,573
0
false
Formula of the regular DNA and RNA bases (A, C, T, U) are not shown.
[]
Formula of the regular DNA and RNA bases (A, C, T, U) are not shown.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Lower left: Cycling arrangement of four guanine into a G-quartet.
[ "1", "2", "3", "4–7", "8–11" ]
65
4,574
0
false
Lower left: Cycling arrangement of four guanine into a G-quartet.
[]
Lower left: Cycling arrangement of four guanine into a G-quartet.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Altering the NH2 group on position 2 will alter the external ring of H-bonds, whereas modifications of the 8-position should leave the H-bond pattern unaffected.
[ "1", "2", "3", "4–7", "8–11" ]
161
4,575
0
false
Altering the NH2 group on position 2 will alter the external ring of H-bonds, whereas modifications of the 8-position should leave the H-bond pattern unaffected.
[]
Altering the NH2 group on position 2 will alter the external ring of H-bonds, whereas modifications of the 8-position should leave the H-bond pattern unaffected.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Altering the carbonyl group at position 6 not only perturbs the central ring of H-bonds, but may also interfere with cation coordination.
[ "1", "2", "3", "4–7", "8–11" ]
137
4,576
0
false
Altering the carbonyl group at position 6 not only perturbs the central ring of H-bonds, but may also interfere with cation coordination.
[]
Altering the carbonyl group at position 6 not only perturbs the central ring of H-bonds, but may also interfere with cation coordination.
true
true
true
true
true
774
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4 B5 B6 B7", "B8 B9 B10 B11" ]
17,452,368
pmid-12831878|pmid-17012276|pmid-13947099|pmid-15079086|pmid-11438689|pmid-15231739|pmid-16142245|NA|pmid-17036128|pmid-17146462|pmid-17226803|pmid-16287312
Lower right: Scheme of the general folding topology of the TG4T tetramolecular parallel quadruplex.
[ "1", "2", "3", "4–7", "8–11" ]
99
4,577
0
false
Lower right: Scheme of the general folding topology of the TG4T tetramolecular parallel quadruplex.
[]
Lower right: Scheme of the general folding topology of the TG4T tetramolecular parallel quadruplex.
true
true
true
true
true
774
1
INTRODUCTION
0
null
null
17,452,368
pmid-5138337|pmid-1390713
A G-quartet and bases tested here.
null
34
4,578
0
false
null
null
A G-quartet and bases tested here.
true
true
true
true
true
775
1
INTRODUCTION
0
null
null
17,452,368
pmid-5138337|pmid-1390713
Top: Chemical formulae of the bases tested here.
null
48
4,579
0
false
null
null
Top: Chemical formulae of the bases tested here.
true
true
true
true
true
775
1
INTRODUCTION
0
null
null
17,452,368
pmid-5138337|pmid-1390713
I = Inosine; 6 = 6-thioguanine; 7 = 7-deazaguanine; 8 = 8-oxoguanine; P = 6MI = 6-methylisoxanthopterin; Q = 3MI = 3-methylisoxanthopterin; M = 6-methyl guanine; X = 8-bromo-guanine.
null
182
4,580
0
false
null
null
I = Inosine; 6 = 6-thioguanine; 7 = 7-deazaguanine; 8 = 8-oxoguanine; P = 6MI = 6-methylisoxanthopterin; Q = 3MI = 3-methylisoxanthopterin; M = 6-methyl guanine; X = 8-bromo-guanine.
true
true
true
true
true
775
1
INTRODUCTION
0
null
null
17,452,368
pmid-5138337|pmid-1390713
Formula of the regular DNA and RNA bases (A, C, T, U) are not shown.
null
68
4,581
0
false
null
null
Formula of the regular DNA and RNA bases (A, C, T, U) are not shown.
true
true
true
true
true
775
1
INTRODUCTION
0
null
null
17,452,368
pmid-5138337|pmid-1390713
Lower left: Cycling arrangement of four guanine into a G-quartet.
null
65
4,582
0
false
null
null
Lower left: Cycling arrangement of four guanine into a G-quartet.
true
true
true
true
true
775
1
INTRODUCTION
0
null
null
17,452,368
pmid-5138337|pmid-1390713
Altering the NH2 group on position 2 will alter the external ring of H-bonds, whereas modifications of the 8-position should leave the H-bond pattern unaffected.
null
161
4,583
0
false
null
null
Altering the NH2 group on position 2 will alter the external ring of H-bonds, whereas modifications of the 8-position should leave the H-bond pattern unaffected.
true
true
true
true
true
775
1
INTRODUCTION
0
null
null
17,452,368
pmid-5138337|pmid-1390713
Altering the carbonyl group at position 6 not only perturbs the central ring of H-bonds, but may also interfere with cation coordination.
null
137
4,584
0
false
null
null
Altering the carbonyl group at position 6 not only perturbs the central ring of H-bonds, but may also interfere with cation coordination.
true
true
true
true
true
775
1
INTRODUCTION
0
null
null
17,452,368
pmid-5138337|pmid-1390713
Lower right: Scheme of the general folding topology of the TG4T tetramolecular parallel quadruplex.
null
99
4,585
0
false
null
null
Lower right: Scheme of the general folding topology of the TG4T tetramolecular parallel quadruplex.
true
true
true
true
true
775
2
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B14", "B15", "B17" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
In the tetramolecular quadruplex configuration (G4-DNA, Figure 1), all strands are parallel, and all guanines are in the anti conformation.
[ "12", "13", "14", "15", "16", "14", "15", "17" ]
139
4,586
0
false
In the tetramolecular quadruplex configuration (G4-DNA, Figure 1), all strands are parallel, and all guanines are in the anti conformation.
[]
In the tetramolecular quadruplex configuration, all strands are parallel, and all guanines are in the anti conformation.
true
true
true
true
true
776
2
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B14", "B15", "B17" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
The conformations of guanines in G4-DNA are very well known due to a number of available high-resolution X-ray and NMR structures.
[ "12", "13", "14", "15", "16", "14", "15", "17" ]
130
4,587
0
false
The conformations of guanines in G4-DNA are very well known due to a number of available high-resolution X-ray and NMR structures.
[]
The conformations of guanines in G4-DNA are very well known due to a number of available high-resolution X-ray and NMR structures.
true
true
true
true
true
776
2
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B14", "B15", "B17" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
This structural wealth might be explained in part by the extraordinary stiffness of the G4-DNA motif (12,13).
[ "12", "13", "14", "15", "16", "14", "15", "17" ]
109
4,588
0
false
This structural wealth might be explained in part by the extraordinary stiffness of the G4-DNA motif.
[ "12,13" ]
This structural wealth might be explained in part by the extraordinary stiffness of the G4-DNA motif.
true
true
true
true
true
776
2
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B14", "B15", "B17" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
On the other hand, less is known concerning the kinetics and thermodynamics of tetramolecular quadruplexes.
[ "12", "13", "14", "15", "16", "14", "15", "17" ]
107
4,589
0
false
On the other hand, less is known concerning the kinetics and thermodynamics of tetramolecular quadruplexes.
[]
On the other hand, less is known concerning the kinetics and thermodynamics of tetramolecular quadruplexes.
true
true
true
true
true
776
2
INTRODUCTION
1
14
[ "B12", "B13", "B14", "B15", "B16", "B14", "B15", "B17" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
Rules have been proposed to describe the properties of simple, short segments such as T2G4T2 (14).
[ "12", "13", "14", "15", "16", "14", "15", "17" ]
98
4,590
1
false
Rules have been proposed to describe the properties of simple, short segments such as T2G4T2.
[ "14" ]
Rules have been proposed to describe the properties of simple, short segments such as T2G4T2.
true
true
true
true
true
776
2
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B14", "B15", "B17" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
In previous studies, we analyzed the kinetics of quadruplex formation with short DNA sequences (15,16).
[ "12", "13", "14", "15", "16", "14", "15", "17" ]
103
4,591
0
false
In previous studies, we analyzed the kinetics of quadruplex formation with short DNA sequences.
[ "15,16" ]
In previous studies, we analyzed the kinetics of quadruplex formation with short DNA sequences.
true
true
true
true
true
776
2
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B14", "B15", "B17" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
The kinetic inertia of these quadruplexes allowed us to study association and dissociation processes independently.
[ "12", "13", "14", "15", "16", "14", "15", "17" ]
115
4,592
0
false
The kinetic inertia of these quadruplexes allowed us to study association and dissociation processes independently.
[]
The kinetic inertia of these quadruplexes allowed us to study association and dissociation processes independently.
true
true
true
true
true
776
2
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B14", "B15", "B17" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
The association rate strongly depended on strand concentration, with an experimentally determined order close to four (14,15,17).
[ "12", "13", "14", "15", "16", "14", "15", "17" ]
129
4,593
0
false
The association rate strongly depended on strand concentration, with an experimentally determined order close to four.
[ "14,15,17" ]
The association rate strongly depended on strand concentration, with an experimentally determined order close to four.
true
true
true
true
true
776
2
INTRODUCTION
1
12
[ "B12", "B13", "B14", "B15", "B16", "B14", "B15", "B17" ]
17,452,368
NA|pmid-12944293|pmid-8672504|pmid-15642696|pmid-16682446|pmid-8672504|pmid-15642696|pmid-16287312|pmid-12490709|NA|pmid-7704525|pmid-16332077|pmid-16433524|pmid-16714449|pmid-16866556|pmid-17040899
The corresponding association rate constant kon decreased with increasing temperature (reflecting a negative activation energy Eon) and increased with ionic strength.
[ "12", "13", "14", "15", "16", "14", "15", "17" ]
166
4,594
0
false
The corresponding association rate constant kon decreased with increasing temperature (reflecting a negative activation energy Eon) and increased with ionic strength.
[]
The corresponding association rate constant kon decreased with increasing temperature (reflecting a negative activation energy Eon) and increased with ionic strength.
true
true
true
true
true
776
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
A number of recent reports demonstrate that tetramolecular quadruplexes may accommodate at least one unusual quartet (18,19).
[ "18", "19", "20", "21", "22", "23", "24" ]
125
4,595
0
false
A number of recent reports demonstrate that tetramolecular quadruplexes may accommodate at least one unusual quartet.
[ "18,19" ]
A number of recent reports demonstrate that tetramolecular quadruplexes may accommodate at least one unusual quartet.
true
true
true
true
true
777
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
DNA quadruplex formation is therefore not restricted to G-repeat sequences.
[ "18", "19", "20", "21", "22", "23", "24" ]
75
4,596
0
false
DNA quadruplex formation is therefore not restricted to G-repeat sequences.
[]
DNA quadruplex formation is therefore not restricted to G-repeat sequences.
true
true
true
true
true
777
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
Rather, the quadruplex fold has a versatile and robust architecture that is accessible to a range of mixed sequences with the potential to form various tetrads or even hexads, heptads and octads.
[ "18", "19", "20", "21", "22", "23", "24" ]
195
4,597
0
false
Rather, the quadruplex fold has a versatile and robust architecture that is accessible to a range of mixed sequences with the potential to form various tetrads or even hexads, heptads and octads.
[]
Rather, the quadruplex fold has a versatile and robust architecture that is accessible to a range of mixed sequences with the potential to form various tetrads or even hexads, heptads and octads.
true
true
true
true
true
777
3
INTRODUCTION
1
18
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
Many articles analyzed these ‘non-G quartets,’ often in the context of parallel tetramolecular quadruplexes.
[ "18", "19", "20", "21", "22", "23", "24" ]
108
4,598
0
false
Many articles analyzed these ‘non-G quartets,’ often in the context of parallel tetramolecular quadruplexes.
[]
Many articles analyzed these ‘non-G quartets,’ often in the context of parallel tetramolecular quadruplexes.
true
true
true
true
true
777
3
INTRODUCTION
1
20
[ "B18", "B19", "B20", "B21", "B22", "B23", "B24" ]
17,452,368
pmid-14747859|pmid-15614794|pmid-10352174|pmid-10772934|pmid-12842044|pmid-1382577|pmid-14604532|pmid-12944293|NA|pmid-15642696|pmid-16682446|pmid-15642696|pmid-8672504|pmid-15642696|pmid-16682446|pmid-16287312|pmid-8672504|pmid-12944293|pmid-15642696
NMR studies have shown that the thymine in the center of the TG2TG2C four-stranded quadruplex forms a thymine quartet (20) and the cytosine in the TG3CGT quadruplex forms a cytosine quartet (21).
[ "18", "19", "20", "21", "22", "23", "24" ]
195
4,599
1
false
NMR studies have shown that the thymine in the center of the TG2TG2C four-stranded quadruplex forms a thymine quartet and the cytosine in the TG3CGT quadruplex forms a cytosine quartet.
[ "20", "21" ]
NMR studies have shown that the thymine in the center of the TG2TG2C four-stranded quadruplex forms a thymine quartet and the cytosine in the TG3CGT quadruplex forms a cytosine quartet.
true
true
true
true
true
777