Datasets:
vgainullin
/
xciting_data

Dataset card Data Studio Files
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2
INTRODUCTION
1
2
[ "b2", "b4" ]
17,142,240
pmid-14980014|pmid-10890390
This ability can be estimated by a method that we term ‘knowledge based cross-validation’ by which we determine how the a priori known subtypes (e.g.
[ "2", "4" ]
149
800
0
false
This ability can be estimated by a method that we term ‘knowledge based cross-validation’ by which we determine how the a priori known subtypes (e.g.
[]
This ability can be estimated by a method that we term ‘knowledge based cross-validation’ by which we determine how the a priori known subtypes (e.g.
true
true
true
true
true
139
2
INTRODUCTION
1
2
[ "b2", "b4" ]
17,142,240
pmid-14980014|pmid-10890390
protein families within a superfamily) can be recognized, based on other known subtypes (2–4).
[ "2", "4" ]
94
801
0
false
protein families within a superfamily) can be recognized, based on other known subtypes.
[ "2–4" ]
protein families within a superfamily) can be recognized, based on other known subtypes.
false
true
true
true
false
139
3
INTRODUCTION
0
null
null
17,142,240
null
In view of the above difficulties and the number of new genomes sequenced, it is critically important to define benchmark datasets for assessing the accuracy of classification algorithms.
null
187
802
0
false
null
null
In view of the above difficulties and the number of new genomes sequenced, it is critically important to define benchmark datasets for assessing the accuracy of classification algorithms.
true
true
true
true
true
140
3
INTRODUCTION
0
null
null
17,142,240
null
The goal of the Protein Classification Benchmark collection is to provide a standardized set of protein data and procedures that makes it easier to compare new methods with the established ones.
null
194
803
0
false
null
null
The goal of the Protein Classification Benchmark collection is to provide a standardized set of protein data and procedures that makes it easier to compare new methods with the established ones.
true
true
true
true
true
140
3
INTRODUCTION
0
null
null
17,142,240
null
The collection is based on two general ideas: (i) since protein groups are highly variable, the performance of an algorithm has to be tested on a wide range of classification tasks, such as the recognition of all the protein families in a given database; (ii) the utility of a classifier is determined by its ability to recognize novel subtypes of the existing proteins.
null
370
804
0
false
null
null
The collection is based on two general ideas: (i) since protein groups are highly variable, the performance of an algorithm has to be tested on a wide range of classification tasks, such as the recognition of all the protein families in a given database; (ii) the utility of a classifier is determined by its ability to recognize novel subtypes of the existing proteins.
true
true
true
true
true
140
3
INTRODUCTION
0
null
null
17,142,240
null
The collection is primarily meant for those interested in developing sequence or structure comparison algorithms and/or machine learning methods for protein classification.
null
172
805
0
false
null
null
The collection is primarily meant for those interested in developing sequence or structure comparison algorithms and/or machine learning methods for protein classification.
true
true
true
true
true
140
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
Group II introns have been detected in eukaryotic organelles as well as in eubacterial genomes as intervening sequences of protein, tRNA or rRNA coding genes.
[ "1", "2", "3" ]
158
806
0
false
Group II introns have been detected in eukaryotic organelles as well as in eubacterial genomes as intervening sequences of protein, tRNA or rRNA coding genes.
[]
Group II introns have been detected in eukaryotic organelles as well as in eubacterial genomes as intervening sequences of protein, tRNA or rRNA coding genes.
true
true
true
true
true
141
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
Common to all group II introns is a conserved secondary structure that consists of six double-helical domains (DI-DVI) radiating from a central wheel (1).
[ "1", "2", "3" ]
154
807
1
false
Common to all group II introns is a conserved secondary structure that consists of six double-helical domains (DI-DVI) radiating from a central wheel.
[ "1" ]
Common to all group II introns is a conserved secondary structure that consists of six double-helical domains (DI-DVI) radiating from a central wheel.
true
true
true
true
true
141
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
Group II introns splice via two sequential transesterifications that in vitro occur in some cases autocatalytically.
[ "1", "2", "3" ]
116
808
0
false
Group II introns splice via two sequential transesterifications that in vitro occur in some cases autocatalytically.
[]
Group II introns splice via two sequential transesterifications that in vitro occur in some cases autocatalytically.
true
true
true
true
true
141
0
INTRODUCTION
1
1
[ "b1", "b2", "b3" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
In vivo, however, splicing is dependent on protein co-factors as was shown by mutant analyses (2,3).
[ "1", "2", "3" ]
100
809
0
false
In vivo, however, splicing is dependent on protein co-factors as was shown by mutant analyses.
[ "2,3" ]
In vivo, however, splicing is dependent on protein co-factors as was shown by mutant analyses.
true
true
true
true
true
141
1
INTRODUCTION
1
4
[ "b4", "b5", "b6" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
In Chlamydomonas reinhardtii chloroplasts, two trans-splicing introns were found in the psaA gene encoding the major P700 chlorophyll a/b-binding protein (4).
[ "4", "5", "6" ]
158
810
1
false
In Chlamydomonas reinhardtii chloroplasts, two trans-splicing introns were found in the psaA gene encoding the major P700 chlorophyll a/b-binding protein.
[ "4" ]
In Chlamydomonas reinhardtii chloroplasts, two trans-splicing introns were found in the psaA gene encoding the major P700 chlorophyll a/b-binding protein.
true
true
true
true
true
142
1
INTRODUCTION
1
5
[ "b4", "b5", "b6" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
In the case of the first intron of the psaA gene, three independently transcribed RNAs associate via tertiary interactions to form a functional group II intron, resulting in trans-splicing of the flanking exon 1 and exon 2 (5).
[ "4", "5", "6" ]
227
811
1
false
In the case of the first intron of the psaA gene, three independently transcribed RNAs associate via tertiary interactions to form a functional group II intron, resulting in trans-splicing of the flanking exon 1 and exon 2.
[ "5" ]
In the case of the first intron of the psaA gene, three independently transcribed RNAs associate via tertiary interactions to form a functional group II intron, resulting in trans-splicing of the flanking exon 1 and exon 2.
true
true
true
true
true
142
1
INTRODUCTION
1
4
[ "b4", "b5", "b6" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
Part of this tripartite group II intron is the tscA RNA that is processed from a chloroplast-encoded precursor RNA.
[ "4", "5", "6" ]
115
812
0
false
Part of this tripartite group II intron is the tscA RNA that is processed from a chloroplast-encoded precursor RNA.
[]
Part of this tripartite group II intron is the tscA RNA that is processed from a chloroplast-encoded precursor RNA.
true
true
true
true
true
142
1
INTRODUCTION
1
6
[ "b4", "b5", "b6" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
Secondary structure predictions revealed that tscA contains domain DII and DIII as well as partial domains DI and DIV of the conserved secondary group II intron structure (6).
[ "4", "5", "6" ]
175
813
1
false
Secondary structure predictions revealed that tscA contains domain DII and DIII as well as partial domains DI and DIV of the conserved secondary group II intron structure.
[ "6" ]
Secondary structure predictions revealed that tscA contains domain DII and DIII as well as partial domains DI and DIV of the conserved secondary group II intron structure.
true
true
true
true
true
142
2
INTRODUCTION
1
7
[ "b7", "b8", "b9", "b11" ]
17,012,281
pmid-10562560|pmid-16115062|pmid-16407333|pmid-15037779|pmid-11437228|pmid-15980199|NA|pmid-12569397|pmid-9077453|pmid-11073993|pmid-10921904|pmid-7565770|pmid-14992573
Mutant work in C.reinhardtii has shown that >14 nuclear genes affect the chloroplast trans-splicing reaction, and complementation of some of the characterized mutants led to the identification of the molecular determinants.
[ "7", "8", "9", "11" ]
223
814
0
false
Mutant work in C.reinhardtii has shown that >14 nuclear genes affect the chloroplast trans-splicing reaction, and complementation of some of the characterized mutants led to the identification of the molecular determinants.
[]
Mutant work in C.reinhardtii has shown that >14 nuclear genes affect the chloroplast trans-splicing reaction, and complementation of some of the characterized mutants led to the identification of the molecular determinants.
true
true
true
true
true
143
2
INTRODUCTION
1
7
[ "b7", "b8", "b9", "b11" ]
17,012,281
pmid-10562560|pmid-16115062|pmid-16407333|pmid-15037779|pmid-11437228|pmid-15980199|NA|pmid-12569397|pmid-9077453|pmid-11073993|pmid-10921904|pmid-7565770|pmid-14992573
Although some of the identified polypeptides are related to proteins involved in nucleic acid metabolisms, this function seems to be non-essential for intron splicing (7,8).
[ "7", "8", "9", "11" ]
173
815
0
false
Although some of the identified polypeptides are related to proteins involved in nucleic acid metabolisms, this function seems to be non-essential for intron splicing.
[ "7,8" ]
Although some of the identified polypeptides are related to proteins involved in nucleic acid metabolisms, this function seems to be non-essential for intron splicing.
true
true
true
true
true
143
2
INTRODUCTION
1
7
[ "b7", "b8", "b9", "b11" ]
17,012,281
pmid-10562560|pmid-16115062|pmid-16407333|pmid-15037779|pmid-11437228|pmid-15980199|NA|pmid-12569397|pmid-9077453|pmid-11073993|pmid-10921904|pmid-7565770|pmid-14992573
Similar to nuclear mRNA splicing, these protein components might be part of a chloroplast splicing complex, because they were found in large stromal or membrane-bound RNA-containing complexes (9–11).
[ "7", "8", "9", "11" ]
199
816
0
false
Similar to nuclear mRNA splicing, these protein components might be part of a chloroplast splicing complex, because they were found in large stromal or membrane-bound RNA-containing complexes.
[ "9–11" ]
Similar to nuclear mRNA splicing, these protein components might be part of a chloroplast splicing complex, because they were found in large stromal or membrane-bound RNA-containing complexes.
true
true
true
true
true
143
3
INTRODUCTION
1
12
[ "b12", "b13", "b14" ]
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
To define further components of a putative ‘chloroplast spliceosome’ in C.reinhardtii, we used the tscA RNA as bait to identify novel intron RNA-binding proteins.
[ "12", "13", "14" ]
162
817
0
false
To define further components of a putative ‘chloroplast spliceosome’ in C.reinhardtii, we used the tscA RNA as bait to identify novel intron RNA-binding proteins.
[]
To define further components of a putative ‘chloroplast spliceosome’ in C.reinhardtii, we used the tscA RNA as bait to identify novel intron RNA-binding proteins.
true
true
true
true
true
144
3
INTRODUCTION
1
12
[ "b12", "b13", "b14" ]
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
Using the yeast three-hybrid system, we isolated a polypeptide that seems to be a novel member of the multifunctional nucleosome assembly protein (NAP) family.
[ "12", "13", "14" ]
159
818
0
false
Using the yeast three-hybrid system, we isolated a polypeptide that seems to be a novel member of the multifunctional nucleosome assembly protein (NAP) family.
[]
Using the yeast three-hybrid system, we isolated a polypeptide that seems to be a novel member of the multifunctional nucleosome assembly protein (NAP) family.
true
true
true
true
true
144
3
INTRODUCTION
1
12
[ "b12", "b13", "b14" ]
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
These well-conserved eukaryotic histone chaperones facilitate, for example, the nucleosome assembly and remodelling of chromatin, and are implicated in transcriptional regulation and cell cycle regulation (12,13).
[ "12", "13", "14" ]
213
819
0
false
These well-conserved eukaryotic histone chaperones facilitate, for example, the nucleosome assembly and remodelling of chromatin, and are implicated in transcriptional regulation and cell cycle regulation.
[ "12,13" ]
These well-conserved eukaryotic histone chaperones facilitate, for example, the nucleosome assembly and remodelling of chromatin, and are implicated in transcriptional regulation and cell cycle regulation.
true
true
true
true
true
144
3
INTRODUCTION
1
12
[ "b12", "b13", "b14" ]
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
Here, we assign a novel function to a NAP-like protein.
[ "12", "13", "14" ]
55
820
0
false
Here, we assign a novel function to a NAP-like protein.
[]
Here, we assign a novel function to a NAP-like protein.
true
true
true
true
true
144
3
INTRODUCTION
1
12
[ "b12", "b13", "b14" ]
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
Laser scanning confocal fluorescence microscopy (LSCFM) and in vitro binding assays demonstrate that chloroplasts of C.reinhardtii contain a NAP-like protein that specifically binds to organellar group II intron RNA and U-rich chloroplast transcripts.
[ "12", "13", "14" ]
251
821
0
false
Laser scanning confocal fluorescence microscopy (LSCFM) and in vitro binding assays demonstrate that chloroplasts of C.reinhardtii contain a NAP-like protein that specifically binds to organellar group II intron RNA and U-rich chloroplast transcripts.
[]
Laser scanning confocal fluorescence microscopy (LSCFM) and in vitro binding assays demonstrate that chloroplasts of C.reinhardtii contain a NAP-like protein that specifically binds to organellar group II intron RNA and U-rich chloroplast transcripts.
true
true
true
true
true
144
3
INTRODUCTION
1
14
[ "b12", "b13", "b14" ]
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
Our data further support the view that during evolution, chloroplasts have acquired novel nuclear components that most probably were not delivered by endosymbiont gene transfer (14).
[ "12", "13", "14" ]
182
822
1
false
Our data further support the view that during evolution, chloroplasts have acquired novel nuclear components that most probably were not delivered by endosymbiont gene transfer.
[ "14" ]
Our data further support the view that during evolution, chloroplasts have acquired novel nuclear components that most probably were not delivered by endosymbiont gene transfer.
true
true
true
true
true
144
0
DISCUSSION
1
53
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
The splicing chemistry and RNA structures of self-splicing group II introns and nuclear pre-mRNA introns are strikingly similar.
[ "53", "7", "11", "54", "55", "8", "56" ]
128
823
0
false
The splicing chemistry and RNA structures of self-splicing group II introns and nuclear pre-mRNA introns are strikingly similar.
[]
The splicing chemistry and RNA structures of self-splicing group II introns and nuclear pre-mRNA introns are strikingly similar.
true
true
true
true
true
145
0
DISCUSSION
1
53
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
Thereby, suggesting some evolutionary relationship between group II introns and the nuclear spliceosomal intron (53).
[ "53", "7", "11", "54", "55", "8", "56" ]
117
824
1
false
Thereby, suggesting some evolutionary relationship between group II introns and the nuclear spliceosomal intron.
[ "53" ]
Thereby, suggesting some evolutionary relationship between group II introns and the nuclear spliceosomal intron.
true
true
true
true
true
145
0
DISCUSSION
1
53
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
Moreover, there is compelling evidence to suggest that chloroplast spliceosomes catalyse intron splicing using a similar mechanism to that reported for nuclear spliceosomes.
[ "53", "7", "11", "54", "55", "8", "56" ]
173
825
0
false
Moreover, there is compelling evidence to suggest that chloroplast spliceosomes catalyse intron splicing using a similar mechanism to that reported for nuclear spliceosomes.
[]
Moreover, there is compelling evidence to suggest that chloroplast spliceosomes catalyse intron splicing using a similar mechanism to that reported for nuclear spliceosomes.
true
true
true
true
true
145
0
DISCUSSION
1
54
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
This suggestion is the result of data obtained form a combination of different experimental approaches that have identified components of a putative chloroplast spliceosome in C.reinhardtii (7–11) and higher plants (54).
[ "53", "7", "11", "54", "55", "8", "56" ]
220
826
1
false
This suggestion is the result of data obtained form a combination of different experimental approaches that have identified components of a putative chloroplast spliceosome in C.reinhardtii and higher plants.
[ "7–11", "54" ]
This suggestion is the result of data obtained form a combination of different experimental approaches that have identified components of a putative chloroplast spliceosome in C.reinhardtii and higher plants.
true
true
true
true
true
145
0
DISCUSSION
1
53
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
Additional support comes from studies with tobacco chloroplasts.
[ "53", "7", "11", "54", "55", "8", "56" ]
64
827
0
false
Additional support comes from studies with tobacco chloroplasts.
[]
Additional support comes from studies with tobacco chloroplasts.
true
true
true
true
true
145
0
DISCUSSION
1
55
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
Nakamura and co-workers (55) identified chloroplast ribonucleoproteins (cpRNPs) that are associated in vivo with various species of chloroplast mRNAs and intron-containing precursor tRNAs.
[ "53", "7", "11", "54", "55", "8", "56" ]
188
828
1
false
Nakamura and co-workers identified chloroplast ribonucleoproteins (cpRNPs) that are associated in vivo with various species of chloroplast mRNAs and intron-containing precursor tRNAs.
[ "55" ]
Nakamura and co-workers identified chloroplast ribonucleoproteins (cpRNPs) that are associated in vivo with various species of chloroplast mRNAs and intron-containing precursor tRNAs.
true
true
true
true
true
145
0
DISCUSSION
1
53
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
They suggested that these stromal RNA–protein complexes promote, for example, RNA splicing, processing or editing.
[ "53", "7", "11", "54", "55", "8", "56" ]
114
829
0
false
They suggested that these stromal RNA–protein complexes promote, for example, RNA splicing, processing or editing.
[]
They suggested that these stromal RNA–protein complexes promote, for example, RNA splicing, processing or editing.
true
true
true
true
true
145
0
DISCUSSION
1
53
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
Previously, the yeast three-hybrid system was used to demonstrate specific binding of proteins to organellar intron RNA (8,56).
[ "53", "7", "11", "54", "55", "8", "56" ]
127
830
0
false
Previously, the yeast three-hybrid system was used to demonstrate specific binding of proteins to organellar intron RNA.
[ "8,56" ]
Previously, the yeast three-hybrid system was used to demonstrate specific binding of proteins to organellar intron RNA.
true
true
true
true
true
145
0
DISCUSSION
1
53
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
In this work, we used the yeast three-hybrid system successfully to screen a C.reinhardtii cDNA library and we were able to detect the novel organellar protein cNAPL that specifically binds to the first psaA group II intron.
[ "53", "7", "11", "54", "55", "8", "56" ]
224
831
0
false
In this work, we used the yeast three-hybrid system successfully to screen a C.reinhardtii cDNA library and we were able to detect the novel organellar protein cNAPL that specifically binds to the first psaA group II intron.
[]
In this work, we used the yeast three-hybrid system successfully to screen a C.reinhardtii cDNA library and we were able to detect the novel organellar protein cNAPL that specifically binds to the first psaA group II intron.
true
true
true
true
true
145
0
DISCUSSION
1
53
[ "b53", "b7", "b11", "b54", "b55", "b8", "b56" ]
17,012,281
pmid-15568970|pmid-10946107|pmid-12955455|pmid-16242989|pmid-10562560|pmid-15037779|pmid-16379013|pmid-10556512|pmid-16115062|pmid-14706817
The binding of cNAPL to domains DII+III and DV+VI of the first psaA intron was further shown in electromobility shift assays.
[ "53", "7", "11", "54", "55", "8", "56" ]
125
832
0
false
The binding of cNAPL to domains DII+III and DV+VI of the first psaA intron was further shown in electromobility shift assays.
[]
The binding of cNAPL to domains DII+III and DV+VI of the first psaA intron was further shown in electromobility shift assays.
true
true
true
true
true
145
1
DISCUSSION
1
57
[ "b57", "b58", "b22", "b59", "b60" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
In several other studies using defined intron domains, separated molecules were found to fold into a structure corresponding to their conformation in the complete active intronic RNA (57,58).
[ "57", "58", "22", "59", "60" ]
191
833
0
false
In several other studies using defined intron domains, separated molecules were found to fold into a structure corresponding to their conformation in the complete active intronic RNA.
[ "57,58" ]
In several other studies using defined intron domains, separated molecules were found to fold into a structure corresponding to their conformation in the complete active intronic RNA.
true
true
true
true
true
146
1
DISCUSSION
1
22
[ "b57", "b58", "b22", "b59", "b60" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
Recent studies have demonstrated that fragmented intron molecules are appropriate targets for gel retardation assays (22).
[ "57", "58", "22", "59", "60" ]
122
834
1
false
Recent studies have demonstrated that fragmented intron molecules are appropriate targets for gel retardation assays.
[ "22" ]
Recent studies have demonstrated that fragmented intron molecules are appropriate targets for gel retardation assays.
true
true
true
true
true
146
1
DISCUSSION
1
57
[ "b57", "b58", "b22", "b59", "b60" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
In EMSA, we observed multiple shifted bands after incubating domains DII+III of tscA RNA with increasing amounts of cNAPL.
[ "57", "58", "22", "59", "60" ]
122
835
0
false
In EMSA, we observed multiple shifted bands after incubating domains DII+III of tscA RNA with increasing amounts of cNAPL.
[]
In EMSA, we observed multiple shifted bands after incubating domains DII+III of tscA RNA with increasing amounts of cNAPL.
true
true
true
true
true
146
1
DISCUSSION
1
59
[ "b57", "b58", "b22", "b59", "b60" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
As was shown for example for the mutated SxlN1 protein of Drosophila, multiple shifted bands probably correspond to the sequential filling of binding sites when protein concentration is increased (59).
[ "57", "58", "22", "59", "60" ]
201
836
1
false
As was shown for example for the mutated SxlN1 protein of Drosophila, multiple shifted bands probably correspond to the sequential filling of binding sites when protein concentration is increased.
[ "59" ]
As was shown for example for the mutated SxlN1 protein of Drosophila, multiple shifted bands probably correspond to the sequential filling of binding sites when protein concentration is increased.
true
true
true
true
true
146
1
DISCUSSION
1
57
[ "b57", "b58", "b22", "b59", "b60" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
Hence, the two shifted bands observed in Figure 2b–d shows non-cooperative binding of cNAPL to domains DII and DIII, thus indicating at least two binding sites.
[ "57", "58", "22", "59", "60" ]
160
837
0
false
Hence, the two shifted bands observed in Figure 2b–d shows non-cooperative binding of cNAPL to domains DII and DIII, thus indicating at least two binding sites.
[]
Hence, the two shifted bands observed in Figure 2b–d shows non-cooperative binding of cNAPL to domains DII and DIII, thus indicating at least two binding sites.
true
true
true
true
true
146
1
DISCUSSION
1
57
[ "b57", "b58", "b22", "b59", "b60" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
However, we were not able to detect a known RNA-binding motif [, (60)] in cNAPL, such as the RNP motif, the K homology motif (KH) or the RGG (Arg-Gly-Gly) box.
[ "57", "58", "22", "59", "60" ]
159
838
0
false
However, we were not able to detect a known RNA-binding motif in cNAPL, such as the RNP motif, the K homology motif (KH) or the RGG (Arg-Gly-Gly) box.
[ ", (60)" ]
However, we were not able to detect a known RNA-binding motif in cNAPL, such as the RNP motif, the K homology motif (KH) or the RGG (Arg-Gly-Gly) box.
true
true
true
true
true
146
1
DISCUSSION
1
57
[ "b57", "b58", "b22", "b59", "b60" ]
17,012,281
pmid-16453785|pmid-3280139|pmid-1707343|pmid-8382803|pmid-8117737|pmid-11406270|NA|NA
Further binding studies with truncated cNAPL constructs could help to determine the exact RNA-binding domain.
[ "57", "58", "22", "59", "60" ]
109
839
0
false
Further binding studies with truncated cNAPL constructs could help to determine the exact RNA-binding domain.
[]
Further binding studies with truncated cNAPL constructs could help to determine the exact RNA-binding domain.
true
true
true
true
true
146
2
DISCUSSION
1
12
[ "b12", "b42", "b61", "b45", "b62", "b63", "b13", "b64", "b65" ]
17,012,281
pmid-10562560|pmid-16115062|pmid-16407333|pmid-15037779|pmid-11437228|pmid-15980199|NA|pmid-12569397|pmid-9077453|pmid-11073993|pmid-10921904|pmid-7565770|pmid-14992573
cNAPL is a member of the multifunctional family of NAPs that are involved in processes which normally take place in the nucleus or the cytoplasm of various eukaryotes (12,42,61).
[ "12", "42", "61", "45", "62", "63", "13", "64", "65" ]
178
840
0
false
cNAPL is a member of the multifunctional family of NAPs that are involved in processes which normally take place in the nucleus or the cytoplasm of various eukaryotes.
[ "12,42,61" ]
cNAPL is a member of the multifunctional family of NAPs that are involved in processes which normally take place in the nucleus or the cytoplasm of various eukaryotes.
false
true
true
true
false
147
2
DISCUSSION
1
12
[ "b12", "b42", "b61", "b45", "b62", "b63", "b13", "b64", "b65" ]
17,012,281
pmid-10562560|pmid-16115062|pmid-16407333|pmid-15037779|pmid-11437228|pmid-15980199|NA|pmid-12569397|pmid-9077453|pmid-11073993|pmid-10921904|pmid-7565770|pmid-14992573
Besides their distinct functions in mitotic events and cytokinesis, NAPs act as histone chaperones, binding to all core histones with a preference for H2A and H2B and working as a deposition factor by transferring NAP1-bound histones to double-stranded DNA.
[ "12", "42", "61", "45", "62", "63", "13", "64", "65" ]
257
841
0
false
Besides their distinct functions in mitotic events and cytokinesis, NAPs act as histone chaperones, binding to all core histones with a preference for H2A and H2B and working as a deposition factor by transferring NAP1-bound histones to double-stranded DNA.
[]
Besides their distinct functions in mitotic events and cytokinesis, NAPs act as histone chaperones, binding to all core histones with a preference for H2A and H2B and working as a deposition factor by transferring NAP1-bound histones to double-stranded DNA.
true
true
true
true
true
147
2
DISCUSSION
1
12
[ "b12", "b42", "b61", "b45", "b62", "b63", "b13", "b64", "b65" ]
17,012,281
pmid-10562560|pmid-16115062|pmid-16407333|pmid-15037779|pmid-11437228|pmid-15980199|NA|pmid-12569397|pmid-9077453|pmid-11073993|pmid-10921904|pmid-7565770|pmid-14992573
In addition to its nucleosome assembly and histone-binding activity, NAP1 as well as plant NAP1-like proteins may be involved in regulating gene expression and therefore cellular differentiation (45,62,63).
[ "12", "42", "61", "45", "62", "63", "13", "64", "65" ]
206
842
0
false
In addition to its nucleosome assembly and histone-binding activity, NAP1 as well as plant NAP1-like proteins may be involved in regulating gene expression and therefore cellular differentiation.
[ "45,62,63" ]
In addition to its nucleosome assembly and histone-binding activity, NAP1 as well as plant NAP1-like proteins may be involved in regulating gene expression and therefore cellular differentiation.
true
true
true
true
true
147
2
DISCUSSION
1
12
[ "b12", "b42", "b61", "b45", "b62", "b63", "b13", "b64", "b65" ]
17,012,281
pmid-10562560|pmid-16115062|pmid-16407333|pmid-15037779|pmid-11437228|pmid-15980199|NA|pmid-12569397|pmid-9077453|pmid-11073993|pmid-10921904|pmid-7565770|pmid-14992573
NAP1 has also been shown to facilitate transcription factor binding by disruption of the histone octamer through the binding of H2A and H2B (13,64).
[ "12", "42", "61", "45", "62", "63", "13", "64", "65" ]
148
843
0
false
NAP1 has also been shown to facilitate transcription factor binding by disruption of the histone octamer through the binding of H2A and H2B.
[ "13,64" ]
NAP1 has also been shown to facilitate transcription factor binding by disruption of the histone octamer through the binding of H2A and H2B.
true
true
true
true
true
147
2
DISCUSSION
1
65
[ "b12", "b42", "b61", "b45", "b62", "b63", "b13", "b64", "b65" ]
17,012,281
pmid-10562560|pmid-16115062|pmid-16407333|pmid-15037779|pmid-11437228|pmid-15980199|NA|pmid-12569397|pmid-9077453|pmid-11073993|pmid-10921904|pmid-7565770|pmid-14992573
NAP1 also shuttles histones H2A and H2B as well as a complex of H2A, H2B, H3 and H4 between the template DNA and nascent RNA during transcription (65).
[ "12", "42", "61", "45", "62", "63", "13", "64", "65" ]
151
844
1
false
NAP1 also shuttles histones H2A and H2B as well as a complex of H2A, H2B, H3 and H4 between the template DNA and nascent RNA during transcription.
[ "65" ]
NAP1 also shuttles histones H2A and H2B as well as a complex of H2A, H2B, H3 and H4 between the template DNA and nascent RNA during transcription.
true
true
true
true
true
147
2
DISCUSSION
1
12
[ "b12", "b42", "b61", "b45", "b62", "b63", "b13", "b64", "b65" ]
17,012,281
pmid-10562560|pmid-16115062|pmid-16407333|pmid-15037779|pmid-11437228|pmid-15980199|NA|pmid-12569397|pmid-9077453|pmid-11073993|pmid-10921904|pmid-7565770|pmid-14992573
To date, however, it is still unknown whether NAP1 interacts directly also with RNA.
[ "12", "42", "61", "45", "62", "63", "13", "64", "65" ]
84
845
0
false
To date, however, it is still unknown whether NAP1 interacts directly also with RNA.
[]
To date, however, it is still unknown whether NAP1 interacts directly also with RNA.
true
true
true
true
true
147
3
DISCUSSION
0
null
null
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
Phylogenetic analysis indicates that cNAPL is related to nuclear localized NAP polypeptides.
null
92
846
0
false
null
null
Phylogenetic analysis indicates that cNAPL is related to nuclear localized NAP polypeptides.
true
true
true
true
true
148
3
DISCUSSION
0
null
null
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
The clustering of cNAPL with algal NAPs and not with NAPs of higher plants could be explained by its chloroplast targeting signal.
null
130
847
0
false
null
null
The clustering of cNAPL with algal NAPs and not with NAPs of higher plants could be explained by its chloroplast targeting signal.
true
true
true
true
true
148
3
DISCUSSION
0
null
null
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
In the case of Thalassiosira NAP, TargetP predicted a 69 amino acid signal sequence, which could not be assigned clearly to any organelle.
null
138
848
0
false
null
null
In the case of Thalassiosira NAP, TargetP predicted a 69 amino acid signal sequence, which could not be assigned clearly to any organelle.
true
true
true
true
true
148
3
DISCUSSION
0
null
null
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
Diatoms, such as T.pseudonana, possess so-called ‘complex plastids’ delineated by four distinct membranes.
null
106
849
0
false
null
null
Diatoms, such as T.pseudonana, possess so-called ‘complex plastids’ delineated by four distinct membranes.
true
true
true
true
true
148
3
DISCUSSION
0
null
null
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
For a nuclear-encoded plastid polypeptide to be directed to the plastids, multiple targeting signals are necessary.
null
115
850
0
false
null
null
For a nuclear-encoded plastid polypeptide to be directed to the plastids, multiple targeting signals are necessary.
true
true
true
true
true
148
3
DISCUSSION
0
null
null
17,012,281
pmid-11437228|pmid-10921904|pmid-14735123
Thus, determining a protein's localization in diatoms using today's prediction programs is difficult.
null
101
851
0
false
null
null
Thus, determining a protein's localization in diatoms using today's prediction programs is difficult.
true
true
true
true
true
148
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
It is now generally accepted that double-membrane-bound chloroplasts are the result of an endosymbiotic event involving a cyanobacterial-like organism early on in evolution.
[ "14", "66", "14" ]
173
852
0
false
It is now generally accepted that double-membrane-bound chloroplasts are the result of an endosymbiotic event involving a cyanobacterial-like organism early on in evolution.
[]
It is now generally accepted that double-membrane-bound chloroplasts are the result of an endosymbiotic event involving a cyanobacterial-like organism early on in evolution.
true
true
true
true
true
149
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
During evolution, the cyanobacterial endosymbiont has lost its autonomy, and this has been accompanied by significant changes of the chloroplast proteome (14,66).
[ "14", "66", "14" ]
162
853
0
false
During evolution, the cyanobacterial endosymbiont has lost its autonomy, and this has been accompanied by significant changes of the chloroplast proteome.
[ "14,66" ]
During evolution, the cyanobacterial endosymbiont has lost its autonomy, and this has been accompanied by significant changes of the chloroplast proteome.
true
true
true
true
true
149
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
A key factor in this process of adoption was the loss of genetic material resulting from gene transfer to the cell nucleus.
[ "14", "66", "14" ]
123
854
0
false
A key factor in this process of adoption was the loss of genetic material resulting from gene transfer to the cell nucleus.
[]
A key factor in this process of adoption was the loss of genetic material resulting from gene transfer to the cell nucleus.
true
true
true
true
true
149
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
The vast majority of proteins in present day chloroplasts are encoded by the host nucleus and require N-terminal presequences that target them back to the chloroplast.
[ "14", "66", "14" ]
167
855
0
false
The vast majority of proteins in present day chloroplasts are encoded by the host nucleus and require N-terminal presequences that target them back to the chloroplast.
[]
The vast majority of proteins in present day chloroplasts are encoded by the host nucleus and require N-terminal presequences that target them back to the chloroplast.
true
true
true
true
true
149
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
Therefore, in order to establish a functional organelle–nucleus interaction, chloroplasts have had to import a set of new proteins to adapt their metabolism to the new conditions.
[ "14", "66", "14" ]
179
856
0
false
Therefore, in order to establish a functional organelle–nucleus interaction, chloroplasts have had to import a set of new proteins to adapt their metabolism to the new conditions.
[]
Therefore, in order to establish a functional organelle–nucleus interaction, chloroplasts have had to import a set of new proteins to adapt their metabolism to the new conditions.
true
true
true
true
true
149
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
Interestingly, a proportion of these proteins do not seem to have been acquired from cyanobacteria (14).
[ "14", "66", "14" ]
104
857
1
false
Interestingly, a proportion of these proteins do not seem to have been acquired from cyanobacteria.
[ "14" ]
Interestingly, a proportion of these proteins do not seem to have been acquired from cyanobacteria.
true
true
true
true
true
149
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
Phylogenetic analysis and database research revealed that no NAP homologues could be identified in prokaryotic organisms.
[ "14", "66", "14" ]
121
858
0
false
Phylogenetic analysis and database research revealed that no NAP homologues could be identified in prokaryotic organisms.
[]
Phylogenetic analysis and database research revealed that no NAP homologues could be identified in prokaryotic organisms.
true
true
true
true
true
149
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
We therefore suggest that cNAPL does not originate from an endosymbiotic gene transfer event and that the chloroplast of C.reinhardtii has gained cNAPL as a novel nuclear-encoded factor.
[ "14", "66", "14" ]
186
859
0
false
We therefore suggest that cNAPL does not originate from an endosymbiotic gene transfer event and that the chloroplast of C.reinhardtii has gained cNAPL as a novel nuclear-encoded factor.
[]
We therefore suggest that cNAPL does not originate from an endosymbiotic gene transfer event and that the chloroplast of C.reinhardtii has gained cNAPL as a novel nuclear-encoded factor.
true
true
true
true
true
149
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
The phylogenetic analysis suggests that cNapl originate from a nuclear Nap gene, and is probably the result of a gene duplication event that occurred after separation of higher plants from green algae.
[ "14", "66", "14" ]
201
860
0
false
The phylogenetic analysis suggests that cNapl originate from a nuclear Nap gene, and is probably the result of a gene duplication event that occurred after separation of higher plants from green algae.
[]
The phylogenetic analysis suggests that cNapl originate from a nuclear Nap gene, and is probably the result of a gene duplication event that occurred after separation of higher plants from green algae.
true
true
true
true
true
149
4
DISCUSSION
1
14
[ "b14", "b66", "b14" ]
17,012,281
pmid-14735123|pmid-12493248|pmid-14735123
We thus propose that cNAPL with its chloroplast transit peptide represents a new type of NAP-like polypeptide.
[ "14", "66", "14" ]
110
861
0
false
We thus propose that cNAPL with its chloroplast transit peptide represents a new type of NAP-like polypeptide.
[]
We thus propose that cNAPL with its chloroplast transit peptide represents a new type of NAP-like polypeptide.
true
true
true
true
true
149
5
DISCUSSION
1
1
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
Many group II introns of plants have lost their self-splicing activity during evolution and thus, recruited host-encoded proteins as splicing factors (1,67).
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
157
862
0
false
Many group II introns of plants have lost their self-splicing activity during evolution and thus, recruited host-encoded proteins as splicing factors.
[ "1,67" ]
Many group II introns of plants have lost their self-splicing activity during evolution and thus, recruited host-encoded proteins as splicing factors.
true
true
true
true
true
150
5
DISCUSSION
1
1
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
The participation of nuclear-encoded proteins in chloroplast splicing could provide a means to control the biogenesis of the photosynthetic apparatus.
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
150
863
0
false
The participation of nuclear-encoded proteins in chloroplast splicing could provide a means to control the biogenesis of the photosynthetic apparatus.
[]
The participation of nuclear-encoded proteins in chloroplast splicing could provide a means to control the biogenesis of the photosynthetic apparatus.
true
true
true
true
true
150
5
DISCUSSION
1
1
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
It has been suggested that these recruited host-encoded proteins probably had other functions in the cell.
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
106
864
0
false
It has been suggested that these recruited host-encoded proteins probably had other functions in the cell.
[]
It has been suggested that these recruited host-encoded proteins probably had other functions in the cell.
true
true
true
true
true
150
5
DISCUSSION
1
1
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
Many of these proteins show some degree of homology to proteins involved in RNA metabolism.
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
91
865
0
false
Many of these proteins show some degree of homology to proteins involved in RNA metabolism.
[]
Many of these proteins show some degree of homology to proteins involved in RNA metabolism.
true
true
true
true
true
150
5
DISCUSSION
1
7
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
For example, Raa2 of C.reinhardtii shows homology to pseudouridine synthetase; however, such enzymatic activity is not required for trans-splicing of psaA RNA (7).
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
163
866
1
false
For example, Raa2 of C.reinhardtii shows homology to pseudouridine synthetase; however, such enzymatic activity is not required for trans-splicing of psaA RNA.
[ "7" ]
For example, Raa2 of C.reinhardtii shows homology to pseudouridine synthetase; however, such enzymatic activity is not required for trans-splicing of psaA RNA.
true
true
true
true
true
150
5
DISCUSSION
1
68
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
Another example is Mss116p of Saccharomyces cerevisiae, which influences the splicing of all nine group I and all four group II introns in mitochondria (68).
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
157
867
1
false
Another example is Mss116p of Saccharomyces cerevisiae, which influences the splicing of all nine group I and all four group II introns in mitochondria.
[ "68" ]
Another example is Mss116p of Saccharomyces cerevisiae, which influences the splicing of all nine group I and all four group II introns in mitochondria.
true
true
true
true
true
150
5
DISCUSSION
1
1
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
Mss116p is related to DEAD-box proteins with RNA chaperone function and may facilitate splicing by resolving misfolded introns.
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
127
868
0
false
Mss116p is related to DEAD-box proteins with RNA chaperone function and may facilitate splicing by resolving misfolded introns.
[]
Mss116p is related to DEAD-box proteins with RNA chaperone function and may facilitate splicing by resolving misfolded introns.
true
true
true
true
true
150
5
DISCUSSION
1
69
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
However, it is generally discussed that proteins involved in splicing and interacting with intron RNAs seem to support RNA folding or to stabilize the active conformation, whereas the catalytic potential is clearly located in the RNA itself (69).
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
246
869
1
false
However, it is generally discussed that proteins involved in splicing and interacting with intron RNAs seem to support RNA folding or to stabilize the active conformation, whereas the catalytic potential is clearly located in the RNA itself.
[ "69" ]
However, it is generally discussed that proteins involved in splicing and interacting with intron RNAs seem to support RNA folding or to stabilize the active conformation, whereas the catalytic potential is clearly located in the RNA itself.
true
true
true
true
true
150
5
DISCUSSION
1
1
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
Furthermore, Mss116p is a bifunctional protein that influences, in addition to splicing of group I and group II introns, some RNA end-processing reactions and translation of a subset of mitochondrial mRNAs.
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
206
870
0
false
Furthermore, Mss116p is a bifunctional protein that influences, in addition to splicing of group I and group II introns, some RNA end-processing reactions and translation of a subset of mitochondrial mRNAs.
[]
Furthermore, Mss116p is a bifunctional protein that influences, in addition to splicing of group I and group II introns, some RNA end-processing reactions and translation of a subset of mitochondrial mRNAs.
true
true
true
true
true
150
5
DISCUSSION
1
1
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
Indeed, for several nuclear-encoded host proteins, it is known that they have additional cellular functions and seem to have been recruited for splicing during evolution (1).
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
174
871
1
false
Indeed, for several nuclear-encoded host proteins, it is known that they have additional cellular functions and seem to have been recruited for splicing during evolution.
[ "1" ]
Indeed, for several nuclear-encoded host proteins, it is known that they have additional cellular functions and seem to have been recruited for splicing during evolution.
true
true
true
true
true
150
5
DISCUSSION
1
1
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
Therefore, it has been questioned whether cNAPL is also a multifunctional protein.
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
82
872
0
false
Therefore, it has been questioned whether cNAPL is also a multifunctional protein.
[]
Therefore, it has been questioned whether cNAPL is also a multifunctional protein.
true
true
true
true
true
150
5
DISCUSSION
1
1
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
The analysed interactions of cNAPL with tscA RNA and domains DV and DVI of the first psaA intron implicate a role for cNAPL as a potential tscA RNA processing factor and also as a splicing factor of the first psaA intron.
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
221
873
0
false
The analysed interactions of cNAPL with tscA RNA and domains DV and DVI of the first psaA intron implicate a role for cNAPL as a potential tscA RNA processing factor and also as a splicing factor of the first psaA intron.
[]
The analysed interactions of cNAPL with tscA RNA and domains DV and DVI of the first psaA intron implicate a role for cNAPL as a potential tscA RNA processing factor and also as a splicing factor of the first psaA intron.
true
true
true
true
true
150
5
DISCUSSION
1
8
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
An example for such a bifunctional protein comes from recent work where Rat1 is required for both processing of tscA RNA as well as for splicing of the first psaA intron (8).
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
174
874
1
false
An example for such a bifunctional protein comes from recent work where Rat1 is required for both processing of tscA RNA as well as for splicing of the first psaA intron.
[ "8" ]
An example for such a bifunctional protein comes from recent work where Rat1 is required for both processing of tscA RNA as well as for splicing of the first psaA intron.
true
true
true
true
true
150
5
DISCUSSION
1
9
[ "b1", "b67", "b7", "b68", "b69", "b1", "b8", "b9", "b70" ]
17,012,281
pmid-15568970|NA|pmid-10562560|pmid-16505350|NA|pmid-15568970|pmid-16115062|pmid-16407333|NA
Another factor involved in tscA RNA processing and splicing of both introns is Raa1-L137H (9), allelic to HN31 (70).
[ "1", "67", "7", "68", "69", "1", "8", "9", "70" ]
116
875
1
false
Another factor involved in tscA RNA processing and splicing of both introns is Raa1-L137H, allelic to HN31.
[ "9", "70" ]
Another factor involved in tscA RNA processing and splicing of both introns is Raa1-L137H, allelic to HN31.
true
true
true
true
true
150
6
DISCUSSION
1
71
[ "b71", "b72", "b69" ]
17,012,281
pmid-2684776|pmid-8670849|NA
cNAPL binds specifically to domains DII and DVI of the first psaA intron.
[ "71", "72", "69" ]
73
876
0
false
cNAPL binds specifically to domains DII and DVI of the first psaA intron.
[]
cNAPL binds specifically to domains DII and DVI of the first psaA intron.
false
true
true
true
false
151
6
DISCUSSION
1
71
[ "b71", "b72", "b69" ]
17,012,281
pmid-2684776|pmid-8670849|NA
Domain DII is a phylogenetically less-conserved region and was assigned as functionally unimportant because of its high degree of sequence and structure variations (71).
[ "71", "72", "69" ]
169
877
1
false
Domain DII is a phylogenetically less-conserved region and was assigned as functionally unimportant because of its high degree of sequence and structure variations.
[ "71" ]
Domain DII is a phylogenetically less-conserved region and was assigned as functionally unimportant because of its high degree of sequence and structure variations.
true
true
true
true
true
151
6
DISCUSSION
1
72
[ "b71", "b72", "b69" ]
17,012,281
pmid-2684776|pmid-8670849|NA
However, Chanfreau and Jacquier (72) could show that the so-called tertiary η–η′ interaction (see also Figure 2a) between DII and DVI of group IIA introns is responsible for a conformational change between the two catalytic transesterification steps.
[ "71", "72", "69" ]
250
878
1
false
However, Chanfreau and Jacquier could show that the so-called tertiary η–η′ interaction (see also Figure 2a) between DII and DVI of group IIA introns is responsible for a conformational change between the two catalytic transesterification steps.
[ "72" ]
However, Chanfreau and Jacquier could show that the so-called tertiary η–η′ interaction between DII and DVI of group IIA introns is responsible for a conformational change between the two catalytic transesterification steps.
true
true
true
true
true
151
6
DISCUSSION
1
71
[ "b71", "b72", "b69" ]
17,012,281
pmid-2684776|pmid-8670849|NA
Interestingly, only a few of the known group IIB introns can potentially form this interaction.
[ "71", "72", "69" ]
95
879
0
false
Interestingly, only a few of the known group IIB introns can potentially form this interaction.
[]
Interestingly, only a few of the known group IIB introns can potentially form this interaction.
true
true
true
true
true
151
6
DISCUSSION
1
69
[ "b71", "b72", "b69" ]
17,012,281
pmid-2684776|pmid-8670849|NA
It is discussed that the majority of the group IIB introns interact with protein factors to change the conformation between the first and the second step (69).
[ "71", "72", "69" ]
159
880
1
false
It is discussed that the majority of the group IIB introns interact with protein factors to change the conformation between the first and the second step.
[ "69" ]
It is discussed that the majority of the group IIB introns interact with protein factors to change the conformation between the first and the second step.
true
true
true
true
true
151
6
DISCUSSION
1
71
[ "b71", "b72", "b69" ]
17,012,281
pmid-2684776|pmid-8670849|NA
The fact that cNAPL interacts with both domains, DII and DVI, implies a role for cNAPL in this conformational change.
[ "71", "72", "69" ]
117
881
0
false
The fact that cNAPL interacts with both domains, DII and DVI, implies a role for cNAPL in this conformational change.
[]
The fact that cNAPL interacts with both domains, DII and DVI, implies a role for cNAPL in this conformational change.
true
true
true
true
true
151
7
DISCUSSION
1
69
[ "b69" ]
17,012,281
NA
Our experiments further demonstrated the binding of cNAPL to domain DV of the first psaA intron.
[ "69" ]
96
882
0
false
Our experiments further demonstrated the binding of cNAPL to domain DV of the first psaA intron.
[]
Our experiments further demonstrated the binding of cNAPL to domain DV of the first psaA intron.
true
true
true
true
true
152
7
DISCUSSION
1
69
[ "b69" ]
17,012,281
NA
Domain DV is the phylogenetically most conserved sequence and essential for the catalytic splicing reaction.
[ "69" ]
108
883
0
false
Domain DV is the phylogenetically most conserved sequence and essential for the catalytic splicing reaction.
[]
Domain DV is the phylogenetically most conserved sequence and essential for the catalytic splicing reaction.
true
true
true
true
true
152
7
DISCUSSION
1
69
[ "b69" ]
17,012,281
NA
DV shows numerous important tertiary interactions and contains important conserved sequence motifs (69).
[ "69" ]
104
884
1
false
DV shows numerous important tertiary interactions and contains important conserved sequence motifs.
[ "69" ]
DV shows numerous important tertiary interactions and contains important conserved sequence motifs.
true
true
true
true
true
152
7
DISCUSSION
1
69
[ "b69" ]
17,012,281
NA
Overall, we assume that cNAPL presumably has a function in the stabilization and correct folding of the catalytic core of the first psaA intron by interacting with tscA RNA and domains DV and DVI.
[ "69" ]
196
885
0
false
Overall, we assume that cNAPL presumably has a function in the stabilization and correct folding of the catalytic core of the first psaA intron by interacting with tscA RNA and domains DV and DVI.
[]
Overall, we assume that cNAPL presumably has a function in the stabilization and correct folding of the catalytic core of the first psaA intron by interacting with tscA RNA and domains DV and DVI.
true
true
true
true
true
152
8
DISCUSSION
1
73
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
In addition, our analyses showed that the binding of cNAPL to tscA RNA was competed efficiently by poly(U) in contrast to other RNA homopolymers.
[ "73", "74", "75", "76", "77", "78", "11" ]
145
886
0
false
In addition, our analyses showed that the binding of cNAPL to tscA RNA was competed efficiently by poly(U) in contrast to other RNA homopolymers.
[]
In addition, our analyses showed that the binding of cNAPL to tscA RNA was competed efficiently by poly(U) in contrast to other RNA homopolymers.
true
true
true
true
true
153
8
DISCUSSION
1
73
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
Moreover, cNAPL binds the 5′-UTR of U-rich chloroplast transcripts psbA, psbD, rbcL and rps4 considerably better than the nuclear transcripts Lhcb1
[ "73", "74", "75", "76", "77", "78", "11" ]
147
887
0
false
Moreover, cNAPL binds the 5′-UTR of U-rich chloroplast transcripts psbA, psbD, rbcL and rps4 considerably better than the nuclear transcripts Lhcb1
[]
Moreover, cNAPL binds the 5′-UTR of U-rich chloroplast transcripts psbA, psbD, rbcL and rps4 considerably better than the nuclear transcripts Lhcb1
true
true
false
true
false
153
8
DISCUSSION
1
73
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
5′-UTR, Lhcb1 3′-UTR, Rps18 and Tba1A.
[ "73", "74", "75", "76", "77", "78", "11" ]
38
888
0
false
5′-UTR, Lhcb1 3′-UTR, Rps18 and Tba1A.
[]
5′-UTR, Lhcb1 3′-UTR, Rps18 and Tba1A.
false
false
true
true
false
153
8
DISCUSSION
1
73
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
It is proven that the 5′-UTRs of chloroplast transcripts contain the cis-acting determinants for the stabilization of plastid transcripts and are essential for initiation of chloroplast translation by binding trans-acting factors (mostly encoded by nuclear genes) and by interaction with the ribosomal preinitiation complex (73).
[ "73", "74", "75", "76", "77", "78", "11" ]
329
889
1
false
It is proven that the 5′-UTRs of chloroplast transcripts contain the cis-acting determinants for the stabilization of plastid transcripts and are essential for initiation of chloroplast translation by binding trans-acting factors (mostly encoded by nuclear genes) and by interaction with the ribosomal preinitiation complex.
[ "73" ]
It is proven that the 5′-UTRs of chloroplast transcripts contain the cis-acting determinants for the stabilization of plastid transcripts and are essential for initiation of chloroplast translation by binding trans-acting factors (mostly encoded by nuclear genes) and by interaction with the ribosomal preinitiation complex.
true
true
true
true
true
153
8
DISCUSSION
1
74
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
For example, the stability of the psbD mRNA depends on a nucleus-encoded TPR protein, which is part of a high-molecular weight complex mediating its function via the psbD 5′-UTR (74).
[ "73", "74", "75", "76", "77", "78", "11" ]
183
890
1
false
For example, the stability of the psbD mRNA depends on a nucleus-encoded TPR protein, which is part of a high-molecular weight complex mediating its function via the psbD 5′-UTR.
[ "74" ]
For example, the stability of the psbD mRNA depends on a nucleus-encoded TPR protein, which is part of a high-molecular weight complex mediating its function via the psbD 5′-UTR.
true
true
true
true
true
153
8
DISCUSSION
1
75
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
For the psbA mRNA it is assumed that a multiprotein complex specifically regulates translation of this mRNA through interaction with a U-rich sequence in the 5′-UTR (75).
[ "73", "74", "75", "76", "77", "78", "11" ]
170
891
1
false
For the psbA mRNA it is assumed that a multiprotein complex specifically regulates translation of this mRNA through interaction with a U-rich sequence in the 5′-UTR.
[ "75" ]
For the psbA mRNA it is assumed that a multiprotein complex specifically regulates translation of this mRNA through interaction with a U-rich sequence in the 5′-UTR.
true
true
true
true
true
153
8
DISCUSSION
1
73
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
Furthermore, there are several proteins in Chlamydomonas binding to 5′-UTRs of chloroplast mRNAs, e.g.
[ "73", "74", "75", "76", "77", "78", "11" ]
102
892
0
false
Furthermore, there are several proteins in Chlamydomonas binding to 5′-UTRs of chloroplast mRNAs, e.g.
[]
Furthermore, there are several proteins in Chlamydomonas binding to 5′-UTRs of chloroplast mRNAs, e.g.
true
true
true
true
true
153
8
DISCUSSION
1
73
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
to 5′-UTRs of atpB, rbcL, rps7 and rps12, that so far have not been characterized and are discussed to be required for translational regulation (76,77).
[ "73", "74", "75", "76", "77", "78", "11" ]
152
893
0
false
to 5′-UTRs of atpB, rbcL, rps7 and rps12, that so far have not been characterized and are discussed to be required for translational regulation.
[ "76,77" ]
to 5′-UTRs of atpB, rbcL, rps7 and rps12, that so far have not been characterized and are discussed to be required for translational regulation.
false
true
true
true
false
153
8
DISCUSSION
1
73
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
However, the cpRNP complexes seem to be not only involved in regulation of translation, but also in distinct steps of post-transcriptional gene expression, e.g.
[ "73", "74", "75", "76", "77", "78", "11" ]
160
894
0
false
However, the cpRNP complexes seem to be not only involved in regulation of translation, but also in distinct steps of post-transcriptional gene expression, e.g.
[]
However, the cpRNP complexes seem to be not only involved in regulation of translation, but also in distinct steps of post-transcriptional gene expression, e.g.
true
true
true
true
true
153
8
DISCUSSION
1
78
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
by facilitating proper RNA folding for intron-containing RNA (78).
[ "73", "74", "75", "76", "77", "78", "11" ]
66
895
1
false
by facilitating proper RNA folding for intron-containing RNA.
[ "78" ]
by facilitating proper RNA folding for intron-containing RNA.
false
true
true
true
false
153
8
DISCUSSION
1
11
[ "b73", "b74", "b75", "b76", "b77", "b78", "b11" ]
17,012,281
NA|pmid-10880449|pmid-15222765|pmid-11158540|pmid-8576143|NA|pmid-15037779
Recently it was demonstrated that there are two RNP complexes in C.reinhardtii that are involved in trans-splicing of psaA, one in the soluble fraction of the chloroplast and the other one associated with chloroplast membranes, which could provide a link to translation (11).
[ "73", "74", "75", "76", "77", "78", "11" ]
275
896
1
false
Recently it was demonstrated that there are two RNP complexes in C.reinhardtii that are involved in trans-splicing of psaA, one in the soluble fraction of the chloroplast and the other one associated with chloroplast membranes, which could provide a link to translation.
[ "11" ]
Recently it was demonstrated that there are two RNP complexes in C.reinhardtii that are involved in trans-splicing of psaA, one in the soluble fraction of the chloroplast and the other one associated with chloroplast membranes, which could provide a link to translation.
true
true
true
true
true
153
9
DISCUSSION
1
78
[ "b78" ]
17,012,281
NA
In conclusion, we have isolated a novel type of group II intron RNA-binding protein using the yeast three-hybrid system.
[ "78" ]
120
897
0
false
In conclusion, we have isolated a novel type of group II intron RNA-binding protein using the yeast three-hybrid system.
[]
In conclusion, we have isolated a novel type of group II intron RNA-binding protein using the yeast three-hybrid system.
true
true
true
true
true
154
9
DISCUSSION
1
78
[ "b78" ]
17,012,281
NA
Phylogenetic analysis indicates that the chloroplast located cNAPL protein is encoded by a nuclear gene that probably has evolved from duplication of an ancestral Nap gene.
[ "78" ]
172
898
0
false
Phylogenetic analysis indicates that the chloroplast located cNAPL protein is encoded by a nuclear gene that probably has evolved from duplication of an ancestral Nap gene.
[]
Phylogenetic analysis indicates that the chloroplast located cNAPL protein is encoded by a nuclear gene that probably has evolved from duplication of an ancestral Nap gene.
true
true
true
true
true
154
9
DISCUSSION
1
78
[ "b78" ]
17,012,281
NA
Moreover, it is proposed that cpRNP complexes are global mediators of chloroplast RNA metabolism, which connect transcription and translation in the chloroplast (78).
[ "78" ]
166
899
1
false
Moreover, it is proposed that cpRNP complexes are global mediators of chloroplast RNA metabolism, which connect transcription and translation in the chloroplast.
[ "78" ]
Moreover, it is proposed that cpRNP complexes are global mediators of chloroplast RNA metabolism, which connect transcription and translation in the chloroplast.
true
true
true
true
true
154