Skip to main content

Table 1 Comparison of SLs and SL RNA genes detected by SLIDR and SLFinder in four eukaryotes (Caenorhabditis elegansCiona intestinalisHydra vulgaris and Schistosoma mansoni)

From: SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data

Species SL Pipeline SL sequence SLs detected SL RNA genes detected
C. elegans Cel-SL1 SLIDR -agtcGGTTTAATTACCCAAGTTTGAG------ 100% (1/1) 100% (10/10)
   SLFinder ggaggGGTTTAATTACCCAAGTTTGAGaaaatg 100% (1/1) 100% (10/10)
    -------------TACCCAAGTTTGAGgtaatc   
C. elegans Cel-SL2 SLIDR ttGGTTTTAACCCAGTTAACCAAG--- a 100% (11/11) 100% (18/18)
   SLFinder -tGGTTTTAACCCAGTTAACCAAGatg 9% (1/11) 44% (8/18)
C. intestinalis Cin-SL SLIDR taaggcATTCTATTTGAATAAG- 100% (1/1) 73% (11/15) b
   SLFinder ----ggATTCTATTTGAATAAGa 100% (1/1) 0% (0/15) c
H. vulgaris Hvu-SL-B1 SLIDR ---cttcggaaaaAAACACATACTGAAACTTTTTAGTCCCTGTGTAATAAG-------- a 17% (2/12) d
   SLFinder cccggACGGAAAAAAACACATACTGAAACTTTTTAGTCCCTGTGTAATAAGaaaaaaat 8% (1/12) 239 d
    -------------------------------------CCCTGTGTAATAAGcaaaaa--   
    -------------------------------------CCCTGTGTAATAAGgtttaa--   
    -------------------------------------CCCTGTGTAATAAGtaaaaaa-   
    --------------------------------------CCTGTGTAATAAGttttaaa-   
    ---------ccgatctCACATACTGAAACT-----------------------------   
S. mansoni Sma-SL SLIDR ctaaccgtCACGGTTTTACTCTTGTGATTTGTTGCATG--- 100% (1/1) 110 d
   SLFinder ----ccgtcacgGTTTTACTCTTGTGATTTGTTGCATGata 100% (1/1) 132 d
  1. Datasets are detailed in Additional file 1: Table S1 and [34]. For each expected SL, the sequences assembled from the RNA-Seq data are presented as alignments, underlining the expected sequence. Lower-case 5′ bases in the SLIDR sequences denote bases supported by fewer than 50% of reads. Numbers of detected out of expected SLs and SL RNA genes are detailed where available
  2. aOnly the single SL sequence identical to the SLFinder sequence is presented
  3. bThe remaining four loci are sequence variants of the SL that are not present in the RNA-Seq libraries
  4. c28 loci were predicted, but none matched functional copies
  5. dSL RNA genes are poorly characterised in the reference genome (see main text)
\