ライフサイエンスコーパス: intron

1 gradation based on Cre-regulated- Artificial Intron).

2 RN1 allele with a deletion in the regulatory intron.

3 xpression by enhanced splicing of a retained intron.

4 t codon is in the previously annotated first intron.

5 he requirement for H2A.Z in splicing of that intron.

6 rphisms increases as one approaches a mobile intron.

7 ated R-loops is dependent on the presence of introns.

8 n differed between retained and constitutive introns.

9 st ensure accurate removal of highly diverse introns.

10 stimulate recruitment and retention of U1 on introns.

11 roliferation by regulating numerous detained introns.

12 pression level and with increasing number of introns.

13 ss for the efficient splicing of a subset of introns.

14 tly differ between constitutive and retained introns.

15 ionary differences in the age and origins of introns.

16 ntisense copies of proviruses located within introns.

17 xons, but, somewhat surprisingly, also avoid introns.

18 diversity in exons that border self-splicing introns.

19 not only the local intron but also adjacent introns.

20 tation and from proviruses integrated within introns.

21 d species suggest an evolutionary analogy to introns.

22 relatively long coding exons and few coding introns.

23 vel ORFs in 5'UTRs, long noncoding RNAs, and introns.

24 ma reesei) alternative, overlapping internal introns.

25 On chromosome 14, TSHR genetic variants in intron 1 could conceivably help explain past findings re

26 The first intronic mutations in the intron 1 GATA site (int-1-GATA) of 5-aminolevulinate syn

27 on-coding hexanucleotide repeat expansion in intron 1 of the C9orf72 gene is the most common cause of

28 Furthermore, germline rearrange-ments in intron 1 of TP53 are associated with LFS and are frequen

29 The G allele of the intron 1 polymorphism rs3176891 was more common in VTE v

30 cohort and identify six new risk variants in introns 1 and 2.

31 The HGE starts from the 3' end of intron 19 and extends into intron 22, possesses enhancer

32 97Gly (x3) and a donor splice site mutation (intron 19).

33 apped the regulatory region located in SMIM1 intron 2 in Swedish blood donors, and observed a strong

34 6 expression in CRC cells by inducing SRSF6(+intron 2) transcripts which were considered to be the pu

35 va1(-4)) and intron 2-retained SRSF6 (SRSF6(+intron 2)) transcripts in CRC tissues and cell lines.

36 ncological ventral antigen 1 (Nova1(-4)) and intron 2-retained SRSF6 (SRSF6(+intron 2)) transcripts i

37 On the other hand, alternative splicing of Intron-2 generates a longer transcript encoding a protei

38 Specifically, alternative polyadenylation at Intron-2 of OXT6 produces a transcript coding for AtCPSF

39 rom the 3' end of intron 19 and extends into intron 22, possesses enhancer histone modification marks

40 tative intronic splicing enhancer present in intron 25, which appeared to function redundantly with t

41 s targeting the polyadenylation signal in AR intron 3 as a strategy to prevent expression of a broad

42 ely by a single polyadenylation signal in AR intron 3.

43 a long terminal repeat element inserted into intron 35 exposes an alternative polyadenylation site, r

44 sversion (T --> A) at the second position of intron 36 of the Col1a1 gene, encoding the type I collag

45 on redundantly with the splice donor site of intron 36.

46 ealed activation of a cryptic splice site in intron 4 resulting in a frame shift and a premature stop

47 inly attributable to the A-44G transition in intron 6.

48 to-C mutation at the first position (G1C) of intron 7.

49 translated region (UTR), suggesting that the intron affects transcription initiation.

50 The Lshid transgene contains a sex-specific intron and as a consequence only females produce LsHID p

51 on) is a web-accessible database that houses intron and exon information of plant genes.

52 ed Element (UCE) that is within the retained intron and overlaps the alternative exon.

53 10 recognizes a diverse set of RNA motifs in introns and exons and regulates alternative splicing.

54 the differential GC content between adjacent introns and exons.

55 ryotic cells must undergo splicing to remove introns and join exons, and splicing elements present a

56 ocess in a single gene coding, which removes introns and joins exons, and splicing branchpoints are i

57 e cluster regions (CCRs), and is enriched in introns and lincRNA loci.

58 sence of canonical splice sites in the mtRNA introns and of core components of the nuclei-encoded spl

59 ce of eukaryotic retroelements, spliceosomal introns and other key components of the spliceosome.

60 nd AG dinucleotides at the 5' and 3' ends of introns and provides insight into the catalytic mechanis

61 g sites (MBSs) are frequently interrupted by introns and therefore require proper splicing to generat

62 using the total RNA kit had more signal for introns and various RNA classes (ncRNA, snRNA, snoRNA) a

63 nnon and Belfort introduce inteins - protein introns - and describe how they escape host proteins, th

64 in genes (including untranslated regions and introns) and 28% (7217) are within 500 bp of a gene.

65 Notably, affected introns are enriched for H2A.Z occupancy and more likely

66 Frequently retained introns are enriched for specific RNA binding protein si

67 ubt that prokaryotic and organellar group II introns are evolutionary related, there are remarkable d

68 Group II introns are found in all three domains of life and are t

69 y identified in organellar genomes, group II introns are found in bacteria, chloroplasts, and mitocho

70 Introns are removed from eukaryotic messenger RNA precur

71 We found that most U12-type introns are retained or misspliced in rgh3 Genes affecte

72 Alternatively spliced introns are the ones that are usually spliced but can be

73 Drug-induced retained introns are typically shorter, displaying higher GC cont

74 Finally, these mutations occur in the same intron as retroviral integration sites in gene therapy-i

75 sequences the same distance upstream of the intron as when the promoter was intact.

76 e alternative loss of either of the internal introns at the DNA level from an alternatively spliced s

77 seed oil blends using the plastid trnL (UAA) intron barcode.

78 Rev protein that mediates nuclear export of intron-bearing late-stage viral mRNAs.

79 emind us, that sequence variants within exon-intron boundaries, which are primarily identified for di

80 disrupts the splicing of not only the local intron but also adjacent introns.

81 The duality of group II introns, capable of carrying out both self-splicing and

82 and provides insight into the biogenesis of intron circles.

83 zizomycotina, we find a variety of predicted intron configurations interrupting the DNA stretch encod

84 n the level of gene expression as long as an intron containing stimulatory sequences was included.

85 recruited to the export machinery or how the intron-containing but unspliced M1 mRNA bypasses the nor

86 splicing isoforms were derived from 128 667 intron-containing full-length FLNC reads, including a la

87 Here we show that splicing of intron-containing genes in cells lacking H2A.Z is impair

88 The expression of intron-containing genes in eukaryotes requires generatio

89 to differential expression analysis of minor intron-containing genes is applicable to other diseases

90 Strikingly, intron-containing genes were most susceptible to CHD1 lo

91 In intron-containing genes, R-loops are bounded between the

92 ivo, with a preference for exon 2 regions of intron-containing pre-mRNAs and poly(A) proximal sites.

93 execute nuclear export of newly transcribed intron-containing pre-tRNAs.

94 of spliceosomes from this abundant class of intron-containing RNAs (the ribosomal protein genes) to

95 of spliceosomes from this abundant class of intron-containing RNAs to otherwise poorly spliced trans

96 Moreover, 144 minor intron-containing RNAs were differentially expressed, in

97 Each intron contains three obligate signals: a 5' splice site

98 e Ophioglossum mitogenome (372 kb), gene and intron content is slightly reduced, including the loss o

99 ss of intron that can only splice in a multi-intron context.

100 ization data for three model RNAs: a group I intron, CsrB and a tRNA.

101 well-known orthologous U12-type spliceosomal intron database U12DB.

102 after its excision, a newly formed canonical intron defined as 'external'.

103 etention of introns, in the framework of an "intron definition" model for splicing.

104 ially recognized in either intron-spanning ('intron definition') or exon-spanning ('exon definition')

105 splicing disruption specific to all U12-type introns detected in blood monocytes from affected indivi

106 y primarily disrupts the removal of detained introns (DIs).

107 Here, we conclude that introns do not necessarily contain 'missing' information

108 16 is positioned to bind and translocate the intron downstream of the branch point to destabilize bra

109 intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing pr

110 PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessibl

111 on can only explain diversity gradients near intron-exon boundaries if the conversion template comes

112 o 21 in the 3' exon, enabling it to pull the intron-exon or ligated exons in a 3' to 5' direction to

113 ource for biologists interested in comparing intron-exon organization and provides valuable insights

114 Conserved intron/exon boundaries, protein structure, and key bindi

115 The identification of an intron/exon-spanning promoter in a hosting gene, resulti

116 intron interrupts the donor of the external intron (experimentally confirmed for Aspergillus nidulan

117 regulates circRNA biogenesis by binding the introns flanking the back-splicing junctions and that th

118 ons have retained their ability to spread to intron-free target sites, often assisted by intron-encod

119 h result in inefficient excision of selected introns from a subset of pre-mRNAs.

120 Surprisingly, removal of introns from a target gene abolishes the requirement for

121 SE2 is required for the splicing of group II introns from chloroplast transcripts.

122 The excision of introns from pre-mRNA is an essential step in mRNA proce

123 f most eukaryotic mRNAs requires splicing of introns from pre-mRNA.

124 , whereby the spliceosome removes non-coding introns from pre-mRNAs and joins exons.

125 The spliceosome excises introns from pre-mRNAs in two sequential transesterifica

126 as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA).

127 In vitro assays further showed that this intron functions as a genomic enhancer where glucocortic

128 RNA splicing of U12-type introns functions in human cell differentiation, but it

129 plex covering the free ends of the two rps12 intron halves.

130 n, but it is not known whether this class of introns has a similar role in plants.

131 snRNPs are affected, and some U12-dependent introns have been reported to be aberrantly spliced in p

132 In fungi, many of these introns have retained their ability to spread to intron-

133 We also found that retained introns, high in GC content, served as substrates for th

134 d by mRNAs that excise the NP1-regulated MVC intron immediately upstream of the internal polyadenylat

135 d to selective retention of a PTC-containing intron in EIF2B5.

136 alternative splicing, followed by alternate "intron in exon." Seven hundred seventy novel transcripti

137 splicing errors increases with the number of introns in a gene and with expression level.

138 trons previously identified, suggesting that introns in the mitochondrial genome of annelids may be m

139 tedly low variation in splicing rates across introns in the same gene, suggesting the presence of gen

140 of the only two genes harboring cis-spliced introns in this organism, and its function is currently

141 potentially responsible for the retention of introns, in the framework of an "intron definition" mode

142 intron retention, particularly of minor U12 introns, in the spinal cord of mice 30 d after SMA induc

143 rter gene fusion in Arabidopsis thaliana The intron increased expression from all transcribed positio

144 x intervening sequences, where an 'internal' intron interrupts one of the sequences essential for spl

145 Some sport a stwintron where the internal intron interrupts the donor of the external intron (expe

146 ng horizontal gene transfer of self-splicing introns into extant fungal populations.

147 ation with Cre recombinase ("on-state"), the intron is crippled and the target gene is disrupted by a

148 Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the f

149 ore, we show that retention of U12-dependent introns is mitigated by ASO treatment of SMA mice and th

150 /ACA class small nucleolar RNA, ACA11, in an intron, is associated with several cancer types, includi

151 NA, resulting in an increase in the retained intron isoform and nonsense mediated decay susceptible i

152 transcription start site and the first exon-intron junction.

153 The exons and exon-intron junctions of present day higher plant's Rca, whic

154 Structures of B, B(act), C, C*, and intron lariat spliceosome complexes revealed mechanisms

155 to the formation and resolution of pre-mRNA intron lariats and therefore suggests that similar mecha

156 SF3B1, prevent accumulation of postcatalytic intron lariats, and contribute to the timely eviction of

157 To understand how exon and intron length and splice site recognition mode impact sp

158 al that splicing fidelity depends largely on intron length together with secondary structure and spli

159 We also found considerable intron length variation and mismatches of alleles detect

160 These introns likely provided the framework for the emergence

161 the last exon of genes besides the ordinary intron locality, thus potentially modifying the end of g

162 Considering the fact that an intron may have multiple branchpoints, we transform the

163 everse transcriptases (RTs) function in both intron mobility and RNA splicing and are evolutionary pr

164 Instead, our findings implicate intron mobility as a direct driver of host gene diversit

165 lent type of AS event (40%) was retention of introns, most of which were supported by multiple cDNA e

166 While this implies that the intron must be transcribed to increase expression, the T

167 genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content.

168 This is the greatest number of introns observed in annelid mtDNA genomes, and possibly

169 STAiR2 originates from the first intron of a tumor suppressor gene.

170 ned regulatory elements and within the first intron of all genes.

171 ns is a GGGGCC repeat expansion in the first intron of C9ORF72 As shown by recent intensive studies,

172 regulatory element (FIRE), within the second intron of Csf1r, is necessary and sufficient to direct m

173 Klf5 binding sites in the promoter and first intron of Dmp1 and Dspp genes that are homologous across

174 ct of Klf5 on Dspp activity was in the first intron of Dspp gene.

175 ST1 bound CATATG/CAGCTG E boxes in the first intron of genes that regulate autophagosome/lysosomal de

176 ly binding to the E-box element in the first intron of HP1gamma gene, and the upregulated HP1gamma, i

177 ermore, the splicing efficiency of the first intron of nad2, encoding for another complex I subunit,

178 .8 x 10(-9)), which resides within the sixth intron of PHB.

179 stant TCF4/beta-catenin-binding sites in the intron of Rnf43 This novel activity of DDB2 was required

180 A "+9.5-like" element resides in an intron of Samd14 (Samd14-Enh) encoding a sterile alpha m

181 NTR-Alu (SVA)-type retrotransposon within an intron of TAF1 This unique insertion coincides with six

182 morphism (rs12519770, P=2.98x10(-)(8)) in an intron of the adhesion GPR98 (G-protein-coupled receptor

183 Expanded GGGGCC repeats in the first intron of the C9orf72 gene represent the most common cau

184 3460075, OR = 0.56, P = 3.8 x 10(-8)) in the intron of the dystrophin gene DMD (X chromosome), and a

185 61,082,153, p = 8.2 x 10(-9)) located in an intron of the FHIT gene.

186 (P = 2.40 x 10(-8)), which is located in an intron of the gene GPM6B.

187 l as decreased DNA methylation in the second intron of the Kappa gene.

188 nucleotide polymorphism (SNP) located in the intron of the long noncoding RNA (lncRNA) LINC00305 by s

189 ritized rs9349379, a common SNP in the third intron of the PHACTR1 gene, as the putative causal varia

190 of WNT4 and SNP rs11918967 is located in the intron of WNT5A.

191 iabetes and fasting glucose levels reside in introns of ADCY5, a gene that encodes adenylate cyclase

192 at defined non-coding regions, such as first introns of genes and regulatory domains, are associated

193 ranscription termination events within first introns of pc genes.

194 Here we identified mutations located deep in introns of POLR3A to be a frequent cause of hereditary s

195 y, these silencing events often occur within introns of transcriptionally active genes, and lead to t

196 can visualize the locations-within exons and introns-of sequence variants to be analyzed and the pred

197 mRNA accumulation, the effect of a UBIQUITIN intron on gene expression was tested from six different

198 Discordant canonical introns, one nt apart, are present in yet other species,

199 Some genome-wide significant loci in introns or noncoding regions could affect regulation of

200 print on the insertion environment of mobile introns or nonrandom patterns of genetic diversity are c

201 SNPs; P < 2.2 x 10(-7)), and were mostly in introns or regulatory regions with predicted effects inc

202 transcription factor through changes in exon-intron organization and thereby supported the evolution

203 ncluding 683 intra-molecularly co-associated intron pairs.

204 Self-splicing introns populate several highly conserved protein-coding

205 Using conservation of intron positions, we determined that the nine Arabidopsi

206 e introns within cox1 is similar to Group II introns previously identified, suggesting that introns i

207 such as exon circularization, first and last intron processing, alternative 5 and 3'ss usage and exon

208 riptome-wide associations between LeafCutter intron quantifications and 40 complex traits increased t

209 GU-AG consensus sequences are used for intron recognition in the majority of cases of pre-mRNA

210 alpha signal joints on TCR excision circles, intron recombination signal sequence k-deleting element

211 ting recombination excision circles, genomic intron recombination signal sequence k-deleting element

212 in situ RNA hybridization (RNA-FISH) of the intron region of immediate early transcripts, we visuali

213 ription factor STAT1 to the enhancer and the intron regions of ROS1 target genes, CXCL1 and GLI1, for

214 splice site (ss) recognition, branching, and intron release, but lacked information on 3'-ss recognit

215 d a particular, transcript-specific order of intron removal in human genes.

216 We propose that defects in intron removal in SMA promote DNA damage in part through

217 Intron removal requires assembly of the spliceosome on p

218 onic region that reduces Pasilla binding and intron removal selectively impairs long-term memory.

219 g are marked by distinct patterns of ordered intron removal.

220 enome, we discover the smallest spliceosomal introns reported for any species.

221 Many mammalian genes contain poorly spliced introns, resulting in nuclear detention of partially spl

222 o-Ser2 RNA polymerase II specifically at the intron retained under hypoxia.

223 These findings suggest that intron-retained mRNAs in the cytoplasm have previously u

224 However, many intron-retained mRNAs were not substrates for nonsense-m

225 xpression through nonsense-mediated decay of intron-retained transcripts.

226 e aberrations accompany increased unspliced (intron-retained) and decreased spliced mRNA of IFNG and

227 virus and woodchuck hepatitis virus), and an intron-retaining transcript encoded by the cellular NXF1

228 is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediat

229 text of fruit development; the percentage of intron retention (IR) is markedly reduced whereas that o

230 Intron retention (IR) occurs when an intron is transcrib

231 Widespread intron retention and markers of the DNA damage response

232 We show elevated U12-intron retention in all examined tissues from SMA mice,

233 Reverse transcriptase PCR demonstrated minor intron retention in all of 9 randomly selected RNAs from

234 ng identified several factors that influence intron retention in EIF2B5: a weak splicing potential at

235 issues from SMA mice, and that U12-dependent intron retention is induced upon siRNA knock-down of SMN

236 Intron retention is the major type of alternative splici

237 nhibition of this signaling pathway leads to intron retention of lipogenic genes, which triggers nons

238 Intron retention was concomitant with a strong induction

239 Intron retention was significantly lower in the absence

240 SSA generally displaying stronger effects on intron retention, and Sudemycins more acute effects on e

241 rotein isoform structure and function (e.g., intron retention, exon skipping).

242 We found evidence of widespread intron retention, particularly of minor U12 introns, in

243 native exon lead to inefficient splicing and intron retention.

244 ng including alternative polyadenylation and intron retention.

245 PHF5A-Y36C alters splicing modulator-induced intron-retention/exon-skipping profile, which correlates

246 our observations using thermostable group II intron reverse transcriptase sequencing (TGIRT-seq) to c

247 as mismatches using a thermostable group II intron reverse transcriptase.

248 Bacterial group II intron reverse transcriptases (RTs) function in both int

249 -switching activity of thermostable group II intron reverse transcriptases (TGIRTs) for DNA-seq libra

250 We analyzed the transcriptome of the intron-rich eukaryote Paramecium tetraurelia.

251 variant H2A.Z in pre-mRNA splicing using the intron-rich model yeast Schizosaccharomyces pombe Using

252 cture of a full-length thermostable group II intron RT in complex with an RNA template-DNA primer dup

253 stinctive biochemical properties of group II intron RTs, and it provides a prototype for many related

254 ntron sequences against the U12-type spliced intron sequence database to examine whether some events

255 First, we investigate a variety of intron sequence-derived features, such as sparse profile

256 NCODE project RNA-Seq data to search spliced intron sequences against the U12-type spliced intron seq

257 mRNA (pre-mRNA) splicing removes non-coding intron sequences to produce mature mRNA.

258 nd attempt to predict branchpoint sites from intron sequences.

259 An evolutionary pathway of 1 nt intron shift, involving an alternatively spliced stwintr

260 iplets among the first and last 50 nt of the introns significantly differ between constitutive and re

261 targets were detected in all fractions, with intron, snoRNA and lncRNA interactions enriched in the n

262 es, which are initially recognized in either intron-spanning ('intron definition') or exon-spanning (

263 upports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe Both

264 bilities in four additional RNAs: a group II intron, Spinach II, 2-MS2 binding domain and glgC 5 UTR.

265 to study sample and population variation in intron splicing.

266 f chloroplast RNA processing beyond group II intron splicing.

267 ed by exonic coconversion, which occurs when introns spread to empty target sites via homologous reco

268 An analysis of the exon/intron structure and protein domains was conducted to su

269 An analysis of the exon-intron structures and conserved motifs provided further

270 Surprisingly, hundreds of cytoplasmic intron targets were detected.

271 We validate an extreme class of intron that can only splice in a multi-intron context.

272 variants in the FAD2 5' untranslated region intron that determine the expression level of the gene.

273 located on the 5' half of the trans-spliced intron that is almost absent in the partially complement

274 he protein, an isoform containing a retained intron that is detained in the nucleus, and an isoform c

275 , self-nonself discrimination depends on the intron that programs the circRNA.

276 Shorter introns that contain enhancers splice early.

277 Mirtrons are introns that form pre-microRNA hairpins after splicing,

278 tes cotranscriptional splicing of suboptimal introns that may otherwise be discarded via proofreading

279 n pre-mRNA is interrupted, on average, by 11 introns that must be spliced out for proper gene express

280 s its sequence is derived from an artificial intron, the cassette is removed by the splicing machiner

281 nate immune sensing of circRNA and highlight introns-the predominant output of mammalian transcriptio

282 isoforms revealed skipped exon and retained intron to be the most abundant alternative splicing even

283 , we mutated the splice sites in an affected intron to consensus and found that this suppressed the r

284 Use of a human intron to express a foreign circRNA sequence abrogates i

285 V tripartite leader (TPL), composed of three introns (TPL 1-3), is critical to the translation of HAd

286 Notably, this intron was expressed in solid tumors in a stage-dependen

287 ncrease expression, the TSS changed when the intron was located in the 5'-untranslated region (UTR),

288 xamples of splicing suppression when the env intron was retained in the 4-kb size class.

289 By comparing retained and constitutive introns, we identified sequence features potentially res

290 of genes and splicing efficiency in over 140 introns were affected.

291 These cytoplasmic introns were found to be highly conserved and introduced

292 th 3' ends within protein-coding regions and introns were less stable than mRNAs that end at 3'-UTR p

293 Interestingly, the introns were of variable sizes suggesting possible evolu

294 d to P5CS1 regulatory sequences in the first intron, which carries a conserved PHR1-binding site (P1B

295 regions of the genome (promoters, UTRs, and introns), while being depleted in coding and intergenic

296 that child abuse is associated in the Kappa intron with a selective reduction in levels of DNA hydro

297 s, and RNA sequencing (RNA-seq) reveals that introns with nonconsensus branch points are particularly

298 in intergenic, 12% in promoters, and 28% in introns, with similar statistics observed in L1 arrest l

299 This study also identified a novel intron within the LANA 5' untranslated region using a sp

300 The sequence of the introns within cox1 is similar to Group II introns previ