TopHat analysis of RNA-Seq data reveals alternative splicing in Arabidopsis thaliana GRP7 (AT2G21660)
This image from IGB 6.6 shows how IGB can capture a rich data scene and convey details about alternative splicing. The image depicts Arabidopsis thaliana GRP7 (AT2G21660) encoding "a small glycine-rich RNA binding protein" that "regulates..circadian oscillations of its own transcript." (Functional annotation comes from The Arabidopsis Information Resource locus page for AT2G21660.) Splicing pattern of GRP7 is complex, as depicted in the image below. Here, junctions predicted by the TopHat spliced alignment program are shown together with the number of reads supporting each junction - this comes from the "score" field of the junction.bed file TopHat produces. 