Protein-Coding Genes and Transposable Elements in
Copy number increases of transposable elements and protein-coding genes in an invasive fish of hybrid origin
... 10,979 genes was assessed using comparative genome hybridization ...Twelve genes showed sig- nificantly higher copy numbers in invasive Cottus compared to both ...three genes related to vision, ...
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Epigenetics and Transposable Elements
... targeting protein coding genes for insertion, causing chromosome breakage, illegitimate recombination and genome rearrangement ...flanking genes in a variety of ways, either by altering ...
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Analysis of Transposable Elements in Coccidioides Species
... the transposable elements (TE) in Coccidioides ...that protein-coding genes within 1 kB of hAT or Gypsy TEs were poorly ...posadasii genes within 1 kB of Gypsy TEs was also ...
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Dual coding of sirnas and mirnas by plant transposable elements
... The miRBase Sequence Database (Griffiths-Jones et al. 2006) contains genome annotations for experimentally characterized miRNA gene sequences from a number of species, including Arabidopsis and rice. Release 10.0 of ...
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C-GATE - catalogue of genes affected by transposable elements
... C-GATE is formatted as shown in Table 1, and each user can either upload an example through an online form or multiple examples by downloading a table and submitting it in the C-GATE forum. A ‘comment’ section allows for ...
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Transposable elements contribute to fungal genes and impact fungal lifestyle
... of transposable elements (TEs) in 625 publicly available fungal genomes from the NCBI database in order to explore their potential roles in genome evolution and correlation with species’ ...as genes, ...
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The DAWGPAWS pipeline for the annotation of genes and transposable elements in plant genomes
... annotate genes in a number of eukaryotic genomes, plant genome anno- tation efforts cannot focus solely on the annotation of genes due to the risk of conflating genes with transposable ...
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Identifying protein-coding genes and synonymous constraint elements using phylogenetic codon models
... We develop methods to identify and characterize short coding regions with highly conserved synonymous sites in mammalian genes, which we call Synonymous Constraint Elem[r] ...
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Evaluating the protein coding potential of exonized transposable element sequences
... as protein coding sequences but they can also be domesticated to serve as regulatory ...a protein coding sequence or it could be a regulatory role such as we propose for anti-sense ...as ...
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The Regulation of Prokaryotic Transposable Elements by the RNA Binding Protein Hfq
... IS Elements from the IS Finder database, one can successfully identify IS Elements containing Hfq binding sites which may implicate Hfq ...identified elements, IS1413, was characterized by ...
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Transposable elements in Drosophila
... They designated this form of off-target gene silencing as “genomic autoimmunity”, an analogous to classic forms of autoimmunity which are caused by an immune re- sponse that incorrectly targets self. Despite the rapid ...
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Identifying protein coding genes in genomic sequences
... or protein sequences onto the genome, which can be obtained using a variety of tools, including sequence-similarity searches, is refined using more sophisticated ‘splice alignment’ algorithms, whose explicit ...
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Detecting positive selection in protein coding genes
... those genes that experienced positive selection sites the affected residues can be inferred and in the m ost interesting cases mapped onto a 3D protein structure if ...
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COMPUTATIONAL PREDICTION OF EUKARYOTIC PROTEIN-CODING GENES
... several genes, a feature (such as an exon) in one gene becomes dependent on the features of other ...different genes, except for genes at some tightly linked loci, such as the locus con- trol region ...
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CHAPTER 20 Transposable Elements
... 2. R plasmids have medical significance, because they carry genes for resistance to antibiotics, and transfer them between bacteria (Figure 20.7). a. Genetic features of R plasmids include: i. The resistance ...
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Manipulating the Xenopusgenome with transposable elements
... of protein expression can be delayed by injecting plasmid constructs in which a promoter drives expression of the introduced gene, thus delaying expression until after the mid-blastula transition when zygotic ...
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DUPLICATED GENES PRODUCING TRANSPOSABLE CONTROLLING ELEMENTS FOR THE MATING-TYPE DIFFERENTIATION IN SACCHAROMYCES CEREVISIAE
... Evidence for the functional mutation of the HMLa and HMRa genes: To con- firm the mutation of H M L a and HMRa to the alternative functional alleles, meiotic segregan[r] ...
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Site-to-site Rate Variation in Protein Coding Genes
... 13 protein coding genes from the completed mitochondrial genomes of a total of 111 taxa sampled from ten animal clades, we find extensive variability of synonymous rates in the majority of ...
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Transcriptome analyses of tumor-adjacent somatic tissues reveal genes co-expressed with transposable elements
... specific transposable elements embedded within introns, the correction is not ...the genes. The genes co- expressed with intronic TEs include pseudogenes, in- tronic transcripts, anti-sense ...
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DNA methylation changes facilitated evolution of genes derived from Mutator like transposable elements
... putative genes in each of the Oryza species, a large proportion of which have evidence of expression and contain chimeric ...Mutator-like transposable element-derived genes are generally GC-rich and ...
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