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1 iants, suggesting the causal variant was non-exonic.
2 Many of these mutations were cryptic, either exonic alterations of splice enhancers or silencers or d
7 timated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of
11 ites, are distributed evenly across distinct exonic and intronic regions, and are difficult to predic
13 g splicing minigenes, we identified multiple exonic and intronic splicing enhancers and silencers tha
14 cation of intronic sequence, loss or gain of exonic and intronic splicing enhancers and silencers, co
15 trates that mCpG provides a stable record of exonic and intronic usage, whereas H3K36me3 is dynamic.
16 l evidence and filters were applied to multi-exonic and mono-exonic putative genes to yield between 2
19 biochemical phenotype, 2 variants in GC--one exonic and one intronic--were associated with serum DBP
22 plification and bi-directional sequencing of exonic and promoter regions and performed acetylcholine
24 As (lincRNAs), intronic overlapping lncRNAs, exonic antisense overlapping lncRNAs, and precursors for
27 r characterize the nature of constrained non-exonic bases with low CNEP scores using additional types
30 .5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic an
32 led to two surprising discoveries: (i) many exonic circRNA (EcircRNA) isoforms share an identical ba
38 provided an effective means to assess small exonic CNV from whole-exome data, indicated that rare 1-
39 uch data could be used to reliably call rare exonic CNV in the size range of 1-30 kilobases (kb), mak
40 s (total of 55 genes) were enriched for rare exonic CNVs among BD cases, but none of these survives c
44 ey anomaly (KA) cases were most enriched for exonic CNVs, encompassing GD-CNVs and novel deletions; o
47 patterns of genetic diversity are caused by exonic coconversion, which occurs when introns spread to
49 oding exons as part of an artificial intron (exonic COINs), greatly simplifying allele design and inc
50 detection of single nucleotide variants and exonic copy number variants in one comprehensive assessm
51 included both single nucleotide variants and exonic copy number variants, such as hemizygous nonsense
52 lity, have 17% lower SSM density compared to exonic cores, even after excluding canonical splice site
53 nical care included high-depth (median 600x) exonic coverage of 410 cancer genes and whole-genome cop
54 t DNA methylation occurred preferentially in exonic CpGs of highly and stably expressed genes involve
55 variants, the method identified 32 potential exonic cryptic splice variants, two of which were experi
56 ative analysis of variant calling methods on exonic data from 202 genes sequenced at 24x in 7,842 ind
60 d that the AMELX missense mutation increased exonic definition of exon 4 and the MMP20 synonymous mut
61 ce A (P = 3.31 x 10(-12)), with a particular exonic deletion (P = 1.59 x 10(-8)) in full linkage dise
64 hift deletions and insertions in WFS1 and an exonic deletion in CISD2 which all altered the respectiv
66 uded a common and sometimes homozygous 61 bp exonic deletion in SLC38A10, three CNVs found in lymphob
68 ea, we discovered a missense mutation and an exonic deletion in the SLC25A46 gene encoding a mitochon
69 and, most importantly, in a male proband, an exonic deletion of the TMLHE (trimethyllysine hydroxylas
70 and specificity >99% in covered regions) and exonic deletions (100% sensitivity and specificity).
71 find among 22,288 individuals that these HP exonic deletions associate with reduced LDL and total ch
72 hole-exome data, indicated that rare 1-30 kb exonic deletions could contribute to risk in up to 7% of
76 e novo CNVs, including single-exon and intra-exonic deletions, as well as interchromosomal duplicatio
78 es as often as common variants, and missense exonic disease mutations that have the least impact on p
83 which somatic events other than mutations in exonic DNA shape its genetic landscape and define its me
85 ting non-exonic variants, we focused on 3334 exonic DNMs for evaluation of their association with the
90 e being in an evolutionarily constrained non-exonic element from an input of over 60,000 epigenomic a
91 assays, we demonstrate that several of these exonic enhancer (eExons) candidates can function as enha
93 is, we compare human-mouse and human-macaque exonic evolutionary rates against experimentally determi
94 Furthermore, our analysis of genes with high exonic expression in brain and low burden of rare mutati
95 hylation level is negatively correlated with exonic expression level, but positively correlated with
96 LASS combines mixture statistical models for exonic feature selection across multiple samples with sp
101 of expression; we also isolated a conserved exonic hox2 enhancer from lamprey that drives segmental
102 restingly, both activities of Tra2 favor the exonic identity of the RNA sequences that encompass its
106 ethylation signals associated with upstream, exonic, intronic and downstream genomic loci from A. mel
109 erefore screened patients without identified exonic lesions for mutations within conserved noncoding
110 DNA FISH, we further show that one of these exonic limb enhancers, Dync1i1 exon 15, has active enhan
114 ce, and large set of SNPs including putative exonic markers associated with rubber related gene homol
115 vival, we analyzed survival effects of tumor exonic missense mutation burden (TEMMB) across 6947 spec
116 hout RTEL1 variants, and the presence of any exonic missense RTEL1 variant was associated with a 42%
117 t liver transplantation, the presence of any exonic missense variant was associated with a longer pos
121 ed in 114 STGD patients with one known ABCA4 exonic mutation revealing, on average, 200 intronic vari
122 er with an intronic MAPT mutation or with an exonic mutation, developed accumulation and extracellula
125 Here, we sought to determine whether LEKTI exonic mutations associated with atopic dermatitis (AD)
128 tenin/LEF-1-mediated transcription, displays exonic mutations in human prostate cancer and promotes c
130 Timothy Syndrome (TS) is caused by very rare exonic mutations of the CACNA1C gene that produce delaye
133 We analyzed 4,964 published disease-causing exonic mutations using a massively parallel splicing ass
134 plex genomic alterations, with a mean of 360 exonic mutations, 165 genomic rearrangements, and 323 se
135 ) data, which are typically used for calling exonic mutations, have also been utilized in detecting D
136 nd in the gene sequence, including two novel exonic mutations: R251L and R396W, leading to substituti
137 equencing, we systematically annotated multi-exonic non-coding RNA (mencRNA) genes transcribed from 1
138 e-associated haploblocks express novel multi-exonic non-coding transcripts that are tissue-specific a
139 h case was characterized by a median of 24.5 exonic nonsynonymous single-nucleotide variations, and t
141 urred in compound heterozygous state with an exonic OPA1 missense variant (p.I382M; NM_015560.2).
142 ur in splice sites near intron borders or in exonic or intronic RNA regulatory silencer or enhancer e
143 LA without signs of PRA did not identify any exonic or splice site variants, suggesting the causal va
144 tions in yet unknown Usher genes or in extra-exonic parts of the known genes - to date a largely unex
145 nd an increase in affected subjects carrying exonic pathogenic CNVs overlapping known loci associated
146 s (SF2 and Rbp1) that activate splicing from exonic positions were tethered intronically they failed
148 ilters were applied to multi-exonic and mono-exonic putative genes to yield between 27 000 and 44 000
149 at the overwhelming majority of intronic and exonic RE are expressed in the same orientation as the g
151 C repeat expansion from five to seven in the exonic region of the gene for cartilage oligomeric matri
152 70 bp poly-A and an 11 bp duplication of the exonic region preceding the poly-A (XM_548088.6:c.2110_2
153 nymous or stop codon gained) were located in exonic regions (13.04 %) and 294 placed in intronic regi
155 ted sequencing of genomic DNA amplified from exonic regions and associated splice intron site junctio
157 WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with va
158 hat increasing the coverage more than 10x in exonic regions does not improve the detection power of t
161 indel discovery and characterization in the exonic regions of the example sequencing data can be com
166 ovel somatic retrotransposon insertions into exonic regions, including an insertion into an exon of t
167 given the high number of SNPs identified in exonic regions, this strategy represents an important to
173 ariant detection did not report 94.2% of the exonic repeat length variations in part because the alig
175 ynonymous variants (NSVs) identified by deep exonic resequencing of 10 genes found by GWAS (IL10, IL2
176 ween a approximately 25-kDa protein and this exonic residue of pre-mRNAs in the arrested bud31 null s
177 repression accompanied by the assembly of an exonic ribonucleoprotein complex with a tightly bound U1
180 ster, evidence for association was found for exonic RVs (p = 0.02 in families, p = 0.28 in NOMAS), wh
183 erparts, suggesting that base-pairing in the exonic segments upstream of retained introns could be a
187 cers of their neighboring genes and that the exonic sequence is necessary for enhancer activity.
188 anscript involved a lineage-specific gain of exonic sequence with no homology to protein coding seque
189 rcular RNA molecules that typically comprise exonic sequences and are spliced at canonical splice sit
195 ' splice site-bound U1 snRNA and neighboring exonic sequences that, in turn, inhibit stable associati
196 e sets, significantly more acquired and lost exonic sequences were detected in wheat than in model gr
203 eted Sequencing Study, we performed targeted exonic sequencing of SCN5A (n=3699, European ancestry in
205 ia to investigate the relationship of 11 630 exonic single-nucleotide polymorphisms (SNPs) and 43 cop
207 sm risk, we generated a comprehensive set of exonic single-nucleotide variants (SNVs) and copy number
208 Seq run, we identified multiple intronic and exonic single-nucleotide variations (SNVs), including on
210 e individuals and uncovered more than 10,000 exonic sites where the RNA sequences do not match that o
211 nizes a GGA-centered motif enriched in RBM10 exonic sites with high affinity and specificity and test
213 hree single nucleotide polymorphisms (SNPs), exonic SNP rs12422149 and intronic SNPs rs1789693 and rs
216 ering and principal component analyses using exonic SNPs consistently revealed two genetic clusters,
217 work highlights the importance of functional exonic SNPs for studying population genetic pattern in a
227 Analysis of exon 12 sequences identified an exonic splice enhancer that binds serine arginine splici
228 nsistent with a role in splicing modulation, exonic splice enhancers have a lower SSM density before
232 in a previously identified set of hexameric exonic splicing enhancer (ESE) sequences compared to the
233 o the LINE1 insertion the inactivation of an exonic splicing enhancer (ESE) within exon 6 is required
235 sequence of CA(G/C/A)CC(C/A) as a potential exonic splicing enhancer for these SRSF3-regulated exons
236 thereby altering the recognition of specific exonic splicing enhancer motifs to drive recurrent mis-s
237 e sequencing led to the identification of an exonic splicing enhancer mutation in exon 7 of CIZ1 (c.7
238 g of the central RNA recognition motif to an exonic splicing enhancer sequence, a phenomenon reversed
239 ysis revealed that Ins44 disrupts a putative exonic splicing enhancer that allows for skipping of exo
240 targeted to the cryptic branch point and an exonic splicing enhancer, U7.BP + 623, was the most effe
243 ne of these SNPs, rs10185378, is a predicted exonic splicing enhancer; significant alteration in the
246 differences in U1 binding or the density of exonic splicing enhancers but may be partially attribute
248 tural features that regulate the exposure of exonic splicing motifs across the transcriptome is not c
250 We present a large-scale characterization of exonic splicing mutations using a new technology that fa
251 ar-splice site synonymous mutations changing exonic splicing regulators and those within frontal cort
252 termine rates of loss or gain of known human exonic splicing regulatory (ESR) sequences associated wi
253 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
256 repetitive GAA motif was identified to be an exonic splicing silencer that controls red light-respons
257 -F1 regulate alternative splicing through an exonic splicing silencer to control splicing machinery a
258 e; however, a C-->T substitution converts an exonic-splicing enhancer (ESE) to a silencer (ESS), caus
259 These results suggest that disruption of exonic stem-loop structures immediately upstream (but no
260 ance in Man (OMIM) genes of up to 0.86 using exonic sub-regions and 0.91 using sub-regions defined by
261 ned with our previous method that identifies exonic tags for GMAS, this study yielded 622 GMAS exons.
262 viduals carried a significant burden of rare exonic (that is, affecting coding regions) CNVs and were
263 ying two alternative promoters, one intronic/exonic, to generate two sequence-overlapping but functio
265 q on 21 human tissues to identify 1775 multi-exonic transcripts from 561 intronic and intergenic hapl
267 hat completely matched both the intronic and exonic U1 binding sequences of the mutated DDC gene coul
268 changed the relative proportions of intronic/exonic/untranslated RNA captured by RNA-seq for most gen
270 aneurysms (IAs) in Nunavik Inuit revealed an exonic variant under weak negative selection to be signi
272 V6 in 4405 childhood ALL cases identified 31 exonic variants (four non-sense, 21 missense, one splice
275 pands the diagnostic tools for detecting non-exonic variants and provides examples of intronic loss-o
276 Our analysis focused on putative functional exonic variants assayed on the Illumina HumanExome BeadC
277 CDI and AAD subjects were determined by MBL2 exonic variants B, C, and D and the haplotypes (LYPB, LY
279 identified and tested 111,592 nonsynonymous exonic variants for association with behavioral disinhib
281 gh-coverage exome-sequencing, we studied the exonic variants in 1265 individuals from the Rotterdam s
282 esting, we strengthen the evidence that rare exonic variants in the ARC (p = 4.0 x 10(-4)) and NMDAR
284 structure to explore whether relatively rare exonic variants influence the burden of depressive sympt
287 Analysis of more than 650,000 intronic and exonic variants revealed widespread patterns of mutation
288 an unbiased genome-wide approach to identify exonic variants segregating with diabetes in a multigene
290 fied from RNA-seq, and comparable numbers of exonic variants were identified in RNA-seq and WES.
293 mes Project database of 1092 individuals for exonic variants within 3 sarcomere genes MHY7, MYBPC3, a
294 n P=.043, and Asian P=.027), suggesting that exonic variants within this gene modify AD susceptibilit
297 he allosteric-like/far-reaching effect of an exonic variation on pre-mRNA splicing that is mediated b
298 -wide screens for CNVs, common variation and exonic variation--are converging on similar sets of path
300 ine/arginine rich (SR) proteins tended to be exonic whereas heterogeneous ribonucleoprotein (hnRNP) r