Identification of binding sites for Tra2β in the mouse transcriptome.

(A) Nucleotide sequences enriched in the Tra2β CLIP tags are enriched in the core motif GAA. The percentage of CLIP tags was plotted against the order of retrieval of individual 6-mers on a logarithmic scale to identify the most frequently occurring 6-mer sequences within the CLIP tags. CLIP tag sequences which contain GAA are indicated in red. All other CLIP tags are shown in blue. (B) Consensus binding site for Tra2β derived from alignment of full length CLIP tags. The consensus was constructed by anchoring CLIP tags around GAA and then performing an alignment. The positions 1–6 which are particularly conserved are shown underneath and discussed in the main text. (C) Pie chart showing percentage of retrieved CLIP tags mapping to different inter- and intragenic locations within the mouse transcriptome. (D) Summary of the top 5 molecular and cellular functions for Tra2β determined by Ingenuity Pathway Analysis. (E) Distribution of Tra2β binding sites relative to the different classes of alternative events annotated on the mouse genome. Alternative events are shown in red, and the constitutive events as yellow boxes (exons) or black lines (introns). Alternative events are annotated according to the UCSC genome browser track Alternative Events (URL: http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=knownAlt&hgsid=212031267).