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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 | 468 | Selenocysteine tRNAs (TCA) | 2 | Possible suppressor tRNAs (CTA,TTA) | 0 | tRNAs with undetermined or unknown isotypes | 1 | Predicted pseudogenes | 0 | Total tRNAs | 471 |
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Intron Summary tRNAs with introns 34 | Pro AGG 1 | Arg TCT 7 | Leu CAA 5 | Ile TAT 6 | Tyr ATA 1 | Tyr GTA 14 |
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Four Box tRNA Sets Isotype | tRNA Count by Anticodon | Total | Ala | AGC 22 | GGC | CGC 4 | TGC 9 | 35 | Gly | ACC | GCC 13 | CCC 9 | TCC 8 | 30 | Pro | AGG 11 | GGG | CGG 4 | TGG 7 | 22 | Thr | AGT 12 | GGT | CGT 6 | TGT 5 | 23 | Val | AAC 8 | GAC | CAC 15 | TAC 7 | 30 |
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| Six Box tRNA Sets Isotype | tRNA Count by Anticodon | Total | Ser | AGA 9 | GGA | CGA 6 | TGA 4 | ACT | GCT 8 |   |   | 27 | Arg | ACG 7 | GCG | CCG 6 | TCG 6 |   |   | CCT 8 | TCT 8 | 35 | Leu | AAG 10 | GAG | CAG 10 | TAG 3 |   |   | CAA 5 | TAA 6 | 34 |
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| Two Box tRNA Sets Isotype | tRNA Count by Anticodon | Total | Phe | AAA | GAA 11 |   |   | 11 | Asn | ATT 2 | GTT 33 |   |   | 35 | Lys |   |   | CTT 20 | TTT 14 | 34 | Asp | ATC | GTC 11 |   |   | 11 | Glu |   |   | CTC 7 | TTC 19 | 26 | His | ATG | GTG 10 |   |   | 10 | Gln |   |   | CTG 9 | TTG 6 | 15 |
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| Two Box & Other tRNA Sets Isotype | tRNA Count by Anticodon | Total | Ile | AAT 13 | GAT 3 |   | TAT 6 | 22 | Met |   |   | CAT 18 |   | 18 | Tyr | ATA 1 | GTA 15 |   |   | 16 | Supres |   |   | CTA | TTA | 0 | Cys | ACA | GCA 27 |   |   | 27 | Trp |   |   | CCA 7 |   | 7 | SelCys |   |   |   | TCA 2 | 2 |
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