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Figure 5 | Genome Biology

Figure 5

From: Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors

Figure 5

Size analysis of coding sequence and UTRs of U2AF65- and PTB-associated mRNA populations. (a) Average size of 5' and 3' UTRs and coding sequence (CDS) for mRNAs in the U2AF65-associated or PTB-associated populations and their respective control (nonassociated) populations (Additional data file 2). For this analysis, information for the longest curated transcript available in EMBL [40], GenBank [41], and RefSeq [42] databases was retrieved for all entries in each population, when available (Additional data file 4). Statistically significant differences between the associated and the respective control populations are indicated. (b) Analysis of putative U2AF65 and PTB binding motifs in selected mRNA populations. The longest curated transcripts for mRNA accessions in the U2AF65-associated or PTB-associated populations and their respective control (nonassociated) populations were searched for putative U2AF65- and PTB-binding motifs. Graphs present average U2AF65 motif density in the U2AF65-associated and control populations, and average PTB motif density in the PTB-associated and control populations. The ratio between values for each associated/control pair is shown. (c) Analysis of the distribution of putative U2AF65- and PTB-binding motifs in the different transcript regions. Graphs present average U2AF65 motif density by transcript region in the U2AF65-associated and control populations and average PTB motif density by transcript region in the PTB-associated and control populations. The ratio between values for each associated/control pair is shown. *P << 0.001. n, population size; n.s., not significant; PTB, polypyrimidine tract binding protein; U2AF, U2 small nuclear RNP auxiliary factor; UTR, untranslated region.

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