Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
xet
 Community
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DISCUSSION
0
null
null
17,170,005
null
Use of the PET and measuring the ratios between predicted exon classes will allow researchers to directly measure the effects of new genefinders.
null
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7,500
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false
null
null
Use of the PET and measuring the ratios between predicted exon classes will allow researchers to directly measure the effects of new genefinders.
true
true
true
true
true
1,218
0
INTRODUCTION
1
1
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Identification of causal genetic variants underlying complex traits is a major goal in genetic studies.
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Identification of causal genetic variants underlying complex traits is a major goal in genetic studies.
[]
Identification of causal genetic variants underlying complex traits is a major goal in genetic studies.
true
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1,219
0
INTRODUCTION
1
1
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Linkage analysis has long been used to discover chromosomal intervals harboring sequence variants that cause variations in quantitative traits.
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143
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Linkage analysis has long been used to discover chromosomal intervals harboring sequence variants that cause variations in quantitative traits.
[]
Linkage analysis has long been used to discover chromosomal intervals harboring sequence variants that cause variations in quantitative traits.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
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A typical quantitative trait locus (QTL) interval usually contains many genes ranging from several dozens to several hundreds, hence it is critical to be able to focus on genetic variants in the interval that are most likely to have functional impacts.
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
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A typical quantitative trait locus (QTL) interval usually contains many genes ranging from several dozens to several hundreds, hence it is critical to be able to focus on genetic variants in the interval that are most likely to have functional impacts.
[]
A typical quantitative trait locus (QTL) interval usually contains many genes ranging from several dozens to several hundreds, hence it is critical to be able to focus on genetic variants in the interval that are most likely to have functional impacts.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
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Among them, nonsynonymous single nucleotide polymorphisms (SNPs) that alter protein sequences and regulatory polymorphisms that affect gene expression are natural high-priority candidates.
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
188
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Among them, nonsynonymous single nucleotide polymorphisms (SNPs) that alter protein sequences and regulatory polymorphisms that affect gene expression are natural high-priority candidates.
[]
Among them, nonsynonymous single nucleotide polymorphisms (SNPs) that alter protein sequences and regulatory polymorphisms that affect gene expression are natural high-priority candidates.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
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17,099,235
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Although regulatory polymorphisms are much more challenging to be identified and characterized, experimental and analytical tools are being actively developed for this purpose (1–4).
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182
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0
false
Although regulatory polymorphisms are much more challenging to be identified and characterized, experimental and analytical tools are being actively developed for this purpose.
[ "1–4" ]
Although regulatory polymorphisms are much more challenging to be identified and characterized, experimental and analytical tools are being actively developed for this purpose.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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Polymorphisms in miRNA target sites (PolymiRTS) represent a specific class of regulatory polymorphisms that may regulate posttranscriptional gene expression.
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
157
7,506
0
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Polymorphisms in miRNA target sites (PolymiRTS) represent a specific class of regulatory polymorphisms that may regulate posttranscriptional gene expression.
[]
Polymorphisms in miRNA target sites (PolymiRTS) represent a specific class of regulatory polymorphisms that may regulate posttranscriptional gene expression.
true
true
true
true
true
1,219
0
INTRODUCTION
1
5
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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A recent work reports that PolymiRTS can underlie the effects of physiological QTLs (pQTLs) that control classic higher order traits (5).
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
137
7,507
1
false
A recent work reports that PolymiRTS can underlie the effects of physiological QTLs (pQTLs) that control classic higher order traits.
[ "5" ]
A recent work reports that PolymiRTS can underlie the effects of physiological QTLs (pQTLs) that control classic higher order traits.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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MicroRNAs (miRNAs) are a family of small RNAs that pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization (6,7).
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
164
7,508
0
false
MicroRNAs (miRNAs) are a family of small RNAs that pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization.
[ "6,7" ]
MicroRNAs (miRNAs) are a family of small RNAs that pair to the transcripts of protein-coding genes and cause translational repression or mRNA destabilization.
true
true
true
true
true
1,219
0
INTRODUCTION
1
7
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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Hundreds of miRNAs have been identified in humans and mice and many of them have been shown to regulate their target genes that control diverse biological processes such as differentiation, proliferation, apoptosis and morphogenesis (7).
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
237
7,509
1
false
Hundreds of miRNAs have been identified in humans and mice and many of them have been shown to regulate their target genes that control diverse biological processes such as differentiation, proliferation, apoptosis and morphogenesis.
[ "7" ]
Hundreds of miRNAs have been identified in humans and mice and many of them have been shown to regulate their target genes that control diverse biological processes such as differentiation, proliferation, apoptosis and morphogenesis.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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PolymiRTS may affect the base-pairing process, hence affect the miRNA-mediated gene repression which in turn cause phenotypic variations.
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
137
7,510
0
false
PolymiRTS may affect the base-pairing process, hence affect the miRNA-mediated gene repression which in turn cause phenotypic variations.
[]
PolymiRTS may affect the base-pairing process, hence affect the miRNA-mediated gene repression which in turn cause phenotypic variations.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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It has been found that miRNA-mediated target mRNA destabilization is widespread in mammals (8–10).
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
98
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0
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It has been found that miRNA-mediated target mRNA destabilization is widespread in mammals.
[ "8–10" ]
It has been found that miRNA-mediated target mRNA destabilization is widespread in mammals.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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Thus, for miRNAs acting by this mechanism, the PolymiRTS may lead to heritable variations in gene expression.
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
109
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Thus, for miRNAs acting by this mechanism, the PolymiRTS may lead to heritable variations in gene expression.
[]
Thus, for miRNAs acting by this mechanism, the PolymiRTS may lead to heritable variations in gene expression.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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Variations in gene expression across a population can be assessed by a newly developed genetical genomics approach (11–13).
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123
7,513
0
false
Variations in gene expression across a population can be assessed by a newly developed genetical genomics approach.
[ "11–13" ]
Variations in gene expression across a population can be assessed by a newly developed genetical genomics approach.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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The genetical genomics approach treats gene expression level as quantitative trait.
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
83
7,514
0
false
The genetical genomics approach treats gene expression level as quantitative trait.
[]
The genetical genomics approach treats gene expression level as quantitative trait.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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Linkage mapping is then used to discover the genetic loci regulating gene expression traits (eQTLs).
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
100
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0
false
Linkage mapping is then used to discover the genetic loci regulating gene expression traits (eQTLs).
[]
Linkage mapping is then used to discover the genetic loci regulating gene expression traits (eQTLs).
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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PolymiRTS may induce a cis-acting eQTL that coincides with the gene's physical location.
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
88
7,516
0
false
PolymiRTS may induce a cis-acting eQTL that coincides with the gene's physical location.
[]
PolymiRTS may induce a cis-acting eQTL that coincides with the gene's physical location.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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We proposed a simple conceptual model (Figure 1) that represents information flow from PolymiRTS to complex trait via cis-acting eQTL.
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
134
7,517
0
false
We proposed a simple conceptual model that represents information flow from PolymiRTS to complex trait via cis-acting eQTL.
[ "Figure 1" ]
We proposed a simple conceptual model that represents information flow from PolymiRTS to complex trait via cis-acting eQTL.
true
true
true
true
true
1,219
0
INTRODUCTION
1
1
[ "b1", "b4", "b5", "b6", "b7", "b7", "b8", "b10", "b11", "b13" ]
17,099,235
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Based on this model scheme, we create a database integrating SNP, phenotype and expression microarray data of human and mouse.
[ "1", "4", "5", "6", "7", "7", "8", "10", "11", "13" ]
126
7,518
0
false
Based on this model scheme, we create a database integrating SNP, phenotype and expression microarray data of human and mouse.
[]
Based on this model scheme, we create a database integrating SNP, phenotype and expression microarray data of human and mouse.
true
true
true
true
true
1,219
1
INTRODUCTION
0
null
null
17,099,235
null
Conceptual QTL model.
null
21
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0
false
null
null
Conceptual QTL model.
true
true
true
true
true
1,220
1
INTRODUCTION
0
null
null
17,099,235
null
A PolymiRTS (triangle) may cause the gene expression variation (diamond) in segregating population and a cis-acting eQTL is observed.
null
133
7,520
0
false
null
null
A PolymiRTS (triangle) may cause the gene expression variation (diamond) in segregating population and a cis-acting eQTL is observed.
true
true
true
true
true
1,220
1
INTRODUCTION
0
null
null
17,099,235
null
The variation in gene expression in turn may cause phenotype variation (rectangle) and a pQTL is observed.
null
106
7,521
0
false
null
null
The variation in gene expression in turn may cause phenotype variation (rectangle) and a pQTL is observed.
true
true
true
true
true
1,220
0
INTRODUCTION
1
1
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
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MORF4 (mortality factor on chromosome 4), MRG15
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
47
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0
false
MORF4, MRG15
[ "mortality factor on chromosome 4" ]
MORF4, MRG15
true
true
false
true
false
1,221
0
INTRODUCTION
1
1
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
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(MORF4-related gene on chromosome 15) and MRGX (MORF4-related gene on chromosome X) are members of the MRG protein family that were first identified as transcription factors involved in cellular senescence (1,2).
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
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0
false
and MRGX are members of the MRG protein family that were first identified as transcription factors involved in cellular senescence.
[ "MORF4-related gene on chromosome 15", "MORF4-related gene on chromosome X", "1,2" ]
and MRGX are members of the MRG protein family that were first identified as transcription factors involved in cellular senescence.
false
true
true
true
false
1,221
0
INTRODUCTION
1
1
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
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Among those MRG proteins, MRG15 (a 37 kDa protein consisting of 323 amino acid residues) is of particular interest because it is expressed in a wide variety of human tissues and its homologues have been identified in many other eukaryotes (2,3).
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
245
7,524
0
false
Among those MRG proteins, MRG15 is of particular interest because it is expressed in a wide variety of human tissues and its homologues have been identified in many other eukaryotes.
[ "a 37 kDa protein consisting of 323 amino acid residues", "2,3" ]
Among those MRG proteins, MRG15 is of particular interest because it is expressed in a wide variety of human tissues and its homologues have been identified in many other eukaryotes.
true
true
true
true
true
1,221
0
INTRODUCTION
1
1
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
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In addition to its involvement in cellular senescence, MRG15 is found to be crucial in embryonic development and cell proliferation.
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
132
7,525
0
false
In addition to its involvement in cellular senescence, MRG15 is found to be crucial in embryonic development and cell proliferation.
[]
In addition to its involvement in cellular senescence, MRG15 is found to be crucial in embryonic development and cell proliferation.
true
true
true
true
true
1,221
0
INTRODUCTION
1
4
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
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Knockout of MRG15 in mice is embryonic lethal and exhibits developmental delay (4).
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
83
7,526
1
false
Knockout of MRG15 in mice is embryonic lethal and exhibits developmental delay.
[ "4" ]
Knockout of MRG15 in mice is embryonic lethal and exhibits developmental delay.
true
true
true
true
true
1,221
0
INTRODUCTION
1
5
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
pmid-9891081|pmid-11290425|pmid-11290425|pmid-10908644|pmid-15798182|pmid-12397079|pmid-11500496|pmid-12391155|pmid-11500496|pmid-12963728|pmid-12175490|pmid-12773392
Cell biological and biochemical studies have shown that MRG15 is most likely to function in chromatin remodeling and transcriptional regulation through participation in two nucleoprotein complexes, MAF1 and MAF2 (MRG15-associated factors 1 and 2, respectively) (5).
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
265
7,527
1
false
Cell biological and biochemical studies have shown that MRG15 is most likely to function in chromatin remodeling and transcriptional regulation through participation in two nucleoprotein complexes, MAF1 and MAF2.
[ "MRG15-associated factors 1 and 2, respectively", "5" ]
Cell biological and biochemical studies have shown that MRG15 is most likely to function in chromatin remodeling and transcriptional regulation through participation in two nucleoprotein complexes, MAF1 and MAF2.
true
true
true
true
true
1,221
0
INTRODUCTION
1
6
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
pmid-9891081|pmid-11290425|pmid-11290425|pmid-10908644|pmid-15798182|pmid-12397079|pmid-11500496|pmid-12391155|pmid-11500496|pmid-12963728|pmid-12175490|pmid-12773392
The C-terminal part of MRG15 has interactions with the tumor suppressor protein retinoblastoma (Rb) and a novel nuclear protein PAM14 (protein associated with MRG15 of 14 kDa) in MAF1 (6).
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
188
7,528
1
false
The C-terminal part of MRG15 has interactions with the tumor suppressor protein retinoblastoma (Rb) and a novel nuclear protein PAM14 in MAF1.
[ "protein associated with MRG15 of 14 kDa", "6" ]
The C-terminal part of MRG15 has interactions with the tumor suppressor protein retinoblastoma (Rb) and a novel nuclear protein PAM14 in MAF1.
true
true
true
true
true
1,221
0
INTRODUCTION
1
7
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
pmid-9891081|pmid-11290425|pmid-11290425|pmid-10908644|pmid-15798182|pmid-12397079|pmid-11500496|pmid-12391155|pmid-11500496|pmid-12963728|pmid-12175490|pmid-12773392
It is also involved in interactions with the HDAC (histone deacetylase) containing transcriptional corepressor mSin3A and the plant homeodomain zinc finger protein Pf1 (7).
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
172
7,529
1
false
It is also involved in interactions with the HDAC (histone deacetylase) containing transcriptional corepressor mSin3A and the plant homeodomain zinc finger protein Pf1.
[ "7" ]
It is also involved in interactions with the HDAC (histone deacetylase) containing transcriptional corepressor mSin3A and the plant homeodomain zinc finger protein Pf1.
true
true
true
true
true
1,221
0
INTRODUCTION
1
6
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
pmid-9891081|pmid-11290425|pmid-11290425|pmid-10908644|pmid-15798182|pmid-12397079|pmid-11500496|pmid-12391155|pmid-11500496|pmid-12963728|pmid-12175490|pmid-12773392
The N-terminal part of MRG15 interacts with hMOF (human male absent on first) in MAF2 (6).
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
90
7,530
1
false
The N-terminal part of MRG15 interacts with hMOF (human male absent on first) in MAF2.
[ "6" ]
The N-terminal part of MRG15 interacts with hMOF (human male absent on first) in MAF2.
true
true
true
true
true
1,221
0
INTRODUCTION
1
8
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
pmid-9891081|pmid-11290425|pmid-11290425|pmid-10908644|pmid-15798182|pmid-12397079|pmid-11500496|pmid-12391155|pmid-11500496|pmid-12963728|pmid-12175490|pmid-12773392
In addition, MRG15 is associated with a mammalian TRRAP/Tip60 HAT (histone acetyltransferase) complex through protein MRGBP (MRG15/MRGX-binding protein) (8).
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
157
7,531
1
false
In addition, MRG15 is associated with a mammalian TRRAP/Tip60 HAT (histone acetyltransferase) complex through protein MRGBP.
[ "MRG15/MRGX-binding protein", "8" ]
In addition, MRG15 is associated with a mammalian TRRAP/Tip60 HAT (histone acetyltransferase) complex through protein MRGBP.
true
true
true
true
true
1,221
0
INTRODUCTION
1
1
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
pmid-9891081|pmid-11290425|pmid-11290425|pmid-10908644|pmid-15798182|pmid-12397079|pmid-11500496|pmid-12391155|pmid-11500496|pmid-12963728|pmid-12175490|pmid-12773392
Several MRG15 homologues in other species, such as MRG1 in Caenorhabditis elegans, MSL3 (male-specific lethal protein 3) in Drosophila, Eaf3p (Esa1p-associated factor 3 protein) in Saccharomyces cerevisiae, Alp13 (altered polarity protein 13) in fission yeast, are also found to be part of multi-subunit HAT/HDAC complex...
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
407
7,532
0
false
Several MRG15 homologues in other species, such as MRG1 in Caenorhabditis elegans, MSL3 in Drosophila, Eaf3p in Saccharomyces cerevisiae, Alp13 in fission yeast, are also found to be part of multi-subunit HAT/HDAC complexes that are involved in transcriptional regulation through chromatin remodeling.
[ "male-specific lethal protein 3", "Esa1p-associated factor 3 protein", "altered polarity protein 13", "9–17" ]
Several MRG15 homologues in other species, such as MRG1 in Caenorhabditis elegans, MSL3 in Drosophila, Eaf3p in Saccharomyces cerevisiae, Alp13 in fission yeast, are also found to be part of multi-subunit HAT/HDAC complexes that are involved in transcriptional regulation through chromatin remodeling.
true
true
true
true
true
1,221
0
INTRODUCTION
1
1
[ "b1", "b2", "b2", "b3", "b4", "b5", "b6", "b7", "b6", "b8", "b9", "b17" ]
17,135,209
pmid-9891081|pmid-11290425|pmid-11290425|pmid-10908644|pmid-15798182|pmid-12397079|pmid-11500496|pmid-12391155|pmid-11500496|pmid-12963728|pmid-12175490|pmid-12773392
However, the exact functions of MRG15 and its homologues in these complexes and the underlying molecular mechanism(s) are unknown.
[ "1", "2", "2", "3", "4", "5", "6", "7", "6", "8", "9", "17" ]
130
7,533
0
false
However, the exact functions of MRG15 and its homologues in these complexes and the underlying molecular mechanism(s) are unknown.
[]
However, the exact functions of MRG15 and its homologues in these complexes and the underlying molecular mechanism(s) are unknown.
true
true
true
true
true
1,221
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
Human MRG15 consists of a putative chromo domain (the N-terminal residues 1–85) and a conserved MRG domain (the C-terminal residues 151–323) which are linked together by a flexible region (residues 86–150) (2).
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
210
7,534
1
false
Human MRG15 consists of a putative chromo domain (the N-terminal residues 1–85) and a conserved MRG domain which are linked together by a flexible region (residues 86–150).
[ "the C-terminal residues 151–323", "2" ]
Human MRG15 consists of a putative chromo domain (the N-terminal residues 1–85) and a conserved MRG domain which are linked together by a flexible region (residues 86–150).
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
The MRG domain is highly conserved among all MRG proteins and the crystal structure of the MRG domain of human MRG15 has recently been determined (18,19).
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
154
7,535
0
false
The MRG domain is highly conserved among all MRG proteins and the crystal structure of the MRG domain of human MRG15 has recently been determined.
[ "18,19" ]
The MRG domain is highly conserved among all MRG proteins and the crystal structure of the MRG domain of human MRG15 has recently been determined.
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
It assumes a fold consisting of mainly Ξ±-helices and appears to function as an adaptor module to interact with other proteins in nuclear protein complexes.
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
155
7,536
0
false
It assumes a fold consisting of mainly Ξ±-helices and appears to function as an adaptor module to interact with other proteins in nuclear protein complexes.
[]
It assumes a fold consisting of mainly Ξ±-helices and appears to function as an adaptor module to interact with other proteins in nuclear protein complexes.
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
Site-directed mutagenesis studies indicate that several hydrophobic residues form a shallow hydrophobic pocket to interact with the N-terminal region of PAM14.
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
159
7,537
0
false
Site-directed mutagenesis studies indicate that several hydrophobic residues form a shallow hydrophobic pocket to interact with the N-terminal region of PAM14.
[]
Site-directed mutagenesis studies indicate that several hydrophobic residues form a shallow hydrophobic pocket to interact with the N-terminal region of PAM14.
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
The exact function of the chromo domain of MRG15 is not yet well understood.
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
76
7,538
0
false
The exact function of the chromo domain of MRG15 is not yet well understood.
[]
The exact function of the chromo domain of MRG15 is not yet well understood.
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
However, the conservation of the chromo domain in many MRG15 homologues underscores its functional importance.
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
110
7,539
0
false
However, the conservation of the chromo domain in many MRG15 homologues underscores its functional importance.
[]
However, the conservation of the chromo domain in many MRG15 homologues underscores its functional importance.
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
Previous biochemical and structural studies have shown that chromo and chromo-like domains (such as Tudor and PWWP domains) are involved in recognition and interaction with histones or other proteins containing modified residues (such as methylated lysines or arginines) in nucleoprotein complexes (such as HAT and HDAC ...
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
489
7,540
0
false
Previous biochemical and structural studies have shown that chromo and chromo-like domains (such as Tudor and PWWP domains) are involved in recognition and interaction with histones or other proteins containing modified residues (such as methylated lysines or arginines) in nucleoprotein complexes (such as HAT and HDAC ...
[ "for reviews see (20–23)" ]
Previous biochemical and structural studies have shown that chromo and chromo-like domains (such as Tudor and PWWP domains) are involved in recognition and interaction with histones or other proteins containing modified residues (such as methylated lysines or arginines) in nucleoprotein complexes (such as HAT and HDAC ...
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
Chromatin-binding proteins HP1 (heterochromatin-binding protein 1) and Pc (Polycomb) chromo domains bind to methylated Lys9 and Lys27 of histone H3 (H3K9 and H3K27), respectively (24–29).
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
187
7,541
0
false
Chromatin-binding proteins HP1 (heterochromatin-binding protein 1) and Pc (Polycomb) chromo domains bind to methylated Lys9 and Lys27 of histone H3, respectively.
[ "H3K9 and H3K27", "24–29" ]
Chromatin-binding proteins HP1 (heterochromatin-binding protein 1) and Pc (Polycomb) chromo domains bind to methylated Lys9 and Lys27 of histone H3, respectively.
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
The highly related HP1 chromo shadow domain can interact with numerous proteins containing a PXVXL motif (30–33).
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
113
7,542
0
false
The highly related HP1 chromo shadow domain can interact with numerous proteins containing a PXVXL motif.
[ "30–33" ]
The highly related HP1 chromo shadow domain can interact with numerous proteins containing a PXVXL motif.
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
Many of these interactions play an important role in directing heterochromatin formation and/or gene silencing (21,30,34).
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
122
7,543
0
false
Many of these interactions play an important role in directing heterochromatin formation and/or gene silencing.
[ "21,30,34" ]
Many of these interactions play an important role in directing heterochromatin formation and/or gene silencing.
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
The yeast Eaf3p chromo domain binds to methylated Lys4 and Lys36 of histone H3 (H3K4 and H3K36) and this interaction links histone deacetylation to phosphorylation of the RNA polymerase II C-terminal domain and thus the transcriptional elongation (14–16).
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
255
7,544
0
false
The yeast Eaf3p chromo domain binds to methylated Lys4 and Lys36 of histone H3 and this interaction links histone deacetylation to phosphorylation of the RNA polymerase II C-terminal domain and thus the transcriptional elongation.
[ "H3K4 and H3K36", "14–16" ]
The yeast Eaf3p chromo domain binds to methylated Lys4 and Lys36 of histone H3 and this interaction links histone deacetylation to phosphorylation of the RNA polymerase II C-terminal domain and thus the transcriptional elongation.
true
true
true
true
true
1,222
1
INTRODUCTION
1
35
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
The human CHD1 (chromo-ATPase/helicase DNA-binding protein 1) double chromo domains cooperate together to bind to methylated H3K4 (35).
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
135
7,545
1
false
The human CHD1 (chromo-ATPase/helicase DNA-binding protein 1) double chromo domains cooperate together to bind to methylated H3K4.
[ "35" ]
The human CHD1 (chromo-ATPase/helicase DNA-binding protein 1) double chromo domains cooperate together to bind to methylated H3K4.
true
true
true
true
true
1,222
1
INTRODUCTION
1
2
[ "b2", "b18", "b19", "b20", "b23", "b24", "b29", "b30", "b33", "b21", "b30", "b34", "b14", "b16", "b35", "b36", "b40" ]
17,135,209
pmid-11290425|pmid-16407074|pmid-17008723|pmid-9640536|pmid-14745831|pmid-11242054|pmid-12897052|pmid-12151603|pmid-14765118|pmid-10655032|pmid-12151603|pmid-12351676|pmid-16286007|pmid-16286008|pmid-16372014|pmid-11135666|pmid-16415788
A number of Tudor, PWWP and other chromo-like domains have also been shown to bind to methylated N-terminal tails of histones or other proteins (36–40).
[ "2", "18", "19", "20", "23", "24", "29", "30", "33", "21", "30", "34", "14", "16", "35", "36", "40" ]
152
7,546
0
false
A number of Tudor, PWWP and other chromo-like domains have also been shown to bind to methylated N-terminal tails of histones or other proteins.
[ "36–40" ]
A number of Tudor, PWWP and other chromo-like domains have also been shown to bind to methylated N-terminal tails of histones or other proteins.
true
true
true
true
true
1,222
2
INTRODUCTION
0
null
null
17,135,209
null
To explore its biological function, we determined the crystal structure of the chromo domain of human MRG15 at 2.2 β„« resolution, which assumes a structure more similar to the Drosophila MOF (dMOF) chromo barrel domain than the typical HP1/Pc chromo domain.
null
256
7,547
0
false
null
null
To explore its biological function, we determined the crystal structure of the chromo domain of human MRG15 at 2.2 β„« resolution, which assumes a structure more similar to the Drosophila MOF (dMOF) chromo barrel domain than the typical HP1/Pc chromo domain.
true
true
true
true
true
1,223
2
INTRODUCTION
0
null
null
17,135,209
null
Using in vitro binding assay, we found that the MRG15 chromo domain can bind to methylated H3K36.
null
97
7,548
0
false
null
null
Using in vitro binding assay, we found that the MRG15 chromo domain can bind to methylated H3K36.
true
true
true
true
true
1,223
2
INTRODUCTION
0
null
null
17,135,209
null
The structural and biochemical data together suggest that the MRG15 chromo domain may function as an adaptor module to interact with a modified histone in a mode different from that of the HP1/Pc chromo domains.
null
211
7,549
0
false
null
null
The structural and biochemical data together suggest that the MRG15 chromo domain may function as an adaptor module to interact with a modified histone in a mode different from that of the HP1/Pc chromo domains.
true
true
true
true
true
1,223
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5" ]
17,204,483
pmid-15333634|pmid-12651953|pmid-4373468|pmid-320212
The recent identification and characterization of an RNA ligase (DraRnl) from the radiation-resistant bacterium Deinococcus radiodurans raised the prospect that RNA end sealing might be pertinent to bacterial physiology (1).
[ "1", "2", "3", "5" ]
224
7,550
1
false
The recent identification and characterization of an RNA ligase (DraRnl) from the radiation-resistant bacterium Deinococcus radiodurans raised the prospect that RNA end sealing might be pertinent to bacterial physiology.
[ "1" ]
The recent identification and characterization of an RNA ligase (DraRnl) from the radiation-resistant bacterium Deinococcus radiodurans raised the prospect that RNA end sealing might be pertinent to bacterial physiology.
true
true
true
true
true
1,224
0
INTRODUCTION
1
2
[ "b1", "b2", "b3", "b5" ]
17,204,483
pmid-15333634|pmid-12651953|pmid-4373468|pmid-320212
DraRnl is a 342 amino acid polypeptide encoded by the D.radiodurans DRB0094 ORF, which is one of several genes transiently up-regulated during recovery from radiation exposure (2).
[ "1", "2", "3", "5" ]
180
7,551
1
false
DraRnl is a 342 amino acid polypeptide encoded by the D.radiodurans DRB0094 ORF, which is one of several genes transiently up-regulated during recovery from radiation exposure.
[ "2" ]
DraRnl is a 342 amino acid polypeptide encoded by the D.radiodurans DRB0094 ORF, which is one of several genes transiently up-regulated during recovery from radiation exposure.
true
true
true
true
true
1,224
0
INTRODUCTION
1
1
[ "b1", "b2", "b3", "b5" ]
17,204,483
pmid-15333634|pmid-12651953|pmid-4373468|pmid-320212
DraRnl, like all other ATP-dependent RNA/DNA ligases, joins 3β€²-OH and 5β€²-PO4 termini via a series of three nucleotidyl transfer steps: (i) the enzyme reacts with ATP to form a covalent ligase-(lysyl-N)-AMP intermediate plus pyrophosphate, (ii) AMP is transferred from ligase-adenylate to the 5β€²-PO4 end to form a polynuc...
[ "1", "2", "3", "5" ]
503
7,552
0
false
DraRnl, like all other ATP-dependent RNA/DNA ligases, joins 3β€²-OH and 5β€²-PO4 termini via a series of three nucleotidyl transfer steps: (i) the enzyme reacts with ATP to form a covalent ligase-(lysyl-N)-AMP intermediate plus pyrophosphate, (ii) AMP is transferred from ligase-adenylate to the 5β€²-PO4 end to form a polynuc...
[ "3–5" ]
DraRnl, like all other ATP-dependent RNA/DNA ligases, joins 3β€²-OH and 5β€²-PO4 termini via a series of three nucleotidyl transfer steps: (i) the enzyme reacts with ATP to form a covalent ligase-(lysyl-N)-AMP intermediate plus pyrophosphate, (ii) AMP is transferred from ligase-adenylate to the 5β€²-PO4 end to form a polynuc...
true
true
true
true
true
1,224
1
INTRODUCTION
1
6
[ "b6", "b8", "b9", "b10", "b12", "b1" ]
17,204,483
pmid-12228725|pmid-12766156|pmid-2444436|pmid-15084599|pmid-10446205|pmid-15333634
There are two distinct branches of the RNA ligase family, exemplified by bacteriophage T4 RNA ligase 1 (Rnl1) and RNA ligase 2 (Rnl2), respectively (6–8).
[ "6", "8", "9", "10", "12", "1" ]
154
7,553
0
false
There are two distinct branches of the RNA ligase family, exemplified by bacteriophage T4 RNA ligase 1 and RNA ligase 2 (Rnl2), respectively.
[ "Rnl1", "6–8" ]
There are two distinct branches of the RNA ligase family, exemplified by bacteriophage T4 RNA ligase 1 and RNA ligase 2 (Rnl2), respectively.
true
true
true
true
true
1,225
1
INTRODUCTION
1
9
[ "b6", "b8", "b9", "b10", "b12", "b1" ]
17,204,483
pmid-12228725|pmid-12766156|pmid-2444436|pmid-15084599|pmid-10446205|pmid-15333634
Whereas Rnl1-like ligases prefer to join single-stranded RNA termini emanating from RNA stems (9), the Rnl2-like ligases display optimal activity in sealing nicks embedded within duplex RNAs or RNA–DNA hybrids (10–12).
[ "6", "8", "9", "10", "12", "1" ]
218
7,554
1
false
Whereas Rnl1-like ligases prefer to join single-stranded RNA termini emanating from RNA stems, the Rnl2-like ligases display optimal activity in sealing nicks embedded within duplex RNAs or RNA–DNA hybrids.
[ "9", "10–12" ]
Whereas Rnl1-like ligases prefer to join single-stranded RNA termini emanating from RNA stems, the Rnl2-like ligases display optimal activity in sealing nicks embedded within duplex RNAs or RNA–DNA hybrids.
true
true
true
true
true
1,225
1
INTRODUCTION
1
6
[ "b6", "b8", "b9", "b10", "b12", "b1" ]
17,204,483
pmid-12228725|pmid-12766156|pmid-2444436|pmid-15084599|pmid-10446205|pmid-15333634
Initial biochemical characterization of DraRnl highlighted functional similarities to Rnl2, e.g.
[ "6", "8", "9", "10", "12", "1" ]
96
7,555
0
false
Initial biochemical characterization of DraRnl highlighted functional similarities to Rnl2, e.g.
[]
Initial biochemical characterization of DraRnl highlighted functional similarities to Rnl2, e.g.
true
true
true
true
true
1,225
1
INTRODUCTION
1
1
[ "b6", "b8", "b9", "b10", "b12", "b1" ]
17,204,483
pmid-12228725|pmid-12766156|pmid-2444436|pmid-15084599|pmid-10446205|pmid-15333634
activity in sealing duplex RNA nicks, but no activity in circularizing short single-stranded RNA substrates (this being the preferred reaction for Rnl1-type ligases) (1).
[ "6", "8", "9", "10", "12", "1" ]
170
7,556
1
false
activity in sealing duplex RNA nicks, but no activity in circularizing short single-stranded RNA substrates.
[ "this being the preferred reaction for Rnl1-type ligases", "1" ]
activity in sealing duplex RNA nicks, but no activity in circularizing short single-stranded RNA substrates.
false
true
true
true
false
1,225
1
INTRODUCTION
1
6
[ "b6", "b8", "b9", "b10", "b12", "b1" ]
17,204,483
pmid-12228725|pmid-12766156|pmid-2444436|pmid-15084599|pmid-10446205|pmid-15333634
Yet, the primary structure of DraRnl reveals novel features and domain arrangements that confound its classification as either Rnl1-like or Rnl2-like.
[ "6", "8", "9", "10", "12", "1" ]
150
7,557
0
false
Yet, the primary structure of DraRnl reveals novel features and domain arrangements that confound its classification as either Rnl1-like or Rnl2-like.
[]
Yet, the primary structure of DraRnl reveals novel features and domain arrangements that confound its classification as either Rnl1-like or Rnl2-like.
true
true
true
true
true
1,225
2
INTRODUCTION
1
7
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
T4 Rnl1 (374 amino acids) and T4 Rnl2 (334 amino acids) are composed of two structural domains (7,13).
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
102
7,558
0
false
T4 Rnl1 and T4 Rnl2 (334 amino acids) are composed of two structural domains.
[ "374 amino acids", "7,13" ]
T4 Rnl1 and T4 Rnl2 (334 amino acids) are composed of two structural domains.
true
true
true
true
true
1,226
2
INTRODUCTION
1
14
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
They have an N-terminal nucleotidyltransferase domain, shared with DNA ligases and mRNA capping enzymes, that includes the six peptide motifs (I, Ia, III, IIIa, IV and V) that define the covalent nucleotidyltransferase superfamily (14).
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
236
7,559
1
false
They have an N-terminal nucleotidyltransferase domain, shared with DNA ligases and mRNA capping enzymes, that includes the six peptide motifs (I, Ia, III, IIIa, IV and V) that define the covalent nucleotidyltransferase superfamily.
[ "14" ]
They have an N-terminal nucleotidyltransferase domain, shared with DNA ligases and mRNA capping enzymes, that includes the six peptide motifs (I, Ia, III, IIIa, IV and V) that define the covalent nucleotidyltransferase superfamily.
true
true
true
true
true
1,226
2
INTRODUCTION
1
7
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
Rnl1 and Rnl2 are distinguished from one another by their C-terminal domains, which adopt unique Ξ±-helical folds that are unrelated to the OB-fold modules appended to the C-termini of the nucleotidyltransferase domains of DNA ligases and RNA capping enzymes.
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
258
7,560
0
false
Rnl1 and Rnl2 are distinguished from one another by their C-terminal domains, which adopt unique Ξ±-helical folds that are unrelated to the OB-fold modules appended to the C-termini of the nucleotidyltransferase domains of DNA ligases and RNA capping enzymes.
[]
Rnl1 and Rnl2 are distinguished from one another by their C-terminal domains, which adopt unique Ξ±-helical folds that are unrelated to the OB-fold modules appended to the C-termini of the nucleotidyltransferase domains of DNA ligases and RNA capping enzymes.
true
true
true
true
true
1,226
2
INTRODUCTION
1
7
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
Available evidence suggests that the biological specificity of polynucleotide ligases is dictated in part by their carboxyl domains.
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
132
7,561
0
false
Available evidence suggests that the biological specificity of polynucleotide ligases is dictated in part by their carboxyl domains.
[]
Available evidence suggests that the biological specificity of polynucleotide ligases is dictated in part by their carboxyl domains.
true
true
true
true
true
1,226
2
INTRODUCTION
1
7
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
In the case of ATP-dependent DNA ligases and RNA capping enzymes, the C-terminal OB domain is required for the initial step of covalent enzyme nucleotidylation at the lysine of motif I (KxDG) (15–18).
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
200
7,562
0
false
In the case of ATP-dependent DNA ligases and RNA capping enzymes, the C-terminal OB domain is required for the initial step of covalent enzyme nucleotidylation at the lysine of motif I (KxDG).
[ "15–18" ]
In the case of ATP-dependent DNA ligases and RNA capping enzymes, the C-terminal OB domain is required for the initial step of covalent enzyme nucleotidylation at the lysine of motif I (KxDG).
true
true
true
true
true
1,226
2
INTRODUCTION
1
19
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
T4 Rnl2 can form ligase-AMP in the absence of its C domain (19), but is then unable to execute the composite RNA nick sealing reaction.
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
135
7,563
1
false
T4 Rnl2 can form ligase-AMP in the absence of its C domain, but is then unable to execute the composite RNA nick sealing reaction.
[ "19" ]
T4 Rnl2 can form ligase-AMP in the absence of its C domain, but is then unable to execute the composite RNA nick sealing reaction.
true
true
true
true
true
1,226
2
INTRODUCTION
1
19
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
The Rnl2 C domain is required for nick recognition and catalysis of nick adenylylation, yet it is not required for phosphodiester formation at a preadenylylated nick (19).
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
171
7,564
1
false
The Rnl2 C domain is required for nick recognition and catalysis of nick adenylylation, yet it is not required for phosphodiester formation at a preadenylylated nick.
[ "19" ]
The Rnl2 C domain is required for nick recognition and catalysis of nick adenylylation, yet it is not required for phosphodiester formation at a preadenylylated nick.
true
true
true
true
true
1,226
2
INTRODUCTION
1
7
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
The remarkable feature of DraRnl is that is has no C domain at all.
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
67
7,565
0
false
The remarkable feature of DraRnl is that is has no C domain at all.
[]
The remarkable feature of DraRnl is that is has no C domain at all.
true
true
true
true
true
1,226
2
INTRODUCTION
1
7
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
Rather, it has a distinctive N-terminal module, which is important for strand joining activity, but has no primary structure similarity to any known polynucleotide ligase (Figure 1).
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
182
7,566
0
false
Rather, it has a distinctive N-terminal module, which is important for strand joining activity, but has no primary structure similarity to any known polynucleotide ligase.
[ "Figure 1" ]
Rather, it has a distinctive N-terminal module, which is important for strand joining activity, but has no primary structure similarity to any known polynucleotide ligase.
true
true
true
true
true
1,226
2
INTRODUCTION
1
1
[ "b7", "b13", "b14", "b15", "b18", "b19", "b19", "b1" ]
17,204,483
pmid-17018278|pmid-16263720|pmid-15582400|pmid-9160746|pmid-9753729|pmid-14962393|pmid-14962393|pmid-15333634
The DraRnl N-terminal module is a putative homolog of the OB-fold of phenylalanyl-tRNA synthetases (1).
[ "7", "13", "14", "15", "18", "19", "19", "1" ]
103
7,567
1
false
The DraRnl N-terminal module is a putative homolog of the OB-fold of phenylalanyl-tRNA synthetases.
[ "1" ]
The DraRnl N-terminal module is a putative homolog of the OB-fold of phenylalanyl-tRNA synthetases.
true
true
true
true
true
1,226
3
INTRODUCTION
0
null
null
17,204,483
null
DraRnl subfamily of RNA ligases.
null
32
7,568
0
false
null
null
DraRnl subfamily of RNA ligases.
true
true
true
true
true
1,227
3
INTRODUCTION
0
null
null
17,204,483
null
The amino acid sequence of DraRnl is aligned to the sequences of homologous proteins from S.avermitilis (Sav) and bacteriophage 44RR.8t (44RR).
null
143
7,569
0
false
null
null
The amino acid sequence of DraRnl is aligned to the sequences of homologous proteins from S.avermitilis (Sav) and bacteriophage 44RR.8t (44RR).
true
true
true
true
true
1,227
3
INTRODUCTION
0
null
null
17,204,483
null
Putative nucleotidyltransferase motifs I, Ia, III, IIIa, IV and V are highlighted in shaded boxes.
null
98
7,570
0
false
null
null
Putative nucleotidyltransferase motifs I, Ia, III, IIIa, IV and V are highlighted in shaded boxes.
true
true
true
true
true
1,227
3
INTRODUCTION
0
null
null
17,204,483
null
The essential motif I lysine nucleophile is denoted by |.
null
57
7,571
0
false
null
null
The essential motif I lysine nucleophile is denoted by |.
true
true
true
true
true
1,227
3
INTRODUCTION
0
null
null
17,204,483
null
Residues subjected to mutational analysis in the present study are denoted by β€’.
null
80
7,572
0
false
null
null
Residues subjected to mutational analysis in the present study are denoted by β€’.
true
true
true
true
true
1,227
3
INTRODUCTION
0
null
null
17,204,483
null
The translation start site of the N-terminal deletion mutant NΞ”126 is indicated by an arrow above the sequence.
null
111
7,573
0
false
null
null
The translation start site of the N-terminal deletion mutant NΞ”126 is indicated by an arrow above the sequence.
true
true
true
true
true
1,227
4
INTRODUCTION
1
1
[ "b1", "b20", "b21", "b22", "b23" ]
17,204,483
pmid-15333634|pmid-2318808|pmid-10618210|pmid-178008|pmid-12522252
DraRnl is a template-directed RNA ligase capable of sealing nicks in which the 3β€²-OH strand is RNA.
[ "1", "20", "21", "22", "23" ]
99
7,574
0
false
DraRnl is a template-directed RNA ligase capable of sealing nicks in which the 3β€²-OH strand is RNA.
[]
DraRnl is a template-directed RNA ligase capable of sealing nicks in which the 3β€²-OH strand is RNA.
true
true
true
true
true
1,228
4
INTRODUCTION
1
1
[ "b1", "b20", "b21", "b22", "b23" ]
17,204,483
pmid-15333634|pmid-2318808|pmid-10618210|pmid-178008|pmid-12522252
DraRnl can join a RNAOH end to a 5β€²-pRNA or 5β€²-pDNA-strand, but it is unable to join when the 3β€²-OH strand is DNA (1).
[ "1", "20", "21", "22", "23" ]
118
7,575
1
false
DraRnl can join a RNAOH end to a 5β€²-pRNA or 5β€²-pDNA-strand, but it is unable to join when the 3β€²-OH strand is DNA.
[ "1" ]
DraRnl can join a RNAOH end to a 5β€²-pRNA or 5β€²-pDNA-strand, but it is unable to join when the 3β€²-OH strand is DNA.
true
true
true
true
true
1,228
4
INTRODUCTION
1
1
[ "b1", "b20", "b21", "b22", "b23" ]
17,204,483
pmid-15333634|pmid-2318808|pmid-10618210|pmid-178008|pmid-12522252
In light of this specificity, it is conceivable that DraRnl contributes to radiation resistance by either repairing broken RNAs or by sealing broken DNAs that have acquired 3β€²-OH RNA termini by ribonucleotide addition (perhaps as a stop-gap measure during double-strand break repair).
[ "1", "20", "21", "22", "23" ]
284
7,576
0
false
In light of this specificity, it is conceivable that DraRnl contributes to radiation resistance by either repairing broken RNAs or by sealing broken DNAs that have acquired 3β€²-OH RNA termini by ribonucleotide addition (perhaps as a stop-gap measure during double-strand break repair).
[]
In light of this specificity, it is conceivable that DraRnl contributes to radiation resistance by either repairing broken RNAs or by sealing broken DNAs that have acquired 3β€²-OH RNA termini by ribonucleotide addition (perhaps as a stop-gap measure during double-strand break repair).
true
true
true
true
true
1,228
4
INTRODUCTION
1
1
[ "b1", "b20", "b21", "b22", "b23" ]
17,204,483
pmid-15333634|pmid-2318808|pmid-10618210|pmid-178008|pmid-12522252
Unlike other polynucleotide ligases, DraRnl relies on manganese (not magnesium) as a cofactor for strand sealing (though either Mg or Mn can support the formation of the DraRnl-AMP intermediate).
[ "1", "20", "21", "22", "23" ]
195
7,577
0
false
Unlike other polynucleotide ligases, DraRnl relies on manganese (not magnesium) as a cofactor for strand sealing (though either Mg or Mn can support the formation of the DraRnl-AMP intermediate).
[]
Unlike other polynucleotide ligases, DraRnl relies on manganese (not magnesium) as a cofactor for strand sealing (though either Mg or Mn can support the formation of the DraRnl-AMP intermediate).
true
true
true
true
true
1,228
4
INTRODUCTION
1
1
[ "b1", "b20", "b21", "b22", "b23" ]
17,204,483
pmid-15333634|pmid-2318808|pmid-10618210|pmid-178008|pmid-12522252
Manganese exerts unique effects on Deinococcus growth, metabolism and radiosensitivity (20,21).
[ "1", "20", "21", "22", "23" ]
95
7,578
0
false
Manganese exerts unique effects on Deinococcus growth, metabolism and radiosensitivity.
[ "20,21" ]
Manganese exerts unique effects on Deinococcus growth, metabolism and radiosensitivity.
true
true
true
true
true
1,228
4
INTRODUCTION
1
22
[ "b1", "b20", "b21", "b22", "b23" ]
17,204,483
pmid-15333634|pmid-2318808|pmid-10618210|pmid-178008|pmid-12522252
Manganese is associated with the Deinococcus genome (22) and extracellular manganese concentration affects genome condensation (23).
[ "1", "20", "21", "22", "23" ]
132
7,579
1
false
Manganese is associated with the Deinococcus genome and extracellular manganese concentration affects genome condensation.
[ "22", "23" ]
Manganese is associated with the Deinococcus genome and extracellular manganese concentration affects genome condensation.
true
true
true
true
true
1,228
5
INTRODUCTION
1
1
[ "b1" ]
17,204,483
pmid-15333634
DraRnl homologs are found in the proteomes of Streptomyces avermitilis, Hahella chejuensis and the Aeromonas phage 44RR2.8t.
[ "1" ]
124
7,580
0
false
DraRnl homologs are found in the proteomes of Streptomyces avermitilis, Hahella chejuensis and the Aeromonas phage 44RR2.8t.
[]
DraRnl homologs are found in the proteomes of Streptomyces avermitilis, Hahella chejuensis and the Aeromonas phage 44RR2.8t.
true
true
true
true
true
1,229
5
INTRODUCTION
1
1
[ "b1" ]
17,204,483
pmid-15333634
A primary structure alignment indicates that they recapitulate the distinctive features of DraRnl.
[ "1" ]
98
7,581
0
false
A primary structure alignment indicates that they recapitulate the distinctive features of DraRnl.
[]
A primary structure alignment indicates that they recapitulate the distinctive features of DraRnl.
true
true
true
true
true
1,229
5
INTRODUCTION
1
1
[ "b1" ]
17,204,483
pmid-15333634
They have a conserved N-terminal module not found in other ligase clades and they terminate ∼30 amino acids downstream of the presumptive counterpart of nucleotidyltransferase motif IV (305EGVVV309 in DraRnl; see Figure 1).
[ "1" ]
223
7,582
0
false
They have a conserved N-terminal module not found in other ligase clades and they terminate ∼30 amino acids downstream of the presumptive counterpart of nucleotidyltransferase motif IV.
[ "305EGVVV309 in DraRnl; see Figure 1" ]
They have a conserved N-terminal module not found in other ligase clades and they terminate ∼30 amino acids downstream of the presumptive counterpart of nucleotidyltransferase motif IV.
true
true
true
true
true
1,229
5
INTRODUCTION
1
1
[ "b1" ]
17,204,483
pmid-15333634
DraRnl and its cousins have an obvious counterpart of motif I that contains the lysine to which AMP becomes covalently attached.
[ "1" ]
128
7,583
0
false
DraRnl and its cousins have an obvious counterpart of motif I that contains the lysine to which AMP becomes covalently attached.
[]
DraRnl and its cousins have an obvious counterpart of motif I that contains the lysine to which AMP becomes covalently attached.
true
true
true
true
true
1,229
5
INTRODUCTION
1
1
[ "b1" ]
17,204,483
pmid-15333634
The motif I Lys165 side chain of DraRnl is essential, insofar as its replacement by alanine abolished RNA nick sealing and ligase adenylylation activities (1).
[ "1" ]
159
7,584
1
false
The motif I Lys165 side chain of DraRnl is essential, insofar as its replacement by alanine abolished RNA nick sealing and ligase adenylylation activities.
[ "1" ]
The motif I Lys165 side chain of DraRnl is essential, insofar as its replacement by alanine abolished RNA nick sealing and ligase adenylylation activities.
true
true
true
true
true
1,229
5
INTRODUCTION
1
1
[ "b1" ]
17,204,483
pmid-15333634
The sequence alignment in Figure 1 highlights the location of candidate DraRnl equivalents of several other nucleotidyltransferase motifs.
[ "1" ]
138
7,585
0
false
The sequence alignment in Figure 1 highlights the location of candidate DraRnl equivalents of several other nucleotidyltransferase motifs.
[]
The sequence alignment in Figure 1 highlights the location of candidate DraRnl equivalents of several other nucleotidyltransferase motifs.
true
true
true
true
true
1,229
6
INTRODUCTION
0
null
null
17,204,483
null
Here, we address the following questions.
null
41
7,586
0
false
null
null
Here, we address the following questions.
true
true
true
true
true
1,230
6
INTRODUCTION
0
null
null
17,204,483
null
What other residues of the DraRnl nucleotidyltransferase domain are essential for sealing?
null
90
7,587
0
false
null
null
What other residues of the DraRnl nucleotidyltransferase domain are essential for sealing?
true
true
true
true
true
1,230
6
INTRODUCTION
0
null
null
17,204,483
null
At which step of the ligation reaction do the essential residues act?
null
69
7,588
0
false
null
null
At which step of the ligation reaction do the essential residues act?
true
true
true
true
true
1,230
6
INTRODUCTION
0
null
null
17,204,483
null
How does the distinctive N domain of DraRnl promote RNA sealing?
null
64
7,589
0
false
null
null
How does the distinctive N domain of DraRnl promote RNA sealing?
true
true
true
true
true
1,230
6
INTRODUCTION
0
null
null
17,204,483
null
Are specific residues in the N domain critical for activity?
null
60
7,590
0
false
null
null
Are specific residues in the N domain critical for activity?
true
true
true
true
true
1,230
6
INTRODUCTION
0
null
null
17,204,483
null
Answering these questions provides new insights to the evolution of polynucleotide ligases.
null
91
7,591
0
false
null
null
Answering these questions provides new insights to the evolution of polynucleotide ligases.
true
true
true
true
true
1,230
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,576,682
pmid-15943979|pmid-12824381|pmid-16962311
Short, linear motifs (SLiMs) play an essential role in the basic functions of many proteins and identifying these motifs is of great interest in expanding our understanding of biological interaction networks (1).
[ "1", "2", "3" ]
212
7,592
1
false
Short, linear motifs (SLiMs) play an essential role in the basic functions of many proteins and identifying these motifs is of great interest in expanding our understanding of biological interaction networks.
[ "1" ]
Short, linear motifs (SLiMs) play an essential role in the basic functions of many proteins and identifying these motifs is of great interest in expanding our understanding of biological interaction networks.
true
true
true
true
true
1,231
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,576,682
pmid-15943979|pmid-12824381|pmid-16962311
They facilitate many fundamental biological tasks, such as subcellular targeting (e.g.
[ "1", "2", "3" ]
86
7,593
0
false
They facilitate many fundamental biological tasks, such as subcellular targeting (e.g.
[]
They facilitate many fundamental biological tasks, such as subcellular targeting (e.g.
true
true
true
true
true
1,231
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,576,682
pmid-15943979|pmid-12824381|pmid-16962311
The DxxLL Endosome-Lysosome-Basolateral sorting signal motif), post-translational modification (e.g.
[ "1", "2", "3" ]
100
7,594
0
false
The DxxLL Endosome-Lysosome-Basolateral sorting signal motif), post-translational modification (e.g.
[]
The DxxLL Endosome-Lysosome-Basolateral sorting signal motif), post-translational modification (e.g.
true
true
true
true
true
1,231
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,576,682
pmid-15943979|pmid-12824381|pmid-16962311
The NxC N-Linked glycosylation site motif) and protein binding
[ "1", "2", "3" ]
62
7,595
0
false
The NxC N-Linked glycosylation site motif) and protein binding
[]
The NxC N-Linked glycosylation site motif) and protein binding
true
true
false
true
false
1,231
0
INTRODUCTION
1
2
[ "B1", "B2", "B3" ]
17,576,682
pmid-15943979|pmid-12824381|pmid-16962311
The (KR)xTQT Dynein Light Chain binding motif](2).
[ "1", "2", "3" ]
50
7,596
1
false
The (KR)xTQT Dynein Light Chain binding motif].
[ "2" ]
The (KR)xTQT Dynein Light Chain binding motif].
true
true
true
true
true
1,231
0
INTRODUCTION
1
1
[ "B1", "B2", "B3" ]
17,576,682
pmid-15943979|pmid-12824381|pmid-16962311
However, our current knowledge of the area is sparse with less than a hundred classes of SLiMs known in eukaryotes.
[ "1", "2", "3" ]
115
7,597
0
false
However, our current knowledge of the area is sparse with less than a hundred classes of SLiMs known in eukaryotes.
[]
However, our current knowledge of the area is sparse with less than a hundred classes of SLiMs known in eukaryotes.
true
true
true
true
true
1,231
0
INTRODUCTION
1
3
[ "B1", "B2", "B3" ]
17,576,682
pmid-15943979|pmid-12824381|pmid-16962311
Estimates have been made that suggest hundreds more are still undiscovered, making the area of SLiM discovery worthy of substantial investment of effort (3).
[ "1", "2", "3" ]
157
7,598
1
false
Estimates have been made that suggest hundreds more are still undiscovered, making the area of SLiM discovery worthy of substantial investment of effort.
[ "3" ]
Estimates have been made that suggest hundreds more are still undiscovered, making the area of SLiM discovery worthy of substantial investment of effort.
true
true
true
true
true
1,231
1
INTRODUCTION
1
4
[ "B4", "B5", "B6" ]
17,576,682
pmid-16845024|pmid-16279839|pmid-16855291
A powerful way to discover novel SLiMs comes from the fact that they are evolutionarily plastic, making them amenable to convergent evolution.
[ "4", "5", "6" ]
142
7,599
0
false
A powerful way to discover novel SLiMs comes from the fact that they are evolutionarily plastic, making them amenable to convergent evolution.
[]
A powerful way to discover novel SLiMs comes from the fact that they are evolutionarily plastic, making them amenable to convergent evolution.
true
true
true
true
true
1,232