ライフサイエンスコーパス: codon

1 -bound fluorescent protein lacking its start codon.

2 wo codons flanking the translation-defective codon.

3 tiated at an upstream ACG near-cognate start codon.

4 was predicted to result in a premature stop codon.

5 slational initiation at an alternative start codon.

6 in a frameshift and a premature termination codon.

7 A sequence close to the transgene initiation codon.

8 ough of the normal translational termination codon.

9 rget these mRNAs at sites distal to the stop codon.

10 esent epitopes downstream of the termination codon.

11 ependent mechanism that utilizes a CUG start codon.

12 ot thought to initiate from the 61 remaining codons.

13 y changing single nucleotides to create stop codons.

14 es reveals purifying selection affecting AUG codons.

15 and promote utilization of suboptimal start codons.

16 ers yeast ribosomes to read-through UGA stop codons.

17 nates transcripts with premature termination codons.

18 es include large clusters of synonymous rare codons.

19 nature of the immediately adjacent flanking codons.

20 , some of which serve as the exclusive start codons.

21 e to antibiotics due to its ten in frame UGA codons.

22 bacteria, capable of reading all three stop codons.

23 e of in vivo ribosome stalling at synonymous codons.

24 d mitoribosome stalling at the corresponding codons.

25 ousands of uORFs initiate with non-AUG start codons.

26 y base-stacking energy over three successive codons.

27 acids can be encoded by multiple synonymous codons.

28 they are translated more slowly than common codons.

29 target gene is disrupted by a series of stop codons.

30 hat is strongly selected against among start codons.

31 f ribosome density downstream of all UGA-Sec codons.

32 h causes a leucine to serine substitution at codon 102 (Human Genome Variation Society nomenclature:

33 Mutations that replaced the lysine at codon 110 and the arginine at codon 111 with alanine cod

34 the lysine at codon 110 and the arginine at codon 111 with alanine codons failed to replicate, and t

35 gly, CTCs harbored various KRAS mutations in codon 12 and 13.

36 harbored a NRAS point mutation (c.35G>A) in codon 12, resulting in a p.G12D substitution.

37 r, patients whose tumors harbor mutant KRAS (codons 12/13, 61 and 146) are often excluded from EGFR-t

38 rom substitution of valine for isoleucine at codon 122 of the transthyretin (TTR) gene (V122I), prese

39 ed prion type 1-2 and cases heterozygous for codon 129 generated intermediate CSF RT-QuIC patterns, w

40 f prion replication occur in a prion protein codon 129 genotype-dependent manner, reflecting the geno

41 ed with specific pairings of the genotype at codon 129 of the prion protein gene and conformational p

42 presented a HRAS point mutation (c.38G>T) in codon 13, resulting in a p.G13V substitution.

43 ighly conserved and a single polymorphism at codon 132 can markedly extend CWD latency when the minor

44 s, exploring the effects of polymorphisms at codon 146 of the goat PRNP gene on resistance to disease

45 at only animals homozygous for asparagine at codon 146 succumb to scrapie under natural conditions.IM

46 5, a change of glutamine to glutamic acid at codon 166 (p.Q166E) has been reported to alter the subst

47 cytosine for a thymine nucleotide (C64T) at codon 22, leading to a premature stop codon (R22X) in th

48 Guanines in codons 243, 244, 245, and 248 were most frequently oxidi

49 Rate constants for non-CpG codons 244 and 243 were not influenced significantly by

50 adduction on G at the major reactive CpG in codon 248 vs. the non-MeC fragment.

51 SK9 by inducing the ribosome to stall around codon 34, mediated by the sequence of the nascent chain

52 m glutamine (Gln, Q) to arginine (Arg, R) at codon 460 of the purinergic P2X7 receptor (P2X7R) has re

53 The best-known mutations at codons 460, 520, or 591 to 607 individually confer 5- to

54 deletion mutations, deletions that involved codons 557 and/or 558, and deletions that led to pTrp557

55 ons, including deletions that affect exon 11 codons 557 and/or 558.

56 mon point and in-frame deletion mutations at codons 591 to 603 remain incompletely characterized.

57 mple is BRAF mutations that occur outside of codon 600 ((non-V600) BRAF mutations).

58 efect in KIR2DP1 is a nucleotide deletion in codon 88.

59 ef clones harboring nonconsensus variants at codon 9 downregulated HLA-B (though not HLA-A) significa

60 tective HLA class I alleles, carriage of Nef codon 9 variants was also associated with reduced ex viv

61 field-collected samples of whole blood from codon 96 glycine/glycine, captive white-tailed deer that

62 t found by LAP in that it was more likely to codon align insertions and deletions and to facilitate t

63 th the rate ranged from 0.22 to 0.59 changes/codon among the 11 genes evaluated.

64 icient strains, sequencing identified 2 stop codon and 3 IS481 locations disrupting the prn gene.

65 that is placed between a translational start codon and a membrane-bound fluorescent protein lacking i

66 One mutation resulted in a premature stop codon and absent protein, while the second mutation repl

67 element that spans the initiating AUG and by codon and amino acid frequency.

68 ons between the first two nucleotides of the codon and anticodon and then is stabilized by base-stack

69 s a lower affinity of binding to the cognate codon and is more efficiently rejected than the fully mo

70 in the GL4 gene resulted in a premature stop codon and led to small seeds and loss of seed shattering

71 a mutation that resulted in a premature stop codon and protein truncation leading to complete loss of

72 n mutations creating a premature termination codon and the degradation of the mutated messenger RNA b

73 1A suppresses initiation at near-cognate UUG codons and AUGs in poor context.

74 Specific codons and codon combinations modulate ribosome speed an

75 t, functional roles for otherwise synonymous codons and enables experimental testing of the impact of

76 significantly enriched in slowly translated codons and evolutionarily conserved.

77 MD) of transcripts containing premature stop codons and related to the ATM and ATR kinases which are

78 monizing selected DNA segments by synonymous codons and reveal additional complexity involved in hete

79 at cause premature STOP codons, loss of STOP codons and single nucleotide polymorphisms, and short in

80 TPT3 into mRNAs with two different unnatural codons and tRNAs with cognate unnatural anticodons, and

81 rate; rather, interactions between adjacent codons and wobble base pairing are key.

82 s were predicted to introduce premature stop codons, and one was predicted to result in read through

83 entre nucleotide G530 stabilizes the cognate codon-anticodon helix, initiating step-wise 'latching' o

84 ons are nonrandom, and mutations at specific codons are associated with specific cancers, as widely d

85 Synonymous rare codons are considered to be sub-optimal for gene express

86 longation rate, so that sequences using fast codons are expected to be less affected by ribosome drop

87 the tRNAs represent rare tRNA species, whose codons are overrepresented in the viral genome.

88 y codon biased and using preferentially fast codons, are highly resilient to ribosome drop-off.

89 The level of FlgM activity produced by any codon arrangement was directly proportional to the degre

90 The various codon arrangements had no apparent effects on flgM mRNA

91 Dual-assignment of codons as termination and elongation codons is used to e

92 ncrease in the rate of mistranslation of Phe codons as Tyr compared to wild type, the increase in mis

93 ion of resistance mutations, particularly in codon Asp835 (D835).

94 encoded by a gene with an in-frame nonsense codon at an essential lysine can be expressed in its nat

95 tural proteins (NS) that share an initiation codon at the left end of the genome and which are indivi

96 at the rotated state with specific pairs of codons at P-A sites serve as RQC substrates.

97 Rare codons at the 5' terminus of coding sequences have been

98 cycle because a mutant virus containing stop codons at the amino terminus of ORF2 does not reactivate

99 acement of the stop codon with 46 additional codons at the C-terminus.

100 The canonical start codon (AUG) and a few near-cognates (GUG, UUG) are consi

101 Codon-based analyses of selection and assessments of cha

102 that bears the unusual premature termination codon besides the canonically spliced OsPCS2a transcript

103 d the impact of CDS recoding using different codon bias tables.

104 he translation machinery, known to be highly codon biased and using preferentially fast codons, are h

105 sfer RNA (tRNA) cognate to the terminal mRNA codon bound to the 70S ribosome.

106 lationally inserted at a predefined UGA opal codon by means of Sec-specific translation machineries.

107 Ribosomes decode mRNA codons by selecting cognate aminoacyl-tRNAs delivered by

108 es, we induced ribosome stalling at specific codons by starving the bacterium Escherichia coli for th

109 activates genes by precisely converting four codons (CAA, CAG, CGA, and TGG) into STOP codons without

110 ovide further evidence that fast-translating codons can be as biologically important as pause sites i

111 Early stop codons can be introduced in approximately 17,000 human g

112 cid substitution (G299V) or a premature stop codon causing strong virulence attenuation in mice.

113 although the usage frequencies of synonymous codons change from organism to organism, codon rarity wi

114 Neither in plasma nor in the liver codon changes were detected at position 282 that cause r

115 We demonstrate that many rare codon cluster positions are indeed conserved within homo

116 The identification of conserved rare codon clusters advances our understanding of distinct, f

117 While proteins with conserved rare codon clusters are structurally and functionally diverse

118 Most conserved rare codon clusters occur within rather than between conserve

119 Specific codons and codon combinations modulate ribosome speed and facilitat

120 ent a new genetic annotation approach termed Codon Consequence Scanner (COCOS).

121 A model explains these codon-context effects by suggesting that codon recogniti

122 egulation of the tRNA cognate to the mutated codon counteracts the effects of the sSNP and rescues pr

123 iling model was that the slow translation of codons decoded by rare tRNAs reduces efficiency.

124 e and cysteine in response to stop and sense codons, depending on the identity element and anticodon

125 Expression of alternative codon-derived DPRs in chick embryonic spinal cord confir

126 ild homozygous for the premature termination codon displayed symptoms consistent with MMIHS.

127 explain the observed ribosome pausing at AAA codons during translation and demonstrate how the s(2) m

128 s of chlB mRNA are changed by RNA editing to codons encoding evolutionarily conserved amino acid resi

129 0 and the arginine at codon 111 with alanine codons failed to replicate, and the pUL33 mutant interac

130 general functional role for synonymous rare codons farther within coding sequences has not yet been

131 ynonymous flgM allele were restricted to two codons flanking the translation-defective codon.

132 NucAmino is more likely to align codons flush with a reference sequence's amino acids and

133 annel Kv1.1 converts an isoleucine to valine codon for amino acid 400, speeding channel recovery from

134 ates (GUG, UUG) are considered as the 'start codons' for translation initiation in Escherichia coli.

135 ) drives the recoding of highly specific UGA codons from stop signals to Sec.

136 ion step of the two tRNALys and the slippery codons from the A- and P- sites.

137 Stop-codon-generating mutations in TcNTR-1 were associated wi

138 signed five segments of the Fab gene with a "codon harmonization" method described by Angov et al. an

139 The sequence encoding mature Pfs25 was codon harmonized for expression in Escherichia coli We p

140 ass I release factors (RFs) in decoding stop codons has evolved beyond a simple tripeptide anticodon

141 Our data suggest that rare codons have a regulatory role only if they are present w

142 conservation of rarity-rather than specific codon identity-could coordinate co-translational folding

143 meshift and subsequent premature termination codon in each.

144 (eIF)2-GTP scans the mRNA leader for an AUG codon in favorable "Kozak" context.

145 tion complex (PIC) scans the mRNA for an AUG codon in favorable context, and AUG recognition stabiliz

146 rnary complex (TC) scans the mRNA for an AUG codon in favorable context.

147 y was found to carry a premature termination codon in Leiomodin1 (LMOD1), a gene preferentially expre

148 ified by linkage analysis: a homozygous stop codon in PI3-kinase p110delta (PIK3CD) and a homozygous

149 reinitiation of translation at a third start codon in SPAST, resulting in synthesis of a novel M187 s

150 -also increase discrimination against an AUG codon in suboptimal Kozak context.

151 n a single IR1 repeat unit, including a stop codon in the EBNA-LP gene.

152 f human L1 loci containing at least one stop codon in their ORF1 sequence.

153 Reconstruction of the evolution of start codons in 36 groups of closely related bacterial and arc

154 cantly weaker than the selection on the same codons in coding sequences, although the switches betwee

155 B1 induced readthrough at all three nonsense codons in cultured cancer cells with TP53 (tumor protein

156 anslation initiation generally occurs at AUG codons in eukaryotes, although it has been shown that no

157 tant allele lines introducing premature stop codons in exon 1, as well as obtained an abcd1 allele fr

158 n of the repertoire exhibited premature stop codons in some elderly subjects, indicating that aging m

159 nstrate that introduction of equivalent stop codons in the full-length human L1 sequence leads to the

160 n our own prior work, we have shown that six codons in VH4-containing genes in B cells from the cereb

161 iminish initiation at near-cognate UUG start codons in yeast mutants in which UUG selection is abnorm

162 n) causes ribosome pausing at the respective codons in yeast.

163 variants, including a premature termination codon, in CRKL.

164 ted in vitro with mRNA harboring a UUG start codon, indicating destabilization of the closed PIN stat

165 nding to PICs reconstituted with a UUG start codon, indicating inappropriate rearrangement to the clo

166 nserved and introduced premature termination codons into coding regions.

167 Furthermore, the premature stop codon introduced by the CHADL frameshift mutation result

168 , the efficiency of translating a particular codon is influenced by the nature of the immediately adj

169 strong secondary structures around the start codon is more dependent on the SD-aSD interaction than w

170 nad5 losing both translation start and stop codons is enriched in the mutant.

171 If the initiation rate for these codons is low, then an AUG-initiated downstream ORF prev

172 Selection on start codons is most pronounced in evolutionarily conserved, h

173 However, purifying selection on start codons is significantly weaker than the selection on the

174 ment of codons as termination and elongation codons is used to expand the genetic code.

175 itate gene inactivation by induction of STOP codons (iSTOP), we provide access to a database of over

176 y in a participant's HIV quasispecies at pol codons K103N, Y181C, G190A, M184 V, or K65R by oligonucl

177 tein motif is dependent on stretches of rare codons, Leu(UUA)-Gly(GGU)-Val(GUA).

178 tation affecting one of five neighboring NF1 codons-Leu844, Cys845, Ala846, Leu847, and Gly848-locate

179 ith translation through a premature UAG stop codon located in a beta-galactosidase reporter.

180 s derived from tRNAs (3'-loop, 5'-loop, anti-codon loop), named tRFs, have been reported in several o

181 equence variations that cause premature STOP codons, loss of STOP codons and single nucleotide polymo

182 Selective pressure favoring the Cys529 codon may have coemerged with the evolution of RV-C and

183 domains optimized by the "one amino acid-one codon" method.

184 erfere with ribosomal function and may cause codon misreading.

185 uencing revealed a homozygous premature stop codon mutation in the gene encoding MYSM1.

186 bosomes along coding sequences, and ribosome codon occupancies.

187 Finally, codon occupancy showed strong positive correlations in c

188 ncorporation at the first and downstream UGA codons occurs with variable efficiencies to control synt

189 In this research, one specific serine codon of the 1Ax1 gene corresponding to the extra cystei

190 e AAV2 genome that is found between the stop codon of the cap gene, which encodes proteins that form

191 Mutation of the start codon of two C-terminal ORFs in an infectious clone redu

192 In some gymnosperms, two codons of chlB mRNA are changed by RNA editing to codons

193 bserved maximal repression with intermediate codon optimality and weak repression with very high or l

194 Codon optimality has been shown to regulate translation

195 ty and weak repression with very high or low codon optimality.

196 ation can be further altered by changing the codon-optimality or 5'UTR of the luciferase reporter.

197 Use of synthetic, codon-optimised DNA enabled overexpression of functional

198 Accordingly, codon optimization correlates with host range across the

199 synonymous substitutions underpin increased codon optimization in a generalist but not a specialist

200 e fungi likely increase natural selection on codon optimization in these species.

201 We conclude that codon optimization is related to the capacity of parasit

202 zation of F in the pre-F conformation and of codon optimization resulting in reduced CpG content and

203 Here, we show that codon optimization underlies genome adaptation in broad

204 nipulation of the protein transport pathway, codon optimization, and co-expression of molecular chape

205 GP was codon optimized and expressed either as a full-length pr

206 Self-complementary AAV cassettes containing codon optimized HLA-G1 (transmembrane) or HLA-G5 (solubl

207 We infused a single intravenous dose of a codon-optimized adeno-associated virus serotype 5 (AAV5)

208 This modified NTF was combined with codon-optimized Escherichia coli BirA in a single T-DNA

209 5' gag sequence in the HIV-1 genome with two codon-optimized gag sequences and found that such substi

210 e genes were consistently enriched in highly codon-optimized genes of generalist but not specialist s

211 The codon-optimized mMOMP gene was co-translated with Delta4

212 Codon-optimized RSV F containing fewer CpG dinucleotides

213 Application of a codon-optimized sequence of the cat gene and a single co

214 er-specific promoter driving expression of a codon-optimized wild-type human FIX gene.

215 ctions when adjacent variants alter the same codon, or when a frame-shifting indel is followed by a f

216 tion (c.565G>T) introducing a premature stop codon (p.Glu189*).

217 rmining packaging specificity do not survive codon pair recoding.

218 This sSNP introduces a codon pairing to a low-abundance tRNA that is particular

219 iants (excess of underrepresented synonymous codon pairs) are nonviable except for P2(Min), a variant

220 genome, translation initiation from non-AUG codons plays an important role in various gene regulatio

221 When located at the first or second codon position, N1-methyladenosine (m1A) and m1G constit

222 When situated at the third codon position, the methylated nucleosides did not compr

223 Exclusion of third codon positions of PCGs improved some node support value

224 ethylguanosine (m6G) at the first and second codon positions was strongly and moderately miscoding, r

225 ns within these new alignments (e.g., genes, codon positions, and structural features) often favor hu

226 (nt) -pairings, one sequesters the gag start codon promoting dimerization while the other sequesters

227 EB harbor at least one premature termination codon (PTC) mutation in COL7A1, and previous studies hav

228 tion that introduces a premature termination codon (PTC) that prevents synthesis of the full-length p

229 ts inclusion creates a premature termination codon (PTC), that leads to a 65kDa truncated protein iso

230 dogenous and exogenous Premature Termination Codon (PTC)-containing mRNA isoforms and its effects are

231 In-frame premature termination codons (PTCs) account for approximately 11% of all disea

232 mRNAs containing premature termination codons (PTCs) are rapidly degraded through nonsense-medi

233 Drug-induced readthrough over premature stop codons (PTCs) is a potentially attractive therapy for ge

234 nd degrades mRNAs with premature termination codons (PTCs).

235 4T) at codon 22, leading to a premature stop codon (R22X) in the albino robust capuchin monkey.

236 lovir susceptibilities of 17 mutants in this codon range were evaluated by use of the same recombinan

237 Translation from non-canonical start codons ranged from 0.007 to 3% relative to translation f

238 ous codons change from organism to organism, codon rarity will be conserved at specific positions in

239 ion termination factor, which increases stop codon read-through allowing ribosomes to translate into

240 Overexpression of Sup35 decreases stop codon read-through and rescues oxidant tolerance consist

241 zed reporter system, we discovered that stop codon readthrough is heterogeneous among single cells, a

242 erones, substrate reduction therapy, or stop codon readthrough).

243 en accident, i.e., the deleterious effect of codon reassignment in the SGC, and the inhibitory effect

244 e unnatural amino acid incorporation via AUG codon reassignment, and copper-catalyzed azide-alkyne cy

245 ese codon-context effects by suggesting that codon recognition by elongation factor-bound aminoacyl-t

246 deciphering the principles for specific stop codon recognition by RFs identified Arg-213 as a crucial

247 Our work highlights the notion that stop codon recognition involves complex interactions with mul

248 ress how the Selenop mRNA can direct dynamic codon redefinition in different regions of the same mRNA

249 te a Salmonella with 1557 synonymous leucine codon replacements across 176 genes, the largest number

250 ceptor ionotropic AMPA 2 (GRIA2), modifies a codon, replacing the genomically encoded glutamine (Q) w

251 sequences, although the switches between the codons result in conservative amino acid substitutions.

252 thus becoming increasingly clear that start codon selection is regulated by many trans-acting initia

253 h is crucial for the scanning and initiation codon selection.

254 pA and CspB were modified to plant-preferred codon sequences and named as SeCspA and SeCspB.

255 Complementation with codon-shuffled RTA constructs did not yield any WT rever

256 We propose complementation by codon shuffling as a means to produce replication-defect

257 ology approach based on a technique known as codon shuffling.

258 ly by cysteine, tryptophan and arginine in a codon-specific manner.

259 revalence was calculated by demographics and codon, stratifying by prior ARV experience.

260 ts have identified rare-to-common synonymous codon substitutions that impair folding of the encoded p

261 adical trap 3-amino tyrosine (NH2Y) by amber codon suppression at positions Y731 or Y730 and investig

262 roteins from a phosphotyrosyl-tRNACUA by UAG codon suppression during in vitro translation.

263 Amber codon suppression for the insertion of non-natural amino

264 ecific incorporation into proteins via amber codon suppression in Escherichia coli and mammalian cell

265 Synonymous codon suppressors that corrected the effect of a transla

266 nter-simple sequence repeat (ISSR) and Start codon targeted (SCoT) markers in genetic diversity of V.

267 Thus, AUG is the optimal start codon that is actively maintained by purifying selection

268 een a sequence element upstream of the start codon (the Shine-Dalgarno sequence [SD]) and a complemen

269 ently incorporated at a predefined UAG amber codon, thereby competing with RF1 rather than RF2.

270 ene, the effects on translation of replacing codons Thr6 and Pro8 of flgM with synonymous alternates

271 esidue of 1Dx5 was substituted by a cysteine codon through site-directed mutagenesis.

272 Mutation of the start codon to a sub-optimal form (GUG or UUG) tends to be com

273 ongation, underscoring the ability of E-site codons to modulate the dynamics of protein synthesis.

274 expansion of the genetic code allows for UGA codons to specify the amino acid selenocysteine (Sec).

275 wn roles in maintaining the accuracy of mRNA codon translation.

276 Finally, we show that codon usage affects protein structure and function in vi

277 ies, such as the ability to view and compare codon usage between individual organisms and across taxo

278 Given the impact of codon usage bias on recombinant gene technologies, this

279 Codon usage biases are found in all eukaryotic and proka

280 ing the recruitment of the ribosomes, or the codon usage establishing the speed of protein elongation

281 echnique relies on the accurate knowledge of codon usage frequencies.

282 suggesting an important role for synonymous codon usage in organism physiology.

283 Codon usage is one of the factors influencing recombinan

284 rimental testing of the impact of synonymous codon usage on the production of functional proteins.

285 er, these results suggest that the effect of codon usage on translation elongation speed is a conserv

286 In addition, codon usage regulates ribosome movement and stalling on

287 Despite the obvious need for accurate codon usage tables, currently available resources are ei

288 ations (DS-Cav1), and we also modified RSV F codon usage to have a lower CpG content and a higher lev

289 h signaling, independently of mRNA levels or codon usage.

290 timization of the tRNA pool to the demand in codon usage.

291 th translation rate modulation by synonymous codon usage.

292 nes with stable mRNA structures, non-optimal codon use, and those whose gene product is cotranslation

293 rrespondence between amino acids and cognate codons was determined by recognition of amino acids by R

294 substitutions uniquely affecting the Glu117 codon were not observed previously.

295 ecognition were not observed, premature stop codons were observed in 7% and 56% of tax sequences from

296 Transfer RNA (tRNA) decodes mRNA codons when aminoacylated (charged) with an amino acid a

297 arboring stall sequences near the initiation codon, which cannot accommodate multiple ribosomes, are

298 oter and the 5' exon with a functional start codon while the bulk of the protein-coding sequence evol

299 luext*46 resulted in replacement of the stop codon with 46 additional codons at the C-terminus.

300 ur codons (CAA, CAG, CGA, and TGG) into STOP codons without DSB formation.