Using the allele frequency spectrum of SNVs from 71,702 whole genome sequences in gnomAD, we find that SNVs introducing new stop codons, or creating stronger translation termination signals in uORFs are under strong selective constraints within 5′UTRs. (nature.com)
Across all cells, hybrids accumulate most strongly in non-coding RNAs and 5′-UTRs of coding sequences. (biorxiv.org)
Both 5' and 3' UTRs are important for regulating translation initiation and mRNA stability. (openstax.org)
The current view of an mRNA is that of a central coding sequence (CDS) flanked by 5′ and 3′ untranslated regions (UTRs). (imim.es)
Genes8
A total of 4,761 perfect and 6,583 imperfect SSRs were present in 3,781 genes (14.11% of the total), corresponding to an overall density across the gene space of 32,5 and 44,9 SSRs/Mbp for perfect and imperfect motifs, respectively. (researchgate.net)
We have now established a new data pre-processing procedure to eliminate artifacts caused by a 5'-RACE library generation process, reanalyzed a previously studied data set defining human immunoglobulin heavy chain genes, and identified novel upstream regions, as well as previously identified upstream regions that may have been identified in error. (lu.se)
Finally, based on the outcomes of the analysis, we define a set of testable hypotheses with respect to the placement of particular alleles in complex IGHV locus haplotypes, and discuss the evolutionary relatedness of particular heavy chain variable genes based on sequences of their upstream regions. (lu.se)
We cloned and sequenced a 924-nt fragment that covered part of the 5′UTR and the VP4/VP2 capsid genes. (plos.org)
The elegant and original use of a probabilistic model of segregating alleles (implemented in the SEX-DETector method) allowed to identify both the sex and self-incompatibility loci [4], while this tool was initially developed for detecting sex-linked genes in species with strictly separated sexes (dioecy) [5]. (peercommunityin.org)
In order to test this hypothesis and understand the molecular basis for hsp70 expression, we compared basal hsp70 mRNA levels in males and females, and analysed the 5′ and 3′ regulatory regions of hsp70 genes in warm- and cold-climate isochromosomal O 3 + 4 + 7 and O ST lines of D. subobscura . (biomedcentral.com)
The expression level of AtS40-1 , AtS40-2 and AtS40-5 genes were induced after 2 days of darkness incubation while AtS40-3 and At-S40-4 showed increased expression only one day after darkness incubation [ 22 ]. (biomedcentral.com)
Functional and evolutionary analyses of genes are usually performed on one or few representatives of their expression products, i.e. transcripts and proteins. (biomedcentral.com)
MRNA11
Engineering chimeric, "humanized" yeast ribosomes for ES9S reveals that an evolutionary change in the sequence of ES9S endows species-specific binding of Hoxa9 mRNA to the ribosome. (nih.gov)
They found that one round of amplification produced approximately 10 3 fold of the estimated amount of starting mRNA, and two rounds produced an approximately 10 5 fold increase. (genomicglossaries.com)
The 3' regulatory regions have a great diversity of cis -regulatory elements directly involved in polyadenylation, stability, transport and mRNA translation, essential to achieve the desired levels of gene expression. (frontiersin.org)
In particular, upstream open reading frames (uORFs) are segments of 5′UTR mRNA sequences that can initiate and terminate translation upstream of protein-coding start codons. (nature.com)
If scanning ribosomes encountering uORFs prematurely initiate translation in the 5′UTR, upon reaching the uORF termination codon the ribosome may dissociate from the mRNA transcript, or the 40 s subunit may resume scanning after the 60 s subunit is lost. (nature.com)
Strikingly, only one single nucleotide polymorphism (SNP) in the 5' untranslated region (UTR) of mRNA strongly impaired translation in the USA300 strain, leading to a strong decrease in the level of HlgC but not in HlgB. (cnrs.fr)
Biomolecular analyses have revealed that a few SNPs in the promoter sequences and only one SNP in the 5' UTR of mRNA induce the differential expression of , drastically impacting mRNA translation. (cnrs.fr)
The three most important steps of pre-mRNA processing are the addition of stabilizing and signaling factors at the 5' and 3' ends of the molecule, and the removal of the introns ( Figure 15.11 ). (openstax.org)
In addition to 5' Cap and 3' Poly-A Tail addition, introns must be precisely removed and exons joined to generate a functional mRNA. (openstax.org)
The 3' ends of guide RNAs have a long poly-U tail, and these U bases are inserted in regions of the pre-mRNA transcript at which the guide RNAs are looped. (openstax.org)
What could be the evolutionary reason for this additional step in pre-mRNA processing? (openstax.org)
Sequence9
Subsequently a bat sarbecovirus-RaTG13, sampled from a Rhinolophus affinis horseshoe bat in 2013 in Yunnan Province-was reported that clusters with SARS-CoV-2 in almost all genomic regions with approximately 96% genome sequence identity 2 . (nature.com)
2020 ). According to previous research model, it was suggested that strand exchange or 5′ leader (5′ UTR) sequence to body (RNA) fusion occurs at TRS during negative sense RNA synthesis (Kim et al. (springeropen.com)
One coding sequence variant (a missense variant) and four non-coding variants (two 5'-untranslated region [UTR] variants and two 3'-UTR variants) were recorded. (genominfo.org)
87(5): 1663-1667] Specifically, the investigators started by priming whole cerebellar RNA with a synthetic oligonucleotide containing a T7 RNA polymerase promoter sequence. (genomicglossaries.com)
Because sequence analysis of the 5′-UTR amplicon showed that this enterovirus strain was closely related to other human enterovirus A strains, another set of consensus primers (5′-TGCCCACAYCARTGGATHAA-3′ and 5′-CCTGACCACTGNGTRTARTA-3′) specific for the viral protein 2-viral protein 3 region of human enterovirus A was used for typing. (blogspot.com)
We studied the probable molecular-evolutionary patterns of AVR-Pib alleles by assaying their DNA-sequence diversification and examining their avirulence to the corresponding Pib resistance gene under natural conditions in China. (researchsquare.com)
When analyzing a fragment of the 5′ UTR, we characterized at least two subspecies of HRV-C: HRV-Cc, which clustered differently from HRV-A and HRV-B, and HRV-Ca, which resulted from previous recombination in this region with sequences related to HRV-A. The full-length sequence of one strain of each HRV-Ca and HRV-Cc subspecies was obtained for comparative analysis. (plos.org)
Mutants showed sequential super-stereotypy in the sense of having more stereotyped and predictable syntactic grooming sequences, and were also more likely to resist disruption of the pattern en route, by returning after a disruption to complete the pattern from the appropriate point in the sequence. (biomedcentral.com)
There are outstanding evolutionary questions on the recent emergence of human coronavirus SARS-CoV-2 including the role of reservoir species, the role of recombination and its time of divergence from animal viruses. (nature.com)
Across a large region of the virus genome, corresponding approximately to ORF1b, it did not cluster with any of the known bat coronaviruses indicating that recombination probably played a role in the evolutionary history of these viruses 5 , 7 . (nature.com)
By investigating two of these receptors during infection by dengue and Zika viruses, scientists from the Institut Pasteur discovered that a precise region of the viral genome was recognized by a receptor known as RIG-I. Their discovery paves the way for the future development of vaccines for these diseases. (pasteur.fr)
Using an RLR-purification technique in conjunction with high-throughput sequencing and bioinformatics analysis, "we demonstrated that a precise region of the genomes of the dengue and Zika viruses (known as the 5' untranslated region) was recognized by RIG-I," explains Nolwenn Jouvenet, a scientist in the Viral Genomics and Vaccination Unit at the Institut Pasteur and last author of the paper. (pasteur.fr)
RNAs2
Secondary structure of the 5′ nontranslated regions of hepatitis C virus and pestivirus genomic RNAs. (microbiologyresearch.org)
Analysis of RNAs enriched in different sub-cellular regions based on SCS spot assignments provides information on RNA localization and further supports the segmentation results. (bilkent.edu.tr)
Differentiation1
This is reinforced by the lack of important differential features in the number and structure of regulatory elements between both arrangements, despite the genetic differentiation observed when the complete 5′ and 3′ regulatory regions were considered. (biomedcentral.com)
Protein4
The missense variant showed pathogenic effects and high evolutionary conservation over the functions of the neuroligin 3 protein. (genominfo.org)
The availability of multiple PAS in the same 3' regulatory region enables the inclusion or exclusion of 3' untranslated region (3'UTR) sequences, resulting in transcripts that may differ in particularities involving post-transcriptional processes such as stability, transport and translation ( Mayr, 2016 ), and even protein localization ( Berkovits and Mayr, 2015 ). (frontiersin.org)
Since multiple transcript and protein variants expressed by the same gene are, by definition, structurally distinct and need not to be functionally equivalent, the concept of gene orthology should be extended to the transcript level in order to describe evolutionary relationships between structurally similar transcript variants. (biomedcentral.com)
Both mobile and virally encoded kinases get excited about the phosphorylation of tegument protein (5, 11, 12), and serines of tegument proteins HSV-1 VP22 are phosphorylated in contaminated cells (11, 12). (thebiotechdictionary.com)
Genomics1
Their genetic determinism and the factors controlling their evolution represent fascinating questions in evolutionary biology and genomics. (peercommunityin.org)
Phylogenetic2
To employ phylogenetic dating methods, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. (nature.com)
The phylogenetic analysis of the 5′-untranslated region (5'UTR) of the GBV-C genome has led to the segregation of viral strains into six genotypes, but incongruent results are frequently obtained depending on the genome region analyzed. (unl.pt)
Genome4
Classically, MHA rely on the amplification by real-time PCR of several regions scattered along the HIV-1 genome, and on their characterization with clade-specific TaqMan probes (also known as hydrolysis probes). (unl.pt)
They are classified into at least three species, HRV-A, HRV-B and HRV-C, which are characterized by sequencing the 5′ untranslated region (UTR) or the VP4/VP2 region of the genome. (plos.org)
Understanding the architecture of the human proteome has the potential to inform the scientist about cellular, structural, and evolutionary mechanisms, and this is critical to elucidating how genome variation contributes to disease. (genewhisperer.com)
The genome analysis showed a newly observed mutation in the 5′ untranslated region of a lagovirus, whose role remains unknown. (biomedcentral.com)
Patterns3
GB virus C (GBV-C) evolutionary patterns revealed by analyses of reference genomes, E2 and NS5B sequences amplified from viral strains circulating in the Lisbon area (Portugal). (unl.pt)
Evolutionary patterns of eastern equine encephalitis virus in North versus South America suggest ecological differences and taxonomic revision. (microbiologyresearch.org)
We compared HCV genotypes among IDUs in Yunnan Province with those from other regions and found that the distribution patterns of HCV genotypes in Yunnan Province were similar to those in southern China, but different from those in eastern China. (cdc.gov)
Proteins1
In addition, after transcription, a wide array of RNA-binding proteins interacts with cis -acting elements located mainly in the 3' untranslated region, determining the fate of mRNAs in eukaryotic cells. (frontiersin.org)
Variants2
Several novel upstream region variants were validated, for instance by their segregation to a single haplotype in heterozygotic subjects. (lu.se)
Beyond the "desirable" morphological traits, undesirable "disease" syndromes may be associated with these genetic loci due to either multiple phenotypic sequelae of specific variants, or associated genetic variants carried within long regions of linkage disequilibrium. (frontiersin.org)
Although a small number of 3' regulatory regions have been identified and validated so far, many studies have shown that plant 3' regulatory regions have a higher potential to regulate gene expression in plants compared to widely used 3' regulatory regions, such as NOS and OCS from Agrobacterium tumefaciens and 35S from cauliflower mosaic virus. (frontiersin.org)
In this review, we discuss the role of 3' regulatory regions in gene expression, and the superior potential that plant 3' regulatory regions have compared to NOS, OCS and 35S 3' regulatory regions. (frontiersin.org)
Alleles1
AVR-Pib alleles evolved to virulent forms from avirulent forms by base substitution and TE insertion of Pot2 and Pot3 in the 5′ untranslated region of AVR-Pib . (researchsquare.com)
Strains1
We conducted a large-scale epidemiologic and evolutionary study of 1,329 E30 strains collected in 22 countries in Europe during 2016-2018. (cdc.gov)
Genomes1
RIG-I Recognizes the 5' Region of Dengue and Zika Virus Genomes, Cell Reports , July 10, 2018. (pasteur.fr)
Species1
RHDV2 causes a disease similar to that due to RHDV, except that the course of the disease and case fatality rates are more variable, and that kittens under 4 weeks old and various hare species can also be infected [ 5 ]. (biomedcentral.com)
Ribosome1
In characterizing ribosome binding to a regulatory element within a Homeobox (Hox) 5' UTR, we identify a modular stem-loop within this element that binds to a single ES, ES9S. (nih.gov)
Initiation2
This consensus region is present at the adjacent of initiation codon. (springeropen.com)
Cap-dependent translation initiation begins when the 40 s ribosomal subunit encounters a start codon as it scans along the 5′UTR. (nature.com)
Transcription1
These samples were also positive by reverse transcription PCR (RT-PCR) with pan-enterovirus primers (5′-CAAGCACTTCTGTBWCCCCGG-3′ and 5′-GAAACACGGACACCCAAAGTAGT-3′) specific for the 5′ untranslated region (5′-UTR) as described ( 3 - 5 ). (blogspot.com)
Upstream2
Inference from large, rearranged immunoglobulin transcriptome data sets offers an opportunity to define the upstream regions (5'-untranslated regions and leader sequences). (lu.se)
Nucleotides upstream (towards the 5'cap) of the translation START codon are part of the 5' untranslated region (5' UTR). (openstax.org)
Downstream1
The non-coding regions downstream of coding sequences (CDS) is usually termed terminators. (frontiersin.org)
Promoter1
In particular, six single-nucleotide-polymorphisms (SNPs) in the promoter region of BnaC07g30920D were associated with the significant reduction of SOC, leading to a 4.7-6.2% reduction of SOCs. (biomedcentral.com)
Analysis1
Marklewitz M , Zirkel F , Kurth A , Drosten C , Junglen S . Evolutionary and phenotypic analysis of live virus isolates suggests arthropod origin of a pathogenic RNA virus family. (microbiologyresearch.org)
Human1
A typical human gene, then, produces multiple transcript isoforms (ten per gene, on average), that can differ both in their coding and untranslated regions. (biomedcentral.com)
Change2
Also he proposed an hereditary model in which the environmental influences are very important as an agents of evolutionary change and proposed the Theory of acquired characters. (intechopen.com)
however, a substitution in the 5′ untranslated region and a change in the potential p23/2C-like helicase cleavage site were observed. (biomedcentral.com)
Approaches1
Bayesian evolutionary rate and divergence date estimates were shown to be consistent for these three approaches and for two different prior specifications of evolutionary rates based on HCoV-OC43 and MERS-CoV. (nature.com)
Findings1
or (2) lower motor findings in two body regions - without an alternative demonstrable cause. (medscape.com)
Important1
Yunnan Province is located in southwestern China and borders on one of the world's most important poppy ( Papaver somniferum ) growing areas and opium producing bases (the 'Golden Triangle,' an area near the border of Laos, Myanmar and Thailand), and has been an important transfer station and drug trafficking route from the Golden Triangle to Yunnan Province and then to other regions of China. (cdc.gov)
Years1
In contrast, the frequencies of subtypes 3b and 1b decreased by almost 50% within 5 years. (cdc.gov)
Early2
Extreme differences in limb length define many of the dog breeds around the world, and the association between specific "short-legged" breeds and premature intervertebral disc degeneration has been documented since the early twentieth century [referenced in ( 4 , 5 )] Skeletal dysplasia is a general term describing abnormalities of growth and development of cartilage and/or bone and associated alterations in stature ( 6 , 7 ). (frontiersin.org)