Genomic tRNA Database: Pan troglodytes (chimp) (Mar 2006)

tRNAscan-SE Analysis of Pan troglodytes (chimp) (Mar 2006)

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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 459
 Selenocysteine tRNAs (TCA) 2
 Possible suppressor tRNAs (CTA,TTA) 2
 tRNAs with undetermined 
 or unknown isotypes 0
 Predicted pseudogenes 0
 Total tRNAs 463
 
 
Intron Summary tRNAs with introns 
 31 Pro 
 AGG 
 1 Val 
 TAC 
 1 Arg 
 TCT 
 5 Leu 
 CAA 
 5 Ile 
 TAT 
 5 Tyr 
 ATA 
 1 Tyr 
 GTA 
 13

Four Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ala AGC 
 29 GGC 
   CGC 
 5 TGC 
 9 43
 Gly ACC 
   GCC 
 11 CCC 
 11 TCC 
 7 29
 Pro AGG 
 10 GGG 
   CGG 
 5 TGG 
 7 22
 Thr AGT 
 9 GGT 
   CGT 
 4 TGT 
 6 19
 Val AAC 
 10 GAC 
   CAC 
 12 TAC 
 9 31  Six Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ser AGA 
 10 GGA 
   CGA 
 3 TGA 
 4 ACT 
 2 GCT 
 9   
     
   28
 Arg ACG 
 7 GCG 
 1 CCG 
 4 TCG 
 6   
     
   CCT 
 6 TCT 
 6 30
 Leu AAG 
 8 GAG 
   CAG 
 6 TAG 
 3   
     
   CAA 
 7 TAA 
 8 32
 Two Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Phe AAA 
   GAA 
 11   
     
   11
 Asn ATT 
 1 GTT 
 30   
     
   31
 Lys   
     
   CTT 
 16 TTT 
 15 31
 Asp ATC 
   GTC 
 13   
     
   13
 Glu   
     
   CTC 
 7 TTC 
 15 22
 His ATG 
   GTG 
 10   
     
   10
 Gln   
     
   CTG 
 10 TTG 
 7 17  Two Box & Other tRNA Sets Isotype tRNA Count by Anticodon Total
 Ile AAT 
 14 GAT 
 1   
   TAT 
 5 20
 Met   
     
   CAT 
 21   
   21
 Tyr ATA 
 1 GTA 
 13   
     
   14
 Supres   
     
   CTA 
 1 TTA 
 1 2
 Cys ACA 
 1 GCA 
 27   
     
   28
 Trp   
     
   CCA 
 7   
   7
 SelCys   
     
     
   TCA 
 2 2

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.