Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
1
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1
INTRODUCTION
1
7
[ "B6", "B7", "B8", "B9", "B10", "B11" ]
18,162,713
pmid-8069912|pmid-8647957|pmid-7795648|pmid-8961624|pmid-14612666|pmid-11242115|NA|pmid-14612666|NA
The encoded protein is a 502 amino-acid long intracellular protein, which is broadly expressed in hematopoietic cells (7).
[ "6", "7", "8", "9", "10", "11" ]
122
42,819
1
false
The encoded protein is a 502 amino-acid long intracellular protein, which is broadly expressed in hematopoietic cells.
[ "7" ]
The encoded protein is a 502 amino-acid long intracellular protein, which is broadly expressed in hematopoietic cells.
true
true
true
true
true
7,421
1
INTRODUCTION
1
6
[ "B6", "B7", "B8", "B9", "B10", "B11" ]
18,162,713
pmid-8069912|pmid-8647957|pmid-7795648|pmid-8961624|pmid-14612666|pmid-11242115|NA|pmid-14612666|NA
The WAS gene was found to be mutated, not only in classic WAS patients, but also in patients with X-linked thrombocytopenia (XLT), which is a clinically mild allelic variant (8, 9).
[ "6", "7", "8", "9", "10", "11" ]
181
42,820
0
false
The WAS gene was found to be mutated, not only in classic WAS patients, but also in patients with X-linked thrombocytopenia (XLT), which is a clinically mild allelic variant.
[ "8, 9" ]
The WAS gene was found to be mutated, not only in classic WAS patients, but also in patients with X-linked thrombocytopenia (XLT), which is a clinically mild allelic variant.
true
true
true
true
true
7,421
1
INTRODUCTION
1
6
[ "B6", "B7", "B8", "B9", "B10", "B11" ]
18,162,713
pmid-8069912|pmid-8647957|pmid-7795648|pmid-8961624|pmid-14612666|pmid-11242115|NA|pmid-14612666|NA
Recent reports have expanded the WAS mutation phenotype to include intermittent XLT, X-linked neutropenia with or without myelodysplasia, or WAS/XLT in females with heterozygous mutations (10, 11).
[ "6", "7", "8", "9", "10", "11" ]
197
42,821
0
false
Recent reports have expanded the WAS mutation phenotype to include intermittent XLT, X-linked neutropenia with or without myelodysplasia, or WAS/XLT in females with heterozygous mutations.
[ "10, 11" ]
Recent reports have expanded the WAS mutation phenotype to include intermittent XLT, X-linked neutropenia with or without myelodysplasia, or WAS/XLT in females with heterozygous mutations.
true
true
true
true
true
7,421
2
INTRODUCTION
0
null
null
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
Many WAS gene mutations have been reported in patients with WAS.
null
64
42,822
0
false
null
null
Many WAS gene mutations have been reported in patients with WAS.
true
true
true
true
true
7,422
2
INTRODUCTION
0
null
null
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
However, little is known about Korean WAS patients in terms of their molecular genetic diagnosis.
null
97
42,823
0
false
null
null
However, little is known about Korean WAS patients in terms of their molecular genetic diagnosis.
true
true
true
true
true
7,422
2
INTRODUCTION
0
null
null
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
In this report, we describe a Korean family with WAS, which was diagnosed as having exon 2 mutation, based on the WAS gene mutation analysis.
null
141
42,824
0
false
null
null
In this report, we describe a Korean family with WAS, which was diagnosed as having exon 2 mutation, based on the WAS gene mutation analysis.
true
true
true
true
true
7,422
2
INTRODUCTION
0
null
null
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
This is the first identified case of a hotspot mutation in exon 2 of WAS in Korea.
null
82
42,825
0
false
null
null
This is the first identified case of a hotspot mutation in exon 2 of WAS in Korea.
true
true
true
true
true
7,422
0
DISCUSSION
1
1
[ "B1", "B8", "B9", "B10", "B11" ]
18,162,713
pmid-7996359|pmid-8032367|pmid-8219187|pmid-11238097|pmid-7996359|pmid-7795648|pmid-8961624|pmid-14612666|pmid-11242115
Mutations of the WAS gene result in 3 distinct phenotypes: the classic WAS triad of thrombocytopenia with small platelets, recurrent infections as a result of immunodeficiency, and eczema (1); the milder XLT variant, characterized predominantly by thromobocytopenia with small platelets (8, 9); and finally, congenital n...
[ "1", "8", "9", "10", "11" ]
397
42,826
1
false
Mutations of the WAS gene result in 3 distinct phenotypes: the classic WAS triad of thrombocytopenia with small platelets, recurrent infections as a result of immunodeficiency, and eczema ; the milder XLT variant, characterized predominantly by thromobocytopenia with small platelets ; and finally, congenital neutropeni...
[ "1", "8, 9", "10, 11" ]
Mutations of the WAS gene result in 3 distinct phenotypes: the classic WAS triad of thrombocytopenia with small platelets, recurrent infections as a result of immunodeficiency, and eczema ; the milder XLT variant, characterized predominantly by thromobocytopenia with small platelets ; and finally, congenital neutropeni...
true
true
true
true
true
7,423
1
DISCUSSION
1
13
[ "B13", "B10", "B13" ]
18,162,713
pmid-8069912|pmid-8647957|pmid-7795648|pmid-8961624|pmid-14612666|pmid-11242115|NA|pmid-14612666|NA
As shown in WASPbase (13), a database of mutations, a total of 441 cases consisted of missense mutations in 179 cases (40.6%), deletions in 92 cases (20.9%), nonsense mutations in 64 cases (14.5%), splicing defects in 64 cases (14.5%), and insertions in 42 cases (9.5%).
[ "13", "10", "13" ]
270
42,827
1
false
As shown in WASPbase, a database of mutations, a total of 441 cases consisted of missense mutations in 179 cases (40.6%), deletions in 92 cases (20.9%), nonsense mutations in 64 cases (14.5%), splicing defects in 64 cases (14.5%), and insertions in 42 cases (9.5%).
[ "13" ]
As shown in WASPbase, a database of mutations, a total of 441 cases consisted of missense mutations in 179 cases (40.6%), deletions in 92 cases (20.9%), nonsense mutations in 64 cases, splicing defects in 64 cases, and insertions in 42 cases (9.5%).
true
true
true
true
true
7,424
1
DISCUSSION
1
13
[ "B13", "B10", "B13" ]
18,162,713
pmid-8069912|pmid-8647957|pmid-7795648|pmid-8961624|pmid-14612666|pmid-11242115|NA|pmid-14612666|NA
The exon distribution of over 5% frequency of mutation was located in exon 2 (27.0%), exon 10 (16.1%), exon 1 (13.8%), exon 4 (9.8%), exon 3 (7.5%), and exon 7 (6.4%).
[ "13", "10", "13" ]
167
42,828
0
false
The exon distribution of over 5% frequency of mutation was located in exon 2 (27.0%), exon 10 (16.1%), exon 1, exon 4 (9.8%), exon 3 (7.5%), and exon 7 (6.4%).
[ "13.8%" ]
The exon distribution of over 5% frequency of mutation was located in exon 2 (27.0%), exon 10, exon 1, exon 4 (9.8%), exon 3 (7.5%), and exon 7 (6.4%).
true
true
true
true
true
7,424
1
DISCUSSION
1
13
[ "B13", "B10", "B13" ]
18,162,713
pmid-8069912|pmid-8647957|pmid-7795648|pmid-8961624|pmid-14612666|pmid-11242115|NA|pmid-14612666|NA
Notably, the frequency at codon 86 in exon 2 was 33.6% (40/119 cases).
[ "13", "10", "13" ]
70
42,829
0
false
Notably, the frequency at codon 86 in exon 2 was 33.6% (40/119 cases).
[]
Notably, the frequency at codon 86 in exon 2 was 33.6%.
true
true
true
true
true
7,424
1
DISCUSSION
1
13
[ "B13", "B10", "B13" ]
18,162,713
pmid-8069912|pmid-8647957|pmid-7795648|pmid-8961624|pmid-14612666|pmid-11242115|NA|pmid-14612666|NA
It is well known that the codon 86 of the WAS gene is the most common missense mutation site responsible for WAS/XLT (10, 13).
[ "13", "10", "13" ]
126
42,830
0
false
It is well known that the codon 86 of the WAS gene is the most common missense mutation site responsible for WAS/XLT.
[ "10, 13" ]
It is well known that the codon 86 of the WAS gene is the most common missense mutation site responsible for WAS/XLT.
true
true
true
true
true
7,424
1
DISCUSSION
1
13
[ "B13", "B10", "B13" ]
18,162,713
pmid-8069912|pmid-8647957|pmid-7795648|pmid-8961624|pmid-14612666|pmid-11242115|NA|pmid-14612666|NA
To our knowledge, this is the first report on the hotspot missense mutation in exon 2 of WAS gene in Korea.
[ "13", "10", "13" ]
107
42,831
0
false
To our knowledge, this is the first report on the hotspot missense mutation in exon 2 of WAS gene in Korea.
[]
To our knowledge, this is the first report on the hotspot missense mutation in exon 2 of WAS gene in Korea.
true
true
true
true
true
7,424
2
DISCUSSION
1
14
[ "B14", "B18", "B15", "B9", "B10", "B13" ]
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
There are several reports on WAS mutations in Korean families (Table 2).
[ "14", "18", "15", "9", "10", "13" ]
72
42,832
0
false
There are several reports on WAS mutations in Korean families (Table 2).
[]
There are several reports on WAS mutations in Korean families (Table 2).
true
true
true
true
true
7,425
2
DISCUSSION
1
14
[ "B14", "B18", "B15", "B9", "B10", "B13" ]
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
As shown in Table 2, the predominant mutations were nonsense mutations and missense mutations (14-18).
[ "14", "18", "15", "9", "10", "13" ]
102
42,833
0
false
As shown in Table 2, the predominant mutations were nonsense mutations and missense mutations.
[ "14-18" ]
As shown in Table 2, the predominant mutations were nonsense mutations and missense mutations.
true
true
true
true
true
7,425
2
DISCUSSION
1
15
[ "B14", "B18", "B15", "B9", "B10", "B13" ]
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
Only one small deletion was reported in exon 10 (15).
[ "14", "18", "15", "9", "10", "13" ]
53
42,834
1
false
Only one small deletion was reported in exon 10.
[ "15" ]
Only one small deletion was reported in exon 10.
true
true
true
true
true
7,425
2
DISCUSSION
1
14
[ "B14", "B18", "B15", "B9", "B10", "B13" ]
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
In this report, we found a missense mutation in exon 2.
[ "14", "18", "15", "9", "10", "13" ]
55
42,835
0
false
In this report, we found a missense mutation in exon 2.
[]
In this report, we found a missense mutation in exon 2.
true
true
true
true
true
7,425
2
DISCUSSION
1
14
[ "B14", "B18", "B15", "B9", "B10", "B13" ]
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
In Korean patients' reports, including our results, mutations in exon 1, 2, 3, 7, 8, and 10 have been involved in WAS.
[ "14", "18", "15", "9", "10", "13" ]
118
42,836
0
false
In Korean patients' reports, including our results, mutations in exon 1, 2, 3, 7, 8, and 10 have been involved in WAS.
[]
In Korean patients' reports, including our results, mutations in exon 1, 2, 3, 7, 8, and 10 have been involved in WAS.
true
true
true
true
true
7,425
2
DISCUSSION
1
14
[ "B14", "B18", "B15", "B9", "B10", "B13" ]
18,162,713
pmid-12894849|pmid-16787874|pmid-15469902|pmid-8961624|pmid-14612666|NA
Therefore, although it is necessary to accumulate mutation data from a large number of patients with WAS, the distribution of mutations may be highly diverse in Korean patients, as had been observed in other reports (9, 10, 13).
[ "14", "18", "15", "9", "10", "13" ]
228
42,837
0
false
Therefore, although it is necessary to accumulate mutation data from a large number of patients with WAS, the distribution of mutations may be highly diverse in Korean patients, as had been observed in other reports.
[ "9, 10, 13" ]
Therefore, although it is necessary to accumulate mutation data from a large number of patients with WAS, the distribution of mutations may be highly diverse in Korean patients, as had been observed in other reports.
true
true
true
true
true
7,425
3
DISCUSSION
1
19
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
A correlation between clinical phenotype and genotype was reported independently by several investigators (19-21), but was not observed by all (22, 23).
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
152
42,838
0
false
A correlation between clinical phenotype and genotype was reported independently by several investigators, but was not observed by all.
[ "19-21", "22, 23" ]
A correlation between clinical phenotype and genotype was reported independently by several investigators, but was not observed by all.
true
true
true
true
true
7,426
3
DISCUSSION
1
19
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
Imai et al.
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
11
42,839
0
false
Imai et al.
[]
Imai et al.
true
true
true
true
true
7,426
3
DISCUSSION
1
19
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
demonstrated that all WAS patients with missense mutations showed WASP-positive expression; in contrast, patients with nonsense mutations, large deletions, small deletions, and small insertions were WASP-negative expression.
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
224
42,840
0
false
demonstrated that all WAS patients with missense mutations showed WASP-positive expression; in contrast, patients with nonsense mutations, large deletions, small deletions, and small insertions were WASP-negative expression.
[]
demonstrated that all WAS patients with missense mutations showed WASP-positive expression; in contrast, patients with nonsense mutations, large deletions, small deletions, and small insertions were WASP-negative expression.
false
true
true
true
false
7,426
3
DISCUSSION
1
19
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
Patients with splicing mutations were either WASP-negative or WASP-positive.
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
76
42,841
0
false
Patients with splicing mutations were either WASP-negative or WASP-positive.
[]
Patients with splicing mutations were either WASP-negative or WASP-positive.
true
true
true
true
true
7,426
3
DISCUSSION
1
24
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
Lack of WASP expression was associated with severe clinical symptoms and poor prognosis (24).
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
93
42,842
1
false
Lack of WASP expression was associated with severe clinical symptoms and poor prognosis.
[ "24" ]
Lack of WASP expression was associated with severe clinical symptoms and poor prognosis.
true
true
true
true
true
7,426
3
DISCUSSION
1
19
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
reported 5 mutational hotspots in the WAS gene from 227 WAS/XLT families with a total of 262 affected members.
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
110
42,843
0
false
reported 5 mutational hotspots in the WAS gene from 227 WAS/XLT families with a total of 262 affected members.
[]
reported 5 mutational hotspots in the WAS gene from 227 WAS/XLT families with a total of 262 affected members.
false
true
true
true
false
7,426
3
DISCUSSION
1
25
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
They also noted that the missense mutation at codon 86 was observed most frequently and associated with mild symptoms (25).
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
123
42,844
1
false
They also noted that the missense mutation at codon 86 was observed most frequently and associated with mild symptoms.
[ "25" ]
They also noted that the missense mutation at codon 86 was observed most frequently and associated with mild symptoms.
true
true
true
true
true
7,426
3
DISCUSSION
1
19
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
Two previous reports (24, 25) showed that there is a strong possibility of establishing an association between genotype and phenotype.
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
134
42,845
0
false
Two previous reports showed that there is a strong possibility of establishing an association between genotype and phenotype.
[ "24, 25" ]
Two previous reports showed that there is a strong possibility of establishing an association between genotype and phenotype.
true
true
true
true
true
7,426
3
DISCUSSION
1
19
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
In spite of advances in the clinical treatment of WAS patients, WAS remains a life-threatening condition, resulting in a poor quality of life and a bad long-term prognosis, especially for those who lack an HLA-matched sibling.
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
226
42,846
0
false
In spite of advances in the clinical treatment of WAS patients, WAS remains a life-threatening condition, resulting in a poor quality of life and a bad long-term prognosis, especially for those who lack an HLA-matched sibling.
[]
In spite of advances in the clinical treatment of WAS patients, WAS remains a life-threatening condition, resulting in a poor quality of life and a bad long-term prognosis, especially for those who lack an HLA-matched sibling.
true
true
true
true
true
7,426
3
DISCUSSION
1
19
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
The discovery of the WAS gene, and the identification of the molecular basis of WAS, have made it possible to provide genetic counseling for at-risk families.
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
158
42,847
0
false
The discovery of the WAS gene, and the identification of the molecular basis of WAS, have made it possible to provide genetic counseling for at-risk families.
[]
The discovery of the WAS gene, and the identification of the molecular basis of WAS, have made it possible to provide genetic counseling for at-risk families.
true
true
true
true
true
7,426
3
DISCUSSION
1
19
[ "B19", "B21", "B22", "B23", "B24", "B25", "B24", "B25" ]
18,162,713
pmid-7579329|pmid-10447259|pmid-8931701|pmid-8682510|pmid-12969986|pmid-15284122|pmid-12969986|pmid-15284122
Therefore, this report on the hotspot missense mutation in exon 2 of WAS gene, will help this patient's parent and his maternal uncle to understand WAS and plan both genetic counseling and family regulation.
[ "19", "21", "22", "23", "24", "25", "24", "25" ]
207
42,848
0
false
Therefore, this report on the hotspot missense mutation in exon 2 of WAS gene, will help this patient's parent and his maternal uncle to understand WAS and plan both genetic counseling and family regulation.
[]
Therefore, this report on the hotspot missense mutation in exon 2 of WAS gene, will help this patient's parent and his maternal uncle to understand WAS and plan both genetic counseling and family regulation.
true
true
true
true
true
7,426
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B3", "B4", "B5" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
Pre-mRNA splicing provides an important window for post-transcriptional control of the transcriptome, with alternative splicing leading to a huge expansion in proteomic diversity (1,2).
[ "1", "2", "3", "3", "4", "5" ]
185
42,849
0
false
Pre-mRNA splicing provides an important window for post-transcriptional control of the transcriptome, with alternative splicing leading to a huge expansion in proteomic diversity.
[ "1,2" ]
Pre-mRNA splicing provides an important window for post-transcriptional control of the transcriptome, with alternative splicing leading to a huge expansion in proteomic diversity.
true
true
true
true
true
7,427
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B3", "B4", "B5" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
The large, multi-complex spliceosome is assembled de novo onto each intron, for which the precise recognition of the intron borders by the spliceosome is essential (3).
[ "1", "2", "3", "3", "4", "5" ]
168
42,850
1
false
The large, multi-complex spliceosome is assembled de novo onto each intron, for which the precise recognition of the intron borders by the spliceosome is essential.
[ "3" ]
The large, multi-complex spliceosome is assembled de novo onto each intron, for which the precise recognition of the intron borders by the spliceosome is essential.
true
true
true
true
true
7,427
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B3", "B4", "B5" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
Each intron is defined by a donor site and an acceptor site at its 5′ and 3′ ends, respectively.
[ "1", "2", "3", "3", "4", "5" ]
96
42,851
0
false
Each intron is defined by a donor site and an acceptor site at its 5′ and 3′ ends, respectively.
[]
Each intron is defined by a donor site and an acceptor site at its 5′ and 3′ ends, respectively.
true
true
true
true
true
7,427
0
INTRODUCTION
1
3
[ "B1", "B2", "B3", "B3", "B4", "B5" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
However, as these core splicing signals are highly degenerative, intron/exon definition requires a network of protein–protein and protein–RNA interactions to ensure that the correct splice sites are recognized and used (3).
[ "1", "2", "3", "3", "4", "5" ]
223
42,852
1
false
However, as these core splicing signals are highly degenerative, intron/exon definition requires a network of protein–protein and protein–RNA interactions to ensure that the correct splice sites are recognized and used.
[ "3" ]
However, as these core splicing signals are highly degenerative, intron/exon definition requires a network of protein–protein and protein–RNA interactions to ensure that the correct splice sites are recognized and used.
true
true
true
true
true
7,427
0
INTRODUCTION
1
1
[ "B1", "B2", "B3", "B3", "B4", "B5" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
Much attention has been focused on the regulation of this process through RNA-binding proteins, which can mediate the effects of splicing enhancers or silencers at a specific site (4,5).
[ "1", "2", "3", "3", "4", "5" ]
186
42,853
0
false
Much attention has been focused on the regulation of this process through RNA-binding proteins, which can mediate the effects of splicing enhancers or silencers at a specific site.
[ "4,5" ]
Much attention has been focused on the regulation of this process through RNA-binding proteins, which can mediate the effects of splicing enhancers or silencers at a specific site.
true
true
true
true
true
7,427
1
INTRODUCTION
1
6
[ "B6", "B7 B8 B9", "B8", "B6", "B10", "B11", "B11", "B12" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
Splicing regulation can also be effected by the presence of secondary structure within the pre-mRNA (6).
[ "6", "7–9", "8", "6", "10", "11", "11", "12" ]
104
42,854
1
false
Splicing regulation can also be effected by the presence of secondary structure within the pre-mRNA.
[ "6" ]
Splicing regulation can also be effected by the presence of secondary structure within the pre-mRNA.
true
true
true
true
true
7,428
1
INTRODUCTION
1
7–9
[ "B6", "B7 B8 B9", "B8", "B6", "B10", "B11", "B11", "B12" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
There is a general consensus that secondary structures within pre-mRNA will be formed locally, rather than over long distances, since folding occurs cotranscriptionally (7–9).
[ "6", "7–9", "8", "6", "10", "11", "11", "12" ]
175
42,855
1
false
There is a general consensus that secondary structures within pre-mRNA will be formed locally, rather than over long distances, since folding occurs cotranscriptionally.
[ "7–9" ]
There is a general consensus that secondary structures within pre-mRNA will be formed locally, rather than over long distances, since folding occurs cotranscriptionally.
true
true
true
true
true
7,428
1
INTRODUCTION
1
8
[ "B6", "B7 B8 B9", "B8", "B6", "B10", "B11", "B11", "B12" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
Cotranscriptional folding of pre-RNA was suggested to occur mainly within a window of about 60 nucleotides downstream of the transcribing polymerase (8).
[ "6", "7–9", "8", "6", "10", "11", "11", "12" ]
153
42,856
1
false
Cotranscriptional folding of pre-RNA was suggested to occur mainly within a window of about 60 nucleotides downstream of the transcribing polymerase.
[ "8" ]
Cotranscriptional folding of pre-RNA was suggested to occur mainly within a window of about 60 nucleotides downstream of the transcribing polymerase.
true
true
true
true
true
7,428
1
INTRODUCTION
1
6
[ "B6", "B7 B8 B9", "B8", "B6", "B10", "B11", "B11", "B12" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
Recently, many specific examples have been documented in which the presence of local secondary structure is shown to affect the splicing outcome (6).
[ "6", "7–9", "8", "6", "10", "11", "11", "12" ]
149
42,857
1
false
Recently, many specific examples have been documented in which the presence of local secondary structure is shown to affect the splicing outcome.
[ "6" ]
Recently, many specific examples have been documented in which the presence of local secondary structure is shown to affect the splicing outcome.
true
true
true
true
true
7,428
1
INTRODUCTION
1
10
[ "B6", "B7 B8 B9", "B8", "B6", "B10", "B11", "B11", "B12" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
For instance, the efficiency of splicing of an intron in the Drosophila Adh gene was reduced when a hairpin structure within the intron was disrupted (10).
[ "6", "7–9", "8", "6", "10", "11", "11", "12" ]
155
42,858
1
false
For instance, the efficiency of splicing of an intron in the Drosophila Adh gene was reduced when a hairpin structure within the intron was disrupted.
[ "10" ]
For instance, the efficiency of splicing of an intron in the Drosophila Adh gene was reduced when a hairpin structure within the intron was disrupted.
true
true
true
true
true
7,428
1
INTRODUCTION
1
11
[ "B6", "B7 B8 B9", "B8", "B6", "B10", "B11", "B11", "B12" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
In the human tau pre-mRNA, a stem structure that occurs locally masks the donor site of exon 10 (11).
[ "6", "7–9", "8", "6", "10", "11", "11", "12" ]
101
42,859
1
false
In the human tau pre-mRNA, a stem structure that occurs locally masks the donor site of exon 10.
[ "11" ]
In the human tau pre-mRNA, a stem structure that occurs locally masks the donor site of exon 10.
true
true
true
true
true
7,428
1
INTRODUCTION
1
6
[ "B6", "B7 B8 B9", "B8", "B6", "B10", "B11", "B11", "B12" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
Silent mutations linked with neurogenerative diseases have been shown to destabilize the stem structure, thereby increasing the availability of the donor site with a concurrent increase in exon 10 inclusion (11,12).
[ "6", "7–9", "8", "6", "10", "11", "11", "12" ]
215
42,860
0
false
Silent mutations linked with neurogenerative diseases have been shown to destabilize the stem structure, thereby increasing the availability of the donor site with a concurrent increase in exon 10 inclusion.
[ "11,12" ]
Silent mutations linked with neurogenerative diseases have been shown to destabilize the stem structure, thereby increasing the availability of the donor site with a concurrent increase in exon 10 inclusion.
true
true
true
true
true
7,428
2
INTRODUCTION
1
13
[ "B13", "B14", "B14" ]
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
A recent analysis of the human genome revealed a correlation between secondary structure encompassing a splice site and alternative splicing, suggesting that local secondary structures frequently modulate alternative splicing by masking splice sites (13).
[ "13", "14", "14" ]
255
42,861
1
false
A recent analysis of the human genome revealed a correlation between secondary structure encompassing a splice site and alternative splicing, suggesting that local secondary structures frequently modulate alternative splicing by masking splice sites.
[ "13" ]
A recent analysis of the human genome revealed a correlation between secondary structure encompassing a splice site and alternative splicing, suggesting that local secondary structures frequently modulate alternative splicing by masking splice sites.
true
true
true
true
true
7,429
2
INTRODUCTION
1
14
[ "B13", "B14", "B14" ]
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
In another human genome-wide analysis, splicing enhancer and silencer signals were found more frequently in a single-stranded than in a double-stranded context (14).
[ "13", "14", "14" ]
165
42,862
1
false
In another human genome-wide analysis, splicing enhancer and silencer signals were found more frequently in a single-stranded than in a double-stranded context.
[ "14" ]
In another human genome-wide analysis, splicing enhancer and silencer signals were found more frequently in a single-stranded than in a double-stranded context.
true
true
true
true
true
7,429
2
INTRODUCTION
1
14
[ "B13", "B14", "B14" ]
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
Correspondingly, the signals were less effective as splicing regulators if incorporated into a double-stranded context, suggesting that local RNA secondary structure is under evolutionary selection (14).
[ "13", "14", "14" ]
203
42,863
1
false
Correspondingly, the signals were less effective as splicing regulators if incorporated into a double-stranded context, suggesting that local RNA secondary structure is under evolutionary selection.
[ "14" ]
Correspondingly, the signals were less effective as splicing regulators if incorporated into a double-stranded context, suggesting that local RNA secondary structure is under evolutionary selection.
true
true
true
true
true
7,429
3
INTRODUCTION
1
15
[ "B15", "B16" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
Long-range base-pairing within pre-mRNA has also been implicated in modulating pre-mRNA splicing in a few cases.
[ "15", "16" ]
112
42,864
0
false
Long-range base-pairing within pre-mRNA has also been implicated in modulating pre-mRNA splicing in a few cases.
[]
Long-range base-pairing within pre-mRNA has also been implicated in modulating pre-mRNA splicing in a few cases.
true
true
true
true
true
7,430
3
INTRODUCTION
1
15
[ "B15", "B16" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
One of the most dramatic examples is offered by the Drosophila Dscam pre-mRNA, where the formation of an intronic stem structure between a region downstream of the donor site, and one of the regions upstream of each of the 48 potential acceptor sites, appears to modulate the binding of splicing regulators and allow for...
[ "15", "16" ]
393
42,865
1
false
One of the most dramatic examples is offered by the Drosophila Dscam pre-mRNA, where the formation of an intronic stem structure between a region downstream of the donor site, and one of the regions upstream of each of the 48 potential acceptor sites, appears to modulate the binding of splicing regulators and allow for...
[ "15" ]
One of the most dramatic examples is offered by the Drosophila Dscam pre-mRNA, where the formation of an intronic stem structure between a region downstream of the donor site, and one of the regions upstream of each of the 48 potential acceptor sites, appears to modulate the binding of splicing regulators and allow for...
true
true
true
true
true
7,430
3
INTRODUCTION
1
15
[ "B15", "B16" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
Such interactions would occur over distances ranging from 1000 to 12 000 nucleotides.
[ "15", "16" ]
85
42,866
0
false
Such interactions would occur over distances ranging from 1000 to 12 000 nucleotides.
[]
Such interactions would occur over distances ranging from 1000 to 12 000 nucleotides.
true
true
true
true
true
7,430
3
INTRODUCTION
1
15
[ "B15", "B16" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
Similarly to short-range interactions, long-range interactions could mask splicing signals or create novel binding sites for protein binding to double-stranded RNA.
[ "15", "16" ]
164
42,867
0
false
Similarly to short-range interactions, long-range interactions could mask splicing signals or create novel binding sites for protein binding to double-stranded RNA.
[]
Similarly to short-range interactions, long-range interactions could mask splicing signals or create novel binding sites for protein binding to double-stranded RNA.
true
true
true
true
true
7,430
3
INTRODUCTION
1
15
[ "B15", "B16" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
They could also affect the context of splicing signals to a greater degree, for example, by looping out an exon, or by bringing distant splice sites in closer proximity to each other.
[ "15", "16" ]
183
42,868
0
false
They could also affect the context of splicing signals to a greater degree, for example, by looping out an exon, or by bringing distant splice sites in closer proximity to each other.
[]
They could also affect the context of splicing signals to a greater degree, for example, by looping out an exon, or by bringing distant splice sites in closer proximity to each other.
true
true
true
true
true
7,430
3
INTRODUCTION
1
16
[ "B15", "B16" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
For instance, GC-rich motifs surrounding alternatively spliced exons in humans were implicated in looping-out these exons and thereby leading to exon skipping, even though the interactions between these motifs would occur over long distances (16).
[ "15", "16" ]
247
42,869
1
false
For instance, GC-rich motifs surrounding alternatively spliced exons in humans were implicated in looping-out these exons and thereby leading to exon skipping, even though the interactions between these motifs would occur over long distances.
[ "16" ]
For instance, GC-rich motifs surrounding alternatively spliced exons in humans were implicated in looping-out these exons and thereby leading to exon skipping, even though the interactions between these motifs would occur over long distances.
true
true
true
true
true
7,430
4
INTRODUCTION
0
null
null
19,465,384
pmid-14698618|pmid-12127448
To determine the extent to which long-range interactions modulate pre-mRNA splicing, we took advantage of the availability of the 12 sequenced Drosophila genomes to perform phylogenetic searches for conserved intronic stem structures.
null
234
42,870
0
false
null
null
To determine the extent to which long-range interactions modulate pre-mRNA splicing, we took advantage of the availability of the 12 sequenced Drosophila genomes to perform phylogenetic searches for conserved intronic stem structures.
true
true
true
true
true
7,431
4
INTRODUCTION
0
null
null
19,465,384
pmid-14698618|pmid-12127448
Specifically, we first searched the D. melonogaster genome for complementary stretches of at least nine nucleotides (hereafter termed ‘boxes’) that could base-pair, with the requirement that each box be located near an intron boundary to maximize the potential for the stem structures to influence splicing.
null
307
42,871
0
false
null
null
Specifically, we first searched the D. melonogaster genome for complementary stretches of at least nine nucleotides (hereafter termed ‘boxes’) that could base-pair, with the requirement that each box be located near an intron boundary to maximize the potential for the stem structures to influence splicing.
true
true
true
true
true
7,431
4
INTRODUCTION
0
null
null
19,465,384
pmid-14698618|pmid-12127448
This set was then narrowed down to those pairs that were also phylogenetically conserved, resulting in 202 pairs of conserved boxes, of which approximately 50% were within alternatively spliced introns.
null
202
42,872
0
false
null
null
This set was then narrowed down to those pairs that were also phylogenetically conserved, resulting in 202 pairs of conserved boxes, of which approximately 50% were within alternatively spliced introns.
true
true
true
true
true
7,431
4
INTRODUCTION
0
null
null
19,465,384
pmid-14698618|pmid-12127448
Several pairs of boxes were experimentally tested within mini-genes to determine whether the stem structures predicted to form over long distances could influence the splicing outcome.
null
184
42,873
0
false
null
null
Several pairs of boxes were experimentally tested within mini-genes to determine whether the stem structures predicted to form over long distances could influence the splicing outcome.
true
true
true
true
true
7,431
4
INTRODUCTION
0
null
null
19,465,384
pmid-14698618|pmid-12127448
Indeed, mutagenesis studies revealed that base-pairing of the boxes was critical in determining the resulting ratio of alternatively spliced mRNAs.
null
147
42,874
0
false
null
null
Indeed, mutagenesis studies revealed that base-pairing of the boxes was critical in determining the resulting ratio of alternatively spliced mRNAs.
true
true
true
true
true
7,431
4
INTRODUCTION
0
null
null
19,465,384
pmid-14698618|pmid-12127448
We suggest that the formation of long-distance secondary structure plays a much greater role in modulating alternative splicing in Drosophila than previously assumed.
null
166
42,875
0
false
null
null
We suggest that the formation of long-distance secondary structure plays a much greater role in modulating alternative splicing in Drosophila than previously assumed.
true
true
true
true
true
7,431
4
INTRODUCTION
0
null
null
19,465,384
pmid-14698618|pmid-12127448
This modulation provides a way of amplifying the alternative splicing repertoire as well as a platform for further regulation in trans.
null
135
42,876
0
false
null
null
This modulation provides a way of amplifying the alternative splicing repertoire as well as a platform for further regulation in trans.
true
true
true
true
true
7,431
0
DISCUSSION
1
28
[ "B28" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
The extent to which secondary structures influence splicing was analyzed in a genome-wide manner, using the strength of phylogenomic comparisons in Drosophila, for which 12 genomes are available (28).
[ "28" ]
200
42,877
1
false
The extent to which secondary structures influence splicing was analyzed in a genome-wide manner, using the strength of phylogenomic comparisons in Drosophila, for which 12 genomes are available.
[ "28" ]
The extent to which secondary structures influence splicing was analyzed in a genome-wide manner, using the strength of phylogenomic comparisons in Drosophila, for which 12 genomes are available.
true
true
true
true
true
7,432
0
DISCUSSION
1
28
[ "B28" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
We uncovered a set of 202 intronic sequence pairs that could engage in thermodynamically stable stems, and that are highly conserved among fruit flies.
[ "28" ]
151
42,878
0
false
We uncovered a set of 202 intronic sequence pairs that could engage in thermodynamically stable stems, and that are highly conserved among fruit flies.
[]
We uncovered a set of 202 intronic sequence pairs that could engage in thermodynamically stable stems, and that are highly conserved among fruit flies.
true
true
true
true
true
7,432
0
DISCUSSION
1
28
[ "B28" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
Our search included base-pairing over relatively long RNA distances.
[ "28" ]
68
42,879
0
false
Our search included base-pairing over relatively long RNA distances.
[]
Our search included base-pairing over relatively long RNA distances.
true
true
true
true
true
7,432
0
DISCUSSION
1
28
[ "B28" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
Experimentally, we demonstrated for three cases that the predicted stem structures influence the outcome of alternative splicing.
[ "28" ]
129
42,880
0
false
Experimentally, we demonstrated for three cases that the predicted stem structures influence the outcome of alternative splicing.
[]
Experimentally, we demonstrated for three cases that the predicted stem structures influence the outcome of alternative splicing.
true
true
true
true
true
7,432
0
DISCUSSION
1
28
[ "B28" ]
19,465,384
pmid-15499012|pmid-18978788|NA|NA|pmid-10916158|pmid-12626338|pmid-17994087
We propose that alternative splicing is often modulated by long-range RNA secondary structures, through a variety of mechanisms that promote specific splice site usage.
[ "28" ]
168
42,881
0
false
We propose that alternative splicing is often modulated by long-range RNA secondary structures, through a variety of mechanisms that promote specific splice site usage.
[]
We propose that alternative splicing is often modulated by long-range RNA secondary structures, through a variety of mechanisms that promote specific splice site usage.
true
true
true
true
true
7,432
1
DISCUSSION
1
10
[ "B10" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
Taking advantage of phylogenetic comparisons, we identified a set of highly conserved complementary sequences that could form stem structures, which we predict could influence splicing.
[ "10" ]
185
42,882
0
false
Taking advantage of phylogenetic comparisons, we identified a set of highly conserved complementary sequences that could form stem structures, which we predict could influence splicing.
[]
Taking advantage of phylogenetic comparisons, we identified a set of highly conserved complementary sequences that could form stem structures, which we predict could influence splicing.
true
true
true
true
true
7,433
1
DISCUSSION
1
10
[ "B10" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
Testing several of these experimentally demonstrated that the stem structures indeed influenced splicing when they occurred in alternatively, but not constitutively, spliced introns.
[ "10" ]
182
42,883
0
false
Testing several of these experimentally demonstrated that the stem structures indeed influenced splicing when they occurred in alternatively, but not constitutively, spliced introns.
[]
Testing several of these experimentally demonstrated that the stem structures indeed influenced splicing when they occurred in alternatively, but not constitutively, spliced introns.
true
true
true
true
true
7,433
1
DISCUSSION
1
10
[ "B10" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
Consistently, there is an enrichment for alternatively spliced introns within our set.
[ "10" ]
86
42,884
0
false
Consistently, there is an enrichment for alternatively spliced introns within our set.
[]
Consistently, there is an enrichment for alternatively spliced introns within our set.
true
true
true
true
true
7,433
1
DISCUSSION
1
10
[ "B10" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
However, we cannot exclude the possibility that constitutive splicing is likewise affected by the presence of the stem structures, but that our over-expression system is technically not able to detect changes in these splicing events upon stem disruption.
[ "10" ]
255
42,885
0
false
However, we cannot exclude the possibility that constitutive splicing is likewise affected by the presence of the stem structures, but that our over-expression system is technically not able to detect changes in these splicing events upon stem disruption.
[]
However, we cannot exclude the possibility that constitutive splicing is likewise affected by the presence of the stem structures, but that our over-expression system is technically not able to detect changes in these splicing events upon stem disruption.
true
true
true
true
true
7,433
1
DISCUSSION
1
10
[ "B10" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
For example, a hairpin structure was found to influence the splicing of the Drosophila Adh pre-mRNA and alter the subsequent protein expression levels, although the changes observed in splicing in vivo when the hairpin was disrupted were only 6% (10).
[ "10" ]
251
42,886
1
false
For example, a hairpin structure was found to influence the splicing of the Drosophila Adh pre-mRNA and alter the subsequent protein expression levels, although the changes observed in splicing in vivo when the hairpin was disrupted were only 6%.
[ "10" ]
For example, a hairpin structure was found to influence the splicing of the Drosophila Adh pre-mRNA and alter the subsequent protein expression levels, although the changes observed in splicing in vivo when the hairpin was disrupted were only 6%.
true
true
true
true
true
7,433
1
DISCUSSION
1
10
[ "B10" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
It is also possible that stem structures are important within constitutively spliced introns for sequestering and thereby silencing cryptic splice sites, thus allowing splicing to occur constitutively.
[ "10" ]
201
42,887
0
false
It is also possible that stem structures are important within constitutively spliced introns for sequestering and thereby silencing cryptic splice sites, thus allowing splicing to occur constitutively.
[]
It is also possible that stem structures are important within constitutively spliced introns for sequestering and thereby silencing cryptic splice sites, thus allowing splicing to occur constitutively.
true
true
true
true
true
7,433
1
DISCUSSION
1
10
[ "B10" ]
19,465,384
pmid-15572659|pmid-12127447|pmid-2840206|pmid-3670310|pmid-2840206|pmid-15572659|pmid-12972637|pmid-9641683|pmid-9641683|pmid-16782711|pmid-12972637
Additionally, some of the introns in our set which are classified as constitutively spliced may actually contain undocumented alternative splicing events, such as those we observed for the Atrophin intron (which had an undocumented alternative acceptor site; Figure 3).
[ "10" ]
269
42,888
0
false
Additionally, some of the introns in our set which are classified as constitutively spliced may actually contain undocumented alternative splicing events, such as those we observed for the Atrophin intron (which had an undocumented alternative acceptor site; Figure 3).
[]
Additionally, some of the introns in our set which are classified as constitutively spliced may actually contain undocumented alternative splicing events, such as those we observed for the Atrophin intron (which had an undocumented alternative acceptor site; Figure 3).
true
true
true
true
true
7,433
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
Why should secondary structures play such a frequent role in regulating alternative splicing?
null
93
42,889
0
false
null
null
Why should secondary structures play such a frequent role in regulating alternative splicing?
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
Modulation of alternative splicing by secondary structures provides a built-in mechanism for balancing the splicing output.
null
123
42,890
0
false
null
null
Modulation of alternative splicing by secondary structures provides a built-in mechanism for balancing the splicing output.
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
Our results exemplify this principle.
null
37
42,891
0
false
null
null
Our results exemplify this principle.
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
In the case of Atrophin alternative splicing, two alternative acceptor sites are used equally well only when a stem structure masks the stronger one of these sites (see Figure 3).
null
179
42,892
0
false
null
null
In the case of Atrophin alternative splicing, two alternative acceptor sites are used equally well only when a stem structure masks the stronger one of these sites (see Figure 3).
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
The use of the stronger acceptor site adds 22 amino acids to the resulting protein, which could change its function.
null
116
42,893
0
false
null
null
The use of the stronger acceptor site adds 22 amino acids to the resulting protein, which could change its function.
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
Thus, the balanced use of the two acceptor sites is ensured by the stem structure formation, without the prerequisite for additional trans-acting factors.
null
154
42,894
0
false
null
null
Thus, the balanced use of the two acceptor sites is ensured by the stem structure formation, without the prerequisite for additional trans-acting factors.
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
In the second case, a stem structure also masks an alternative splice site in the CG33298 intron; however, the splicing outcome of this event differs from that of Atrophin, since the masked splice site is highly suppressed and only used to a small degree.
null
255
42,895
0
false
null
null
In the second case, a stem structure also masks an alternative splice site in the CG33298 intron; however, the splicing outcome of this event differs from that of Atrophin, since the masked splice site is highly suppressed and only used to a small degree.
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
When the stem is prevented from forming, there is an almost complete switch of splicing to the previously masked splice site (which is predicted to be the stronger one).
null
169
42,896
0
false
null
null
When the stem is prevented from forming, there is an almost complete switch of splicing to the previously masked splice site (which is predicted to be the stronger one).
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
Thus, several parameters determine how alternative splicing can be modulated by secondary structure formation, such as splice site strength, splice site competitiveness due to positioning, and regulation through the kinetics and thermodynamics of secondary structure formation.
null
277
42,897
0
false
null
null
Thus, several parameters determine how alternative splicing can be modulated by secondary structure formation, such as splice site strength, splice site competitiveness due to positioning, and regulation through the kinetics and thermodynamics of secondary structure formation.
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
This complexity is evident for the Nmnat intron, in which the stem loop was required to approximate a distal splice site, and to reduce the competitiveness of a proximal splice site, in order to allow usage of both splice sites (see Figure 4).
null
243
42,898
0
false
null
null
This complexity is evident for the Nmnat intron, in which the stem loop was required to approximate a distal splice site, and to reduce the competitiveness of a proximal splice site, in order to allow usage of both splice sites (see Figure 4).
true
true
true
true
true
7,434
2
DISCUSSION
0
null
null
19,465,384
pmid-18579871|pmid-18020710|pmid-18020710
Thus, the formation of stem structures over long ranges of RNA greatly amplifies the potential for alternative splice site choices.
null
131
42,899
0
false
null
null
Thus, the formation of stem structures over long ranges of RNA greatly amplifies the potential for alternative splice site choices.
true
true
true
true
true
7,434
3
DISCUSSION
1
29
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
Modulation of alternative splicing by stem structures also opens the possibility for directed regulation.
[ "29", "30", "31", "32" ]
105
42,900
0
false
Modulation of alternative splicing by stem structures also opens the possibility for directed regulation.
[]
Modulation of alternative splicing by stem structures also opens the possibility for directed regulation.
true
true
true
true
true
7,435
3
DISCUSSION
1
29
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
Regulation could come through the propensity of the secondary RNA structures themselves to change, in response to different cellular situations.
[ "29", "30", "31", "32" ]
144
42,901
0
false
Regulation could come through the propensity of the secondary RNA structures themselves to change, in response to different cellular situations.
[]
Regulation could come through the propensity of the secondary RNA structures themselves to change, in response to different cellular situations.
true
true
true
true
true
7,435
3
DISCUSSION
1
29
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
For example, changes in transcription rate could change the kinetics of stem formation, leading to specific changes in the alternative splicing outcome.
[ "29", "30", "31", "32" ]
152
42,902
0
false
For example, changes in transcription rate could change the kinetics of stem formation, leading to specific changes in the alternative splicing outcome.
[]
For example, changes in transcription rate could change the kinetics of stem formation, leading to specific changes in the alternative splicing outcome.
true
true
true
true
true
7,435
3
DISCUSSION
1
29
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
This would be somewhat similar to the bacterial attenuators which are regulated by ribosome pausing (29).
[ "29", "30", "31", "32" ]
105
42,903
1
false
This would be somewhat similar to the bacterial attenuators which are regulated by ribosome pausing.
[ "29" ]
This would be somewhat similar to the bacterial attenuators which are regulated by ribosome pausing.
true
true
true
true
true
7,435
3
DISCUSSION
1
29
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
Additional regulation could likewise come from the binding of trans-acting factors, such as proteins and small RNAs.
[ "29", "30", "31", "32" ]
116
42,904
0
false
Additional regulation could likewise come from the binding of trans-acting factors, such as proteins and small RNAs.
[]
Additional regulation could likewise come from the binding of trans-acting factors, such as proteins and small RNAs.
true
true
true
true
true
7,435
3
DISCUSSION
1
29
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
Regulation through local RNA structures has been demonstrated for the yeast ribosomal L30 protein, which binds a structure in its own pre-mRNA that resembles its rRNA target.
[ "29", "30", "31", "32" ]
174
42,905
0
false
Regulation through local RNA structures has been demonstrated for the yeast ribosomal L30 protein, which binds a structure in its own pre-mRNA that resembles its rRNA target.
[]
Regulation through local RNA structures has been demonstrated for the yeast ribosomal L30 protein, which binds a structure in its own pre-mRNA that resembles its rRNA target.
true
true
true
true
true
7,435
3
DISCUSSION
1
30
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
L30 binding prevents subsequent U2 snRNP association, thereby auto-regulating its own pre-mRNA splicing (30).
[ "29", "30", "31", "32" ]
109
42,906
1
false
L30 binding prevents subsequent U2 snRNP association, thereby auto-regulating its own pre-mRNA splicing.
[ "30" ]
L30 binding prevents subsequent U2 snRNP association, thereby auto-regulating its own pre-mRNA splicing.
true
true
true
true
true
7,435
3
DISCUSSION
1
29
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
Splicing regulation has also been demonstrated in plants and fungi to occur by riboswitches modulated by the binding of thiamine pyrophosphate (TPP) in some pre-mRNAs that encode proteins involved in TPP metabolism, thereby changing the alternative splicing outcome (31,32).
[ "29", "30", "31", "32" ]
274
42,907
0
false
Splicing regulation has also been demonstrated in plants and fungi to occur by riboswitches modulated by the binding of thiamine pyrophosphate (TPP) in some pre-mRNAs that encode proteins involved in TPP metabolism, thereby changing the alternative splicing outcome.
[ "31,32" ]
Splicing regulation has also been demonstrated in plants and fungi to occur by riboswitches modulated by the binding of thiamine pyrophosphate (TPP) in some pre-mRNAs that encode proteins involved in TPP metabolism, thereby changing the alternative splicing outcome.
true
true
true
true
true
7,435
3
DISCUSSION
1
29
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
The kinetics of stem structure formation could also be regulated by sequestering binding sites of single-stranded RNA-binding proteins (intronic splicing enhancers and silencers).
[ "29", "30", "31", "32" ]
179
42,908
0
false
The kinetics of stem structure formation could also be regulated by sequestering binding sites of single-stranded RNA-binding proteins (intronic splicing enhancers and silencers).
[]
The kinetics of stem structure formation could also be regulated by sequestering binding sites of single-stranded RNA-binding proteins (intronic splicing enhancers and silencers).
true
true
true
true
true
7,435
3
DISCUSSION
1
29
[ "B29", "B30", "B31", "B32" ]
19,465,384
pmid-16213213|pmid-12655015|pmid-7007895|pmid-18570876|pmid-18006684|pmid-17468745
Such regulation could then affect the ratio of splicing isoforms produced and would have a strong potential to fine-tune sensitive splicing events.
[ "29", "30", "31", "32" ]
147
42,909
0
false
Such regulation could then affect the ratio of splicing isoforms produced and would have a strong potential to fine-tune sensitive splicing events.
[]
Such regulation could then affect the ratio of splicing isoforms produced and would have a strong potential to fine-tune sensitive splicing events.
true
true
true
true
true
7,435
4
DISCUSSION
1
33
[ "B33", "B34" ]
19,465,384
pmid-14698618|pmid-12127448
The high degree of conservation of not only the RNA structure but also the complementary sequences (almost always 100%) in our dataset is remarkable.
[ "33", "34" ]
149
42,910
0
false
The high degree of conservation of not only the RNA structure but also the complementary sequences (almost always 100%) in our dataset is remarkable.
[]
The high degree of conservation of not only the RNA structure but also the complementary sequences (almost always 100%) in our dataset is remarkable.
true
true
true
true
true
7,436
4
DISCUSSION
1
33
[ "B33", "B34" ]
19,465,384
pmid-14698618|pmid-12127448
Indeed, although the search allowed for up to three mismatches in a 9 nt stretch, the boxes usually differed by at most one nucleotide between the species (Figures 2–4, and Supplementary Table S2).
[ "33", "34" ]
197
42,911
0
false
Indeed, although the search allowed for up to three mismatches in a 9 nt stretch, the boxes usually differed by at most one nucleotide between the species (Figures 2–4, and Supplementary Table S2).
[]
Indeed, although the search allowed for up to three mismatches in a 9 nt stretch, the boxes usually differed by at most one nucleotide between the species (Figures 2–4, and Supplementary Table S2).
true
true
true
true
true
7,436
4
DISCUSSION
1
33
[ "B33", "B34" ]
19,465,384
pmid-14698618|pmid-12127448
This is quite surprising since the Drosophila species analyzed here have been diverging for over 40 million years of evolution.
[ "33", "34" ]
127
42,912
0
false
This is quite surprising since the Drosophila species analyzed here have been diverging for over 40 million years of evolution.
[]
This is quite surprising since the Drosophila species analyzed here have been diverging for over 40 million years of evolution.
true
true
true
true
true
7,436
4
DISCUSSION
1
33
[ "B33", "B34" ]
19,465,384
pmid-14698618|pmid-12127448
One possible explanation for this extreme conservation is that sequence evolutionary rate is slower in base-paired regions because two simultaneous mutations are needed to maintain secondary structure.
[ "33", "34" ]
201
42,913
0
false
One possible explanation for this extreme conservation is that sequence evolutionary rate is slower in base-paired regions because two simultaneous mutations are needed to maintain secondary structure.
[]
One possible explanation for this extreme conservation is that sequence evolutionary rate is slower in base-paired regions because two simultaneous mutations are needed to maintain secondary structure.
true
true
true
true
true
7,436
4
DISCUSSION
1
33
[ "B33", "B34" ]
19,465,384
pmid-14698618|pmid-12127448
This effect has been reported previously in bacterial terminators and attenuators (33).
[ "33", "34" ]
87
42,914
1
false
This effect has been reported previously in bacterial terminators and attenuators.
[ "33" ]
This effect has been reported previously in bacterial terminators and attenuators.
true
true
true
true
true
7,436
4
DISCUSSION
1
33
[ "B33", "B34" ]
19,465,384
pmid-14698618|pmid-12127448
However, it is also possible that the strong conservation we observe reflects further interactions with trans-acting factors for one or both of the sequences of each pair, in addition to a direct role of the stem structures on splicing.
[ "33", "34" ]
236
42,915
0
false
However, it is also possible that the strong conservation we observe reflects further interactions with trans-acting factors for one or both of the sequences of each pair, in addition to a direct role of the stem structures on splicing.
[]
However, it is also possible that the strong conservation we observe reflects further interactions with trans-acting factors for one or both of the sequences of each pair, in addition to a direct role of the stem structures on splicing.
true
true
true
true
true
7,436
4
DISCUSSION
1
34
[ "B33", "B34" ]
19,465,384
pmid-14698618|pmid-12127448
Indeed, sequence covariation over the evolution of ribosomal RNA structure was very strong and allowed these structures to be resolved through comparative modeling (34).
[ "33", "34" ]
169
42,916
1
false
Indeed, sequence covariation over the evolution of ribosomal RNA structure was very strong and allowed these structures to be resolved through comparative modeling.
[ "34" ]
Indeed, sequence covariation over the evolution of ribosomal RNA structure was very strong and allowed these structures to be resolved through comparative modeling.
true
true
true
true
true
7,436
4
DISCUSSION
1
33
[ "B33", "B34" ]
19,465,384
pmid-14698618|pmid-12127448
Since our search would not have included stem structures that have been conserved structurally with covariation, we could predict that such a group would further expand our list of stem structures that could influence splicing.
[ "33", "34" ]
227
42,917
0
false
Since our search would not have included stem structures that have been conserved structurally with covariation, we could predict that such a group would further expand our list of stem structures that could influence splicing.
[]
Since our search would not have included stem structures that have been conserved structurally with covariation, we could predict that such a group would further expand our list of stem structures that could influence splicing.
true
true
true
true
true
7,436
5
DISCUSSION
1
8
[ "B8", "B35", "B35", "B36" ]
19,465,384
pmid-2840206|pmid-15989962|pmid-15989962|pmid-11994740
By allowing the distance between the boxes to be determined by intron length, we have considered long-range as well as short-range interactions, despite the common belief that the long-range interactions are less likely to occur.
[ "8", "35", "35", "36" ]
229
42,918
0
false
By allowing the distance between the boxes to be determined by intron length, we have considered long-range as well as short-range interactions, despite the common belief that the long-range interactions are less likely to occur.
[]
By allowing the distance between the boxes to be determined by intron length, we have considered long-range as well as short-range interactions, despite the common belief that the long-range interactions are less likely to occur.
true
true
true
true
true
7,437