Genomic tRNA Database: Pongo pygmaeus abelii (orangutan) (July 2007)

tRNAscan-SE Analysis of Pongo pygmaeus abelii (orangutan) (July 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 468
 Selenocysteine tRNAs (TCA) 2
 Possible suppressor tRNAs (CTA,TTA) 0
 tRNAs with undetermined 
 or unknown isotypes 1
 Predicted pseudogenes 0
 Total tRNAs 471
 
 
Intron Summary tRNAs with introns 
 34 Pro 
 AGG 
 1 Arg 
 TCT 
 7 Leu 
 CAA 
 5 Ile 
 TAT 
 6 Tyr 
 ATA 
 1 Tyr 
 GTA 
 14

Four Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ala AGC 
 22 GGC 
   CGC 
 4 TGC 
 9 35
 Gly ACC 
   GCC 
 13 CCC 
 9 TCC 
 8 30
 Pro AGG 
 11 GGG 
   CGG 
 4 TGG 
 7 22
 Thr AGT 
 12 GGT 
   CGT 
 6 TGT 
 5 23
 Val AAC 
 8 GAC 
   CAC 
 15 TAC 
 7 30  Six Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ser AGA 
 9 GGA 
   CGA 
 6 TGA 
 4 ACT 
   GCT 
 8   
     
   27
 Arg ACG 
 7 GCG 
   CCG 
 6 TCG 
 6   
     
   CCT 
 8 TCT 
 8 35
 Leu AAG 
 10 GAG 
   CAG 
 10 TAG 
 3   
     
   CAA 
 5 TAA 
 6 34
 Two Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Phe AAA 
   GAA 
 11   
     
   11
 Asn ATT 
 2 GTT 
 33   
     
   35
 Lys   
     
   CTT 
 20 TTT 
 14 34
 Asp ATC 
   GTC 
 11   
     
   11
 Glu   
     
   CTC 
 7 TTC 
 19 26
 His ATG 
   GTG 
 10   
     
   10
 Gln   
     
   CTG 
 9 TTG 
 6 15  Two Box & Other tRNA Sets Isotype tRNA Count by Anticodon Total
 Ile AAT 
 13 GAT 
 3   
   TAT 
 6 22
 Met   
     
   CAT 
 18   
   18
 Tyr ATA 
 1 GTA 
 15   
     
   16
 Supres   
     
   CTA 
   TTA 
   0
 Cys ACA 
   GCA 
 27   
     
   27
 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.