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As special conservation elements, we identified Priority Areas for Conservation of species using five criteria: species richness, geographic rarity, species vulnerability, a Combined Index of these three criteria, and a Standardised Biodiversity Index (SBI) that integrate the three criteria and four studied taxa.
The major elements we identified in the stable mRNAs are GA-rich (SE1), CA-rich (SE2 4) or CU-rich (SE5 and 6).
Most of the elements we identified contained frequent stop codons or/and frameshifts in the coding regions, and appeared fragmented.
In the case of CACTA elements, we identified 125 transposase-like sequences, whereas 55 were isolated for Mutator-like elements.
The elements we identified can be divided into 1,725 families based on the similarity of their nucleotide sequence.
When analyzing the binding sites common to amphioxus 2B and Ciona 2D0.5 elements, we identified several Ets sites in the 2B sequence.
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As a first step towards functional characterization of protein-coding genes with predicted structurally-conserved elements in their 3' and 5' untranslated regions (UTRs) and introns, we identified enriched Gene Ontology (GO) terms with GO::TermFinder [42]. Figure 7 indicates potential biological functions for the structured elements we identify.
Here, using a combination of sequence profile analysis and contextual information from genomes of viruses and other selfish elements we identify a novel family of polymerases related to superfamily A DNA polymerases and mitochondrial/phage T7-like RNA polymerases.
In switch 2 element, we identified one substantial change in the loop region between the two helices of the GTP-bound system (see Figure 6A).
The CMITE-IN element also seems to be a mobile element: we identified a pair of alleles from A. palmata, with and without CMITE-IN element, which suggest that the CMITE-IN can be excised at the position of its protoelement-derived TTAAs (Fig. 2d, bottom).
TremG, the 7th Tc1/mariner element we identified, has 6 copies in Pb03 and 11 in Pb18.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com