For calculation of the time to the most recent ancestor (TMRCA) for specific clades in the phylogeny, ρ statistics (mean divergence from inferred ancestral haplotype) were used with a coding region (nts 577 16023) mutation rate estimate of one transition per 5138 years [ 45].
Articles were assessed using a coding sheet adapted for the region which included themes on: Governance Arrangements, Financial Arrangements, Delivery Arrangements, and Implementation Strategies.
Exon duplication is one widely used mechanism for adding a coding region within an existing gene.
For the remaining genomes, we collected the ZΔ G values for the first 30 bases in each ORF from Gu et al. (2010), available at http://openwetware.org/wiki/Wilke:Data_Sets. In certain analyses, we also examined ZΔ G for regions upstream of a coding region, using a sliding window approach for 30 base windows starting 10, 20, and 30 bases upstream of the coding region.
Alternatively, the use of dsRNA against a coding region of a protein known not to be involved in mitosis could also help to discard unspecific effects.
The term locus is used here as a synonym for a coding region of the genome.
These methods demonstrate that log odds ratios based on codon conservation can be used to indicate the possibility of a coding region existing in the alignment of human and mouse sequences [ 15, 16].
The inferred CDS were used to make a coding region-only data set for subsequent divergence analysis.
To assess the copy number and integrity of the transgene, we analyzed Tg-250SB by Southern blot using MOR42-3 coding region as a probe, which cross-hybridizes to highly homologous gene MOR42-1 (97% identical).
However, by using the coding region of dog BCMP1 a significant match was identified with genomic sequences assigned to human chromosome 8 (clone RP11-31H18, EMBL/GenBacc acc. #: AC041003).
