ライフサイエンスコーパス: intron

1 g is interrupted by another intron (internal intron).

2 hether located in a heterologous promoter or intron.

3 stability, necessitating splicing of a novel intron.

4 he 5'-donor element of another (external) U2 intron.

5 he spliceosome is required for removal of an intron.

6 ficant mutations in 5'Smu as well as the JH4 intron.

7 new functional splice sites within an extant intron.

8 ctional intron donor element of the ancestor intron.

9 to produce mature mRNA and an excised lariat intron.

10 acilitating splicing of an upstream adjacent intron.

11 mid and stimulates retrotransposition of the intron.

12 sive expansion of GAA repeats into its first intron.

13 ite, alternative 3' splice site and retained intron.

14 ers that are separated by the first exon and intron.

15 f certain mitochondrial and plastid group II introns.

16 ptic cleavage/polyadenylation sites in first introns.

17 MS19 is 62 kb, consisting of 20 exons and 19 introns.

18 in exons while passively depleting them from introns.

19 nterrupted genes that contain frameshifts or introns.

20 ne methylation, are sometimes located within introns.

21 g sequences are often interrupted by U2-type introns.

22 ising by splicing and debranching from short introns.

23 d in mencRNA exons, but not the promoters or introns.

24 s that facilitate the splicing of organellar introns.

25 ript shortening through APA in 3'UTRs and in introns.

26 general chaperone for mitochondrial group I introns.

27 ve of intron 1 position, OSRE1 deletion from intron 1 abolishes hyperosmotic enhancer activity.

28 positioning and the presence of an OSRE1 in intron 1 are required for precise enhancement of hyperos

29 showed higher OXTR methylation levels in the intron 1 area compared with neurotypical subjects.

30 ther, these results indicate the enhancer in intron 1 binds YY1 and suggest YY1 provides a scaffold f

31 Intron 1 includes a single, functional copy of an osmore

32 osmotic induction of glutamine synthetase by intron 1 is position dependent.

33 disease that are rescued when the entire FXN intron 1 is removed, and not with the excision of the ex

34 ely through its binding site 5'-GGCTCG-3' in intron 1 of Igf2.

35 But irrespective of intron 1 position, OSRE1 deletion from intron 1 abolishe

36 These findings indicate that proper intron 1 positioning and the presence of an OSRE1 in int

37 red a novel osmosensitive mechanism by which intron 1 positively mediates glutamine synthetase transc

38 fied a polymorphic 3-kb region within LILRB1 intron 1 that is epigenetically marked as an active enha

39 y conserved SOX9-binding enhancer located in intron 1 was necessary to drive transcription of Snorc i

40 insertion site into the rat gene just beyond intron 1.

41 In the mutants, intron 12 retention leads to expression of a truncated e

42 points within or adjacent to Alu elements in intron 15; producing partial gene duplications, inversio

43 ied, which is activated upon HIF1 binding to intron 18 of the EGFR gene in cell lines in which EGFR w

44 y a replacement of the segment of DNA within intron 2 of hCYP11B2 with the corresponding region of th

45 Recently, a pentanucleotide expansion in intron 2 of RFC1 was identified as the genetic cause of

46 7) were genotyped for the promoter 5-HTTLPR, intron 2 VNTR and rs25531 polymorphisms by PCR-based met

47 to p300, NFkappaB, and CEBPalpha than to WT intron 2.

48 ontaining either the intron conversion or WT intron 2.

49 transfection in H295R cells compared with WT intron 2.

50 pressure compared with TG mice containing WT intron 2.

51 It associates with intron 24 of Apob pre-mRNA, with the 3'UTR of Uqcrb, and

52 rget of NFI and has NFI-binding sites in its intron 3 region.

53 n the Blimp1 gene at a 24-kb upstream and an intron-3 element.

54 mmary, we have identified a G->A mutation in intron 6 of C8A as a predominant cause of C8alpha-gamma

55 sequencing revealed a G->A point mutation in intron 6, upstream of the exon 7 acceptor site.

56 substrates, containing 333 nt of the C8alpha intron 6/exon 7 boundary, in an in vitro splicing assay.

57 amprey nprl3, which corresponds to the NPRL3 intron 7 MCS-R1 enhancer of jawed vertebrates.

58 an erythroid-specific enhancer is located in intron 7 of lamprey nprl3, which corresponds to the NPRL

59 thylation of FK506 binding protein 5 (FKBP5) intron 7, site 6 compared with Jewish comparison volunte

60 s the previously observed decrement in FKBP5 intron 7, site 6 methylation in Holocaust offspring.

61 These retained introns affect transcripts in multiple cellular pathways

62 emophilia A by NHEJ knock-in of BDDF8 at Alb introns after AAV-mediated delivery of editing component

63 nuclear ribonucleoproteins (snRNPs) mark an intron and recruit the U4/U6.U5 tri-snRNP.

64 es, one spanning an exceptionally long first intron and the other spanning exons, we identify two cla

65 ays, one operating on the plastid trnL (UAA) intron and the other targeting its inner P6 loop in nest

66 ers (ESEs) are enriched in exons relative to introns and bind splicing activators.

67 in RNA mis-splicing, enrichment for retained introns and disruption of the transcriptional control of

68 l regions including promoters, coding exons, introns and distal intergenic regions.

69 minantly affecting short and high GC-content introns and genes involved in brain disorders.

70 mic loci and contained numerous spliceosomal introns and large duplications, suggesting tight assimil

71 sus sequence features for all introns, small introns and large introns for each genome.

72 e proximal polyadenylation signals (PASs) in introns and last exons.

73 the predominant circRNAs had longer flanking introns and more Alu elements than other circRNAs in the

74 putative progenitors of nuclear spliceosomal introns and use the same two-step splicing pathway.

75 nRT is encoded within a eubacterial group II intron, and it has been shown to efficiently copy highly

76 ce modules are neural networks scoring exon, intron, and splice sites, trained on distinct large-scal

77 t of long noncoding RNAs, RNAs with retained introns, and a subgroup of protein-coding mRNAs in the c

78 in gene expression via measurements of gene introns, and detect rare transcripts and quantify cell-t

79 se genes is likely associated with the three introns, and intron loss is likely reverse transcriptase

80 from short transcripts that tend to have few introns, and we validate this with reporter constructs.

81 ed it on 24 eukaryotic genomes to create the Intron Annotation and Orthology Database (IAOD).

82 y, the exonic segments flanking the retained introns appeared to be more enriched in a previously ide

83 which generates a non-polyadenylated stable intron appearing to be a conserved feature of betaherpes

84 rkeyi, the donor elements of the constituent introns are abutting and the complex intervening sequenc

85 Different classes of introns are excised by the U2-type or the U12-type splic

86 pre-messenger RNAs and long non-coding RNAs, introns are removed through the process of RNA splicing.

87 Group II introns are self-splicing ribozymes and mobile genetic e

88 Strikingly, almost all detained introns are spliced more efficiently when O-GlcNAc level

89 nalyses show that lncRNAs containing cryptic introns are targeted by the conserved Pir2(ARS2) protein

90 Group II introns are the putative progenitors of nuclear spliceos

91 Spliceosomal introns are ubiquitous non-coding RNAs that are typicall

92 Group II introns are ubiquitous self-splicing ribozymes and retro

93 al evidence for OXTR hypermethylation in the intron area as a potential biomarker for adults with ASD

94 and splicing of the adjacent upstream third intron, as well as regions outside the classical motifs

95 Introns associated with new exon creation are significan

96 It reports the dinucleotides around the intron boundary and displays the consensus sequence feat

97 In one class of complex introns called [D] stwintrons, an (internal) U2 intron i

98 As neoepitopes originating from retained introns can be presented on the cancer cell surface, the

99 o multiple GCAUG and GCACG motifs in a xol-1 intron, causing intron retention or partial exon deletio

100 We created intronIC, a program for assigning intron class to all introns in a given genome, and used

101 e TSEN complex, but is not required for tRNA intron cleavage in vitro.

102 trate that loops immediately upstream of the introns contain pre-mRNA-specific splicing enhancers, th

103 instead promoting the retention of flanking introns containing repeated SRSF7 binding sites.

104 ruitment of RNA polymerase II (Pol II) to an intron-containing gene, which is rescued by spt8Delta.

105 to elevated minor intron retention in minor intron-containing genes that regulate cell cycle.

106 Interestingly, translation of intron-containing mRNAs was up-regulated.

107 wed transcriptome alterations that suggested intron content-dependent regulation of gene expression.

108 from the adrenals of TG mice containing the intron conversion binds more strongly to p300, NFkappaB,

109 Reporter constructs containing the intron conversion had increased promoter activity on tra

110 We found that TG mice containing the intron conversion have (a) increased plasma aldosterone

111 These results uncover a functional role of intron conversion in hCYP11B2 and suggest a new paradigm

112 The intron conversion is formed by a replacement of the segm

113 We show here that the intron conversion is located in an open chromatin form a

114 s of the hCYP11B2 gene containing either the intron conversion or WT intron 2.

115 In some humans, hCYP11B2 undergoes a unique intron conversion whose function is largely unclear.

116 in the exonic segments upstream of retained introns could be a means for occlusion of ESEs.

117 hod for the coordinated analysis of exon and intron data by investigating their relationship within i

118 This coordinated analysis of exon and intron data offers strong evidence for significant diffe

119 y expression data from the combined exon and intron data.

120 simultaneous consideration of both exon and intron data.

121 analyze the differences between the exon and intron definition scenarios and find that exon definitio

122 ng and noncoding genes frequently ignore any intron-derived miRNA.

123 Intron detention in precursor RNAs serves to regulate ex

124 How detained intron (DI) splicing is controlled is poorly understood.

125 sm may involve duplication of the functional intron donor element of the ancestor intron.

126 We further show that introns drive selection of both proximal and distal vari

127 The recognized role of introns during translation, and the presence of substant

128 s a ribonucleoprotein (RNP) complex with the intron-encoded protein (IEP), which is essential for spl

129 cold, splicing is partially restored by the intron-encoded protein (IEP).

130 gn RNA on the genome and accurately discover introns, especially with long reads.

131 splicing biomarker peptides with one single intron event and one exon skipping event were identified

132 ive splicing events, especially for retained intron events since this is the most common type of alte

133 intervening sequences can constitute complex introns excised by consecutive splicing reactions.

134 egulates alternative splicing (predominantly intron exclusion) of several genes including those essen

135 l start and stop positions do not match with intron-exon boundaries, reinforcing the model that they

136 The intron-exon structure of the NPIP gene family has change

137 is-elements, conserved motif identification, intron/exon structural patterns and gene ontology classi

138 nitors, but phylogenetics and differences in intron/exon structure suggest that they may have acquire

139 ized transgenic (TG) mice containing all the introns, exons, and 5'- and 3'-flanking regions of the h

140 evolution of the two classes of spliceosomal introns, finding support for the class conversion model

141 d to circRNA biogenesis, including length of introns flanking circularized exons, repetitive elements

142 res for all introns, small introns and large introns for each genome.

143 o promote the splicing of all but two of the introns found in angiosperm chloroplast genomes.

144 Insertion of the sex-specifically spliced intron from the C. hominivorax transformer gene within t

145 The spliceosome removes introns from messenger RNA precursors (pre-mRNA).

146 of mitochondrial genome evolution including intron gain and loss, extensive patterns of genetic code

147 A plethora of introns have been inferred by computational analyses as

148 and rs2004776), located at +507 and +1164 in intron I of the human AGT (hAGT) gene, are associated wi

149 on and RNA editing in back-splicing flanking introns; (ii) a two-stage DE approach of circRNAs based

150 ypermutation is almost negligible at the JH4 intron in AID(S38A/S38A)MSH2(-/-) mouse B cells, and, co

151 emical and structural data have captured the intron in multiple conformations at different stages of

152 on and splicing lead to a paucity of excised intron in the cold, levels of relaxase mRNA are maintain

153 a program for assigning intron class to all introns in a given genome, and used it on 24 eukaryotic

154 Typically, miRNA is expressed from introns in cellular genes, but there is no intron readil

155 Further, neighboring introns in human cells tend to be spliced concurrently,

156 majority of the approximately 20 chloroplast introns in land plants.

157 icing events are coordinated across numerous introns in metazoan RNA transcripts requires quantitativ

158 ntial roles in splicing group I and group II introns in mitochondria and chloroplasts.

159 del explaining the low abundance of U12-type introns in modern genomes.

160 structural information we show that retained introns in mouse are commonly flanked by a short ( 70 nu

161 es splicing of the highly conserved detained introns in OGT and OGA to control mRNA abundance in orde

162 ing, which occurs with higher efficiency for introns in protein-coding genes than for those in noncod

163 ons, including the formation of exons within introns in proximity to Alu elements.

164 al MoATG genes were identified with retained introns in their mRNA transcripts, corresponding with a

165 etention of ~200 introns, including multiple introns in TUBGCP6, a central component of the gamma-TuR

166 ss of WBP11 results in the retention of ~200 introns, including multiple introns in TUBGCP6, a centra

167 h could be caused by the length expansion of introns inserted by transposon elements.

168 uted in all genomic regions including exons, introns, intergenic, TTS (transcription termination site

169 volved in splicing is interrupted by another intron (internal intron).

170 rescue is achieved by inserting sex-specific introns into the coding sequences of antibiotic-resistan

171 rons called [D] stwintrons, an (internal) U2 intron is nested within the 5'-donor element of another

172 The level of this circularized intron is reduced in the islets of rodent diabetes model

173 The splicing of tRNA introns is a critical step in pre-tRNA maturation.

174 The origin of spliceosomal introns is a vexing problem.

175 own about how splicing of bacterial group II introns is influenced by environmental conditions.

176 SAEs as a common driver in recombination of intron-lacking genes during mitogenome evolution.

177 siae, the 3'-end sequences of at least three intron-lacking mitochondrial genes exhibit elevated nucl

178 ysis, gene set enrichment analysis, and exon-intron landscape analysis, we examined the impact of dru

179 Finally, the intron length and abundance of Alu elements positively c

180 ces existing throughout phylogeny, including intron-less genes and inactive germline processed pseudo

181 stasis, there is a global change in detained intron levels.

182 plasmid-encoded Lactococcus lactis group II intron, Ll.LtrB, splicing enables expression of the intr

183 ikely associated with the three introns, and intron loss is likely reverse transcriptase mediated.

184 are maintained, partially due to diminished intron-mediated mRNA targeting, allowing intron spread b

185 atched change characterization for exons and introns (MEI), is its straightforward applicability to e

186 We hypothesize that the high exon to intron motif ratios necessary for ESE function were crea

187 Total intron number and intron position are two predominant fe

188 oncurrently, implying that splicing of these introns occurs cooperatively.

189 runcating variant in FLG and a SNP within an intron of GSDMB) had evidence for differential associati

190 ference technology, we identified the second intron of IncRNA, PVT1, as a unique bona fide gained enh

191 druplex-forming sequence (PQFS) in the first intron of the Atg7 gene folds into a G4.

192 he deletion of the P1BS motif from the first intron of the barley 5'-UTR led to a significant increas

193 linkage disequilibrium block, located in the intron of the BCL2 gene, which reached genome-wide signi

194 itized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant.

195 llele of rs10508884, which is situated in an intron of the CXCL12 gene, increased the rate of immunog

196 ce of expanded (GAA)(n) repeats in the first intron of the FXN gene [V.

197 xpansion of the GAA/TTC repeats in the first intron of the FXN gene causes Friedreich's ataxia.

198 containing the lariat sequence of the second intron of the insulin gene.

199 able number tandem repeat (VNTR) in the last intron of WDR7, which exhibits striking variability in b

200 cated in between genes (36.7%) or within the introns of genes (42.4%).

201 ruses from those 4 donors were mapped to the introns of the MATR3, ZNF268, ZNF721/ABCA11P, and ABCA11

202 neighboring gene promoter such as within an intron or exon.

203 umulation to a similar degree from within an intron or when introduced into the 5'-UTR and coding seq

204 Here we show that RNase H ASOs targeted to introns or exons robustly reduce the level of spliced RN

205 s identified through gene phylogeny and exon/intron phase analysis.

206 atterns differ between exitrons and retained introns, pointing to their distinct regulation.

207 red for the nuclear export of intronless and intron-poor mRNAs and lncRNAs.

208 , tiny intergenic regions, and is remarkably intron-poor, as more than 80% of coding genes are intron

209 Total intron number and intron position are two predominant features that correl

210 yeast genus Lipomyces, the most 5' terminal intron position is occupied by one of three complex inte

211 The retained intron pre-mRNAs display a number of characteristics, in

212 f substantial RNA-Seq counts attributable to introns, provide the rationale for the simultaneous cons

213 While the intron provides the species discrimination ability, the

214 m introns in cellular genes, but there is no intron readily apparent in BKPyV from which the miRNA co

215 iscover inactivation of tumor suppressors in intron regions and that tissue type and subtype indicate

216 diately upstream (but not downstream) of the introns regulate alternative splicing events, likely thr

217 In archaea and eukaryotes, tRNA intron removal is catalyzed by the tRNA splicing endonuc

218 downstream gene body incorporates a cryptic intron required for repression of that gene.

219 e to canonical AUG-mediated translation from intron-retained GGCCTG repeat RNAs.

220 ied to quantify the stability of spliced and intron-retained transcripts on a genome-wide scale.

221 T cell activation, although the stability of intron-retained transcripts remained relatively constant

222 Beyond substantiating that intron-retained transcripts were considerably less stabl

223 aphid feeding induced alternatively spliced intron-retaining CCA1a/b transcripts, which are normally

224 Motivated by our previous finding that intron retention (IR) could lead to transcript instabili

225 that PpPHY4 and PphnRNP-F1 coregulate 70% of intron retention (IR) events in response to red light.

226 Intron retention (IR) in cancer was for a long time over

227 ed RNA splicing defects involving widespread intron retention affecting almost 2000 transcripts in C9

228 lates with disease progression and establish intron retention as a hallmark of PCa stemness and aggre

229 ctivation of exon skipping and repression of intron retention being the most common splicing events i

230 Moreover, we identify an intron retention event in FUS itself that is associated

231 These intron retention events appear not to alter overall expr

232 We also observe a strong downregulation of intron retention events associated with SF3B1 mutation.

233 limb size is reduced owing to elevated minor intron retention in minor intron-containing genes that r

234 model for ALS pathogenesis whereby aberrant intron retention in SFPQ transcripts contributes to FUS

235 nd methylation at the C9orf72 locus, reduced intron retention in the edited lines and abolished patho

236 Intron retention is associated with greater nuclear abun

237 lly, we find that mutant FUS directly alters intron retention levels in RNA-binding proteins.

238 and GCACG motifs in a xol-1 intron, causing intron retention or partial exon deletion, thereby elimi

239 anisms, alternative splicing (AS; especially intron retention) and alternative polyadenylation (APA),

240 c splicing enhancers and silencers, complete intron retention, hypomorphic alleles, and combinations

241 e analysis after PI demonstrates broad-scale intron retention, suggestive of spliceosome interference

242 ects, such as alternative exon inclusion and intron retention, were characterized in CDK7-inhibited c

243 NDC1 cassette exon that regulates pan-cancer intron retention.

244 expression of the interrupted host gene and intron retromobility.

245 nic and primarily localized within the first intron, revealing this position as a common feature asso

246 Here, we used thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) comb

247 for native refolding of a misfolded group I intron ribozyme by CYT-19, a Neurospora crassa DEAD-box

248 In the cell, the intron RNA forms a ribonucleoprotein (RNP) complex with

249 suggesting that a kinetic trap prevents the intron RNA from assuming its native state.

250 Although structures of spliced group II intron RNAs and RNP complexes have been characterized, s

251 miRNA-sized RNAs, and putatively structured intron RNAs of potential biological, evolutionary, and b

252 tif instances, conserved domains in group II intron RNAs, and the tRNA mimicry of IRES RNAs.

253 e, including a family of full-length excised intron RNAs, subsets of which correspond to mirtron pre-

254 structures of endogenously produced group II intron RNPs trapped in their pre-catalytic state.

255 atches and the high processivity of group II intron RTs enable synthesis of full-length DNA copies of

256 Ll.LtrB, splicing enables expression of the intron's host relaxase protein.

257 constitutive exons but are flanked by longer intron sequences.

258 developing the role of using both exons and intron sequencing counts in studies of gene regulatory p

259 RegSNPs-intron showed excellent performance in evaluating the pa

260 Both repeat content and intron size are major contributors to the observed diffe

261 ficantly larger than the genome-wide average intron size.

262 lays the consensus sequence features for all introns, small introns and large introns for each genome

263 suggest that the miRNA is expressed from an intron spliced out of these greater-than-genome-size pri

264 th a significant reduction in transcripts of intron-spliced isoforms in the MoHMT1 mutant strain.

265 y the intrinsic cold sensitivity of group II intron splicing and the role of the IEP for cold-stress

266 Intron splicing of a nascent mRNA transcript by spliceos

267 Our insights into the mechanism of group II intron splicing parallels functional data on the spliceo

268 proteins and RNAs that meticulously promotes intron splicing through the formation of eight intermedi

269 demonstrate that O-GlcNAc controls detained intron splicing to tune system-wide gene expression, pro

270 he structural basis of IEP-assisted group II intron splicing, but also provide parallels to evolution

271 ow that low temperatures can inhibit Ll.LtrB intron splicing.

272 bal impact of the minor spliceosome on major intron splicing.

273 ient conditions fluctuate, controls detained intron splicing.

274 hed intron-mediated mRNA targeting, allowing intron spread by conjugal transfer.

275 Spliceosomal twin introns (stwintrons) are introns where any of the three

276 Here we show that intron-targeted ASOs and, to a lesser extent, exon-targe

277 Surprisingly, intron-targeted ASOs reduce the level of pre-mRNA associ

278 evidence that the miRNA is expressed from an intron that is generated by RNA polymerase II transcribi

279 (CFM1), promotes the splicing of most of the introns that had not previously been shown to require a

280 nce can affect IME; the same three synthetic introns that increase mcherry protein concentration by a

281 is controlled through an autoregulated minor intron, tightly correlating Srsf10 with minor spliceosom

282 t also maintenance of horizontal plasmid and intron transfer under cold-shock.

283 enesis of mature tRNAs and circularized tRNA introns (tricRNAs) in vivo.

284 or spliceosomes control splicing of distinct intron types and are thought to act largely independent

285 bidopsis thaliana and showed that nearly all introns undergo co-transcriptional splicing, which occur

286 equences consistent of differently nested U2 intron units, as demonstrated in L. lipofer, L. suomiens

287 r incorporating the significance of exon and intron variability and further developing the role of us

288 mportantly, the observed changes in exon and intron variability with statistically significant false

289 Here, we show that three AT-rich introns were retained in the TNP2-like transposase genes

290 Spliceosomal twin introns (stwintrons) are introns where any of the three consensus sequences invol

291 enomic complementary DNAs (gencDNAs) lacking introns, which integrate into locations distinct from ge

292 ate that the maize CFM1 ortholog is bound to introns whose splicing is disrupted in the cfm1 mutant.

293 tid ribosomes but instead associate with the introns whose splicing they promote.

294 co-transcriptional splicing efficiency, and introns with alternative 5' or 3' splice sites are less

295 n nascent RNAs than in mature RNAs, and that introns with increased splicing defects in mature RNAs a

296 encoding trans-acting proteins lead to more introns with increased splicing defects in nascent RNAs

297 wo of which arise from excision of a cryptic intron within the amyloid-forming repeat (RPT) domain, l

298 aused by a trinucleotide CTG expansion in an intron within the TCF4 gene.

299 ism mediates gene repression through cryptic introns within lncRNAs.

300 inding regions (-25 kb, -20 kb, and IRF8 6th intron) within the IRF8 locus.