Genomic tRNA Database: Danio rerio (Zebrafish) (danRer5 July 2007)

tRNAscan-SE Analysis of Danio rerio (Zebrafish) (danRer5 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 12752
 Selenocysteine tRNAs (TCA) 14
 Possible suppressor tRNAs (CTA,TTA) 16
 tRNAs with undetermined 
 or unknown isotypes 20
 Predicted pseudogenes 0
 Total tRNAs 12802
 
 
Intron Summary tRNAs with introns 
 823 Ala 
 TGC 
 1 Gly 
 CCC 
 4 Gly 
 TCC 
 2 Pro 
 AGG 
 8 Val 
 AAC 
 1 Arg 
 TCT 
 247 Leu 
 AAG 
 4 Leu 
 TAG 
 5 Leu 
 CAA 
 184 Leu 
 TAA 
 5 Phe 
 AAA 
 1 Lys 
 TTT 
 3 Asp 
 GTC 
 1 Ile 
 AAT 
 1 Ile 
 TAT 
 115 Met 
 CAT 
 1 Tyr 
 ATA 
 4 Tyr 
 GTA 
 236

Four Box tRNA Sets Isotype Anticodon Count Total
 Ala AGC 
 92 GGC 
 4 CGC 
 112 TGC 
 368 576
 Gly ACC 
 9 GCC 
 846 CCC 
 273 TCC 
 48 1176
 Pro AGG 
 327 GGG 
 2 CGG 
 195 TGG 
 226 750
 Thr AGT 
 369 GGT 
 10 CGT 
 73 TGT 
 305 757
 Val AAC 
 234 GAC 
 6 CAC 
 231 TAC 
 227 698  Six Box tRNA Sets Isotype Anticodon Count Total
 Ser AGA 
 374 GGA 
 2 CGA 
 90 TGA 
 193 ACT 
 15 GCT 
 454   
     
   1128
 Arg ACG 
 214 GCG 
 26 CCG 
 64 TCG 
 106   
     
   CCT 
 67 TCT 
 251 728
 Leu AAG 
 301 GAG 
 3 CAG 
 307 TAG 
 271   
     
   CAA 
 192 TAA 
 63 1137
 Two Box tRNA Sets Isotype Anticodon Count Total
 Phe AAA 
 10 GAA 
 210   
     
   220
 Asn ATT 
 24 GTT 
 1136   
     
   1160
 Lys   
     
   CTT 
 1012 TTT 
 557 1569
 Asp ATC 
 1 GTC 
 161   
     
   162
 Glu   
     
   CTC 
 256 TTC 
 243 499
 His ATG 
 10 GTG 
 410   
     
   420
 Gln   
     
   CTG 
 287 TTG 
 108 395  Two Box & Other tRNA Sets Isotype Anticodon Count Total
 Ile AAT 
 282 GAT 
 10   
   TAT 
 129 421
 Met   
     
   CAT 
 524   
   524
 Tyr ATA 
 5 GTA 
 246   
     
   251
 Supres   
     
   CTA 
 10 TTA 
 6 16
 Cys ACA 
 8 GCA 
 122   
     
   130
 Trp   
     
   CCA 
 51   
   51
 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.