Genomic tRNA Database: Equus caballus (horse) (Jan 2007)

tRNAscan-SE Analysis of Equus caballus (horse) (Jan 2007)

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>> tRNA Alignments

>> FASTA Seqs

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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 499
 Selenocysteine tRNAs (TCA) 4
 Possible suppressor tRNAs (CTA,TTA) 0
 tRNAs with undetermined 
 or unknown isotypes 0
 Predicted pseudogenes 0
 Total tRNAs 503
 
 
Intron Summary tRNAs with introns 
 32 Arg 
 TCT 
 6 Leu 
 CAA 
 6 Glu 
 CTC 
 1 Ile 
 TAT 
 4 Tyr 
 ATA 
 1 Tyr 
 GTA 
 14

Four Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ala AGC 
 27 GGC 
   CGC 
 8 TGC 
 10 45
 Gly ACC 
   GCC 
 10 CCC 
 8 TCC 
 5 23
 Pro AGG 
 10 GGG 
   CGG 
 3 TGG 
 7 20
 Thr AGT 
 9 GGT 
   CGT 
 3 TGT 
 7 19
 Val AAC 
 12 GAC 
 3 CAC 
 16 TAC 
 6 37  Six Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ser AGA 
 12 GGA 
   CGA 
 4 TGA 
 4 ACT 
   GCT 
 12   
     
   32
 Arg ACG 
 10 GCG 
 1 CCG 
 4 TCG 
 5   
     
   CCT 
 7 TCT 
 6 33
 Leu AAG 
 8 GAG 
   CAG 
 3 TAG 
 5   
     
   CAA 
 6 TAA 
 4 26
 Two Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Phe AAA 
   GAA 
 13   
     
   13
 Asn ATT 
 1 GTT 
 21   
     
   22
 Lys   
     
   CTT 
 18 TTT 
 15 33
 Asp ATC 
 1 GTC 
 10   
     
   11
 Glu   
     
   CTC 
 50 TTC 
 11 61
 His ATG 
 1 GTG 
 12   
     
   13
 Gln   
     
   CTG 
 10 TTG 
 6 16  Two Box & Other tRNA Sets Isotype tRNA Count by Anticodon Total
 Ile AAT 
 20 GAT 
     
   TAT 
 4 24
 Met   
     
   CAT 
 23   
   23
 Tyr ATA 
 1 GTA 
 14   
     
   15
 Supres   
     
   CTA 
   TTA 
   0
 Cys ACA 
   GCA 
 26   
     
   26
 Trp   
     
   CCA 
 7   
   7
 SelCys   
     
     
   TCA 
 4 4

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.