ライフサイエンスコーパス: splice site

1 n of nucleotide 'C' at position -3 of the 3' splice site.

2 Each transposon carries one splice site.

3 the recognition of weak Py-tracts at the 3' splice site.

4 exon skipping, or by creating a new cryptic splice site.

5 ing of U1-70K (snRNP70) to the downstream 5' splice site.

6 conserved, and closely distributed to the 3' splice site.

7 ns that fail to reconstitute an efficient 5' splice site.

8 Our data also do not support it being a splice site.

9 s: a 5' splice site, a branch site, and a 3' splice site.

10 side before its release from the pre-mRNA 5' splice site.

11 lic attack of the branch adenosine at the 5' splice site.

12 49T > G, predicted to generate a novel donor splice site.

13 mutated SF3B1 residues contact the pre-mRNA splice site.

14 the spliceosomal U1 snRNP to a suboptimal 5' splice site.

15 e forms a hairpin that weakly tethers the 5' splice site.

16 ancy and more likely to contain nonconsensus splice sites.

17 xonic sequences and are spliced at canonical splice sites.

18 regulatory signals, including a role for RNA splice sites.

19 ome must distinguish optimal from suboptimal splice sites.

20 am of transcription start sites and flanking splice sites.

21 in both coding and noncoding sequences like splice sites.

22 and affected by mutations outside consensus splice sites.

23 NA) splicing through disruption of consensus splice sites.

24 know the tertiary structures surrounding the splice sites.

25 , but also can promote use of alternative 5' splice sites.

26 and utilize alternative branch sites and 3' splice sites.

27 anonical introns, lacking conventional GT-AG splice sites.

28 he splicing substrate to disengage candidate splice sites.

29 e-tunes relative affinities of mismatched 5'-splice sites.

30 reds of introns with adjacent alternative 3' splice sites.

31 ein particle called U1 snRNP engages with 5' splice sites.

32 the altered splicing of introns with weak 5' splice sites.

33 exonic cores, even after excluding canonical splice sites.

34 we identified 14 different novel variants (2 splice site, 2 frameshift and 10 missense changes) in GN

35 e tract (PPT) and AG dinucleotides at the 3' splice site (3'ss).

36 samples, we show that hundreds of cryptic 3' splice sites (3'SSs) are used in cancers with SF3B1 muta

37 aberrant pre-mRNA splicing using cryptic 3' splice sites (3'SSs), but the mechanism of their selecti

38 omoted by cytosine at rs609621 in the NSE 3' splice-site (3'ss), which is predominant in high cancer

39 The selection of 3 splice sites (3ss) is an essential early step in mammali

40 er N1 (ISS-N1), located downstream of the 5' splice site (5'ss) of exon 7.

41 e first catalytic step of splicing at the 5' splice site (5'ss).

42 intron contains three obligate signals: a 5' splice site, a branch site, and a 3' splice site.

43 r results provide a mechanism for exon 16 3' splice site activation in which a coordinated effort amo

44 tification of global locations of endogenous splice-site activation by lariat sequencing confirms the

45 Our findings suggest that cryptic splice-site activation is more common than previously th

46 Splice-site activation was predicted for 129 (28%) of th

47 The 3'-splice site AG dinucleotide is recognized through non-Wa

48 n-trapping assays with constructs containing splice site alleles revealed errors in splicing.

49 s that are more than 30 nucleotides from any splice site alter splicing nine times as often as common

50 ading to frame shifts, nonsense, missense or splice-site alterations.

51 Splice site analysis of rs12252_C was performed using PI

52 c) and identified 2 deleterious mutations (1 splice site and 1 nonsense mutation) and 1 missense muta

53 olves U6atac and U12 interaction with the 5' splice site and branch site regions of a U12-dependent i

54 o acid residues, leading to perturbed normal splice site and exon recognition.

55 through non-Watson-Crick pairing with the 5' splice site and the branch-point adenosine.

56 ells were characterized by particularly weak splice sites and by upstream binding sites for Polypyrim

57 Moreover, when both splice sites and poly(A) signals were mutated, polyadeny

58 mputational analysis of DNA sequences around splice sites and poly-A signals is able to explain sever

59 vely, the strong nucleosome positioning over splice sites and surrounding putative transcription fact

60 tely sensitive to the sequence context of 3' splice sites and to small structural differences between

61 tial correlation of CAGE clusters with donor splice sites and with poly(A) sites.

62 nsense, and frameshift mutations, as well as splice-site and deletion mutations.

63 terozygous KMT2D mutation (50% nonsense, 20% splice site, and 30% missense mutations), and 70% of the

64 c variants (four non-sense, 21 missense, one splice site, and five frameshift variants) that were pot

65 contain cytosine-rich sequences near the 5' splice site, and have suboptimal splice sites in the imp

66 th achromatopsia include missense, nonsense, splice site, and single-nucleotide deletion or duplicati

67 ogether to identify the 5 splice site, the 3 splice site, and the branchsite (BS) of nascent pre-mRNA

68 onation of alternative promoters, enhancers, splice sites, and termination signals.

69 CA-RNA are within 50 nucleotides of 5' or 3' splice sites, and the vast majority of exons harboring m

70 After exclusion of pathogenic coding, splice-site, and copy-number variations, a parallel appr

71 terious ARMC9 variants (stop-gain, missense, splice-site, and single-exon deletion) in 11 individuals

72 ation of gene promoter elements, intron/exon splicing sites, and SH RNAs, location of RNA degradation

73 s regard, we found that DNA sequences at RNA splice sites are hypersensitive to digestion by MNase bu

74 other variants that may create or eliminate splice sites are often clinically classified as variants

75 uctionist approach focused on how individual splice sites are recognized.

76 epithelial transition (MET) near the exon 14 splice sites are recurrent in lung adenocarcinoma and ca

77 the catalytic stage of splicing, suboptimal splice sites are repressed by the DEAH-box ATPases Prp16

78 level, our results implicate non-synonymous, splice site as well as stop-altering single-nucleotide v

79 regions, such as 5' untranslated regions and splicing sites, as well as in genes previously not predi

80 Once the 3' splice site at ancient Alu-exons reaches a stable phase,

81 propose a role for Cwc21p positioning the 3' splice site at the transition to the second step conform

82 rassa TER intron contains a non-canonical 5'-splice site AUAAGU that alone prevents the second step o

83 In contrast, a non-canonical 5' splice site blocks the second transesterification reacti

84 U2AF and U1 snRNP binding to the target exon splice sites but blocked U2 snRNP assembly in HeLa nucle

85 exons in the affected genes contain weak 5' splice sites, but are otherwise indistinguishable from a

86 ion of regulatory RNA cis elements in the 3' splice site by the U2 auxiliary factor (U2AF).

87 ( *)), c.247_250del (p.Asn83Hisfs( *)4), and splice site c.830+2_830+3insT mutations lead to C-termin

88 ; p.Pro166His and c.1229A>G; p.Asp410Gly), 1 splice site (c.1282A>C p.Ser428Arg), 1 frameshift (c.470

89 , c.2352_2353insC (p.Arg785Glnfs( *)23), and splice-site, c.4549-1G>A, mutations were identified.

90 in SMOC2 promotes the utilization of cryptic splice sites, causing its incorporation into transcripts

91 nse, three extension mutations, six putative splice site changes, and seven changes that lead to a co

92 ne expression, while allowing flexibility in splice site choice with the nonribosomal protein transcr

93 imultaneously affects transcription rate and splicing site choice can explain the alternative splicin

94 ift toward usage of the adjacent proximal 3' splice site (closer to the 5' end of the intron).

95 that at least 84.1% of these predicted novel splice sites could be validated.

96 mplest organisms that possess mammalian-like splice site degeneracy.

97 and simple library prep and high resolution splice site detection.

98 suggesting SFPS might be involved in the 3' splice site determination.

99 used RNA-seq aligners rely on the consensus splice site dinucleotide motifs to map reads across spli

100 equently, genomic variants that create novel splice site dinucleotides may produce splice junction RN

101 ides evidence of mutations outside consensus splice sites disrupting splicing and introduces the conc

102 interactions between the branch helix and 5'-splice site dock the branch adenosine into the active si

103 nd stabilize a conformation competent for 3'-splice site docking, thereby promoting exon ligation.

104 ne AF cohort, 9 rare missense variants and 1 splice site donor variant were detected.

105 ce of U6 snRNA, which base-pairs with the 5'-splice site during catalytic activation, forms a hairpin

106 ZRSR2 is involved in the recognition of 3'-splice site during the early stages of spliceosome assem

107 ation signals, identification of alternative splicing sites, etc.

108 One 9-bp duplication and one splice-site, five missense, and two nonsense variants in

109 of eukaryotic genes, the spliceosome selects splice sites for intron excision and exon ligation.

110 owing to competition with a reconstituted 5' splice site formed at the RS-site after the first splici

111 atures such as transcription start sites and splicing sites from histone marks.

112 cells preferring to splice at the distal 3' splice site (furthest from the 5' end of the intron) and

113 g on cassette exons: binding close to the 5' splice site generally promoted exon inclusion, whereas b

114 . pombe TER intron contains the canonical 5'-splice site GUAUGU, the N. crassa TER intron contains a

115 IFITM3 rs12252_C, a putative alternate splice site, has been associated with influenza severity

116 r RNA production occurs at major spliceosome splice sites; however, we find the first examples of dev

117 ions with obvious exonic coding or canonical splice site impact.

118 on (c.1909+22G>A), which activates a cryptic splice site in a tissue and stage of development-specifi

119 rnal deletion due to activation of a cryptic splice site in exon 9 of the gene (c.1090_1129del; p.Val

120 in patients revealed activation of a cryptic splice site in intron 4 resulting in a frame shift and a

121 termed VEGFAxxxb that utilise an alternative splice site in the final exon have been widely reported,

122 b (resulting from alternative usage of a 3' splice site in the terminal exon) is protective for kidn

123 ce of the latter correlation, we mutated the splice sites in an affected intron to consensus and foun

124 determined that two competing alternative 5' splice sites in exon 12 yield Esrp1 isoforms with differ

125 tion decreases RNP complex formation at most splice sites in exon-intron junctions throughout the gen

126 midine (Py) signals of the major class of 3' splice sites in human gene transcripts remains incomplet

127 near the 5' splice site, and have suboptimal splice sites in the impacted intron, suggesting that a c

128 The presence of canonical splice sites in the mtRNA introns and of core components

129 Detecting specific splice sites in this large sequence pool is the responsi

130 Thus, identifying splicing sites in DNA/RNA sequences is significant for b

131 so uncovered thousands of previously unknown splice sites, indicating pervasive splicing; yet most of

132 miR-16 expression by introducing three novel splicing sites instead of the missing 5' terminal splici

133 ely on hyperstabilization of the U6 snRNA-5' splice site interaction to impede the 2nd step of splici

134 a2 expression using translation blocking and splice-site interfering morpholinos.

135 novel elements of RNA processing-alternative splice sites, introns, and cleavage sites-which are ofte

136 The 5'-splice site is cleaved but remains close to the catalyti

137 The other splice site is co-opted from the gene sequence that is d

138 situated between the branch point and the 3' splice site is crucial for inclusion.

139 st introns are gone nearly as soon as the 3' splice site is transcribed and that introns have distinc

140 ce that use of germline-specific proximal 3' splice sites is conserved across Caenorhabditis species.

141 We show that evolutionary progression of 3' splice sites is coupled with longer repressive uridine t

142 around the start codon upstream of the first splice site: it preferentially decorates more structured

143 antisense DNA strands) of DNA methylation at splice site junctions in A. mellifera MeDIP-Seq datasets

144 Due to its ability to query novel splice sites, JunctionSeq is still able to detect these

145 The del12 mutation activates a cryptic splice site, leading to a frameshift mutation and a prem

146 bundles A and B and C, D, E, F, and G via a splicing site located in the BC loop.

147 tify a recurrent homozygous c.408+1G>A donor splice site loss-of-function mutation in DDRGK domain co

148 esting that specific changes in the pre-mRNA splicing sites may be a mechanism by which MAP escapes h

149 at retained introns tend to have a weaker 5' splice site, more Gs in their poly-pyrimidine tract and

150 ted organs, and, accordingly, tuba start and splice site morphants showed various ciliary mutant phen

151 that U2AF1 mutations alter the preferred 3' splice site motif in patients, in cell culture, and in v

152 BCB11 mutations - Glu297Gly (x3) and a donor splice site mutation (intron 19).

153 re-attributes the phenotypes to an essential splice site mutation affecting adgra2 (gpr124) splicing

154 siblings were compound heterozygotes with a splice site mutation c.1220 + 1G>C (IVS13 + 1 G>C).

155 verified by Sanger sequencing, identified a splice site mutation c.212 + 1 G > T in the SNX10 gene e

156 ompound heterozygous for p.Gly131Glu and the splice site mutation c.240-1G>C, previously reported in

157 e second family identified a distinct, novel splice site mutation c.643 + 1G > A, that perfectly segr

158 Screening for splice site mutation c.828+3A>T in the peripherin 2 (PRP

159 A similarly delivered ASO targeting a causal splice site mutation for Usher syndrome corrects gene ex

160 enital adrenal hyperplasia, and an essential splice site mutation in a proband with partial lipodystr

161 Finally, we report a deletion and a splice site mutation in IFT74, inherited under a recessi

162 ied a novel locus, JBTS23, with a homozygous splice site mutation in KIAA0586 (alias TALPID3), a know

163 The PRPH2 c.828+3A>T splice site mutation is a frequent cause of inherited re

164 The effect of the splice site mutation on the PRPH2 transcript was analyze

165 By using a binary splice site mutation suppressor assay we demonstrate tha

166 Results of testing for splice site mutation, haplotypes, and alternate transcri

167 al pattern despite the presence of the donor splice site mutation, likely due to the action of a puta

168 utation (c.496C>T [p.Arg166*]) and a de novo splice-site mutation (c.2572-2A>G), whereas the other be

169 In the latter case, we found a homozygous splice-site mutation (c.735+2T>C) in CEP104.

170 A conserved splice-site mutation in 1 copy of the suppressor of fuse

171 We found that a splice-site mutation in the component of the transcripti

172 , Reln(CTRdel), carries a chemically induced splice-site mutation that truncates the C-terminal regio

173 hat exclusively express MPc by inserting the splice-site mutation.

174 in, frame shift, initiation codon (INIT) and splice site mutations (n = 930, OR = 1.3, P = 1.5xE-5).

175 NER alterations, including nonsynonymous or splice site mutations and homozygous deletions of NER ge

176 ants, including rare or uncommon missense or splice site mutations in 9 and homozygous synonymous var

177 ere compound heterozygous for frameshift and splice site mutations leading to reduced, but not absent

178 proteins to the NP1 open reading frame, and splice site mutations that prevented their expression in

179 Frameshifting and splice site mutations were common, found in 4 of 5 patie

180 No nonsense or essential splice site mutations were found in 2,479 controls, whil

181 third family were compound heterozygous for splice-site mutations c.700+1G>T and c.4002+1G>A.

182 CPAMD8 splice-site mutations caused aberrant pre-mRNA splicing

183 Two splice-site mutations were identified, including homozyg

184 nse mutations, 9 frameshift mutations, and 5 splice-site mutations.

185 Among them, three are splicing site mutations, four are nonsense mutations, se

186 Disease-causing mutations can often occur in splice sites near intron borders or in exonic or introni

187 nding assays, shows that the selection of 5'-splice site nucleotides by U1 snRNP is achieved predomin

188 ort RNA duplex is established between the 5' splice site of a pre-mRNA and the 5' end of the U1 snRNA

189 sociated single nucleotide polymorphism in a splice site of ANK3.

190 enotype of the A-to-G substitution in the 3' splice site of BBS8 exon 2A (IVS1-2A>G mutation) in the

191 ions were identified over time except for 5' splice site of exon 10.

192 nd interfering with that of U2AF65 at the 3' splice site of exon 7.

193 actions within U1 snRNP, and show how the 5' splice site of pre-mRNA is recognised by U1 snRNP.

194 In contrast, the internal C-terminal splice site of TyrRSDeltaE2-3 prevented either dimerizat

195 We proved that the 5' splice sites of CD46 cassette exons 7 and 8 encoding ext

196 tely identified 168 of 180 (93.3%) canonical splice sites of five genes.

197 Splicing factor 1 (SF1) recognizes 3' splice sites of the major class of introns as a ternary

198 er than previous estimates, with alternative splice sites on average activated at approximately 3% th

199 lead to a premature stop, disrupt canonical splice sites, or lead to insertions/deletions that shift

200 ribe pathogenic mutations in splice factors, splice sites, or regulatory sequences.

201 The c.1164-1G>A splice-site, p.Gln358SerfsTer13 frameshift, and p.Gln376

202 m a bridging structure that enforces correct splice site pairing.

203 on-coupled splicing of RNAs in which weak 5' splice sites predominate, enabling diversification of hu

204 ingers give rise to different alterations in splice site preference and largely distinct downstream s

205 exon inclusion, whereas binding near the 3' splice site promoted either exon skipping or inclusion.

206 Private exons often arise from cryptic splice sites providing an important clue for variant pri

207 U1 snRNP plays a critical role in 5'-splice site recognition and is a frequent target of alte

208 cations have been proposed to play a role in splice site recognition and regulation.

209 ted SF1 loop are required for cooperative 3' splice site recognition by the SF1-U2AF(65) complex (whe

210 e the molecular mechanism and dynamics of 3' splice site recognition by U2AF65 and the role of U2AF35

211 The mechanism of 3'-splice site recognition during exon ligation has remaine

212 to determine how mutations affecting the 3' splice site recognition factor U2AF1 alter its normal ro

213 To understand how exon and intron length and splice site recognition mode impact splicing, we measure

214 f several of these mutations on splicing and splice site recognition, functional connections linking

215 or the function of positioned nucleosomes in splice site recognition.

216 ociates with the snRNAs that are involved in splice site recognition.

217 d SR proteins, which then promotes efficient splice-site recognition and subsequent spliceosome assem

218 SR family of splicing factors for efficient splice-site recognition, but this idea is incompatible w

219 e steps by re-splicing at ratchet points--5' splice sites recreated after splicing.

220 sette exons, thus driving a novel pathway of splice site regulation within the mammalian transcriptom

221 ions (sm) smA1' and smD1' at the A1' and D1' splice sites, respectively.

222 lation on its associations with U2AF(65) and splice-site RNAs are likely to influence pre-mRNA splici

223 affinities for either optimal or suboptimal splice-site RNAs.

224 contain a cryptic site, known as a recursive splice site (RS-site), that enables a multi-step process

225 length together with secondary structure and splice site score.

226 untranslated region activated HPV16 late 5'-splice site SD3632 and resulted in production of HPV16 L

227 that bypassed the suppressed HPV16 late, 5'-splice site SD3632; produced elevated levels of RNA-bind

228 the intervening years has revealed that both splice site selection and splicing itself are much more

229 Our microarray analysis shows changes in 3' splice site selection at elevated temperature in a subse

230 alternative splicing, including alternative splice site selection for over half of all annotated int

231 Research into the problem of splice site selection has followed a reductionist approa

232 hanism whereby SRm300/SRRM2, might influence splice site selection in human cells.

233 own recently to alter branch site (BS) or 3' splice site selection in splicing.

234 higher organisms, but the regulation of the splice site selection remains incompletely understood.

235 hexamer sequence motifs measurably influence splice site selection when positioned within alternative

236 the level of RNA splicing via alternative 5' splice site selection within exon 2 to produce either th

237 cause snRNP70 is a key early regulator of 5' splice site selection, our results suggest a model in wh

238 ition varies based on proteins that modulate splice site selection.

239 MDS patient samples demonstrate aberrant 3' splice-site selection associated with increased nonsense

240 ch as the CDC2-like kinase 1 (CLK1), weakens splice-site selection.

241 The unique N. crassa TER 5'-splice site sequence is evolutionarily conserved in TERs

242 Optimization of splice site sequences or mutation of nearby cytosines el

243 16 that targets SRSF1, it did not affect the splice site shifting activity of SRSF1.

244 f molecular recognition for a major class of splice site signals.

245 The splice site single nucleotide polymorphism (rs41283526)

246 94 splice junctions had splice site SNPs associated with GWAS signals of human t

247 the splice-modulating potential of canonical splice-site SNVs.

248 Using splice site-specific antisense morpholino oligos, we inh

249 d Rex-knockout HTLV-1 molecular clones using splice site-specific quantitative reverse transcription

250 of these viral mRNAs was confirmed by using splice site-specific RT-PCR with ex vivo samples.

251 Splice site specification is controlled by interactions

252 Among them, alternative 3 ': splice site (SS) and 5 ': SS account for more than 30% o

253 iceosome complexes revealed mechanisms of 5'-splice site (ss) recognition, branching, and intron rele

254 The spliceosome must identify the correct splice sites (SS) and branchsite (BS) used during splici

255 Eleven MAPT gene splice site stem loop mutations were identified over tim

256 Splice site strength correlated with IR among stable but

257 Experimental enhancement of splice-site strength in mini-gene constructs overcomes t

258 latory functions, we found that de novo near-splice site synonymous mutations changing exonic splicin

259 Dense methylation near the Karma splice site (termed the Good Karma epiallele) predicts n

260 cing in germline cells occurs at proximal 3' splice sites that lack a preceding polypyrimidine tract,

261 spliceosome work together to identify the 5 splice site, the 3 splice site, and the branchsite (BS)

262 Adjacent alternative 3' splice sites, those separated by </=18 nucleotides, prov

263 Most chimeras use canonical splicing sites, thus are likely products of 'intergenic

264 ajor splice donors (MSDs) can activate novel splice sites to produce HIV-1 transcripts, and cells wit

265 inants of the differential sensitivity of 3' splice sites to these drugs.

266 s the use of the growing annotation of known splice sites, transcription start and end sites, or full

267 o novel variants include nine missense, four splice site, two non-sense, one insertion and six gross

268 s, we identified 244,246 coding-sequence and splice-site ultra-rare variants (URVs) that were unique

269 Splice site usage has been mapped exhaustively across di

270 ce of chromatin factors on cotranscriptional splice site usage remains unclear.

271 fic regulation of neurexin transcription and splice-site usage.

272 A splice site variant (c.502-2A>G) in the FHL1 gene was hi

273 nts in DCPS in three affected individuals; a splice site variant (c.636+1G>A) that results in an in-f

274 shift (p.[A1048fs*13], p.[L849Afs*3]), and a splice site variant (c.761 + 2T>A).

275 nsive extramacular drusen, carried essential splice site variant CFH 1:196648924 (IVS6+1G>A) or misse

276 Targeted analysis showed that this splice site variant cosegregated with disease in the fam

277 ently described RAB28 gene, the c.172 + 1G>C splice site variant in IVS2 and the missense c.T651G:p.C

278 We also identified a heterozygous splice site variant in the nuclear envelope gene SYNE1 i

279 Sequencing cDNA showed the splice site variant led to skipping of exons 6 of the FH

280 Our data suggest that a novel FHL1 splice site variant results in the absence of FHL1A and

281 ved in fibroblasts from a patient carrying a splice site variant; functional studies in yeast confirm

282 onymous and 1% gain or loss of stop codon or splice site variant] in 16 751 genes with the strongest

283 2_Glyfs( *)51]) in one family and a putative splice-site variant (c.3985+5C>A) in the other.

284 mphoblasts from the patient carrying a SYNE1 splice-site variant displayed changes in nuclear morphol

285 Proband 1 inherited a splice-site variant that results in skipping of exon 13,

286 n spectrum includes frameshift, missense and splice site variants and one single-exon deletion.

287 assays were performed for two non-canonical splice site variants and revealed missplicing for the mu

288 cted 28 low-frequency missense, nonsense and splice site variants that were enriched in the pre-eclam

289 or allele frequency <0.5%) nonsynonymous and splice-site variants in 2 arrhythmia susceptibility gene

290 Novel non-synonymous/splice-site variants in extracellular matrix genes were

291 e patients harbored heterozygous nonsense or splice-site variants in the nucleoporin genes NUP37, NUP

292 Rare missense, truncating or splice-site variants shared by the 3 relatives were sele

293 ns were defined as nonsense, frameshift, and splice-site variants, along with missense variants resul

294 s or compound heterozygous) nonsynonymous or splice-site variations in 6 cardiomyopathy-associated ge

295 ow likely distant mutations around annotated splice sites were to disrupt splicing.

296 ed U1 snRNAs, complementary to mutated donor splice sites, were able to improve exon definition very

297 e mutation in the DTNA gene produces a novel splice site which skips exon 21 and leads to a shorter a

298 positions 120739/121012 and encodes a single splice site, which is shared with the 3'-coterminal K14-

299 The splicing reaction requires definition of splice sites, which are initially recognized in either i

300 king, and restructures the pairing of the 5' splice site with the U6 snRNA ACAGAGA region.