Fig. 3

BLAT alignment of sequenced cDNA from UN21936 and assembled transcripts to the reference genome. Screenshot was captured from the UCSC Genome Browser. Dark boxes represent exons while thin lines are introns. The empty RefSeq Genes, Ensembl Gene Predictions, Horse ESTs, and Non-Horse RefSeq tracks indicate that there has never been expression or computational predictions placed here. Although the amplicon shows three mismatches to the reference (shown as vertical red lines on the SangerSequence data), this sequence aligned perfectly to the sequence from the de novo assembled transcript (RawAssemblySequence)