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About 33% (381) of these genes are processed (181) or unprocessed (200) pseudogenes, and an additional 276 non-coding RNAs contain lincRNAs (118), microRNAs (38), and snoRNAs (120).
Primary miRNAs (pri-miRNAs), transcribed either as independent genes or as introns of coding genes, are processed to form precursor hairpin loops (pre-miRNAs) and then mature miRNAs by the RNAse III enzymes Drosha and Dicer respectively.
Over 40% of plant genes (Arabidopsis thaliana and Oryza sativa) and over 90% of human genes are processed by alternative splicing to generate multiple and assorted mature mRNA molecules [ 3- 6].
In Caenorhabditis elegans, the 22 nucleotide endogenous miRNA encoded by lin-4 and let-7 genes are processed by Dcr-1 and these small RNAs regulate lin-14 and lin-41 linked timing of developmental stages in the nematode life cycle [ 24].
Here, we are using the same candidate gene sets as described at the beginning of Section " Gene aggregation evaluation", but the candidate genes are processed by the MA-kNN wrapper, and the outcome is then evaluated by the three performance measures as in Section " Parsimony model" (Tables 3, 4 and 5) and Section " Gene aggregation evaluation" (Figs. 2, 3, 4, 5, 6, 7 and 8).
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The list of potential miRNA target genes and MIRNA genes was processed by a bulk query of the MPSS [85] web portal (http://mpss.udel.edu).edu
Large-scale identification of wheat resistance genes were processed by comparative transcriptomic analysis.
Differentially expressed genes were processed using DEGseq and screened according to the criteria FC >2 and p-value <0.05.
The biological processes, KEGG path, gene cellular localization, and molecular function annotation of the 471 genes were processed through ClueGo [ 29] plug-in of Cytoscape [ 87].
The initial transcript of a gene is processed by a delicate piece of cellular machinery known as a spliceosome, which strips out all the introns and joins the exons together.
It has been previously shown that the protein product from an engineered tomato prosystemin gene is processed in tobacco, thus suggesting that the components responsible for its post-translational modifications are present in this species.
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