Examples of new UTRs revealed by novel contigs. (A) Novel contig whose expression is correlated with that of chinmo. The region illustrated includes the 3′ portion of the annotated chinmo gene and all of its downstream neighbor, cpb. Signal graphs for the transcripts are shown for eight cell lines. (Red bar) The position of the novel contig; a region of continuously overlapping paired-end sequences (blue line) connects the novel contig to chinmo. (B) Novel contig that appears to encode a novel 3′ exon for Fs(2)Ket. The display is similar to panel A, showing the convergently transcribed genes Fs(2)Ket and CG9310. Much of the region between the two genes is covered by a transposable element and is therefore masked from both tiling array and RNA-seq analysis. However, paired-end RNA-seq showed multiple clones in all four of the lines that were analyzed in which one end lies in the 3′ region of the annotated Fs(2)Ket transcript and the other end lies in the novel contig 7 kb away; the dashed blue line indicates the region that is bridged by these clones. The novel contig also contains overlapping paired-end clones that extend into the annotated CG9310 transcript. These data indicate that the contig probably corresponds to novel overlapping 3′ regions from the two genes. (C) A contig that corresponds to a novel 5′ exon for Prestin, a gene for which only the coding region was previously annotated. (From top to bottom) The novel contig (red bar); a novel splice junction identified from RNA-seq data from S2-DRSC RNA; the FlyBase v5.12 annotation for Prestin, which includes only the coding region (purple); a Prestin transcript from the unpublished annotation MB8 (MJ van Baren, L Langton, CL Comstock, BC Koebbe, and MR Brent, unpubl.; http://www.modencode.org/), which used the RNA-seq splicing data as input for the annotation (blue and white); sequence of a full-length cDNA clone MIP14411 (GenBank accession no. BT120083) retrieved by targeting with the FB 5.12 gene model; and pattern of transcripts from RNA-seq analysis of S2-DRSC cells.
