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1 ORF CT588 has a strong sequence similarity to RsbU cytop
2 ORF translation rate is strongly correlated with its mRN
4 aining 2,692 synonymous mutations in 9 of 11 ORFs did not lose temperature sensitivity, remained gene
6 e data set involving 10,635 nsSNPs from 2154 ORFs in the human genome and recognized disease-associat
10 the RNAPII CTD at Ser2 residues in the cat-3 ORF region during transcription elongation and deletion
11 R34 (medium-reiteration-frequency-family-34) ORF], with unprecedented characteristics, because it is
12 mRNAs encoding E', GP2, or ORF5a as their 5' ORF as well as sg mRNAs encoding six previously unreport
13 ur results indicate that selection of HHV-6B ORFs for immunotherapy should consider this expanded pan
15 nits of secondary structure that vary across ORF boundaries such that adjacent ORFs on the same mRNA
16 ipts contain multiple translationally active ORFs, and also that most isoforms contain unique combina
17 ary across ORF boundaries such that adjacent ORFs on the same mRNA molecule are structurally distinct
18 map to exons 2 and 3 of POLG but also affect ORF-Y provides potential clinical significance to this f
21 s reported being expressed from an alternate ORF in the mitochondrial genome and inhibiting apoptosis
22 uss progress in the detection of alternative ORFs as well as in the understanding of functions and th
24 With only the sequence information of an ORF, MiPepid is able to predict whether it encodes a mic
26 ription vector used in the RG system with an ORF encoding NSP3 fused to a fluorescent reporter protei
27 ; dsRNA2 dsRNA is 1,524 bp in length with an ORF that encodes 434 amino acids (molecular mass of 46.9
28 in the CdSe core peak UV-vis absorption and ORF wavelengths, and increases their peak cross-sections
29 nsity of the CdSe core UV-vis absorption and ORF, but it reduces the QD fluorescence depolarization.
30 le CRISPR/Cas9-mediated loss of function and ORF/cDNA driven rescue screens, and cell-based models of
31 encoded upstream and downstream of annotated ORFs, from alternative start sites nested within annotat
32 ernative start sites nested within annotated ORFs and from RNAs previously considered noncoding, it i
37 ient protein expression from an intact BHLF1 ORF required the EBV posttranscriptional regulator prote
45 n the 5' mRNA leaders, and amongst canonical ORFs during the activation of the zygotic translatome at
47 uffer the translation of canonical canonical ORFs; and show that, in general, small ORFs in mRNAs dis
51 shed essential genes and 82 highly conserved ORFs that have no known gene products or assigned functi
52 alignment of mammalian sequences containing ORF-Y revealed that the CUG codon has a strong initiatio
53 on phenotype allowed us to identify two core ORFs, so far without any assigned function, as responsib
54 ngle peptide expressed from both the cryptic ORF and wild-type genomes, suggesting a potential new ge
56 nthetic genome in which 71 conserved cryptic ORFs were simultaneously disrupted is viable but with ~5
58 ons is low, then an AUG-initiated downstream ORF prevents the generation of shorter, AUG-initiated is
60 The peptides encoded by these downstream ORFs (dORFs) are often poorly conserved across evolution
62 nt RNA polymerase (RdRp), whereas the dsRNA2 ORF sequence showed homology with the putative capsid pr
64 yces cerevisiae has isolated several dubious ORFs whose deletions mitigated the protein burden effect
67 veral in-frame internal ORFs within existing ORFs, resulting in N-terminally truncated products, as w
68 n conclusion, SCD patients with the FCGR2Cnc-ORF polymorphism have over a 3-fold lower risk for RBC a
72 , absorption, and on-resonance-fluorescence (ORF) activities of CdSe/CdS core/shell fluorescent QDs a
73 thematical model for calculating fluorophore ORF and scattering cross sections has been developed tha
74 e experimental separation of the fluorophore ORF and photon scattering features in the fluorophore re
77 l of de novo gene birth where a fully formed ORF existed before the regulatory element to activate tr
79 six previously unreported alternative frame ORFs or 14 previously unreported C-terminal ORFs of know
83 nce encoded in the first open reading frame (ORF) and accumulation of the reporter gene product in to
85 pan-cancer fusion genes, open reading frame (ORF) assignment, and retention search of 39 protein feat
87 additional uninterrupted open reading frame (ORF) covering almost the entire length of the reverse co
88 assumptions, such as one open reading frame (ORF) encodes one protein and minimal lengths for transla
90 e approximately 1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested with
91 (TCV) coat protein (CP) open reading frame (ORF) has been found to promote internal expression of th
92 replication, although an open reading frame (ORF) is retained among an unknown percentage of EBV isol
93 ty of the putative BWRF1 open reading frame (ORF) is retained in over 80% of strains, and deletions t
95 le at least one reliable open reading frame (ORF) model has been assigned for every coding gene, the
96 is, we replaced the NSP3 open reading frame (ORF) of the segment 7 (pT7/NSP3) transcription vector us
97 of a frameshift into the open reading frame (ORF) of the target gene which truncates the coding seque
99 683 bp in length with an open reading frame (ORF) that encodes 539 amino acids (molecular mass of 62.
100 6 nucleotides of the NSs open reading frame (ORF) were needed to ensure the efficient termination of
101 e or by truncating the X open reading frame (ORF), had little effect on the infectious virus titer of
102 sites or shifting of the open reading frame (ORF), leading to a variety of human diseases and conside
103 triplet-long overlapping open reading frame (ORF), which we call POLGARF (POLG Alternative Reading Fr
106 and only four putative open reading frames (ORF), vB_RpoMi-Mini becomes the smallest ssDNA phage amo
110 can also predict novel open reading frames (ORFs) from regular ribosome profiling (rRibo-seq) data a
111 nd variable (accessory) open reading frames (ORFs) grouped at fixed regions in their genomes; however
112 alf of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being puta
115 We subjected various open reading frames (ORFs) in the genome of respiratory syncytial virus (RSV)
117 that were localized in open reading frames (ORFs) likely associated with host cell entry and exit be
120 y to generate candidate Open Reading Frames (ORFs) resulting from Cytidine to Uridine (c->u) editing
122 dentified 315 potential open reading frames (ORFs) within the genome, including the 11 established es
123 nscripts with competent open reading frames (ORFs), and can be found in the peripheral blood CD4(+) T
124 lly carry promoter-less open reading frames (ORFs), encoding proteins with various functions includin
125 the coding potential of open reading frames (ORFs), including many short ORFs that were previously pr
126 dentify hundreds of new open reading frames (ORFs), including upstream ORFs (uORFs) and internal ORFs
127 ng 128 unique predicted open reading frames (ORFs), many of which were most closely related to herpes
128 repeat epitopes in two open reading frames (ORFs), one translated from the 5' cap, and the other fro
129 n addition to canonical open reading frames (ORFs), thousands of translated small ORFs (containing le
130 of actively translated open reading frames (ORFs), to the quantification of translational efficiency
132 (dsDNA) genome with 31 open reading frames (ORFs), whose predicted gene products show little homolog
139 onally encode two major open reading frames (ORFs): Rep and capsid protein (CP) characteristic of a t
141 sequences of these genes show no functional ORFs, but include segments of different protein coding g
144 b locus, consisting of the hp1369 and hp1370 ORFs, encodes for a truncated and inactive MTase in H. p
145 called ORF-less GCs, contain no identifiable ORF with a small number shown to be involved in antisens
149 including upstream ORFs (uORFs) and internal ORFs (iORFs), generating a complete unbiased atlas of HH
150 a regulatory role, several in-frame internal ORFs within existing ORFs, resulting in N-terminally tru
152 ence (SPHINX 1.8), with an iteron before its ORF, was evaluated here for its expression in neural cel
153 on is approximately 10-fold smaller than its ORF counterparts for all the six model fluorophores, but
156 potentially deattenuating mutations in the L ORF as well as, surprisingly, many appearing in other OR
159 One identified provirus has full-length ORFs for all genes, and thus could potentially be replic
162 domain, resulting from the splicing of MCMV ORFs m131 and m129 MCK-2 is essential for full MCMV infe
163 ases were not close to DNA methyltransferase ORFs, strongly supporting modification dependent activit
164 s and large-scale DNA synthesis, one or more ORFs of a microbial pathogen can be recoded by different
165 nd L, which in common had CPO of one or more ORFs of proteins of the polymerase complex, exhibited gl
166 reading frame in the FCGR2C gene (FCGR2C.nc-ORF) was strongly associated with a decreased alloimmuni
168 g tools for classifying coding and noncoding ORFs were built on datasets in which "normal-sized" prot
170 of Canada goose coronavirus include 6 novel ORFs, a partial duplication of the 4 gene and a presumpt
176 ration and detection of promoter activity of ORF-less GCs from Treponema bacteria and the development
177 In this study, the promoter activity of ORF-less GCs, previously recovered from the oral metagen
178 dicated that operonic mRNAs are comprised of ORF-wide units of secondary structure that vary across O
179 y(A) site utilization, with increased use of ORF-proximal poly(A) sites resulting in shorter 3' mRNA
181 explain translation of the vast majority of ORFs as well as N-terminal extensions (NTEs) and truncat
184 tion, we detected signatures of selection on ORF 5a and on a small subset of sites in the genome.
188 e developed a new approach to classify phage ORFs into ten major classes of structural proteins or in
189 that are synonymous with respect to the POLG ORF and found that most of these variants cause amino ac
194 Nidovirales express their structural protein ORFs from a nested set of 3' subgenomic mRNAs (sg mRNAs)
195 also represents a rare example of the proto-ORF model of de novo gene birth where a fully formed ORF
196 thesis by activating translation of the psbJ ORF, that this function is conserved in Arabidopsis LPE1
199 sitive NanK enzymes belong to the Repressor, ORF, Kinase (ROK) family, but many lack the canonical Zn
204 High-level GFP accumulation from the second ORF facilitates identification of transplastomic events
208 Max A (with CPO of NS1, NS2, N, P, M, and SH ORFs), Max B (with CPO of G and F), Max L (with CPO of L
209 trast, we detected selection focused on SHFV ORFs 5a and 5, which encode putative membrane proteins.
210 tated polycysteine-encoding leaderless short ORF architectures responded to cysteine limitation, reve
213 ng actively translating ORFs including short ORFs on multiple published datasets across species inclu
215 that polycysteine-encoding leaderless short ORFs function as cysteine-responsive attenuators of oper
216 reading frames (ORFs), including many short ORFs that were previously presumed to be non-translating
218 l coordination by ribosomes on sensory short ORFs illustrates one utility of the many unannotated sho
219 tion of translating ORFs, specifically short ORFs, from Ribo-seq data, remains challenging due to its
221 derless mRNAs often encode unannotated short ORFs as the first gene of a polycistronic transcript.
223 ble with the main function of upstream short ORFs being to buffer the translation of canonical canoni
224 especially prevalent amongst upstream short ORFs located in the 5' mRNA leaders, and amongst canonic
228 e EMBO Journal, Wu et al characterized small ORFs in the 3' untranslated regions (3' UTRs) of human a
229 nical ORFs; and show that, in general, small ORFs in mRNAs display markers compatible with an evoluti
230 frames (ORFs), thousands of translated small ORFs (containing less than 100 codons) have been identif
233 tend the catalog of in vivo translated small ORFs, and to reveal the translational regulation of both
234 RNA-binding proteins, encode potential Split-ORFs, some of which are expressed under specific cellula
236 hich we show is essential to remove spurious ORFs and to distinguish coding from pseudogene regions.
237 h for quantification of the fluorophore SSF, ORF, and scattering depolarization and anisotropy using
238 velength region, and they all exhibit strong ORF emission in the wavelength regions where the QDs bot
239 ional regions, with accessory and structural ORFs containing the highest structural density in the vi
249 ap completely prevents the expression of the ORF and avoids expression of C-terminal truncated protei
250 (2017) report that ribosomes translating the ORF that encodes the copper pump frequently frameshift a
253 for PUA domain containing endonucleases, the ORFs for DUF3427 fusion proteins were frequently found i
256 long polyadenosine (polyA) runs within their ORFs, distinguishing the parasite from its hosts and oth
258 ow individual RNA structures formed by these ORFs are affected by the differences in genomic and subg
259 omic mRNAs (sg mRNAs), and for most of these ORFs, a single genomic transcription regulatory sequence
260 No function has been described for this ORF, yet the absence of stops is conserved across divers
264 the serendipitous discoveries of translated ORFs encoded upstream and downstream of annotated ORFs,
266 ins, methods for predicting short translated ORFs must be trained independently from those for longer
267 ct, but we also detect genes with translated ORFs on multiple transcript isoforms, including targets
268 a method for detecting actively translating ORFs by directly leveraging the three-nucleotide periodi
269 er methods at detecting actively translating ORFs including short ORFs on multiple published datasets
271 g frames and revealed the translation of two ORFs (ORF4b and ORF4c on sgmRNA IR), which are widely co
273 ucleotide polymorphism within the AD169 UL55 ORF, resulting in a D275Y amino acid exchange within gly
274 gh-throughput method to discover unannotated ORFs, elucidates evolutionarily conserved and unique tra
277 SPR-Cas9 targeting of the conserved upstream ORF present in the mRNA leader derepress PRL protein syn
278 egulated mRNAs, 30% had one or more upstream ORF (uORF) that influenced the number of ribosomes on th
280 ycin (TOR) promotes reinitiation at upstream ORFs (uORFs) in genes that play important roles in stem
283 en reading frames (ORFs), including upstream ORFs (uORFs) and internal ORFs (iORFs), generating a com
289 ccumulation of transcripts just at the viral ORFs, while vsRNAs spanned the entire genome, showing a
290 lished without interrupting any of the viral ORFs, yielding recombinant viruses that likely express t
292 ted deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblas
294 e variants of poliovirus type 1 (PV1), whose ORF (6,189 nucleotides) carried up to 1,297 "Max" mutati
295 reen utilized the most extensive genome-wide ORF collection to date, covering 90% of human, nonredund
299 2 influenza viruses were full-length, with X-ORFs encoding 61 amino acids; however, those of equine-o