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
6
DISCUSSION
1
23
[ "B23", "B44", "B52" ]
17,284,463
pmid-10395892|pmid-1566578|pmid-11433350
It is known that uAUGs can inhibit translation in several ways.
[ "23", "44", "52" ]
63
10,200
0
false
It is known that uAUGs can inhibit translation in several ways.
[]
It is known that uAUGs can inhibit translation in several ways.
true
true
true
true
true
1,626
6
DISCUSSION
1
23
[ "B23", "B44", "B52" ]
17,284,463
pmid-10395892|pmid-1566578|pmid-11433350
When they are recognized by translational machinery, a futile cycle can occur, such that only the ribosomes skipping the uAUG (leaky scanning) can reach the main ORF.
[ "23", "44", "52" ]
166
10,201
0
false
When they are recognized by translational machinery, a futile cycle can occur, such that only the ribosomes skipping the uAUG (leaky scanning) can reach the main ORF.
[]
When they are recognized by translational machinery, a futile cycle can occur, such that only the ribosomes skipping the uAUG (leaky scanning) can reach the main ORF.
true
true
true
true
true
1,626
6
DISCUSSION
1
23
[ "B23", "B44", "B52" ]
17,284,463
pmid-10395892|pmid-1566578|pmid-11433350
Accordingly, the level of inhibition is directly related to the context for translation initiation: the better an uAUG is recognized, the greater the resulting inhibition (23).
[ "23", "44", "52" ]
176
10,202
1
false
Accordingly, the level of inhibition is directly related to the context for translation initiation: the better an uAUG is recognized, the greater the resulting inhibition.
[ "23" ]
Accordingly, the level of inhibition is directly related to the context for translation initiation: the better an uAUG is recognized, the greater the resulting inhibition.
true
true
true
true
true
1,626
6
DISCUSSION
1
23
[ "B23", "B44", "B52" ]
17,284,463
pmid-10395892|pmid-1566578|pmid-11433350
Even in conditions of optimal uAUG recognition, a small percentage of ribosomes, after translation of the uORF, can continue scanning for start sites (reinitiation), eventually reaching the AUG of the main ORF (44,52).
[ "23", "44", "52" ]
218
10,203
0
false
Even in conditions of optimal uAUG recognition, a small percentage of ribosomes, after translation of the uORF, can continue scanning for start sites (reinitiation), eventually reaching the AUG of the main ORF.
[ "44,52" ]
Even in conditions of optimal uAUG recognition, a small percentage of ribosomes, after translation of the uORF, can continue scanning for start sites (reinitiation), eventually reaching the AUG of the main ORF.
true
true
true
true
true
1,626
7
DISCUSSION
1
53
[ "B53", "B50" ]
17,284,463
pmid-15777708|pmid-11707416
Despite efficient translation of the uORF, the main cistron remains translated.
[ "53", "50" ]
79
10,204
0
false
Despite efficient translation of the uORF, the main cistron remains translated.
[]
Despite efficient translation of the uORF, the main cistron remains translated.
true
true
true
true
true
1,627
7
DISCUSSION
1
53
[ "B53", "B50" ]
17,284,463
pmid-15777708|pmid-11707416
Several mechanisms can explain the translation of the downstream cistron by internal ribosome entry, ribosome reinitiation and leaky scanning.
[ "53", "50" ]
142
10,205
0
false
Several mechanisms can explain the translation of the downstream cistron by internal ribosome entry, ribosome reinitiation and leaky scanning.
[]
Several mechanisms can explain the translation of the downstream cistron by internal ribosome entry, ribosome reinitiation and leaky scanning.
true
true
true
true
true
1,627
7
DISCUSSION
1
53
[ "B53", "B50" ]
17,284,463
pmid-15777708|pmid-11707416
The stronger suppression of uAUGs with respect to uORFs can be partially explained by the fact that initiation at the main ORF may occur only by leaky scanning in uAUG-containing transcripts, whereas both leaky scanning and ribosome reinitiation may allow initiation at the AUG of main uORF-containing transcripts (53).
[ "53", "50" ]
319
10,206
1
false
The stronger suppression of uAUGs with respect to uORFs can be partially explained by the fact that initiation at the main ORF may occur only by leaky scanning in uAUG-containing transcripts, whereas both leaky scanning and ribosome reinitiation may allow initiation at the AUG of main uORF-containing transcripts.
[ "53" ]
The stronger suppression of uAUGs with respect to uORFs can be partially explained by the fact that initiation at the main ORF may occur only by leaky scanning in uAUG-containing transcripts, whereas both leaky scanning and ribosome reinitiation may allow initiation at the AUG of main uORF-containing transcripts.
true
true
true
true
true
1,627
7
DISCUSSION
1
53
[ "B53", "B50" ]
17,284,463
pmid-15777708|pmid-11707416
Figure 7 shows that the uAUG toeprint binds exactly to each AUG site, confirming the prior experiments.
[ "53", "50" ]
103
10,207
0
false
Figure 7 shows that the uAUG toeprint binds exactly to each AUG site, confirming the prior experiments.
[]
Figure 7 shows that the uAUG toeprint binds exactly to each AUG site, confirming the prior experiments.
true
true
true
true
true
1,627
7
DISCUSSION
1
53
[ "B53", "B50" ]
17,284,463
pmid-15777708|pmid-11707416
These toeprints show the same Kozak sequence rule.
[ "53", "50" ]
50
10,208
0
false
These toeprints show the same Kozak sequence rule.
[]
These toeprints show the same Kozak sequence rule.
true
true
true
true
true
1,627
7
DISCUSSION
1
53
[ "B53", "B50" ]
17,284,463
pmid-15777708|pmid-11707416
In the case of reinitiation, they must first initiate translation at an uAUG codon.
[ "53", "50" ]
83
10,209
0
false
In the case of reinitiation, they must first initiate translation at an uAUG codon.
[]
In the case of reinitiation, they must first initiate translation at an uAUG codon.
true
true
true
true
true
1,627
7
DISCUSSION
1
53
[ "B53", "B50" ]
17,284,463
pmid-15777708|pmid-11707416
Therefore, when cycloheximide is added to arrest translation elongation before ribosomes can initiate translation, ribosomes should collect at the uAUG codon but not at the downstream AUG.
[ "53", "50" ]
188
10,210
0
false
Therefore, when cycloheximide is added to arrest translation elongation before ribosomes can initiate translation, ribosomes should collect at the uAUG codon but not at the downstream AUG.
[]
Therefore, when cycloheximide is added to arrest translation elongation before ribosomes can initiate translation, ribosomes should collect at the uAUG codon but not at the downstream AUG.
true
true
true
true
true
1,627
7
DISCUSSION
1
50
[ "B53", "B50" ]
17,284,463
pmid-15777708|pmid-11707416
However, in the case of leaky scanning, they will load at the downstream start codon without prior translation of an uORF (50).
[ "53", "50" ]
127
10,211
1
false
However, in the case of leaky scanning, they will load at the downstream start codon without prior translation of an uORF.
[ "50" ]
However, in the case of leaky scanning, they will load at the downstream start codon without prior translation of an uORF.
true
true
true
true
true
1,627
7
DISCUSSION
1
53
[ "B53", "B50" ]
17,284,463
pmid-15777708|pmid-11707416
Therefore, whether Cyh is added to the translation reaction prior to initiation or under steady-state conditions, ribosomes will stall at both the uAUG and main AUG codons.
[ "53", "50" ]
172
10,212
0
false
Therefore, whether Cyh is added to the translation reaction prior to initiation or under steady-state conditions, ribosomes will stall at both the uAUG and main AUG codons.
[]
Therefore, whether Cyh is added to the translation reaction prior to initiation or under steady-state conditions, ribosomes will stall at both the uAUG and main AUG codons.
true
true
true
true
true
1,627
8
DISCUSSION
0
null
null
17,284,463
null
In conclusion, we provide evidence that mouse MOR expression is inhibited at the translational level by the presence of uORFs.
null
126
10,213
0
false
null
null
In conclusion, we provide evidence that mouse MOR expression is inhibited at the translational level by the presence of uORFs.
true
true
true
true
true
1,628
8
DISCUSSION
0
null
null
17,284,463
null
Mainly, the uAUG#3 in the 5′-UTR of the MOR mRNA functions efficiently as a translation initiation site.
null
104
10,214
0
false
null
null
Mainly, the uAUG#3 in the 5′-UTR of the MOR mRNA functions efficiently as a translation initiation site.
true
true
true
true
true
1,628
8
DISCUSSION
0
null
null
17,284,463
null
However, all three uAUGs synergistically regulate translation of the main AUG.
null
78
10,215
0
false
null
null
However, all three uAUGs synergistically regulate translation of the main AUG.
true
true
true
true
true
1,628
8
DISCUSSION
0
null
null
17,284,463
null
The MOR uORF uses a mechanism independent of peptide sequence, and translational repression of MOR uORF is not dependent on the intercistronic region.
null
150
10,216
0
false
null
null
The MOR uORF uses a mechanism independent of peptide sequence, and translational repression of MOR uORF is not dependent on the intercistronic region.
true
true
true
true
true
1,628
8
DISCUSSION
0
null
null
17,284,463
null
Furthermore, leaky scanning is involved in inhibition of physiological AUG-initiated MOR translation, resulting in weak expression of MOR under normal conditions.
null
162
10,217
0
false
null
null
Furthermore, leaky scanning is involved in inhibition of physiological AUG-initiated MOR translation, resulting in weak expression of MOR under normal conditions.
true
true
true
true
true
1,628
8
DISCUSSION
0
null
null
17,284,463
null
These uORFs have the potential to exert a major impact on MOR gene expression, and some, but not all, serve as important regulatory elements under normal conditions.
null
165
10,218
0
false
null
null
These uORFs have the potential to exert a major impact on MOR gene expression, and some, but not all, serve as important regulatory elements under normal conditions.
true
true
true
true
true
1,628
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4" ]
17,584,794
pmid-16601727|pmid-15343339|pmid-16683017|pmid-15637633
One of the principal challenges in analyzing genomic sequences is to identify patterns, or ‘motifs,’ that represent functional elements (1).
[ "1", "2–4" ]
140
10,219
1
false
One of the principal challenges in analyzing genomic sequences is to identify patterns, or ‘motifs,’ that represent functional elements.
[ "1" ]
One of the principal challenges in analyzing genomic sequences is to identify patterns, or ‘motifs,’ that represent functional elements.
true
true
true
true
true
1,629
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4" ]
17,584,794
pmid-16601727|pmid-15343339|pmid-16683017|pmid-15637633
An important use of sequence motifs is to represent sites where transcriptional regulatory proteins bind and modulate expression of genes.
[ "1", "2–4" ]
138
10,220
0
false
An important use of sequence motifs is to represent sites where transcriptional regulatory proteins bind and modulate expression of genes.
[]
An important use of sequence motifs is to represent sites where transcriptional regulatory proteins bind and modulate expression of genes.
true
true
true
true
true
1,629
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4" ]
17,584,794
pmid-16601727|pmid-15343339|pmid-16683017|pmid-15637633
There are many algorithms for finding such motifs.
[ "1", "2–4" ]
50
10,221
0
false
There are many algorithms for finding such motifs.
[]
There are many algorithms for finding such motifs.
true
true
true
true
true
1,629
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4" ]
17,584,794
pmid-16601727|pmid-15343339|pmid-16683017|pmid-15637633
Given the same input data, these algorithms often discover different motifs, with no one algorithm consistently recovering all biologically significant patterns.
[ "1", "2–4" ]
161
10,222
0
false
Given the same input data, these algorithms often discover different motifs, with no one algorithm consistently recovering all biologically significant patterns.
[]
Given the same input data, these algorithms often discover different motifs, with no one algorithm consistently recovering all biologically significant patterns.
true
true
true
true
true
1,629
0
INTRODUCTION
1
2–4
[ "B1", "B2 B3 B4" ]
17,584,794
pmid-16601727|pmid-15343339|pmid-16683017|pmid-15637633
Several studies have demonstrated that it is possible to achieve higher accuracy and sensitivity by combining the results from multiple motif discovery programs (2–4).
[ "1", "2–4" ]
167
10,223
1
false
Several studies have demonstrated that it is possible to achieve higher accuracy and sensitivity by combining the results from multiple motif discovery programs.
[ "2–4" ]
Several studies have demonstrated that it is possible to achieve higher accuracy and sensitivity by combining the results from multiple motif discovery programs.
true
true
true
true
true
1,629
0
INTRODUCTION
1
1
[ "B1", "B2 B3 B4" ]
17,584,794
pmid-16601727|pmid-15343339|pmid-16683017|pmid-15637633
However, this approach requires considerable computational overhead for managing data in a variety of formats and for clustering and scoring the large number of discovered motifs.
[ "1", "2–4" ]
179
10,224
0
false
However, this approach requires considerable computational overhead for managing data in a variety of formats and for clustering and scoring the large number of discovered motifs.
[]
However, this approach requires considerable computational overhead for managing data in a variety of formats and for clustering and scoring the large number of discovered motifs.
true
true
true
true
true
1,629
1
INTRODUCTION
1
5
[ "B5" ]
17,584,794
pmid-16332710
WebMOTIFS is a user-friendly web-based program that makes it easy to follow the current ‘best practice’ in motif discovery.
[ "5" ]
123
10,225
0
false
WebMOTIFS is a user-friendly web-based program that makes it easy to follow the current ‘best practice’ in motif discovery.
[]
WebMOTIFS is a user-friendly web-based program that makes it easy to follow the current ‘best practice’ in motif discovery.
true
true
true
true
true
1,630
1
INTRODUCTION
1
5
[ "B5" ]
17,584,794
pmid-16332710
A single web-based form facilitates data entry.
[ "5" ]
47
10,226
0
false
A single web-based form facilitates data entry.
[]
A single web-based form facilitates data entry.
true
true
true
true
true
1,630
1
INTRODUCTION
1
5
[ "B5" ]
17,584,794
pmid-16332710
WebMOTIFS automatically performs motif discovery on these data with several programs.
[ "5" ]
85
10,227
0
false
WebMOTIFS automatically performs motif discovery on these data with several programs.
[]
WebMOTIFS automatically performs motif discovery on these data with several programs.
true
true
true
true
true
1,630
1
INTRODUCTION
1
5
[ "B5" ]
17,584,794
pmid-16332710
The results from these programs are scored and integrated, and the most significant motifs are provided in an easily interpreted graphic output.
[ "5" ]
144
10,228
0
false
The results from these programs are scored and integrated, and the most significant motifs are provided in an easily interpreted graphic output.
[]
The results from these programs are scored and integrated, and the most significant motifs are provided in an easily interpreted graphic output.
true
true
true
true
true
1,630
1
INTRODUCTION
1
5
[ "B5" ]
17,584,794
pmid-16332710
WebMOTIFS also offers users the opportunity to analyze their data with THEME (5), a Bayesian motif discovery program that incorporates prior knowledge about the biochemical properties of many DNA-binding domains.
[ "5" ]
212
10,229
1
false
WebMOTIFS also offers users the opportunity to analyze their data with THEME, a Bayesian motif discovery program that incorporates prior knowledge about the biochemical properties of many DNA-binding domains.
[ "5" ]
WebMOTIFS also offers users the opportunity to analyze their data with THEME, a Bayesian motif discovery program that incorporates prior knowledge about the biochemical properties of many DNA-binding domains.
true
true
true
true
true
1,630
1
INTRODUCTION
1
5
[ "B5" ]
17,584,794
pmid-16332710
The THEME approach is much more powerful than de novo motif discovery programs in mammalian species, and reveal both the motif and the class of DNA-binding protein that regulates a set of sequences.
[ "5" ]
198
10,230
0
false
The THEME approach is much more powerful than de novo motif discovery programs in mammalian species, and reveal both the motif and the class of DNA-binding protein that regulates a set of sequences.
[]
The THEME approach is much more powerful than de novo motif discovery programs in mammalian species, and reveal both the motif and the class of DNA-binding protein that regulates a set of sequences.
true
true
true
true
true
1,630
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
Proper gene expression depends on precisely orchestrated interactions between nucleic acids and nucleic acid-binding proteins.
[ "1", "2", "3", "4" ]
126
10,231
0
false
Proper gene expression depends on precisely orchestrated interactions between nucleic acids and nucleic acid-binding proteins.
[]
Proper gene expression depends on precisely orchestrated interactions between nucleic acids and nucleic acid-binding proteins.
true
true
true
true
true
1,631
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
In fact, virtually every step of gene expression involves the activities of both sequence-specific and general nucleic acid-binding proteins.
[ "1", "2", "3", "4" ]
141
10,232
0
false
In fact, virtually every step of gene expression involves the activities of both sequence-specific and general nucleic acid-binding proteins.
[]
In fact, virtually every step of gene expression involves the activities of both sequence-specific and general nucleic acid-binding proteins.
true
true
true
true
true
1,631
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
For example, transcription of DNA to RNA employs helicases, transcription factors, RNA polymerase, 5′-capping enzymes, poly (A) polymerase and numerous other proteins required to process the nascent mRNA transcript (1,2).
[ "1", "2", "3", "4" ]
221
10,233
0
false
For example, transcription of DNA to RNA employs helicases, transcription factors, RNA polymerase, 5′-capping enzymes, poly (A) polymerase and numerous other proteins required to process the nascent mRNA transcript.
[ "1,2" ]
For example, transcription of DNA to RNA employs helicases, transcription factors, RNA polymerase, 5′-capping enzymes, poly (A) polymerase and numerous other proteins required to process the nascent mRNA transcript.
true
true
true
true
true
1,631
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
All of these factors must recognize nucleic acids in some manner.
[ "1", "2", "3", "4" ]
65
10,234
0
false
All of these factors must recognize nucleic acids in some manner.
[]
All of these factors must recognize nucleic acids in some manner.
true
true
true
true
true
1,631
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B4" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
Then numerous mRNA-binding proteins are required to escort transcripts out of the nucleus and, ultimately, to coordinate protein translation (3).
[ "1", "2", "3", "4" ]
145
10,235
1
false
Then numerous mRNA-binding proteins are required to escort transcripts out of the nucleus and, ultimately, to coordinate protein translation.
[ "3" ]
Then numerous mRNA-binding proteins are required to escort transcripts out of the nucleus and, ultimately, to coordinate protein translation.
true
true
true
true
true
1,631
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B4" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
Thus, gene expression relies heavily on nucleic acid-binding proteins, with major roles for proteins that bind to mRNA.
[ "1", "2", "3", "4" ]
119
10,236
0
false
Thus, gene expression relies heavily on nucleic acid-binding proteins, with major roles for proteins that bind to mRNA.
[]
Thus, gene expression relies heavily on nucleic acid-binding proteins, with major roles for proteins that bind to mRNA.
true
true
true
true
true
1,631
0
INTRODUCTION
1
4
[ "B1", "B2", "B3", "B4" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
In keeping with this workload, proteins have evolved a vast array of domains that mediate interactions with RNA, including but not limited to the hnRNP K homology (KH) domain, RNA recognition motifs (RRMs), arginine-rich motifs, and zinc-finger motifs (4).
[ "1", "2", "3", "4" ]
256
10,237
1
false
In keeping with this workload, proteins have evolved a vast array of domains that mediate interactions with RNA, including but not limited to the hnRNP K homology (KH) domain, RNA recognition motifs (RRMs), arginine-rich motifs, and zinc-finger motifs.
[ "4" ]
In keeping with this workload, proteins have evolved a vast array of domains that mediate interactions with RNA, including but not limited to the hnRNP K homology (KH) domain, RNA recognition motifs (RRMs), arginine-rich motifs, and zinc-finger motifs.
true
true
true
true
true
1,631
1
INTRODUCTION
1
4
[ "B4", "B4", "B5", "B6" ]
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
Many RNA-binding domains are abundant and highly conserved across species.
[ "4", "4", "5", "6" ]
74
10,238
0
false
Many RNA-binding domains are abundant and highly conserved across species.
[]
Many RNA-binding domains are abundant and highly conserved across species.
true
true
true
true
true
1,632
1
INTRODUCTION
1
4
[ "B4", "B4", "B5", "B6" ]
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
In fact, Chen and Varani have estimated that about 1.5–2% of the human genome is composed of proteins that contain RRM domains, the most abundant and well-characterized of the RNA-binding domains (4).
[ "4", "4", "5", "6" ]
200
10,239
1
false
In fact, Chen and Varani have estimated that about 1.5–2% of the human genome is composed of proteins that contain RRM domains, the most abundant and well-characterized of the RNA-binding domains.
[ "4" ]
In fact, Chen and Varani have estimated that about 1.5–2% of the human genome is composed of proteins that contain RRM domains, the most abundant and well-characterized of the RNA-binding domains.
true
true
true
true
true
1,632
1
INTRODUCTION
1
4
[ "B4", "B4", "B5", "B6" ]
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
RNA-binding motifs are typically recognized and defined on the basis of their conserved primary amino acid sequence, but the degree of sequence conservation among different motifs varies widely (4).
[ "4", "4", "5", "6" ]
198
10,240
1
false
RNA-binding motifs are typically recognized and defined on the basis of their conserved primary amino acid sequence, but the degree of sequence conservation among different motifs varies widely.
[ "4" ]
RNA-binding motifs are typically recognized and defined on the basis of their conserved primary amino acid sequence, but the degree of sequence conservation among different motifs varies widely.
true
true
true
true
true
1,632
1
INTRODUCTION
1
4
[ "B4", "B4", "B5", "B6" ]
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
Although some major residues are defined functionally, others have been identified strictly on the basis of sequence conservation or homology (5,6).
[ "4", "4", "5", "6" ]
148
10,241
0
false
Although some major residues are defined functionally, others have been identified strictly on the basis of sequence conservation or homology.
[ "5,6" ]
Although some major residues are defined functionally, others have been identified strictly on the basis of sequence conservation or homology.
true
true
true
true
true
1,632
1
INTRODUCTION
1
4
[ "B4", "B4", "B5", "B6" ]
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
A key question is whether these conserved residues are actually critical for protein function, and therefore whether sequence conservation alone can be used as a measure of functional significance.
[ "4", "4", "5", "6" ]
197
10,242
0
false
A key question is whether these conserved residues are actually critical for protein function, and therefore whether sequence conservation alone can be used as a measure of functional significance.
[]
A key question is whether these conserved residues are actually critical for protein function, and therefore whether sequence conservation alone can be used as a measure of functional significance.
true
true
true
true
true
1,632
2
INTRODUCTION
1
7
[ "B7", "B7", "B8" ]
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
One remarkably versatile and highly conserved RNA-binding motif is the KH domain (7).
[ "7", "7", "8" ]
85
10,243
1
false
One remarkably versatile and highly conserved RNA-binding motif is the KH domain.
[ "7" ]
One remarkably versatile and highly conserved RNA-binding motif is the KH domain.
true
true
true
true
true
1,633
2
INTRODUCTION
1
7
[ "B7", "B7", "B8" ]
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
KH domains, which were originally identified as a repeated sequence in the hnRNP K protein (7), are ∼70 amino acids in length, with a characteristic pattern of hydrophobic residues, a GXXG segment and a variable loop.
[ "7", "7", "8" ]
217
10,244
1
false
KH domains, which were originally identified as a repeated sequence in the hnRNP K protein, are ∼70 amino acids in length, with a characteristic pattern of hydrophobic residues, a GXXG segment and a variable loop.
[ "7" ]
KH domains, which were originally identified as a repeated sequence in the hnRNP K protein, are ∼70 amino acids in length, with a characteristic pattern of hydrophobic residues, a GXXG segment and a variable loop.
true
true
true
true
true
1,633
2
INTRODUCTION
1
7
[ "B7", "B7", "B8" ]
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
KH domains are often found in multiple copies per protein.
[ "7", "7", "8" ]
58
10,245
0
false
KH domains are often found in multiple copies per protein.
[]
KH domains are often found in multiple copies per protein.
true
true
true
true
true
1,633
2
INTRODUCTION
1
7
[ "B7", "B7", "B8" ]
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
There is strong evidence that KH domains are critically important to the function of those proteins that contain them.
[ "7", "7", "8" ]
118
10,246
0
false
There is strong evidence that KH domains are critically important to the function of those proteins that contain them.
[]
There is strong evidence that KH domains are critically important to the function of those proteins that contain them.
true
true
true
true
true
1,633
2
INTRODUCTION
1
8
[ "B7", "B7", "B8" ]
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
For example, fragile X syndrome, a leading cause of inherited mental retardation, can arise from a missense mutation of Ile304Asn in the second KH domain of the FMRP protein (8).
[ "7", "7", "8" ]
178
10,247
1
false
For example, fragile X syndrome, a leading cause of inherited mental retardation, can arise from a missense mutation of Ile304Asn in the second KH domain of the FMRP protein.
[ "8" ]
For example, fragile X syndrome, a leading cause of inherited mental retardation, can arise from a missense mutation of Ile304Asn in the second KH domain of the FMRP protein.
true
true
true
true
true
1,633
2
INTRODUCTION
1
8
[ "B7", "B7", "B8" ]
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
Indeed, the Ile304Asn mutation is associated with a severe clinical phenotype (8).
[ "7", "7", "8" ]
82
10,248
1
false
Indeed, the Ile304Asn mutation is associated with a severe clinical phenotype.
[ "8" ]
Indeed, the Ile304Asn mutation is associated with a severe clinical phenotype.
true
true
true
true
true
1,633
2
INTRODUCTION
1
7
[ "B7", "B7", "B8" ]
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
Thus, there is evidence that mutations in KH domains can cause human disease, which underscores the importance of defining what constitutes a functional KH domain.
[ "7", "7", "8" ]
163
10,249
0
false
Thus, there is evidence that mutations in KH domains can cause human disease, which underscores the importance of defining what constitutes a functional KH domain.
[]
Thus, there is evidence that mutations in KH domains can cause human disease, which underscores the importance of defining what constitutes a functional KH domain.
true
true
true
true
true
1,633
3
INTRODUCTION
1
9
[ "B9", "B10 B11 B12 B13 B14", "B15", "B16" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Some proteins contain both conserved KH domains that include the GXXG motif, as well as what have been termed diverged KH domains, in which the GXXG motif is interrupted or altered (9).
[ "9", "10–14", "15", "16" ]
185
10,250
1
false
Some proteins contain both conserved KH domains that include the GXXG motif, as well as what have been termed diverged KH domains, in which the GXXG motif is interrupted or altered.
[ "9" ]
Some proteins contain both conserved KH domains that include the GXXG motif, as well as what have been termed diverged KH domains, in which the GXXG motif is interrupted or altered.
true
true
true
true
true
1,634
3
INTRODUCTION
1
10–14
[ "B9", "B10 B11 B12 B13 B14", "B15", "B16" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Although the structures of a number of conserved KH domains have been solved (10–14), there has been little functional analysis of diverged KH domains.
[ "9", "10–14", "15", "16" ]
151
10,251
1
false
Although the structures of a number of conserved KH domains have been solved, there has been little functional analysis of diverged KH domains.
[ "10–14" ]
Although the structures of a number of conserved KH domains have been solved, there has been little functional analysis of diverged KH domains.
true
true
true
true
true
1,634
3
INTRODUCTION
1
15
[ "B9", "B10 B11 B12 B13 B14", "B15", "B16" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Recent evidence suggests possible synergistic binding to mRNA targets by the three KH domains of hnRNP K protein (15), thereby enhancing interaction with the nucleic acid substrate.
[ "9", "10–14", "15", "16" ]
181
10,252
1
false
Recent evidence suggests possible synergistic binding to mRNA targets by the three KH domains of hnRNP K protein, thereby enhancing interaction with the nucleic acid substrate.
[ "15" ]
Recent evidence suggests possible synergistic binding to mRNA targets by the three KH domains of hnRNP K protein, thereby enhancing interaction with the nucleic acid substrate.
true
true
true
true
true
1,634
3
INTRODUCTION
1
16
[ "B9", "B10 B11 B12 B13 B14", "B15", "B16" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Chmiel and colleagues (16) drew a similar conclusion from their work with the Drosophila PSI protein, which contains four KH domains.
[ "9", "10–14", "15", "16" ]
133
10,253
1
false
Chmiel and colleagues drew a similar conclusion from their work with the Drosophila PSI protein, which contains four KH domains.
[ "16" ]
Chmiel and colleagues drew a similar conclusion from their work with the Drosophila PSI protein, which contains four KH domains.
true
true
true
true
true
1,634
3
INTRODUCTION
1
9
[ "B9", "B10 B11 B12 B13 B14", "B15", "B16" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
While these findings do shed light on the functional importance of KH domain clustering in proteins, they fail to address the functional significance of KH domain sequence conservation or divergence.
[ "9", "10–14", "15", "16" ]
199
10,254
0
false
While these findings do shed light on the functional importance of KH domain clustering in proteins, they fail to address the functional significance of KH domain sequence conservation or divergence.
[]
While these findings do shed light on the functional importance of KH domain clustering in proteins, they fail to address the functional significance of KH domain sequence conservation or divergence.
true
true
true
true
true
1,634
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
As a first step towards addressing whether GXXG is essential for KH domain function, we explored the roles of conserved and diverged KH domains in Scp160p, a multiple KH domain protein in S. cerevisiae.
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
202
10,255
0
false
As a first step towards addressing whether GXXG is essential for KH domain function, we explored the roles of conserved and diverged KH domains in Scp160p, a multiple KH domain protein in S. cerevisiae.
[]
As a first step towards addressing whether GXXG is essential for KH domain function, we explored the roles of conserved and diverged KH domains in Scp160p, a multiple KH domain protein in S. cerevisiae.
true
true
true
true
true
1,635
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
Scp160p includes 14 KH domains (17), only seven of which contain a strictly conserved GXXG motif (KH 2, 8–12 and 14).
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
117
10,256
1
false
Scp160p includes 14 KH domains, only seven of which contain a strictly conserved GXXG motif (KH 2, 8–12 and 14).
[ "17" ]
Scp160p includes 14 KH domains, only seven of which contain a strictly conserved GXXG motif.
true
true
true
true
true
1,635
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
The other seven KH domains are diverged, with interruptions or alterations of the GXXG motif.
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
93
10,257
0
false
The other seven KH domains are diverged, with interruptions or alterations of the GXXG motif.
[]
The other seven KH domains are diverged, with interruptions or alterations of the GXXG motif.
true
true
true
true
true
1,635
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
Although the exact function of Scp160p and its orthologs, known as vigilins in higher eukaryotes, is not known, recent work suggests a role for this protein in modulating the metabolism of specific mRNA targets in the cytoplasm (18,19).
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
236
10,258
0
false
Although the exact function of Scp160p and its orthologs, known as vigilins in higher eukaryotes, is not known, recent work suggests a role for this protein in modulating the metabolism of specific mRNA targets in the cytoplasm.
[ "18,19" ]
Although the exact function of Scp160p and its orthologs, known as vigilins in higher eukaryotes, is not known, recent work suggests a role for this protein in modulating the metabolism of specific mRNA targets in the cytoplasm.
true
true
true
true
true
1,635
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
Consistent with this postulated function, much of Scp160p is found in large protein complexes associated with soluble or membrane-bound polyribosomes (17,20–25).
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
161
10,259
0
false
Consistent with this postulated function, much of Scp160p is found in large protein complexes associated with soluble or membrane-bound polyribosomes.
[ "17,20–25" ]
Consistent with this postulated function, much of Scp160p is found in large protein complexes associated with soluble or membrane-bound polyribosomes.
true
true
true
true
true
1,635
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
The goal of the present study was to explore two questions.
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
59
10,260
0
false
The goal of the present study was to explore two questions.
[]
The goal of the present study was to explore two questions.
true
true
true
true
true
1,635
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
First, are diverged KH domains essential for Scp160p function?
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
62
10,261
0
false
First, are diverged KH domains essential for Scp160p function?
[]
First, are diverged KH domains essential for Scp160p function?
true
true
true
true
true
1,635
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
Second, can diverged KH domains functionally replace conserved KH domains?
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
74
10,262
0
false
Second, can diverged KH domains functionally replace conserved KH domains?
[]
Second, can diverged KH domains functionally replace conserved KH domains?
true
true
true
true
true
1,635
4
INTRODUCTION
1
17
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
To address these questions, we deleted and/or interchanged conserved and diverged KH domains of Scp160p, then expressed these variant alleles in yeast.
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
151
10,263
0
false
To address these questions, we deleted and/or interchanged conserved and diverged KH domains of Scp160p, then expressed these variant alleles in yeast.
[]
To address these questions, we deleted and/or interchanged conserved and diverged KH domains of Scp160p, then expressed these variant alleles in yeast.
true
true
true
true
true
1,635
4
INTRODUCTION
1
23
[ "B17", "B18", "B19", "B17", "B20 B21 B22 B23 B24 B25", "B23", "B17", "B20 B21 B22 B23 B24 B25" ]
17,264,125
pmid-9363784|pmid-12654998|pmid-9139664|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294|pmid-14530432|pmid-9363784|pmid-11278502|pmid-10710424|pmid-11410665|pmid-14530432|pmid-15012629|pmid-15356294
We applied a combination of previously defined genetic (23) and biochemical (17,20–25) assays to the strains expressing these mutated alleles to discern the functional capacity of each encoded Scp160p protein.
[ "17", "18", "19", "17", "20–25", "23", "17", "20–25" ]
209
10,264
1
false
We applied a combination of previously defined genetic and biochemical assays to the strains expressing these mutated alleles to discern the functional capacity of each encoded Scp160p protein.
[ "23", "17,20–25" ]
We applied a combination of previously defined genetic and biochemical assays to the strains expressing these mutated alleles to discern the functional capacity of each encoded Scp160p protein.
true
true
true
true
true
1,635
5
INTRODUCTION
0
null
null
17,264,125
pmid-16381856|pmid-9600884
Our results demonstrated that the answer to each of our two questions was yes.
null
78
10,265
0
false
null
null
Our results demonstrated that the answer to each of our two questions was yes.
true
true
true
true
true
1,636
5
INTRODUCTION
0
null
null
17,264,125
pmid-16381856|pmid-9600884
Both conserved and diverged KH domains were essential for Scp160p function, and diverged KH domains were capable of functioning in place of conserved KH domains.
null
161
10,266
0
false
null
null
Both conserved and diverged KH domains were essential for Scp160p function, and diverged KH domains were capable of functioning in place of conserved KH domains.
true
true
true
true
true
1,636
0
DISCUSSION
1
24
[ "B24" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
The goal of this study was to explore whether diverged KH domains are as important for Scp160p function as conserved domains, and also whether diverged KH domains can functionally replace conserved KH domains in Scp160p.
[ "24" ]
220
10,267
0
false
The goal of this study was to explore whether diverged KH domains are as important for Scp160p function as conserved domains, and also whether diverged KH domains can functionally replace conserved KH domains in Scp160p.
[]
The goal of this study was to explore whether diverged KH domains are as important for Scp160p function as conserved domains, and also whether diverged KH domains can functionally replace conserved KH domains in Scp160p.
true
true
true
true
true
1,637
0
DISCUSSION
1
24
[ "B24" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
Our results yielded two important conclusions.
[ "24" ]
46
10,268
0
false
Our results yielded two important conclusions.
[]
Our results yielded two important conclusions.
true
true
true
true
true
1,637
0
DISCUSSION
1
24
[ "B24" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
First, diverged KH domains can be as critical for function as conserved KH domains.
[ "24" ]
83
10,269
0
false
First, diverged KH domains can be as critical for function as conserved KH domains.
[]
First, diverged KH domains can be as critical for function as conserved KH domains.
true
true
true
true
true
1,637
0
DISCUSSION
1
24
[ "B24" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
Specifically, we demonstrated, as others have hypothesized (24), that at least one diverged KH domain in Scp160p, KH13, is essential for Scp160p function, despite its lack of the GXXG motif.
[ "24" ]
190
10,270
1
false
Specifically, we demonstrated, as others have hypothesized, that at least one diverged KH domain in Scp160p, KH13, is essential for Scp160p function, despite its lack of the GXXG motif.
[ "24" ]
Specifically, we demonstrated, as others have hypothesized, that at least one diverged KH domain in Scp160p, KH13, is essential for Scp160p function, despite its lack of the GXXG motif.
true
true
true
true
true
1,637
0
DISCUSSION
1
24
[ "B24" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
Second, there can be considerable functional overlap between diverged and conserved KH domains.
[ "24" ]
95
10,271
0
false
Second, there can be considerable functional overlap between diverged and conserved KH domains.
[]
Second, there can be considerable functional overlap between diverged and conserved KH domains.
true
true
true
true
true
1,637
0
DISCUSSION
1
24
[ "B24" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
In particular, we observed that add-back of the diverged KH13 domain sequence to an Scp160p variant missing conserved KH14 partially restored both presumed mRNP formation and polyribosome association, and also restored close to 50% wild-type complementation.
[ "24" ]
258
10,272
0
false
In particular, we observed that add-back of the diverged KH13 domain sequence to an Scp160p variant missing conserved KH14 partially restored both presumed mRNP formation and polyribosome association, and also restored close to 50% wild-type complementation.
[]
In particular, we observed that add-back of the diverged KH13 domain sequence to an Scp160p variant missing conserved KH14 partially restored both presumed mRNP formation and polyribosome association, and also restored close to 50% wild-type complementation.
true
true
true
true
true
1,637
0
DISCUSSION
1
24
[ "B24" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
It is also important to note, however, that no ‘add-back’ variant was able to restore fully wild-type levels of SCP160 function when measured by our biochemical or quantitative complementation assays.
[ "24" ]
200
10,273
0
false
It is also important to note, however, that no ‘add-back’ variant was able to restore fully wild-type levels of SCP160 function when measured by our biochemical or quantitative complementation assays.
[]
It is also important to note, however, that no ‘add-back’ variant was able to restore fully wild-type levels of SCP160 function when measured by our biochemical or quantitative complementation assays.
true
true
true
true
true
1,637
0
DISCUSSION
1
24
[ "B24" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
Furthermore, the variants studied here showed differing levels of biochemical function with regard to presumed mRNP formation and polyribosome association.
[ "24" ]
155
10,274
0
false
Furthermore, the variants studied here showed differing levels of biochemical function with regard to presumed mRNP formation and polyribosome association.
[]
Furthermore, the variants studied here showed differing levels of biochemical function with regard to presumed mRNP formation and polyribosome association.
true
true
true
true
true
1,637
0
DISCUSSION
1
24
[ "B24" ]
17,264,125
pmid-16822967|pmid-10772858|pmid-16141059|pmid-15853794|pmid-15012629
These results highlight the distinction between the shared and unique roles of individual KH domains in a multi-KH-domain protein; though they may be repeated, these units are not simply interchangeable.
[ "24" ]
203
10,275
0
false
These results highlight the distinction between the shared and unique roles of individual KH domains in a multi-KH-domain protein; though they may be repeated, these units are not simply interchangeable.
[]
These results highlight the distinction between the shared and unique roles of individual KH domains in a multi-KH-domain protein; though they may be repeated, these units are not simply interchangeable.
true
true
true
true
true
1,637
1
DISCUSSION
0
null
null
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
Another noteworthy conclusion from our results is that neither the sheer number of KH domains nor the total protein size defines Scp160p function.
null
146
10,276
0
false
null
null
Another noteworthy conclusion from our results is that neither the sheer number of KH domains nor the total protein size defines Scp160p function.
true
true
true
true
true
1,638
1
DISCUSSION
0
null
null
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
For example, each of the add-back alleles included a total of 14 KH domains, yet there was enormous disparity in their degrees of function.
null
139
10,277
0
false
null
null
For example, each of the add-back alleles included a total of 14 KH domains, yet there was enormous disparity in their degrees of function.
true
true
true
true
true
1,638
1
DISCUSSION
0
null
null
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
Furthermore, as illustrated in Figure 2, the variant Scp160p proteins were not all the same size, even after add-back, because KH domain 13 is almost twice the size of any of the other KH domains.
null
196
10,278
0
false
null
null
Furthermore, as illustrated in Figure 2, the variant Scp160p proteins were not all the same size, even after add-back, because KH domain 13 is almost twice the size of any of the other KH domains.
true
true
true
true
true
1,638
1
DISCUSSION
0
null
null
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
This disparity means that the variants missing KH13 with either a KH6 add-back or a KH14 add-back were both approximately the same size as the variant protein that was simply missing KH14, with no add-back, and yet the function of these proteins differed dramatically (Figures 3–5).
null
282
10,279
0
false
null
null
This disparity means that the variants missing KH13 with either a KH6 add-back or a KH14 add-back were both approximately the same size as the variant protein that was simply missing KH14, with no add-back, and yet the function of these proteins differed dramatically (Figures 3–5).
true
true
true
true
true
1,638
1
DISCUSSION
0
null
null
17,264,125
pmid-15853794|pmid-15853794|pmid-15231733|pmid-15257761
Clearly, size alone does not define Scp160p function.
null
53
10,280
0
false
null
null
Clearly, size alone does not define Scp160p function.
true
true
true
true
true
1,638
2
DISCUSSION
0
null
null
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
One of the interesting observations from the data we present here is that SCP160 function is not binary; the variants we have created and tested clearly uncouple different aspects of Scp160p function.
null
200
10,281
0
false
null
null
One of the interesting observations from the data we present here is that SCP160 function is not binary; the variants we have created and tested clearly uncouple different aspects of Scp160p function.
true
true
true
true
true
1,639
2
DISCUSSION
0
null
null
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
For example, all four of the add-back alleles we tested restored at least partial ability of Scp160p to form presumed mRNPs, but only three restored at least partial ability of the protein to associate with polyribosomes.
null
221
10,282
0
false
null
null
For example, all four of the add-back alleles we tested restored at least partial ability of Scp160p to form presumed mRNPs, but only three restored at least partial ability of the protein to associate with polyribosomes.
true
true
true
true
true
1,639
2
DISCUSSION
0
null
null
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
Finally, of all the variant alleles tested, only one, SCP160Δ14.13, restored significant function as measured using our genetic complementation assay.
null
150
10,283
0
false
null
null
Finally, of all the variant alleles tested, only one, SCP160Δ14.13, restored significant function as measured using our genetic complementation assay.
true
true
true
true
true
1,639
2
DISCUSSION
0
null
null
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
The simplest interpretation of these results would be that SCP160 function, as measured by the complementation assay, is a complex variable.
null
140
10,284
0
false
null
null
The simplest interpretation of these results would be that SCP160 function, as measured by the complementation assay, is a complex variable.
true
true
true
true
true
1,639
2
DISCUSSION
0
null
null
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
An ability to form presumed mRNPs appears to be a prerequisite for polyribosome association, and polyribosome association appears to be necessary but not sufficient for full function in vivo.
null
191
10,285
0
false
null
null
An ability to form presumed mRNPs appears to be a prerequisite for polyribosome association, and polyribosome association appears to be necessary but not sufficient for full function in vivo.
true
true
true
true
true
1,639
2
DISCUSSION
0
null
null
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
It is also interesting to note that the allele demonstrating the strongest ability to complement scp160δ eap1δ
null
110
10,286
0
false
null
null
It is also interesting to note that the allele demonstrating the strongest ability to complement scp160δ eap1δ
true
true
false
true
false
1,639
2
DISCUSSION
0
null
null
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
synthetic lethality (SCP160Δ14.13) was not the same allele that showed the greatest association with polyribosomes (SCP160Δ13.14).
null
130
10,287
0
false
null
null
synthetic lethality (SCP160Δ14.13) was not the same allele that showed the greatest association with polyribosomes (SCP160Δ13.14).
false
true
true
true
false
1,639
2
DISCUSSION
0
null
null
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
Furthermore, the most genetically functional of all of the add-back alleles tested was SCP160Δ14.13, in which a conserved KH domain was replaced by a diverged KH domain.
null
169
10,288
0
false
null
null
Furthermore, the most genetically functional of all of the add-back alleles tested was SCP160Δ14.13, in which a conserved KH domain was replaced by a diverged KH domain.
true
true
true
true
true
1,639
2
DISCUSSION
0
null
null
17,264,125
pmid-8464704|pmid-8464704|pmid-10496225
These data clearly demonstrate that the GXXG motif cannot be essential for the function of every KH domain in Scp160p.
null
118
10,289
0
false
null
null
These data clearly demonstrate that the GXXG motif cannot be essential for the function of every KH domain in Scp160p.
true
true
true
true
true
1,639
3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Here we have used Scp160p in yeast as a model to study conserved and diverged KH motifs within a multi-KH-domain protein.
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
121
10,290
0
false
Here we have used Scp160p in yeast as a model to study conserved and diverged KH motifs within a multi-KH-domain protein.
[]
Here we have used Scp160p in yeast as a model to study conserved and diverged KH motifs within a multi-KH-domain protein.
true
true
true
true
true
1,640
3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Scp160p is most closely related to a family of proteins in higher eukaryotes, known as vigilins (9).
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
100
10,291
1
false
Scp160p is most closely related to a family of proteins in higher eukaryotes, known as vigilins.
[ "9" ]
Scp160p is most closely related to a family of proteins in higher eukaryotes, known as vigilins.
true
true
true
true
true
1,640
3
DISCUSSION
1
30
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
First identified in chicken (30), vigilin homologues have now been found in species ranging from Neurospora crassa to humans (9,17,19,21,22,30–32)(GenPept 7493335; GenPept 7899383).
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
181
10,292
1
false
First identified in chicken, vigilin homologues have now been found in species ranging from Neurospora crassa to humans.
[ "30", "9,17,19,21,22,30–32", "GenPept 7493335; GenPept 7899383" ]
First identified in chicken, vigilin homologues have now been found in species ranging from Neurospora crassa to humans.
true
true
true
true
true
1,640
3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Like Scp160p, these proteins contain both conserved and diverged KH domains, and as with Scp160p, the diverged KH domains of vigilin have an interrupted GXXG.
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
158
10,293
0
false
Like Scp160p, these proteins contain both conserved and diverged KH domains, and as with Scp160p, the diverged KH domains of vigilin have an interrupted GXXG.
[]
Like Scp160p, these proteins contain both conserved and diverged KH domains, and as with Scp160p, the diverged KH domains of vigilin have an interrupted GXXG.
true
true
true
true
true
1,640
3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Interestingly, the positions of the diverged KH domains in the human, mouse, and chicken vigilins, and to some extent also in the Drosophila melanogaster DDP1 sequence, have been conserved, but that conservation does not extend to SCP160 (Figure 6).
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
249
10,294
0
false
Interestingly, the positions of the diverged KH domains in the human, mouse, and chicken vigilins, and to some extent also in the Drosophila melanogaster DDP1 sequence, have been conserved, but that conservation does not extend to SCP160 (Figure 6).
[]
Interestingly, the positions of the diverged KH domains in the human, mouse, and chicken vigilins, and to some extent also in the Drosophila melanogaster DDP1 sequence, have been conserved, but that conservation does not extend to SCP160 (Figure 6).
true
true
true
true
true
1,640
3
DISCUSSION
1
33
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Nonetheless, fly DDP1 is apparently adequate to rescue the abnormal DNA-content phenotype in scp160Δ yeast (33).
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
112
10,295
1
false
Nonetheless, fly DDP1 is apparently adequate to rescue the abnormal DNA-content phenotype in scp160Δ yeast.
[ "33" ]
Nonetheless, fly DDP1 is apparently adequate to rescue the abnormal DNA-content phenotype in scp160Δ yeast.
true
true
true
true
true
1,640
3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
While anecdotal, this evidence further supports the conclusion that the presence versus absence of a GXXG motif does not define the functional capacity of every KH domain, at least within the context of a multi-KH-domain protein.
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
229
10,296
0
false
While anecdotal, this evidence further supports the conclusion that the presence versus absence of a GXXG motif does not define the functional capacity of every KH domain, at least within the context of a multi-KH-domain protein.
[]
While anecdotal, this evidence further supports the conclusion that the presence versus absence of a GXXG motif does not define the functional capacity of every KH domain, at least within the context of a multi-KH-domain protein.
true
true
true
true
true
1,640
3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Figure 6.Domain structures of multi-KH-domain-containing proteins.
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
66
10,297
0
false
Figure 6.Domain structures of multi-KH-domain-containing proteins.
[]
Figure 6.Domain structures of multi-KH-domain-containing proteins.
true
true
true
true
true
1,640
3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Domain portions of the proteins are not drawn to scale.
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
55
10,298
0
false
Domain portions of the proteins are not drawn to scale.
[]
Domain portions of the proteins are not drawn to scale.
true
true
true
true
true
1,640
3
DISCUSSION
1
9
[ "B9", "B30", "B9", "B17", "B19", "B21", "B22", "B30 B31 B32", "B33" ]
17,264,125
pmid-10331606|pmid-8612276|pmid-10369774|pmid-9302998|pmid-10368286|pmid-16004877|pmid-15527774|pmid-16428607|pmid-10331606|pmid-1606952|pmid-10331606|pmid-9363784|pmid-9139664|pmid-10710424|pmid-11410665|pmid-1606952|pmid-8168838|pmid-10805729|pmid-10393197
Numbered, filled boxes represent conserved KH domains; numbered, open boxes represent diverged KH domains.
[ "9", "30", "9", "17", "19", "21", "22", "30–32", "33" ]
106
10,299
0
false
Numbered, filled boxes represent conserved KH domains; numbered, open boxes represent diverged KH domains.
[]
Numbered, filled boxes represent conserved KH domains; numbered, open boxes represent diverged KH domains.
true
true
true
true
true
1,640