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  • locus
  • In order to get round this problem, annotators also require some sort of protein evidence, such as whether the locus has sequence similarity to orthologues from other species, whether the resulting gene product contains Pfam functional domains, or whether experimental data is available from published papers, large-scale interaction studies or mass spectrometry experiments. (blogspot.com)
  • Coding and non-coding variants in the LOXL1 locus increase risk for developing XFG, though the functional effects remain poorly characterized. (arvojournals.org)
  • The goal of this work was to identify the genes and pathways regulated by the two genes in this locus: the non-coding lncRNA LOXL1-AS1 and the protein coding gene LOXL1 . (arvojournals.org)
  • A pbpA pbpH double mutant containing a xylose-regulated pbpH gene inserted into the chromosome at the amyE locus was constructed. (vt.edu)
  • 2018
  • 2018). The issue is the same problem that I discussed in recent posts [ Disappearing genes: a paper is refuted before it is even published ] [ Nature falls (again) for gene hype ]. (blogspot.com)
  • genomic
  • We use the Drosophila genomic data to distinguish between factors that increase the strength of purifying selection on proteins and factors that affect the amount of positive selection experienced by proteins. (carleton.ca)
  • This section includes genomic Reference Sequences (RefSeqs) from all assemblies on which this gene is annotated, such as RefSeqs for chromosomes and scaffolds (contigs) from both reference and alternate assemblies. (nih.gov)
  • sequences
  • C. parvum and C. hominis protein coding gene nucleotide and amino acid sequences were downloaded from CryptoDB [ 12 ] ( http://cryptodb.org/cryptodb/ ) release 3.2. (hindawi.com)
  • N. Goldman and Z. Yang, "A codon-based model of nucleotide substitution for protein-coding DNA sequences," Molecular Biology and Evolution , vol. 11, no. 5, pp. 725-736, 1994. (hindawi.com)
  • A codon based model of nucleotide substitution for proteincoding DNA sequences. (currentprotocols.com)
  • Overlapping loci from the two gene sets were analyzed by calculating the intersection and union of their respective coding (exon) sequences to determine if they represented the same gene. (biomedcentral.com)
  • In the opposite situation, RNA-seq data identified 215 transcriptional units with strong homology to known mammalian gene sequences, but not included in the in silico equine gene sets. (biomedcentral.com)
  • Accurate modelling of substitution processes in protein-coding sequences is often hampered by the computational burdens associated with full codon models. (beds.ac.uk)
  • While the modelling of evolutionary processes in non-coding sequences has received much attention from a context-dependence point of view in the last two decades, the same cannot be said for modelling approaches for coding sequences, at least not in terms of developed model-based approaches. (beds.ac.uk)
  • For example, in the case of analyzing protein-coding sequences, one needs to make sure to incorporate codon models as well as codon partition models in the model selection procedure. (beds.ac.uk)
  • functional
  • When these predicted genes are examined more closely they turn out to be artifacts-they are not functional genes. (blogspot.com)
  • A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. (currentprotocols.com)
  • Gene ontology annotation was used to evaluate the functional and structural categories of genes expressed in either a stable or tissue-restricted pattern. (biomedcentral.com)
  • sequence
  • In order to qualify as a real gene you have to show that the potential sequence has all the characteristics of real genes. (blogspot.com)
  • Investigating proteincoding sequence evolution with probabilistic codon substitution models. (currentprotocols.com)
  • A sequence alignment of the predicted product of pbpH against the microbial protein database demonstrated that the most similar protein in B. subtilis is PBP2A and in E. coli is PBP2. (vt.edu)
  • variation
  • The authors looked for local regulatory variation in a number of genes, and found one instance where the putative regulatory variant mapped to a protein-coding SNP inside the gene. (gnxp.com)
  • Variation in genes coding for AMP-activated protein kinase (AMPK) and breast cancer risk in the European Prospective Investigation on Cancer (EPIC). (diva-portal.org)
  • Using a tagging approach and selecting SNPs we covered all the common genetic variation of these genes. (diva-portal.org)
  • putative
  • The next best evidence is that the putative gene is under negative selection with respect to potential homologues in other species. (blogspot.com)
  • conclusion
  • Finally, we observe that the substitution patterns in both datasets are drastically different, leading to the conclusion that combined analysis of these two genes using a single model may not be advisable from a context-dependent point of view. (beds.ac.uk)
  • transcripts
  • Genes and transcripts may change their status between releases as annotators adjust the annotation to the available evidence. (blogspot.com)
  • substitution
  • Finally, the evolutionary tendencies of RNA editing in different gene groups were estimated using the nonsynonymous-synonymous substitution rate selection mode. (biomedcentral.com)
  • evolutionary
  • The evolutionary history of a gene can be very informative about its function. (biomedcentral.com)
  • Several contributing factors have been implicated in evolutionary rate heterogeneity among proteins, but their evolutionary mechanisms remain poorly characterized. (carleton.ca)
  • mainly
  • In higher plants, RNA editing mainly occurs in the protein-encoding genes of mitochondria and chloroplasts and it mostly converts C to U, although hornwort and fern have abundant U to C editing. (biomedcentral.com)
  • The genes found in all fungi except Saccharomycotina are slightly better characterised and predicted to encode mainly enzymes. (biomedcentral.com)
  • chromatin
  • And what´s more, they provide evidence that chromodomains, a form of molecular Velcro, read the histone code by distinguishing between two similar locations on the histone tail, a flexible protein chain that pokes through the tightly folded chromatin complex. (innovations-report.com)
  • HP1 is a protein associated with heterochromatin, a condensed form of chromatin that silences genes. (innovations-report.com)
  • cellular
  • AMP-activated protein kinase (AMPK) is an energy sensing/signalling intracellular protein which is activated by an increase in the cellular AMP:ATP ratio after ATP depletion. (diva-portal.org)
  • regulate
  • Biologists find that long non-coding RNA molecules are necessary to regulate differentiation of embryonic stem cells into cardiac cells. (lsrf.org)
  • On a little further study, they found the story goes like this-- the gene itself (AMN1) is a regulator of two other genes (DSE1 and DSE2) in a network, and those genes, in turn, regulate AMN1. (gnxp.com)
  • The coding change in the gene keeps it from playing its proper role in the network, so DSE1 and DSE2 are upregulated and, in turn, up-regulate AMN1. (gnxp.com)
  • genetic
  • The one precursor one siRNA model might not be valid for all sRNA genes, leaving the question: what are the genetic/epigenetic features of the sRNA genes that differentiate their sRNA precursors production and processing? (psu.edu)
  • SNPs
  • We observed no statistically significant association between the SNPs in the PRKAs genes and BC risk and BMI after correction for multiple testing. (diva-portal.org)
  • Genotyping of 16 single-nucleotide polymorphisms (SNPs) of eight "canonic" SR protein-coding genes were performed with the use of the Illumina Infinium Beadchip platform. (fertstertforum.com)
  • methylation
  • The research reported in the Genes & Development paper focuses on a chemical reaction called methylation that occurs on histone H3 (histones are made of four subunits called H2A, H2B, H3 and H4). (innovations-report.com)
  • metabolic
  • Whereas "housekeeping genes" are under purifying selection to conserve many metabolic functions, genes that enable the parasite to adapt to different host environments may evolve more rapidly. (hindawi.com)
  • 2001
  • These results motivated us to describe a set of 2001 potential non-coding genes based on features such as weak conservation, a lack of protein features, or ambiguous annotations from major databases, all of which correlated with low peptide detection across the seven experiments. (nih.gov)
  • In 2001, Allis´ laboratory at the University of Virginia (he joined Rockefeller in March 2003) showed that a protein called HP1 docks to methylated Lys9. (innovations-report.com)
  • cell viability
  • However, these genes underpin numerous core biological processes and are indispensable for cell viability. (frontiersin.org)
  • The idea is to disrupt every gene and screen to see if it's required for cell viability in culture. (blogspot.com)
  • Pathway
  • Pathway analysis identified enrichment of genes involved in UV response, proteasome complex formation, ECM constituents and downstream targets of TGF-β1 with LOXL1-AS1 KD. (arvojournals.org)
  • encode
  • We hypothesized that genes that are up-regulated in the uterine endometrium at the initiation of conceptus elongation in cattle, and that encode for secreted proteins, contribute to the composition of the uterine luminal fluid (ULF) and ultimately, drive conceptus elongation. (biomedcentral.com)
  • conservation
  • We found a strong relationship between detection in proteomics experiments and both gene family age and cross-species conservation. (nih.gov)
  • At the opposite end of the scale, we identified almost no peptides for genes that have appeared since primates, for genes that did not have any protein-like features or for genes with poor cross-species conservation. (nih.gov)
  • The percentage of gene products detected in proteomics experiments as a function of gene conservation. (nih.gov)
  • Gene conservation is expressed using MI score, displayed in bins. (nih.gov)
  • The 'missing' genes are those where the conservation was so poor that INERTIA was not able to generate a score. (nih.gov)