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Table 2 Summary of TATE copy analyzes from the distinct genomes presenting at least one potentially encoding copy

From: Study of VIPER and TATE in kinetoplastids and the evolution of tyrosine recombinase retrotransposons

Species No of analyzed copies No of copies with at least one potentially encoding ORF No of copies with the three potentially encoding ORFs No of potential encoding copies with YR and RT/RT related domains No of copies with SDRs Structure of SDRs size in base pairs, percentage of identity No of putative autonomous copies* Mean identity among copies in nu (total) and aa levels (for each ORF)**
B. saltans 5 2 2 *one ORF with the three genes 0 1 5′ → A1, A2 3′ → B1 → B2 A: 73 bp, 99%; B: 161 bp, 81% 0 nu: na Gag-like, YR, RT/RH (2, 1464 aa): 49%
T. theileri 15 7 4 0 1 (incomplete/missing data) 5′ → A1 3′ → A2 A: 91 bp, 100%;; B: missing data 0 nu: na Gag-like: na YR (3, 584 aa): 45.3% RT/RH (4, 698 aa): 86.9%
C. fasciculata 15 7 4 0 0 na 0 nu: na Gag -like (3, 240 aa): 31.1% YR (7, 727 aa): 44.8% RT/RH (3, 473 aa): 53.6%
C. mellificae 11 3 1 1 1 (incomplete/missing data) 5′ → A1 3′ → A2 A: 357 bp, 100%; B: missing data 0 nu: na Gag-like (2, 240 aa): 25.6% YR (3, 434 aa): 36.3% RT/RH: 1 sequence
S. culicis 15 1 1 0 0 na 0 1 sequence
Lep. pyrrhocoris 15 11 4 0 0 na 0 nu: na Gag-like (5, 194 aa): 29.7% YR (10, 468 aa): 48.9% RT/RH (8, 882 aa): 55.6%
L. braziliensis 15 15 7 6 1 5′ → A1 3′ → B1 → A2 → B2 A: 381 bp, 96%; B: 294 bp, 99% ? nu: 90% Gag-like (8, 450 aa): 73.3% YR (15, 982 aa): 95.6% RT/RH (14, 954 aa): 96%
  1. *putative autonomous copies are those containing the tree expected ORFs plus direct repeats
  2. **identity was estimated only for regions with confident alignment. The number of sequences and the size of alignment is shown in parenthesis
  3. ? the copy where the SDRs were identified presents a frameshift mutation in the third ORF, however, we do not rule out the possibility that the genome could have additional copies that were not detected due to assembling issues