Figure 3.

Transcripts can be aligned to the mouse genome assembly using BLAT search at the UCSC Genome Browser. Aligning regions (usually exons) are shown as black blocks. The aligning regions are connected by lines representing gaps (usually spliced-out introns), with arrowheads indicating the direction of transcription. (a) The alignment of TCs and DTs associated with MGI gene Ncam1(MGI:97281) to the annotated Ncam1 gene on chromosome 9 shows that alternative spliced exons and alternative poly(A) addition sites cause multiple transcripts from one gene. The tracks of *TC640342 and *DT.487850 are matches with lower percentage identity over a shorter region of the sequence. (b) The alignment of TCs and DTs associated with the MGI gene Dtna (MGI:106039) to the annotated Dtna gene on chromosome 18 demonstrates that three alternative promoters are actively used, as suggested by published experimental results.