Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
paragraph_index
int64
sec
string
p_has_citation
int64
cites
string
citeids
list
pmid
int64
cited_id
string
sentences
string
all_sent_cites
list
sent_len
int64
sentence_batch_index
int64
sent_has_citation
float64
qc_fail
bool
cited_sentence
string
cites_in_sentence
list
cln_sentence
string
is_cap
bool
is_alpha
bool
ends_wp
bool
cit_qc
bool
lgtm
bool
__index_level_0__
int64
4
DISCUSSION
1
19
[ "B19", "B3", "B20 B21 B22", "B1", "B23" ]
17,459,886
pmid-12669795|pmid-14615184|NA|pmid-7568673|NA|pmid-12850441|pmid-15956662
An initial concern with ITS was the fact that there are typically several hundred copies of the ribosomal RNA locus in tandem in the nuclear genome (19)—hence there was the potential for intragenomic variation.
[ "19", "3", ",20–22", "1", "23" ]
210
10,400
1
false
An initial concern with ITS was the fact that there are typically several hundred copies of the ribosomal RNA locus in tandem in the nuclear genome —hence there was the potential for intragenomic variation.
[ "19" ]
An initial concern with ITS was the fact that there are typically several hundred copies of the ribosomal RNA locus in tandem in the nuclear genome —hence there was the potential for intragenomic variation.
true
true
true
true
true
1,660
4
DISCUSSION
1
19
[ "B19", "B3", "B20 B21 B22", "B1", "B23" ]
17,459,886
pmid-12669795|pmid-14615184|NA|pmid-7568673|NA|pmid-12850441|pmid-15956662
It is now clear that, except as described below, these repeats are subject to ‘concerted evolution’ (3,20–22), the result of a poorly understood process of homogenization that renders the ITS repeats of an organism identical over very short evolutionary time.
[ "19", "3", ",20–22", "1", "23" ]
259
10,401
0
false
It is now clear that, except as described below, these repeats are subject to ‘concerted evolution’, the result of a poorly understood process of homogenization that renders the ITS repeats of an organism identical over very short evolutionary time.
[ "3,20–22" ]
It is now clear that, except as described below, these repeats are subject to ‘concerted evolution’, the result of a poorly understood process of homogenization that renders the ITS repeats of an organism identical over very short evolutionary time.
true
true
true
true
true
1,660
4
DISCUSSION
1
19
[ "B19", "B3", "B20 B21 B22", "B1", "B23" ]
17,459,886
pmid-12669795|pmid-14615184|NA|pmid-7568673|NA|pmid-12850441|pmid-15956662
Intragenomic variation, if present at all, is typically only in very few extremely variable positions that are never paired in secondary structure.
[ "19", "3", ",20–22", "1", "23" ]
147
10,402
0
false
Intragenomic variation, if present at all, is typically only in very few extremely variable positions that are never paired in secondary structure.
[]
Intragenomic variation, if present at all, is typically only in very few extremely variable positions that are never paired in secondary structure.
true
true
true
true
true
1,660
4
DISCUSSION
1
1
[ "B19", "B3", "B20 B21 B22", "B1", "B23" ]
17,459,886
pmid-12669795|pmid-14615184|NA|pmid-7568673|NA|pmid-12850441|pmid-15956662
Thus, the ITS2 can be treated as a single gene (1).
[ "19", "3", ",20–22", "1", "23" ]
51
10,403
1
false
Thus, the ITS2 can be treated as a single gene.
[ "1" ]
Thus, the ITS2 can be treated as a single gene.
true
true
true
true
true
1,660
4
DISCUSSION
1
19
[ "B19", "B3", "B20 B21 B22", "B1", "B23" ]
17,459,886
pmid-12669795|pmid-14615184|NA|pmid-7568673|NA|pmid-12850441|pmid-15956662
For an exhaustive analysis of ITS2 intragenomic variation, see Pröschold et al.
[ "19", "3", ",20–22", "1", "23" ]
79
10,404
0
false
For an exhaustive analysis of ITS2 intragenomic variation, see Pröschold et al.
[]
For an exhaustive analysis of ITS2 intragenomic variation, see Pröschold et al.
true
true
true
true
true
1,660
5
DISCUSSION
1
3
[ "B3", "B24" ]
17,459,886
pmid-14615184|pmid-14615185
The other potential problems, discussed at length in Alvarez and Wendel (3) and Bailey et al.
[ "3", "24" ]
93
10,405
1
false
The other potential problems, discussed at length in Alvarez and Wendel and Bailey et al.
[ "3" ]
The other potential problems, discussed at length in Alvarez and Wendel and Bailey et al.
true
true
true
true
true
1,661
5
DISCUSSION
1
24
[ "B3", "B24" ]
17,459,886
pmid-14615184|pmid-14615185
(24), concern hybridization and polyploidy.
[ "3", "24" ]
43
10,406
1
false
, concern hybridization and polyploidy.
[ "24" ]
, concern hybridization and polyploidy.
false
false
true
true
false
1,661
5
DISCUSSION
1
3
[ "B3", "B24" ]
17,459,886
pmid-14615184|pmid-14615185
Clearly if two organisms differing in their ITS2 sequences hybridize and crossover occurs, the outcome can confuse the phylogenetic analysis.
[ "3", "24" ]
141
10,407
0
false
Clearly if two organisms differing in their ITS2 sequences hybridize and crossover occurs, the outcome can confuse the phylogenetic analysis.
[]
Clearly if two organisms differing in their ITS2 sequences hybridize and crossover occurs, the outcome can confuse the phylogenetic analysis.
true
true
true
true
true
1,661
5
DISCUSSION
1
3
[ "B3", "B24" ]
17,459,886
pmid-14615184|pmid-14615185
There may ultimately be more than one locus of rDNA genes in the nucleus, there may be mixed ITS2 sequences within and between arrays, resulting from differing parents and from crossingover, and there may even be pseudogene sequences of ITS resulting from degeneration of one set.
[ "3", "24" ]
280
10,408
0
false
There may ultimately be more than one locus of rDNA genes in the nucleus, there may be mixed ITS2 sequences within and between arrays, resulting from differing parents and from crossingover, and there may even be pseudogene sequences of ITS resulting from degeneration of one set.
[]
There may ultimately be more than one locus of rDNA genes in the nucleus, there may be mixed ITS2 sequences within and between arrays, resulting from differing parents and from crossingover, and there may even be pseudogene sequences of ITS resulting from degeneration of one set.
true
true
true
true
true
1,661
5
DISCUSSION
1
3
[ "B3", "B24" ]
17,459,886
pmid-14615184|pmid-14615185
Non-functional pseudogenes, in fact, are readily recognizable by their imperfect 5.8S and for absence of some or all of the relatively conserved regions of ITS2, aspects obvious from transcript secondary structure knowledge.
[ "3", "24" ]
224
10,409
0
false
Non-functional pseudogenes, in fact, are readily recognizable by their imperfect 5.8S and for absence of some or all of the relatively conserved regions of ITS2, aspects obvious from transcript secondary structure knowledge.
[]
Non-functional pseudogenes, in fact, are readily recognizable by their imperfect 5.8S and for absence of some or all of the relatively conserved regions of ITS2, aspects obvious from transcript secondary structure knowledge.
true
true
true
true
true
1,661
5
DISCUSSION
1
3
[ "B3", "B24" ]
17,459,886
pmid-14615184|pmid-14615185
Hybridization, polyploidy and their consequences, more common in plants than in animals, can engender confusion, but such situations are generally recognizable and already suspected in particular groups under study.
[ "3", "24" ]
215
10,410
0
false
Hybridization, polyploidy and their consequences, more common in plants than in animals, can engender confusion, but such situations are generally recognizable and already suspected in particular groups under study.
[]
Hybridization, polyploidy and their consequences, more common in plants than in animals, can engender confusion, but such situations are generally recognizable and already suspected in particular groups under study.
true
true
true
true
true
1,661
5
DISCUSSION
1
3
[ "B3", "B24" ]
17,459,886
pmid-14615184|pmid-14615185
The resulting ITS sequences, containing two or more repeat types, may then actually prove highly informative in resolving the phylogenetic problems.
[ "3", "24" ]
148
10,411
0
false
The resulting ITS sequences, containing two or more repeat types, may then actually prove highly informative in resolving the phylogenetic problems.
[]
The resulting ITS sequences, containing two or more repeat types, may then actually prove highly informative in resolving the phylogenetic problems.
true
true
true
true
true
1,661
6
DISCUSSION
0
null
null
17,459,886
null
The conservation of basic hallmarks of ITS2 structure across great taxonomic spans has inspired several novel approaches to handling major taxonomic categories.
null
160
10,412
0
false
null
null
The conservation of basic hallmarks of ITS2 structure across great taxonomic spans has inspired several novel approaches to handling major taxonomic categories.
true
true
true
true
true
1,662
6
DISCUSSION
0
null
null
17,459,886
null
Recently, Landis and Gargas (submitted for publication) have proposed a method for identification of all fungi to species, using just PCR and a set of sequential 20-mer primers designed from the first half of the ITS2, reflecting the specificity and stability of helix I, II and the 5′portion of III.
null
300
10,413
0
false
null
null
Recently, Landis and Gargas (submitted for publication) have proposed a method for identification of all fungi to species, using just PCR and a set of sequential 20-mer primers designed from the first half of the ITS2, reflecting the specificity and stability of helix I, II and the 5′portion of III.
true
true
true
true
true
1,662
7
DISCUSSION
1
25
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
For the four-helix model of ITS2, using the hallmarks of the helix II pyrimidine mismatch and the longer helix III with TGGT on the 5′ side, Schultz et al.
[ "25", "2", "26", "27", "28", "29", "30" ]
155
10,414
0
false
For the four-helix model of ITS2, using the hallmarks of the helix II pyrimidine mismatch and the longer helix III with TGGT on the 5′ side, Schultz et al.
[]
For the four-helix model of ITS2, using the hallmarks of the helix II pyrimidine mismatch and the longer helix III with TGGT on the 5′ side, Schultz et al.
true
true
true
true
true
1,663
7
DISCUSSION
1
25
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
(25) have automated GenBank searching for ITS2 sequences and their folding.
[ "25", "2", "26", "27", "28", "29", "30" ]
75
10,415
1
false
have automated GenBank searching for ITS2 sequences and their folding.
[ "25" ]
have automated GenBank searching for ITS2 sequences and their folding.
false
true
true
true
false
1,663
7
DISCUSSION
1
25
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
Subsequently, Wolf et al.
[ "25", "2", "26", "27", "28", "29", "30" ]
25
10,416
0
false
Subsequently, Wolf et al.
[]
Subsequently, Wolf et al.
true
true
true
true
true
1,663
7
DISCUSSION
1
2
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
(2) and Schultz et al.
[ "25", "2", "26", "27", "28", "29", "30" ]
22
10,417
1
false
and Schultz et al.
[ "2" ]
and Schultz et al.
false
true
true
true
false
1,663
7
DISCUSSION
1
26
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
(26) have extended automation and set up a website (http://its2.bioapps.biozentrum.uni-wuerzburg.de) with eukaryote-wide representation of exemplar ITS2 folds.
[ "25", "2", "26", "27", "28", "29", "30" ]
159
10,418
1
false
have extended automation and set up a website with eukaryote-wide representation of exemplar ITS2 folds.
[ "26", "http://its2.bioapps.biozentrum.uni-wuerzburg.de" ]
have extended automation and set up a website with eukaryote-wide representation of exemplar ITS2 folds.
false
true
true
true
false
1,663
7
DISCUSSION
1
27
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
In addition, there is a growing literature on programs to handle simultaneously sequence alignments and their secondary structure characteristics, as in Siebert and Backofen (27), Seibel et al.
[ "25", "2", "26", "27", "28", "29", "30" ]
193
10,419
1
false
In addition, there is a growing literature on programs to handle simultaneously sequence alignments and their secondary structure characteristics, as in Siebert and Backofen, Seibel et al.
[ "27" ]
In addition, there is a growing literature on programs to handle simultaneously sequence alignments and their secondary structure characteristics, as in Siebert and Backofen, Seibel et al.
true
true
true
true
true
1,663
7
DISCUSSION
1
25
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
Wolf et al.
[ "25", "2", "26", "27", "28", "29", "30" ]
11
10,420
0
false
Wolf et al.
[]
Wolf et al.
true
true
true
true
true
1,663
7
DISCUSSION
1
25
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
Biffen et al.
[ "25", "2", "26", "27", "28", "29", "30" ]
13
10,421
0
false
Biffen et al.
[]
Biffen et al.
true
true
true
true
true
1,663
7
DISCUSSION
1
30
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
(30) provide a recent example of the application of such programs, plus an interesting analysis of the types and rates of compensatory base change in SSU versus ITS.
[ "25", "2", "26", "27", "28", "29", "30" ]
165
10,422
1
false
provide a recent example of the application of such programs, plus an interesting analysis of the types and rates of compensatory base change in SSU versus ITS.
[ "30" ]
provide a recent example of the application of such programs, plus an interesting analysis of the types and rates of compensatory base change in SSU versus ITS.
false
true
true
true
false
1,663
7
DISCUSSION
1
25
[ "B25", "B2", "B26", "B27", "B28", "B29", "B30" ]
17,459,886
pmid-15769870|pmid-16244129|NA|pmid-15972285|pmid-17101042|NA|NA
These methods appear to work best for relatively short ITS2 sequences, averaging ∼200 nt, and thus have proven particularly applicable to plants and green algae, fungi, dinoflagellates and some metazoan groups.
[ "25", "2", "26", "27", "28", "29", "30" ]
210
10,423
0
false
These methods appear to work best for relatively short ITS2 sequences, averaging ∼200 nt, and thus have proven particularly applicable to plants and green algae, fungi, dinoflagellates and some metazoan groups.
[]
These methods appear to work best for relatively short ITS2 sequences, averaging ∼200 nt, and thus have proven particularly applicable to plants and green algae, fungi, dinoflagellates and some metazoan groups.
true
true
true
true
true
1,663
8
DISCUSSION
1
31
[ "B31", "B6", "B8", "B32", "B5", "B33", "B34", "B35" ]
17,459,886
pmid-10896128|NA|NA|pmid-9873081|pmid-9060392|pmid-11821917|pmid-15022773|NA
A unique advantage of the ITS2 as a choice for sequencing is that the resulting alignment contains information related to the level of the biological species (31).
[ "31", "6", "8", "32", "5", "33", "34", "35" ]
163
10,424
1
false
A unique advantage of the ITS2 as a choice for sequencing is that the resulting alignment contains information related to the level of the biological species.
[ "31" ]
A unique advantage of the ITS2 as a choice for sequencing is that the resulting alignment contains information related to the level of the biological species.
true
true
true
true
true
1,664
8
DISCUSSION
1
31
[ "B31", "B6", "B8", "B32", "B5", "B33", "B34", "B35" ]
17,459,886
pmid-10896128|NA|NA|pmid-9873081|pmid-9060392|pmid-11821917|pmid-15022773|NA
This is an empirical observation that has borne up for all eukaryote groups investigated so far.
[ "31", "6", "8", "32", "5", "33", "34", "35" ]
96
10,425
0
false
This is an empirical observation that has borne up for all eukaryote groups investigated so far.
[]
This is an empirical observation that has borne up for all eukaryote groups investigated so far.
true
true
true
true
true
1,664
8
DISCUSSION
1
31
[ "B31", "B6", "B8", "B32", "B5", "B33", "B34", "B35" ]
17,459,886
pmid-10896128|NA|NA|pmid-9873081|pmid-9060392|pmid-11821917|pmid-15022773|NA
The fundamental correlation arises from the highly conserved regions of sequence.
[ "31", "6", "8", "32", "5", "33", "34", "35" ]
81
10,426
0
false
The fundamental correlation arises from the highly conserved regions of sequence.
[]
The fundamental correlation arises from the highly conserved regions of sequence.
true
true
true
true
true
1,664
8
DISCUSSION
1
31
[ "B31", "B6", "B8", "B32", "B5", "B33", "B34", "B35" ]
17,459,886
pmid-10896128|NA|NA|pmid-9873081|pmid-9060392|pmid-11821917|pmid-15022773|NA
In taxonomic groups with fairly short ITS2 sequences, where these are all identical, the organisms are observed to be able to intercross experimentally, and if no compensatory base change is present, at least to some degree.
[ "31", "6", "8", "32", "5", "33", "34", "35" ]
224
10,427
0
false
In taxonomic groups with fairly short ITS2 sequences, where these are all identical, the organisms are observed to be able to intercross experimentally, and if no compensatory base change is present, at least to some degree.
[]
In taxonomic groups with fairly short ITS2 sequences, where these are all identical, the organisms are observed to be able to intercross experimentally, and if no compensatory base change is present, at least to some degree.
true
true
true
true
true
1,664
8
DISCUSSION
1
31
[ "B31", "B6", "B8", "B32", "B5", "B33", "B34", "B35" ]
17,459,886
pmid-10896128|NA|NA|pmid-9873081|pmid-9060392|pmid-11821917|pmid-15022773|NA
For groups with longer sequences, the additional regions appear to show lesser evolutionary constraint, so that one must limit the comparison to only the most conserved paired positions (the 10 basal pairings in II and the 18 pairings including and immediately surrounding the highly conserved 5′ sequence of helix III);...
[ "31", "6", "8", "32", "5", "33", "34", "35" ]
423
10,428
0
false
For groups with longer sequences, the additional regions appear to show lesser evolutionary constraint, so that one must limit the comparison to only the most conserved paired positions ; these should be identical, or lack any compensatory base change, for any interbreeding to be possible.
[ "the 10 basal pairings in II and the 18 pairings including and immediately surrounding the highly conserved 5′ sequence of helix III" ]
For groups with longer sequences, the additional regions appear to show lesser evolutionary constraint, so that one must limit the comparison to only the most conserved paired positions ; these should be identical, or lack any compensatory base change, for any interbreeding to be possible.
true
true
true
true
true
1,664
8
DISCUSSION
1
5
[ "B31", "B6", "B8", "B32", "B5", "B33", "B34", "B35" ]
17,459,886
pmid-10896128|NA|NA|pmid-9873081|pmid-9060392|pmid-11821917|pmid-15022773|NA
Such an analysis requires a plethora of data, not only ITS2 sequences but experimental interbreeding data; yet examples have been found among protists (6,8,32), plants (5) and animals (33,34) to test the hypothesis.
[ "31", "6", "8", "32", "5", "33", "34", "35" ]
215
10,429
1
false
Such an analysis requires a plethora of data, not only ITS2 sequences but experimental interbreeding data; yet examples have been found among protists, plants and animals to test the hypothesis.
[ "6,8,32", "5", "33,34" ]
Such an analysis requires a plethora of data, not only ITS2 sequences but experimental interbreeding data; yet examples have been found among protists, plants and animals to test the hypothesis.
true
true
true
true
true
1,664
8
DISCUSSION
1
31
[ "B31", "B6", "B8", "B32", "B5", "B33", "B34", "B35" ]
17,459,886
pmid-10896128|NA|NA|pmid-9873081|pmid-9060392|pmid-11821917|pmid-15022773|NA
An additional data set arises from the clades of angiosperms endemic to either the Hawaiian Islands or to Macaronesia, where only a limited evolutionary time has been available to produce the endemic genera and species groups now present.
[ "31", "6", "8", "32", "5", "33", "34", "35" ]
238
10,430
0
false
An additional data set arises from the clades of angiosperms endemic to either the Hawaiian Islands or to Macaronesia, where only a limited evolutionary time has been available to produce the endemic genera and species groups now present.
[]
An additional data set arises from the clades of angiosperms endemic to either the Hawaiian Islands or to Macaronesia, where only a limited evolutionary time has been available to produce the endemic genera and species groups now present.
true
true
true
true
true
1,664
8
DISCUSSION
1
35
[ "B31", "B6", "B8", "B32", "B5", "B33", "B34", "B35" ]
17,459,886
pmid-10896128|NA|NA|pmid-9873081|pmid-9060392|pmid-11821917|pmid-15022773|NA
Breeding studies have suggested that none of these groups has managed to evolve to the point of sexual isolation (35).
[ "31", "6", "8", "32", "5", "33", "34", "35" ]
118
10,431
1
false
Breeding studies have suggested that none of these groups has managed to evolve to the point of sexual isolation.
[ "35" ]
Breeding studies have suggested that none of these groups has managed to evolve to the point of sexual isolation.
true
true
true
true
true
1,664
8
DISCUSSION
1
31
[ "B31", "B6", "B8", "B32", "B5", "B33", "B34", "B35" ]
17,459,886
pmid-10896128|NA|NA|pmid-9873081|pmid-9060392|pmid-11821917|pmid-15022773|NA
Comparisons of the ITS2 sequences, in the nine genus and species swarms where ITS2 is available, now agree that all have the expected ITS2 nucleotide identity (Coleman, in preparation).
[ "31", "6", "8", "32", "5", "33", "34", "35" ]
185
10,432
0
false
Comparisons of the ITS2 sequences, in the nine genus and species swarms where ITS2 is available, now agree that all have the expected ITS2 nucleotide identity (Coleman, in preparation).
[]
Comparisons of the ITS2 sequences, in the nine genus and species swarms where ITS2 is available, now agree that all have the expected ITS2 nucleotide identity (Coleman, in preparation).
true
true
true
true
true
1,664
9
DISCUSSION
1
36
[ "B36" ]
17,459,886
pmid-3779840
In sum, ITS2 is present in essentially all eukaryotes, and even when truncated, the region is still sufficient to allow identification to species and lower.
[ "36" ]
156
10,433
0
false
In sum, ITS2 is present in essentially all eukaryotes, and even when truncated, the region is still sufficient to allow identification to species and lower.
[]
In sum, ITS2 is present in essentially all eukaryotes, and even when truncated, the region is still sufficient to allow identification to species and lower.
true
true
true
true
true
1,665
9
DISCUSSION
1
36
[ "B36" ]
17,459,886
pmid-3779840
There is no evidence of any horizontal gene transfer (36).
[ "36" ]
58
10,434
1
false
There is no evidence of any horizontal gene transfer.
[ "36" ]
There is no evidence of any horizontal gene transfer.
true
true
true
true
true
1,665
9
DISCUSSION
1
36
[ "B36" ]
17,459,886
pmid-3779840
ITS2 PCR and sequencing are straight forward, and there is rarely any excessive length.
[ "36" ]
87
10,435
0
false
ITS2 PCR and sequencing are straight forward, and there is rarely any excessive length.
[]
ITS2 PCR and sequencing are straight forward, and there is rarely any excessive length.
true
true
true
true
true
1,665
9
DISCUSSION
1
36
[ "B36" ]
17,459,886
pmid-3779840
A recognizable short pyrimidine bulge-containing helix (‘helix II’) and downstream, a longer helix with highly conserved nucleotide motif on the 5′ side (‘helix III’) are essentially universally present.
[ "36" ]
203
10,436
0
false
A recognizable short pyrimidine bulge-containing helix (‘helix II’) and downstream, a longer helix with highly conserved nucleotide motif on the 5′ side (‘helix III’) are essentially universally present.
[]
A recognizable short pyrimidine bulge-containing helix (‘helix II’) and downstream, a longer helix with highly conserved nucleotide motif on the 5′ side (‘helix III’) are essentially universally present.
true
true
true
true
true
1,665
9
DISCUSSION
1
36
[ "B36" ]
17,459,886
pmid-3779840
For the full biochemical understanding of how ribosomal RNA processing occurs, the many ITS alignments available should prove invaluable to test models, and those few eukaryotes groups (e.g.
[ "36" ]
190
10,437
0
false
For the full biochemical understanding of how ribosomal RNA processing occurs, the many ITS alignments available should prove invaluable to test models, and those few eukaryotes groups (e.g.
[]
For the full biochemical understanding of how ribosomal RNA processing occurs, the many ITS alignments available should prove invaluable to test models, and those few eukaryotes groups (e.g.
true
true
true
true
true
1,665
9
DISCUSSION
1
36
[ "B36" ]
17,459,886
pmid-3779840
Acropora corals) lacking helix III and hence its detailed guidance role in processing pose a further challenge since they obviously produce ribosomes.
[ "36" ]
150
10,438
0
false
Acropora corals) lacking helix III and hence its detailed guidance role in processing pose a further challenge since they obviously produce ribosomes.
[]
Acropora corals) lacking helix III and hence its detailed guidance role in processing pose a further challenge since they obviously produce ribosomes.
true
true
true
true
true
1,665
9
DISCUSSION
1
36
[ "B36" ]
17,459,886
pmid-3779840
Furthermore, thanks to its conserved secondary structure aspects, one has a guide, from sequence and structure alone, to the group of taxa probably capable of interbreeding.
[ "36" ]
173
10,439
0
false
Furthermore, thanks to its conserved secondary structure aspects, one has a guide, from sequence and structure alone, to the group of taxa probably capable of interbreeding.
[]
Furthermore, thanks to its conserved secondary structure aspects, one has a guide, from sequence and structure alone, to the group of taxa probably capable of interbreeding.
true
true
true
true
true
1,665
9
DISCUSSION
1
36
[ "B36" ]
17,459,886
pmid-3779840
This correlation allows interesting comparisons of breeding potential with the idiosyncracies of taxonomic practice at the species level across eukaryote groups.
[ "36" ]
161
10,440
0
false
This correlation allows interesting comparisons of breeding potential with the idiosyncracies of taxonomic practice at the species level across eukaryote groups.
[]
This correlation allows interesting comparisons of breeding potential with the idiosyncracies of taxonomic practice at the species level across eukaryote groups.
true
true
true
true
true
1,665
9
DISCUSSION
1
36
[ "B36" ]
17,459,886
pmid-3779840
The ITS2, once considered a highly variable and largely uninteresting locus, has proven in fact to be one containing eukaryote-wide homology, undoubtedly a consequence of its guidance role in what must be a eukaryote-wide biochemistry of ribosome formation.
[ "36" ]
257
10,441
0
false
The ITS2, once considered a highly variable and largely uninteresting locus, has proven in fact to be one containing eukaryote-wide homology, undoubtedly a consequence of its guidance role in what must be a eukaryote-wide biochemistry of ribosome formation.
[]
The ITS2, once considered a highly variable and largely uninteresting locus, has proven in fact to be one containing eukaryote-wide homology, undoubtedly a consequence of its guidance role in what must be a eukaryote-wide biochemistry of ribosome formation.
true
true
true
true
true
1,665
0
INTRODUCTION
1
1
[ "b1" ]
17,135,193
pmid-10839820
Membrane transporters are a large group of proteins that span the cell membrane and form an intricate system of pumps and channels through which they deliver essential nutrients, eject waste products and assist the cell to sense environmental conditions.
[ "1" ]
254
10,442
0
false
Membrane transporters are a large group of proteins that span the cell membrane and form an intricate system of pumps and channels through which they deliver essential nutrients, eject waste products and assist the cell to sense environmental conditions.
[]
Membrane transporters are a large group of proteins that span the cell membrane and form an intricate system of pumps and channels through which they deliver essential nutrients, eject waste products and assist the cell to sense environmental conditions.
true
true
true
true
true
1,666
0
INTRODUCTION
1
1
[ "b1" ]
17,135,193
pmid-10839820
Transporters represent a large and diverse group of proteins that differ in membrane topology, energy coupling mechanism and substrate specificities.
[ "1" ]
149
10,443
0
false
Transporters represent a large and diverse group of proteins that differ in membrane topology, energy coupling mechanism and substrate specificities.
[]
Transporters represent a large and diverse group of proteins that differ in membrane topology, energy coupling mechanism and substrate specificities.
true
true
true
true
true
1,666
0
INTRODUCTION
1
1
[ "b1" ]
17,135,193
pmid-10839820
They play indispensable roles in the fundamental cellular processes of all organisms (1).
[ "1" ]
89
10,444
1
false
They play indispensable roles in the fundamental cellular processes of all organisms.
[ "1" ]
They play indispensable roles in the fundamental cellular processes of all organisms.
true
true
true
true
true
1,666
1
INTRODUCTION
1
2
[ "b2", "b4", "b5" ]
17,135,193
pmid-9533881|NA|pmid-14681414
With the advent of the genomics era, comprehensive genome-wide bioinformatic comparisons of predicted membrane transporters across a range of organisms in all three domains of life have become possible.
[ "2", "4", "5" ]
202
10,445
0
false
With the advent of the genomics era, comprehensive genome-wide bioinformatic comparisons of predicted membrane transporters across a range of organisms in all three domains of life have become possible.
[]
With the advent of the genomics era, comprehensive genome-wide bioinformatic comparisons of predicted membrane transporters across a range of organisms in all three domains of life have become possible.
true
true
true
true
true
1,667
1
INTRODUCTION
1
2
[ "b2", "b4", "b5" ]
17,135,193
pmid-9533881|NA|pmid-14681414
Previously, we have reported a series of comparative analyses of transport systems in a collection of prokaryotic and eukaryotic organisms (2–4).
[ "2", "4", "5" ]
145
10,446
0
false
Previously, we have reported a series of comparative analyses of transport systems in a collection of prokaryotic and eukaryotic organisms.
[ "2–4" ]
Previously, we have reported a series of comparative analyses of transport systems in a collection of prokaryotic and eukaryotic organisms.
true
true
true
true
true
1,667
1
INTRODUCTION
1
2
[ "b2", "b4", "b5" ]
17,135,193
pmid-9533881|NA|pmid-14681414
We started a web portal showing our bioinformatic prediction of transporters in sequenced genomes back in 1996, and have had a continual web presence since then.
[ "2", "4", "5" ]
161
10,447
0
false
We started a web portal showing our bioinformatic prediction of transporters in sequenced genomes back in 1996, and have had a continual web presence since then.
[]
We started a web portal showing our bioinformatic prediction of transporters in sequenced genomes back in 1996, and have had a continual web presence since then.
true
true
true
true
true
1,667
1
INTRODUCTION
1
5
[ "b2", "b4", "b5" ]
17,135,193
pmid-9533881|NA|pmid-14681414
The current incarnation of TransportDB dates back to 2002, when we moved to a relational database structure and greatly enhanced the available features (5).
[ "2", "4", "5" ]
156
10,448
1
false
The current incarnation of TransportDB dates back to 2002, when we moved to a relational database structure and greatly enhanced the available features.
[ "5" ]
The current incarnation of TransportDB dates back to 2002, when we moved to a relational database structure and greatly enhanced the available features.
true
true
true
true
true
1,667
1
INTRODUCTION
1
2
[ "b2", "b4", "b5" ]
17,135,193
pmid-9533881|NA|pmid-14681414
The aim of TransportDB is to present the comprehensive transporter profiles of each sequenced prokaryotic and eukaryotic organisms, as well as to provide comparative and phylogenetic tools to view, search, compare and download the transporter data in an easy-to-navigate format.
[ "2", "4", "5" ]
278
10,449
0
false
The aim of TransportDB is to present the comprehensive transporter profiles of each sequenced prokaryotic and eukaryotic organisms, as well as to provide comparative and phylogenetic tools to view, search, compare and download the transporter data in an easy-to-navigate format.
[]
The aim of TransportDB is to present the comprehensive transporter profiles of each sequenced prokaryotic and eukaryotic organisms, as well as to provide comparative and phylogenetic tools to view, search, compare and download the transporter data in an easy-to-navigate format.
true
true
true
true
true
1,667
1
INTRODUCTION
1
2
[ "b2", "b4", "b5" ]
17,135,193
pmid-9533881|NA|pmid-14681414
We describe in this paper the data content and web features of TransportDB, with a focus on the recent additions and improvements.
[ "2", "4", "5" ]
130
10,450
0
false
We describe in this paper the data content and web features of TransportDB, with a focus on the recent additions and improvements.
[]
We describe in this paper the data content and web features of TransportDB, with a focus on the recent additions and improvements.
true
true
true
true
true
1,667
0
INTRODUCTION
0
null
null
17,686,787
pmid-9228948
RNAs are capable of carrying out a multitude of diverse biological functions.
null
77
10,451
0
false
null
null
RNAs are capable of carrying out a multitude of diverse biological functions.
true
true
true
true
true
1,668
0
INTRODUCTION
0
null
null
17,686,787
pmid-9228948
Many biologically active RNAs have to adopt intricate 3D structures that rival protein structures in their complexity to be functional in a cellular environment.
null
161
10,452
0
false
null
null
Many biologically active RNAs have to adopt intricate 3D structures that rival protein structures in their complexity to be functional in a cellular environment.
true
true
true
true
true
1,668
1
INTRODUCTION
1
1
[ "B1", "B2" ]
17,686,787
pmid-15811793|pmid-9751704
Folding of RNA chains into compact globular 3D structures represents a problem.
[ "1", "2" ]
79
10,453
0
false
Folding of RNA chains into compact globular 3D structures represents a problem.
[]
Folding of RNA chains into compact globular 3D structures represents a problem.
true
true
true
true
true
1,669
1
INTRODUCTION
1
1
[ "B1", "B2" ]
17,686,787
pmid-15811793|pmid-9751704
Due to the polyanionic character of the RNA phosphodiester backbone, it inevitably brings negative charges in close proximity to each other.
[ "1", "2" ]
140
10,454
0
false
Due to the polyanionic character of the RNA phosphodiester backbone, it inevitably brings negative charges in close proximity to each other.
[]
Due to the polyanionic character of the RNA phosphodiester backbone, it inevitably brings negative charges in close proximity to each other.
true
true
true
true
true
1,669
1
INTRODUCTION
1
1
[ "B1", "B2" ]
17,686,787
pmid-15811793|pmid-9751704
This results in highly unfavorable electrostatic interactions that are anisotropically distributed in the folded form of the RNA.
[ "1", "2" ]
129
10,455
0
false
This results in highly unfavorable electrostatic interactions that are anisotropically distributed in the folded form of the RNA.
[]
This results in highly unfavorable electrostatic interactions that are anisotropically distributed in the folded form of the RNA.
true
true
true
true
true
1,669
1
INTRODUCTION
1
1
[ "B1", "B2" ]
17,686,787
pmid-15811793|pmid-9751704
Therefore, divalent metal ions in general and Mg2+ with its favorable charge/size ratio in particular (1) play an important role in RNA folding.
[ "1", "2" ]
144
10,456
1
false
Therefore, divalent metal ions in general and Mg2+ with its favorable charge/size ratio in particular play an important role in RNA folding.
[ "1" ]
Therefore, divalent metal ions in general and Mg2+ with its favorable charge/size ratio in particular play an important role in RNA folding.
true
true
true
true
true
1,669
1
INTRODUCTION
1
1
[ "B1", "B2" ]
17,686,787
pmid-15811793|pmid-9751704
Mg2+-ions not only stabilize the final structure through either direct coordination (inner sphere contact) with negatively charged groups of the RNA or in a water-mediated interaction (outer sphere contact) with the hexahydrated ion (Mg(H2O)62+).
[ "1", "2" ]
246
10,457
0
false
Mg2+-ions not only stabilize the final structure through either direct coordination (inner sphere contact) with negatively charged groups of the RNA or in a water-mediated interaction (outer sphere contact) with the hexahydrated ion 62+).
[ "Mg(H2O" ]
Mg2+-ions not only stabilize the final structure through either direct coordination (inner sphere contact) with negatively charged groups of the RNA or in a water-mediated interaction (outer sphere contact) with the hexahydrated ion 62+).
true
true
true
true
true
1,669
1
INTRODUCTION
1
2
[ "B1", "B2" ]
17,686,787
pmid-15811793|pmid-9751704
They also influence the rate of folding, stabilize folding intermediates or destabilize alternative conformations (2).
[ "1", "2" ]
118
10,458
1
false
They also influence the rate of folding, stabilize folding intermediates or destabilize alternative conformations.
[ "2" ]
They also influence the rate of folding, stabilize folding intermediates or destabilize alternative conformations.
true
true
true
true
true
1,669
2
INTRODUCTION
1
3
[ "B3" ]
17,686,787
NA|pmid-16931335|pmid-17440909|pmid-17175531|pmid-15610857
Riboswitches control the expression of a significant number of bacterial genes by binding with high affinity and specificity to small metabolite molecules.
[ "3" ]
155
10,459
0
false
Riboswitches control the expression of a significant number of bacterial genes by binding with high affinity and specificity to small metabolite molecules.
[]
Riboswitches control the expression of a significant number of bacterial genes by binding with high affinity and specificity to small metabolite molecules.
true
true
true
true
true
1,670
2
INTRODUCTION
1
3
[ "B3" ]
17,686,787
NA|pmid-16931335|pmid-17440909|pmid-17175531|pmid-15610857
To achieve the binding specificity and affinity required for their function, the ligand binding or aptamer domains of these RNA elements must fold into intricate tertiary structures.
[ "3" ]
182
10,460
0
false
To achieve the binding specificity and affinity required for their function, the ligand binding or aptamer domains of these RNA elements must fold into intricate tertiary structures.
[]
To achieve the binding specificity and affinity required for their function, the ligand binding or aptamer domains of these RNA elements must fold into intricate tertiary structures.
true
true
true
true
true
1,670
2
INTRODUCTION
1
3
[ "B3" ]
17,686,787
NA|pmid-16931335|pmid-17440909|pmid-17175531|pmid-15610857
This is illustrated in a number of X-ray structures of aptamer domain/ligand complexes of different riboswitches (3).
[ "3" ]
117
10,461
1
false
This is illustrated in a number of X-ray structures of aptamer domain/ligand complexes of different riboswitches.
[ "3" ]
This is illustrated in a number of X-ray structures of aptamer domain/ligand complexes of different riboswitches.
true
true
true
true
true
1,670
2
INTRODUCTION
1
3
[ "B3" ]
17,686,787
NA|pmid-16931335|pmid-17440909|pmid-17175531|pmid-15610857
In many cases, the X-ray structures revealed the presence of defined Mg2+-binding sites.
[ "3" ]
88
10,462
0
false
In many cases, the X-ray structures revealed the presence of defined Mg2+-binding sites.
[]
In many cases, the X-ray structures revealed the presence of defined Mg2+-binding sites.
true
true
true
true
true
1,670
3
INTRODUCTION
1
4
[ "B4", "B5", "B6 B7 B8", "B9", "B10" ]
17,686,787
pmid-16871614|pmid-15862294|pmid-16962976|pmid-16728979|pmid-16675665|pmid-16484375|pmid-16990543|pmid-10373367|pmid-16351072
For instance for the thiamine pyrophosphate (TPP)-sensing riboswitch it was shown that Mg2+ binding is absolutely required for TPP binding (4) and cannot be replaced by monovalent ions or Ca2+ (5).
[ "4", "5", "6–8", "9", "10" ]
197
10,463
1
false
For instance for the thiamine pyrophosphate (TPP)-sensing riboswitch it was shown that Mg2+ binding is absolutely required for TPP binding and cannot be replaced by monovalent ions or Ca2+.
[ "4", "5" ]
For instance for the thiamine pyrophosphate (TPP)-sensing riboswitch it was shown that Mg2+ binding is absolutely required for TPP binding and cannot be replaced by monovalent ions or Ca2+.
true
true
true
true
true
1,671
3
INTRODUCTION
1
4
[ "B4", "B5", "B6 B7 B8", "B9", "B10" ]
17,686,787
pmid-16871614|pmid-15862294|pmid-16962976|pmid-16728979|pmid-16675665|pmid-16484375|pmid-16990543|pmid-10373367|pmid-16351072
The X-ray structure of the thiC TPP-sensing riboswitch from Arabidopsis thaliana bound to TPP reveals that one Mg2+-ion chelates oxygen atoms in the pyrophosphate moiety of TPP and links them to the RNA whereas there are two bridging Mg2+-ions in the X-ray structure of the thiM TPP-sensing riboswitch from Escherichia c...
[ "4", "5", "6–8", "9", "10" ]
337
10,464
0
false
The X-ray structure of the thiC TPP-sensing riboswitch from Arabidopsis thaliana bound to TPP reveals that one Mg2+-ion chelates oxygen atoms in the pyrophosphate moiety of TPP and links them to the RNA whereas there are two bridging Mg2+-ions in the X-ray structure of the thiM TPP-sensing riboswitch from Escherichia c...
[]
The X-ray structure of the thiC TPP-sensing riboswitch from Arabidopsis thaliana bound to TPP reveals that one Mg2+-ion chelates oxygen atoms in the pyrophosphate moiety of TPP and links them to the RNA whereas there are two bridging Mg2+-ions in the X-ray structure of the thiM TPP-sensing riboswitch from Escherichia c...
true
true
true
true
true
1,671
3
INTRODUCTION
1
6–8
[ "B4", "B5", "B6 B7 B8", "B9", "B10" ]
17,686,787
pmid-16871614|pmid-15862294|pmid-16962976|pmid-16728979|pmid-16675665|pmid-16484375|pmid-16990543|pmid-10373367|pmid-16351072
The presence of bridging Mg2+-ions in the X-ray structures is consistent with the strict Mg2+ requirements for TPP binding to the TPP-sensing riboswitch (6–8).
[ "4", "5", "6–8", "9", "10" ]
159
10,465
1
false
The presence of bridging Mg2+-ions in the X-ray structures is consistent with the strict Mg2+ requirements for TPP binding to the TPP-sensing riboswitch.
[ "6–8" ]
The presence of bridging Mg2+-ions in the X-ray structures is consistent with the strict Mg2+ requirements for TPP binding to the TPP-sensing riboswitch.
true
true
true
true
true
1,671
3
INTRODUCTION
1
4
[ "B4", "B5", "B6 B7 B8", "B9", "B10" ]
17,686,787
pmid-16871614|pmid-15862294|pmid-16962976|pmid-16728979|pmid-16675665|pmid-16484375|pmid-16990543|pmid-10373367|pmid-16351072
In contrast, the GlmS riboswitch—a ribozyme that undergoes a self-cleavage reaction in the presence of glucosamine-6-phosphate (GlcN6P)—does not strictly require Mg2+ for the self-cleavage reaction.
[ "4", "5", "6–8", "9", "10" ]
198
10,466
0
false
In contrast, the GlmS riboswitch—a ribozyme that undergoes a self-cleavage reaction in the presence of glucosamine-6-phosphate (GlcN6P)—does not strictly require Mg2+ for the self-cleavage reaction.
[]
In contrast, the GlmS riboswitch—a ribozyme that undergoes a self-cleavage reaction in the presence of glucosamine-6-phosphate (GlcN6P)—does not strictly require Mg2+ for the self-cleavage reaction.
true
true
true
true
true
1,671
3
INTRODUCTION
1
9
[ "B4", "B5", "B6 B7 B8", "B9", "B10" ]
17,686,787
pmid-16871614|pmid-15862294|pmid-16962976|pmid-16728979|pmid-16675665|pmid-16484375|pmid-16990543|pmid-10373367|pmid-16351072
Here, Mg2+ can be substituted by either other divalent metal ions or Co(NH3)63+ and to some extend by high concentrations of monovalent ions (9) indicating that the metal ion is not involved in catalysis but only in electrostatic stabilization of the structure consistent with the X-ray structure of this complex (10).
[ "4", "5", "6–8", "9", "10" ]
318
10,467
1
false
Here, Mg2+ can be substituted by either other divalent metal ions or Co(NH3)63+ and to some extend by high concentrations of monovalent ions indicating that the metal ion is not involved in catalysis but only in electrostatic stabilization of the structure consistent with the X-ray structure of this complex.
[ "9", "10" ]
Here, Mg2+ can be substituted by either other divalent metal ions or Co(NH3)63+ and to some extend by high concentrations of monovalent ions indicating that the metal ion is not involved in catalysis but only in electrostatic stabilization of the structure consistent with the X-ray structure of this complex.
true
true
true
true
true
1,671
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
The purine-sensing riboswitches are among the smallest riboswitches found so far.
[ "11", "12", "13–15" ]
81
10,468
0
false
The purine-sensing riboswitches are among the smallest riboswitches found so far.
[]
The purine-sensing riboswitches are among the smallest riboswitches found so far.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
All purine riboswitches fold into a three-way junction (Figure 1A) where central structural elements such as the ligand-binding core region and the loops L2 and L3 that cap helices II and III, respectively, show a very high degree of sequence conservation.
[ "11", "12", "13–15" ]
256
10,469
0
false
All purine riboswitches fold into a three-way junction (Figure 1A) where central structural elements such as the ligand-binding core region and the loops L2 and L3 that cap helices II and III, respectively, show a very high degree of sequence conservation.
[]
All purine riboswitches fold into a three-way junction where central structural elements such as the ligand-binding core region and the loops L2 and L3 that cap helices II and III, respectively, show a very high degree of sequence conservation.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
However, despite the sequence conservation and similarity in structure, the adenine-sensing riboswitch binds adenine with high specificity while the guanine-sensing riboswitch binds guanine.
[ "11", "12", "13–15" ]
190
10,470
0
false
However, despite the sequence conservation and similarity in structure, the adenine-sensing riboswitch binds adenine with high specificity while the guanine-sensing riboswitch binds guanine.
[]
However, despite the sequence conservation and similarity in structure, the adenine-sensing riboswitch binds adenine with high specificity while the guanine-sensing riboswitch binds guanine.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
This specificity is mediated by a single nucleotide in the ligand-binding core region which is a cytidin in the guanine-sensing riboswitch and a uridine in the adenine-sensing riboswitch (11,12).
[ "11", "12", "13–15" ]
195
10,471
0
false
This specificity is mediated by a single nucleotide in the ligand-binding core region which is a cytidin in the guanine-sensing riboswitch and a uridine in the adenine-sensing riboswitch.
[ "11,12" ]
This specificity is mediated by a single nucleotide in the ligand-binding core region which is a cytidin in the guanine-sensing riboswitch and a uridine in the adenine-sensing riboswitch.
true
true
true
true
true
1,672
4
INTRODUCTION
1
13–15
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
It was shown that the purine ligand is bound to this specific nucleotide in the core region by forming an intermolecular Watson–Crick base pair (13–15).
[ "11", "12", "13–15" ]
152
10,472
1
false
It was shown that the purine ligand is bound to this specific nucleotide in the core region by forming an intermolecular Watson–Crick base pair.
[ "13–15" ]
It was shown that the purine ligand is bound to this specific nucleotide in the core region by forming an intermolecular Watson–Crick base pair.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
Figure 1.Adenine binding the adenine-sensing riboswitch and complete imino resonance assignment.
[ "11", "12", "13–15" ]
96
10,473
0
false
Figure 1.Adenine binding the adenine-sensing riboswitch and complete imino resonance assignment.
[]
Figure 1.Adenine binding the adenine-sensing riboswitch and complete imino resonance assignment.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
(A) Secondary structure of the aptamer domain of the pbuE adenine-sensing riboswitch from B. subtilis where loops L2 and L3 are boxed.
[ "11", "12", "13–15" ]
134
10,474
0
false
(A) Secondary structure of the aptamer domain of the pbuE adenine-sensing riboswitch from B. subtilis where loops L2 and L3 are boxed.
[]
(A) Secondary structure of the aptamer domain of the pbuE adenine-sensing riboswitch from B. subtilis where loops L2 and L3 are boxed.
false
false
true
true
false
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
The sequence of L2 and L3 of the xpt–pbuX guanine-sensing riboswitch from B. subtilis is shown below in separate boxes.
[ "11", "12", "13–15" ]
119
10,475
0
false
The sequence of L2 and L3 of the xpt–pbuX guanine-sensing riboswitch from B. subtilis is shown below in separate boxes.
[]
The sequence of L2 and L3 of the xpt–pbuX guanine-sensing riboswitch from B. subtilis is shown below in separate boxes.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
Nucleotides that are different in the guanine-sensing riboswitch compared to the adenine-sensing riboswitch are shaded in gray.
[ "11", "12", "13–15" ]
127
10,476
0
false
Nucleotides that are different in the guanine-sensing riboswitch compared to the adenine-sensing riboswitch are shaded in gray.
[]
Nucleotides that are different in the guanine-sensing riboswitch compared to the adenine-sensing riboswitch are shaded in gray.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
(B) Imino region of a 1H,15N-HSQC spectrum of the aptamer domain of the adenine-sensing riboswitch RNA in complex with adenine and complete imino resonance assignment in the absence of Mg2+ at 10°C.
[ "11", "12", "13–15" ]
198
10,477
0
false
(B) Imino region of a 1H,15N-HSQC spectrum of the aptamer domain of the adenine-sensing riboswitch RNA in complex with adenine and complete imino resonance assignment in the absence of Mg2+ at 10°C.
[]
(B) Imino region of a 1H,15N-HSQC spectrum of the aptamer domain of the adenine-sensing riboswitch RNA in complex with adenine and complete imino resonance assignment in the absence of Mg2+ at 10°C.
false
false
true
true
false
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
The signal of the H9N9 imino group of adenine is labeled in blue.
[ "11", "12", "13–15" ]
65
10,478
0
false
The signal of the H9N9 imino group of adenine is labeled in blue.
[]
The signal of the H9N9 imino group of adenine is labeled in blue.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
(C) HNN-COSY experiment of the RNA–adenine complex in the absence of Mg2+ at 10°C.
[ "11", "12", "13–15" ]
82
10,479
0
false
(C) HNN-COSY experiment of the RNA–adenine complex in the absence of Mg2+ at 10°C.
[]
(C) HNN-COSY experiment of the RNA–adenine complex in the absence of Mg2+ at 10°C.
false
false
true
true
false
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
The correlation from the hydrogen bond donor (N-H, black resonances) to the hydrogen bond acceptor (N, red resonances) is indicated by dashed lines for RNA–adenine intermolecular hydrogen bonds and for selected tertiary interactions.
[ "11", "12", "13–15" ]
233
10,480
0
false
The correlation from the hydrogen bond donor (N-H, black resonances) to the hydrogen bond acceptor (N, red resonances) is indicated by dashed lines for RNA–adenine intermolecular hydrogen bonds and for selected tertiary interactions.
[]
The correlation from the hydrogen bond donor (N-H, black resonances) to the hydrogen bond acceptor (N, red resonances) is indicated by dashed lines for RNA–adenine intermolecular hydrogen bonds and for selected tertiary interactions.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
Schematic drawing of the intermolecular base triple (D) involving adenine recognition by U74 and U51 from the adenine-sensing riboswitch, (E) the interaction between U49 and A76, and (F) the long-range reversed-Hoogsteen A65:U34 base pair.
[ "11", "12", "13–15" ]
239
10,481
0
false
Schematic drawing of the intermolecular base triple (D) involving adenine recognition by U74 and U51 from the adenine-sensing riboswitch, (E) the interaction between U49 and A76, and (F) the long-range reversed-Hoogsteen A65:U34 base pair.
[]
Schematic drawing of the intermolecular base triple (D) involving adenine recognition by U74 and U51 from the adenine-sensing riboswitch, (E) the interaction between U49 and A76, and (F) the long-range reversed-Hoogsteen A65:U34 base pair.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
All hydrogen bonds are indicated by dashed lines.
[ "11", "12", "13–15" ]
49
10,482
0
false
All hydrogen bonds are indicated by dashed lines.
[]
All hydrogen bonds are indicated by dashed lines.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
Hydrogen bonds including the hydrogen bond donor and the hydrogen bond acceptor which are detected and annotated in (C) are shown in red.
[ "11", "12", "13–15" ]
137
10,483
0
false
Hydrogen bonds including the hydrogen bond donor and the hydrogen bond acceptor which are detected and annotated in (C) are shown in red.
[]
Hydrogen bonds including the hydrogen bond donor and the hydrogen bond acceptor which are detected and annotated in (C) are shown in red.
true
true
true
true
true
1,672
4
INTRODUCTION
1
11
[ "B11", "B12", "B13 B14 B15" ]
17,686,787
pmid-12787499|pmid-14718920|pmid-15549109|pmid-15610857|pmid-15665103|pmid-16931335|pmid-17440909|pmid-14718920|pmid-17175531|pmid-16201765|pmid-17440909|pmid-17200422
The adenine ligand is shown in blue.
[ "11", "12", "13–15" ]
36
10,484
0
false
The adenine ligand is shown in blue.
[]
The adenine ligand is shown in blue.
true
true
true
true
true
1,672
5
INTRODUCTION
0
null
null
17,686,787
null
Adenine binding the adenine-sensing riboswitch and complete imino resonance assignment.
null
87
10,485
0
false
null
null
Adenine binding the adenine-sensing riboswitch and complete imino resonance assignment.
true
true
true
true
true
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
(A) Secondary structure of the aptamer domain of the pbuE adenine-sensing riboswitch from B. subtilis where loops L2 and L3 are boxed.
null
134
10,486
0
false
null
null
(A) Secondary structure of the aptamer domain of the pbuE adenine-sensing riboswitch from B. subtilis where loops L2 and L3 are boxed.
false
false
true
true
false
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
The sequence of L2 and L3 of the xpt–pbuX guanine-sensing riboswitch from B. subtilis is shown below in separate boxes.
null
119
10,487
0
false
null
null
The sequence of L2 and L3 of the xpt–pbuX guanine-sensing riboswitch from B. subtilis is shown below in separate boxes.
true
true
true
true
true
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
Nucleotides that are different in the guanine-sensing riboswitch compared to the adenine-sensing riboswitch are shaded in gray.
null
127
10,488
0
false
null
null
Nucleotides that are different in the guanine-sensing riboswitch compared to the adenine-sensing riboswitch are shaded in gray.
true
true
true
true
true
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
(B) Imino region of a 1H,15N-HSQC spectrum of the aptamer domain of the adenine-sensing riboswitch RNA in complex with adenine and complete imino resonance assignment in the absence of Mg2+ at 10°C.
null
198
10,489
0
false
null
null
(B) Imino region of a 1H,15N-HSQC spectrum of the aptamer domain of the adenine-sensing riboswitch RNA in complex with adenine and complete imino resonance assignment in the absence of Mg2+ at 10°C.
false
false
true
true
false
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
The signal of the H9N9 imino group of adenine is labeled in blue.
null
65
10,490
0
false
null
null
The signal of the H9N9 imino group of adenine is labeled in blue.
true
true
true
true
true
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
(C) HNN-COSY experiment of the RNA–adenine complex in the absence of Mg2+ at 10°C.
null
82
10,491
0
false
null
null
(C) HNN-COSY experiment of the RNA–adenine complex in the absence of Mg2+ at 10°C.
false
false
true
true
false
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
The correlation from the hydrogen bond donor (N-H, black resonances) to the hydrogen bond acceptor (N, red resonances) is indicated by dashed lines for RNA–adenine intermolecular hydrogen bonds and for selected tertiary interactions.
null
233
10,492
0
false
null
null
The correlation from the hydrogen bond donor (N-H, black resonances) to the hydrogen bond acceptor (N, red resonances) is indicated by dashed lines for RNA–adenine intermolecular hydrogen bonds and for selected tertiary interactions.
true
true
true
true
true
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
Schematic drawing of the intermolecular base triple (D) involving adenine recognition by U74 and U51 from the adenine-sensing riboswitch, (E) the interaction between U49 and A76, and (F) the long-range reversed-Hoogsteen A65:U34 base pair.
null
239
10,493
0
false
null
null
Schematic drawing of the intermolecular base triple (D) involving adenine recognition by U74 and U51 from the adenine-sensing riboswitch, (E) the interaction between U49 and A76, and (F) the long-range reversed-Hoogsteen A65:U34 base pair.
true
true
true
true
true
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
All hydrogen bonds are indicated by dashed lines.
null
49
10,494
0
false
null
null
All hydrogen bonds are indicated by dashed lines.
true
true
true
true
true
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
Hydrogen bonds including the hydrogen bond donor and the hydrogen bond acceptor which are detected and annotated in (C) are shown in red.
null
137
10,495
0
false
null
null
Hydrogen bonds including the hydrogen bond donor and the hydrogen bond acceptor which are detected and annotated in (C) are shown in red.
true
true
true
true
true
1,673
5
INTRODUCTION
0
null
null
17,686,787
null
The adenine ligand is shown in blue.
null
36
10,496
0
false
null
null
The adenine ligand is shown in blue.
true
true
true
true
true
1,673
6
INTRODUCTION
1
16
[ "B16", "B17", "B14", "B13", "B14", "B15", "B18", "B17" ]
17,686,787
pmid-16650860|pmid-16931335|pmid-15610857|pmid-15549109|pmid-15610857|pmid-15665103|pmid-17175531|pmid-16931335|pmid-17200422|pmid-10606276|pmid-11274387
The importance of Mg2+-ions for ligand binding to these riboswitches is less clear.
[ "16", "17", "14", "13", "14", "15", "18", "17" ]
83
10,497
0
false
The importance of Mg2+-ions for ligand binding to these riboswitches is less clear.
[]
The importance of Mg2+-ions for ligand binding to these riboswitches is less clear.
true
true
true
true
true
1,674
6
INTRODUCTION
1
16
[ "B16", "B17", "B14", "B13", "B14", "B15", "B18", "B17" ]
17,686,787
pmid-16650860|pmid-16931335|pmid-15610857|pmid-15549109|pmid-15610857|pmid-15665103|pmid-17175531|pmid-16931335|pmid-17200422|pmid-10606276|pmid-11274387
Thermodynamic studies of ligand binding supported a requirement for the presence of Mg2+ in the case of hypoxanthine binding to the guanine-sensing riboswitch (16) and FRET studies of the pbuE adenine-sensing riboswitch from B. subtilis suggested an important role for Mg2+ in ligand binding (17).
[ "16", "17", "14", "13", "14", "15", "18", "17" ]
297
10,498
1
false
Thermodynamic studies of ligand binding supported a requirement for the presence of Mg2+ in the case of hypoxanthine binding to the guanine-sensing riboswitch and FRET studies of the pbuE adenine-sensing riboswitch from B. subtilis suggested an important role for Mg2+ in ligand binding.
[ "16", "17" ]
Thermodynamic studies of ligand binding supported a requirement for the presence of Mg2+ in the case of hypoxanthine binding to the guanine-sensing riboswitch and FRET studies of the pbuE adenine-sensing riboswitch from B. subtilis suggested an important role for Mg2+ in ligand binding.
true
true
true
true
true
1,674
6
INTRODUCTION
1
16
[ "B16", "B17", "B14", "B13", "B14", "B15", "B18", "B17" ]
17,686,787
pmid-16650860|pmid-16931335|pmid-15610857|pmid-15549109|pmid-15610857|pmid-15665103|pmid-17175531|pmid-16931335|pmid-17200422|pmid-10606276|pmid-11274387
Specifically, Mg2+ was required for the formation of the long-range base-pairing interactions between nucleotides in loop 2 and 3.
[ "16", "17", "14", "13", "14", "15", "18", "17" ]
130
10,499
0
false
Specifically, Mg2+ was required for the formation of the long-range base-pairing interactions between nucleotides in loop 2 and 3.
[]
Specifically, Mg2+ was required for the formation of the long-range base-pairing interactions between nucleotides in loop 2 and 3.
true
true
true
true
true
1,674