Genomic tRNA Database: Rattus norvegicus (rn4 Nov 2004)

tRNAscan-SE Analysis of Rattus norvegicus (rn4 Nov 2004)

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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 437
 Selenocysteine tRNAs (TCA) 1
 Possible suppressor tRNAs (CTA,TTA) 0
 tRNAs with undetermined 
 or unknown isotypes 6
 Predicted pseudogenes 0
 Total tRNAs 444
 
 
Intron Summary tRNAs with introns 
 23 Thr 
 AGT 
 1 Arg 
 TCT 
 6 Leu 
 CAA 
 3 Phe 
 AAA 
 1 Asp 
 ATC 
 1 Ile 
 TAT 
 3 Tyr 
 GTA 
 8

Four Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ala AGC 
 34 GGC 
 2 CGC 
 4 TGC 
 15 55
 Gly ACC 
   GCC 
 15 CCC 
 5 TCC 
 9 29
 Pro AGG 
 30 GGG 
   CGG 
 3 TGG 
 6 39
 Thr AGT 
 9 GGT 
   CGT 
 3 TGT 
 5 17
 Val AAC 
 8 GAC 
   CAC 
 7 TAC 
 5 20  Six Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ser AGA 
 8 GGA 
   CGA 
 3 TGA 
 4 ACT 
 1 GCT 
 9   
     
   25
 Arg ACG 
 6 GCG 
   CCG 
 3 TCG 
 5   
     
   CCT 
 9 TCT 
 8 31
 Leu AAG 
 6 GAG 
   CAG 
 14 TAG 
 4   
     
   CAA 
 3 TAA 
 2 29
 Two Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Phe AAA 
 1 GAA 
 7   
     
   8
 Asn ATT 
   GTT 
 14   
     
   14
 Lys   
     
   CTT 
 17 TTT 
 9 26
 Asp ATC 
 1 GTC 
 15   
     
   16
 Glu   
     
   CTC 
 10 TTC 
 10 20
 His ATG 
   GTG 
 12   
     
   12
 Gln   
     
   CTG 
 9 TTG 
 5 14  Two Box & Other tRNA Sets Isotype tRNA Count by Anticodon Total
 Ile AAT 
 12 GAT 
     
   TAT 
 3 15
 Met   
     
   CAT 
 13   
   13
 Tyr ATA 
   GTA 
 8   
     
   8
 Supres   
     
   CTA 
   TTA 
   0
 Cys ACA 
   GCA 
 38   
     
   38
 Trp   
     
   CCA 
 8   
   8
 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.