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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