Figure 1.
Xbp1's partial transcript sequence, including the non-canonical 26 nt spliced region (highlighted on right).
Figure 2.
Illustration of a hypothetical potentially novel spliced region with two supporting reads.
Below the gene are two examples that RSW would disregard: a split read pair mapped to the incorrect strand (gray) and a split read pair mapped with a 0 or 1 bp gap (orange).
Table 1.
Bowtie Mapping statistics for Ire1α+/− samples treated with Tg and Dtt.
Figure 3.
UCSC custom track view for Xbp1 26 nt spliced region in mouse embryonic fibroblast cells and qRT-PCR results.
“Het” = Ire1α+/−; “KO” = Ire1α−/−. a = 500 nM Thapsigargin 4 hrs; b = 1 mM Dithiothreitol 4 hrs; For both a and b, Het reads are on top and KO reads are on the bottom. Red vertical lines indicate the 26 nt spliced region.
Table 2.
The number of reads aligned to Xbp1's 26 bp splice junction by our “Read-Split-Walk” (RSW) algorithm for Ire1α+/− and Ire1α−/− samples.
Figure 4.
Comparison of supporting reads for Xbp1's 26 nt splice junction site in the Dithiothreitol (Dtt) sample from RSW, Exonerate and the Unix “grep” command.
Table 3.
STAR results on the region where Xbp1 is located.
Table 4.
Counts of spliced regions detected by RSW and proteomics from the SKBR3 cell line.