Genomic tRNA Database: Macaca mulatta (Rhesus Jan 2006)

tRNAscan-SE Analysis of Macaca mulatta (Rhesus Jan 2006)

>> Main Overview

>> tRNAs by Isotype

>> tRNAs by Locus

>> Secondary Structures

>> tRNA Alignments

>> FASTA Seqs

>> Run Options/Stats

>> Analysis Notes

>> 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 378
 Selenocysteine tRNAs (TCA) 1
 Possible suppressor tRNAs (CTA,TTA) 0
 tRNAs with undetermined 
 or unknown isotypes 0
 Predicted pseudogenes 0
 Total tRNAs 379
 
 
Intron Summary tRNAs with introns 
 23 Arg 
 TCT 
 4 Leu 
 CAA 
 3 Ile 
 TAT 
 5 Tyr 
 GTA 
 11

Four Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ala AGC 
 15 GGC 
 1 CGC 
 5 TGC 
 8 29
 Gly ACC 
   GCC 
 11 CCC 
 7 TCC 
 5 23
 Pro AGG 
 8 GGG 
   CGG 
 4 TGG 
 5 17
 Thr AGT 
 8 GGT 
   CGT 
 4 TGT 
 6 18
 Val AAC 
 6 GAC 
   CAC 
 12 TAC 
 7 25  Six Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ser AGA 
 9 GGA 
   CGA 
 4 TGA 
 5 ACT 
   GCT 
 8   
     
   26
 Arg ACG 
 7 GCG 
   CCG 
 4 TCG 
 5   
     
   CCT 
 5 TCT 
 5 26
 Leu AAG 
 9 GAG 
   CAG 
 5 TAG 
 4   
     
   CAA 
 3 TAA 
 4 25
 Two Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Phe AAA 
   GAA 
 9   
     
   9
 Asn ATT 
 1 GTT 
 18   
     
   19
 Lys   
     
   CTT 
 12 TTT 
 13 25
 Asp ATC 
   GTC 
 14   
     
   14
 Glu   
     
   CTC 
 6 TTC 
 11 17
 His ATG 
   GTG 
 10   
     
   10
 Gln   
     
   CTG 
 10 TTG 
 5 15  Two Box & Other tRNA Sets Isotype tRNA Count by Anticodon Total
 Ile AAT 
 10 GAT 
 4   
   TAT 
 5 19
 Met   
     
   CAT 
 17   
   17
 Tyr ATA 
   GTA 
 11   
     
   11
 Supres   
     
   CTA 
   TTA 
   0
 Cys ACA 
   GCA 
 26   
     
   26
 Trp   
     
   CCA 
 7   
   7
 SelCys   
     
     
   TCA 
 1 1

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.