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Transcript
What constitutes an ‘alternative TSS’? . . . any . . . any Case 1 This includes: First exon shows novel splice structure (likely real) . . . any . . . any Condition: x>100 bp Case 2 (optional; default: not included *) • • • . . . any . . . any First exon is significant variation on existing exon (but may also be artifact) Genes with a single TSS: by default, longest form included for multi-exon transcripts only Case 2 events account for ~40% of the cases (genes with a single TSS not included) Event “signature” is the in-boundary of the first exon (see below). Therefore, different events may lead to the same transcription start site in genomic coordinates: Event 1001 Event 1002 . . . any Different events, same genomic TSS . . . any Example 1: Alternative TSS at Uqcrc1 Cufflinks t1, t2, t3 t4 t5 What constitutes a ‘skipped’ (cassette) exon? (X)SKIP ‘on’ ‘off’ X X X X (X)MSKIP ‘on’ ‘off’ • • • • Transfrags must belong to the same gene, have the same orientation Both transfrags must contain >=3 exons X – exact boundary match for SKIP, approximate (simple exon overlap) for XSKIP - event “pattern” or “signature” (column 7) Example 2: ‘Skipped’ exons at Sp140 s1 s2 What constitutes a ‘retained intron’? (X)IR ‘off’ ‘on’ (X)MIR any … any … ‘off’ any … any … any … any … ‘on’ any … any … X X X X What if the event involves a terminal exon? 1. Long (‘on’) exon? No – APA! ‘off’ any … ‘on’ any … any … ‘off’ ‘on’ X any … any … X any … X X 2. Short (‘off’) exon? Yes - IR! ‘off’ any … ‘on’ any … any … X • • ‘off’ ‘on’ any … any … X any … X X Transfrags must belong to the same gene, have the same orientation Both transfrags must contain >=3 exons What constitutes an ‘alternative exon end’? (X)AE 3’ end any … (5’ exon end must match) any … X … any 5’ end (3’ exon end must match) … any X Both ends X • • X Transfrags must belong to the same gene, have the same orientation Both transfrags must contain >=3 exons; only internal exons can be AE Relationship to a reference gene (column 19) 5’ 3’ =2 (identical) ~2 (overlap) ~2 (overlap) >2 (intronic) <1 (out of range)
