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These genes, coded on opposite strands, overlap in the ancestral gene arrangement by seven residues, comprising the 3′ ends of both amino acyl stems.
Genes on opposite strands overlap (e.g., nad2 and trnC), are contiguous (e.g., trnQ and trnM), or are separated by some nucleotides (e.g., trnT and trnP) or intergenic spacers (e.g., trnS2 and nad1).
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Transcripts were joined in several ways including on opposite strands overlapping in the 3' UTR, and on the same strand with some overlapping reads (possibly due to the repetitive nature of the genome).
In contrast, using GeF-seq, the distributions of sequence tags on the plus and − strands overlapped in the middle of the two ChAP-seq peaks (Fig. 3B).
Sites of 10-bp overlap were defined as regions within a 3' UTR cluster where the first 10 bases of sequences aligned to the plus and minus strands overlapped each other.
We identified 71,210 same-strand overlapping gene pairs (Table 1).
The Airn promoter lies in the second intron of Igf2r, and Airn transcription occurs from the opposite strand overlapping Igf2r exons 1 and 2 [ 5- 7].
Kingsford et al. [ 13] explained this phase distribution in opposite-strand overlapping genes by the frequency of reverse-complementary stop codons in coding sequences.
d the shorter gene is fully contained in the longer gene (but transcribed from the opposite DNA strand) Overlapping gene pairs on different strands (groups 1-3) actually form sense-antisense (SA) pairs.
We identified two pairs of opposite strand overlapping coding loci in human and mouse, which could potentially serve as antisense with respect to each other: PAX3 and CCDS140 is one pair, and ZHX3 and PLCG1 the other.
The gau ORF is always found in the same reading frame, which is in the antisense strand overlapping the cox1 gene in such a way that the third position of the cox1 gene codons are complementary to the third position of the gau ORF triplets.
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