Genomic tRNA Database: Danio rerio (Zebrafish) (Zv8 Apr 2009)

tRNAscan-SE Analysis of Danio rerio (Zebrafish) (Zv8 Apr 2009)

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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 12244
 Selenocysteine tRNAs (TCA) 14
 Possible suppressor tRNAs (CTA,TTA) 15
 tRNAs with undetermined 
 or unknown isotypes 19
 Predicted pseudogenes 0
 Total tRNAs 12292
 
 
Intron Summary tRNAs with introns 
 813 Gly 
 CCC 
 3 Gly 
 TCC 
 2 Pro 
 AGG 
 7 Val 
 AAC 
 2 Arg 
 TCT 
 247 Leu 
 AAG 
 4 Leu 
 TAG 
 8 Leu 
 CAA 
 234 Leu 
 TAA 
 8 Phe 
 AAA 
 1 Lys 
 TTT 
 3 Asp 
 GTC 
 1 Ile 
 AAT 
 1 Ile 
 TAT 
 61 Met 
 CAT 
 2 Tyr 
 ATA 
 4 Tyr 
 GTA 
 225

Four Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ala AGC 
 92 GGC 
 4 CGC 
 112 TGC 
 368 576
 Gly ACC 
 11 GCC 
 836 CCC 
 268 TCC 
 47 1162
 Pro AGG 
 315 GGG 
 2 CGG 
 180 TGG 
 205 702
 Thr AGT 
 359 GGT 
 10 CGT 
 66 TGT 
 290 725
 Val AAC 
 232 GAC 
 6 CAC 
 227 TAC 
 230 695  Six Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Ser AGA 
 336 GGA 
 2 CGA 
 80 TGA 
 209 ACT 
 14 GCT 
 424   
     
   1065
 Arg ACG 
 203 GCG 
 24 CCG 
 59 TCG 
 107   
     
   CCT 
 104 TCT 
 252 749
 Leu AAG 
 270 GAG 
 4 CAG 
 300 TAG 
 244   
     
   CAA 
 241 TAA 
 73 1132
 Two Box tRNA Sets Isotype tRNA Count by Anticodon Total
 Phe AAA 
 10 GAA 
 197   
     
   207
 Asn ATT 
 24 GTT 
 1045   
     
   1069
 Lys   
     
   CTT 
 953 TTT 
 525 1478
 Asp ATC 
 1 GTC 
 150   
     
   151
 Glu   
     
   CTC 
 245 TTC 
 225 470
 His ATG 
 10 GTG 
 387   
     
   397
 Gln   
     
   CTG 
 266 TTG 
 105 371  Two Box & Other tRNA Sets Isotype tRNA Count by Anticodon Total
 Ile AAT 
 258 GAT 
 10   
   TAT 
 75 343
 Met   
     
   CAT 
 522   
   522
 Tyr ATA 
 5 GTA 
 236   
     
   241
 Supres   
     
   CTA 
 9 TTA 
 6 15
 Cys ACA 
 9 GCA 
 136   
     
   145
 Trp   
     
   CCA 
 44   
   44
 SelCys   
     
     
   TCA 
 14 14

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.