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1 ORF translation rate is strongly correlated with its mRN
2 aining 2,692 synonymous mutations in 9 of 11 ORFs did not lose temperature sensitivity, remained gene
5 rent pXO1 plasmid (having 181,677 bp and 217 ORFs) is extremely stable under the same growth conditio
6 ained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an unrelated geno
8 e identified for the majority of the SHFV 3' ORFs, and four previously identified TRSs were found not
10 R34 (medium-reiteration-frequency-family-34) ORF], with unprecedented characteristics, because it is
11 mRNAs encoding E', GP2, or ORF5a as their 5' ORF as well as sg mRNAs encoding six previously unreport
15 ARS-CoV designated as open reading frame-9b (ORF-9b) localizes to mitochondria and causes mitochondri
17 nits of secondary structure that vary across ORF boundaries such that adjacent ORFs on the same mRNA
18 ipts contain multiple translationally active ORFs, and also that most isoforms contain unique combina
20 ary across ORF boundaries such that adjacent ORFs on the same mRNA molecule are structurally distinct
23 e designed primers and probe did not amplify ORF of the E genes for some closely related and more pat
25 ped hamster hypothalamus, which contained an ORF of 570 bp encoding two RFamide-related peptide (RFRP
26 is: insertion of iterated AAA codons into an ORF diminishes protein expression more than insertion of
27 as novel candidate adaptors together with an ORF factor designated as regulator of human erythroid ce
28 rt ORFs, each of which was located within an ORF ("ORF-within-ORF"), including one not previously rec
29 ORFs shorter than approximately 590 nt, and ORFs for which the total time required to complete elong
30 coprotein E (ORF68), we identified antigenic ORFs that may be useful components of subunit vaccines.
34 t study reported that the protein encoded by ORF CT009 interacts with MreB despite low sequence simil
35 tase or hexanucleotide expansion in C9orf72 (ORF 72 on chromosome 9) the two most frequent causes of
36 tream open reading frames (uORFs), canonical ORFs shorter than approximately 590 nt, and ORFs for whi
37 panning the viral protease, RdRP, and capsid ORFs and isolated individual recombinant RNA genomes tha
38 oding exons and encode truncated or chimeric ORFs translated into products with predicted abnormal or
39 come the limitations associated with cloning ORFs from a genome that remains incompletely annotated,
41 s, they maintained translationally competent ORFs, involving elements of gag, pol, env, rev, and nef
45 entifying in both genomes numerous conserved ORFs not included in the published annotation of coding
46 all three ILEs, the first 5.1 kb (containing ORFs 1-4) were structurally conserved and contained thre
51 ons is low, then an AUG-initiated downstream ORF prevents the generation of shorter, AUG-initiated is
54 F) prevents HPV18 233^416 splicing in the E6 ORF through interaction with a host splicing factor, hnR
56 A, was tolerated when introduced into either ORF within the intragenomic replicon, but unlike many ot
58 n conclusion, SCD patients with the FCGR2Cnc-ORF polymorphism have over a 3-fold lower risk for RBC a
59 on on fluorophore on-resonance fluorescence (ORF) and resonance Rayleigh scattering (RRS) is limited
61 thematical model for calculating fluorophore ORF and scattering cross sections has been developed tha
62 fundamental parameters including fluorophore ORF cross sections and quantum yields have been quantifi
63 large-scale systematic study on fluorophore ORF and RRS using the conventional UV-vis extinction and
64 e experimental separation of the fluorophore ORF and photon scattering features in the fluorophore re
67 six previously unreported alternative frame ORFs or 14 previously unreported C-terminal ORFs of know
68 y in containing an extra open reading frame (ORF) (named ORFX), between ORF6 and ORF7, which has no h
72 tomegalovirus (CMV) UL11 open reading frame (ORF) encodes a putative type I transmembrane glycoprotei
73 e approximately 1,100 bp open reading frame (ORF) encoding the envelope proteins is fully nested with
74 d RRV26-95, although the open reading frame (ORF) encoding the KSHV ORFK15 homolog was disrupted in R
76 findings that the entire open reading frame (ORF) for the large (L) envelope protein that is essentia
77 (TCV) coat protein (CP) open reading frame (ORF) has been found to promote internal expression of th
78 n initiation of the main open reading frame (ORF) in an mRNA transcript has been reported to be regul
79 a cotranscribed upstream open reading frame (ORF) in GBS strain 515 reduced bacterial adherence to VK
80 tains a primate-specific open reading frame (ORF) in the antisense orientation that we named ORF0.
81 ty of the putative BWRF1 open reading frame (ORF) is retained in over 80% of strains, and deletions t
83 iridae) contains a large open reading frame (ORF) of 3,494 codons translatable as a polyprotein and t
84 of a frameshift into the open reading frame (ORF) of the target gene which truncates the coding seque
87 identified ESS at the E7 open reading frame (ORF) prevents HPV18 233^416 splicing in the E6 ORF throu
89 in the p38 coat protein open reading frame (ORF) that arose in response to a mutation in the asymmet
90 6 nucleotides of the NSs open reading frame (ORF) were needed to ensure the efficient termination of
91 NCODE lncRNAs acquire an open reading frame (ORF) when their structure is extended with CaptureSeq.
92 deleted the entire US28 open reading frame (ORF), deleted all four of the viral GPCR ORFs, or delete
95 e large tegument protein open reading frame (ORF)64, gained the capacity to stimulate the DNA-activat
96 ability of nearly every open reading frame (ORF; approximately 5,300 ORFs) to induce heritable trait
97 eletion of the gene 9GL (open reading frame [ORF] B119L) in highly virulent ASFV Malawi-Lil-20/1 prod
98 HV-1/EP713 contains two open reading frames (ORF), each encoding an autocatalytic papain-like leader
99 in the overlapping P/C open reading frames (ORFs) (C(Delta170)) or a temperature-sensitive missense
100 nscribed with two novel open reading frames (ORFs) (termed ORF1 and ORF2 herein) conserved only in M.
101 mutations were found in open reading frames (ORFs) 1a, 2, and 6 in the RVRp22 genome based on full-le
103 milar and contained 217 open reading frames (ORFs) and 220 ORFs, respectively, while Basilisk has an
104 ks that overlap dubious open reading frames (ORFs) and are likely to include previously unrecognized
105 automatically maintains open reading frames (ORFs) and does not require linkers, adaptors, sequence h
106 lack long or conserved open reading frames (ORFs) and which have been termed long non-coding RNAs (l
107 anscription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expressio
108 ed the presence of five open reading frames (ORFs) corresponding to the genes for the N, P, M, G, and
109 can also predict novel open reading frames (ORFs) from regular ribosome profiling (rRibo-seq) data a
110 ) plasmid consisting of open reading frames (ORFs) GBAA_pXO1_0020 to GBAA_pXO1_0023 is not stably mai
111 alf of the 32 annotated open reading frames (ORFs) have no homologs in databases (ORFans), being puta
113 iliary protein-encoding open reading frames (ORFs) in HTLV-3, the latest HTLV to be discovered, is un
115 ith unusually divergent open reading frames (ORFs) in the conserved region of rpoA, the gene encoding
116 cription from all eight open reading frames (ORFs) in the terminal repeat was investigated in IgM(+)
119 that were localized in open reading frames (ORFs) likely associated with host cell entry and exit be
120 er, is recruited to the open reading frames (ORFs) of actively transcribed genes genome wide, suggest
121 ion, the protein coding open reading frames (ORFs) of certain individual mRNAs exhibited resistance t
122 ter translation of long open reading frames (ORFs) on cellular mRNAs, reinitiation occurs efficiently
124 ion of products from 27 open reading frames (ORFs) previously designated "predicted," "uncharacterize
126 t cloning of Drosophila open-reading frames (ORFs) that are regulated by upstream activation sequence
127 ries a number of unique open reading frames (ORFs) that have not yet been investigated regarding thei
128 loss of protein-coding open reading frames (ORFs) that progress from individual missense mutations t
129 d up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation amo
130 roteins encoded by HCMV open reading frames (ORFs) UL47 and UL48 and identifying the binding domains
131 ates for the individual open reading frames (ORFs) were highest in the regions encoding the attachmen
132 ng 128 unique predicted open reading frames (ORFs), many of which were most closely related to herpes
133 of the 70 annotated VZV open reading frames (ORFs), suggesting that defective virus transcription doe
134 gth and contained eight open reading frames (ORFs), while the ILE from FH4 was 16 233 bp in length an
135 enome with 32 predicted open reading frames (ORFs), YSLV6 has a 24,837-bp genome with 29 predicted OR
140 pping peptides spanning open reading frames [ORFs] 1-3) was used in interferon-gamma (IFN-gamma) T-ce
142 ts with ORF54 gene deletions, Delta54L (full ORF deletion) and Delta54S (partial internal deletion).
144 sequences of these genes show no functional ORFs, but include segments of different protein coding g
145 me (ORF), deleted all four of the viral GPCR ORFs, or deleted three of the HCMV GPCRs but not the US2
151 ons inconsistencies between newly identified ORFs and pre-existing annotations of coding-regions.
152 Overall, our findings strongly implicate ORF-associated RSC in governing Pol II function and in m
153 69PUK1-like pseudogenes with stop codons in ORFs.PUK1orthologs and other pseudogenes also displayed
154 nction, ~9% of the peptides are conserved in ORFs in mouse transcripts, as are 74% of pseudogene pept
155 genomes were designed in which the indicated ORFs were recoded: Min A (NS1, NS2, N, P, M, and SH), Mi
157 presence of helicases in the stress-induced ORFs identified by cDNA microarray indicates that helica
159 ence (SPHINX 1.8), with an iteron before its ORF, was evaluated here for its expression in neural cel
160 on is approximately 10-fold smaller than its ORF counterparts for all the six model fluorophores, but
161 ained either wild-type (WT) K1, a deleted K1 ORF (KSHVDeltaK1), stop codons within the K1 ORF (KSHV-K
162 ORF (KSHVDeltaK1), stop codons within the K1 ORF (KSHV-K15xSTOP), or a revertant K1 virus (KSHV-K1REV
165 potentially deattenuating mutations in the L ORF as well as, surprisingly, many appearing in other OR
170 ae) contains species with multiple rpoA-like ORFs that show evidence of ongoing inter-paralog gene co
171 PLATO uses ribosome display (RD) to link ORF-derived mRNA molecules to the proteins they encode,
172 ct with an overlapping site early in the lrp ORF, while GcvB acts upstream at two independent sites i
173 ghly abundant transcript containing the mccA ORF and a longer minor transcript containing mccA and do
175 domain, resulting from the splicing of MCMV ORFs m131 and m129 MCK-2 is essential for full MCMV infe
176 In this study, the DJ-1 superfamily member ORF 19.251/GLX3 from Candida albicans is shown to posses
178 emature termination codons (PTCs) in an mRNA ORF inactivate gene function by causing production of a
179 reading frame in the FCGR2C gene (FCGR2C.nc-ORF) was strongly associated with a decreased alloimmuni
181 L2-dsRNA/SsMBV1 comprises two nonoverlapping ORFs (ORFA and ORFB) encoding two hypothetical proteins
182 lated pre-mRNAs, some of which contain novel ORFs, were typically intronless, <2 Kb in length, expres
184 These findings suggest that these novel ORFs may play a role in recombination in these two close
186 dicated that operonic mRNAs are comprised of ORF-wide units of secondary structure that vary across O
187 p29, derived from the N-terminal portion of ORF A, functions as a suppressor of RNA silencing, while
191 Previous studies have predicted thousands of ORFs in 5'UTRs, the vast majority of which have unknown
192 tion, we detected signatures of selection on ORF 5a and on a small subset of sites in the genome.
193 genome of Tetrahymena thermophila, the only ORF sharing similarities with FARs is fused to an acyltr
194 s, each of which was located within an ORF ("ORF-within-ORF"), including one not previously recognize
198 hrough two (or three) completely overlapping ORFs (shifting to a new reading frame at the end of each
202 st that the second-site mutations in the p38 ORF exert positive effects through a similar downstream
203 ortion of viral transcripts, fusing the pipo ORF in frame with the 5' third of the polyprotein ORF.
207 LV6 has a 24,837-bp genome with 29 predicted ORFs, and YSLV7 has a 23,193-bp genome with 26 predicted
209 NAs from PLC/PRF/5 cells, while an L protein ORF that was truncated and fused to inverted precore seq
210 Nidovirales express their structural protein ORFs from a nested set of 3' subgenomic mRNAs (sg mRNAs)
212 hown to contain 132,831 bp with 145 putative ORFs (open reading frames) of at least 50 amino acids.
213 Among these unique ORFs are two putative ORFs, ORF011 and ORF012, which are found at the extreme
215 gion that harbors a short proline codon-rich ORF--termed mgtP--the translation of which is predicted
216 mgtA mRNA contains a 17-codon, proline-rich ORF, mgtL, whose translation regulates the transcription
218 linically relevant mutations in HBsAg and rt ORFs, successfully treated with a combination of nucleot
220 trast, we detected selection focused on SHFV ORFs 5a and 5, which encode putative membrane proteins.
221 which the time taken to translate the short ORF, impacted by distance, sequence, and structure, not
222 e also detected the expression of four short ORFs, each of which was located within an ORF ("ORF-with
223 le as a polyprotein and two embedded shorter ORFs in the -1 frame: PISPO, of 230 codons, and PIPO, of
225 olytic microbes; yet the function of a small ORF, kdgF, which cooccurs with the genes for these enzym
231 h for quantification of the fluorophore SSF, ORF, and scattering depolarization and anisotropy using
239 omiscuous glycosyltransferase encoded by the ORF atu2297, with UDP-glucose or UDP-glucuronic acid as
241 Surprisingly, the release of p48 from the ORF B-encoded polyprotein was not prevented by mutation
242 epitope tags (or regulatory regions) in the ORF library strains, which further extends the potential
243 A premature termination codon (PTC) in the ORF of an mRNA generally leads to production of a trunca
245 ap completely prevents the expression of the ORF and avoids expression of C-terminal truncated protei
246 ubiquitin-specific protease activity of the ORF UL48 protein was functional in the complex, cleaving
248 r AIP4 expression substantially reversed the ORF-9b-mediated reduction of MAVS and the suppression of
251 (2017) report that ribosomes translating the ORF that encodes the copper pump frequently frameshift a
254 nt with such a role, Pol II occupancy in the ORFs of weakly transcribed genes is drastically reduced
255 eletion of, or start codon mutations in, the ORFs for the peptides in the DeltarcrR-NP background res
257 promoter strength driving expression of the ORFs was largely unchanged and the mRNA half-lives were
258 tes could produce transcripts bringing these ORFs in frame with the upstream polyprotein, thus leadin
259 omic mRNAs (sg mRNAs), and for most of these ORFs, a single genomic transcription regulatory sequence
260 ically localized, which indicates that these ORFs came from the nucleus or (less likely) a cryptic en
270 UAS sites); the resulting GAL4-inducible UAS-ORF plasmid library is then used to generate Drosophila
274 ntified a viral protein encoded by the UL148 ORF (UL148) that influences the ratio of gH/gL/gO to gH/
275 A substantial number of these unannotated ORFs are evolutionarily conserved, and some produce stab
278 oteins in other rhabdoviruses and an unknown ORF of 111 amino acids located between the G- and L-prot
280 ranslated region (UTR) generates an upstream ORF (uORF) that affects both the background expression o
281 ng ribosome bypass of an inhibitory upstream ORF (uORF) situated in the 5'-leader of the CHOP mRNA.
282 egulated mRNAs, 30% had one or more upstream ORF (uORF) that influenced the number of ribosomes on th
284 ycin (TOR) promotes reinitiation at upstream ORFs (uORFs) in genes that play important roles in stem
287 to the evidence that the removal of upstream ORFs by RNA processing is not typically required for the
288 so exposed the inhibitory effect of upstream ORFs on the translation of downstream protein-coding reg
289 cription factor ATF4 through paired upstream ORFs (uORFs) plays an important role in eukaryotic gene
293 ne the regulatory features by which upstream ORFs (uORFs) direct downstream translation control and e
294 y as infection with viruses lacking the US28 ORF alone or in combination with the remaining HCMV-enco
296 Therefore, we suggest that these two viral ORFs are involved in the same mechanism or pathway that
297 system, we demonstrate the role of two viral ORFs, ORF18 and ORF30, in regulating viral gene expressi
298 ted deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblas
299 e variants of poliovirus type 1 (PV1), whose ORF (6,189 nucleotides) carried up to 1,297 "Max" mutati
300 which was located within an ORF ("ORF-within-ORF"), including one not previously recognized or known
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