Genomic tRNA Database: Caenorhabditis brenneri (Jan 2007)

tRNAscan-SE Analysis of Caenorhabditis brenneri (Jan 2007)

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>> Genome Seq

tRNA Gene Summary

tRNA-derived SINEs are found in a number of eukaryotes especially mammalian genomes. After manual inspection and analysis, we apply the following filter to this genome for eliminating these tRNA-derived elements from true tRNAs. If the tRNA candidates have hits in both tRNAscan and Eufind first-pass scanners, we use a combination of at least 20 bits COVE score, 10 bits HMM score, and 5 bits 2' structure score to define a true tRNA. If the tRNA candidates only have hits in one of the first-pass scanners, the threshold of a true tRNA will be 55 bits COVE score.



tRNAs Decoding Standard 20 AA 1076
 Selenocysteine tRNAs (TCA) 0
 Possible suppressor tRNAs (CTA,TTA) 1
 tRNAs with undetermined 
 or unknown isotypes 19
 Predicted pseudogenes 0
 Total tRNAs 1096
 
 
Intron Summary tRNAs with introns 
 51 Leu 
 CAA 
 15 Phe 
 GAA 
 1 Ile 
 GAT 
 2 Ile 
 TAT 
 7 Tyr 
 ATA 
 2 Tyr 
 GTA 
 24

Four Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ala AGC 
 34 GGC 
 1 CGC 
 7 TGC 
 10 52
 Gly ACC 
   GCC 
 35 CCC 
 25 TCC 
 68 128
 Pro AGG 
 11 GGG 
 4 CGG 
 8 TGG 
 50 73
 Thr AGT 
 32 GGT 
 3 CGT 
 9 TGT 
 17 61
 Val AAC 
 35 GAC 
   CAC 
 15 TAC 
 8 58  Six Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ser AGA 
 19 GGA 
   CGA 
 9 TGA 
 13 ACT 
   GCT 
 14   
     
   55
 Arg ACG 
 33 GCG 
   CCG 
 24 TCG 
 17   
     
   CCT 
 11 TCT 
 13 98
 Leu AAG 
 32 GAG 
   CAG 
 10 TAG 
 9   
     
   CAA 
 15 TAA 
 7 73
 Two Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Phe AAA 
   GAA 
 22   
     
   22
 Asn ATT 
   GTT 
 32   
     
   32
 Lys   
     
   CTT 
 50 TTT 
 26 76
 Asp ATC 
   GTC 
 33   
     
   33
 Glu   
     
   CTC 
 37 TTC 
 35 72
 His ATG 
   GTG 
 23   
     
   23
 Gln   
     
   CTG 
 13 TTG 
 41 54  Two Box & Other tRNA Sets Isotype tRNA Count by Anticodon Total
 Ile AAT 
 36 GAT 
 2   
   TAT 
 27 65
 Met   
     
   CAT 
 29   
   29
 Tyr ATA 
 2 GTA 
 25   
     
   27
 Supres   
     
   CTA 
 1 TTA 
   1
 Cys ACA 
 3 GCA 
 20   
     
   23
 Trp   
     
   CCA 
 22   
   22
 SelCys   
     
     
   TCA 
   0

The Genomic tRNA Database is curated by Todd Lowe and Patricia Chan. Please email lowe@soe.ucsc.edu with any questions and comments. To submit corrections, please use our Bug and Request Tracking System.