ライフサイエンスコーパス: splice junction

1 a 5'-OH on the -N(3')pp(5')G end to form the splice junction.

2 generation of a 3',5'-phosphodiester at the splice junction.

3 is then linked to the 5'-OH end to form the splice junction.

4 forming a (thio)ester bond at the N-terminal splice junction.

5 ning a 2'-PO(4), 3'-5' phosphodiester at the splice junction.

6 aining a 2'-PO4, 3'-5' phosphodiester at the splice junction.

7 e extein position adjacent to the N-terminal splice junction.

8 due to a G.U pair that forms at the intron's splice junction.

9 rm the initial (thio)ester at the N-terminal splice junction.

10 on DNA3'pp5'G to form a 3'-5' phosphodiester splice junction.

11 seq dataset, and rescues 39% of noncanonical splice junctions.

12 report mRNA fragments containing one or few splice junctions.

13 ng more than 5 bases across the 8b/7 or 8b/5 splice junctions.

14 high accuracy and efficiency while detecting splice junctions.

15 al splice sites, we also identified 35 novel splice junctions.

16 ns containing CAG trinucleotides at their 3' splice junctions.

17 orithm for the alignment of RNA-seq reads to splice junctions.

18 s with typical GT/AG boundaries defining the splice junctions.

19 hose that fail to share promoters, exons and splice junctions.

20 from the expressions of individual exons and splice junctions.

21 th random sequences in the exon bases at the splice junctions.

22 Drosophila melanogaster and across predicted splice junctions.

23 oducts were cloned and sequenced to identify splice junctions.

24 cript-confirmed alternative and constitutive splice junctions.

25 hat does not rely on unmapped reads or known splice junctions.

26 he formation of a stable EJC-mRNA complex at splice junctions.

27 8, 21, and 22) with preservation of ORFs and splice junctions.

28 ntron boundaries possess the consensus GT/AG splice junctions.

29 ound as far as 200 nucleotides away from the splice junctions.

30 , which in many studies does not include all splice junctions.

31 hat mammalian Ire1 can precisely cleave both splice junctions.

32 s, and can be searched for patterns near the splice junctions.

33 s revealed no mutations in coding regions or splice junctions.

34 y conserved AG sequence normally found at 3' splice junctions.

35 1.7-fold deeper median read depth over those splice junctions.

36 ifferential usage of both exonic regions and splice junctions.

37 r impedes expression quantification of novel splice junctions.

38 fect of variants both proximal and distal to splice junctions.

39 site dinucleotide motifs to map reads across splice junctions.

40 ation and a reduced false discovery rate for splice junctions.

41 cleotides located in the regions adjacent to splice-junctions.

42 kdown of the scissile bond at the N-terminal splicing junction.

43 A zinc atom was discovered at the C-terminal splicing junction.

44 we called 40 gene fusions among over 120,000 splicing junctions.

45 T-qPCR using divergent primers spanning back-splicing junctions.

46 s, and 2'-phosphotransferase to transfer the splice junction 2'-phosphate from ligated tRNA to NAD, p

47 variants at any site in the coding sequence, splice junctions, 5' untranslated region, or 3' untransl

48 species, owing to their low sensitivity and splice junction accuracy.

49 junction complex (EJC) that is assembled at splice junctions after splicing is completed.

50 f 61% of alternative and 74% of constitutive splice junctions, albeit with broad confidence intervals

51 viduals, we identified 506 personal specific splice junctions, among which 437 were novel splice junc

52 new variants, one of which is within a donor splice junction and cosegregates with affected members.

53 l per million mapped reads, for quantitating splice junction and gene expression.

54 rosourea changed a conserved nucleotide at a splice junction and severely reduced splicing of sox9a t

55 e reveals how Tpt1 recognizes a 2'-PO(4) RNA splice junction and the mechanism of RNA phospho-ADP-rib

56 but highly variable efficiency and cost for splice junction and variant detection between all platfo

57 In addition, we found 7881 novel splice junctions and 2301 differentially used alternativ

58 All intron/exon splice junctions and all intron sizes are conserved with

59 tic splice acceptors adjacent to the natural splice junctions and apparently interfere with exon reco

60 tion method assigns likelihood values to all splice junctions and assigns the most probable alignment

61 hat splice with high efficiency at different splice junctions and at higher temperatures.

62 ing RNA-Seq data to a genome relies on known splice junctions and cannot identify novel ones.

63 e STR database demonstrated repeats spanning splice junctions and identified SNPs within repeat eleme

64 across samples analyzed; and (iii) exon-exon splice junctions and indels (features) in columnar forma

65 Splice junctions and mapped reads were also found from i

66 We analyzed the structure of 5'-splice junctions and observed commonalities between spec

67 e targeted hundreds to thousands of pre-mRNA splice junctions and obtained high-precision detection o

68 d human variant in all known exons, introns, splice junctions and promoter regions.

69 ribonuclease Ire1p cleaves HAC1 mRNA at both splice junctions and tRNA ligase joins the two exons tog

70 ons to WormBase annotations and identify new spliced junctions and genes not part of any WormBase ann

71 ript assembly is to accurately determine the splicing junctions and boundaries of the expressed trans

72 ation peaks in coding and noncoding regions, splicing junctions and splicing regulatory sequences.

73 sis by binding the introns flanking the back-splicing junctions and that this control can be reproduc

74 s, 9 were found in an intron (none involving splice junctions), and 6 were found in an exon (Gly39Glu

75 ge counts (for genes, exons, and known/novel splice-junctions), and browser tracks.

76 oups, a G.U pair that occurs at the intron's splice junction, and a G.A pair.

77 nformation about intron and exon structures, splice junctions, and 5' and 3' untranslated regions (UT

78 cing, to examine protein-coding regions, RNA splice junctions, and 5' untranslated region (UTR) exons

79 formational analysis of the coding sequence, splice junctions, and a portion of the 3' untranslated r

80 sumed core promoter regions, all exon-intron splice junctions, and a portion of the 3'-untranslated r

81 D For fine-mapping, we sequenced WFS1 exons, splice junctions, and conserved noncoding sequences in s

82 subjects were used to resequence NPR3 exons, splice junctions, and flanking regions.

83 without ASD, particularly in exons and near splice junctions, and in genes related to the developmen

84 nd KSHV have identified conserved promoters, splice junctions, and novel genes.

85 ification of at least 94% of simulated novel splice junctions, and provided as much as 1.7-fold deepe

86 validating completely novel proteins, novel splice junctions, and single amino acid variants using s

87 g (selection on alternatively spliced genes, splice junctions, and spliceosome-bound sites) and trans

88 All exons, splice junctions, and the 5'-flanking region of GSTP1 we

89 s, the nucleotide distributions around their splice junctions, and the frequencies of occurrence of s

90 arry any mutations in the SHP-1 gene-coding, splice-junction, and promoter regions.

91 tures that demarcate open reading frames and splicing junctions, and define authentic microRNA-bindin

92 ability to identify a higher number of real splicing junctions, and provides highly annotated output

93 Thus nonconsensus splice junctions are critical to stage-specific exclusio

94 lly critical amino acids involved at the two splice junctions are cysteine, serine, or threonine.

95 Because the nucleotides that flank splice junctions are nonrandom, it has been proposed tha

96 ether the consensus nucleotides flanking the splice junctions are remnants of the original protosplic

97 Averaging across all six tissues, 90% of the splice junctions are supported by short reads from match

98 ocedure, has two exclusive features: 1) only splicing junctions are involved in the assembling proced

99 e models, and even in the most comprehensive splice junction array only 69% lead to identifiable mode

100 f an isoform deconvolution model on exon and splice junction arrays and in RNA-Seq.

101 ended to other exon arrays, tiling arrays or splice junction arrays.

102 d 15% of alternative and 67% of constitutive splice junctions as conserved; however, these numbers ar

103 gle-nucleotide variant (SNV) loci and nearby splice junctions, assessing the co-occurrence of variant

104 nomic DNA identified a mutation in the donor splice junction at the end of dystrophin exon 62.

105 t this approach identifies personal specific splice junctions at a low false positive rate.

106 supersplat empirically identifies potential splice junctions at a rate of approximately 11.4 million

107 ng analysis uncovered more than 10,000 novel splice junctions at each stage and revealed that many kn

108 regions are conserved: (1) the nonconsensus splice junctions at either end of exon 18; (2) exon 18 i

109 Initial splice junctions at nucleotides 279 and 333 were analogo

110 licing, a stop codon (TAG) is located at the splice junction between exons 16 and 17, resulting in de

111 to be overexpressed, defined by an exon-exon splice junction between exons 8 and 10 (junc8.10) and th

112 IDH 1-B was formed by splice junctions between exon W, exon X, and exon Y.

113 Mutations at the N- and C-terminal splicing junctions, blocking in vivo protein splicing, a

114 between U1-C and the RNA backbone around the splice junction but U1-C makes no base-specific contacts

115 cleophiles, (b) activation of the N-terminal splice junction by a variant Block B motif that includes

116 ing dinucleotides shifted from the annotated splice junction by one position.

117 tion occurs by nucleophilic attack on the 5' splice junction by the 2' hydroxyl of an internal adenos

118 t inactivation of Cys(160) at the C-terminal splice junction by the chelation of zinc affects both th

119 nt works by increasing alignment of reads to splice junctions by short lengths, and that potential al

120 ques and identified 1,753 previously unknown splice junctions called by at least 5 reads.

121 Splice-junction centric analysis of RNA-Seq data provide

122 The splice-junction centric approach that this software enab

123 Asn cyclization, which results in C-terminal splice junction cleavage.

124 in pre-mRNA or luciferase reporter pre-mRNA, splicing junctions clustered at or near expected splice

125 Most splice junctions conform to consensus sequences for such

126 All intron/exon splice junctions conform to the GT/AG rule.

127 b gene contains 12 introns and 13 exons; all splice junctions conform to the gt/ag rule.

128 All INMT exon-intron splice junctions conformed to the "GT-AG" rule, and no c

129 All splice junctions conformed to the GT/AG rule, except tha

130 NA, leading to the creation of a proximal 3'-splice junction containing a non-canonical adenosine-ino

131 veloped to quantify the expression levels of splice junction Delta(9,10), a segment of the breast can

132 Splice junctions derived from eight breast cancer RNA-se

133 or Splicing and Transcriptome Analysis) is a splice junction detection algorithm specifically designe

134 ormatics pipeline uses MapSplice, an RNA-seq splice junction detection algorithm, to detect and quant

135 el pipeline based on TopHat2 combined with a splice junction detection algorithm, which we have named

136 Novel splice junction detection indicated that the GABAB1 gene

137 However, splice junction detection significantly improves as the

138 heir sequences, including donor and acceptor splice junctions, determined.

139 ely eliminated) is absolute at the 5' and 3' splice junction dinucleotides, and averages 72% in base

140 stics of two-pass alignment, which separates splice junction discovery from quantification.

141 we present supersplat, a method for unbiased splice-junction discovery through empirical RNA-seq data

142 Determination of the intron-exon splice junctions established that the gene is encoded by

143 Determination of the intron-exon splicing junctions established that the mouse TS gene (T

144 g, RNA-seq can support reliable detection of splice junctions except for those that are present at ve

145 RNA sequencing and genome-wide annotation of splice junctions--extreme compaction and loss of associa

146 struct only in the context of the endogenous splice junctions flanking the splice junctions of the sk

147 All of exon-intron splice junctions follow the GT-AG rule.

148 nking the LAT sequence revealed the expected splice junction for LAT excision in RNA from sensory neu

149 HPV18 splice sites/splice junctions for both early and late transcripts wer

150 tilizing this method all 79 coding exons and splice junctions for the muscle dystrophin gene, along w

151 The GABA(B)R2 gene lacks canonical splice junctions for the reported variants.

152 ->C transversion in the invariant AG of a 3' splice junction, found in 38 of 115 alleles, and a C-->T

153 deep neural network that accurately predicts splice junctions from an arbitrary pre-mRNA transcript s

154 the mapping, detection and quantification of splice junctions from multi-exon reads.

155 a computational method, SpliceMap, to detect splice junctions from RNA-seq data.

156 hly efficient and sensitive tool to identify splicing junctions from RNA-Seq data.

157 plex problem requiring the identification of splice junctions, gene boundaries, and alternative splic

158 NA splicing that removes the 2'-PO(4) at the splice junction generated by fungal tRNA ligase.

159 94 splice junctions had splice site SNPs associated with GW

160 The residues at the splice junctions have a profound effect on splicing and

161 The complete ZIP8 mRNA and intron-exon splice junctions have no nucleotide differences between

162 To maximize GABAB1 splice junction identification, we combined gene specifi

163 An invariant splice junction in all members of the NR family except L

164 The proband of Family 1 had an altered splice junction in Intron 1 (g.502011G>C; c.405-1G>C) an

165 a single nucleotide deletion that altered a splice junction in Intron 10 (g.66622del; c.1361+4del).

166 a(1) inteins: (a) cleavage at the N-terminal splice junction in the absence of all standard N- and C-

167 ing exonic splicing enhancers found near the splice junction in the gene, reveals that these (short D

168 We sequenced TRPV4 coding regions and splice junctions in 271 patients with CMT2 and 151 patie

169 We have discovered that positions of splice junctions in genes are constrained by the toleran

170 llore et al. offers a comprehensive study of splice junctions in humans by re-analyzing over 21,500 p

171 ect mismatches, microindels and noncanonical splice junctions in mapped transcripts using the referen

172 We compared GABAB1 splice junctions in prefrontal cortices from 14 alcoholi

173 Mutations within the coding regions and splice junctions in the dystrophin gene only account for

174 Thus we infer that it is the positions of splice junctions in the gene that must be under constrai

175 h LINE and SINE elements forming the most RE splice junctions in the human OFC.

176 nucleotides comprising coding sequences and splice junctions in the mouse genome were covered at lea

177 Residues proximal to the intein-splicing junction in both N- and C-terminal exteins can

178 amplified fragments showed an exon 9-exon 11 splice junction, indicating that the entire exon 10 sequ

179 ted base conversion in the intron 22/exon 23 splice junction induces alternative splicing and the pro

180 We have shown that splice junctions inferred by UnSplicer are in better agr

181 ytic nucleophiles at their N- and C-terminal splice junctions, inteins are able to excise out of prec

182 Controlled cleavage at the C-terminal splice junction involving cyclization of Asn154 was achi

183 NA sequences proximal to the intron 1-exon 2 splice junction is altered by the SNP and represents a p

184 The removal of the 2'-PO(4) at the splice junction is catalyzed by the essential enzyme Tpt

185 t suggests that the precise structure of the splice junction is crucial in retaining the balance betw

186 c-73(e936) messages containing the wild-type splice junction is increased to 33% with a corresponding

187 The accurate mapping of reads that span splice junctions is a critical component of all analytic

188 Mutations within the +/-KTS splice junction lead to severe urogenital developmental

189 a minimum, and run in parallel with gene and splice-junction level quantification.

190 c alcohol altered exon/intron expression and splice junction levels.

191 We identified 171 genes and eight splicing junctions located within four genes (SNX19, ARL

192 Here, using an original hybrid tiling and splice junction microarray that includes alternate allel

193 Splice junction microarrays and RNA-seq are two popular

194 oduced new strategies, reads per kilobase of splice junction model per million mapped reads and reads

195 n mutation associated with CESD is an exon 8 splice junction mutation (c.894G>A; E8SJM), which expres

196 The mineralization was associated with a splice junction mutation at the 3' end of exon 14 of the

197 We identified a splice junction mutation in the ERLIN2 gene-a component

198 An X-CGD patient in which a splice junction mutation results in an in-frame deletion

199 hypomorphic allele of GDSL lipase carrying a splice junction mutation, thus highlighting the potentia

200 G784 --> A in exon 8 (Gly262 --> Ser), and 2 splice junction mutations at the 5' end of intron 1, gt

201 We have identified single nucleotide splice junction mutations in Herc2 in three independent

202 120 patients for all possible ATM coding and splice junction mutations.

203 s were associated with LINCL, comprising six splice-junction mutations, 11 missense mutations, 3 nons

204 splice junctions, among which 437 were novel splice junctions not documented in current human transcr

205 he absence of all standard N- and C-terminal splice junction nucleophiles, (b) activation of the N-te

206 with a CAG codon (glutamine) inserted at the splice junction of exons 4 and 5, was found both in SLE

207 the alleles of 56010G>A, a SNP within the 3' splice junction of intron 7, are strongly associated wit

208 sversion occurs at the -1 position of the 5' splice junction of intron 7.

209 ontains a single G to A transition at the 3' splice junction of intron III resulting in missplicing a

210 A peptide nucleic acid (PNA) targeting a splice junction of the murine PTEN primary transcript wa

211 mic deletion within intron 2 close to the 5' splice junction of the SOD1 gene was identified in three

212 ectly sequenced the entire coding region and splice junctions of 5 cardiac ion channel genes, SCN5A,

213 enotype, we resequenced the coding exons and splice junctions of 58 genes in 379 obese and 378 lean i

214 ay-format multiplex detection of alternative splice junctions of breast cancer susceptibility gene 1

215 Mutation search in exons and splice junctions of candidate genes CTAG2, GAB3, MPP1, F

216 em-loop structures predicted to form at both splice junctions of HAC1 mRNA are required and sufficien

217 The entire coding region and intronic splice junctions of p73 were examined in 54 cancer cell

218 ibonucleic acid sequencing, the coding exons/splice junctions of PKP2, DSP, DSG2, DSC2, and TMEM43 we

219 ypothesis, we sequenced all coding exons and splice junctions of RLBP1.

220 in PCR products containing the 15 exons and splice junctions of the mouse Faah gene.

221 the endogenous splice junctions flanking the splice junctions of the skipped exon.

222 al analysis of most of the coding region and splice junctions of TOR1A and TOR1B did not reveal addit

223 When the splicing junctions of the 27-nt repeat containing intron

224 Mutations at splice junctions often cause exon skipping, short deleti

225 JC) is a macromolecular complex deposited at splice junctions on mRNAs as a consequence of splicing.

226 In the absence of endogenous splice junctions, only mutant transcript was detected.

227 ermine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5'- and

228 complex (EJC) that is deposited upstream of spliced junctions orchestrates downstream events in the

229 A set of 43 337 splice junction pairs was extracted from mammalian GenBa

230 of the entire genomic region from individual splice junction pairs, using a novel algorithm that uses

231 orphism (SAP) peptides, 2 INDEL peptides, 49 splice junction peptides, and 75 novel transcript-derive

232 suring expression levels of several exons or splice junctions per gene.

233 In mammalian cells, splice junctions play a dual role in mRNA quality contro

234 Here, we show that the exon sequences at the splice junctions play a significant, previously unrecogn

235 not due to aberrations in the coding region, splice junctions, polyadenylation signals, or core promo

236 Allele frequencies of the exon 3 and exon 6 splice junction polymorphisms were determined and found

237 Comparisons against TopHat and other splice junction prediction software on real and simulate

238 nd annotation, strand-specific RNA-seq data, splice junction predictions (based on RNA-seq), phosphop

239 Splice junctions present in the GABA(B)R1 gene sequence

240 (P = 0.001) and were more likely to rely on splice junctions provided by them, than were known genes

241 e GWAS-eQTL analysis against gene, exon, and splice-junction quantifications.

242 ile attacks a peptide bond at the N-terminal splice junction rather than a (thio)ester bond, alleviat

243 RNA splicing, the structural features of the splice junctions recognized by Ire1p differ from those r

244 Genomic sequencing of splice junction regions of the Ikaros gene was performed

245 st the vglut3 ATG start site or the affected splice junction replicate the asteroid phenotype.

246 xperiment and recovered more than 72% of the splice junctions reported by the annotation-based softwa

247 nd degradation rates of each transcript at a splice junction resolution during the LPS response of mo

248 We identified splice junctions resulting from splicing of primary tran

249 novel splice site dinucleotides may produce splice junction RNA-seq reads that cannot be mapped to t

250 s with identical placements and a typical 5' splice junction sequence, GTNNGY.

251 the mutations identified are in noninvariant splice-junction sequences.

252 ts were found in this gene, one in the donor splice junction site of intron C.

253 One point mutation at a splice junction site results in transcripts that encode

254 nd other variants that differ at the alleged splice junction site.

255 he flanking regions of the circular RNA back-spliced junction sites.

256 g noncoding RNAs (lncRNAs) and 154,281 known splicing junction sites were selected for targeted seque

257 allenging to accurately map RNA-seq reads to splice junctions (SJs), which is a critically important

258 ol called SCANVIS for scoring and annotating splice junctions (SJs), with an efficient visualization

259 rom rRNA-depleted RNA-seq data based on back-splicing junction-spanning reads, computational tools to

260 ependence," whereby residues surrounding the splice junction strongly affect splicing efficiency, lim

261 At each splice junction suggested by split sequencing reads, rea

262 nucleotides directed against the tau exon 10 splice junctions suppress inclusion of tau exon 10.

263 We find evidence for many more splice junctions than are annotated in WormBase, with ma

264 e additional deletion of a G nucleotide at a splice junction that attenuates levels of mutant p53 to

265 d additional gene-boundary data and recovers splice junctions that are invisible to other methods.

266 We identified splice junctions that could be generated only from prima

267 We have identified hundreds of splice junctions that exhibit distinct splicing patterns

268 rison of the nucleotide sequences around the splice junctions that flank old (shared by two or more m

269 nt functional regions in DNA sequences (e.g. splice junctions that signal the beginning and end of tr

270 In contrast to the splicing junctions that can be efficiently detected from

271 th putative errors and ambiguous location of splice junctions the verified dataset includes 22 489 en

272 ent splicing requires nucleotide bias at the splice junction; the preferred usage produces a distribu

273 ng pathway to yield the requisite N-terminal splice junction (thio)ester.

274 f candidate processed transcripts, including splice junctions, trans-spliced leader sequences, and po

275 To improve detection of splice junctions, TrueSight uses information on statisti

276 ide association study of gene expression and splice junction usage in HGSOC-relevant tissue types (N

277 ct and quantify differential and unannotated splice junction usage.

278 In some cases, there is variation in the splice junctions used.

279 sequenced its 5'-flanking region, exons, and splice junctions using 60 DNA samples from African-Ameri

280 persplat for de novo empirical annotation of splice junctions using the reference monocot plant Brach

281 We also found a splicing junction variant (IVS24-7delGTTT) in all 19 pat

282 an labels chosen to clearly discriminate the splice junctions via specific target identification.

283 For example, the total number of confirmed splice junctions was raised from 70,911 to over 98,000.

284 By priming off of the splice junction, we developed a quantitative RT-PCR assa

285 Using reads aligned across splice junctions, we determined that alternative splicin

286 tein splicing and cleavage at the N-terminal splice junction were inhibited in the presence of zinc i

287 All exons and the flanking splice junctions were screened by direct sequencing.

288 Furthermore, canonical GT-AG splice junctions were used significantly less frequently

289 More than 95% of FlyBase genes and 90% of splicing junctions were observed.

290 -globin intron into the K8beta exon 3-exon 4 splice junction, which promoted splicing of K8beta intro

291 cked splicing and cleavage at the N-terminal splice junction, while substitution of the intein C-term

292 overall transcript structures and individual splice junctions, while performing competitively in dete

293 3'-cyclic phosphate and 5'-OH ends to form a splice junction with a 2'-OH, 3',5'-phosphodiester.

294 perimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborat

295 e structures and is capable of finding novel splice junctions with high sensitivity and specificity.

296 E splicing occurs largely at canonical GT-AG splice junctions with LINE and SINE elements forming the

297 se composition between sites flanking the 5'-splice junction, with the potential to create a subset o

298 designed to bind to the 3' end of the exon 6 splice junction within the primary CD40 transcript.

299 In addition, we verified 6010 exon-exon splice junctions within existing WormBase gene models.

300 ble of detecting differential usage of novel splice junctions without the need for an additional isof