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2 tion (p = 0.024; pleiotropic SNPs more often exonic [14.5% versus 4.9% for nonpleiotropic, trait-asso
7 timated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of
11 plicing-driven selective pressure constrains exonic and intronic sequences, especially those distant
13 g splicing minigenes, we identified multiple exonic and intronic splicing enhancers and silencers tha
14 trates that mCpG provides a stable record of exonic and intronic usage, whereas H3K36me3 is dynamic.
15 inical and molecular genetic data, including exonic and near intron/exon boundaries of DCM genes, wer
17 biochemical phenotype, 2 variants in GC--one exonic and one intronic--were associated with serum DBP
18 plification and bi-directional sequencing of exonic and promoter regions and performed acetylcholine
21 As (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for
24 .5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic an
26 hat approximately 60% of target bases in the exonic 'catch', and approximately 80% in the regional ca
27 led to two surprising discoveries: (i) many exonic circRNA (EcircRNA) isoforms share an identical ba
30 provided an effective means to assess small exonic CNV from whole-exome data, indicated that rare 1-
31 uch data could be used to reliably call rare exonic CNV in the size range of 1-30 kilobases (kb), mak
32 s (total of 55 genes) were enriched for rare exonic CNVs among BD cases, but none of these survives c
36 patterns of genetic diversity are caused by exonic coconversion, which occurs when introns spread to
38 oding exons as part of an artificial intron (exonic COINs), greatly simplifying allele design and inc
40 detection of single nucleotide variants and exonic copy number variants in one comprehensive assessm
41 included both single nucleotide variants and exonic copy number variants, such as hemizygous nonsense
42 ty, have 17% lower SSM density compared to exonic cores, even after excluding canonical splice site
43 nical care included high-depth (median 600x) exonic coverage of 410 cancer genes and whole-genome cop
44 t DNA methylation occurred preferentially in exonic CpGs of highly and stably expressed genes involve
45 variants, the method identified 32 potential exonic cryptic splice variants, two of which were experi
46 ative analysis of variant calling methods on exonic data from 202 genes sequenced at 24x in 7,842 ind
48 ce A (P = 3.31 x 10(-12)), with a particular exonic deletion (P = 1.59 x 10(-8)) in full linkage dise
51 uded a common and sometimes homozygous 61 bp exonic deletion in SLC38A10, three CNVs found in lymphob
53 ea, we discovered a missense mutation and an exonic deletion in the SLC25A46 gene encoding a mitochon
54 and, most importantly, in a male proband, an exonic deletion of the TMLHE (trimethyllysine hydroxylas
55 and specificity >99% in covered regions) and exonic deletions (100% sensitivity and specificity).
56 find among 22,288 individuals that these HP exonic deletions associate with reduced LDL and total ch
57 hole-exome data, indicated that rare 1-30 kb exonic deletions could contribute to risk in up to 7% of
61 e novo CNVs, including single-exon and intra-exonic deletions, as well as interchromosomal duplicatio
65 es as often as common variants, and missense exonic disease mutations that have the least impact on p
68 which somatic events other than mutations in exonic DNA shape its genetic landscape and define its me
71 ting non-exonic variants, we focused on 3334 exonic DNMs for evaluation of their association with the
73 a mild-moderate mental retardation syndrome, exonic duplications in the gene for vasoactive intestina
77 ss activation in which binding of RBM25 with exonic element CGGGCA may stabilize the pre-mRNA-U1 snRN
78 assays, we demonstrate that several of these exonic enhancer (eExons) candidates can function as enha
79 entified binding of SRp20 and SF2/ASF to the exonic enhancers and CUG-BP1 to the exonic silencer by R
81 is, we compare human-mouse and human-macaque exonic evolutionary rates against experimentally determi
82 Furthermore, our analysis of genes with high exonic expression in brain and low burden of rare mutati
83 hylation level is negatively correlated with exonic expression level, but positively correlated with
88 of expression; we also isolated a conserved exonic hox2 enhancer from lamprey that drives segmental
89 restingly, both activities of Tra2 favor the exonic identity of the RNA sequences that encompass its
94 ethylation signals associated with upstream, exonic, intronic and downstream genomic loci from A. mel
96 e genomes and each of the component classes (exonic, intronic, and nongenic regions) have similar top
98 erefore screened patients without identified exonic lesions for mutations within conserved noncoding
99 DNA FISH, we further show that one of these exonic limb enhancers, Dync1i1 exon 15, has active enhan
104 ce, and large set of SNPs including putative exonic markers associated with rubber related gene homol
107 ed in 114 STGD patients with one known ABCA4 exonic mutation revealing, on average, 200 intronic vari
108 er with an intronic MAPT mutation or with an exonic mutation, developed accumulation and extracellula
112 tenin/LEF-1-mediated transcription, displays exonic mutations in human prostate cancer and promotes c
114 Timothy Syndrome (TS) is caused by very rare exonic mutations of the CACNA1C gene that produce delaye
115 We analyzed 4,964 published disease-causing exonic mutations using a massively parallel splicing ass
116 plex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 se
117 ) data, which are typically used for calling exonic mutations, have also been utilized in detecting D
118 nd in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substituti
119 s were obtained with a target containing the exonic N279K mutation which strengthens a splicing enhan
120 e-associated haploblocks express novel multi-exonic non-coding transcripts that are tissue-specific a
121 h case was characterized by a median of 24.5 exonic nonsynonymous single-nucleotide variations, and t
123 urred in compound heterozygous state with an exonic OPA1 missense variant (p.I382M; NM_015560.2).
124 ur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer e
125 tions in yet unknown Usher genes or in extra-exonic parts of the known genes - to date a largely unex
126 nd an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated
130 s (SF2 and Rbp1) that activate splicing from exonic positions were tethered intronically they failed
132 at the overwhelming majority of intronic and exonic RE are expressed in the same orientation as the g
133 ive CTCF binding sites in the hTERT proximal exonic region (PER) and determine their functional relev
135 C repeat expansion from five to seven in the exonic region of the gene for cartilage oligomeric matri
136 nymous or stop codon gained) were located in exonic regions (13.04 %) and 294 placed in intronic regi
138 ted sequencing of genomic DNA amplified from exonic regions and associated splice intron site junctio
140 hat increasing the coverage more than 10x in exonic regions does not improve the detection power of t
142 indel discovery and characterization in the exonic regions of the example sequencing data can be com
147 ovel somatic retrotransposon insertions into exonic regions, including an insertion into an exon of t
148 with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can for
154 tivated cryptic 5' or 3' splice sites within exonic regions; the third mutation activated a downstrea
155 ariant detection did not report 94.2% of the exonic repeat length variations in part because the alig
156 ynonymous variants (NSVs) identified by deep exonic resequencing of 10 genes found by GWAS (IL10, IL2
157 ed the entire coding region of JAK1 by total exonic resequencing of bone marrow DNA samples from 94 p
158 ween a approximately 25-kDa protein and this exonic residue of pre-mRNAs in the arrested bud31 null s
159 repression accompanied by the assembly of an exonic ribonucleoprotein complex with a tightly bound U1
166 cers of their neighboring genes and that the exonic sequence is necessary for enhancer activity.
167 anscript involved a lineage-specific gain of exonic sequence with no homology to protein coding seque
168 rcular RNA molecules that typically comprise exonic sequences and are spliced at canonical splice sit
169 g purifying selection in their genomic loci, exonic sequences and promoter regions, with greater than
170 benchmark, we show that it produces shuffled exonic sequences having folding free energy closer to na
176 ' splice site-bound U1 snRNA and neighboring exonic sequences that, in turn, inhibit stable associati
178 e sets, significantly more acquired and lost exonic sequences were detected in wheat than in model gr
185 eted Sequencing Study, we performed targeted exonic sequencing of SCN5A (n=3699, European ancestry in
187 ng these single nucleotide polymorphisms and exonic single nucleotide polymorphisms rs6517137 and rs1
189 ia to investigate the relationship of 11 630 exonic single-nucleotide polymorphisms (SNPs) and 43 cop
191 sm risk, we generated a comprehensive set of exonic single-nucleotide variants (SNVs) and copy number
192 Seq run, we identified multiple intronic and exonic single-nucleotide variations (SNVs), including on
195 e individuals and uncovered more than 10,000 exonic sites where the RNA sequences do not match that o
196 nizes a GGA-centered motif enriched in RBM10 exonic sites with high affinity and specificity and test
198 hree single nucleotide polymorphisms (SNPs), exonic SNP rs12422149 and intronic SNPs rs1789693 and rs
201 ering and principal component analyses using exonic SNPs consistently revealed two genetic clusters,
202 work highlights the importance of functional exonic SNPs for studying population genetic pattern in a
203 e for allelic imbalance at multiple reporter exonic SNPs in CD6 for two samples heterozygous at the m
213 Analysis of exon 12 sequences identified an exonic splice enhancer that binds serine arginine splici
214 nsistent with a role in splicing modulation, exonic splice enhancers have a lower SSM density before
215 ort hairpin RNA (shRNA) complementary to the exonic splicing chaperone SRp40 expressed 30% less SRp40
217 Finally, we report the presence of a novel exonic splicing enhancer (ESE) element within the 5'-pro
220 n in the Adam17 gene that ablates a putative exonic splicing enhancer (ESE) sequence in exon 7 result
221 o the LINE1 insertion the inactivation of an exonic splicing enhancer (ESE) within exon 6 is required
224 ied a splicing regulatory element in exon 3 (exonic splicing enhancer 2 (ESE2)), but we had not deter
225 g mutations within exon 11, we detected both exonic splicing enhancer and exonic splicing silencer el
226 We now show that the change creates a new exonic splicing enhancer element and increases the amoun
227 mical approaches underscore the relevance of exonic splicing enhancer loss and silencer gain in inher
228 cleotide change), which lies in a suggestive exonic splicing enhancer motif in exon 1, was common onl
229 thereby altering the recognition of specific exonic splicing enhancer motifs to drive recurrent mis-s
230 e sequencing led to the identification of an exonic splicing enhancer mutation in exon 7 of CIZ1 (c.7
231 g of the central RNA recognition motif to an exonic splicing enhancer sequence, a phenomenon reversed
232 ysis revealed that Ins44 disrupts a putative exonic splicing enhancer that allows for skipping of exo
233 of a serine/arginine-rich (SR) protein to an exonic splicing enhancer, thereby inhibiting splicing at
234 at an exonic GGG motif overlapped a critical exonic splicing enhancer, which was predicted to bind th
235 ne of these SNPs, rs10185378, is a predicted exonic splicing enhancer; significant alteration in the
236 ole of auxiliary cis-acting elements such as exonic splicing enhancers (ESE) and exonic splicing sile
237 rom constitutive SREs, since only 18% of our exonic splicing enhancers (ESEs) are contained in consti
238 promote spliceosome formation by recognizing exonic splicing enhancers (ESEs) during pre-mRNA splicin
239 d repressors mapped four physically distinct exonic splicing enhancers (ESEs) within HIPK3-T, each co
242 RNA is defined by three GAA motif-containing exonic splicing enhancers and a G/GU-rich intronic splic
243 tutions in constitutive exons tend to create exonic splicing enhancers and to disrupt exonic splicing
244 differences in U1 binding or the density of exonic splicing enhancers but may be partially attribute
245 sting that engagement of the SR protein with exonic splicing enhancers can regulate phosphoryl conten
247 onymous substitutions that disrupt predicted exonic splicing enhancers or create predicted exonic spl
249 We present a large-scale characterization of exonic splicing mutations using a new technology that fa
250 ar-splice site synonymous mutations changing exonic splicing regulators and those within frontal cort
251 termine rates of loss or gain of known human exonic splicing regulatory (ESR) sequences associated wi
252 in somatic tissues due to the function of an exonic splicing silencer (ESS) complex present on the 5'
255 ntronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splici
258 such as exonic splicing enhancers (ESE) and exonic splicing silencers (ESS) in human inherited disea
259 Es include exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enha
260 ate exonic splicing enhancers and to disrupt exonic splicing silencers, implying positive selection f
262 e; however, a C-->T substitution converts an exonic-splicing enhancer (ESE) to a silencer (ESS), caus
263 ) exon as being uniquely densely packed with exonic-splicing enhancers (ESEs), rendering this exon hy
264 ned with our previous method that identifies exonic tags for GMAS, this study yielded 622 GMAS exons.
265 ying two alternative promoters, one intronic/exonic, to generate two sequence-overlapping but functio
267 q on 21 human tissues to identify 1775 multi-exonic transcripts from 561 intronic and intergenic hapl
268 hat completely matched both the intronic and exonic U1 binding sequences of the mutated DDC gene coul
272 V6 in 4405 childhood ALL cases identified 31 exonic variants (four non-sense, 21 missense, one splice
273 pands the diagnostic tools for detecting non-exonic variants and provides examples of intronic loss-o
274 Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadC
275 CDI and AAD subjects were determined by MBL2 exonic variants B, C, and D and the haplotypes (LYPB, LY
277 identified and tested 111,592 nonsynonymous exonic variants for association with behavioral disinhib
279 gh-coverage exome-sequencing, we studied the exonic variants in 1265 individuals from the Rotterdam s
280 We therefore assessed the frequency of LRRK2 exonic variants in individuals with and without PD, to i
282 structure to explore whether relatively rare exonic variants influence the burden of depressive sympt
286 Analysis of more than 650,000 intronic and exonic variants revealed widespread patterns of mutation
287 an unbiased genome-wide approach to identify exonic variants segregating with diabetes in a multigene
289 fied from RNA-seq, and comparable numbers of exonic variants were identified in RNA-seq and WES.
292 mes Project database of 1092 individuals for exonic variants within 3 sarcomere genes MHY7, MYBPC3, a
293 n P=.043, and Asian P=.027), suggesting that exonic variants within this gene modify AD susceptibilit
296 he allosteric-like/far-reaching effect of an exonic variation on pre-mRNA splicing that is mediated b
297 -wide screens for CNVs, common variation and exonic variation--are converging on similar sets of path
299 nce motifs and have distinct preferences for exonic versus intronic or coding versus untranslated tra
300 ine/arginine rich (SR) proteins tended to be exonic whereas heterogeneous ribonucleoprotein (hnRNP) r
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