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FST estimates over all populations by locus were also small and not significant (FST ≤0.0026, P≥0.110).
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All CDSs found at the 3DS locus were also compared by Blastn against the complete sets of gene models from rice and Brachypodium downloaded from ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/ (RGAP 6.1) and http://ftp.brachypodium.org/ (Bradi_1.0).
Regulatory elements of the Rad23a locus were also readily detected by FAIRE in untreated and α-amanitin treated fetal liver cells (Figure S3).
As mentioned in the introduction, the M- and P-specific genes controlled by the mat1 locus are also induced by pheromone.
Typically the closest gene is identified as the gene of interest, but that is not a foolproof algorithm, and the pathways affected by the genetic locus are also not necessarily immediately apparent [ 13].
Note that the expression level of p19 Arf, another transcript produced by the Ink4a/Arf gene locus, was also increased in the SMGs of mice lacking Bmi-1, albeit to a lesser extent (Fig. S1A).
The existence of this locus is also supported by the finding of PmHhb-related exonic sequences in the trace archives of the Pm genome sequence project (kaki, Fig. 1A and phylogenetic tree in Fig. 2A).
The stability of the integrated MSP-1 locus was also shown by Southern analysis during 35 days of successive passages, demonstrating that no reversion to the wild type had occurred.
One predicted CNV locus was also evaluated by direct PCR of two genomic segments within the putative deletion region using the following primer pairs: (PLSCR1exon amplicon) forward 5'-TCTAAACCCAGGATTAGCAAGAA-3', reverse 5'-CCATGTAATTTTGATAGGGTATTTCA-3' and (CFA23CNV44Mb amplicon) forward 5'-TGTAAACCTCATTTCACTTACATGG-3', reverse 5'-GGTCCATGGAGGACTCTCTCT-3'.
The presence of a single mating-type a-idiomorph locus was also confirmed by gDNA-based Southern blotting.
This single putative TbUGP locus was also confirmed by Southern blotting of restriction endonuclease digested genomic DNA (data not shown).
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