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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 | 499 | Selenocysteine tRNAs (TCA) | 4 | Possible suppressor tRNAs (CTA,TTA) | 0 | tRNAs with undetermined or unknown isotypes | 0 | Predicted pseudogenes | 0 | Total tRNAs | 503 |
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Intron Summary tRNAs with introns 32 | Arg TCT 6 | Leu CAA 6 | Glu CTC 1 | Ile TAT 4 | Tyr ATA 1 | Tyr GTA 14 |
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Four Box tRNA Sets Isotype | tRNA Count by Anticodon | Total | Ala | AGC 27 | GGC | CGC 8 | TGC 10 | 45 | Gly | ACC | GCC 10 | CCC 8 | TCC 5 | 23 | Pro | AGG 10 | GGG | CGG 3 | TGG 7 | 20 | Thr | AGT 9 | GGT | CGT 3 | TGT 7 | 19 | Val | AAC 12 | GAC 3 | CAC 16 | TAC 6 | 37 |
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| Six Box tRNA Sets Isotype | tRNA Count by Anticodon | Total | Ser | AGA 12 | GGA | CGA 4 | TGA 4 | ACT | GCT 12 |   |   | 32 | Arg | ACG 10 | GCG 1 | CCG 4 | TCG 5 |   |   | CCT 7 | TCT 6 | 33 | Leu | AAG 8 | GAG | CAG 3 | TAG 5 |   |   | CAA 6 | TAA 4 | 26 |
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| Two Box tRNA Sets Isotype | tRNA Count by Anticodon | Total | Phe | AAA | GAA 13 |   |   | 13 | Asn | ATT 1 | GTT 21 |   |   | 22 | Lys |   |   | CTT 18 | TTT 15 | 33 | Asp | ATC 1 | GTC 10 |   |   | 11 | Glu |   |   | CTC 50 | TTC 11 | 61 | His | ATG 1 | GTG 12 |   |   | 13 | Gln |   |   | CTG 10 | TTG 6 | 16 |
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| Two Box & Other tRNA Sets Isotype | tRNA Count by Anticodon | Total | Ile | AAT 20 | GAT |   | TAT 4 | 24 | Met |   |   | CAT 23 |   | 23 | Tyr | ATA 1 | GTA 14 |   |   | 15 | Supres |   |   | CTA | TTA | 0 | Cys | ACA | GCA 26 |   |   | 26 | Trp |   |   | CCA 7 |   | 7 | SelCys |   |   |   | TCA 4 | 4 |
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