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. 2009 Nov 20;38(Database issue):D600–D606. doi: 10.1093/nar/gkp1046

Figure 2.

Figure 2.

MouseIndelDB custom track at UCSC mouse genome browser. Polymorphic SINE and L1 retrotransposons at a region of mouse chromosome 1 are shown on the MouseIndelDB custom track displayed at the UCSC mouse genome browser (mm9 assembly). Three WGS sequence traces from DBA/2J mice each skip over a single polymorphic SINE retrotransposon, present in the reference (designated as REF-IN) genome but absent from DBA (top, labeled as REF-IN, red rectangles, trace IDs 1090731691, 1101700443 and 109988639). The reference SINE element can be seen on the conventional RepeatMasker track (bottom). In addition, a nearby mapped sequence trace from the 129X1 strain indicates an insertional polymorphism present in that alternative (ALT-IN) strain but absent from the reference C57 genome (blue rectangle, labeled as ALT-IN, trace ID 1073424193). In the latter case, a 50-nt thin projection (thin blue rectangle, right) indicates the genomic junction and relative position of the previously unreported L1 retrotransposon integrant in the 129X1 genome. Superimposed arrows indicate the direction of sequence trace alignments compared with the reference genome.