Genomic tRNA Database: Strongylocentrotus purpuratus (Sea urchin) (Version 2.1)

tRNAscan-SE Analysis of Strongylocentrotus purpuratus (Sea urchin) (Version 2.1)

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>> 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 1065
 Selenocysteine tRNAs (TCA) 0
 Possible suppressor tRNAs (CTA,TTA) 1
 tRNAs with undetermined 
 or unknown isotypes 2
 Predicted pseudogenes 0
 Total tRNAs 1068
 
 
Intron Summary tRNAs with introns 
 39 Ser 
 ACT 
 1 Ile 
 TAT 
 13 Tyr 
 GTA 
 24

Four Box tRNA Sets Isotype Anticodon Count Total
 Ala AGC 
 32 GGC 
   CGC 
 7 TGC 
 17 56
 Gly ACC 
   GCC 
 42 CCC 
 4 TCC 
 33 79
 Pro AGG 
 19 GGG 
   CGG 
 9 TGG 
 21 49
 Thr AGT 
 27 GGT 
   CGT 
 9 TGT 
 21 57
 Val AAC 
 20 GAC 
   CAC 
 16 TAC 
 11 47  Six Box tRNA Sets Isotype Anticodon Count Total
 Ser AGA 
 25 GGA 
   CGA 
 6 TGA 
 15 ACT 
 1 GCT 
 17   
     
   64
 Arg ACG 
 29 GCG 
   CCG 
 1 TCG 
 19   
     
   CCT 
 19 TCT 
 18 86
 Leu AAG 
 18 GAG 
   CAG 
 5 TAG 
 8   
     
   CAA 
 2 TAA 
 14 47
 Two Box tRNA Sets Isotype Anticodon Count Total
 Phe AAA 
 2 GAA 
     
     
   2
 Asn ATT 
   GTT 
 39   
     
   39
 Lys   
     
   CTT 
 42 TTT 
 57 99
 Asp ATC 
   GTC 
 82   
     
   82
 Glu   
     
   CTC 
 29 TTC 
 26 55
 His ATG 
   GTG 
 26   
     
   26
 Gln   
     
   CTG 
 21 TTG 
 17 38  Two Box & Other tRNA Sets Isotype Anticodon Count Total
 Ile AAT 
 69 GAT 
 2   
   TAT 
 22 93
 Met   
     
   CAT 
 73   
   73
 Tyr ATA 
   GTA 
 24   
     
   24
 Supres   
     
   CTA 
   TTA 
 1 1
 Cys ACA 
   GCA 
 31   
     
   31
 Trp   
     
   CCA 
 18   
   18
 SelCys   
     
     
   TCA 
   0

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.