Table 2.

Alternative gene splicing associated with SF3B1 mutations in uveal melanoma

Gene symbolGene namePossible alternative event (HTA2/GenoSplice EASANA)Harbour and colleagues RNA-Seq (GenoSplice EASANA)Present study RNA-Seq (DEXSeq/MATS)qRT-PCR Validation
ABCC5ATP-binding cassette, sub-family C (CFTR/MRP), member 5Retention of intron 5
CRNDEColorectal neoplasia differentially expressed (non-protein coding)Alternative acceptor site (exon 4)
UQCCUbiquinol-cytochrome c reductase complex chaperoneAlternative terminal exons
GUSBP11Glucuronidase, beta pseudogene 11Cassette exon 7
ANKHD1Ankyrin repeat and KH domain containing 1Alternative acceptors site (exon 3)
ADAM12ADAM metallopeptidase domain 12Alternative terminal exons (exon 18 vs. exon 19)
F8Coagulation factor VIII, procoagulant componentAlternative first exons (exon 23 vs. exon 24)
GAS8Growth arrest-specific 8Alternative terminal exons (exon 12 vs. exon 13)

NOTE: For each gene indicated, the table presents the prediction of alternative splicing by the GenoSplice EASANA visualization interface in our HTA2 data and the RNA-Seq data by Harbour and colleagues (9). Also shown is the prediction of these events by DEXSeq and/or MATS in our RNA-Seq data and validation of the events by PCR.

Abbreviation: qRT-PCR, quantitative real-time PCR.