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Firstly, one to six transcribed CojaIIB loci were identified in each Coja haplotype, of which one or two of them was the major coding locus.
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This is in agreement with the emerging general view that in a given condition, the transcriptome from protein coding loci is dominated by one major transcript per gene and often that same transcript is expressed across many cell-types [ 52].
DNA sequences of up- and downstream coding loci were used as queries for BLAST searches of the L. major genome in GeneDB.
Fig. 3 Averaged overall major codes.
This distinction is necessary since promoter loci harbor substantially more diversity than coding loci (see Table S5 from Supplementary Material).
Interestingly, rbcL-a in some cases proved better than other coding loci as a barcode.
Coding loci: Known_CDS, Novel_CDS, Putative_CDS, NMD.
This corresponds to 774,002 protein coding loci and 31,237 miRNA coding loci across all species under analysis.
Loci were allowed unlinked substitution models (Table 2) and the 3 coding loci were partitioned by codon position.
In some coding loci, 2 3 coding variants were accompanied by anywhere from 1 to 50 non-coding variants.
A major limitation of the CCDS data set is that not all protein-coding loci or coding splice variants are currently represented in the CCDS data set.
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