Cufflinks predicted a large number of novel single-exon transcripts (56,719). During the mapping of sequence reads using Life Technologies LifeScope software, spliced reads were only included for the annotated genes, which prevented the construction of novel multi-exon transcripts. After filtering the novel transcripts according to a minimum length (>130 bp) and FPKM value (>5), a total of 13,660 novel candidate transcripts were identified (Figure 2). Furthermore, Cufflinks predicted 38,418 new isoforms, 1595 transcripts with generic overlap with reference genes, and 1311 transcripts with exonic overlap with reference on the opposite strand (Figure 2). For 448 of these opposite strand transcripts in the oviduct and for 787 in the testis, the FPKM was >1. Functional analysis of these genes did not indicate any enriched GO terms, but they do represent possible regulatory sequences for expressed genes in the testis and oviduct.