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Table 2 Spliced leader identification (SLIDR) results in seven nematodes and three other eukaryotes

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

Species Reference Bioproject QC reads Sm motif regex SLs (detected | expected) Novel SLs SL RNA genes (detected | expected)
Caenorhabditis elegans GCF_000224145.3 PRJNA270896 150,041,952 .{40,55}AC?T{4,6}G 12 | 12 28 | 28
  GCF_000002985.6a PRJEB28364 45,443,137 .{40,55}AC?T{4,6}G 12 | 12 28 | 28
Caenorhabditis briggsae PRJNA10731.WBPS5 PRJNA104933 21,265,790 .{20,60}AT{4,6}G 2 | 7 11 | 18 + 
   PRJNA489172 78,497,095 .{20,60}AT{4,6}G 6 | 7 26 | 18 + 
   PRJNA231838 59,271,467 .{20,60}AT{4,6}G 7 | 7 27 | 18 + 
Pristionchus pacificus Hybrid1 SRP039388 81,387,873 .{40,55}[AG]T{4,6}[AG] 7 | 11 6 210 | 203
  GCA_000180635.3 PRJNA338247 330,856,071 .{40,55}[AG]T{4,6}[AG] 6 | 11 10 660 | 203
Meloidogyne hapla PRJNA29083.WBPS14 PRJNA229407 169,404,394 .{30,80}AT{4,6}G 5 | 5 10 14 | ?
   PRJEB14142 62,113,573 .{30,80}AT{4,6}G 5 | 5 9 13 | ?
Trichinella spiralis PRJNA12603.WBPS10 PRJNA510020 201,164,867 .{20,50}AT{4,6}G 15 | 15 22 | 48
Trichuris muris PRJEB126.WBPS15 PRJEB1054 115,460,947 .{25,50}AT{4,6}G 13 | 13 3 20 | 13
Prionchulus punctatus de novo Trinity1 PRJEB7585 71,087,651 .{25,60}AC?T{4,6}G 2 | 6 2 | ?
Ciona intestinalis GCF_000224145.3_KH PRJNA396771 108,760,969 .{2,25}AGCTTTGG 1 | 1 11 | 15
     .{20,50}AT{4,6}G 1 | 1 1 1 | 15
   PRJNA297221 49,713,049 .{2,25}AGCTTTGG 1 | 1 11 | 15
   PRJNA433724 19,072,215 .{2,25}AGCTTTGG 1 | 1 11 | 15
   PRJNA376667 194,089,029 .{2,25}AGCTTTGG 1 | 1 2 14 | 15
     .{20,50}AT{4,6}G 1 | 1 1 3 | 15
Hydra vulgaris Hm105 PRJNA497966 125,523,578 .{10,35}[AG]ATTTT[CG][AG] 2 | 12 2 3 | ?
   PRJNA641135 35,234,240 .{10,35}[AG]ATTTT[CG][AG] 3 | 12 2 4 | ?
Schistosoma mansoni PRJEA36577.WBPS14 PRJNA225599 38,015,650 .{10,30}AGTTTTCTTTGG 1 | 1 110 | ?
  1. Identifiers for reference genomes/transcriptomes and RNA-Seq libraries are presented alongside numbers of quality-trimmed reads (QC), the Sm motif regular expression notation used to filter SLs, numbers of expected SLs detected, numbers of novel SLs identified and numbers of expected SL RNA genes detected. Question marks and pluses represent unknown or poorly characterised SL RNA gene numbers
  2. aTranscriptome reference
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