Genomic tRNA Database: Glycine max (soybean) (Glyma0 preliminary release)

tRNAscan-SE Analysis of Glycine max (soybean) (Glyma0 preliminary release)

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>> Genome DB

>> 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 933
 Selenocysteine tRNAs (TCA) 0
 Possible suppressor tRNAs (CTA,TTA) 0
 tRNAs with undetermined 
 or unknown isotypes 0
 Predicted pseudogenes 0
 Total tRNAs 933
 
 
Intron Summary tRNAs with introns 
 39 Ser 
 TGA 
 1 Met 
 CAT 
 18 Tyr 
 GTA 
 20

Four Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ala AGC 
 24 GGC 
   CGC 
 8 TGC 
 17 49
 Gly ACC 
   GCC 
 32 CCC 
 9 TCC 
 18 59
 Pro AGG 
 21 GGG 
   CGG 
 5 TGG 
 31 57
 Thr AGT 
 10 GGT 
 8 CGT 
 5 TGT 
 13 36
 Val AAC 
 22 GAC 
 13 CAC 
 13 TAC 
 9 57  Six Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ser AGA 
 15 GGA 
 2 CGA 
 6 TGA 
 15 ACT 
   GCT 
 35   
     
   73
 Arg ACG 
 20 GCG 
   CCG 
 5 TCG 
 9   
     
   CCT 
 14 TCT 
 24 72
 Leu AAG 
 16 GAG 
   CAG 
 7 TAG 
 12   
     
   CAA 
 55 TAA 
 9 99
 Two Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Phe AAA 
   GAA 
 24   
     
   24
 Asn ATT 
 2 GTT 
 28   
     
   30
 Lys   
     
   CTT 
 22 TTT 
 20 42
 Asp ATC 
   GTC 
 40   
     
   40
 Glu   
     
   CTC 
 24 TTC 
 17 41
 His ATG 
   GTG 
 25   
     
   25
 Gln   
     
   CTG 
 13 TTG 
 21 34  Two Box & Other tRNA Sets Isotype tRNA Count by Anticodon Total
 Ile AAT 
 31 GAT 
     
   TAT 
 8 39
 Met   
     
   CAT 
 74   
   74
 Tyr ATA 
   GTA 
 29   
     
   29
 Supres   
     
   CTA 
   TTA 
   0
 Cys ACA 
   GCA 
 28   
     
   28
 Trp   
     
   CCA 
 25   
   25
 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.