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Table 1 Transfer tRNAs in Dermatophagoides farinae and D. pteronyssinus

From: Improved tRNA prediction in the American house dust mite reveals widespread occurrence of extremely short minimal tRNAs in acariform mites

Ana Cnb tRNA Strc Lend Ante Strf TRNg ARWh BLASTi Prevj Cfk 5' overlapl 3' overlapm
1-3 y Asp/D + 54 GTC tv Y Y D   y - ATP8 (1)
4-7 y Gly/G + 57 TCC tv Y Y G   y - ND3 (1)
8-14 n Arg/R + 49 TCG d - y R tvn   ND3 (1) -
15-18 y Met/M + 52 CAT tv y - M    - -
19-25 y Ser2/S2 + 52 TGA d - y S2, W tvo   - -
26-28 y Cys/C - 53 GCA d Y Y C A   - -
29-32 y Pro/P + 57 TGG tv Y y P    - -
33-40 n Tyr/Y + 55 GTA d - y Y V p   - K (10)
41-44 y Lys/K + 62 TTT c/tv y y K, W, C, L2 tvq   Y(10) N(1),-
45-47 y Asn/N + 55 GTT tv Y Y N   y K(1) -
48-53 n Val/Vr + 52 TAC d - - V, Y, l-rRNA l-rRNA   s-rRNA(3,2) -
54-57 y Trp/W + 58 TCA tv Y Y W, S2, F   y - -
58-61 - -s + 44 'GGT' - - - - Y   - -
62-67 y Thr/T - 55 TGT tv Y y T    - ND6 (1)
68-70 y His/H + 56 GTG tv Y Y H   y - ND5 (1)
71-77 y Phe/F + 55 GAA tv Y Y F, W   y - -
78-80 y Ser1/S1 - 52 TCT d -t y S1, S2 du   -, Q (2)v -
81-83 y Gln/Q - 54 TTG tv Y Y Q, W    -, I (2)v -, S1(2)v
84-88 y Ile/I - 53 GAT tv y - I    - -, Q (2)v
89-92 y Glu/E - 54 TTC tv y Y E, W tvw y - ND2 (1)
93-95 y Leu1/L1 - 55 TAG tv Y Y L1 tvx   - -
96-100 n Ala/Ay + 50 TGC d - y -z C aa   - -
101-103 y Leu2/L2 + 57 TAA tv Y Y L2    - COX1(1)
  1. a refers to IDs from the detailed analyses (Additional file 5)
  2. b Canonical, can be found confidently either in tRNAscan-SE or ARWEN
  3. c Strand
  4. d Length (D. farinae only)
  5. e Anticodon
  6. f tRNA secondary structure: tv = TV-replacement loop tRNA, d = D-replacement loop tRNA, c = cloverleaf tRNA
  7. g tRNAscan-SE analysis: Y = high score or unambiguous tRNA; y = low score or ambiguous tRNA; - = failed to find any tRNAs
  8. h ARWEN analysis: designations as for tRNAscan-SE
  9. i BLAST similarity search of tRNA anticodon helix restricted to mitochondrial genomes of arthropods
  10. j Previously inferred for D. pteronyssinus, if either gene region (bold) or its secondary structure is different from our reconstruction
  11. k The 5' end of a tRNA is confirmed by EST data (a polyadenylated site immediately upstream of the tRNA 5' end). For others tRNAs these data are not available. Approximated if EST data are missing in one species.
  12. l in all cases overlaps with the 3' end of a gene. The overlap length (nt) is given in parentheses. tRNAs genes are given using single letter designations. If different in the two species, given as two values separated by a comma, for D. farinae and D. pteronyssinus, respectively.
  13. m In all cases overlaps with 5' end of a gene; format as in previous column
  14. n 17 nt overlap with ND3 3' end
  15. o 12 nt overlap with 3' end tRNA-Met
  16. p 5' end overlaps with 5' of tRNA-Lys by 7 nt, 3' end overlaps with 3' end of tRNA-Pro by 11 nt
  17. q 3' part is different from our structure
  18. r putative; alternatively part of l-rRNA start where it forms stable secondary structure with 6-nt "anticodon", variable loop, and 5-nt stem.
  19. s not a tRNA, non-coding region between tRNA-Trp and ND1
  20. t also tRNA-Ser2
  21. u 3' acceptor and T-stems are separated by 1 nt. These two stems are not separated in our structure (as in the typical tRNA)
  22. v D. pteronyssinus only
  23. w 5' acceptor stem and D-stem (3 bp) are separated by 1 nt. These two stems are separated by 2 nt (as in the typical tRNA); D-stem is 4 bp-long in our structure; and the acceptor stem is situated at n-1 position in our structure
  24. x 3-bp D-stem (4-bp in our structure)
  25. y alternatively non-coding region between tRNA L1-tRNA L1-L2 structure
  26. z one hit on Steganacarus magnus may represent tRNA-Ala (originally designated as non-translated intergenic spacer).
  27. aa cloverleaf, 3' end overlaps with tRNA-Leu1 by 5 nt.