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Table 3 Operon prediction (SLOPPR) results in four nematode and two tunicate species

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

Species Genome Bioproject QC reads SL reads SL genes (%) Reference operons Predicted operons Specificity | sensitivity Operonic genes Intercistronic distance (bp)
Caenorhabditis elegans GCF_000224145.3 PRJNA270896 621,744,295 937,587 52 1542 345 86% | 19% 721 99
Caenorhabditis briggsae CB3 PRJNA104933 21,265,790 209,005 27 1034 840 81% | 66% 1847 342
   PRJNA231838 59,271,467 286,520 36 1034 752 81% | 59% 1631 332
  CB4 PRJNA104933 21,265,790 235,001 38 48 921 5% | 96% 2058 111
   PRJNA231838 59,271,467 289,834 41 48 750 5% | 81% 1626 110
Pristionchus pacificus Hybrid1 SRP039388 81,387,873 438,557 20 2219 190 61% | 5% 382 981
   PRJNA338247 330,856,071 312,718 28 2219 205 50% | 5% 414 872
Trichuris muris PRJEB126.WBPS15 PRJEB1054 115,460,947 168,727 35 2 718 a 1492 418
Ciona intestinalis KH PRJNA376667 194,089,029 452,505 51 1328 1172 94% | 83% 2563 1
Oikopleura dioica GCA_000209535.1 PRJNA269316, PRJDB5668 250,361,592 5,860,107 9 1765 464 98% | 26% 1017 31
  1. Identifiers for reference genomes and paired-end RNA-Seq libraries are presented alongside numbers of quality-trimmed reads (QC), numbers of reads with a spliced leader (SL), percentage of genes receiving an SL, numbers of available reference operons, numbers of predicted operons, specificity (predicted operons matching reference operons), sensitivity (fraction of reference operons detected), numbers of operonic genes, and median intercistronic distance among operonic genes. Downstream operonic genes were required to have SL2:SL1 read ratio 2, and upstream operonic genes were not required to be SL trans-spliced. Since the two tunicates C. intestinalis and O. dioica do not use SL2-type trans-splicing, operonic genes were obtained by filtering SL trans-spliced genes by intercistronic distance (cut-offs: 84 bp for C. intestinalis and 60 bp for O. dioica; see main text)
  2. aNot calculated due to low sample size (n = 2)
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