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Exact(6)
In contrast to multiple coding exons of the Ugt1 and Ugt2 genes, the open reading frame of each of the Ugt5 genes (except Ugt5g2) is encoded by a single large exon (Fig. 1B).
We kept only copies in which the closest match was an Ensembl peptide with multiple coding exons (putative parental genes).
V1Rs are typically encoded by a single coding exon (~900-1000 base pairs) and are distantly related to bitter taste receptors whereas V2Rs are encoded by multiple coding exons and are closely related to Ca2+-sensing receptors [ 19– 219.
These genes were further investigated for characteristics that would support their annotation as host genes, including whether the gene was Previously Known, had multiple coding exons, overlapped a spliced transcript alignment, and had InterPro domain matches (Additional file 8).
We also consider whether exon splice junctions are aligned; this test yields slightly higher conservation rates, as may be expected, but only applies to proteins with multiple coding exons 87-900% of proteins from mouse, cow, and zebrafish have human ortholog with at least 3 coding exons).
We examined, in detail, all cases that were not purely duplication events, specifically those events that exhibited evidence of exon acquisition (see Methods): 1) cases with multiple coding exons, and 2) cases that showed evidence of contributions from retrocopy ORFs in the antisense direction.
Similar(54)
The Type I retrocopies contributed domains, in either the sense or antisense orientation, to known multiple coding exon genes [ 74] or to those found in the Refseq database [ 75].
We only included the gene pairs of the Ensembl peptides with multiple coding exon (parental gene) as the best hit of the merged sequence (new gene), as these can prevent the single exon gene, e.g., olfactory receptor genes, from becoming the "parent" gene.
In BRCA2, the design coverage was 96.1%, with multiple regions within coding exons 4, 5, 7, 8, 9, 10, 11, 12, 14, 15, 18, 19, 21 and 26 missed as well as multiple exon-intron boundaries totaling 408 bp of missed sequence.
For example, the mRNA gene could be broken down into introns and exons with multiple coding variants and noncoding variants that control mRNA splicing.
Of the 726 candidate retrocopies whose expression was supported by many transcripts, 624 were composed of single protein coding exons and 102 contained multiple protein coding exons.
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